Patent Publication Number: US-2019194677-A1

Title: Transgenic plants and a transient transformation system for genome-wide transcription factor target discovery

Description:
This application is a continuation of U.S. patent application Ser. No. 14/457,402 filed on Aug. 12, 2014, which claims the benefit of U.S. Provisional Application No. 61/865,438 filed on Aug. 13, 2013 and U.S. Provisional Application 62/011,729 filed on Jun. 13, 2014, the entire contents of each of which are incorporated by reference herein in their entireties. 
    
    
     1. INTRODUCTION 
     This invention relates to plant genes regulated by transcription factors that control the gene network response to an environmental perturbation or signal, and the manipulation of the expression of these “response genes” and/or their regulatory transcription factors in transgenic plants to confer a desired phenotype. The invention also relates to a rapid technique named “TARGET” (Transient Assay Reporting Genome-wide Effects of Transcription factors) for determining such “response genes” and their regulatory transcription factors as well as the structure of the involved gene regulatory networks (GRN)—including “transient” targets of transcription factors (TF)—by transiently perturbing the expression of the transcription factors of interest and the signals they transduce in protoplasts of any plant species. 
     2. BACKGROUND 
     Determining the fundamental structure of gene regulatory networks (GRN) is a major challenge of systems biology. In particular, inferring GRN structure from comprehensive gene expression and transcription factor (TF)-promoter interaction datasets has become an increasingly sought after aim in both fundamental and agronomical research in plant biology (Bonneau et al, 2007, Cell 131:1354-1365; Ruffel et al., 2010, Plant Physiol 152:445-452). A crucial step for the assessment of GRN is the identification of the direct TF-target genes. 
     Transgenic plant lines expressing tagged versions of the TF-of-interest can be used together with transcriptomic and DNA-binding analyses to obtain high-confidence lists of direct targets (see e.g., Mönke et al., 2012, Nucleic acids research 40:8240-825). However, the generation of such transgenics can be a limiting factor, especially in large-scale studies or in non-model species. 
     Another major challenge in systems biology is the generation of gene regulatory networks (GRNs) that describe, and ideally, predict how the network will respond to perturbation. Currently, the global structure of a GRN is modeled by inferring regulatory relationships between transcription factors (TFs) and their target genes from genomic data (Krouk et al., 2010, Genome Biology 11:R123; Brady et al., 2011, Molecular Systems Biology 7:459; Petricka et al., 2011, Trends in Cell Biology 21:442). While diverse experimental approaches have been devised to validate interactions between specific TFs and their targets (Matallana-Ramirez et al., 2013, Molecular Plant [epub ahead of print, doi: 10.1093/mp/sst012]; Bargmann et al., 2013, Molecular Plant 6(3):978; Gorte et al., 2011, Plant Transcription Factors, vol. 754, pp. 119-141; Iwata et al., 2011, Plant Transcription Factors, vol. 754, pp. 107-117; Wehner et al., 2011, Frontiers in Plant Science 2:68), the “gold standard” in the field has been to identify primary TF-targets as genes that are both transcriptionally regulated and whose promoter region is bound by the TF of interest (Oh et al., 2009, The Plant Cell Online 21:403). However, a GRN built purely on this “gold standard” rule (Reeves et al., 2011, Plant Molecular Biology 75:347; Gorski et al., 2011, Nucleic Acids Research 39:9536; Hull et al., 2013, BMC Genomics 14:92; Fujisawa et al., 2011, Planta 235:1107), renders a static network that only includes targets stably bound by a TF under the studied conditions, and likely underestimates the dynamic interactions occurring in vivo. 
     For example, in higher plants, fluctuating nitrogen levels in the soil cause rapid and dramatic changes in plant gene expression. Nitrogen is both a metabolic nutrient and signal that broadly and rapidly reprograms genome-wide responses. While genomic responses to nitrogen have been studied for many years, only a small number of genes in nitrogen genome-wide reprogramming have been identified. The unidentified genes represent the so-called “dark matter” of such metabolic regulatory circuits, a crucial problem in understanding system-wide genetic regulation in many fields. 
     3. SUMMARY 
     Plant genes regulated by transcription factors that control the gene network response to an environmental perturbation or signal (e.g., nitrogen, water, sunlight, oxygen, temperature) are described. These genes respond rapidly to their environment, but surprisingly, there is no evidence of direct transcription factor interaction. More particularly, the large class of genes described herein (and exemplified in Tables 1, 2, 19, 20, and 23) respond to the perturbation of a regulatory transcription factor and the signal it transduces, but in fact are not stably bound to the transcription factor, and yet are most relevant to the signal induced in vivo—in other words, they represent members of the “dark matter” of metabolic regulatory circuits. The invention involves the transgenic manipulation of these “response genes” and/or the genes encoding their regulatory transcription factors in plants so that their respective gene products are either overexpressed or underexpressed in the plant in order to confer a desired phenotype; e.g., increased N usage (to enhance plant growth/biomass) or N storage/yield (to enhance N storage and/or protein accumulation in seeds of seed crops). 
     The invention is based, in part, on the development of a rapid technique named “TARGET” (Transient Assay Reporting Genome-wide Effects of Transcription factors) that uses transient transformation of a plasmid containing a glucocorticoid receptor (GR)-tagged TF in protoplasts to study the genome-wide effects of TF activation. The TARGET system can be used to rapidly retrieve information on direct TF target genes in less than two week&#39;s time. The technique can be used as a part of various experimental designs, as show in  FIG. 1 . The core of the technique makes use of an isolated nucleic acid molecule encoding a chimeric protein comprising a transcription factor fused to a domain comprising an inducible cellular localization signal and an independently expressed selectable marker. A host cell such as a plant protoplast may then be transiently transfected with the nucleic acid molecule. The selectable marker allows for the determination of which cells have been successfully transfected. The TF-inducible signal fusion is sequestered in one cellular location until this retention mechanism is released through treatment with a localization-inducing signal, such as a small molecule. To determine the transcription factor response in the presence of an environmental signal, pre-treatment with such a signal may optionally be performed before the treatment with the cellular localization-inducing signal. mRNA transcripts may then be measured by microarray analysis or other suitable method in those cells identified to be successfully transfected by means of the selectable marker. To distinguish between primary and secondary response genes, a translation inhibitor such as cyclohexamide may optionally be used to inhibit translation of mRNA. Likewise, to determine the binding properties of the transcription factors to their target sequences, an additional step of ChIP-Seq analysis may be optionally added concurrently to microarray analysis which detects mRNAs of TF targets. ChIP-Seq analysis may be done on the same cell samples as the microarray analysis. 
     While not intending to be bound to any theory of operation, using the TARGET system, gene networks have been identified that are regulated by TFs via transient associations with the target gene. Unexpectedly, these transient TF targets were found to be biologically relevant in controlling responsiveness to the applied signal/pertubation/cue. The target genes of interest are referred to herein as “response genes” that are regulated by what is referred to herein as their transiently associated “touch and go” or “hit and run” transcription factors. Conventional wisdom has focused on the “Golden Set” of genes stably bound and regulated by a TF, and has failed to uncover these transient associations described herein. 
     As a proof-of-principle candidate, the well-studied transcription factor, Abscicic acid insensitive 3 (ABI3) was investigated using TARGET, as described in more detail herein in Section 6 (Example 1). The de novo identification of the abscisic acid response element (ABRE) and a majority of the previously classified direct targets was established by use of the TARGET method, confirming its applicability. The TARGET system was then further modified, as described in further detail in Sections 7 and 10 (Examples 2 and 5), to identify genes transiently bound and regulated by the TF of the system in response to an environmental signal. These modifications allowed for the discovery of a “hit-and-run” (“touch-and-go”) mode-of-action for a proof-of-principle transcription factor candidate, bZIP1, where bZIP1 “hits” its target, initiates transcription, then dissociates (“run”), leaving the transcription going on even without bZIP1 binding to the promoter. As evidence that transcription of a gene initiated by “the Hit” continues after “the Run,” an affinity-tagged UTP was used to label and capture newly synthesized mRNA, as described in Section 11 (Example 6). By adding this UTP affinity label at a time-point when bZIP1 is not detectably bound, it was determined that response genes were still actively transcribed. Section 12 (Example 7) describes the discovery that the transient TF-targets detected specifically in the TARGET cell-based system make a unique contribution to understanding how signal transduction occurs in planta, while eluding detection in planta. 
     In Section 8 (Example 3), a method for identifying nitrogen-regulated connections conserved across model species and crops is detailed. This method is a rapid way to assess whether the function of a gene of interest is conserved across species and enables the enhancement of the translational discoveries of the TARGET system. The method of Section 8 may be used as an alternative or supplement to using the TARGET system directly in protoplasts of crops or other plant species. Section 9 (Example 4) also describes a method for identifying networks conserved across species to identify translational targets that may be used as an alternative or supplement to the TARGET system. 
     One advantage of the TARGET system is the ability to study gene regulatory networks and targets of transcription factors in a transient assay system, which means the method can be applied to plants that cannot be stably transformed. Protoplasts can be made from any plant species, and a transcription factor of interest can be transiently expressed to identify its targets genome-wide. Target genes of transcription factors can be rapidly identified because the method does not rely on the use of transgenic plants, which normally have to be stably transformed. Also, the TARGET technique allows for cross-species studies in order to analyze evolutionary conserved networks using genes from a poorly characterized plant genus or species in a better characterized model genus, such as  Arabidopsis,  which has a fully sequenced genome and has microarray chip data available. This also has important implications for translational studies of gene function, from data-rich models (e.g.  Arabidopsis ) to data-poor crops. By providing the ability to do reciprocal cross species genetic network comparisons, the TARGET technique allows for the determination of TF-target connections that are evolutionarily conserved and therefore likely the most important elements of transcription factor networks. The optional modifications to the TARGET system confers the further advantage of the ability to detect gene networks that are controlled transiently in response to environmental signals by TF interactions that have been previously ignored. TF regulation is not always associated with stable TF binding. The TARGET system uncovers TF targets that would otherwise be missed in other systems that require TF binding to identify gene targets. The TARGET system allows for the identification of the functional mode of action for any TF within and across species. 
     The most recent advance in the field of nitrogen-signaling uncovered a master transcription factor, NLP7, which when mutated, affects &gt;58% of the nitrogen-responsive genes in plants, yet can be shown to bind to only 10% of these targets. This conundrum represents a general problem in the field of transcription, and a particular problem in metabolic signaling, where TF binding is a poor indicator of system-wide gene regulation. In fact, most GRN studies have focused on determining when and how TF binding does, or does not, result in activation of its target genes. Such TF-binding approaches have missed the “dark matter” of signal transduction. The TARGET system has revealed that the largest class of genes responding to the perturbation of a TF and a signal it transduces are in fact not stably bound to the TF, and this class of genes which has the most relevance to the signal transduced has been missed in all TF studies to date. Several unique aspects of the system described enable the discovery of this large set of primary TF targets that are regulated by, but do not stably bind to the TF. 
     In one embodiment, the present invention is directed to a transgenic plant that ectopically expresses one or more touch and go (hit and run) transcription factor genes and exhibits a desired phenotype, wherein the said one or more genes comprises a polynucleotide that encodes At1g01060, At1g01720, At1g13300, At1g15100, At1g22070, At1g25550, At1g25560, At1g29160, At1g43160, At1g51700, At1g51950, At1g53910, At1g66140, At1g68670, At1g68840, At1g74660, At1g74840, At1g75390, At1g77450, At1g80840, At2g04880, At2g20570, At2g22430, At2g22850, At2g24570, At2g25000, At2g28510, At2g28550, At2g30250, At2g33710, At2g38470, At2g46830, At3g01560, At3g04070, At3g06590, At3g20770, At3g25790, At3g46130, At3g47620, At3g51920, At3g54620, At3g60490, At3g61150, At3g61890, At3g62420, At4g17490, At4g17500, At4g24240, At4g27410, At4g31800, At4g34590, At4g36540, At4g37180, At4g37260, At4g37610, At4g37730, At5g05410, At5g06800, At5G10030, At5g13080, At5g14540, At5g24800, At5g39610, At5g44190, At5g47230, At5g48655, At5g49450, At5g49520, At5g56270, At5g60850, At5g63790, At5G65210, or At5g65640. In another embodiment, the present invention is directed to a transgenic plant that ectopically expresses one or more touch and go (hit and run) transcription factor genes and exhibits a desired phenotype, wherein the said one or more genes comprises a polynucleotide that encodes At1g01060, At1g01720, At1g13300, At1g15100, At1g25550, At1g25560, At1g29160, At1g51700, At1g51950, At1g53910, At1g66140, At1g68670, At1g68840, At1g74660, At1g75390, At1g77450, At1g80840, At2g04880, At2g22850, At2g24570, At2g28510, At2g28550, At2g30250, At2g33710, At3g04070, At3g06590, At3g20770, At3g25790, At3g46130, At3g47620, At3g51920, At3g54620, At3g60490, At3g62420, At4g17490, At4g24240, At4g27410, At4g31800, At4g34590, At4g36540, At4g37180, At4g37610, At4g37730, At5g05410, At5g06800, At5G10030, At5g13080, At5g39610, At5g47230, At5g49520, At5g56270, At5g60850, At5g63790, At5G65210, or At5g65640. 
     In one embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker. In another embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the nucleic acid molecule is a DNA plasmid. In yet another embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the domain comprising an inducible nuclear localization signal is glucocorticoid receptor. In yet another embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the nucleic acid molecule is a DNA plasmid and the domain comprising an inducible nuclear localization signal is glucocorticoid receptor. 
     In one embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the selectable marker is a fluorescent selection marker. In another embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the nucleic acid molecule is a DNA plasmid, and wherein the selectable marker is a fluorescent selection marker. In yet another embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the domain comprising an inducible nuclear localization signal is glucocorticoid receptor. In yet another embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the nucleic acid molecule is a DNA plasmid, the domain comprising an inducible nuclear localization signal is glucocorticoid receptor, and the selectable marker is a fluorescent selection marker. 
     In one embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the selectable marker is green fluorescent protein, yellow fluorescent protein, red fluorescent protein, cyan fluorescent protein, or blue fluorescent protein. In another embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the nucleic acid molecule is a DNA plasmid, and wherein the selectable marker is a green fluorescent protein, yellow fluorescent protein, red fluorescent protein, cyan fluorescent protein, or blue fluorescent protein. In yet another embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the domain comprising an inducible nuclear localization signal is glucocorticoid receptor. In yet another embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the nucleic acid molecule is a DNA plasmid, the domain comprising an inducible nuclear localization signal is glucocorticoid receptor, and the selectable marker is green fluorescent protein, yellow fluorescent protein, red fluorescent protein, cyan fluorescent protein, or blue fluorescent protein. 
     In one embodiment, the present invention is directed to an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the isolated nucleic acid is DNA plasmid pBeaconRFP_GR, which comprises the nucleotide sequence of SEQ ID NO: 1. 
     In one embodiment, the present invention is directed to a host cell comprising an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker. 
     In one embodiment, the present invention is directed to a host cell comprising an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the host cell is a plant protoplast. 
     In one embodiment, the present invention is directed to a host cell comprising an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the host cell is a plant protoplast, and wherein the plant protoplast is derived from one of the following genuses:  Acorus, Aegilops, Allium, Amborella, Antirrhinum, Apium, Arabidopsis, Arachis, Beta, Betula, Brassica, Capsicum, Ceratopteris, Citrus, Cryptomeria, Cycas, Descurainia, Eschscholzia, Eucalyptus, Glycine, Gossypium, Hedyotis, Helianthus, Hordeum, Ipomoea, Lactuca, Linum, Liriodendron, Lotus, Lupinus, Lycopersicon, Medicago, Mesembryanthemum, Nicotiana, Nuphar, Pennisetum, Persea, Phaseolus, Physcomitrella, Picea, Pinus, Poncirus, Populus, Prunus, Robinia, Rosa, Saccharum, Schedonorus, Secale, Sesamum, Solanum, Sorghum, Stevia, Thellungiella, Theobroma, Triphysaria, Triticum, Vitis, Zea,  or  Zinnia.    
     In one embodiment, the present invention is directed to a host cell comprising an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the host cell is transfected with the nucleic acid molecule. 
     In one embodiment, the present invention is directed to a host cell comprising an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the host cell is transiently transfected with the nucleic acid molecule. 
     In one embodiment, the present invention is directed to a host cell comprising an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the host cell is derived from a genus that is different from the genus from which the transcription factor is derived from. 
     In one embodiment, the present invention is directed to a host cell comprising an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible nuclear localization signal; and (b) an independently expressed selectable marker, wherein the host cell is a plant protoplast derived from the genus  Arabidopsis  and the transcription factor is derived from the genus  Zea.    
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; and (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor. 
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor; and (v) identifying direct target genes of the transcription factor using a method comprising: (a) contacting the host cells with cyclohexamide; and (b) detecting the level of mRNA expressed in the host cells; wherein an alteration in the level of the mRNA expressed in the host cells treated with cyclohexamide compared to the level of the mRNA expressed in the host cells not treated with cyclohexamide indicates the identification of direct target genes of the transcription factor. 
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; and (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor, wherein the host cell is a plant protoplast. 
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor; and (v) identifying direct target genes of the transcription factor using a method comprising: (a) contacting the host cells with cyclohexamide; and (b) detecting the level of mRNA expressed in the host cells; wherein an alteration in the level of the mRNA expressed in the host cells treated with cyclohexamide compared to the level of the mRNA expressed in the host cells not treated with cyclohexamdie indicates the identification of direct target genes of the transcription factor, wherein the host cell is a plant protoplast. 
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; and (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor, wherein the host cell is a plant protoplast derived from one of the following genuses:  Acorus, Aegilops, Allium, Amborella, Antirrhinum, Apium, Arabidopsis, Arachis, Beta, Betula, Brassica, Capsicum, Ceratopteris, Citrus, Cryptomeria, Cycas, Descurainia, Eschscholzia, Eucalyptus, Glycine, Gossypium, Hedyotis, Helianthus, Hordeum, Ipomoea, Lactuca, Linum, Liriodendron, Lotus, Lupinus, Lycopersicon, Medicago, Mesembryanthemum, Nicotiana, Nuphar, Pennisetum, Persea, Phaseolus, Physcomitrella, Picea, Pinus, Poncirus, Populus, Prunus, Robinia, Rosa, Saccharum, Schedonorus, Secale, Sesamum, Solanum, Sorghum, Stevia, Thellungiella, Theobroma, Triphysaria, Triticum, Vitis, Zea,  or  Zinnia.    
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor; and (v) identifying direct target genes of the transcription factor using a method comprising: (a) contacting the host cells with cyclohexamide; and (b) detecting the level of mRNA expressed in the host cells; wherein an alteration in the level of the mRNA expressed in the host cells treated with cyclohexamide compared to the level of the mRNA expressed in the host cells not treated with cyclohexamide indicates the identification of direct target genes of the transcription factor, wherein the host cell is a plant protoplast derived from one of the following genuses:  Acorus, Aegilops, Allium, Amborella, Antirrhinum, Apium, Arabidopsis, Arachis, Beta, Betula, Brassica, Capsicum, Ceratopteris, Citrus, Cryptomeria, Cycas, Descurainia, Eschscholzia, Eucalyptus, Glycine, Gossypium, Hedyotis, Helianthus, Hordeum, Ipomoea, Lactuca, Linum, Liriodendron, Lotus, Lupinus, Lycopersicon, Medicago, Mesembryanthemum, Nicotiana, Nuphar, Pennisetum, Persea, Phaseolus, Physcomitrella, Picea, Pinus, Poncirus, Populus, Prunus, Robinia, Rosa, Saccharum, Schedonorus, Secale, Sesamum, Solanum, Sorghum, Stevia, Thellungiella, Theobroma, Triphysaria, Triticum, Vitis, Zea,  or  Zinnia.    
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; and (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor, wherein the host cells are transiently transfected with the nucleic acid molecules. 
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; and (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor, wherein the agent that induces nuclear localization of the chimeric protein is dexamethasone. 
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; and (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor, wherein the step of detecting host cells that express the selectable marker is performed by Fluorescence Activated Cell Sorting (FACS). 
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; and (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor, wherein the step of detecting the level of mRNA expressed in the host cells is performed by quantitative PCR, high throughput sequencing, or gene microarrays. 
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; and (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor, wherein the host cell is derived from a genus that is different from the genus from which the transcription factor is derived from. 
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; and (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor, wherein the host cell is a plant protoplast derived from the genus  Arabidopsis  and the transcription factor is derived from the genus  Zea.    
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting plant protoplasts with a DNA plasmid that encodes (a) a chimeric protein comprising a transcription factor fused to a glucocorticoid receptor; and (b) an independently expressed red fluorescent protein; (ii) detecting the plant protoplasts that express the red fluorescent protein by performing Fluorescence Activated Cell Sorting.(FACS); (iii) contacting the plant protoplasts that express the red fluorescent protein with an dexamethasone; and (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the plant protoplasts that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the plant protoplasts that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor. 
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor; and (v) detecting transcription factor binding to genomic DNA in the host cells. 
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; and (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor, and wherein the transcription factor is not ABI3. 
     In one embodiment, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with a nucleic acid molecule described above; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces nuclear localization of the chimeric protein; (iv) detecting the level of mRNA expressed in the host cells, wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor; and (v) detecting transcription factor binding to genomic DNA in the host cells, wherein the transcription factor is not ABI3. 
     3.1. TERMINOLOGY 
     Units, prefixes, and symbols may be denoted in their SI accepted form. Unless otherwise indicated, nucleic acids are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxyl orientation, respectively. Numeric ranges recited within the specification are inclusive of the numbers defining the range and include each integer within the defined range. Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes. Unless otherwise provided for, software, electrical, and electronics terms as used herein are as defined in The New IEEE Standard Dictionary of Electrical and Electronics Terms (5th edition, 1993). The terms defined below are more fully defined by reference to the specification as a whole. 
     As used herein, the term “agronomic” includes, but is not limited to, changes in root size, vegetative yield, seed yield or overall plant growth. Other agronomic properties include factors desirable to agricultural production and business. 
     By “amplified” is meant the construction of multiple copies of a nucleic acid sequence or multiple copies complementary to the nucleic acid sequence using at least one of the nucleic acid sequences as a template. Amplification systems include the polymerase chain reaction (PCR) system, ligase chain reaction (LCR) system, nucleic acid sequence based amplification (NASBA, Cangene, Mississauga, Ontario), Q-Beta Replicase systems, transcription-based amplification system (TAS), and strand displacement amplification (SDA). See, e.g., Diagnostic Molecular Microbiology: Principles and Applications, D. H. Persing et al., Ed., 1993, American Society for Microbiology, Washington, D.C. The product of amplification is termed an amplicon. 
     As used herein, “antisense orientation” includes reference to a duplex polynucleotide sequence that is operably linked to a promoter in an orientation where the antisense strand is transcribed. The antisense strand is sufficiently complementary to an endogenous transcription product such that translation of the endogenous transcription product is often inhibited. 
     In its broadest sense, a “delivery system,” as used herein, is any vehicle capable of facilitating delivery of a nucleic acid (or nucleic acid complex) to a cell and/or uptake of the nucleic acid by the cell. 
     The term “ectopic” is used herein to mean abnormal subcellular (e.g., switch between organellar and cytosolic localization), cell-type, tissue-type and/or developmental or temporal expression (e.g., light/dark) patterns for the particular gene or enzyme in question. Such ectopic expression does not necessarily exclude expression in tissues or developmental stages normal for said enzyme but rather entails expression in tissues or developmental stages not normal for the said enzyme. 
     By “endogenous nucleic acid sequence” and similar terms, it is intended that the sequences are natively present in the recipient plant genome and not substantially modified from its original form. 
     The term “exogenous nucleic acid sequence” as used herein refers to a nucleic acid foreign to the recipient plant host or, native to the host if the native nucleic acid is substantially modified from its original form. For example, the term includes a nucleic acid originating in the host species, where such sequence is operably linked to a promoter that differs from the natural or wild-type promoter. 
     By “encoding” or “encoded”, with respect to a specified nucleic acid, is meant comprising the information for translation into the specified protein. A nucleic acid encoding a protein may comprise non-translated sequences (e.g., introns) within translated regions of the nucleic acid, or may lack such intervening non-translated sequences (e.g., as in cDNA). The information by which a protein is encoded is specified by the use of codons. Typically, the amino acid sequence is encoded by the nucleic acid using the “universal” genetic code. However, variants of the universal code, such as are present in some plant, animal, and fungal mitochondria, the bacterium  Mycoplasma capricolum,  or the ciliate Macronucleus, may be used when the nucleic acid is expressed therein. 
     When the nucleic acid is prepared or altered synthetically, advantage can be taken of known codon preferences of the intended host where the nucleic acid is to be expressed. For example, although nucleic acid sequences of the present invention may be expressed in both monocotyledonous and dicotyledonous plant species, sequences can be modified to account for the specific codon preferences and GC content preferences of monocotyledons or dicotyledons as these preferences have been shown to differ (Murray et al., 1989, Nucl. Acids Res. 17: 477-498). Thus, the maize preferred codon for a particular amino acid may be derived from known gene sequences from maize. Maize codon usage for 28 genes from maize plants is listed in Table 4 of Murray et al., supra. 
     By “fragment” is intended a portion of the nucleotide sequence. Fragments of the modulator sequence will generally retain the biological activity of the native suppressor protein. Alternatively, fragments of the targeting sequence may or may not retain biological activity. Such targeting sequences may be useful as hybridization probes, as antisense constructs, or as co-suppression sequences. Thus, fragments of a nucleotide sequence may range from at least about 20 nucleotides, about 50 nucleotides, about 100 nucleotides, and up to the full-length nucleotide sequence of the invention. 
     As used herein “full-length sequence” in reference to a specified polynucleotide or its encoded protein means having the entire amino acid sequence of, a native (non-synthetic), endogenous, biologically active form of the specified protein. Methods to determine whether a sequence is full-length are well known in the art including such exemplary techniques as northern or western blots, primer extension, 51 protection, and ribonuclease protection. See, e.g., Plant Molecular Biology: A Laboratory Manual, Clark, Ed., 1997, Springer-Verlag, Berlin. Comparison to known full-length homologous (orthologous and/or paralogous) sequences can also be used to identify full-length sequences of the present invention. Additionally, consensus sequences typically present at the 5′ and 3′ untranslated regions of mRNA aid in the identification of a polynucleotide as full-length. For example, the consensus sequence ANNNNAUGG, where the underlined codon represents the N-terminal methionine, aids in determining whether the polynucleotide has a complete 5′ end. Consensus sequences at the 3′ end, such as polyadenylation sequences, aid in determining whether the polynucleotide has a complete 3′ end. 
     The term “gene activity” refers to one or more steps involved in gene expression, including transcription, translation, and the functioning of the protein encoded by the gene. 
     The term “genetic modification” as used herein refers to the introduction of one or more exogenous nucleic acid sequences as well as regulatory sequences, into one or more plant cells, which in certain cases can generate whole, sexually competent, viable plants. The term “genetically modified” or “genetically engineered” as used herein refers to a plant which has been generated through the aforementioned process. Genetically modified plants of the invention are capable of self-pollinating or cross-pollinating with other plants of the same species so that the foreign gene, carried in the germ line, can be inserted into or bred into agriculturally useful plant varieties. 
     As used herein, “heterologous” in reference to a nucleic acid is a nucleic acid that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention. For example, a promoter operably linked to a heterologous structural gene is from a species different from that from which the structural gene was derived, or, if from the same species, one or both are substantially modified from their original form. A heterologous protein may originate from a foreign species or, if from the same species, is substantially modified from its original form by deliberate human intervention. 
     By “host cell” is meant a cell that contains a vector and supports the replication and/or expression of the vector. Host cells may be prokaryotic cells such as  E. coli,  or eukaryotic cells such as yeast, plant, insect, amphibian, or mammalian cells. Preferably, host cells are monocotyledonous or dicotyledonous plant cells. A particularly preferred monocotyledonous host cell is a maize host cell. 
     The term “introduced” in the context of inserting a nucleic acid into a cell, means “transfection” or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA). 
     The term “isolated” refers to material, such as a nucleic acid or a protein, which is: (1) substantially or essentially free from components which normally accompany or interact with it as found in its natural environment The isolated material optionally comprises material not found with the material in its natural environment; or (2) if the material is in its natural environment, the material has been synthetically altered or synthetically produced by deliberate human intervention and/or placed at a different location within the cell. The synthetic alteration or creation of the material can be performed on the material within or apart from its natural state. For example, a naturally-occurring nucleic acid becomes an isolated nucleic acid if it is altered or produced by non-natural, synthetic methods, or if it is transcribed from DNA which has been altered or produced by non-natural, synthetic methods. See, e.g., Compounds and Methods for Site Directed Mutagenesis in Eukaryotic Cells, Kmiec, U.S. Pat. No. 5,565,350; In vivo Homologous Sequence Targeting in Eukaryotic Cells; Zarling et al., PCT/US93/03868. The isolated nucleic acid may also be produced by the synthetic re-arrangement (“shuffling”) of a part or parts of one or more allelic forms of the gene of interest Likewise, a naturally-occurring nucleic acid (e.g., a promoter) becomes isolated if it is introduced to a different locus of the genome. Nucleic acids which are “isolated,” as defined herein, are also referred to as “heterologous” nucleic acids. 
     As used herein, the term “marker” refers to a gene encoding a trait or a phenotype which permits the selection of, or the screening for, a plant or plant cell containing the marker. 
     As used herein, “nucleic acid” includes reference to a deoxyribonucleotide or ribonucleotide polymer, or chimeras thereof, in either single- or double-stranded form, and unless otherwise limited, encompasses known analogues having the essential nature of natural nucleotides in that they hybridize to single-stranded nucleic acids in a manner similar to naturally occurring nucleotides (e.g., peptide nucleic acids). 
     By “nucleic acid library” is meant a collection of isolated DNA or RNA molecules which comprise and substantially represent the entire transcribed fraction of a genome of a specified organism or of a tissue from that organism. Construction of exemplary nucleic acid libraries, such as genomic and cDNA libraries, is taught in standard molecular biology references such as Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology, Vol. 152, Academic Press, Inc., San Diego, Calif (Berger); Sambrook et al., 1989, Molecular Cloning—A Laboratory Manual, 2nd ed., Vol. 1-3; and Current Protocols in Molecular Biology, F. M. Ausubel et al., Eds., 1994, Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley &amp; Sons, Inc. 
     As used herein “operably linked” includes reference to a functional linkage between a promoter and a second sequence, wherein the promoter sequence initiates and mediates transcription of the DNA sequence corresponding to the second sequence. Generally, operably linked means that the nucleic acid sequences being linked are contiguous and, where necessary to join two protein coding regions, contiguous and in the same reading frame. 
     The term “orthologous” as used herein describes a relationship between two or more polynucleotides or proteins. Two polynucleotides or proteins are “orthologous” to one another if they are derived from a common ancestral gene and serve a similar function in different organisms. In general, orthologous polynucleotides or proteins will have similar catalytic functions (when they encode enzymes) or will serve similar structural functions (when they encode proteins or RNA that form part of the ultrastructure of a cell). 
     The term “overexpression” is used herein to mean above the normal expression level in the particular tissue, all and/or developmental or temporal stage for said enzyme/expressed protein product. 
     As used herein, the term “plant” is used in its broadest sense, including, but is not limited to, any species of woody, ornamental or decorative, crop or cereal, fruit or vegetable plant, and algae (e.g.,  Chlamydomonas reinhardtii ). Non-limiting examples of plants include plants from the genus  Arabidopsis  or the genus  Oryza.  Other examples include plants from the genuses  Acorus, Aegilops, Allium, Amborella, Antirrhinum, Apium, Arachis, Beta, Betula, Brassica, Capsicum, Ceratopteris, Citrus, Cryptomeria, Cycas, Descurainia, Eschscholzia, Eucalyptus, Glycine, Gossypium, Hedyotis, Helianthus, Hordeum, Ipomoea, Lactuca, Linum, Liriodendron, Lotus, Lupinus, Lycopersicon, Medicago, Mesembryanthemum, Nicotiana, Nuphar, Pennisetum, Persea, Phaseolus, Physcomitrella, Picea, Pinus, Poncirus, Populus, Prunus, Robinia, Rosa, Saccharum, Schedonorus, Secale, Sesamum, Solanum, Sorghum, Stevia, Thellungiella, Theobroma, Triphysaria, Triticum, Vitis, Zea,  or  Zinnia. ” Plants included in the invention are any plants amenable to transformation techniques, including gymnosperms and angiosperms, both monocotyledons and dicotyledons. Examples of monocotyledonous angiosperms include, but are not limited to, asparagus, field and sweet corn, barley, wheat, rice, sorghum, onion, pearl millet, rye and oats and other cereal grains. Examples of dicotyledonous angiosperms include, but are not limited to tomato, tobacco, cotton, rapeseed, field beans, soybeans, peppers, lettuce, peas, alfalfa, clover, cole crops or  Brassica oleracea  (e.g., cabbage, broccoli, cauliflower, brussel sprouts), radish, carrot, beets, eggplant, spinach, cucumber, squash, melons, cantaloupe, sunflowers and various ornamentals. Examples of woody species include poplar, pine, sequoia, cedar, oak, etc. Still other examples of plants include, but are not limited to, wheat, cauliflower, tomato, tobacco, corn, petunia, trees, etc. As used herein, the term “cereal crop” is used in its broadest sense. The term includes, but is not limited to, any species of grass, or grain plant (e.g., barley, corn, oats, rice, wild rice, rye, wheat, millet, sorghum, triticale, etc.), non-grass plants (e.g., buckwheat flax, legumes or soybeans, etc.). As used herein, the term “crop” or “crop plant” is used in its broadest sense. The term includes, but is not limited to, any species of plant or algae edible by humans or used as a feed for animals or used, or consumed by humans, or any plant or algae used in industry or commerce. As used herein, the term “plant” also refers to either a whole plant, a plant part, or organs (e.g., leaves, stems, roots, etc.), a plant cell, or a group of plant cells, such as plant tissue, plant seeds and progeny of same. Plantlets are also included within the meaning of “plant.” The class of plants which can be used in the methods of the invention is generally as broad as the class of higher plants amenable to transformation techniques, including both monocotyledonous and dicotyledonous plants. 
     The term “plant cell” as used herein refers to protoplasts, gamete producing cells, and cells which regenerate into whole plants. Plant cell, as used herein, further includes, without limitation, cells obtained from or found in: seeds, suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, and microspores. Plant cells can also be understood to include modified cells, such as protoplasts, obtained from the aforementioned tissues. 
     As used herein, “polynucleotide” includes reference to a deoxyribopolynucleotide, ribopolynucleotide, or chimeras or analogs thereof that have the essential nature of a natural deoxy- or ribo-nucleotide in that they hybridize, under stringent hybridization conditions, to substantially the same nucleotide sequence as naturally occurring nucleotides and/or allow translation into the same amino acid(s) as the naturally occurring nucleotide(s). A polynucleotide can be full-length or a subsequence of a native or heterologous structural or regulatory gene. Unless otherwise indicated, the term includes reference to the specified sequence as well as the complementary sequence thereof. Thus, DNAs or RNAs with backbones modified for stability or for other reasons are “polynucleotides” as that term is intended herein. Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two examples, are polynucleotides as the term is used herein. It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill in the art. The term polynucleotide as it is employed herein embraces such chemically-, enzymatically- or metabolically-modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including among other things, simple and complex cells. 
     The terms “polypeptide”, “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analogue of a corresponding naturally-occurring amino acid, as well as to naturally-occurring amino acid polymers. The essential nature of such analogues of naturally-occurring amino acids is that, when incorporated into a protein, that protein is specifically reactive to antibodies elicited to the same protein but consisting entirely of naturally occurring amino acids. The terms “polypeptide”, “peptide” and “protein” are also inclusive of modifications including, but not limited to, glycosylation, lipid attachment, sulfation, gamma-carboxylation of glutamic acid residues, hydroxylation and ADP-ribosylation. Further, this invention contemplates the use of both the methionine-containing and the methionine-less amino terminal variants of the protein of the invention. 
     As used herein “promoter” includes reference to a region of DNA upstream from the start of transcription and involved in recognition and binding of RNA polymerase and other proteins to initiate transcription. A “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell. Exemplary plant promoters include, but are not limited to, those that are obtained from plants, plant viruses, and bacteria which comprise genes expressed in plant cells such Agrobacterium or Rhizobium. Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, or seeds. Such promoters are referred to as “tissue preferred.” Promoters which initiate transcription only in certain tissue are referred to as “tissue specific.” A “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves. An “inducible” or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions or the presence of light Tissue specific, tissue preferred, cell type specific, and inducible promoters represent the class of “non-constitutive” promoters. A “constitutive” promoter is a promoter which is active under most environmental conditions. 
     As used herein “recombinant” includes reference to a cell or vector that has been modified by the introduction of a heterologous nucleic acid, or to a cell derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found in identical form within the native (non-recombinant) form of the cell, or exhibit altered expression of native genes, as a result of deliberate human intervention. The term “recombinant” as used herein does not encompass the alteration of the cell or vector by events (e.g., spontaneous mutation, natural transformation, transduction, or transposition) occurring without deliberate human intervention. 
     As used herein, a “recombinant expression cassette” is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements which permit transcription of a particular nucleic acid in a host cell. The recombinant expression cassette can be incorporated into a plasmid, chromosome, mitochondrial DNA, plastid DNA, virus, or nucleic acid fragment Typically, the recombinant expression cassette portion of an expression vector includes, among other sequences, a nucleic acid to be transcribed, and a promoter. 
     The term “regulatory sequence” as used herein refers to a nucleic acid sequence capable of controlling the transcription of an operably associated gene. Therefore, placing a gene under the regulatory control of a promoter or a regulatory element means positioning the gene such that the expression of the gene is controlled by the regulatory sequence(s). Because a microRNA binds to its target, it is a post transcriptional mechanism for regulating levels of mRNA. Thus, an miRNA can also be considered a “regulatory sequence” herein. Not just transcription factors. 
     The term “residue” or “amino acid residue” or “amino acid” are used interchangeably herein to refer to an amino acid that is incorporated into a protein, polypeptide, or peptide (collectively “protein”). The amino acid may be a naturally occurring amino acid and, unless otherwise limited, may encompass non-natural analogs of natural amino acids that can function in a similar manner as naturally occurring amino acids. 
     The term “tissue-specific promotor” is a polynucleotide sequence that specifically binds to transcription factors expressed primarily or only in such specific tissue. 
     The term “selectively hybridizes” includes reference to hybridization, under stringent hybridization conditions, of a nucleic acid sequence to a specified nucleic acid target sequence to a detectably greater degree (e.g., at least 2-fold over background) than its hybridization to non-target nucleic acid sequences and to the substantial exclusion of non-target nucleic acids. Selectively hybridizing sequences typically have about at least 80% sequence identity, preferably 90% sequence identity, and most preferably 100% sequence identity (i.e., complementary) with each other. 
     As used herein, a “stem-loop motif” or a “stem-loop structure,” sometimes also referred to as a “hairpin structure,” is given its ordinary meaning in the art, i.e., in reference to a single nucleic acid molecule having a secondary structure that includes a double-stranded region (a “stem” portion) composed of two regions of nucleotides (of the same molecule) forming either side of the double-stranded portion, and at least one “loop” region, comprising uncomplemented nucleotides (i.e., a single-stranded region). 
     The term “stringent conditions” or “stringent hybridization conditions” includes reference to conditions under which a probe will selectively hybridize to its target sequence, to a detectably greater degree than to other sequences (e.g., at least 2-fold over background). Stringent conditions are sequence-dependent and will be different in different circumstances. By controlling the stringency of the hybridization and/or washing conditions, target sequences can be identified which are 100% complementary to the probe (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing). Generally, a probe is less than about 1000 nucleotides in length, optionally less than 500 nucleotides in length. 
     Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in lx to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C. 
     Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the T m  can be approximated from the equation of Meinkoth and Wahl, 1984, Anal. Biochem., 138:267-284: T m =81.5° C+16.6 (log M)+0.41 (%GC)-0.61 (% form)-500/L; where M is the molarity of monovalent cations, %GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The T m  is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. T m  is reduced by about 1° C. for each 1% of mismatching; thus, T m , hybridization and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with ≥90% identity are sought, the T m  can be decreased 10° C. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (T m ) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermal melting point (T m ); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point (T m ); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point (T m ). Using the equation, hybridization and wash compositions, and desired T m , those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a T m  of less than 45° C. (aqueous solution) or 32° C. (formamide solution) it is preferred to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen, 1993, Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2 “Overview of principles of hybridization and the strategy of nucleic acid probe assays”, Elsevier, N.Y.; and Current Protocols in Molecular Biology, Chapter 2, Ausubel et al., Eds., 1995, Greene Publishing and Wiley-Interscience, New York. Hybridization and/or wash conditions can be applied for at least 10, 30, 60, 90, 120, or 240 minutes. 
     As used herein, “transcription factor” (“TF”) includes reference to a protein which interacts with a DNA regulatory element to affect expression of a structural gene or expression of a second regulatory gene. “Transcription factor” may also refer to the DNA encoding said transcription factor protein. The function of a transcription factor may include activation or repression of transcription initiation. 
     The term “transfection,” as used herein, refers to the introduction of a nucleic acid into a cell. The term “transient transfection,’ as used herein, refers to the introduction of a nucleic acid into a cell, wherein the nucleic acids introduced into the transfected cell are not permanently incorporated into the cellular genome. 
     As used herein, “transgenic plant” includes reference to a plant which comprises within its genome a heterologous polynucleotide or which lacks, by means of homologous recombination or other methods, a native polynucleotide. Generally, the heterologous polynucleotide is stably integrated within the genome such that the polynucleotide is passed on to successive generations. The heterologous polynucleotide may be integrated into the genome alone or as part of a recombinant expression cassette. “Transgenic” is used herein to include any cell, cell line, callus, tissue, plant part or plant, the genotype of which has been altered by the presence of heterologous nucleic acid or lacks a native nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic. The term “transgenic” as used herein does not encompass the alteration of the genome (chromosomal or extra-chromosomal) by conventional plant breeding methods or by naturally occurring events such as random cross-fertilization, non-recombinant viral infection, non-recombinant bacterial transformation, non-recombinant transposition, or spontaneous mutation. 
     The term “underexpression” is used herein to mean below the normal expression level in the particular tissue, all and/or developmental or temporal stage for said enzyme/expressed protein product. 
     As used herein, “vector” includes reference to a nucleic acid used in introduction of a polynucleotide of the present invention into a host cell. Vectors are often replicons. Expression vectors permit transcription of a nucleic acid inserted therein. 
     The following terms are used to describe the sequence relationships between a polynucleotide/polypeptide of the present invention with a reference polynucleotide/polypeptide: (a) “reference sequence”, (b) “comparison window”, (c) “sequence identity”, and (d) “percentage of sequence identity”. 
     (a) As used herein, “reference sequence” is a defined sequence used as a basis for sequence comparison with a polynucleotide/polypeptide of the present invention. A reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence. 
     (b) As used herein, “comparison window” includes reference to a contiguous and specified segment of a polynucleotide/polypeptide sequence, wherein the polynucleotide/polypeptide sequence may be compared to a reference sequence and wherein the portion of the polynucleotide/polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Generally, the comparison window is at least 20 contiguous nucleotides/amino acids residues in length, and optionally can be 30, 40, 50, 100, or longer. Those of skill in the art understand that to avoid a high similarity to a reference sequence due to inclusion of gaps in the polynucleotide/polypeptide sequence, a gap penalty is typically introduced and is subtracted from the number of matches. 
     Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman, 1981, Adv. Appl. Math. 2: 482; by the homology alignment algorithm of Needleman and Wunsch, 1970, J. Mol. Biol. 48: 443; by the search for similarity method of Pearson and Lipman, 1988, Proc. Natl. Acad. Sci. 85: 2444; by computerized implementations of these algorithms, including, but not limited to: CLUSTAL in the PC/Gene program by Intelligenetics, Mountain View, Calif.; GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis., USA; the CLUSTAL program is well described by Higgins and Sharp, 1988, Gene 73: 237-244; Higgins and Sharp, 1989, CABIOS 5: 151-153; Corpet et al., 1988, Nucleic Acids Research 16: 10881-90; Huang et al., 1992, Computer Applications in the Biosciences 8: 155-65; and Pearson et al., 1994, Methods in Molecular Biology 24: 307-331. 
     The BLAST family of programs which can be used for database similarity searches includes: BLASTN for nucleotide query sequences against nucleotide database sequences; BLASTX for nucleotide query sequences against protein database sequences; BLASTP for protein query sequences against protein database sequences; TBLASTN for protein query sequences against nucleotide database sequences; and TBLASTX for nucleotide query sequences against nucleotide database sequences. See, Current Protocols in Molecular Biology, Chapter 19, Ausubel et al., Eds., 1995, Greene Publishing and Wiley-Interscience, New York. 
     Software for performing BLAST analyses is publicly available, e.g., through the National Center for Biotechnology Information (world-wide web at ncbi.nlm.nih.gov). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold. These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always &gt;0) and N (penalty score for mismatching residues; always &lt;0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff &amp; Henikoff, 1989, Proc. Natl. Acad. Sci. USA 89:10915). 
     In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin &amp; Altschul, 1993, Proc. Natl. Acad. Sci. USA 90:5873-5877). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. 
     BLAST searches assume that proteins can be modeled as random sequences. However, many real proteins comprise regions of nonrandom sequences which may be homopolymeric tracts, short-period repeats, or regions enriched in one or more amino acids. Such low-complexity regions may be aligned between unrelated proteins even though other regions of the protein are entirely dissimilar. A number of low-complexity filter programs can be employed to reduce such low-complexity alignments. For example, the SEG (Wooten and Federhen, 1993, Comput. Chem., 17:149-163) and XNU (Claverie and States, 1993, Comput. Chem., 17:191-201) low-complexity filters can be employed alone or in combination. 
     Unless otherwise stated, nucleotide and protein identity/similarity values provided herein are calculated using GAP (GCG Version 10) under default values. 
     GAP (Global Alignment Program) can also be used to compare a polynucleotide or polypeptide of the present invention with a reference sequence. GAP uses the algorithm of Needleman and Wunsch (J. Mol. Biol. 48: 443-453,1970) to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. GAP considers all possible alignments and gap positions and creates the alignment with the largest number of matched bases and the fewest gaps. It allows for the provision of a gap creation penalty and a gap extension penalty in units of matched bases. GAP must make a profit of gap creation penalty number of matches for each gap it inserts. If a gap extension penalty greater than zero is chosen, GAP must, in addition, make a profit for each gap inserted of the length of the gap times the gap extension penalty. Default gap creation penalty values and gap extension penalty values in Version 10 of the Wisconsin Genetics Software Package for protein sequences are 8 and 2, respectively. For nucleotide sequences the default gap creation penalty is 50 while the default gap extension penalty is 3. The gap creation and gap extension penalties can be expressed as an integer selected from the group of integers consisting of from 0 to 100. Thus, for example, the gap creation and gap extension penalties can each independently be: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60 or greater. 
     GAP presents one member of the family of best alignments. There may be many members of this family, but no other member has a better quality. GAP displays four figures of merit for alignments: Quality, Ratio, Identity, and Similarity. The Quality is the metric maximized in order to align the sequences. Ratio is the quality divided by the number of bases in the shorter segment Percent Identity is the percent of the symbols that actually match. Percent Similarity is the percent of the symbols that are similar. Symbols that are across from gaps are ignored. A similarity is scored when the scoring matrix value for a pair of symbols is greater than or equal to 0.50, the similarity threshold. The scoring matrix used in Version 10 of the Wisconsin Genetics Software Package is BLOSUM62 (see Henikoff &amp; Henikoff, 1989, Proc. Natl. Acad. Sci. USA 89:10915). 
     Multiple alignment of the sequences can be performed using the CLUSTAL method of alignment (Higgins and Sharp, 1989, CABIOS. 5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwise alignments using the CLUSTAL method are KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. 
     (c) As used herein, “sequence identity” or “identity” in the context of two nucleic acid or polypeptide sequences includes reference to the residues in the two sequences which are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences which differ by such conservative substitutions are said to have “sequence similarity” or “similarity”. Means for making this adjustment are well-known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., according to the algorithm of Meyers and Miller, 1988, Computer Applic. Biol. Sci., 4:11-17, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif., USA). 
     Polynucleotide sequences having “substantial identity” are those sequences having at least about 50%, 60% sequence identity, generally 70% sequence identity, preferably at least 80%, more preferably at least 90%, and most preferably at least 95%, compared to a reference sequence using one of the alignment programs described above. Preferably sequence identity is determined using the default parameters determined by the program. Substantial identity of amino acid sequences generally means sequence identity of at least 50%, more preferably at least 70%, 80%, 90%, and most preferably at least 95%. Nucleotide sequences are generally substantially identical if the two molecules hybridize to each other under stringent conditions. 
     (d) As used herein, “percentage of sequence identity” means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. 
     As used herein, the term “transgenic,” when used in reference to a plant (i.e., a “transgenic plant”) refers to a plant that contains at least one heterologous gene in one or more of its cells, or that lacks at least one native gene, such as by means of homologous recombination, in one or more of its cells. 
     As used herein, “substantially complementary,” in reference to nucleic acids, refers to sequences of nucleotides (which may be on the same nucleic acid molecule or on different molecules) that are sufficiently complementary to be able to interact with each other in a predictable fashion, for example, producing a generally predictable secondary structure, such as a stem-loop motif. In some cases, two sequences of nucleotides that are substantially complementary may be at least about 75% complementary to each other, and in some cases, are at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, or 100% complementary to each other. In some cases, two molecules that are sufficiently complementary may have a maximum of 40 mismatches (e.g., where one base of the nucleic acid sequence does not have a complementary partner on the other nucleic acid sequence, for example, due to additions, deletions, substitutions, bulges, etc.), and in other cases, the two molecules may have a maximum of 30 mismatches, 20 mismatches, 10 mismatches, or 7 mismatches. In still other cases, the two sufficiently complementary nucleic acid sequences may have a maximum of 0, 1, 2, 3, 4, 5, or 6 mismatches. 
     By “variants” is intended substantially similar sequences. For “variant” nucleotide sequences, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of the modulator of the invention. Variant nucleotide sequences include synthetically derived sequences, such as those generated, for example, using site-directed mutagenesis. Generally, variants of a particular nucleotide sequence of the invention will have at least about 40%, 50%, 60%, 65%, 70%, generally at least about 75%, 80%, 85%, preferably at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, and more preferably at least about 98%, 99% or more sequence identity to that particular nucleotide sequence as determined by sequence alignment programs described elsewhere herein using default parameters. By “variant” protein is intended a protein derived from the native protein by deletion or addition of one or more amino acids to the N-terminal and/or C-terminal end of the native protein; deletion or addition of one or more amino acids at one or more sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein. Such variants may result from, for example, genetic polymorphism or human manipulation. Conservative amino acid substitutions will generally result in variants that retain biological function 
     As used herein, the term “yield” or “plant yield” refers to increased plant growth, and/or increased biomass. In one embodiment, increased yield results from increased growth rate and increased root size. In another embodiment, increased yield is derived from shoot growth. In still another embodiment, increased yield is derived from fruit growth. 
    
    
     
       4. DESCRIPTION OF THE FIGURES 
         FIG. 1 . Experimental scheme for TF and signal perturbation (A) and parallel RNA-Seq and ChIP-Seq analysis (B) of bZIP1 primary targets. (A) A GR::TF fusion protein is overexpressed in a protoplast and its location is restricted to the cytoplasm by Hsp90. DEX-treatment, releases the GR::TF from Hsp90 allowing TF entry to nucleus, where the TF binds and regulates its target genes (Bargmann et al., 2013, Molecular Plant 6(3):978; Eklund et al., 2010, Plant Cell 22:349). In the presence of CHX, translation is blocked so that gene expression level changes are caused solely by the TF association with primary targets, and not downstream effectors. (B) Prior to the GR::TF nuclear import, a pre-treatment with a signal (e.g. N) could result in post-translational modifications of the TF and/or transcriptional/post-translational effects on its TF partners (TF2). (C) Experimental design for temporal induction of TF and/or signal followed by identification of primary bZIP1 targets by either Microarray or ChIP-Seq analysis in the TARGET cell-based system (Bargmann et al., 2013, Molecular Plant 6(3):978). CHX: cycloheximide; DEX: dexamethasone; N: nitrogen; GR: glucocorticoid receptor. 
         FIG. 2 . Diagram of the pBeaconRFP_GR vector. The pBeaconRFP_GR vector contains a red fluorescent protein (RFP) positive selection cassette and a Gateway recombination cassette that is in frame with the rat glucocorticoid receptor (GR) fusion protein. The plasmid is used to transfect protoplast suspensions, followed by treatment with dexamethasone and/or cycloheximide and cell-sorting of successful transformants for transcriptomic analysis. 
         FIG. 3 . Preliminary analysis and microarray validation. (A) Timecourse qPCR analysis of PER1 and CRU3 induction by DEX in the presence of CHX. (B) The induction of six genes found to be significantly induced by ABI3 activation in the microarray was verified by qPCR analysis of independent transformations. Averages +/−SEM are presented, ns-not significant, **p&lt;0.01, ***p&lt;0.001 t-test DEX-treatment n=3. 
         FIG. 4 . Promoter analysis of genes directly up-regulated by ABI3. (A) Spatial representation of RY-repeat, ABRE , G-box and bZIP-core CREs in the promoters of the 186 direct ABI3 up-regulated genes. Genes were ordered by fold induction. (B) Relative binding-site density distribution for the CREs in A 1000 bp upstream of the transcription start site in the 186 direct up-regulated genes. (C) Statistical overrepresentation of CREs in direct up-regulated genes. A sliding window of 30 genes was applied to calculate significance according to a hypergeometric test. Black dotted line indicates log fold change of the 186 genes. (D) The ABRE, G-box and bZIP-core elements. 
         FIG. 5 . qPCR quantification of CRU3 transcript levels in protoplasts transformed with pBeaconRFP_GR-ABI3 or an empty vector control and treated with DEX and/or CHX. Averages +/−SEM are presented, ns-not significant, *p&lt;0.05, ***p&lt;0.001 t-test DEX-treatment n=3. 
         FIG. 6 . qPCR quantification of PER1 transcript levels in protoplasts transformed with pBeaconRFP_GR-ABI3 or an empty vector control and treated with DEX and/or CHX. Averages +/−SEM are presented, ns-not significant, *p&lt;0.05, ***p&lt;0.001 t-test DEX-treatment n=3.  FIG. 6 . Proposed model of the interaction between the  Arabidopsis  circadian clock and N-assimilatory pathway. Arrows indicate influences that affect the function of the two processes. Black arrow: Clock function would affect N-assimilation. This influence is at least partly due to the direct regulatory role of CCA1 on N-assimilation. Grey arrow: N-assimilation would influence clock function through downstream metabolites such as Glu, Gln and possibly other N-metabolites. 
         FIG. 7 . The intersection of 186 genes identified by TARGET as directly up-regulated by ABI3 and genes identified by previous studies as direct up-regulated targets of ABI3 (98 genes;), up-regulated targets of VP1 (51 genes) and ABI5 (59 genes). 
         FIG. 8 . Network model of putative ABI3 connections to its direct up-regulated target genes via the RY-repeat motif (CATGCA) and through interaction with ABRE binding factors (ABFs) and ABRE (ACGTGKC) or the more degenerate G-box (CACGTG) and bZIP core (ACGTG) elements. Target genes (circles) are sized according to their strength of induction. 
         FIG. 9 . Weight matrix representation of the ABRE-like (CACGTGKC) motif retrieved by the MotifSampler and MEME algorithms from the 1 kb upstream of the transcription start sites of the top fifty direct up-regulated ABI3 targets, Ze=7.19 and Ze=7.11, respectively. 
         FIG. 10 . Identification of primary targets of bZIP1 by either Microarray or ChIP-Seq and integration of results. (A) Bioinformatics pipeline used to analyze the transcriptome data for transcriptionally regulated genes and the ChIP-Seq data for bZIP1-bound genes. Data from both sources were then integrated to decipher the binding and regulation dynamics. (B) Identification of primary targets regulated by bZIP1 in the presence of cycloheximide (to block secondary targets) and (C) their associated cis-regulatory motifs. (D) Identification of bZIP1-bound genes by ChIP-Seq (E) and their associated cis-regulatory motifs. 
         FIG. 11 . Three distinct classes of bZIP1 primary targets identified by integration of microarray and ChIP-SEQ data (A) TF primary targets identified by either bZIP1-induced regulation in the presence of CHX (microarray) or bZIP1 binding (ChIP-SEQ) led to the identification of three distinct classes of bZIP1 primary targets: (I) “Poised” TF-bound but not regulated, (II) “Active” TF-bound and regulated, and (III) “Transient” TF-regulated but no binding, which can further be divided into subclasses based on the direction of regulation. Note that 187 bZIP1-bound TF-targets are not on the ATH1 microarray. The over-represented GO terms (FDR &lt;0.01) for each subclass are listed. The significance of overlap with the N-responsive genes, or genes regulated by N*bZIP1 interaction was calculated for each subclass by hypergeometric distribution. (B) Comparison of the subclasses with previous reported bZIP1 regulated genes in planta (Kang et al., 2010, Molecular Plant 3:361), steady-state N-regulated genes (Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939), and early/transient N-regulated genes (Krouk et al., 2010, Genome Biology 11:R123). (C) Enrichment of mRNA of different half-lives (Chiba et al., 2013, Plant &amp; cell physiology. 54:180) in Class II and Class III of bZIP1 primary targets (filtered to only contain genes that are regulated by DEX in the presence and absence of CHX). The number of genes overlapping in each comparison is listed and the significance of the overlap is noted. Any overlap significance &lt;0.01 is highlighted. 
         FIG. 12 . A model for three modes of temporal TF Action of bZIP1 on primary target genes: “poised”, “active” and “transient”. This model illustrates temporal modes of action of bZIP1 with the three different classes of primary gene targets-I “poised”, II “active”, and III “transient” (A) and significantly over-represented cis-element motifs in each class (B). The significance of the over-representation of known bZIP binding motifs (hybrid ACGT box [ACG]ACGT[GC] (Kang et al., 2010, Molecular Plant 3:361) and GCN4 binding motif (Onodera et al., 2001, Journal of Biological Chemistry 276:14139)) are listed. The significance of specific cis-motifs enriched in each subclass, compared to other classes, is shown as a heat-map. 
         FIG. 13 . Heatmap showing the expression profiles of nitrogen (N)-responsive genes in the TARGET cell-based system (Bargmann et al., 2013, Molecular Plant 6(3):978) identified by microarray. The GO terms over-represented (FDR adjusted pval&lt;0.05) were identified for the N up-regulated and N down-regulated genes. 
         FIG. 14 . Genes regulated in response to DEX treatment (i.e. DEX-induced TF nuclear import) (FDR&lt;0.05) and with a significant N*DEX interaction (pval&lt;0.01) from ANOVA analysis. (A) Heatmap showing four distinct clusters were observed and their significantly enriched GO terms are listed. (B) Gene regulatory network constructed from the genes in (A) and bZIP1 using Multinetwork feature in VirtualPlant (Katari et al., 2010, Plant Physiology 152:500). 
         FIG. 15 . bZIP1 targets identified in this study validate the predicted bZIP1 targets based on network analysis of in planta N-treatment transcriptome data (Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939). 27 genes were predicted to be the targets of bZIP1 of which 14 were confirmed by this study. 
         FIG. 16 . The comparison of the genes of the 5 subclasses with (A) DEX regulated genes in the absence of CHX and (B) previously reported Carbon (C)- and Light (L)-regulated gene lists identified from roots and shoots (Krouk et al., 2009, PLoS Computational Biology 5:e1000326). The number of genes overlapping in each comparison is listed and the significance of the overlap noted. A significance of overlap &lt;0.01 is highlighted. 
         FIG. 17 . Cis-regulatory motif analysis of the subclasses of bZIP1 target genes. The significance of over-representation of known cis-regulatory motifs were calculated for each subclass, and if the significance in at least one subclass is smaller than 0.01, the motif is listed and significance shown as a heatmap (A). From this collection of significant motifs, relatively enriched motifs in each subclass were selected by the pattern match algorithm PTM in Mev (B). The motifs enriched in the subgroups were also identified by PTM for the following subgroups: activated subgroup, repressed subgroup, bound and regulated subgroup, and no binding but regulated subgroup (C). 
         FIG. 18 . Enrichment of mRNA of different half-lives (34) in Class II and Class III of bZIP1 primary target genes. The Class II and Class III genes here are filtered to only contain genes that are also regulated by DEX in the absence of CHX. Number of genes overlapping in each comparison is listed and the significance of the overlap noted. A significance of overlap &lt;0.01 is highlighted. 
         FIG. 19 . Schematic diagram of the data mining approach used in this study. Briefly,  O. sativa  (rice) and  A. thaliana  plants were grown for 12 days before treatment with nitrogen. Genome-wide analysis using Affymetrix chips has been used in order to quantify mRNA levels. Modeling of microarray data, using ANOVA and ortholog and network analysis (detailed in Methods), were used to identify a core translational network. 
         FIG. 20 . Number of N-responsive genes in  O. sativa  and  A. thaliana  with ortholog information in the other species (*E-value cutoff 1e −20 ). 
         FIG. 21 . Flowchart of N-regulated rice core correlated network analysis process. 
         FIG. 22 . NutriNet Modules: Constructing maize N-regulatory networks exploiting  Arabidopsis  Network Knowledge. 
         FIG. 23 . A NutriNet Module: Core N-regulatory module conserved between maize and  Arabidopsis  includes previously validated transcription factor hubs (CCA1, GLK1, and bZIP) (Gutierrez et al., 2008, Proc Natl Acad Sci USA 105(12):4939; Baulcombe, 2010, Science 327(5967):761). 
         FIGS. 24 . Experimental scheme for TF (A) and N-signal perturbation (B), and parallel RNA-Seq and ChIP-Seq analysis (C &amp; D) of bZIP1 primary targets. (A) A GR::TF fusion protein is overexpressed in protoplasts and its location is restricted to the cytoplasm by Hsp90. DEX-treatment releases the GR::TF from Hsp90 allowing TF entry to the nucleus, where the TF binds to and regulates its target genes. CHX blocks translation. Thus, when DEX-induced TF import is performed in the presence of CHX, changes in transcript levels are attributed to the direct interaction of the target with the TF of interest. (B) Prior to DEX-induction of GR::TF nuclear import, pre-treatment with a signal (e.g. N-nutrient signal) could result in posttranslational modifications of the TF and/or transcriptional/post-translational effects on its TF partners (e.g. TF2). Genes whose response to TF-induced regulation (by DEX) is altered by CHX treatment were removed from the study to eliminate potential side effects of CHX. (C) Experimental design for identification of primary bZIP1 targets by either Microarray or ChIP-Seq analysis in the cell-based TARGET system (11, 26). CHX: cycloheximide; DEX: dexamethasone; N: nitrogen; GR: glucocorticoid receptor. (D) Bioinformatics pipeline to identify bZIP1 primary targets based on transcriptional response or TF binding. bZIP1-regulated genes were identified by ATH1 arrays. bZIP1-bound genes were identified by ChIP-Seq analysis. The integrated datasets were analyzed for the functional significance of classes of genes grouped based on TF-binding and/or TF-regulation. 
         FIG. 25 . Nitrogen-responsive genes in the cell-based TARGET system. A heat map showing the expression profiles of 328 nitrogen (N)-responsive genes in the TARGET cell-based system as identified by microarray in this study. The GO terms over-represented (FDR adjusted p-val&lt;0.05) were identified for the genes up-regulated or down-regulated in response to the N-signal perturbation. 
         FIG. 26 . Validation of N-response in TARGET system. The 328 N-responsive genes in the cell-based TARGET system show significant overlaps with previously reported N-response gene in roots of whole plants and in seedlings. The significance of overlap between any two of these N-responsive sets is determined by the Genesect tool inVirtualPlant Platform (www virtualplant.org). 
         FIGS. 27 . Primary targets of bZIP1 are identified by either TF-activation or TF-binding. (A) Cluster analysis of bZIP1 primary target genes identified by their upregulation or down-regulation by DEX-induced bZIP1 nuclear import in  Arabidopsis  root protoplasts sequentially treated with inorganic N, CHX and DEX. bZIP motifs and other cismotifs are significantly over-represented in the promoters of bZIP1 primary target genes identified by transcriptional response (B), or by bZIP1 binding (D). (C) Examples of primary targets bound transiently by bZIP1 based on time-course ChIP-Seq. 
         FIG. 28 . Genes influenced by a significant N-signal x bZIP1 interaction in the cell-based TARGET system. Genes regulated in response to DEX-induced bZIP1 nuclear import (FDR&lt;0.05) and with a significant N-signal*bZIP1 interaction (p-val&lt;0.01) from ANOVA analysis. Heat map showing four distinct clusters of genes regulated by a N-signal×bZIP1 interaction. Note that two of the “early response” genes shown to bind transiently to bZIP1 (NLP3 and LBD39, see  FIG. 29C ), are in cluster 1 of the genes regulated by a N-signal×bZIP1 interaction. 
         FIGS. 29 . Class III transient targets of bZIP1 are uniquely associated with rapid N signaling. (A) Primary bZIP1 targets identified by either bZIP1-induced regulation or bZIP1-binding assayed in the same root protoplasts samples. Intersection of these datasets revealed three distinct classes of primary targets: (Class I) “Poised”, TF-bound but not regulated, (Class II) “Stable”, TF-bound and regulated, and (Class III) “Transient”, TF-regulated but no detectable binding. Classes II and III are subdivided into activated or repressed, with their associated over-represented GO terms (FDR &lt;0.01) listed. (B) bZIP1 primary targets detected in protoplasts were compared with bZIP1 regulated genes in planta. The size of overlap is listed and significance is indicated by asterisks (highlight: p-val&lt;0.001)). (C) bZIP1 primary targets detected in protoplasts were compared with and N-regulated genes in plants. The size of overlap is listed and significance is indicated by asterisks (highlight: p-val&lt;0.001)). Class III “transient” targets are uniquely enriched in genes related to rapid N-signaling. (D) Class IIIA target genes (NLP3 and NRT2.1) show transient bZIP1 binding at 1 and 5 minutes after nuclear import of bZIP1, but not at later time-points (30 and 60 min). 
         FIG. 30 . Class III bZIP1 transient targets are specifically enriched in co-inherited cis-motif elements. The significance of the over-representation of the known bZIP binding motifs hybrid ACGT box, and GCN4 binding motif, are listed for each class of bZIP1 primary targets. In addition to these bZIP binding sites, the significance of enrichment of co-inherited cis-regulatory motifs is shown as a heat-map specific to each subclass. 
         FIG. 31 . Over-represented GO terms in each of the bZIP1 target classes. The set of genes from each class of bZIP1 targets were analyzed for over-representation of GO terms using the BioMaps feature of VirtualPlant (www.virtualplant.org). All classes of bZIP1 targets have an over-representation of GO terms related to “Stress” and “Stimulus”. When sub-divided by direction of regulation, Class IIA loses all significant GO terms. In addition to the stress terms, Class I is over-represented for genes responding to “biotic stress” and “divalent ion transport”. Class IIIA shows specific enrichment of GO terms for “Amino acid metabolism,” hence showing an enrichment of genes related to the N-signal. Class IIIB has specific enrichment of genes related to cell death and phosphorus metabolism. 
         FIG. 32 . A network of biological processes represented by Class III transient bZIP1 targets. The set of genes from Class III “transient” bZIP1 targets were analyzed for over-representation of GO terms using the Bingo plugin in Cytoscape (Smoot et al., 2011,  Bioinformatics  27(3):431-432). In addition to terms related to “Stress” and “Stimulus” which are found in all 3 classes of bZIP1 targets, the Class III transient targets also shows class-specific enrichment of GO terms both for “nitrogen metabolism” and the “regulation of nitrogen compound metabolism”, hence showing an enrichment of genes related to the N-signal. Class III transient targets also show overrepresentation of genes involved in “defense response”, “phosphorylation” and “regulation of metabolism.” 
         FIG. 33 . bZIP1 as a pioneer TF for N-uptake/assimilation pathway genes. Global analysis of bZIP1 targets reveals that it regulates multiple genes encoding for the Nuptake/assimilation pathway. Multiple genes encoding nitrate transporters and isoenzymes in the N-assimilation pathway are represented by hexagonal nodes. The nodes targeted by bZIP1 are connected with red arrows. Thickness of the arrow is proportional to the number of genes in that node that are targeted by bZIP1. The IDs of the targeted genes are listed adjacent to the node. This pathway overview suggests that bZIP1 is a master regulator of the N-assimilation pathway. The pathway was constructed in Cytoscape (www.cytoscape.org) based on KEGG annotation (www.genome.jp/kegg/). Node abbreviations: NRT: Nitrate transporters; AMT: Ammonia transporters; GDH: Glutamate dehydrogenases; GOGAT: Glutamate synthases; GS: Glutamine synthetases; ASN: Asparagine synthetases. 
         FIG. 34 . A “Hit-and-Run” transcription model enables bZIP1 to rapidly and catalytically activate genes in response to a N-signal. The transient mode-of-action for Class III bZIP1 targets follows a classic model for “hit-and-run” transcription. In this model, transient interactions of bZIP1 with Class III targets (the “hit”), lead to recruitment of the transcription machinery and possibly other TFs. Next, the transient nature of the bZIP1-target interaction (the “run”) enables bZIP1 to catalytically activate a large set of rapidly induced genes (e.g. target 2 . . . target n) biologically relevant to rapid transduction of the N-signal. 
         FIGS. 35 . 4sU RNA tagging. (A) Dot blot showing that protoplasts are able to use 4sU for RNA synthesis in 20 min after the addition of 4sU. (B) Overlap of the actively transcribed genes regulated by bZIP1 (rows) with the three classes of bZIP1 targets (columns). The size of the overlap of two gene sets (labeled by the row and the column) was indicated by the numbers. The significance of overlap was indicated as: **: p&lt;0.01; ***: p&lt;0.001 (shade). (C). Time-series ChIP-seq showing the transient binding of bZIP1 to NLP3 at 1-5 min after nuclear import of bZIP1. (D) 4sU tagging showing that NLP3 is transcribed due to bZIP1 at both 20 min and 5 hr after nuclear import of bZIP1. 
         FIG. 36 . Transient bZIP1 targets detected in TARGET cell-based system (inner circle) are predicted to regulate secondary targets of TF1 identified in planta (outer circle). 
         FIG. 37 . The Network Walking Pipeline. Network inference links transient TF2 targets of TF1, detected only in the cell-based TARGET system, to secondary TF targets (gene Z) detected only by in planta TF1 perturbation. 
     
    
    
     5. DETAILED DESCRIPTION 
     The present invention involves plant genes that are regulated by transcription factors that control the gene network response to an environmental perturbation or signal (e.g., nitrogen, water, sunlight, oxygen, temperature). These genes respond rapidly to their environment, but surprisingly, there is no evidence of direct transcription factor interaction. More particularly, the large class of genes described herein (and exemplified in Tables 1, 2, 19, 20, and 23) respond to the perturbation of a regulatory transcription factor and the signal it transduces, but in fact are not stably bound to the transcription factor, and yet are most relevant to the signal induced in vivo—in other words, they represent members of the “dark matter” of metabolic regulatory circuits. In some embodiments, these “response genes” are transgenically manipulated so that their respective gene products are either overexpressed or underexpressed in a plant in order to confer a desired phenotype. In other embodiments, the genes encoding the transcription factors regulating these “response genes” are transgenically manipulated so that their respective gene products are either overexpressed or underexpressed in a plant in order to confer a desired phenotype. In a particular embodiment, the desired phenotype is increased nitrogen usage, which may be desired to enhance plant growth. In another embodiment, the desired phenotype is increased nitrogen storage, which may be desired to enhance the storage of nitrogen in seeds of seed crops. In yet other embodiments, the desired phenotype is 
     In certain embodiments, the transgenically manipulated response gene is one or more of the following (also listed in Tables 1 and 2): At3g28510, At1g73260, At1g22400, At1g80460, At1g05570, At5g22570, At5g65110, At1g24440, At5g04310, At3g16150, At4g13430, At1g08090, At5g57655, At1g62660, At3g14050, At5g18670, At1g15380, At5g56870, At2g43400, At3g28510, At1g73260, At1g22400, At1g80460, At1g05570, At5g22570, At5g65110, At1g24440, At5g04310, At3g16150, At4g13430, At1g08090, At5g57655, At1g62660, At3g14050, At5g18670, At1g15380, At5g56870, At2g43400, At3g28510, At1g73260, At1g22400, At1g80460, At1g05570, At5g22570, At5g65110, At1g24440, At5g04310, At3g16150, At4g13430, At1g08090, At5g57655, At1g62660, At3g14050, At5g18670, At1g15380, At5g56870, At2g43400, At3g28510, At1g73260, At1g22400, At1g80460, At1g05570, At5g22570, At5g65110, At1g24440, At5g04310, At3g16150, At4g13430, At1g08090, At5g57655, At1g62660, At3g14050, At5g18670, At1g15380, At5g56870, or At2g43400. 
     In certain embodiments, the transgenically manipulated TF is one or more of the following (also listed in Table 3): At1g01060, At1g01720, At1g13300, At1g15100, At1g22070, At1g25550, At1g25560, At1g29160, At1g43160, At1g51700, At1g51950, At1g53910, At1g66140, At1g68670, At1g68840, At1g74660, At1g74840, At1g75390, At1g77450, At1g80840, At2g04880, At2g20570, At2g22430, At2g22850, At2g24570, At2g25000, At2g28510, At2g28550, At2g30250, At2g33710, At2g38470, At2g46830, At3g01560, At3g04070, At3g06590, At3g20770, At3g25790, At3g46130, At3g47620, At3g51920, At3g54620, At3g60490, At3g61150, At3g61890, At3g62420, At4g17490, At4g17500, At4g24240, At4g27410, At4g31800, At4g34590, At4g36540, At4g37180, At4g37260, At4g37610, At4g37730, At5g05410, At5g06800, At5G10030, At5g13080, At5g14540, At5g24800, At5g39610, At5g44190, At5g47230, At5g48655, At5g49450, At5g49520, At5g56270, At5g60850, At5g63790, At5G65210, or At5g65640. 
     In certain embodiments, the transgenically manipulated plant is a species of woody, ornamental, decorative, crop, cereal, fruit, or vegetable. In other embodiments, the plant is a species of one of the following genuses:  Acorus, Aegilops, Allium, Amborella, Antirrhimum, Apium, Arabidopsis, Arachis, Arachis, Beta, Betula, Brassica, Capsicum, Ceratopteris, Citrus, Cryptomeria, Cycas, Descurainia, Eschscholzia, Eucalyptus, Glycine, Gossypium, Hedyotis, Helianthus, Hordeum, Ipomoea, Lactuca, Linum, Liriodendron, Lotus, Lupinus, Lycopersicon, Medicago, Mesembryanthemum, Nicotiana, Nuphar, Pennisetum, Persea, Phaseolus, Physcomitrella, Picea, Pinus, Poncirus, Populus, Prunus, Robinia, Rosa, Saccharum, Schedonorus, Secale, Sesamum, Solanum, Sorghum, Stevia, Thellungiella, Theobroma, Triphysaria, Triticum, Vitis, Zea,  or  Zinnia.    
     The invention is based, in part, on the development of a rapid technique named “TARGET” that uses transient expression of a glucocorticoid receptor (GR)-tagged TF in protoplasts to study the genome-wide effects of TF activation. In some embodiments, the TARGET system can retrieve information on direct target genes in less than two weeks time. Multiple experimental designs exist for use of the TARGET system, as shown in  FIG. 1 . In some embodiments, the present invention is directed to a method for identifying target genes of a transcription factor comprising: (i) transfecting host cells with an isolated nucleic acid molecule that encodes (a) a chimeric protein comprising a transcription factor fused to a domain comprising an inducible cellular localization signal; and (b) an independently expressed selectable marker; (ii) detecting host cells that express the selectable marker; (iii) contacting the host cells that express the selectable marker with an agent that induces localization (e.g. counters sequestration in the cytoplasm and/or targets to the nucleus, mitochondria, or chloroplasts) of the chimeric protein; and (iv) detecting the level of mRNA expressed in the host cells; wherein an alteration in the level of the mRNA expressed in the host cells that have nuclear localization of the chimeric protein compared to the level of the mRNA expressed in the host cells that do not have nuclear localization of the chimeric protein indicates the identification of target genes of the transcription factor. 
     In certain embodiments, the method of the present invention further comprises identifying direct target genes of the transcription factor comprising: (v) contacting the host cells with cyclohexamide; and (vi) detecting the level of mRNA expressed in the host cells; wherein an alteration in the level of the mRNA expressed in the host cells treated with cyclohexamide compared to the level of the mRNA expressed in the host cells not treated with cyclohexamide indicates the identification of direct target genes of the transcription factor. 
     In some embodiments, the nucleic acid molecule utilized in the methods of the invention is a DNA plasmid. In some embodiments, the domain comprising an inducible cellular localization signal encoded by the nucleic acid molecule used in the method of the invention is glucocorticoid receptor and the agent that allows for nuclear localization of the chimeric protein is dexamethasone. Dexamethasone prevents sequestration of the GR-TF fusion in the cytoplasm, allowing for localization to the nucleus. In some embodiments, the cellular localization signal encoded by the nucleic acid molecule allows for localization to the chloroplast or mitochondria upon treatment with the inducing agent. 
     In one embodiment, a) an isolated nucleic acid encoding a GR-TF fusion construct and an independently expressed selectable marker (e.g. a fluorescent protein such as RFP) is transiently transfected into plant protoplasts; b) treatment of the protoplasts with dexamethasone releases the GR-TF fusion from sequestration in the cytoplasm, allowing the TF to reach target genes; c) protoplasts that have been transiently transfected are identified by means of the detectable signal gene (e.g. by fluorescence activated cell sorting (FACS) to determine the presence of a fluorescent protein such as RFP); d) mRNA transcripts are measured from the transiently transfected protoplasts through use of a microarray analysis. 
     In some embodiments, the protoplasts are optionally exposed to an environmental signal, such as nitrogen, before treatment with dexamethasone, allowing for the measurement of transcription factor activity in response to the signal. In some embodiments, protoplasts may optionally be treated with cyclohexamide prior to or concurrently with dexamethasone treatment, which blocks translation, allowing for the distinction of primary target genes, which are still expressed in the presence of cyclohexamide, from secondary target genes, which are not expressed in the presence of cyclohexamide. In some embodiments, TF binding to response genes in transiently transfected protoplasts may optionally be analyzed using ChIP-Seq. In some embodiments, ChIP-Seq or microarray analysis is performed at differing time points after an environmental signal in order to determine temporal changes in TF binding or gene expression. 
     In certain embodiments, gene networks are identified that are regulated by TFs which demonstrate only transient association with a target gene. The identified TFs that regulate a target gene but are only transiently associated with that target gene can be referred to as “touch and go” or “hit and run” TFs. Touch and go (hit and run) TFs are implicated when (i) one or more particular gene transcript levels are perturbed when the TF-fusion construct is transiently expressed and released from sequestration in the cytoplasm, and (ii) stable binding to the gene or genes is not detected by ChIP SEQ analysis. In some embodiments, these touch and go (hit and run) TFs regulate genes that control responsiveness to an environmental signal, perturbation, or cue. The identified genes targeted by these transiently-associating TFs in response to an environmental signal, perturbation, or cue can be referred to as “response genes.” “Response genes” are implicated when, in the presence of an environmental signal, perturbation, or cue, “touch and go” (hit and run) TFs perturb the levels of one or more particular gene transcript yet do not stably bind the gene as measured by ChIP-Seq analysis. The identification of a particular response gene or set of genes may vary with time after the protoplast is exposed to the environmental signal, perturbation, or cue. 
     The present invention uses nucleic acid molecules, compositions and methods for determining the target genes of transcription factors and the structure of gene regulatory networks (GRN) by transiently expressing transcription factors of interest in host cells, such as protoplasts. The protoplasts can be isolated and utilized from virtually any plant genus and species in the methods of the invention so that target genes and gene regulatory networks in poorly characterized plant genus and species can be studied. The methods of the invention allow for cross-species studies in order to analyze evolutionary conserved networks using genes from a poorly characterized plant genus or species in a better characterized model genus, such as  Arabidopsis,  which has a fully sequenced genome and has microarray chip data available. By providing the ability to do reciprocal cross species genetic network comparisons, the TARGET technique allows for the determination of what is evolutionary conserved and therefore likely the most important elements of transcription factor networks. 
     In some embodiments, the selectable marker encoded by the nucleic acid molecule used in the method of the invention is a fluorescent selection marker. A fluorescent selection marker that can be used in the method of the invention includes, but is not limited to, green fluorescent protein, yellow fluorescent protein, red fluorescent protein, cyan fluorescent protein, or blue fluorescent protein. In a specific embodiment, the fluorescent selection marker used in the method of the invention is red fluorescent protein. In certain embodiments, the step of detecting host cells that express the selectable marker is performed by Fluorescence Activated Cell Sorting (“FACS”). 
     In a specific embodiment, the nucleic acid molecule utilized in the methods of the invention is DNA plasmid pBeaconRFP_GR, which comprises the nucleotide sequence of SEQ ID NO: 1. 
     In certain embodiments, the host cell utilized in the methods of the present invention are transiently transfected with the nucleic acid molecules of the invention. In some embodiments, the host cell utilized in the methods of the present invention is a plant protoplast. In particular embodiments, the plant protoplast is derived from one of the following genuses:  Acorus, Aegilops, Allium, Amborella, Antirrhinum, Apium, Arabidopsis, Arachis, Beta, Betula, Brassica, Capsicum, Ceratopteris, Citrus, Cryptomeria, Cycas, Descurainia, Eschscholzia, Eucalyptus, Glycine, Gossypium, Hedyotis, Helianthus, Hordeum, Ipomoea, Lactuca, Linum, Liriodendron, Lotus, Lupinus, Lycopersicon, Medicago, Mesembryanthemum, Nicotiana, Nuphar, Pennisetum, Persea, Phaseolus, Physcomitrella, Picea, Pinus, Poncirus, Populus, Prunus, Robinia, Rosa, Saccharum, Schedonorus, Secale, Sesamum, Solanum, Sorghum, Stevia, Thellungiella, Theobroma, Triphysaria, Triticum, Vitis, Zea,  or  Zinnia.  In some embodiments, the host cell is derived from a genus that is different from the genus from which the transcription factor is derived from. For example, the host cell is a plant protoplast derived from the genus  Arabidopsis  and the transcription factor is derived from the genus  Zea.    
     5.1. Response Genes and Transcription Factors 
     The tables below list transcription factors and response genes for which expression may be modified in transgenic plants to produce desired phenotypes. In Section 5.2, methods for the production of transgenic plants with modified expression of one or more of these genes are enumerated. 
     Table 1 shows 20 genes that are (1) ClassIIIA, i.e. no TF binding but TF-activated and (2) transiently upregulated by N. These genes are examples of “response” genes. Table 2 shows 14 genes that are (1) ClassIIIA, i.e. no binding but activated and (2) early (9-20 min) upregulated by N. These are also “response” genes. Table 3 lists “touch and go” (“hit and run”) transcription factors that may be utilized with the TARGET system to discover more response genes, which may be modified in transgenic plants to create a desired phenotype. Likewise, the transcription factor genes listed in Table 3 may themselves be modified in transgenic plants to create a desired phenotype. 
     
       
         
           
               
               
             
               
                 TABLE 1 
               
               
                   
               
               
                 PUB LOCUS 
                 ANNOTATION 
               
               
                   
               
             
            
               
                 At3g28510 
                 P-loop containing nucleoside triphosphate hydrolases  
               
               
                   
                 superfamily protein 
               
               
                 At1g73260 
                 ATKTI1, KTI1, kunitz trypsin inhibitor 1 
               
               
                 At1g22400 
                 ATUGT85A1, UGT85A1, UDP-Glycosyltransferase  
               
               
                   
                 superfamily protein 
               
               
                 At1g80460 
                 GLI1, NHO1, Actin-like ATPase superfamily protein 
               
               
                 At1g05570 
                 ATGSL06, ATGSL6, CALS1, GSL06, GSL6, callose  
               
               
                   
                 synthase 1 
               
               
                 At5g22570 
                 ATWRKY38, WRKY38, WRKY DNA-binding  
               
               
                   
                 protein 38 
               
               
                 At5g65110 
                 ACX2, ATACX2, acyl-CoA oxidase 2 
               
               
                 At1g24440 
                 RING/U-box superfamily protein 
               
               
                 At5g04310 
                 Pectin lyase-like superfamily protein 
               
               
                 At3g16150 
                 N-terminal nucleophile aminohydrolases  
               
               
                   
                 (Ntn hydrolases superfamily protein) 
               
               
                 At4g13430 
                 ATLEUC1, IIL1 isopropyl malate isomerase large  
               
               
                   
                 subunit 1 
               
               
                 At1g08090 
                 ACH1, ATNRT2.1, ATNRT2: 1, LIN1, NRT2, NRT2.1,  
               
               
                   
                 NRT2: 1, NRT2; 1AT, nitrate transporter 2:1 
               
               
                 At5g57655 
                 xylose isomerase family protein 
               
               
                 At1g62660 
                 Glycosyl hydrolases family 32 protein 
               
               
                 At3g14050 
                 AT-RSH2, ATRSH2, RSH2, RELA/SPOT homolog 2 
               
               
                 At5g18670 
                 BAM9, BMY3, beta-amylase 3 
               
               
                 At1g15380 
                 Lactoylglutathione lyase/glyoxalase I family protein 
               
               
                 At5g56870 
                 BGAL4, beta-galactosidase 4 
               
               
                 At2g43400 
                 ETFQO, electron-transfer flavoprotein:ubiquinone  
               
               
                   
                 oxidoreductase 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
               
             
               
                 TABLE 2 
               
               
                   
               
               
                 PUB LOCUS 
                 ANNOTATION 
               
               
                   
               
             
            
               
                 At1g62660: 
                 Glycosyl hydrolases family 32 protein 
               
               
                 At3g49940: 
                 LBD38, LOB domain-containing protein 38 
               
               
                 At5g10210: 
                 CONTAINS InterPro DOMAIN/s: C2 calcium-dependent  
               
               
                   
                 membrane targeting (InterPro: IPR000008); BEST  
               
               
                   
                 Arabidopsis thaliana protein match is: unknown protein 
               
               
                   
                 (TAIR: AT5G65030.1); Has 1807 Blast hits to 1807  
               
               
                   
                 proteins in 277 species: Archae-0; Bacteria-0;  
               
               
                   
                 Metazoa-736; Fungi-347; Plants-385; Viruses-0;  
               
               
                   
                 Other Eukaryotes-339 (source: NCBI BLink). 
               
               
                 At1g07150: 
                 MAPKKK13, mitogen-activated protein kinase kinase  
               
               
                   
                 kinase 13 
               
               
                 At3g20320: 
                 TGD2, trigalactosyldiacylglycerol2 
               
               
                 At2g43400: 
                 ETFQO, electron-transfer flavoprotein:ubiquinone  
               
               
                   
                 oxidoreductase 
               
               
                 At1g22400: 
                 ATUGT85A1, UGT85A1, UDP-Glycosyltransferase  
               
               
                   
                 superfamily protein 
               
               
                 At1g05570: 
                 ATGSL06, ATGSL6, CALS1, GSL06, GSL6, callose  
               
               
                   
                 synthase 1 
               
               
                 At4g38490: 
                 unknown protein; Has 30201 Blast hits to 17322 proteins  
               
               
                   
                 in 780 species: Archae-12; Bacteria-1396; Metazoa-  
               
               
                   
                 17338; Fungi-3422; Plants-5037; Viruses-0; Other 
               
               
                   
                 Eukaryotes-2996 (source: NCBI BLink). 
               
               
                 At4g37540: 
                 LBD39, LOB domain-containing protein 39 
               
               
                 At5g65110: 
                 ACX2, ATACX2, acyl-CoA oxidase 2 
               
               
                 At5g04310: 
                 Pectin lyase-like superfamily protein 
               
               
                 At4g39780: 
                 Integrase-type DNA-binding superfamily protein 
               
               
                 At5g51550: 
                 EXL3, EXORDIUM like 3 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
               
               
             
               
                 TABLE 3 
               
               
                   
               
               
                 PUB LOCUS 
                 Name/Symbol 
                 Annotation 
               
               
                   
               
             
            
               
                 At1g01060 
                 myb-related transcription factor 
                 LHY encodes a myb-related putative transcription 
               
               
                   
                 (LHY) 
                 factor involved in circadian rhythm along with 
               
               
                   
                   
                 another myb transcription factor CCA1 
               
               
                 At1g01720 
                 putative transcriptional activator 
                 Belongs to a large family of putative transcriptional 
               
               
                   
                 with NAC domain (ANAC002) 
                 activators with NAC domain. Transcript level 
               
               
                   
                   
                 increases in response to wounding and abscisic acid. 
               
               
                   
                   
                 ATAF1 attentuates ABA signaling and sythesis. 
               
               
                   
                   
                 Mutants are hyposensitive to ABA 
               
               
                 At1g13300 
                 HRS1 
                 Overexpression confers hypersensitivity to low 
               
               
                   
                   
                 phosphate-elicited inhibition of primary root growth 
               
               
                 At1g15100 
                 Ring-H2 finger A2A (RHA2A) 
                 Encodes a putative RING-H2 finger protein RHA2a. 
               
               
                 At1g22070 
                 bZIP1 family transcription factor 
                 Encodes a transcription factor. Like other TGAla- 
               
               
                   
                 (TGA3) 
                 related factors, TGA3 has a highly conserved bZIP 
               
               
                   
                   
                 region and exhibits similar DNA-binding properties. 
               
               
                 At1g25550 
                 HHO3 
                 myb-like transcription factor family protein 
               
               
                 At1g25560 
                 putative AP2-domain containing 
                 Encodes a member of the RAV transcription factor 
               
               
                   
                 transcription factor (TEM1) 
                 family that contains AP2 and B3 binding domains. 
               
               
                   
                   
                 Involved in the regulation of flowering under long 
               
               
                   
                   
                 days. Loss of function results in early flowering. 
               
               
                   
                   
                 Overexpression causes late flowering and repression 
               
               
                   
                   
                 of expression of FT. TBDvel transcriptional regulator 
               
               
                   
                   
                 involved in ethylene signaling Promoter bound by 
               
               
                   
                   
                 EIN3. EDF1 in turn, binds to promoter elements in 
               
               
                   
                   
                 ethylene responsive genes. 
               
               
                 At1g29160 
                 Dof-type zinc finger domain- 
                   
               
               
                   
                 containing protein 
                   
               
               
                 At1g43160 
                 AP2 domain-containing protein 
                 encodes a member of the ERF (ethylene response 
               
               
                   
                 RAP2.6 (RAP2.6) 
                 factor) subfamily B-4 of ERF/AP2 transcription 
               
               
                   
                   
                 factor family (RAP2.6). The protein contains one 
               
               
                   
                   
                 AP2 domain 
               
               
                 At1g51700 
                 Dof-type zinc finger domain- 
                 Encodes dof zinc finger protein (adof1). 
               
               
                   
                 containing protein (ADOF1) 
                   
               
               
                 At1g51950 
                 IAA18, indole-3-acetic acid 
                 Auxin responsive 
               
               
                   
                 inducible 18 
                   
               
               
                 At1g53910 
                 AP2 domain-containing protein 
                 Encodes a member of the ERF (ethylene response 
               
               
                   
                 RAP2.12 (RAP2.12) 
                 factor) subfamily B-2 of ERF/AP2 transcription 
               
               
                   
                   
                 factor family (RAP2.12). The protein contains one 
               
               
                   
                   
                 AP2 domain. There are 5 members in this subfamily 
               
               
                   
                   
                 including RAP2.2 AND RAP2.12. Involved in 
               
               
                   
                   
                 oxygen sensing. 
               
               
                 At1g66140 
                 zinc finger protein 4 transcription 
                   
               
               
                   
                 factor (ZFP4) 
                   
               
               
                 At1g68670 
                 HHO2 
                 myb-like transcription factor family protein 
               
               
                 At1g68840 
                 regulator of ATPase of the vacuolar 
                 Rav2 is part of a complex that has been named 
               
               
                   
                 membrane (RAV2) 
                 ‘regulator of the (H+)-ATPase of the vacuolar and 
               
               
                   
                   
                 endosomal membranes’ (RAVE) 
               
               
                 At1g74660 
                 Mini zinc finger 1 transcription 
                   
               
               
                   
                 factor (MIF1) 
                   
               
               
                 At1g74840 
                 MYB 
                 Homeodomain-like superfamily protein 
               
               
                 At1g75390 
                 AtbZIP44, bZIP44, basic leucine- 
                   
               
               
                   
                 zipper 44 
                   
               
               
                 At1g77450 
                 NAC45 
                 NAC domain containing protein 32 (NAC032); 
               
               
                   
                   
                 FUNCTIONS IN: sequence-specific DNA binding 
               
               
                   
                   
                 transcription factor activity; INVOLVED IN: 
               
               
                   
                   
                 multicellular organismal development, regulation of 
               
               
                   
                   
                 transcription 
               
               
                 At1g80840 
                 WRKY40 
                 Pathogen-induced transcription factor. Binds W-box 
               
               
                   
                   
                 sequences in vitro. Forms protein complexes with 
               
               
                   
                   
                 itself and with WRKY40 and WRKY60. 
               
               
                   
                   
                 Coexpression with WRKY18 or WRKY60 made 
               
               
                   
                   
                 plants more susceptible to both  P. syringae  and  
               
               
                   
                   
                   B. cinerea . 
               
               
                 At2g04880 
                 WRKY1 
                 Encodes WRKY1, a member of the WRKY 
               
               
                   
                   
                 transcription factors in plants involved in disease 
               
               
                   
                   
                 resistance, abiotic stress, senescence as well as in 
               
               
                   
                   
                 some developmental processes. WRKY1 is involved 
               
               
                   
                   
                 in the salicylic acid signaling pathway. The crystal 
               
               
                   
                   
                 structure of the WRKY1 C-terminal domain revealed 
               
               
                   
                   
                 a zinc-binding site and identified the DNA-binding 
               
               
                   
                   
                 residues of WRKY1. 
               
               
                 At2g20570 
                 golden2-like transcription factor 
                 Encodes GLK1, Golden2-like 1, one of a pair of 
               
               
                   
                 (GLK1) 
                 partially redundant nuclear transcription factors that 
               
               
                   
                   
                 regulate chloroplast development in a cell- 
               
               
                   
                   
                 autonomous manner. GLK2, Golden2-like 2, is 
               
               
                   
                   
                 encoded by At5g44190. GLK1 and GLK2 regulate 
               
               
                   
                   
                 the expression of the photosynthetic apparatus. 
               
               
                 At2g22430 
                 ATHB6 
                 Encodes a homeodomain leucine zipper class I (HD- 
               
               
                   
                   
                 Zip I) protein that is a target of the protein 
               
               
                   
                   
                 phosphatase ABI1 and regulates hormone responses 
               
               
                   
                   
                 in Arabidopsis. 
               
               
                 At2g22850 
                 AtbZIP6, bZIP6, basic leucine- 
                   
               
               
                   
                 zipper 6 
                   
               
               
                 At2g24570 
                 WRKY17 
                   
               
               
                 At2g25000 
                 WRKY60 
                 Pathogen-induced transcription factor. Forms protein 
               
               
                   
                   
                 complexes with itself and with WRKY40 
               
               
                 At2g28510 
                 Dof-type zinc finger domain 
                 Dof-type zinc finger DNA-binding family protein 
               
               
                   
                 containing protein 
                   
               
               
                 At2g28550 
                 RAP2.7/TOE1 
                 related to AP2.7 (RAP2.7) 
               
               
                 At2g30250 
                 WRKY25 
                 member of WRKY Transcription Factor; Group I. 
               
               
                   
                   
                 Located in nucleus. Involved in response to various 
               
               
                   
                   
                 abiotic stresses-especially salt stress 
               
               
                 At2g33710 
                 AP2-33 
                 encodes a member of the ERF (ethylene response 
               
               
                   
                   
                 factor) subfamily B-4 of ERF/AP2 transcription 
               
               
                   
                   
                 factor family. The protein contains one AP2 domain 
               
               
                 At2g38470 
                 WRKY33 
                 Member of the plant WRKY transcription factor 
               
               
                   
                   
                 family. Regulates the antagonistic relationship 
               
               
                   
                   
                 between defense pathways mediating responses to  
               
               
                   
                   
                   P. syringae  and necrotrophic fungal pathogens. Located 
               
               
                   
                   
                 in nucleus. Involved in response to various abiotic 
               
               
                   
                   
                 stresses-especially salt stress. 
               
               
                 At2g46830 
                 myb-related transcription factor 
                 Encodes a transcriptional repressor that performs 
               
               
                   
                 (CCA1) 
                 overlapping functions with LHY in a regulatory 
               
               
                   
                   
                 feedback loop that is closely associated with the 
               
               
                   
                   
                 circadian oscillator of Arabidopsis. 
               
               
                 At3g01560 
                 TTF1 
                 Ubiquitin-associated/translation elongation factor 
               
               
                   
                   
                 EF1B, N-terminal 
               
               
                 At3g04070 
                 NAC transcription factor family 
                 NAC domain containing protein 47 (NAC047); 
               
               
                   
                 (ANAC047) 
                 FUNCTIONS IN: sequence-specific DNA binding 
               
               
                   
                   
                 transcription factor activity; INVOLVED IN: 
               
               
                   
                   
                 multicellular organismal development, regulation of 
               
               
                   
                   
                 transcription 
               
               
                 At3g06590 
                 Basic helix-loop-helix (bHLH)  
                   
               
               
                   
                 DNA binding superfamily  
                   
               
               
                   
                 protein 
                   
               
               
                 At3g20770 
                 EIN3 
                 Encodes EIN3 (ethylene-insensitive3), a nuclear 
               
               
                   
                   
                 transcription factor that initiates downstream 
               
               
                   
                   
                 transcriptional cascades for ethylene responses. 
               
               
                 At3g25790 
                 HHO1 
                 myb-like transcription factor family protein 
               
               
                 At3g46130 
                 ATMYB48, ATMYB48-1, 
                   
               
               
                   
                 ATMYB48-2, ATMYB48-3, 
                   
               
               
                   
                 MYB48, myb domain protein 48 
                   
               
               
                 At3g47620 
                 AtTCP14, TCP14, TEOSINTE 
                   
               
               
                   
                 BRANCHED, cycloidea and PCF 
                   
               
               
                   
                 (TCP) 14 
                   
               
               
                 At3g51920 
                 Calmodulin-like protein 9 (CAM9) 
                 encodes a divergent member of calmodulin, which is 
               
               
                   
                   
                 an EF-hand family of Ca2+-binding proteins. 
               
               
                 At3g54620 
                 bZIP25 
                   
               
               
                 At3g60490 
                 Integrase-type DNA-binding 
                   
               
               
                   
                 superfamily protein 
                   
               
               
                 At3g61150 
                 HBZIP 
                 Encodes a homeobox-leucine zipper family protein 
               
               
                   
                   
                 belonging to the HD-ZIP IV family. 
               
               
                 At3g61890 
                 ATHB12 
                 Encodes a homeodomain leucine zipper class I (HD- 
               
               
                   
                   
                 Zip I) protein. Loss of function mutant has 
               
               
                   
                   
                 abnormally shaped leaves and stems. 
               
               
                 At3g62420 
                 bZIP53 
                 Encodes a group-S bZIP transcription factor. Forms 
               
               
                   
                   
                 heterodimers with group-C bZIP transcription 
               
               
                   
                   
                 factors. The heterodimers bind to the ACTCAT cis- 
               
               
                   
                   
                 element of proline dehydrogenase gene. 
               
               
                 At4g17490 
                 ethylene-responsive element binding 
                 Encodes a member of the ERF (ethylene response 
               
               
                   
                 factor 6 (ERF6) 
                 factor) subfamily B-3 of ERF/AP2 transcription 
               
               
                   
                   
                 factor family (ATERF-6). The protein contains one 
               
               
                   
                   
                 AP2 domain. There are 18 members in this subfamily 
               
               
                   
                   
                 including ATERF-1, ATERF-2, AND ATERF-5. It is 
               
               
                   
                   
                 involved in the response to reactive oxygen species 
               
               
                   
                   
                 and light stress. 
               
               
                 At4g17500 
                 ethylene-responsive element-binding 
                 Encodes a member of the ERF (ethylene response 
               
               
                   
                 protein 1 (ERF1) 
                 factor) subfamily B-3 of ERF/AP2 transcription 
               
               
                   
                   
                 factor family (ATERF-1). The protein contains one 
               
               
                   
                   
                 AP2 domain. 
               
               
                 At4g24240 
                 WRKY7 
                 Encodes a Ca-dependent calmodulin binding protein. 
               
               
                   
                   
                 Sequence similarity to the WRKY transcription 
               
               
                   
                   
                 factor gene family. 
               
               
                 At4g27410 
                 NAC transcription factor family 
                 Encodes a NAC transcription factor induced in 
               
               
                   
                 (RD26) 
                 response to dessication. It is localized to the nucleus 
               
               
                   
                   
                 and acts as a transcriptional activator in ABA- 
               
               
                   
                   
                 mediated dehydration response. 
               
               
                 At4g31800 
                 WRKY18 
                 Pathogen-induced transcription factor. Binds W-box 
               
               
                   
                   
                 sequences in vitro. Forms protein complexes with 
               
               
                   
                   
                 itself and with WRKY40 and WRKY60 
               
               
                 At4g34590 
                 ATB2, AtbZIP11, BZIP11, GBF6, 
                   
               
               
                   
                 G-box binding factor 6 
                   
               
               
                 At4g36540 
                 BEE2, BR enhanced expression 2 
                   
               
               
                 At4g37180 
                 HHO5 
                   
               
               
                 At4g37260 
                 myb family transcription factor 
                 Member of the R2R3 factor gene family. 
               
               
                   
                 (MYB73) 
                   
               
               
                 At4g37610 
                 BT5 
                 BTB and TAZ domain protein. Located in cytoplasm 
               
               
                   
                   
                 and expressed in fruit, flower and leaves. 
               
               
                 At4g37730 
                 AtbZIP7, bZIP7, basic leucine- 
                   
               
               
                   
                 zipper 7 
                   
               
               
                 At5g05410 
                 DRE-binding protein 2A (DREB2A) 
                 Encodes a transcription factor that specifically binds 
               
               
                   
                   
                 to DRE/CRT cis elements (responsive to drought and 
               
               
                   
                   
                 low-temperature stress). Belongs to the DREB 
               
               
                   
                   
                 subfamily A-2 of ERF/AP2 transcription factor 
               
               
                   
                   
                 family (DREB2A) 
               
               
                 At5g06800 
                 myb-like HTH transcriptional 
                   
               
               
                   
                 regulator family protein 
                   
               
               
                 At5G10030 
                 TGA4 
                   
               
               
                 At5g13080 
                 ATWRKY75, WRKY75, WRKY 
                   
               
               
                   
                 DNA-binding protein 75 
                   
               
               
                 At5g14540 
                 TTF2 
                 proline-rich family protein contains proline rich 
               
               
                   
                   
                 extensin domains 
               
               
                 At5g24800 
                 bZIP1 transcription factor family 
                 Encodes bZIP protein BZO2H2. 
               
               
                   
                 protein (bZIP9) 
                   
               
               
                 At5g39610 
                 NAC6 
                 Encodes a NAC-domain transcription factor. 
               
               
                   
                   
                 Positively regulates aging-induced cell death and 
               
               
                   
                   
                 senescence in leaves. This gene is upregulated in 
               
               
                   
                   
                 response to salt stress in wildtype as well as NTHK1 
               
               
                   
                   
                 transgenic lines although in the latter case the 
               
               
                   
                   
                 induction was drastically reduced 
               
               
                 At5g44190 
                 myb family transcription factor 
                 Encodes GLK2, Golden2-like 2, one of a pair of 
               
               
                   
                 (GLK2) 
                 partially redundant nuclear transcription factors that 
               
               
                   
                   
                 regulate chloroplast development in a cell- 
               
               
                   
                   
                 autonomous manner. GLK1, Golden2-like 1, is 
               
               
                   
                   
                 encoded by At2g20570. GLK1 and GLK2 regulate 
               
               
                   
                   
                 the expression of the photosynthetic apparatus. 
               
               
                 At5g47230 
                 AP2-6 
                 encodes a member of the ERF (ethylene response 
               
               
                   
                   
                 factor) subfamily B-3 of ERF/AP2 transcription 
               
               
                   
                   
                 factor family (ATERF-5). The protein contains one 
               
               
                   
                   
                 AP2 domain 
               
               
                 At5g48655 
                 C3HC4 RING 
                 RING/U-box superfamily protein 
               
               
                 At5g49450 
                 bZIP1 transcription factor family 
                 Encodes a transcription activator is a positive 
               
               
                   
                 protein (bZIP1) 
                 regulator of plant tolerance to salt, osmotic and 
               
               
                   
                   
                 drought stresses. 
               
               
                 At5g49520 
                 ATWRKY48, WRKY48, WRKY 
                   
               
               
                   
                 DNA-binding protein 48 
                   
               
               
                 At5g56270 
                 ATWRKY2, WRKY2, WRKY 
                   
               
               
                   
                 DNA-binding protein 2 
                   
               
               
                 At5g60850 
                 Dof-type zinc finger domain 
                 Encodes a zinc finger protein. 
               
               
                   
                 containing protein (OBF4) 
                   
               
               
                 At5g63790 
                 NAC transcription factor family 
                 Encodes a member of the NAC family of 
               
               
                   
                 (ANAC102) 
                 transcription factors. ANAC102 appears to have a 
               
               
                   
                   
                 role in mediating response to low oxygen stress 
               
               
                   
                   
                 (hypoxia) in germinating seedlings. 
               
               
                 At5G65210 
                 TGA1 
                   
               
               
                 At5g65640 
                 BHLH093 
                 beta HLH protein 93 (bHLH093) 
               
               
                   
               
            
           
         
       
     
     5.2. Transgenic Plants 
     5.2.1. Modulation of Gene Expression 
     The methods of the invention involve modulation of the expression of one, two, three or more target nucleotide sequences (i.e., target genes) in a host cell, such as a plant protoplast. That is, the expression of a target nucleotide sequence of interest may be increased or decreased. 
     The target nucleotide sequences may be endogenous or exogenous in origin. By “modulate expression of a target gene” is intended that the expression of the target gene is increased or decreased relative to the expression level in a host cell that has not been altered by the methods described herein. 
     By “increased or over expression” is intended that expression of the target nucleotide sequence is increased over expression observed in conventional transgenic lines for heterologous genes and over endogenous levels of expression for homologous genes. Heterologous or exogenous genes comprise genes that do not occur in the host cell of interest in its native state. Homologous or endogenous genes are those that are natively present in the plant genome. Generally, expression of the target sequence is substantially increased. That is expression is increased at least about 25%-50%, preferably about 50%-100%, more preferably about 100%, 200% and greater. 
     By “decreased expression” or “underexpression” it is intended that expression of the target nucleotide sequence is decreased below expression observed in conventional transgenic lines for heterologous genes and below endogenous levels of expression for homologous genes. Generally, expression of the target nucleotide sequence of interest is substantially decreased. That is expression is decreased at least about 25%-50%, preferably about 50%-100%, more preferably about 100%, 200% and greater. 
     Expression levels may be assessed by determining the level of a gene product by any method known in the art including, but not limited to determining the levels of the RNA and protein encoded by a particular target gene. For genes that encode proteins, expression levels may determined, for example, by quantifying the amount of the protein present in plant cells, or in a plant or any portion thereof. Alternatively, it desired target gene encodes a protein that has a known measurable activity, then activity levels may be measured to assess expression levels. 
     5.2.2. Transfection 
     Any method or delivery system may be used for the delivery and/or transfection of the nucleic acid vectors encoding any of the genes of interest of the present invention in the host cell, e.g., plant protoplast. The vectors may be delivered to the host cell either alone, or in combination with other agents. Transient expression systems may also be used. Homologous recombination may also be used. 
     Transfection may be accomplished by a wide variety of means, as is known to those of ordinary skill in the art. Such methods include, but are not limited to,  Agrobacterium -mediated transformation (e.g., Komari et al., 1998, Curr. Opin. Plant Biol., 1:161), particle bombardment mediated transformation (e.g., Finer et al., 1999, Curr. Top. Microbiol. Immunol., 240:59), protoplast electroporation (e.g., Bates, 1999, Methods Mol. Biol., 111:359), viral infection (e.g., Porta and Lomonossoff, 1996, Mol. Biotechnol. 5:209), microinjection, and liposome injection. Other exemplary delivery systems that can be used to facilitate uptake by a cell of the nucleic acid include calcium phosphate and other chemical mediators of intracellular transport, microinjection compositions, and homologous recombination compositions (e.g., for integrating a gene into a preselected location within the chromosome of the cell). Alternative methods may involve, for example, the use of liposomes, electroporation, or chemicals that increase free (or “naked”) DNA uptake, transformation using viruses or pollen and the use of microprojection. Standard molecular biology techniques are common in the art (e.g., Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, New York). 
     One of skill in the art will be able to select an appropriate vector for introducing the encoding nucleic acid sequence in a relatively intact state. Thus, any vector which will produce a host cell, e.g., plant protoplast, carrying the introduced encoding nucleic acid should be sufficient. The selection of the vector, or whether to use a vector, is typically guided by the method of transformation selected. 
     The transformation of plants cells in accordance with the invention may be carried out in essentially any of the various ways known to those skilled in the art of plant molecular biology. (See, for example, Methods of Enzymology, Vol. 153, 1987, Wu and Grossman, Eds., Academic Press, incorporated herein by reference). 
     Plant cells can comprise two or more nucleotide sequence constructs. Any means for producing a plant cell, e.g., protoplast, comprising the nucleotide sequence constructs described herein are encompassed by the present invention. For example, a nucleotide sequence encoding the modulator can be used to transform a plant cell at the same time as the nucleotide sequence encoding the precursor RNA. The nucleotide sequence encoding the precursor mRNA can be introduced into a plant cell that has already been transformed with the modulator nucleotide sequence. Likewise, viral vectors may be used to express gene products by various methods generally known in the art. Suitable plant viral vectors for expressing genes should be self-replicating, capable of systemic infection in a host, and stable. Additionally, the viruses should be capable of containing the nucleic acid sequences that are foreign to the native virus forming the vector. 
     Homologous recombination may be used as a method of gene inactivation. 
     The particular choice of a transformation technology will be determined by its efficiency to transform certain plant species as well as the experience and preference of the person practicing the invention with a particular methodology of choice. It will be apparent to the skilled person that the particular choice of a transformation system to introduce nucleic acid into plant cells is not essential to or a limitation of the invention, nor is the choice of technique for plant regeneration. 
       Agrobacterium.  The nucleic acid sequences utilized in the present invention can be introduced into plant cells using Ti plasmids of  Agrobacterium tumefaciens  ( A. tumefaciens ), root-inducing (Ri) plasmids of  Agrobacterium rhizogenes  ( A. rhizogenes ), and plant virus vectors. For reviews of such techniques see, for example, Weissbach &amp; Weissbach, 1988, Methods for Plant Molecular Biology, Academic Press, New York, Section VIII, pp. 421-463; and Grierson &amp; Corey, 1988, Plant Molecular Biology, 2d Ed., Blackie, London, Ch. 7-9, and Horsch et al., 1985, Science, 227:1229. 
     In using an  A. tumefaciens  culture as a transformation vehicle, it is most advantageous to use a non-oncogenic strain of  Agrobacterium  as the vector carrier so that normal non-oncogenic differentiation of the transformed tissues is possible. It is also preferred that the  Agrobacterium  harbor a binary Ti plasmid system. Such a binary system comprises 1) a first Ti plasmid having a virulence region essential for the introduction of transfer DNA (T-DNA) into plants, and 2) a chimeric plasmid. The chimeric plasmid contains at least one border region of the T-DNA region of a wild-type Ti plasmid flanking the nucleic acid to be transferred. Binary Ti plasmid systems have been shown effective in the transformation of plant cells (De Framond, Biotechnology, 1983, 1:262; Hoekema et al., 1983, Nature, 303:179). Such a binary system is preferred because it does not require integration into the Ti plasmid of  A. tumefaciens,  which is an older methodology. 
     In some embodiments, a disarmed Ti-plasmid vector carried by  Agrobacterium  exploits its natural gene transferability (EP-A-270355, EP-A-01 16718, Townsend et al., 1984, NAR, 12:8711, U.S. Pat. No. 5,563,055). 
     Methods involving the use of  Agrobacterium  in transformation according to the present invention include, but are not limited to: 1) co-cultivation of  Agrobacterium  with cultured isolated protoplasts; 2) transformation of plant cells or tissues with  Agrobacterium;  or 3) transformation of seeds, apices or meristems with  Agrobacterium.    
     In addition, gene transfer can be accomplished by in planta transformation by  Agrobacterium,  as described by Bechtold et al., (C. R. Acad. Sci. Paris, 1993, 316:1194). This approach is based on the vacuum infiltration of a suspension of  Agrobacterium  cells. 
     In certain embodiments, nucleic acid molecule is introduced into plant cells by infecting such plant cells, an explant, a meristem or a seed, with transformed  A. tumefaciens  as described above. Under appropriate conditions known in the art, the transformed plant cells are grown to form shoots, roots, and develop further into plants. 
     Other methods described herein, such as microprojectile bombardment, electroporation and direct DNA uptake can be used where  Agrobacterium  is inefficient or ineffective. Alternatively, a combination of different techniques may be employed to enhance the efficiency of the transformation process, e.g., bombardment with  Agrobacterium -coated microparticles (EP-A-486234) or microprojectile bombardment to induce wounding followed by co-cultivation with  Agrobacterium  (EP-A-486233). 
     CaMV. In some embodiments, cauliflower mosaic virus (CaMV) is used as a vector for introducing a desired nucleic acid into plant cells (U.S. Pat. No. 4,407,956). CaMV viral DNA genome can be inserted into a parent bacterial plasmid creating a recombinant DNA molecule which can be propagated in bacteria. After cloning, the recombinant plasmid again can be cloned and further modified by introduction of the desired nucleic acid sequence. The modified viral portion of the recombinant plasmid can then be excised from the parent bacterial plasmid, and used to inoculate the plant cells or plants. 
     Mechanical and Chemical Means. In some embodiments, a nucleic acid molecule of the invention is introduced into a plant cell using mechanical or chemical means. Exemplary mechanical and chemical means are provided below. 
     As used herein, the term “contacting” refers to any means of introducing a nucleic acid molecule into a plant cell, including chemical and physical means as described above. Preferably, contacting refers to introducing the nucleic acid or vector containing the nucleic acid into plant cells (including an explant, a meristem or a seed), via  A. tumefaciens  transformed with the nucleic acid molecule. 
     Microinjection. In one embodiment, the nucleic acid molecule can be mechanically transferred into the plant cell by microinjection using a micropipette. See, e.g., WO 92/09696, WO 94/00583, EP 331083, EP 175966, Green et al., 1987, Plant Tissue and Cell Culture, Academic Press, Crossway et al., 1986, Biotechniques 4:320-334. 
     PEG. In other embodiment, the nucleic acid can also be transferred into the plant cell by using polyethylene glycol (PEG) which forms a precipitation complex with genetic material that is taken up by the cell. 
     Electroporation. Electroporation can be used, in another set of embodiments, to deliver a nucleic acid to the cell (see, e.g., Fromm et al., 1985, PNA5, 82:5824). “Electroporation,” as used herein, is the application of electricity to a cell, such as a plant protoplast, in such a way as to cause delivery of a nucleic acid into the cell without killing the cell. Typically, electroporation includes the application of one or more electrical voltage “pulses” having relatively short durations (usually less than 1 second, and often on the scale of milliseconds or microseconds) to a media containing the cells. The electrical pulses typically facilitate the non-lethal transport of extracellular nucleic acids into the cells. The exact electroporation protocols (such as the number of pulses, duration of pulses, pulse waveforms, etc.), will depend on factors such as the cell type, the cell media, the number of cells, the substance(s) to be delivered, etc., and can be determined by those of ordinary skill in the art. Electroporation is discussed in greater detail in, e.g., EP 290395, WO 8706614, Riggs et al., 1986, Proc. Natl. Acad. Sci. USA 83:5602-5606; D′Halluin et al., 1992, Plant Cell 4:1495-1505). Other forms of direct DNA uptake can also be used in the methods provided herein, such as those discussed in, e.g., DE 4005152, WO 9012096, U.S. Pat. No. 4,684,611, Paszkowski et al., 1984, EMBO J. 3:2717-2722. 
     Ballistic and Particle Bombardment. Another method for introducing a nucleic acid molecule is high velocity ballistic penetration by small particles with the nucleic acid to be introduced contained either within the matrix of such particles, or on the surface thereof (Klein et al., 1987, Nature 327:70). Genetic material can be introduced into a cell using particle gun (“gene gun”) technology, also called microprojectile or microparticle bombardment. In this method, small, high-density particles (microprojectiles) are accelerated to high velocity in conjunction with a larger, powder-fired macroprojectile in a particle gun apparatus. The microprojectiles have sufficient momentum to penetrate cell walls and membranes, and can carry RNA or other nucleic acids into the interiors of bombarded cells. It has been demonstrated that such microprojectiles can enter cells without causing death of the cells, and that they can effectively deliver foreign genetic material into intact tissue. Bombardment transformation methods are also described in Sanford et al. (Techniques 3:3-16, 1991) and Klein et al. (Bio/Techniques 10:286, 1992). Although, typically only a single introduction of a new nucleic acid sequence(s) is required, this method particularly provides for multiple introductions. 
     Particle or microprojectile bombardment are discussed in greater detail in, e.g., the following references: U.S. Pat. No. 5,100,792, EP-A-444882, EP-A-434616; Sanford et al., U.S. Pat. No. 4,945,050; Tomes et al., 1995, “Direct DNA Transfer into Intact Plant Cells via Microprojectile Bombardment,” in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg and Phillips (Springer-Verlag, Berlin); and McCabe et al., 1988, Biotechnology 6:923-926. 
     Colloidal Dispersion. In other embodiments, a colloidal dispersion system may be used to facilitate delivery of a nucleic acid into the cell. As used herein, a “colloidal dispersion system” refers to a natural or synthetic molecule, other than those derived from bacteriological or viral sources, capable of delivering to and releasing the nucleic acid to the cell. Colloidal dispersion systems include, but are not limited to, macromolecular complexes, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. One example of a colloidal dispersion system is a liposome. Liposomes are artificial membrane vessels. It has been shown that large unilamellar vessels (“LUV”), which-range in size from 0.2 to 4.0 microns, can encapsulate large macromolecules within the aqueous interior and these macromolecules can be delivered to cells in a biologically active form (e.g., Fraley et al., 1981, Trends Biochem. Sci., 6:77). 
     Lipids. Lipid formulations for the transfection and/or intracellular delivery of nucleic acids are commercially available, for instance, from QIAGEN, for example as EFFECTENE® (a non-liposomal lipid with a special DNA condensing enhancer) and SUPER-FECT® (a novel acting dendrimeric technology) as well as Gibco BRL, for example, as LIPOFECTIN® and LIPOFECTACE®, which are formed of cationic lipids such as N-[1-(2,3-dioleyloxy)-propyl]-N,N,N-trimethylammonium chloride (“DOTMA”) and dimethyl dioctadecylammonium bromide (“DDAB”). Liposomes are well known in the art and have been widely described in the literature, for example, in Gregoriadis, G., 1985, Trends in Biotechnology 3:235-241; Freeman et al., 1984, Plant Cell Physiol. 29:1353). 
     Other Methods. In addition to the above, other physical methods for the transformation of plant cells are reviewed in the following and can be used in the methods provided herein. Oard, 1991, Biotech. Adv. 9:1-11. See generally, Weissinger et al., 1988, sAnn. Rev. Genet. 22:421-477; Sanford et al., 1987, Particulate Science and Technology 5:27-37; Christou et al., 1988, Plant Physiol. 87:671-674; McCabe et al., 1988, Bio/Technology 6:923-926; Finer and McMullen, 1991, In vitro Cell Dev. Biol. 27P:175-182; Singh et al., 1998, Theor. Appl. Genet. 96:319-324; Datta et al., 1990, Biotechnology 8:736-740; Klein et al., 1988, Proc. Natl. Acad. Sci. USA 85:4305-4309; Klein et al., 1988, Biotechnology 6:559-563; Tomes, U.S. Pat. No. 5,240,855; Buising et al., U.S. Pat. Nos. 5,322,783 and 5,324,646; Klein et al., 1988, Plant Physiol. 91:440-444; Fromm et al., 1990, Biotechnology 8:833-839; Hooykaas-Van Slogteren et al., 1984, Nature (London) 311:763-764; Bytebier et al., 1987, Proc. Natl. Acad. Sci. USA 84:5345-5349; De Wet et al., 1985, The Experimental Manipulation of Ovule Tissues, ed. Chapman et al. (Longman, N.Y.), pp. 197-209; Kaeppler et al., 1990, Plant Cell Reports 9:415-418 and Kaeppler et al., 1992, Theor. Appl. Genet. 84:560-566; Li et al., 1993, Plant Cell Reports 12:250-255 and Christou and Ford, 1995, Annals of Botany 75:407-413; Osjoda et al., 1996, Nature Biotechnology 14:745-750; all of which are herein incorporated by reference. 
     5.2.3. Nucleic Acid Constructs 
     The nucleic acid molecules of the invention may be provided in nucleotide sequence constructs or expression cassettes for expression in the plant cell of interest. The cassette will include 5′ and 3′ regulatory sequences operably linked to an encoding nucleotide sequence of the invention. 
     The expression cassette may additionally contain at least one additional gene to be co-transformed into the organism. Alternatively, the additional gene(s) can be provided on multiple expression cassettes. 
     In certain embodiments, an expression cassette can be used with a plurality of restriction sites for insertion of the sequences of the invention to be under the transcriptional regulation of the regulatory regions. The expression cassette can additionally contain selectable marker genes (see below). 
     The expression cassette will generally include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region, a DNA sequence of the invention, and a transcriptional and translational termination region functional in plants. The transcriptional initiation region, the promoter, may be native or analogous or foreign or heterologous to the plant host. Additionally, the promoter may be the natural sequence or alternatively a synthetic sequence. By “foreign” is intended that the transcriptional initiation region is not found in the native plant into which the transcriptional initiation region is introduced. As used herein, a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence. 
     The termination region may be native with the transcriptional initiation region, may be native with the operably linked DNA sequence of interest, or may be derived from another source. Convenient termination regions are available from the Ti-plasmid of  A. tumefaciens,  such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al., 1991, Mol. Gen. Genet. 262:141-144; Proudfoot, 1991, Cell 64:671-674; Sanfacon et al., 1991, Genes Dev. 5:141-149; Mogen et al., 1990, Plant Cell 2:1261-1272; Munroe et al., 1990, Gene 91:151-158; Ballas et al., 1989, Nucleic Acids Res. 17:7891-7903; and Joshi et al., 1987, Nucleic Acid Res. 15:9627-9639. 
     In some embodiments, a nucleic acid can be delivered to the cell in a vector. As used herein, a “vector” is any vehicle capable of facilitating the transfer of the nucleic acid to the cell such that the nucleic acid can be processed and/or expressed in the cell. The vector may transport the nucleic acid to the cells with reduced degradation, relative to the extent of degradation that would result in the absence of the vector. The vector optionally includes gene expression sequences or other components (such as promoters and other regulatory elements) able to enhance expression of the nucleic acid within the cell. The invention also encompasses the cells transfected with these vectors, including those cells previously described. 
     To commence a transformation process in certain embodiments, it is first necessary to construct a suitable vector and properly introduce it into the plant cell. Vector(s) employed in the present invention for transformation of a plant cell include an encoding nucleic acid sequence operably associated with a promoter, such as a leaf-specific promoter. Details of the construction of vectors utilized herein are known to those skilled in the art of plant genetic engineering. 
     In general, vectors useful in the invention include, but are not limited to, plasmids, phagemids, viruses, other vehicles derived from viral or bacterial sources that have been manipulated by the insertion or incorporation of the nucleotide sequences (or precursor nucleotide sequences) of the invention. Viral vectors useful in certain embodiments include, but are not limited to, nucleic acid sequences from the following viruses: retroviruses; adenovirus, or other adeno-associated viruses; mosaic viruses such as tobamoviruses; potyviruses, nepoviruses, and RNA viruses such as retroviruses. One can readily employ other vectors not named but known to the art. Some viral vectors can be based on non-cytopathic eukaryotic viruses in which non-essential genes have been replaced with the nucleotide sequence of interest. Non-cytopathic viruses include retroviruses, the life cycle of which involves reverse transcription of genomic viral RNA into DNA with subsequent proviral integration into host cellular DNA. 
     Genetically altered retroviral expression vectors can have general utility for the high-efficiency transduction of nucleic acids. Standard protocols for producing replication-deficient retroviruses (including the steps of incorporation of exogenous genetic material into a plasmid, transfection of a packaging cell lined with plasmid, production of recombinant retroviruses by the packaging cell line, collection of viral particles from tissue culture media, and infection of the cells with viral particles) are well known to those of ordinary skill in the art. Examples of standard protocols can be found in Kriegler, M., 1990, Gene Transfer and Expression, A Laboratory Manual, W.H. Freeman Co., New York, or Murry, E. J. Ed., 1991, Methods in Molecular Biology, Vol. 7, Humana Press, Inc., Cliffton, N.J. 
     Another-example of a virus for certain applications is the adeno-associated virus, which is a double-stranded DNA virus. The adeno-associated virus can be engineered to be replication-deficient and is capable of infecting a wide range of-cell types and species. The adeno-associated virus further has advantages, such as heat and lipid solvent stability; high transduction frequencies in cells of diverse lineages; and/or lack of superinfection inhibition, which may allow multiple series of transductions. 
     Another vector suitable for use with the method provided herein is a plasmid vector. Plasmid vectors, have been extensively described in the art and are well-known to those of skill in the art. See, e.g., Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press. These plasmids may have a promoter compatible with the host cell, and the plasmids can express a peptide from a gene operatively encoded within the plasmid. Some commonly used plasmids include pBR322, pUC18, pUC19, pRC/CMV, SV40, and pBlueScript. Other plasmids are well-known to those of ordinary skill in the art. Additionally, plasmids may be custom-designed, for example, using restriction enzymes and ligation reactions, to remove and add specific fragments of DNA or other nucleic acids, as necessary. The present invention also includes vectors for producing nucleic acids or precursor nucleic acids containing a desired nucleotide sequence (which can, for instance, then be cleaved or otherwise processed within the cell to produce a precursor miRNA). These vectors may include a sequence encoding a nucleic acid and an in vivo expression element, as further described below. In some cases, the in vivo expression element includes at least one promoter. 
     Where appropriate, the gene(s) for enhanced expression may be optimized for expression in the transformed plant. That is, the genes can be synthesized using plant-preferred codons corresponding to the plant of interest. Methods are available in the art for synthesizing plant-preferred genes. See, for example, U.S. Pat. Nos. 5,380,831, and 5,436,391, and Murray et al., 1989, Nucleic Acids Res. 17:477-498. 
     Additional sequence modifications are known to enhance gene expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well-characterized sequences that may be deleterious to gene expression. The G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When desired, the sequence is modified to avoid predicted hairpin secondary mRNA structures. However, it is recognized that in the case of nucleotide sequences encoding the miRNA precursors, one or more hairpin and other secondary structures may be desired for proper processing of the precursor into a mature miRNA and/or for the functional activity of the miRNA in gene silencing. 
     The expression cassettes can additionally contain 5′ leader sequences in the expression cassette construct. Such leader sequences can act to enhance translation. Translation leaders are known in the art and include: picornavirus leaders, for example, EMCV leader (Encephalomyocarditis 5′ noncoding region) (Elroy-Stein et al., 1989, PNAS USA 86:6126-6130); potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) (Allison et al., 1986); MDMV leader (Maize Dwarf Mosaic Virus); Virology 154:9-20), and human immunoglobulin heavy-chain binding protein (BiP), (Macejak et al., 1991, Nature 353:90-94); untranslated leader from the coat protein miRNA of alfalfa mosaic virus (AMV RNA 4) (Jobling et al., 1987, Nature 325:622-625); tobacco mosaic virus leader (TMV) (Gallie et al., 1989, Molecular Biology of RNA, ed. Cech (Liss, New York), pp. 237-256); and maize chlorotic mottle virus leader (MCMV) (Lommel et al., 1991, Virology 81:382-385). See also, Della-Cioppa et al., 1987, Plant Physiol. 84:965-968. 
     In preparing the expression cassette, the various DNA fragments can be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers can be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved. 
     5.2.4. Host Cells 
     Provided herein are host cells that contain a vector, e.g., a DNA plasmid and support the replication and/or expression of the vector. Host cells may be prokaryotic cells such as  E. coli,  or eukaryotic cells such as yeast, plant, insect, amphibian, or mammalian cells. In some embodiments, host cells are monocotyledonous or dicotyledonous plant cells. In other embodiments monocotyledonous host cell is a maize host cell. In certain embodiments, the host cell utilized in the methods of the present invention are transiently transfected with the nucleic acid molecules of the invention. 
     In preferred embodiments, the host cell utilized in the methods of the present invention is a plant protoplast. Plant protoplasts are plant cells that had their entire plant cell wall enzymatically removed prior to the introduction of the molecule of interest. The complete removal of the cell wall disrupts the connection between cells producing a homogenous suspension of individualized cells which allows more uniform and large scale transfection experiments. This comprises, but is not restricted to protoplast fusion, electroporation, liposome-mediated transfection, and polyethylene glycol-mediated transfection. Protoplast preparation is therefore a very reliable and inexpensive method to produce millions of cells. 
     In particular embodiments, the plant protoplast is derived from one of the following genuses:  Acorus, Aegilops, Allium, Amborella, Antirrhinum, Apium, Arabidopsis, Arachis, Beta, Betula, Brassica, Capsicum, Ceratopteris, Citrus, Cryptomeria, Cycas, Descurainia, Eschscholzia, Eucalyptus, Glycine, Gossypium, Hedyotis, Helianthus, Hordeum, Ipomoea, Lactuca, Linum, Liriodendron, Lotus, Lupinus, Lycopersicon, Medicago, Mesembryanthemum, Nicotiana, Nuphar, Pennisetum, Persea, Phaseolus, Physcomitrella, Picea, Pinus, Poncirus, Populus, Prunus, Robinia, Rosa, Saccharum, Schedonorus, Secale, Sesamum, Solanum, Sorghum, Stevia, Thellungiella, Theobroma, Triphysaria, Triticum, Vitis, Zea,  or  Zinnia.  In some embodiments, the host cell is derived from a genus that is different from the genus from which the transcription factor is derived from. For example, the host cell is a plant protoplast derived from the genus  Arabidopsis  and the transcription factor is derived from the genus  Zea.    
     Also provided herein are plant cells having the nucleotide sequence constructs of the invention. A further aspect of the present invention provides a method of making such a plant cell involving introduction of a vector including the construct into a plant cell. For integration of the construct into the plant genome, such introduction will be followed by recombination between the vector and the plant cell genome to introduce the sequence of nucleotides into the genome. RNA encoded by the introduced nucleic acid construct may then be transcribed in the cell and descendants thereof, including cells in plants regenerated from transformed material. A gene stably incorporated into the genome of a plant is passed from generation to generation to descendants of the plant, so such descendants should show the desired phenotype. 
     Optionally, germ line cells may be used in the methods described herein rather than, or in addition to, somatic cells. The term “germ line cells” refers to cells in the plant organism which can trace their eventual cell lineage to either the male or female reproductive cell of the plant. Other cells, referred to as “somatic cells” are cells which give rise to leaves, roots and vascular elements which, although important to the plant, do not directly give rise to gamete cells. Somatic cells, however, also may be used. With regard to callus and suspension cells which have somatic embryogenesis, many or most of the cells in the culture have the potential capacity to give rise to an adult plant. If the plant originates from single cells or a small number of cells from the embryogenic callus or suspension culture, the cells in the callus and suspension can therefore be referred to as germ cells. In the case of immature embryos which are prepared for treatment by the methods described herein, certain cells in the apical meristem region of the plant have been shown to produce a cell lineage which eventually gives rise to the female and male reproductive organs. With many or most species, the apical meristem is generally regarded as giving rise to the lineage that eventually will give rise to the gamete cells. An example of a non-gamete cell in an embryo would be the first leaf primordia in corn which is destined to give rise only to the first leaf and none of the reproductive structures. 
     5.2.5. Promoters and Other Regulatory Sequences 
     In the broad method of the invention, the nucleic acid molecule of the invention is operably linked with a promoter. It may be desirable to introduce more than one copy of a polynucleotide into a plant cell for enhanced expression. 
     In general, promoters are found positioned 5′ (upstream) of the genes that they control. Thus, in the construction of promoter gene combinations, the promoter is preferably positioned upstream of the gene and at a distance from the transcription start site that approximates the distance between the promoter and the gene it controls in the natural setting. As is known in the art, some variation in this distance can be tolerated without loss of promoter function. Similarly, the preferred positioning of a regulatory element, such as an enhancer, with respect to a heterologous gene placed under its control reflects its natural position relative to the structural gene it naturally regulates. 
     Thus, the nucleic acid, in one embodiment, is operably linked to a gene expression sequence, which directs the expression of the nucleic acid within the cell. A “gene expression sequence,” as used herein, is any regulatory nucleotide sequence, such as a promoter sequence or promoter-enhancer combination, which facilitates the efficient transcription and translation of the nucleotide sequence to which it is operably linked. The gene expression sequence may, for example, be a eukaryotic promoter or a viral promoter, such as a constitutive or inducible promoter. Promoters and enhancers consist of short arrays of DNA sequences that interact specifically with cellular proteins involved in transcription, for instance, as discussed in Maniatis et al., 1987, Science 236:1237. Promoter and enhancer elements have been isolated from a variety of eukaryotic sources including genes in plant, yeast, insect and mammalian cells and viruses (analogous control elements, i.e., promoters, are also found in prokaryotes). In some embodiments, the nucleic acid is linked to a gene expression sequence which permits expression of the nucleic acid in a plant cell. A sequence which permits expression of the nucleic acid in a plant cell is one which is selectively active in the particular plant cell and thereby causes the expression of the nucleic acid in these cells. Those of ordinary skill in the art will be able to easily identify promoters that are capable of expressing a nucleic acid in a cell based on the type of plant cell. 
     A number of promoters can be used in the practice of the invention. The promoters can be selected based on the desired outcome. Generally, the nucleotide sequence and the modulator sequences can be combined with promoters of choice to alter gene expression if the target sequences in the tissue or organ of choice. Thus, the nucleotide sequence or modulator nucleotide sequence can be combined with constitutive, tissue-preferred, inducible, developmental, or other promoters for expression in plants depending upon the desired outcome. 
     The selection of a particular promoter and enhancer depends on what cell type is to be used and the mode of delivery. For example, a wide variety of promoters have been isolated from plants and animals, which are functional not only in the cellular source of the promoter, but also in numerous other plant species. There are also other promoters (e.g., viral and Ti-plasmid) which can be used. For example, these promoters include promoters from the Ti-plasmid, such as the octopine synthase promoter, the nopaline synthase promoter, the mannopine synthase promoter, and promoters from other open reading frames in the T-DNA, such as ORF7, etc. Promoters isolated from plant viruses include the 35S promoter from cauliflower mosaic virus. Promoters that have been isolated and reported for use in plants include ribulose-1,3-biphosphate carboxylase small subunit promoter, phaseolin promoter, etc. Thus, a variety of promoters and regulatory elements may be used in the expression vectors of the present invention. 
     Promoters useful in the compositions and methods provided herein include both natural constitutive and inducible promoters as well as engineered promoters. The CaMV promoters are examples of constitutive promoters. Other constitutive mammalian promoters include, but are not limited to, polymerase promoters as well as the promoters for the following genes: hypoxanthine phosphoribosyl transferase (“HPTR”), adenosine deaminase, pyruvate kinase, and alpha-actin. 
     Promoters useful as expression elements of the invention also include inducible promoters. Inducible promoters are expressed in the presence of an inducing agent. For example, a metallothionein promoter can be induced to promote transcription in the presence of certain metal ions. Other inducible promoters are known to those of ordinary skill in the art. The in vivo expression element can include, as necessary, 5′ non-transcribing and 5′ non-translating sequences involved with the initiation of transcription, and can optionally include enhancer sequences or upstream activator sequences. 
     For example, in some embodiments an inducible promoter is used to allow control of nucleic acid expression through the presentation of external stimuli (e.g., environmentally inducible promoters), as discussed below. Thus, the timing and amount of nucleic acid expression can be controlled in some cases. Non-limiting examples of expression systems, promoters, inducible promoters, environmentally inducible promoters, and enhancers are well known to those of ordinary skill in the art. Examples include those described in International Patent Application Publications WO 00/12714, WO 00/11175, WO 00/12713, WO 00/03012, WO 00/03017, WO 00/01832, WO 99/50428, WO 99/46976 and U.S. Pat. Nos. 6,028,250, 5,959,176, 5,907,086, 5,898,096, 5,824,857, 5,744,334, 5,689,044, and 5,612,472. A general descriptions of plant expression vectors and reporter genes can also be found in Gruber et al., 1993, “Vectors for Plant Transformation,” in Methods in Plant Molecular Biology &amp; Biotechnology, Glich et al., Eds., p. 89-119, CRC Press. 
     For plant expression vectors, viral promoters that can be used in certain embodiments include the 35S RNA and 19S RNA promoters of CaMV (Brisson et al., Nature, 1984, 310:511; Odell et al., Nature, 1985, 313:810); the full-length transcript promoter from Figwort Mosaic Virus (FMV) (Gowda et al., 1989, J. Cell Biochem., 13D: 301) and the coat protein promoter to TMV (Takamatsu et al., 1987, EMBO J. 6:307). Alternatively, plant promoters such as the light-inducible promoter from the small subunit of ribulose bis-phosphate carboxylase (ssRUBISCO) (Coruzzi et al., 1984, EMBO J., 3:1671; Broglie et al., 1984, Science, 224:838); mannopine synthase promoter (Velten et al., 1984, EMBO J., 3:2723) nopaline synthase (NOS) and octopine synthase (OCS) promoters (carried on tumor-inducing plasmids of  Agrobacterium tumefaciens ) or heat shock promoters, e.g., soybean hsp17.5-E or hsp17.3-B (Gurley et al., 1986, Mol. Cell. Biol., 6:559; Severin et al., 1990, Plant Mol. Biol., 15:827) may be used. Exemplary viral promoters which function constitutively in eukaryotic cells include, for example, promoters from the simian virus, papilloma virus, adenovirus, human immunodeficiency virus, Rous sarcoma virus, cytomegalovirus, the long terminal repeats of Moloney leukemia virus and other retroviruses, and the thymidine kinase promoter of herpes simplex virus. Other constitutive promoters are known to those of ordinary skill in the art. 
     To be most useful, an inducible promoter should 1) provide low expression in the absence of the inducer; 2) provide high expression in the presence of the inducer; 3) use an induction scheme that does not interfere with the normal physiology of the plant; and 4) have no effect on the expression of other genes. Examples of inducible promoters useful in plants include those induced by chemical means, such as the yeast metallothionein promoter which is activated by copper ions (Mett et al., Proc. Natl. Acad. Sci., U.S.A., 90:4567, 1993); In2-1 and In2-2 regulator sequences which are activated by substituted benzenesulfonamides, e.g., herbicide safeners (Hershey et al., Plant Mol. Biol., 17:679, 1991); and the GRE regulatory sequences which are induced by glucocorticoids (Schena et al., Proc. Natl. Acad Sci., U.S.A., 88:10421, 1991). Other promoters, both constitutive and inducible will be known to those of skill in the art. 
     A number of inducible promoters are known in the art. For resistance genes, a pathogen-inducible promoter can be utilized. Such promoters include those from pathogenesis-related proteins (PR proteins), which are induced following infection by a pathogen; e.g., PR proteins, SAR proteins, beta-1,3-glucanase, chitinase, etc. See, for example, Redolfi et al., 1983, Neth. J. Plant Pathol. 89:245-254; Uknes et al., 1992, Plant Cell 4:645-656; and Van Loon, 1985, Plant Mol. Virol. 4:111-116. Of particular interest are promoters that are expressed locally at or near the site of pathogen infection. See, for example, Marineau et al., 1987, Plant Mol. Biol. 9:335-342; Matton et al., 1989, Molecular Plant-Microbe Interactions 2:325-331; Somsisch et al., 1986, Proc. Natl. Acad. Sci. USA 83:2427-2430; Somsisch et al., 1988, Mol. Gen. Genet. 2:93-98; and Yang, 1996, Proc. Natl. Acad. Sci. USA 93:14972-14977. See also, Chen et al., 1996, Plant J. 10:955-966; Zhang et al., 1994, Proc. Natl. Acad. Sci. USA 91:2507-2511; Warner et al., 1993, Plant J. 3:191-201; Siebertz et al., 1989, Plant Cell 1:961-968; U.S. Pat. No. 5,750,386; Cordero et al., 1992, Physiol. Mol. Plant Path. 41:189-200; and the references cited therein. 
     Additionally, as pathogens find entry into plants through wounds or insect damage, a wound-inducible promoter may be used in the DNA constructs of the invention. Such wound-inducible promoters include potato proteinase inhibitor (pin II) gene (Ryan, 1990, Ann. Rev. Phytopath. 28:425-449; Duan et al., 1996, Nature Biotechnology 14:494-498); wun1 and wun2, U.S. Pat. No. 5,428,148; win1 and win2 (Stanford et al., 1989, Mol. Gen. Genet. 215:200-208); systemin (McGurl et al., 1992, Science 225:1570-1573); WIPI (Rohmeier et al., 1993, Plant Mol. Biol. 22:783-792; Eckelkamp et al., 1993, FEBS Letters 323:73-76); MPI gene (Corderok et al., 1994, Plant J. 6(2):141-150); and the like. Such references are herein incorporated by reference. 
     Chemical-regulated promoters can be used to modulate the expression of a gene in a plant through the application of an exogenous chemical regulator. Depending upon the objective, the promoter may be a chemical-inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression. Chemical-inducible promoters are known in the art and include, but are not limited to, the maize In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR-1 a promoter, which is activated by salicylic acid. Other chemical-regulated promoters of interest include steroid-responsive promoters (see, for example, the glucocorticoid-inducible promoter in Schena et al., 1991, Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis et al., 1998, Plant J. 14(2):247-257) and tetramiR167e-inducible and tetramiR167e-repressible promoters (see, for example, Gatz et al., 1991, Mol. Gen. Genet. 227:229-237, and U.S. Pat. Nos. 5,814,618 and 5,789,156), herein incorporated by reference. 
     Where enhanced expression in particular tissues is desired, tissue-preferred promoters can be utilized. Tissue-preferred promoters include those described by Yamamoto et al., 1997, Plant J. 12(2):255-265; Kawamata et al., 1997, Plant Cell Physiol. 38(7):792-803; Hansen et al., 1997, Mol. Gen Genet. 254(3):337-343; Russell et al., 1997, Transgenic Res. 6(2):157-168; Rinehart et al., 1996, Plant Physiol. 112(3):1331-1341; Van Camp et al., 1996, Plant Physiol. 112(2):525-535; Canevascini et al., 1996, Plant Physiol. 12(2):513-524; Yamamoto et al., 1994, Plant Cell Physiol. 35(5):773-778; Lam, 1994, Results Probl. Cell Differ. 20:181-196; Orozco et al., 1993, Plant Mol. Biol. 23(6): 1129-1138; Matsuoka et al., 1993, Proc Natl. Acad. Sci. USA 90(20):9586-9590; and Guevara-Garcia et al., 1993, Plant J 4(3):495-505. 
     The particular promoter selected should be capable of causing sufficient expression to result in the production of an effective amount of structural gene product in the plant cell to cause upregulation of genes as compared to wild type. The promoters used in the vector constructs of the present invention may be modified, if desired, to affect their control characteristics. In certain embodiments, chimeric promoters can be used. 
     There are promoters known which limit expression to particular plant parts or in response to particular stimuli. One skilled in the art will know of many such plant part-specific promoters which would be useful in the present invention. In certain embodiments, to provide pericycle-specific expression, any of a number of promoters from genes in  Arabidopsis  can be used. In some embodiments, the promoter from one (or more) of the following genes may be used: (i) At1g11080, (ii) At3g60160, (iii) At1g24575, (iv) At3g45160, or (v) At1g23130. In specific embodiments, (vi) promoter elements from the GFP-marker line used in Gifford et al. (in preparation) will be used (see also, Bonke et al., 2003, Nature 426, 181-6; Tian et al., 2004, Plant Physiol 135, 25-38). Several of the predicted genes have a number of potential orthologs in rice and poplar and thus are predicted that they will be applicable for use in crop species; (i) Os04g44410, Os10g39560, Os06g51370, Os02g42310, Os01g22980, Os05g06660, and Poptr1#568263, Poptr1 #555534, Poptr1#365170; (ii) Os04g49900, Os04g49890, Os01g67580, and Poptr1#87573, Poptr1#80582, Poptr1#565079, Poptr1#99223. 
     Promoters used in the nucleic acid constructs of the present invention can be modified, if desired, to affect their control characteristics. For example, the CaMV 35S promoter may be ligated to the portion of the ssRUBISCO gene that represses the expression of ssRUBISCO in the absence of light, to create a promoter which is active in leaves but not in roots. The resulting chimeric promoter may be used as described herein. For purposes of this description, the phrase “CaMV 35S” promoter thus includes variations of CaMV 35S promoter, e.g., promoters derived by means of ligation with operator regions, random or controlled mutagenesis, etc. Furthermore, the promoters may be altered to contain multiple “enhancer sequences” to assist in elevating gene expression. 
     An efficient plant promoter that may be used in specific embodiments is an “overproducing” or “overexpressing” plant promoter. Overexpressing plant promoters that can be used in the compositions and methods provided herein include the promoter of the small sub-unit (“ss”) of the ribulose-1,5-biphosphate carboxylase from soybean (e.g., Berry-Lowe et al., 1982, J. Molecular &amp; App. Genet., 1:483), and the promoter of the chorophyll a-b binding protein. These two promoters are known to be light-induced in eukaryotic plant cells. For example, see Cashmore, Genetic Engineering of plants: An Agricultural Perspective, p. 29-38; Coruzzi et al., 1983, J. Biol. Chem., 258:1399; and Dunsmuir et al., 1983, J. Molecular &amp; App. Genet., 2:285. 
     The promoters and control elements of, e.g., SUCS (root nodules; broadbean; Kuster et al., 1993, Mol Plant Microbe Interact 6:507-14) for roots can be used in compositions and methods provided herein to confer tissue specificity. 
     In certain embodiment, two promoter elements can be used in combination, such as, for example, (i) an inducible element responsive to a treatment that can be provided to the plant prior to N-fertilizer treatment, and (ii) a plant tissue-specific expression element to drive expression in the specific tissue alone. 
     Any promoter of other expression element described herein or known in the art may be used either alone or in combination with any other promoter or other expression element described herein or known in the art. For example, promoter elements that confer tissue specific expression of a gene can be used with other promoter elements conferring constitutive or inducible expression. 
     5.2.6. Isolating Related Promoter Sequences 
     Promoter and promoter control elements that are related to those described in herein can also be used in the compositions and methods provided herein. Such related sequence can be isolated utilizing (a) nucleotide sequence identity; (b) coding sequence identity of related, orthologous genes; or (c) common function or gene products. 
     Relatives can include both naturally occurring promoters and non-natural promoter sequences. Non-natural related promoters include nucleotide substitutions, insertions or deletions of naturally-occurring promoter sequences that do not substantially affect transcription modulation activity. For example, the binding of relevant DNA binding proteins can still occur with the non-natural promoter sequences and promoter control elements of the present invention. 
     According to current knowledge, promoter sequences and promoter control elements exist as functionally important regions, such as protein binding sites, and spacer regions. These spacer regions are apparently required for proper positioning of the protein binding sites. Thus, nucleotide substitutions, insertions and deletions can be tolerated in these spacer regions to a certain degree without loss of function. 
     In contrast, less variation is permissible in the functionally important regions, since changes in the sequence can interfere with protein binding. Nonetheless, some variation in the functionally important regions is permissible so long as function is conserved. 
     The effects of substitutions, insertions and deletions to the promoter sequences or promoter control elements may be to increase or decrease the binding of relevant DNA binding proteins to modulate transcript levels of a polynucleotide to be transcribed. Effects may include tissue-specific or condition-specific modulation of transcript levels of the polypeptide to be transcribed. Polynucleotides representing changes to the nucleotide sequence of the DNA-protein contact region by insertion of additional nucleotides, changes to identity of relevant nucleotides, including use of chemically-modified bases, or deletion of one or more nucleotides are considered encompassed by the present invention. 
     Typically, related promoters exhibit at least 80% sequence identity, preferably at least 85%, more preferably at least 90%, and most preferably at least 95%, even more preferably, at least 96%, at least 97%, at least 98% or at least 99% sequence identity. Such sequence identity can be calculated by the algorithms and computers programs described above. 
     Usually, such sequence identity is exhibited in an alignment region that is at least 75% of the length of a sequence or corresponding full-length sequence of a promoter described herein; more usually at least 80%; more usually, at least 85%, more usually at least 90%, and most usually at least 95%, even more usually, at least 96%, at least 97%, at least 98% or at least 99% of the length of a sequence of a promoter described herein. 
     The percentage of the alignment length is calculated by counting the number of residues of the sequence in region of strongest alignment, e.g., a continuous region of the sequence that contains the greatest number of residues that are identical to the residues between two sequences that are being aligned. The number of residues in the region of strongest alignment is divided by the total residue length of a sequence of a promoter described herein. These related promoters may exhibit similar preferential transcription as those promoters described herein. 
     In certain embodiments, a promoter, such as a leaf-preferred or leaf-specific promoter, can be identified by sequence homology or sequence identity to any root specific promoter identified herein. In other embodiments, orthologous genes identified herein as leaf-specific genes (e.g., the same gene or different gene that if functionally equivalent) for a given species can be identified and the associated promoter can also be used in the compositions and methods provided herein. For example, using high, medium or low stringency conditions, standard promoter rules can be used to identify other useful promoters from orthologous genes for use in the compositions and methods provided herein. In specific embodiments, the orthologous gene is a gene expressed only or primarily in the root, such as pericycle cells. 
     Polynucleotides can be tested for activity by cloning the sequence into an appropriate vector, transforming plants with the construct and assaying for marker gene expression. Recombinant DNA constructs can be prepared, which comprise the polynucleotide sequences of the invention inserted into a vector suitable for transformation of plant cells. The construct can be made using standard recombinant DNA techniques (Sambrook et al., 1989) and can be introduced to the species of interest by  Agrobacterium -mediated transformation or by other means of transformation as referenced below. 
     The vector backbone can be any of those typical in the art such as plasmids, viruses, artificial chromosomes, BACs, YACs and PACs and vectors of the sort described by (a) BAC: Shizuya et al., 1992, Proc. Natl. Acad. Sci. USA 89: 8794-8797; Hamilton et al., 1996, Proc. Natl. Acad. Sci. USA 93: 9975-9979; (b) YAC: Burke et al., 1987, Science 236:806-812; (c) PAC: Stemberg N. et al., 1990, Proc Natl Acad Sci USA. January; 87(1):103-7; (d) Bacteria-Yeast Shuttle Vectors: Bradshaw et al., 1995, Nucl Acids Res 23: 4850-4856; (e) Lambda Phage Vectors: Replacement Vector, e.g., Frischauf et al., 1983, J. Mol. Biol. 170: 827-842; or Insertion vector, e.g., Huynh et al., 1985, In: Glover N M (ed) DNA Cloning: A practical Approach, Vol. 1 Oxford: IRL Press; T-DNA gene fusion vectors: Walden et al., 1990, Mol Cell Biol 1: 175-194; and (g) Plasmid vectors: Sambrook et al., infra. 
     Typically, the construct comprises a vector containing a sequence of the present invention operationally linked to any marker gene. The polynucleotide was identified as a promoter by the expression of the marker gene. Although many marker genes can be used, Green Fluorescent Protein (GFP) is preferred. The vector may also comprise a marker gene that confers a selectable phenotype on plant cells. The marker may encode biocide resistance, particularly antibiotic resistance, such as resistance to kanamycin, G418, bleomycin, hygromycin, or herbicide resistance, such as resistance to chlorosulfuron or phosphinotricin (see below). Vectors can also include origins of replication, scaffold attachment regions (SARs), markers, homologous sequences, introns, etc. 
     5.2.7. Cell-Type Preferential Transcription 
     Specific promoters may be used in the compositions and methods provided herein. As used herein, “specific promoters” refers to a subset of promoters that have a high preference for modulating transcript levels in a specific tissue or organ or cell and/or at a specific time during development of an organism. By “high preference” is meant at least 3-fold, preferably 5-fold, more preferably at least 10-fold still more preferably at least 20-fold, 50-fold or 100-fold increase in transcript levels under the specific condition over the transcription under any other reference condition considered. Typical examples of temporal and/or tissue or organ specific promoters of plant origin that can be used in the compositions and methods of the present invention, include RCc2 and RCc3, promoters that direct root-specific gene transcription in rice (Xu et al., 1995, Plant Mol. Biol. 27:237 and TobRB27, a root-specific promoter from tobacco (Yamamoto et al., 1991, Plant Cell 3:371). Examples of tissue-specific promoters under developmental control include promoters that initiate transcription only in certain tissues or organs, such as roots 
     “Preferential transcription” is defined as transcription that occurs in a particular pattern of cell types or developmental times or in response to specific stimuli or combination thereof. Non-limitative examples of preferential transcription include: high transcript levels of a desired sequence in root tissues; detectable transcript levels of a desired sequence in certain cell types during embryogenesis; and low transcript levels of a desired sequence under drought conditions. Such preferential transcription can be determined by measuring initiation, rate, and/or levels of transcription. 
     Typically, promoter or control elements, which provide preferential transcription in cells, tissues, or organs of a root, produce transcript levels that are statistically significant as compared to other cells, organs or tissues. For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay. 
     5.2.8. Selection and Identification of Transfected Host Cells 
     The method of the present invention comprises detecting host cells that express a selectable marker. In certain embodiments, the step of detecting host cells that express the selectable marker is performed by Fluorescence Activated Cell Sorting (FACS) in the methods of the present invention. Fluorescence activated cell sorting (FACS) is a well-known method for separating particles, including cells, based on the fluorescent properties of the particles (see, e.g., Kamarch, 1987, Methods Enzymol, 151:150-165). Laser excitation of fluorescent moieties in the individual particles results in a small electrical charge allowing electromagnetic separation of positive and negative particles from a mixture. In one embodiment, cell surface marker-specific antibodies or ligands are labeled with distinct fluorescent labels. Cells are processed through the cell sorter, allowing separation of cells based on their ability to bind to the antibodies used. FACS sorted particles may be directly deposited into individual wells of 96-well or 384-well plates to facilitate separation and cloning. 
     Also, desired plants may be obtained by engineering the disclosed gene constructs into a variety of plant cell types, including but not limited to, protoplasts, tissue culture cells, tissue and organ explants, pollens, embryos as well as whole plants. In an embodiment of the present invention, the engineered plant material is selected or screened for transformants (those that have incorporated or integrated the introduced gene construct(s)) following the approaches and methods described below. An isolated transformant may then be regenerated into a plant. Alternatively, the engineered plant material may be regenerated into a plant or plantlet before subjecting the derived plant or plantlet to selection or screening for the marker gene traits. Procedures for regenerating plants from plant cells, tissues or organs, either before or after selecting or screening for marker gene(s), are well known to those skilled in the art. 
     A transformed plant cell, callus, tissue or plant may be identified and isolated by selecting or screening the engineered plant material for traits encoded by the marker genes present on the transforming DNA. For instance, selection may be performed by growing the engineered plant material on media containing inhibitory amount of the antibiotic or herbicide to which the transforming gene construct confers resistance. Further, transformed plants and plant cells may also be identified by screening for the activities of any visible marker genes (e.g., the 3-glucuronidase, luciferase, B or C1 genes) that may be present on the recombinant nucleic acid constructs of the present invention. Such selection and screening methodologies are well known to those skilled in the art. 
     Physical and biochemical methods also may be also to identify plant or plant cell transformants containing the gene constructs of the present invention. These methods include but are not limited to: 1) Southern analysis or PCR amplification for detecting and determining the structure of the recombinant DNA insert; 2) Northern blot, Si RNase protection, primer-extension or reverse transcriptase-PCR amplification for detecting and examining RNA transcripts of the gene constructs; 3) enzymatic assays for detecting enzyme or ribozyme activity, where such gene products are encoded by the gene construct; 4) protein gel electrophoresis, Western blot techniques, immunoprecipitation, or enzyme-linked immunoassays, where the gene construct products are proteins. Additional techniques, such as in situ hybridization, enzyme staining, and immunostaining, also may be used to detect the presence or expression of the recombinant construct in specific plant organs and tissues. The methods for doing all these assays are well known to those skilled in the art. 
     5.2.9. Plant Regeneration 
     Following transformation, a plant may be regenerated, e.g., from single cells, callus tissue or leaf discs, as is standard in the art. Almost any plant can be entirely regenerated from cells, tissues, and organs of the plant. Available techniques are reviewed in Vasil et al., 1984, in Cell Culture and Somatic Cell Genetics of Plants, Vols. I, II, and III, Laboratory Procedures and Their Applications (Academic Press); and Weissbach et al., 1989, Methods For Plant Mol. Biol. 
     The transformed plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. 
     Normally, a plant cell is regenerated to obtain a whole plant from the transformation process. The term “growing” or “regeneration” as used herein means growing a whole plant from a plant cell, a group of plant cells, a plant part (including seeds), or a plant piece (e.g., from a protoplast, callus, or tissue part). 
     Regeneration from protoplasts varies from species to species of plants, but generally a suspension of protoplasts is first made. In certain species, embryo formation can then be induced from the protoplast suspension. The culture media will generally contain various amino acids and hormones, necessary for growth and regeneration. Examples of hormones utilized include auxins and cytokinins. Efficient regeneration will depend on the medium, on the genotype, and on the history of the culture. If these variables are controlled, regeneration is reproducible. 
     Regeneration also occurs from plant callus, explants, organs or parts. Transformation can be performed in the context of organ or plant part regeneration (see Methods in Enzymology, Vol. 118 and Klee et al., Annual Review of Plant Physiology, 38:467, 1987). Utilizing the leaf disk-transformation-regeneration method of Horsch et al., Science, 227:1229, 1985, disks are cultured on selective media, followed by shoot formation in about 2-4 weeks. Shoots that develop are excised from calli and transplanted to appropriate root-inducing selective medium. Rooted plantlets are transplanted to soil as soon as possible after roots appear. The plantlets can be repotted as required, until reaching maturity. 
     In vegetatively propagated crops, the mature transgenic plants are propagated by utilizing cuttings or tissue culture techniques to produce multiple identical plants. Selection of desirable transgenics is made and new varieties are obtained and propagated vegetatively for commercial use. 
     In seed propagated crops, mature transgenic plants can be self crossed to produce a homozygous inbred plant. The resulting inbred plant produces seed containing the newly introduced foreign gene(s). These seeds can be grown to produce plants that would produce the selected phenotype, e.g., increased lateral root growth, uptake of nutrients, overall plant growth and/or vegetative or reproductive yields. 
     Parts obtained from the regenerated plant, such as flowers, seeds, leaves, branches, fruit, and the like are included in the invention, provided that these parts comprise cells comprising the isolated nucleic acid of the present invention. Progeny and variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced nucleic acid sequences. Transgenic plants expressing the selectable marker can be screened for transmission of the nucleic acid of the present invention by, for example, standard immunoblot and DNA detection techniques. Transgenic lines are also typically evaluated on levels of expression of the heterologous nucleic acid. Expression at the RNA level can be determined initially to identify and quantitate expression-positive plants. Standard techniques for RNA analysis can be employed and include PCR amplification assays using oligonucleotide primers designed to amplify only the heterologous RNA templates and solution hybridization assays using heterologous nucleic acid-specific probes. The RNA-positive plants can then analyzed for protein expression by Western immunoblot analysis using the specifically reactive antibodies of the present invention. In addition, in situ hybridization and immunocytochemistry according to standard protocols can be done using heterologous nucleic acid specific polynucleotide probes and antibodies, respectively, to localize sites of expression within transgenic tissue. Generally, a number of transgenic lines are usually screened for the incorporated nucleic acid to identify and select plants with the most appropriate expression profiles. 
     A preferred embodiment is a transgenic plant that is homozygous for the added heterologous nucleic acid; i.e., a transgenic plant that contains two added nucleic acid sequences, one gene at the same locus on each chromosome of a chromosome pair. A homozygous transgenic plant can be obtained by sexually mating (selfing) a heterozygous transgenic plant that contains a single added heterologous nucleic acid, germinating some of the seed produced and analyzing the resulting plants produced for altered expression of a polynucleotide of the present invention relative to a control plant (i.e., native, non-transgenic). Back-crossing to a parental plant and out-crossing with a non-transgenic plant are also contemplated. 
     Transformed plant cells which are derived by any of the above transformation techniques can be cultured to regenerate a whole plant which possesses the transformed genotype. Such regeneration techniques often rely on manipulation of certain phytohormones in a tissue culture growth medium. For transformation and regeneration of maize see, Gordon-Kamm et al., 1990, The Plant Cell, 2:603-618. 
     Plants cells transformed with a plant expression vector can be regenerated, e.g., from single cells, callus tissue or leaf discs according to standard plant tissue culture techniques. It is well known in the art that various cells, tissues, and organs from almost any plant can be successfully cultured to regenerate an entire plant. Plant regeneration from cultured protoplasts is described in Evans et al., 1983, Protoplasts Isolation and Culture, Handbook of Plant Cell Culture, Macmillan Publishing Company, New York, pp. 124-176; and Binding, Regeneration of Plants, Plant Protoplasts, 1985, CRC Press, Boca Raton, pp. 21-73. 
     The regeneration of plants containing the foreign gene introduced by  Agrobacterium  from leaf explants can be achieved as described by Horsch et al., 1985, Science, 227:1229-1231. In this procedure, transformants are grown in the presence of a selection agent and in a medium that induces the regeneration of shoots in the plant species being transformed as described by Fraley et al., 1983, Proc. Natl. Acad. Sci. (U.S.A.), 80:4803. This procedure typically produces shoots within two to four weeks and these transformant shoots are then transferred to an appropriate root-inducing medium containing the selective agent and an antibiotic to prevent bacterial growth. Transgenic plants of the present invention may be fertile or sterile. 
     The regeneration of plants from either single plant protoplasts or various explants is well known in the art. See, for example, Methods for Plant Molecular Biology, A. Weissbach and H. Weissbach, eds., 1988, Academic Press, Inc., San Diego, Calif. This regeneration and growth process includes the steps of selection of transformant cells and shoots, rooting the transformant shoots and growth of the plantlets in soil. For maize cell culture and regeneration see generally, The Maize Handbook, Freeling and Walbot, Eds., 1994, Springer, N.Y. 1994; Corn and Corn Improvement, 3rd edition, Sprague and Dudley Eds., 1988, American Society of Agronomy, Madison, Wis. 
     5.2.10. Plants 
     The present invention also provides a plant comprising a plant cell as disclosed. Transformed seeds and plant parts are also encompassed. 
     In addition to a plant, the present invention provides any clone of such a plant, seed, selfed or hybrid progeny and descendants, and any part of any of these, such as cuttings, seed. The invention provides any plant propagule, that is any part which may be used in reproduction or propagation, sexual or asexual, including cuttings, seed and so on. Also encompassed by the invention is a plant which is a sexually or asexually propagated off-spring, clone or descendant of such a plant, or any part or propagule of said plant, off-spring, clone or descendant. Plant extracts and derivatives are also provided. 
     Any species of woody, ornamental or decorative, crop or cereal, fruit or vegetable plant, and algae (e.g.,  Chlamydomonas reinhardtii ) may be used in the compositions and methods provided herein. Non-limiting examples of plants include plants from the genus  Arabidopsis  or the genus  Oryza.  Other examples include plants from the genuses  Acorus, Aegilops, Allium, Amborella, Antirrhinum, Apium, Arachis, Beta, Betula, Brassica, Capsicum, Ceratopteris, Citrus, Cryptomeria, Cycas, Descurainia, Eschscholzia, Eucalyptus, Glycine, Gossypium, Hedyotis, Helianthus, Hordeum, Ipomoea, Lactuca, Linum, Liriodendron, Lotus, Lupinus, Lycopersicon, Medicago, Mesembryanthemum, Nicotiana, Nuphar, Pennisetum, Persea, Phaseolus, Physcomitrella, Picea, Pinus, Poncirus, Populus, Prunus, Robinia, Rosa, Saccharum, Schedonorus, Secale, Sesamum, Solanum, Sorghum, Stevia, Thellungiella, Theobroma, Triphysaria, Triticum, Vitis, Zea,  or  Zinnia.    
     Plants included in the invention are any plants amenable to transformation techniques, including gymnosperms and angiosperms, both monocotyledons and dicotyledons. 
     Examples of monocotyledonous angiosperms include, but are not limited to, asparagus, field and sweet corn, barley, wheat, rice, sorghum, onion, pearl millet, rye and oats and other cereal grains. 
     Examples of dicotyledonous angiosperms include, but are not limited to tomato, tobacco, cotton, rapeseed, field beans, soybeans, peppers, lettuce, peas, alfalfa, clover, cole crops or  Brassica oleracea  (e.g., cabbage, broccoli, cauliflower, brussel sprouts), radish, carrot, beets, eggplant, spinach, cucumber, squash, melons, cantaloupe, sunflowers and various ornamentals. 
     Examples of woody species include poplar, pine, sequoia, cedar, oak, etc. 
     Still other examples of plants include, but are not limited to, wheat, cauliflower, tomato, tobacco, corn, petunia, trees, etc. 
     In certain embodiments, plants of the present invention are crop plants (for example, cereals and pulses, maize, wheat, potatoes, tapioca, rice, sorghum, millet, cassaya, barley, pea, and other root, tuber, or seed crops. Exemplary cereal crops used in the compositions and methods of the invention include, but are not limited to, any species of grass, or grain plant (e.g., barley, corn, oats, rice, wild rice, rye, wheat, millet, sorghum, triticale, etc.), non-grass plants (e.g., buckwheat flax, legumes or soybeans, etc.). Grain plants that provide seeds of interest include oil-seed plants and leguminous plants. Other seeds of interest include grain seeds, such as corn, wheat, barley, rice, sorghum, rye, etc. Oil seed plants include cotton, soybean, safflower, sunflower,  Brassica,  maize, alfalfa, palm, coconut, etc. Other important seed crops are oil-seed rape, sugar beet, maize, sunflower, soybean, and sorghum. Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc. 
     Horticultural plants to which the present invention may be applied may include lettuce, endive, and vegetable brassicas including cabbage, broccoli, and cauliflower, and carnations and geraniums. The present invention may also be applied to tobacco, cucurbits, carrot, strawberry, sunflower, tomato, pepper, chrysanthemum, poplar, eucalyptus, and pine. 
     The present invention may be used for transformation of other plant species, including, but not limited to, corn ( Zea mays ), canola ( Brassica napus, Brassica rapa  ssp.), alfalfa ( Medicago sativa ), rice ( Oryza sativa ), rye ( Secale cereale ), sorghum ( Sorghum bicolor, Sorghum vulgare ), sunflower ( Helianthus annuus ), wheat ( Triticum aestivum ), soybean ( Glycine max ), tobacco ( Nicotiana tabacum, Nicotiana benthamiana ), potato ( Solanum tuberosum ), peanuts ( Arachis hypogaea ), cotton ( Gossypium hirsutum ), sweet potato ( Ipomoea batatus ), cassaya ( Manihot esculenta ), coffee ( Coffea  spp.), coconut ( Cocos nucifera ), pineapple ( Ananas comosus ), citrus trees ( Citrus  spp.), cocoa ( Theobroma cacao ), tea ( Camellia sinensis ), banana ( Musa  spp.), avocado ( Persea americana ), fig ( Ficus casica ), guava ( Psidium guajava ), mango ( Mangifera indica ), olive ( Olea europaea ), papaya ( Carica papaya ), cashew ( Anacardium occidentale ), macadamia ( Macadamia integrifolia ), almond ( Prunus amygdalus ), sugar beets ( Beta vulgaris ), oats, barley,  Arabidopsis  spp., vegetables, ornamentals, and conifers. 
     5.2.11. Cultivation 
     Methods of cultivation of plants are well known in the art. For example, for the cultivation of wheat see Alcoz et al., 1993, Agronomy Journal 85:1198-1203; Rao and Dao, 1992, J. Am. Soc. Agronomy 84:1028-1032; Howard and Lessman, 1991, Agronomy Journal 83:208-211; for the cultivation of corn see Tollenear et al., 1993, Agronomy Journal 85:251-255; Straw et al., Tennessee Farm and Home Science: Progress Report, Spring 1993, 166:20-24; Miles, S. R., 1934, J. Am. Soc. Agronomy 26:129-137; Dara et al., 1992, J. Am. Soc. Agronomy 84:1006-1010; Binford et al., 1992, Agronomy Journal 84:53-59; for the cultivation of soybean see Chen et al., 1992, Canadian Journal of Plant Science 72:1049-1056; Wallace et al., 1990, Journal of Plant Nutrition 13:1523-1537; for the cultivation of rice see Oritani and Yoshida, 1984, Japanese Journal of Crop Science 53:204-212; for the cultivation of linseed see Diepenbrock and Porksen, 1992, Industrial Crops and Products 1:165-173; for the cultivation of tomato see Grubinger et al., 1993, Journal of the American Society for Horticultural Science 118:212-216; Cerne, M., 1990, Acta Horticulture 277:179-182; for the cultivation of pineapple see Magistad et al., 1932, J. Am. Soc. Agronomy 24:610-622; Asoegwu, S. N., 1988, Fertilizer Research 15:203-210; Asoegwu, S. N., 1987, Fruits 42:505-509; for the cultivation of lettuce see Richardson and Hardgrave, 1992, Journal of the Science of Food and Agriculture 59:345-349; for the cultivation of mint see Munsi, P. S., 1992, Acta Horticulturae 306:436-443; for the cultivation of camomile see Letchamo, W., 1992, Acta Horticulturae 306:375-384; for the cultivation of tobacco see Sisson et al., 1991, Crop Science 31:1615-1620; for the cultivation of potato see Porter and Sisson, 1991, American Potato Journal, 68:493-505; for the cultivation of  brassica  crops see Rahn et al., 1992, Conference “Proceedings, second congress of the European Society for Agronomy”Warwick Univ., p.424-425; for the cultivation of banana see Hegde and Srinivas, 1991, Tropical Agriculture 68:331-334; Langenegger and Smith, 1988, Fruits 43:639-643; for the cultivation of strawberries see Human and Kotze, 1990, Communications in Soil Science and Plant Analysis 21:771-782; for the cultivation of songhum see Mahalle and Seth, 1989, Indian Journal of Agricultural Sciences 59:395-397; for the cultivation of plantain see Anjorin and Obigbesan, 1985, Conference “International Cooperation for Effective Plantain and Banana Research” Proceedings of the third meeting. Abidjan, Ivory Coast, p. 115-117; for the cultivation of sugar cane see Yadav, R. L., 1986, Fertiliser News 31:17-22; Yadav and Sharma, 1983, Indian Journal of Agricultural Sciences 53:38-43; for the cultivation of sugar beet see Draycott et al., 1983, Conference “Symposium Nitrogen and Sugar Beet” International Institute for Sugar Beet Research—Brussels Belgium, p. 293-303. See also Goh and Haynes, 1986, “Nitrogen and Agronomic Practice” in Mineral Nitrogen in the Plant-Soil System, Academic Press, Inc., Orlando, Fla., p. 379-468; Engelstad, O. P., 1985, Fertilizer Technology and Use, Third Edition, Soil Science Society of America, p.633; Yadav and Sharmna, 1983, Indian Journal of Agricultural Sciences, 53:3-43. 
     5.2.12. Products of Transgenic Plants 
     Engineered plants exhibiting the desired physiological and/or agronomic changes can be used directly in agricultural production. 
     Thus, provided herein are products derived from the transgenic plants or methods of producing transgenic plants provided herein. In certain embodiments, the products are commercial products. Some non-limiting example include genetically engineered trees for e.g., the production of pulp, paper, paper products or lumber; tobacco, e.g., for the production of cigarettes, cigars, or chewing tobacco; crops, e.g., for the production of fruits, vegetables and other food, including grains, e.g., for the production of wheat, bread, flour, rice, corn; and canola, sunflower, e.g., for the production of oils or biofuels. 
     In certain embodiments, commercial products are derived from a genetically engineered (e.g., comprising overexpression of GLK1 in the vegetative tissues of the plant) species of woody, ornamental or decorative, crop or cereal, fruit or vegetable plant, and algae (e.g.,  Chlamydomonas reinhardtii ), which may be used in the compositions and methods provided herein. Non-limiting examples of plants include plants from the genus  Arabidopsis  or the genus  Oryza.  Other examples include plants from the genuses  Acorus, Aegilops, Allium, Amborella, Antirrhinum, Apium, Arachis, Beta, Betula, Brassica, Capsicum, Ceratopteris, Citrus, Cryptomeria, Cycas, Descurainia, Eschscholzia, Eucalyptus, Glycine, Gossypium, Hedyotis, Helianthus, Hordeum, Ipomoea, Lactuca, Linum, Liriodendron, Lotus, Lupinus, Lycopersicon, Medicago, Mesembryanthemum, Nicotiana, Nuphar, Pennisetum, Persea, Phaseolus, Physcomitrella, Picea, Pinus, Poncirus, Populus, Prunus, Robinia, Rosa, Saccharum, Schedonorus, Secale, Sesamum, Solanum, Sorghum, Stevia, Thellungiella, Theobroma, Triphysaria, Triticum, Vitis, Zea,  or  Zinnia.    
     In some embodiments, commercial products are derived from a genetically engineered gymnosperms and angiosperms, both monocotyledons and dicotyledons. Examples of monocotyledonous angiosperms include, but are not limited to, asparagus, field and sweet corn, barley, wheat, rice, sorghum, onion, pearl millet, rye and oats and other cereal grains. Examples of dicotyledonous angiosperms include, but are not limited to tomato, tobacco, cotton, rapeseed, field beans, soybeans, peppers, lettuce, peas, alfalfa, clover, cole crops or  Brassica oleracea  (e.g., cabbage, broccoli, cauliflower, brussel sprouts), radish, carrot, beets, eggplant, spinach, cucumber, squash, melons, cantaloupe, sunflowers and various ornamentals. 
     In certain embodiments, commercial products are derived from a genetically engineered woody species, such as poplar, pine, sequoia, cedar, oak, etc. 
     In other embodiments, commercial products are derived from a genetically engineered plant including, but are not limited to, wheat, cauliflower, tomato, tobacco, corn, petunia, trees, etc. 
     In certain embodiments, commercial products are derived from a genetically engineered crop plants, for example, cereals and pulses, maize, wheat, potatoes, tapioca, rice, sorghum, millet, cassaya, barley, pea, and other root, tuber, or seed crops. In one embodiment, commercial products are derived from a genetically engineered cereal crops, including, but are not limited to, any species of grass, or grain plant (e.g., barley, corn, oats, rice, wild rice, rye, wheat, millet, sorghum, triticale, etc.), non-grass plants (e.g., buckwheat flax, legumes or soybeans, etc.). In another embodiments, commercial products are derived from a genetically engineered grain plants that provide seeds of interest, oil-seed plants and leguminous plants. In other embodiments, commercial products are derived from a genetically engineered grain seed plants, such as corn, wheat, barley, rice, sorghum, rye, etc. In yet other embodiments, commercial products are derived from a genetically engineered oil seed plants, such as cotton, soybean, safflower, sunflower,  Brassica,  maize, alfalfa, palm, coconut, etc. In certain embodiments, commercial products are derived from a genetically engineered oil-seed rape, sugar beet, maize, sunflower, soybean, or sorghum. In some embodiments, commercial products are derived from a genetically engineered leguminous plants, such as beans and peas (e.g., guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc.) 
     In certain embodiments, commercial products are derived from a genetically engineered horticultural plant of the present invention, such as lettuce, endive, and vegetable brassicas including cabbage, broccoli, and cauliflower, and carnations and geraniums; tomato, tobacco, cucurbits, carrot, strawberry, sunflower, tomato, pepper, chrysanthemum, poplar, eucalyptus, and pine. 
     In still other embodiments, commercial products are derived from a genetically engineered corn ( Zea mays ), canola ( Brassica napus, Brassica rapa  ssp.), alfalfa ( Medicago sativa ), rice ( Oryza sativa ), rye ( Secale cereale ), sorghum ( Sorghum bicolor, Sorghum vulgare ), sunflower ( Helianthus annuus ), wheat ( Triticum aestivum ), soybean ( Glycine max ), tobacco ( Nicotiana tabacum, Nicotiana benthamiana ), potato ( Solanum tuberosum ), peanuts ( Arachis hypogaea ), cotton ( Gossypium hirsutum ), sweet potato ( Ipomoea batatus ), cassaya ( Manihot esculenta ), coffee ( Coffea  spp.), coconut ( Cocos nucifera ), pineapple ( Ananas comosus ), citrus trees ( Citrus  spp.), cocoa ( Theobroma cacao ), tea ( Camellia sinensis ), banana ( Musa  spp.), avocado ( Persea americana ), fig ( Ficus casica ), guava ( Psidium guajava ), mango ( Mangifera indica ), olive ( Olea europaea ), papaya ( Carica papaya ), cashew ( Anacardium occidentale ), macadamia ( Macadamia integrifolia ), almond ( Prunus amygdalus ), sugar beets ( Beta vulgaris ), oats, barley,  Arabidopsis  spp., vegetables, ornamentals, and conifers. 
     5.3. Components of the Target System 
     The TARGET system utilizes a nucleic acid encoding a chimeric protein comprising a transcription factor fused to a domain comprising an inducible cellular localization signal and an independently expressed selectable marker. Nucleic acids for use with the target system may be plasmids or other appropriate nucleic acid constructs as described in Section 5.2.3. The TARGET system also comprises methods of measuring mRNA expression levels and may additionally comprise methods of detecting TF binding to gene targets. 
     5.3.1. Transcription Factors 
     The transcription factor component chimeric protein encoded by the nucleic acid construct may be, but is not limited to, one of those listed in Table 3. The transcription factor used is not limited to nuclear transcription factors, but may also include proteins that modulate mitochondrial or chloroplast gene expression. 
     5.3.2. Localization Signals and Inducing Agents 
     The glucorticoid receptor (GR) may be used as the inducible cellular localization signal in the chimeric protein encoded by the nucleic acid construct. In the case of the a TF-GR chimeric protein, dexamethasone may be used as the inducing agent. Alternately, another glucocorticoid may be used instead of dexamethasone. Treatment with dexamethasone releases the glucocorticoid receptor from sequestration in the cytoplasm, allowing the TF-GR fusion protein to access its target genes (e.g., in the nucleus). The GR is not the only such inducible cellular localization signal that may be used in this method. Any receptor component or other protein known in the art that is capable of being released from sequestration or otherwise re-localized to the destination of the transcription factor component by treatment of the protoplasts with an inducing agent may potentially be used in the TARGET system. 
     5.3.3. Expression System and Selectable Markers 
     Using any gene transfer technique, such as the above-listed techniques (of Section 5.2), an expression vector harboring the nucleic acid may be transformed into a cell to achieve temporary or prolonged expression. Any suitable expression system may be used, so long as it is capable of undergoing transformation and expressing of the precursor nucleic acid in the cell. In one embodiment, a pET vector (Novagen, Madison, Wis.), or a pBI vector (Clontech, Palo Alto, Calif.) is used as the expression vector. In some embodiments an expression vector further encoding a green fluorescent protein (“GFP”) is used to allow simple selection of transfected cells and to monitor expression levels. Non-limiting examples of such vectors include Clontech&#39;s “Living Colors Vectors” pEYFP and pEYFP-C. 
     The recombinant construct of the present invention may include a selectable marker for propagation of the construct. For example, a construct to be propagated in bacteria preferably contains an antibiotic resistance gene, such as one that confers resistance to kanamycin, tetracycline, streptomycin, or chloramphenicol. Suitable vectors for propagating the construct include plasmids, cosmids, bacteriophages or viruses, to name but a few. 
     In some embodiments, the selectable marker encoded by the nucleic acid molecule used in the method of the invention is a fluorescent selection marker. A fluorescent selection marker that can be used in the method of the invention includes, but is not limited to, green fluorescent protein, yellow fluorescent protein, red fluorescent protein, cyan fluorescent protein, or blue fluorescent protein. In a specific embodiment, the fluorescent selection marker used in the method of the invention is red fluorescent protein. In certain embodiments, the step of detecting host cells that express the selectable marker is performed by Fluorescence Activated Cell Sorting (FACS). Any selectable marker known in the art that may be encoded in the nucleic acid construct and which is selectable using a cell sorting or other selection technique may be used to identify those cells that have expressed the nucleic acid construct containing the chimeric protein. 
     In addition, the recombinant constructs may include plant-expressible selectable or screenable marker genes for isolating, identifying or tracking of plant cells transformed by these constructs. Selectable markers include, but are not limited to, genes that confer antibiotic resistances (e.g., resistance to kanamycin or hygromycin) or herbicide resistance (e.g., resistance to sulfonylurea, phosphinothricin, or glyphosate). Screenable markers include, but are not limited to, the genes encoding .beta.-glucuronidase (Jefferson, 1987, Plant Molec Biol. Rep 5:387-405), luciferase (Ow et al., 1986, Science 234:856-859), B and C1 gene products that regulate anthocyanin pigment production (Goff et al., 1990, EMBO J 9:2517-2522). 
     In some cases, a selectable marker may be included with the nucleic acid being delivered to the cell. A selectable marker may refer to the use of a gene that encodes an enzymatic or other detectable activity (e.g., luminescence or fluorescence) that confers the ability to distinguish cells expressing the nucleic acid construct from those that do not. A selectable marker may confer resistance to an antibiotic or drug upon the cell in which the selectable marker is expressed. Selectable markers may be “dominant” in some cases; a dominant selectable marker encodes an enzymatic or other activity (e.g., luminescence or fluorescence) that can be detected in any cell or cell line. 
     In some embodiments, the marker gene is an antibiotic resistance gene whereby the appropriate antibiotic can be used to select for transformed cells from among cells that are not transformed. Examples of suitable selectable markers include adenosine deaminase, dihydrofolate reductase, hygromycin-B-phosphotransferase, thymidine kinase, xanthine-guanine phospho-ribosyltransferase and amino-glycoside 3′-0-phosphotransferase II. Other suitable markers will be known to those of skill in the art. 
     5.3.4. Detecting the Level of mRNA Expressed in Host Cells 
     The methods of the present invention comprise a step of detecting the level of mRNA expressed in the host cells of the invention. 
     In some embodiments, the level of mRNA expressed in host cells is determined by quantitative real-time PCR (qPCR), a method for DNA amplification in which fluorescent dyes are used to detect the amount of PCR product after each PCR cycle. (Higuchi et al., 1992; Simultaneous amplification and detection of specific DNA-sequences. Bio-Technology 10(4), 413-417].). The qPCR method has become the tool of choice for many scientists because of method&#39;s dynamic range, accuracy, high sensitivity, specificity and speed. Quantitative PCR is carried out in a thermal cycler with the capacity to illuminate each sample with a beam of light of a specified wavelength and detect the fluorescence emitted by the excited fluorochrome. The thermal cycler is also able to rapidly heat and chill samples thereby taking advantage of the physicochemical properties of the nucleic acids and DNA polymerase. 
     In some embodiments, the level of mRNA expressed in host cells is determined by high high throughput sequencing (Next-generation sequencing; also ‘Next-gen sequencing’ or NGS). =NGS methods are highly parallelized processes that enable the sequencing of thousands to millions of molecules at once. Popular NGS methods include pyrosequencing developed by 454 Life Sciences (now Roche), which makes use of luciferase to read out signals as individual nucleotides are added to DNA templates, Illumina sequencing that uses reversible dye-terminator techniques that adds a single nucleotide to the DNA template in each cycle and SOLiD sequencing by Life Technologies that sequences by preferential ligation of fixed-length oligonucleotides. 
     In some embodiments, the level of mRNA expressed in host cells is determined by gene microarrays. A microarray works by exploiting the ability of a given mRNA molecule to bind specifically to, or hybridize to, the DNA template from which it originated. By using an array containing many DNA samples, it can be determined in a single experiment, the expression levels of hundreds or thousands of genes within a cell by measuring the amount of mRNA bound to each site on the array. With the aid of a computer, the amount of mRNA bound to the spots on the microarray is precisely measured, generating a profile of gene expression in the cell. 
     5.3.5. Detecting TF Binding to Gene Targets 
     In some embodiments, the method comprises detection of the level of TF binding to gene targets by ChIP-Seq analysis. ChIP-Seq analysis utilizes chromatin immunoprecipitation in parallel with DNA sequencing to map the binding sites of a TF or other protein of interest. First, protein interactions with chromatin are cross-linked and fragmented. Then, immunoprecipitation is used to isolate the TF with bound chromatin/DNA. The associated chromatin/DNA fragments are sequenced to determine the gene location of protein binding. Other assays known in the art may be used to detect the location of TF binding to genomic regions of DNA. 
     In some embodiments, the yeast one hybrid method may be used. The yeast one hybrid method detects protein-DNA interactions, and may be adapted for use in plants. The DNA binding domains unveiled by ChIP-Seq may be cloned upstream of a reporter gene in a vector or may be introduced into the plant genome by homologous recombination, which allows the transcription factor to interact with the DNA element in a natural environment. A fusion protein containing a constitutive TF activation domain and the DNA binding domain of the TF of interest may then be expressed, and the interaction of the binding domain with the DNA will be detected by reporter gene expression. The yeast one hybrid method can thus be used in some embodiments as a way to interrogate the relationship between binding and activation, as only the binding domain of the TF of interest is used in the fusion protein in the heterologous system. 
     5.3.6. Identifying Conserved Connections Across Species 
     In some embodiments, gene networks conserved between  Arabidopsis  (or another model species) and a species of interest may be determined by a data mining approach. In this approach,  Arabidopsis  plants are grown under the same conditions as plants from another species of interest, including perturbation of environmental signals (e.g. nitrogen). RNA is then extracted from the roots and shoots of the plants, and cDNA synthesized from the extracted RNA. A microarray analysis and filtering approach may be used to determine the genes of each species regulated by the environmental signal when compared with control conditions. An ortholog analysis may then determine the genes orthologous between the two species. Data integration and network analysis then allows for the determination of a core translational network. In some embodiments, the response genes in a species of plant for which a protoplast system is not feasible may be discovered by using such a data mining approach, as described, in combination with the TARGET system for  Arabidopsis  or another species used as a model. 
     6. EXAMPLE 1 
     6.1. Introduction 
     A rapid technique to study the genome-wide effects of TF activation in protoplasts that uses transient expression of a glucocorticoid receptor (GR)-tagged TF has been developed in the present invention. This system can be used to rapidly retrieve information on direct target genes in less than two week&#39;s time. As a proof-of-principle candidate, the well-studied transcription factor, Abscicic acid insensitive 3 (ABI3; Koornneef et al., 1989, Plant physiology, 90:463-469; Mönke et al., 2012, Nucleic acids research 40:8240-8254) was used. The de novo identification of the abscisic acid response element (ABRE) and a majority of the previously classified direct targets was established by use of this method. This technique was named TARGET, for Transient Assay Reporting Genome-wide Effects of Transcription factors. 
     Technically, plant protoplasts are transfected with a plasmid (pBeaconRFP_GR) that expresses the TF-of-interest fused to GR, which allows the controlled entry of the chimeric GR-TF into the nucleus by addition of the GR-ligand dexamethasone (DEX; Schena and Yamamoto, 1988, Science 241:965-967). In addition, the vector contains a separate expression cassette with a positive fluorescent selection marker (red fluorescent protein; RFP) which enables fluorescence activated cell sorting (FACS) of successfully transformed protoplasts (see  FIG. 2 ; Bargmann and Birnbaum, 2009, Plant physiology 149:1231-1239). This purification step allows reliable qPCR or transcriptomic analysis of multiple independent transfections, which would otherwise be hampered by the presence of a population of untransformed cells that varies from experiment to experiment. Lastly, the effect of target gene induction by DEX treatment is measured in the presence or absence of the translation inhibitor cycloheximide (CHX), allowing for the distinction of direct and indirect target genes of the TF under study. pBeaconRFP_GR-ABI3 was used to transfect protoplasts prepared from the roots of  Arabidopsis  seedlings, where ABI3, known largely for its role in seed development, has also been shown to be involved in development (Brady et al., 2003, The Plant journal: for cell and molecular biology 34:67-75). 
     6.2. Materials and Methods 
     Plant materials and treatment. Wild-type  Arabidopsis thaliana  seed (Col-0,  Arabidopsis  Biological Resource Center) was sterilized by 5 min incubation with 96% ethanol followed by 20 min incubation with 50% household bleach and rinsing with sterile water. Seeds were plated on square 10×10 cm plates (Fisher Scientific) with MS-agar (2.2 g/l Murashige and Skoog Salts [Sigma-Aldrich], 1% [w/v] sucrose, 1% [w/v] agar, 0.5 g/lIViES hydrate [Sigma-Aldrich], pH 5.7 with KOH) on top of a sterile nylon mesh (NITEX 03-100/47, Sefar filtration Inc.) to facilitate harvesting of the roots. Seeds were plated in two dense rows. Plates were vernalized for 2 days at 4° C. in the dark and placed vertically in an Advanced Intellus environmental controller (Percival) set to 35 μmol/m 2 *sec −1  and 22° C. with an 18 h-light/6 h-dark regime. 
     Vector construction. pBeaconRFP_GR was constructed by PCR amplification of the glucocorticoid receptor from pJCGLOX (Joubes et al., 2004, The Plant Journal 37: 889-896) with primers GR-F and GR-R, both with an SpeI restriction site, using Phusion polymerase (New England Biolabs). The PCR product was ligated into the SpeI site upstream of the GATEWAY (Invitrogen) cassette in pBeaconRFP (Bargmann and Birnbaum, 2009; Plant physiology 149:1231-1239). The orientation of the insert was checked by PCR. The pBeaconRFP_GR vector (as well as the pMON999_mRFP control vector, containing only 35S::mRFP) will be made available through the VIB website: http://gateway.psb.ugent.be/. 
     ABI3 cDNA was PCR amplified with primers ABI3_AttB1 and ABI3_AttB2, and subsequently re-amplified with primers AttB1 and AttB2 using Phusion polymerase. The PCR product was recombined into pDONR221 using BP clonase and subsequently shuttled into pBeaconRFP_GR with LR clonase (Invitrogen). 
     Protoplast preparation, transfection, treatment and cell sorting. Protoplast were prepared, transfected and sorted as described in Bargmann and Birnbaum, 2009; Plant physiology 149:1231-1239; and Bargmann and Birnbaum, 2010, JoVE. Briefly, roots of 10-day-old seedling were harvested and treated with cell wall digesting enzymes (Cellulase and Macerozyme; Yakult, Japan) for 3 hours. Cells were filtered, washed and 106 cells were transfected with a polyethylene glycol treatment using 50 μg of plasmid DNA and incubated at room temperature overnight. Protoplast suspensions were pretreated with 35 μM cycloheximide (CHX; Sigma-Aldrich) for 30 min, after which 10 μM dexamethasone (DEX; Sigma-Aldrich) was added and cells were incubated at room temperature. Controls were treated with solvent alone. A 10 mM DEX stock was dissolved in ethanol and a 50 mM CHX stock was dissolved in dimethylsulfoxide, both were stored at −20° C. All transfections and treatments were performed in triplicate. Treated protoplasts suspensions were sorted with a FACSAria (BD Biosciences), using 488 nm excitation and measuring emission at 530/30 nm for green fluorescence and 610/20 nm for red fluorescence. RFP-positive cells were sorted directly into RNA extraction buffer. Twenty thousand RFPpositive cells (+/−10% of sorted events were RFP-positive under these experimental conditions) were then isolated by FACS and RNA was extracted for transcript analysis by qPCR. 
     A temporal qPCR analysis of PER1 and CRU3 induction by DEX in the presence of CHX was performed after a 1-hour, 5-hour and overnight (16-hour) incubation (see  FIG. 3A ). Results indicated that, although induction could be seen as early as 1 hour after the addition of DEX for CRU3, the expression of both PER1 and CRU3 continued to increase after 5 and 16 hours (see  FIG. 3A ). In order to achieve a large fold-change in expression between control and treatment, microarray analysis was performed after an overnight treatment. 
     qPCR and microarray analysis. RNA was extracted using an RNeasy Micro Kit with RNase-free DNase Set according to the manufacturer&#39;s instructions (QIAGEN). RNA was quantified with a Bioanalyzer (Agilent Technologies). Gene expression was determined by quantitative real-time PCR (LightCycler; Roche Diagnostics) using gene-specific primers and LightCycler FastStart DNA Master SYBR Green (Roche Diagnostics). Expression levels of tested genes were normalized to expression levels of theACT2/8 and CLATHRIN genes as described in (Krouk et al., 2006 Plant Physiol 142:1075-1086). For microarray analysis, RNA was amplified and labeled with WT-Ovation Pico RNA Amplification System and FL-Ovation cDNA Biotin Module V2, respectively (NuGEN). The labeled cDNA was hybridized, washed and stained on an ATH-121501  Arabidopsis  full genome microarray using a Hybridization Control Kit, a GeneChip Hybridization, Wash, and Stain Kit, a GeneChip Fluidics Station 450 and a GeneChip Scanner (Affymetrix). The microarray data reported in this paper have been deposited in the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) database, (accession #GSE33344). Raw microarray data was normalized using MAS5.0 (scaling factor of 250, Flexarray; http://www.gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?1=e). Data was logged prior to running a Tukey post hoc test on the significance coefficients of a two way ANOVA carried out on CHX versus DEX treatment (in-house [R] script) for differential responses to DEX with or without CHX on non-ambiguous probesets. Heatmaps were created using Multiple Experiment Viewer software (TIGR; http://www.tm4.org/mev/). For the overlap analysis with previously identified targets of ABI3 (Mönke et al., 2012, Nucleic acids research 40:8240-8254), VP1 (Suzuki et al., 2003, Plant physiology 132:1664-1677) and ABI5 (Reeves et al., 2011, Plant molecular biology, 75:347-363), distance between non-parametric distributions (one from the overlap of sampled input gene sets and one from two randomly sampled sets of genes represented on the ATH1 array) was calculated using the genesect [R] script (Krouk et al., 2010, Genome biology 11:R123). For the overlap with VP1 targets, the background consisted of genes represented on both the ATH1- and the 8k AG array [Affymetrix] used by Suzuki and co-workers. 
     GO-term and promoter analysis. GO-term analysis was performed online using the BioMaps function on the VirtualPlant website (www.virtualplant.org) with a default corrected p-value cutoff on the Fisher exact test of p&lt;10-3 (Katari et al., 2010; Plant Physiology, 152:500-515). To determine enrichment of known promoter motifs, the number of 1 kb upstream promoters, out of the top fifty ABI3 up-regulated genes, having one or more of the motifs described in the PLACE database was counted (http://www.dna.affrc.go.jp/PLACE/). p-values were generated using hypergeometric distribution, and values were FDR corrected using an FDR q-value cutoff of 0.01.promoter element enrichment analysis was performed using [R] (http://www.r-project.org/). For the sliding window analysis for promoter element enrichment (see  FIG. 4 ), significance was calculated using the hypergeometric test, comparing the number of motif occurrences in a 30-gene window to the number expected by chance, which was derived from the propensity of the motif in the promoters of all genes nonambiguously represented on the ATH1 chips. The search for recurring promoter motifs was performed using the Cistome website (http://bar.utoronto.ca/cistome/cgibin/BAR_Cistome.cgi). Motif Sampler and MEME were used to look for recurring 8-mer motifs in the 1000 bp upstream of the top fifty direct up-regulated genes with the following significance parameters: Ze cutoff 3.0, functional depth cutoff 0.35, proportion of genes the motif should be found in 0.5. 
     6.3. Results 
     As a first test of the TARGET system, the expression of known direct ABI3 targets PER1 and CRU3 were assayed by qPCR. Compared to control gene expression, both PER1 and CRU3 showed significant induction of transcript levels upon DEX treatment in the ABI3-GR transfected protoplasts in the presence of CHX ( FIGS. 5 and 6 ). PER1 and CRU3 expression in protoplasts transformed with an empty vector control showed no significant induction by DEX treatment ( FIGS. 5 and 6 ). Significant induction of CRU3 expression could only be measured when CHX was present, indicating that the effects of CHX may in some cases facilitate ABI3 function. Enhancement of ABA signaling output by protein synthesis inhibitors, that could explain this phenomenon, has been noted before by independent studies (Reeves et al., 2011, Plant molecular biology 75:347-363). For the transcriptomic analysis, using ATH1 Genome Array chips, a two-way analysis of variance (ANOVA) was performed, followed by a Tukey post hoc test to identify genes whose expression is differentially regulated in response to DEX treatment in the absence or presence of CHX (p&lt;0.05, fold change&gt;1.5). Genes found to be significantly regulated by DEX treatment in the empty vector control were omitted from further analysis. This analysis yielded a total of 668 unique genes whose expression was affected by DEX-induced nuclear localization of ABI3; 227 regulated genes without CHX and 458 regulated genes with CHX (microarray results were validated by qPCR). There was just a 17-gene overlap with and without CHX, reiterating that (as was seen for CRU3 in preliminary qPCR analysis) there are many genes whose response to GR-ABI3 was facilitated by the presence of the protein synthesis inhibitor CHX. The 210 genes regulated only in the absence of CHX were categorized as putative indirect targets of ABI3, whereas the 458 genes regulated in the presence of CHX (186 induced and 272 repressed genes) were designated as putative direct targets of ABI3. 
     The list of 186 putative direct up-regulated genes was highly significantly enriched for genes previously identified as direct targets of ABI3 in whole plant studies (Ze=54.3), as well as targets of the maize homolog VIVIPAROUS1 (Ze=20.8) and co-regulator ABIS (Ze=20.9) ( FIGS. 7 and 8 ; (Mönke et al., 2012, Nucleic acids research 40:8240-8254; Reeves et al., 2011, Plant molecular biology 75:347-363; Suzuki et al., 2003, Plant physiology 132:1664-1677). These substantial intersections indicate that the activation of ABI3 in protoplasts reflects the effects attributed to this transcriptional regulator in in planta studies. The list also showed a significant overrepresentation of GO-terms, including response to ABA, response to water deprivation, lipid storage and embryo development (no significant overlap or enrichments were found in the lists of indirect targets or direct down-regulated targets). Furthermore, promoter analysis of the fifty most strongly induced direct up-regulated genes found significant enrichment of previously identified ABRE-like elements and the RY-repeat motif ( FIG. 8 ). De novo searches for recurring motifs within these promoters (using two independent algorithms, MEW and MotifSampler) yielded the recovery of the CACGTGKC ABRE ( FIG. 9 ). These results show the TARGET system can be used successfully to investigate TF function in protoplasts with significance to whole plants. 
     6.4. Discussion 
     One advantage of the TARGET system lies in the speed at which identification of genome-wide TF targets can be performed. A candidate TF can now be scrutinized for its target genes in a genome in a matter of weeks rather than the months required for the generation of stable transgenic plant lines. The TARGET transient transformation system can also be used purely as a verification of specific TF-target interactions by qPCR, much as yeast-one-hybrid (Y1H) assays are often used, but now in the context of endogenous gene activation in plant cells rather than promoter binding in a yeast strain. The TARGET approach brings the convenience of microbiological systems like Y1H to the genome-wide transcriptomic capabilities of in planta studies. Another advantage of the use of protoplast transformation in the TARGET system is that it can be done in a wide range of species where the generation of transgenic plant lines is either impossible or problematic and more time-consuming (Sheen et al., 2001, Plant physiology 127:1466-1475). The TARGET system combined with RNA sequencing, can enable rapid and systematic assessment of TF function in numerous plant species, for example in important crop model species. 
     This system is not a replacement for in-depth studies using transcriptional- and chromatin immuno-precipitation (ChIP) analyses in transgenic plants. Rather, TARGET is rapid tool for GRN investigations that may have uses in particular circumstances. There are considerations associated with the use of this system. On its own, a genome-wide analysis will yield results that contain false-positives and false-negatives. Identification of direct regulated genes by TARGET is therefore not unequivocal, additional assays for direct TF-target interaction (e.g. ChIP, Y1H, gel shift assays) are required for definitive identification of TF targets. The functionality of the chimeric GR-TF is not tested in this system, other than by the substance of the results. CHX treatment by itself may have effects on transcription that influence the DEX effect on certain direct target genes. Lastly, the cellular dissociation procedure itself may induce gene expression responses that could conceal the effects of TF activation. One can envisage two ways of using the TARGET system; either in combination with other techniques to get high confidence target lists for a particular TF, or as a high-throughput analysis of numerous TFs in a given GRN to get a broad view of putative interactions. 
     Overall, the results presented here demonstrate that TARGET represents a novel and rapid transient system for TF investigation that can be used to help map GRN. Important indications of TF operation, such as direct target genes, biological function by GO-term associations and cis-regulatory elements involved in its action, can be obtained in a rapid and straightforward manner. The proof-of-principle analysis with ABI3 offers a new dataset of transcripts affected by this TF, adding to the understanding of the downstream significance of this central regulator. 
     The pBeaconRFP_GR vector will be made available through the VIB website (http://gateway.psb.ugent.be/). 
     7. EXAMPLE 2 
     7.1. Introduction 
     Evidence for temporal, signal induced TF-target associations that involve the rapid and transient induction of genes related to the signal has been developed in the present invention. This discovery was enabled by a combination of conceptual and technical advances in a cell-based system, which enabled overexpression of a specific TF of interest and temporal induction of its nuclear localization. By temporally inducing TF nuclear localization using dexamethasone (DEX) in the presence of cycloheximide (CHX) to block translation, identification of the primary targets of a TF of interest was possible, based on either TF-regulation or TF-binding assayed in the same samples, exposed to a signal. Moreover, the perturbation of both the TF and the signal it transduces uncovered three distinct TF modes-of-action, “poised”, “active” and “transient”, the latter encompassing signal-dependent, transient TF-target associations. This discovery was made for bZIP1 (BASIC LEUCINE ZIPPER 1), a TF implicated as an integrator of cellular and metabolic signaling in  Arabidopsis  and shared in other eukayrotes (Weltmeier et al., 2008, Plant Molecular Biology 69:107; Sun et al., 2011, Journal of Plant Research 125:429; Baena-Gonzalez et al., 2007, Nature 448:938; Kietrich et al., 2011, The Plant Cell 23:381; Kang et al., 2010, Molecular Plant 3:361; Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A., 105:4939; Obertello et al., 2010, BMC systems biology 4:111). The discovery of this new class of“transient”, signal-induced TF-target interactions opens a window into TF network dynamics that has been missed in previous TF studies in plants and animals. The inclusion of such context-dependent TF-target interactions in GRNs, will improve the predictive capability of GRN models to generate hypotheses that will direct future experimental efforts in living systems. 
     7.2. Materials and Methods 
     Plant Materials and DNA Constructs. Wild-type  Arabidopsis thaliana  seeds [Columbia ecotype (Col-0)] were vapor-phase sterilized, vernalized for 3 days, then 1 ml of seeds were sown on 24 agar plates containing MS [2.2 g/l custom made Murashige and Skoog salts without N or sucrose [Sigma-Aldrich]; 1% [w/v] sucrose; 0.5 g/l MES hydrate [Sigma-Aldrich]; 1 mM KNO 3 ; 2% [w/v] agar; pH 5.7 with HCl]. Plants were grown vertically in an Intellus environment controller [Percival Scientific, Perry, Iowa] set to 35 μmol m −2  s −1  and 16 h-light/8 h-dark regime at constant 22° C. bZIP1 [At5g49450] cDNA in pENTR was obtained from the REGIA collection (Paz-Ares et al., 2002, Comparative and functional genomics 3:102) and was then cloned into the destination vector pBeaconRFP_GR (Bargmann et al., 2013, Molecular Plant 6(3):978) by LR recombination [Life Technologies]. 
     Protoplast Preparation, Transfection, Treatment and Cell Sorting. Protoplasts were prepared, transfected and sorted as previously described (Bargmann et al., 2013, Molecular Plant 6(3):978; Yoo et al., 2007, Nature Protocols 2:1565; Bargmann et al., 2009, Plant physiology 149:1231). Briefly, roots of 10-day-old seedlings were harvested and treated with cell wall digesting enzymes [Cellulase and Macerozyme; Yakult, Japan] for 4 h. Cells were filtered and washed then transfected with 40 μg of pBeaconRFP_GR::bZIP1 plasmid DNA per 1×10 6  cells facilitated by polyethylene glycol treatment [PEG; Fluka 81242] for 25 minutes (Bargmann et al., 2013, Molecular Plant 6(3):978). Cells were washed drop-wise, concentrated by centrifugation, then resuspended in wash solution for overnight incubation at room temperature. Protoplast suspensions were treated sequentially with a N-signal treatment of either a 20 mM KNO 3  and 20 mM NH 4 NO 3  solution [N] or 20 mM KCl [control] for 2 h, either cycloheximide [CHX] [35 μM in DMSO; Sigma-Aldrich] or solvent alone as mock for 20 min, and then with either dexamethasone [DEX] [10 μM in EtOH; Sigma-Aldrich] or solvent alone as mock for 4 h at room temperature. Treated protoplast suspensions were sorted as in (Bargmann et al., 2009, Plant physiology 149:1231): approximately 10,000 RFP-positive cells were sorted directly into RLT buffer [QIAGEN]. 
     RNA Extraction And Microarray. RNA was extracted from protoplasts [6 replicates: 3 treatment replicates and 2 biological replicates] using an RNeasy Micro Kit with RNase-free DNaseI Set [QIAGEN] and quantified on a Bioanalyzer RNA Pico Chip [Agilent Technologies]. RNA was then converted into cDNA, amplified and labeled with Ovation Pico WTA System V2 [NuGEN] and Encore Biotin Module [NuGEN], respectively. The labeled cDNA was hybridized, washed and stained on an ATH1-121501  Arabidopsis  Genome Array [Affymetrix] using a Hybridization Control Kit [Affymetrix], a GeneChip Hybridization, Wash, and Stain Kit [Affymetrix], a GeneChip Fluidics Station 450 and a GeneChip Scanner [Affymetrix]. 
     Analysis of microarray data with CHX treatment: Microarray intensities were normalized using the GCRMA [http://www.bioconductor.org/packages/2.11/bioc/html/germa.html] package. Differentially expressed genes were then determined by a 3-way ANOVA with N, DEX and biological replicates as factors. The raw p-value from ANOVA was adjusted by False Discovery Rate [FDR] to control for multiple testing (Benjamini et al., 2005, Genetics 171:783). Genes significantly regulated by N and/or bZIP1 were then selected with a FDR cutoff of 5% while genes significantly regulated by the interaction of N and bZIP1 [NXbZIP1] were selected with a p-val [ANOVA] cutoff of 0.01. Only unambiguous probes were included. Heatmaps were created using Multiple Experiment Viewer software [TIGR; http://www.tm4.org/mev/]. The significance of overlaps of gene sets were calculated using the genesect [R] script (Krouk et al., 2010, Genome Biology 11:R123) or the hypergeometric method [R]. 
     Analysis of microarray data without CHX treatment: Analysis was identical to with CHX except a 2-way ANOVA with N and bZIP1 as factors was used to identify differentially expressed genes. 
     Micro Chromatin Immunoprecipitation. For each combination of protoplast treatments (see above), an unsorted suspension of protoplasts containing approximately 5,000-10,000 GR::bZIP1 transfected cells was incubated with gentle rotation in 1% formahaldeyde in W5 buffer for 7 minutes, then washed with W5 buffer and frozen in liquid N2. μChIP was performed according to Dahl et al, 2008 (Dahl et al., 2008, Nucleic Acids Research, 36:e15) with a few modifications. The GR::bZIP1-DNA complexes were captured using anti-GR antibody [GR [P-20]-Santa Cruz biotech] bound to Protein A beads [Life Biotechnologies]. A washing step with LiCl buffer [0.25M LiCl, 1% Na deoxycholate, 10 mM Tris-HCl (pH8), 1% NP-40] was added in between the wash with RIPA buffer and TE (Dahl et al., 2008, Nucleic Acids Research, 36:e15). After elution from the beads, the ChIP material and the INPUT DNA were cleaned and concentrated using QIAGEN MinElute Kit [QIAGEN]. The protoplast suspension used for micro ChIP was not FACS sorted to maintain a comparable incubation time between the samples that were used for microarray analyses and for micro ChIP. Additionally, FACS sorting of transformed cells was not required to identify DNA targets, as it is required for microarray studies. 
     ChIP-Seq library prep. The ChIP DNA and Input DNA were prepared for Illumina HiSeq sequencing platform following the Illumina ChIP-Seq protocol [Illumina, San Diego, Calif.] with modifications. Barcoded adaptors and enrichment primers [BiOO Scientific, TX, USA] were used according to the manufacturer&#39;s protocol. The concentration and the quality of the libraries was determined by the Qubit Fluorometric DNA Assay [InVitrogen, NY, USA], DNA 12000 Bioanalzyer chip [Agilent, Calif., USA] and KAPA Quant Library Kit for Illumina [KAPA Biosystems, Mass., USA]. A total of 8 libraries were then pooled equimolarly and sequenced on two lanes of an Illumina HiSeq platform for 100 cycles in paired-end configuration [Cold Spring Harbor Lab, N.Y.]. 
     ChIP-Seq Analysis. Reads obtained from the four treatments were filtered and aligned to the  Arabidopsis thaliana  genome [TAIR10] and clonal reads were removed. The ChIP alignment data was compared to its partner Input DNA and peaks were called using the QuEST package (Valouev et al., 2008, Nature Methods 5:829.) with a ChIP seeding enrichment ≥5, and extension and background enrichments ≥2. These regions were overlapped with the genome annotation to identify genes within 500 bp downstream of the peak. The gene lists from multiple treatments were largely overlapping sets and hence were pooled to generate a single list of 850 genes that show significant binding of bZIP1. Due to technical issues, the experimental design used for ChIP-Seq precludes the observation of significant differences between the genes bound by bZIP1 under the different treatment conditions. This is because the samples fixed for ChIP included a variable number of transfected cells that were not sorted by FACS. 
     Cis-element Motif Analysis. 1 Kb regions upstream of the TSS (Transcription Start Site) for target genes were extracted based on TAIR10 annotation and submitted to the Elefinder program (Li et al., 2011, Plant physiology 156:2124.) or MEME (53) to determine over-representation of known binding sites. (Different parameters used in specific cases were notified in the paper if applicable). The E-value of significance for each motif was used to cluster the occurrence of motifs in the various subsets using the HCL algorithm in MeV (Saeed et al., 2006, Methods in Enzymology 411:134). Motifs that show a higher specificity to a particular category or a sub-group were identified with the PTM algorithm in MeV. De novo motif identification was performed on 1 Kb upstream sequence of the genes regulated by bZIP1 from microarray and ChIP-Seq data separately using the MEME suite (Bailey et al., 2009, Nucleic Acids Research 37:W202). 
     7.3. Results 
     Perturbation of a TF and the signal it transduces uncovers context-dependent primary TF target genes. To discern mechanisms by which TFs controlling GRNs respond to a signal perceived in vivo, both a TF (bZIP1) and a metabolic signal that it transduces (nitrogen, N) were perturbed (Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939; Obertello et al., 2010, BMC systems biology 4:111). The  Arabidopsis  TF bZIP1 was transiently overexpressed as a glucocorticoid receptor fusion (35S::GR-bZIP1) in a rapid cell-based system called TARGET (Transient Assay Reporting Genome-wide Effects of Transcription factors) (Bargmann et al., 2013, Molecular Plant 6(3):978) and genome-wide responses were monitored ( FIG. 1 ). The GR-TF fusion enabled temporal induction of the nuclear localization of the TF using dexamethasone (DEX), as performed previously in planta (Eklund et al., 2010, Plant Cell 22:349) and in the cell-based TARGET system (Bargmann et al., 2013, Molecular Plant 6(3):978). In detail,  Arabidopsis  root protoplast cells overexpressing the 35S::GR-bZIP fusion protein were sequentially treated as follows: i) pre-treatment with an external metabolic signal (nitrogen, +/−N), followed by ii) CHX to block the synthesis of proteins, and iii) DEX to induce bZIP1 nuclear import of the GR-TF fusion ( FIG. 1 ). Importantly, the addition of CHX blocks translation of mRNAs of bZIP1 primary targets, enabling identification of primary TF targets based solely on their TF-induced regulation (Bargmann et al., 2013, Molecular Plant 6(3):978; et al., 2010, Plant Cell 22:349). This sequence of treatments enabled identification of i) bZIP1 primary targets based on either TF-induced gene regulation or TF-binding and ii) the “context-dependence” of TF-target gene regulation (i.e. response to both TF and signal perturbation). Discovery of bZIP1 primary targets by either gene regulation or promoter binding. Transcriptome analysis using ATH1 Affymetrix Gene Chips was performed on cells transfected with 35S::GR-bZIP1 and subjected to the N, CHX and DEX treatments shown in  FIG. 1C , in order to identify the primary targets regulated by bZIP1 in the context of the N-signal it transduces. ANOVA analysis identified 1,218 genes significantly regulated (FDR&lt;0.05) in response to DEX-induced bZIP1 nuclear import ( FIG. 10A ;  FIG. 10B ; Table 4 and 5). 328 genes responded significantly to the N-signal in protoplasts, and show significant intersections with N-responses observed with a similar N-treatment (NH 4 NO 3 ) and/or similar tissue (root) in planta (pval&lt;0.001) ( FIG. 13 ; Table 4) (Krouk et al., 2010, Genome biology 11:R123; Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939; Palenchar et al., 2004, Genome Biology 5:R91; Gutierrez et al., 2007, Genome Biology 8:R7). With regard to signal perturbation, the N-responsive genes (328 genes) ( FIG. 13 ) identified in the cell-based system, overlap significantly with the N-responsive genes identified from in planta studies (Krouk et al., 2010, Genome biology 11:R123; Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939; Palenchar et al., 2004, Genome Biology 5:R91; Gutierrez et al., 2007, Genome Biology 8:R7) with a similar N-treatment (NH4NO3) and/or similar tissue (root) (pval&lt;0.001 by Genesect) underscoring their in planta relevance. These N-responsive genes were also significantly enriched (pval=8.8E−13) with genes responsive to N across all root cell-types (Gifford et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:803), suggesting the root protoplasts used in this study has an even representation of different root cell types. 
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Genes identified by ANOVA and ChIP-Seq analysis. 
               
            
           
           
               
               
            
               
                 Category of Genes 
                 Number of Genes 
               
               
                   
               
            
           
           
               
            
               
                 Microarray Analysis 
               
            
           
           
               
               
               
            
               
                 Significantly 
                 Nitrogen (FDR &lt; 0.05) 
                 328 
               
               
                 regulated by 
                 bZIP1* (FDR &lt; 0.05) 
                 1218 
               
               
                 ANOVA factor 
                 NitrogenXbZIP1 (pval &lt; 0.01) 
                 108 
               
               
                   
                 bZIP1* (FDR &lt; 0.05) AND 
                 48 
               
               
                   
                 NitrogenXbZIP1* (pval &lt; 0.01) 
               
            
           
           
               
            
               
                 ChIP-SEQ Analysis 
               
            
           
           
               
               
            
               
                 bZIP1 bound genes* 
                 850 
               
               
                   
               
               
                 *genes considered as TF primary targets in this study. 
               
            
           
         
       
     
     
       
         
           
               
               
               
             
               
                   
                 TABLE 5 
               
               
                   
                   
               
               
                   
                 Term 
                 p-value 
               
               
                   
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 A. Significantly over-represented GO terms in the 
               
               
                 DEX up-regulated genes (+CHX) 
               
            
           
           
               
               
               
            
               
                 GO:0042221 
                 response to chemical stimulus 
                 1.75E−07 
               
               
                 GO:0050896 
                 response to stimulus 
                 1.75E−07 
               
               
                 GO:0009628 
                 response to abiotic stimulus 
                 2.22E−05 
               
               
                 GO:0009310 
                 amine catabolic process 
                 3.66E−05 
               
               
                 GO:0010033 
                 response to organic substance 
                 5.33E−05 
               
               
                 GO:0009063 
                 cellular amino acid catabolic process 
                 0.000127 
               
               
                 GO:0016054 
                 organic acid catabolic process 
                 0.000239 
               
               
                 GO:0046395 
                 carboxylic acid catabolic process 
                 0.000239 
               
               
                 GO:0009719 
                 response to endogenous stimulus 
                 0.000436 
               
               
                 GO:0006950 
                 response to stress 
                 0.000529 
               
               
                 GO:0009651 
                 response to salt stress 
                 0.000747 
               
               
                 GO:0044282 
                 small molecule catabolic process 
                 0.000899 
               
               
                 GO:0080167 
                 response to karrikin 
                 0.000899 
               
               
                 GO:0009725 
                 response to hormone stimulus 
                 0.00146 
               
               
                 GO:0006970 
                 response to osmotic stress 
                 0.00171 
               
               
                 GO:0009081 
                 branched chain family amino acid 
                 0.00197 
               
               
                   
                 metabolic process 
               
               
                 GO:0009737 
                 response to abscisic acid stimulus 
                 0.00553 
               
            
           
           
               
            
               
                 B. Significantly over-represented GO terms in the 
               
               
                 DEX down-regulated genes (+CHX) 
               
            
           
           
               
               
               
            
               
                 GO:0050896 
                 response to stimulus 
                 8.89E−16 
               
               
                 GO:0006952 
                 defense response 
                 6.77E−12 
               
               
                 GO:0042221 
                 response to chemical stimulus 
                 6.77E−12 
               
               
                 GO:0006950 
                 response to stress 
                 1.19E−10 
               
               
                 GO:0010033 
                 response to organic substance 
                 5.79E−10 
               
               
                 GO:0051707 
                 response to other organism 
                 3.57E−09 
               
               
                 GO:0009607 
                 response to biotic stimulus 
                 1.37E−08 
               
               
                 GO:0051704 
                 multi-organism process 
                 1.37E−08 
               
               
                 GO:0010200 
                 response to chitin 
                 2.84E−08 
               
               
                 GO:0009620 
                 response to fungus 
                 1.24E−07 
               
               
                 GO:0031347 
                 regulation of defense response 
                 3.60E−07 
               
               
                 GO:0080134 
                 regulation of response to stress 
                 3.72E−07 
               
               
                 GO:0002376 
                 immune system process 
                 3.79E−06 
               
               
                 GO:0009743 
                 response to carbohydrate stimulus 
                 1.72E−05 
               
               
                 GO:0048583 
                 regulation of response to stimulus 
                 1.96E−05 
               
               
                 GO:0009719 
                 response to endogenous stimulus 
                 2.45E−05 
               
               
                 GO:0050832 
                 defense response to fungus 
                 2.95E−05 
               
               
                 GO:0009611 
                 response to wounding 
                 9.30E−05 
               
               
                 GO:0031348 
                 negative regulation of defense response 
                 0.000105 
               
               
                 GO:0045087 
                 innate immune response 
                 0.000151 
               
               
                 GO:0006955 
                 immune response 
                 0.000172 
               
               
                 GO:0009753 
                 response to jasmonic acid stimulus 
                 0.000241 
               
               
                 GO:0002682 
                 regulation of immune system process 
                 0.000326 
               
               
                 GO:0031408 
                 oxylipin biosynthetic process 
                 0.00076 
               
               
                 GO:0045088 
                 regulation of innate immune response 
                 0.00125 
               
               
                 GO:0050776 
                 regulation of immune response 
                 0.00125 
               
               
                 GO:0016310 
                 phosphorylation 
                 0.00135 
               
               
                 GO:0031407 
                 oxylipin metabolic process 
                 0.0014 
               
               
                 GO:0006468 
                 protein phosphorylation 
                 0.00169 
               
               
                 GO:0006793 
                 phosphorus metabolic process 
                 0.00194 
               
               
                 GO:0006796 
                 phosphate metabolic process 
                 0.00194 
               
               
                 GO:0009695 
                 jasmonic acid biosynthetic process 
                 0.0022 
               
               
                 GO:0008219 
                 cell death 
                 0.00326 
               
               
                 GO:0009694 
                 jasmonic acid metabolic process 
                 0.00326 
               
               
                 GO:0009725 
                 response to hormone stimulus 
                 0.00326 
               
               
                 GO:0009863 
                 salicylic acid mediated signaling pathway 
                 0.00326 
               
               
                 GO:0016265 
                 death 
                 0.00326 
               
               
                 GO:0050794 
                 regulation of cellular process 
                 0.00326 
               
               
                 GO:0071446 
                 cellular response to salicylic acid stimulus 
                 0.00326 
               
               
                 GO:0009737 
                 response to abscisic acid stimulus 
                 0.00331 
               
               
                 GO:0006334 
                 nucleosome assembly 
                 0.00467 
               
               
                 GO:0034728 
                 nucleosome organization 
                 0.00467 
               
               
                 GO:0010941 
                 regulation of cell death 
                 0.00486 
               
               
                 GO:0048584 
                 positive regulation of response to stimulus 
                 0.00497 
               
               
                 GO:0065004 
                 protein-DNA complex assembly 
                 0.00529 
               
               
                 GO:0071824 
                 protein-DNA complex subunit organization 
                 0.00529 
               
               
                 GO:0042742 
                 defense response to bacterium 
                 0.0057 
               
               
                 GO:0060548 
                 negative regulation of cell death 
                 0.0057 
               
               
                 GO:0045727 
                 positive regulation of translation 
                 0.00575 
               
               
                 GO:0009409 
                 response to cold 
                 0.00577 
               
               
                 GO:0031349 
                 positive regulation of defense response 
                 0.00577 
               
               
                 GO:0009751 
                 response to salicylic acid stimulus 
                 0.00661 
               
               
                 GO:0050789 
                 regulation of biological process 
                 0.00785 
               
               
                 GO:0010185 
                 regulation of cellular defense response 
                 0.00856 
               
               
                 GO:0010193 
                 response to ozone 
                 0.00856 
               
               
                 GO:0032270 
                 positive regulation of cellular protein 
                 0.00856 
               
               
                   
                 metabolic process 
               
               
                 GO:0051247 
                 positive regulation of protein metabolic 
                 0.00856 
               
               
                   
                 process 
               
               
                 GO:0012501 
                 programmed cell death 
                 0.00886 
               
               
                   
               
            
           
         
       
     
     Forty-eight bZIP1 primary targets (FDR&lt;0.05) were uncovered that show a significant TF×N-signal interaction (pval&lt;0.01) (Table 6). These genes responding to bZIP1×N interactions form four distinct expression clusters ( FIG. 14A ) that can be viewed as a context-dependent bZIP1 GRN ( FIG. 14B ). Intriguingly, cluster 4 genes, whose induction is completely dependent on the bZIP1×N interaction, are enriched with N-regulated biological processes such as auxin stimulus, circadian, and response to organic substance ( FIG. 14A ). These 1,218 genes (including the 48 bZIP1×N responsive genes) are deemed to be primary targets of bZIP1, as gene responses to DEX-induced TF nuclear import were assayed in the presence of CHX, which blocks regulation of secondary targets controlled by other TFs downstream of bZIP1 (Bargmann et al., 2013, Molecular Plant 6(3):978). Thus, bZIP1 primary targets are expected to be regulated in response to TF perturbation under both +CHX and −CHX conditions. A significant overlap (pval&lt;0.001) was observed between the bZIP1-regulated genes identified in +CHX samples and −CHX samples. 
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 Genes that are regualted by DEX (FDR &lt; 0.05) and also regulated 
               
               
                 by the interaction of N and DEX (pval &lt; 0.01) forming 4 clusters 
               
               
                 based on their expression patterns by Hierachical clustering in Mev 
               
            
           
           
               
               
               
            
               
                 Locus 
                 Symbol 
                 Fullname 
               
               
                   
               
               
                 A. Cluster 1 
                   
                   
               
               
                 AT4G39190 
               
               
                 AT1G55610 
                 BRL1 
                 BRI1 like 
               
               
                 AT3G49350 
               
               
                 AT3G23820 
                 GAE6 
                 UDP-D-glucuronate 4-epimerase 6 
               
               
                 AT4G33960 
               
               
                 AT5G54470 
                 BBX29 
                 B-box domain protein 29 
               
               
                 AT2G26390 
               
               
                 B. Cluster 2 
               
               
                 AT3G59900 
                 ARGOS 
                 AUXIN-REGULATED GENE INVOLVED 
               
               
                   
                   
                 IN ORGAN SIZE 
               
               
                 AT5G39710 
                 EMB2745 
                 EMBRYO DEFECTIVE 2745 
               
               
                 AT4G28940 
               
               
                 AT4G30560 
                 ATCNGC9 
                 cyclic nucleotide gated channel 9 
               
               
                 AT3G15520 
               
               
                 AT1G56510 
                 ADR2 
                 ACTIVATED DISEASE RESISTANCE 2 
               
               
                 AT2G39900 
                 WLIM2a 
                 WLIM2a 
               
               
                 AT3G63390 
               
               
                 AT3G14360 
               
               
                 AT3G53280 
                 CYP71B5 
                 cytochrome p45 71b5 
               
               
                 AT5G61210 
                 ATSNAP33 
               
               
                 C. Cluster 3 
               
               
                 AT2G04500 
               
               
                 AT3G05210 
                 ERCC1 
               
               
                 AT3G30396 
               
               
                 AT1G13280 
                 AOC4 
                 allene oxide cyclase 4 
               
               
                 AT2G28630 
                 KCS12 
                 3-ketoacyl-CoA synthase 12 
               
               
                 AT4G33420 
               
               
                 AT2G31380 
                 BBX25 
                 B-box domain protein 25 
               
               
                 AT3G60290 
               
               
                 AT2G02700 
               
               
                 AT5G64100 
               
               
                 AT4G37240 
               
               
                 AT4G20350 
               
               
                 AT1G64160 
                 AtDIR5 
               
               
                 AT1G15050 
                 IAA34 
                 indole-3-acetic acid inducible 34 
               
               
                 AT1G10090 
               
               
                 AT1G13270 
                 MAP1B 
                 METHIONINE AMINOPEPTIDASE 1B 
               
               
                 AT3G55150 
                 ATEXO7H1 
                 exocyst subunit exo7 family protein H1 
               
               
                 AT3G48650 
               
               
                 AT2G39570 
                 ACR9 
                 ACT domain repeats 9 
               
               
                 AT2G24130 
               
               
                 AT5G28050 
               
               
                 AT4G25620 
               
               
                 AT1G21410 
                 SKP2A 
               
               
                 AT1G01490 
               
               
                 D. Cluster 4 
               
               
                 AT3G60690 
               
               
                 AT3G48360 
                 ATBT2 
               
               
                 AT4G37540 
                 LBD39 
                 LOB domain-containing protein 39 
               
               
                 AT5G59350 
               
               
                 AT5G04630 
                 CYP77A9 
                 cytochrome P45, family 77, subfamily A, 
               
               
                   
                   
                 polypeptide 9 
               
               
                 AT4G38340 
               
               
                   
               
            
           
         
       
     
     To next identify primary bZIP1 targets whose promoter was bound by the GR-bZIP1 fusion protein either directly or indirectly through an interacting TF partner in a protein complex, a micro-ChIP protocol (Dahl et al., 2008, Nucleic Acids Research 36:e15) was adapted using anti-GR antibodies to pull down genomic regions bound to bZIP1 ( FIG. 1C ). Micro-ChIP and transcriptome data were derived from cells expressing 35S::GR-bZIP1 in parallel ( FIG. 1C ). Genic regions enriched in the ChIP DNA bound to GR-bZIP1 (peak seeding&gt;=5 fold; extension &gt;=2 fold) compared to the background (input DNA), were identified using the QuEST peak-calling algorithm (Valouev et al., 2008, Nature Methods 5:829) ( FIG. 10A ). This analysis identified 850 target genes with significant bZIP1 binding (FDR &lt;0.05) ( FIG. 10D ), which includes several validated bZIP1 target genes (e.g. ASN1 and ProDH) previously uncovered by ChIP-qPCR in planta (Dietrich et al., 2011, The Plant Cell 23:381-395). 
     It was confirmed that the 1,218 genes responding to bZIP1 perturbation and the 850 genes with significant binding to bZIP1 are enriched in bZIP1 primary targets by cis-regulatory motif analysis using MEME (Bailey et al., 2009, Nucleic Acids Research 37:W202) and elefinder (Li et al., 2011, Plant physiology 156:2124), which searches for known bZIP1 binding sites. Genes induced or bound by bZIP1 (644 genes) showed a highly significant overrepresentation of “G/C-box” ( FIG. 10  C&amp;E), a cis-element previously shown to bind bZIP1 in vitro (Kang et al., 2010, Molecular Plant 3:361). A distinct bZIP-binding motif called the “GCN4 binding motif&#39; (Onodera et al., 2001, The Journal of Biological Chemistry 276:14139) was significantly over-represented in the 574 genes repressed in response to bZIP1 perturbation ( FIG. 10C ). The GCN4 motif has been reported to mediate nitrogen and amino acid starvation sensing in both yeast and plants (Hill et al., 1986, Science 234:451; Muller et al., 1993, The Plant Journal: for cell and molecular biology 4:343), suggesting a functional conservation between bZIP1 and nutrient sensing. Lastly, the FORC A  motif, previously implicated in integrating light and defense signaling (Evrard et al., 2009. BMC Plant Biology 9:2), was shown to be over-represented in the 850 bZIP1 bound genes ( FIG. 10E ), consistent with the known role of bZIP1 in planta (Baena-Gonzalez et al., 2007, Nature 448:938; Kang et al., 2010, Molecular Plant 3:361; Hanson et al., 2007, The Plant Journal 53:935). 
     Identification of temporal modes of bZIP1 primary target gene regulation. Mechanisms underlying temporal, signal-mediated modes of TF action were identified by integrating results from transcriptome and ChIP-Seq, and then performing analysis of signal context, biological function, and cis-element enrichment in bZIP1 primary target genes ( FIG. 10A ). bZIP1-regulated primary TF targets (1,218 genes) were compared with the bZIP1-bound TF-targets (663 out of 850 genes, because 187 are not on the ATH1 microarray) ( FIG. 11A ). This analysis identified three classes of primary TF targets ( FIG. 11A ) that represent distinct modes-of-action for bZIP1: Class I: 473 genes with TF binding only; Class II: 190 genes that are TF bound and regulated; and Class III: 1,028 genes that are regulated by, but not bound to the TF ( FIG. 11A ). All three classes of bZIP1 primary targets are: i) enriched in known bZIP1 binding sites ( FIG. 12B ); ii) overlap significantly with genes previously shown to be regulated by bZIP1 from in planta studies (Kang et al., 2010, Molecular Plant 3:361; Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939) ( FIG. 11B ;  FIG. 15 ); iii) shared significant GO terms associated with known bZIP1 functions (e.g. Stimulus/Stress) ( FIG. 11A ); and iv) overlap with genes induced by carbon-starvation and darkness (Krouk et al., 2009, PLoS Computer Biology 5:e1000326) ( FIG. 16 ), which is consistent with the known role of bZIP1 in planta (Baena-Gonzalez et al., 2007, Nature 448:938; Kang et al., 2010, Molecular Plant 3:361; Hanson et al., 2007, The Plant Journal 53:935). In addition to these common features, the three classes of bZIP1 primary target genes show distinguishing features. 
     In planta cross-validation of the three classes of bZIP1 primary targets. The in vivo relevance of all three classes of bZIP1 primary targets was validated based on comparison to targets identified in planta in i) a constitutive bZIP1 overexpression line (Kang et al., 2010, Molecular Plant 3:361) (122/449 genes; p-val&lt;0.001) ( FIG. 11B ) and ii) predicted from an organic-N regulatory network (Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939) (14/27 genes; p-val&lt;0.001) ( FIG. 15 ). Additionally, the potential relevance was determined for each bZIP1-target class in the signaling pathways previously associated with bZIP1 regulation in planta, including sugar (Kang et al., 2010, Molecular Plant 3:361) and light (Baena-Gonzalez et al., 2007, Nature 448:938). Intersections with genes repressed by carbon (C) and light (L) (Krouk et al., 2009, PLoS Computer Biology 5:e1000326) in roots and shoots ( FIG. 16 ) were highly significant (p-val&lt;0.001) across all three classes of bZIP1 primary targets identified. This result is consistent with previous reports that bZIP1 is a master regulator in response to light and sugar starvation (Weltmeier et al., 2008, Plant Molecular Biology 69:107; Baena-Gonzalez et al., 2007, Nature 448:938; Kang et al., 2010, Molecular Plant 3:361; Hanson et al., 2007, The Plant Journal 53:935). 
     Cis-element analysis of the three classes of bZIP1 targets. Cis-element analysis of each of the three subclasses of bZIP1 regulated gene targets show enrichment of known bZIP binding sites ( FIG. 12B ). Genes that either bind to bZIP1 or are activated by bZIP1 (Class I, IIA and IIIA), show significant over-representation of the known bZIP1 binding site “ACGT” box: including G-box, C-box or hybrid G/C-box (Kang et al., 2010, Molecular Plant 3:361) ( FIG. 12B ;  FIG. 17 ). By contrast, genes that are repressed by bZIP1 do not have the canonical “ACGT” core, and instead posses the GCN4 binding motif for the bZIP family—as well as a W-box ( FIG. 12B ;  FIG. 17 ). Interestingly, the GCN4 motif was reported to mediate nitrogen and amino acid starvation sensing in both yeast and plants (Onodera et al., 2001, The Journal of Biological Chemistry 276:14139; Hill et al., 1986, Science 234:451; Muller et al., 1993, The Plant Journal: for cell and molecular biology 4:343), suggesting a link between bZIP1 and nutrient sensing. A non-exclusive alternative interpretation is that bZIP1 may work with a WRKY family partner to repress primary target genes. 
     Class I “poised” bZIP1 targets: TF Binding, No regulation. This class of bZIP1 primary targets were specifically and significantly overrepresented in genes involved in “regulation of transcription” and “calcium transport” (FDR&lt;0.01) ( FIG. 11A ). These functions suggest that bZIP1 may serve as a master TF, that is bound to and “poised” to activate these downstream regulatory genes in response to a signal not provided in the experimental set-up, or that requires a TF partner not present in root cell protoplasts. 
     Class II “active” bZIP1 targets: TF Binding and Regulation. The 190 primary bZIP1 target genes in Class II, represents a 29% overlap (p-val&lt;0.001) between the transcriptome and ChIP-Seq data, which compares favorably to such overlaps in other TF studies in planta (23% ABI3 (Monke et al., 2012, Nucleic Acids Research 40:8240); 25% PIL5 (Oh et al., 2009, The Plant Cell Online 21:403)). Class II genes are the classical “gold standard” set that are the only primary targets identified in other TF studies that require TF-binding to define primary targets. For bZIP1, these primary targets in Class II have an overrepresentation in genes involved in “response to stress/stimulus” (FDR&lt;0.01), which was a term common to all three classes of bZIP1 targets. No class-specific GO-terms were identified for these “classic” Class II bZIP1 primary target genes ( FIG. 11A ). 
     Class III “transient” bZIP1 targets: TF Regulation, but no detectable TF binding. Unexpectedly, the Class III bZIP1 primary target genes, that are regulated by, but not detectably bound to the TF, turned out to be the largest set of bZIP1 primary target genes (1,028) detected in this study. The Class III genes were identified as primary bZIP1 targets based on gene regulation in response to the nuclear import of bZIP1 performed in the presence of CHX (to block activation of secondary targets), but were not detected in the parallel ChIP-Seq analysis to be bound by bZIP1 directly or indirectly in a protein complex containing bZIP1. In either scenario—direct binding of bZIP1 to its gene target or bZIP1 binding via interacting TF partners—the bZIP1 target gene should be detected by ChIP-Seq if the interaction is stable. This led to the hypothesis that the Class III primary bZIP1 target genes that are regulated in response to DEX-induced bZIP1 nuclear import may be the result of a transient TF-target association not detectable by ChIP-Seq at the time of sampling. A series of results supports this view, and also indicates that the Class III “transient” bZIP1 primary targets are most relevant to the function of bZIP1 in transducing the N-signal provided. First, the Class III “transient” bZIP1 primary target genes show a substantial (117/328) and the most significant overlap with N-responsive genes ( FIG. 13 ) identified in the study (Class IIIA: pval=2e−41; Class IIIB: pval=2e−29) compared to Classes I and II ( FIG. 11A ). Second, out of the 48 primary targets regulated by bZIP1×N interaction ( FIG. 14 ),  47  of these belong to Class III: Class IIIA (29 genes regulated by bZIP1×N interaction) (pval=5e−22) and Class IIIB (18 genes regulated by bZIP1×N interaction) (pval=5e−12) ( FIG. 11A ). This suggests that the bZIP1 regulation of Class III genes is likely modified by the N-signal, which may involve a post-translational modification of bZIP1 and/or by translational/transcription effects on its interacting partners ( FIG. 1B ). Third, only Class III bZIP1 primary targets showed a significant enrichment in genes involved in processes related to the N-signal including “amino acid metabolism”, “phosphorus metabolism” and “signal transduction” (FDR&lt;0.01) ( FIG. 11A ). Lastly, but most importantly, only Class IIIA bZIP1 primary targets are specifically enriched with genes that respond to N in a transient and rapid manner in planta ( FIG. 11B ) (Krouk et al., 2010, Genome Biology 11:R123), as discussed in detail below. 
     Class III “transient” bZIP1 target genes show an early and transient N-response in planta. To assess the significance of the three classes of bZIP1 targets identified in this cell-based system, the classes were compared to studies that have implicated bZIP1 as a master hub in mediating responses to N nutrient signals in planta (Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939; Obertello et al., 2010, BMC Systems Biology 4:111). Indeed, all three classes of bZIP1 primary targets identified in this cell-based system were significantly enriched (pval&lt;0.001) in genes regulated by an identical nitrogen treatment (NH 4 NO 3 ) in an in planta study ( FIG. 11B ) (Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939). The link between temporal N nutrient signaling and the bZIP1 “transient” mode of action was investigated by comparing all three Classes of bZIP1 primary targets to a fine-scale, time-series dataset that uncovered dynamic N-responsive genes in roots (Krouk et al., 2010, Genome Biology 11:R123). This analysis shows that only Class IIIA “transient” bZIP1 targets genes are rapidly and transiently regulated by nitrogen treatments in planta, as follows: i) Rapid N-induction: Only Class IIIA “transient” bZIP1 primary targets show a significant overlap (pval&lt;0.001) with early nitrate-responsive genes induced within 6 minutes following N-treatment (Krouk et al., 2009, PLoS Computer Biology 5:e1000326) ( FIG. 11B ). ii) Transient N-induction: Only Class IIIA “transient” bZIP1 activated targets are distinguished by their significant overlap (pval&lt;0.001) with genes that show a transient response to nitrate-induction in roots from the in planta time-course study (Krouk et al., 2010, Genome Biology 11:R123) ( FIG. 11B ). Specifically, 20 Class IIIA bZIP1 primary target genes (Table 1) are transiently N-induced in planta, and specific gene induction kinetics (3-20 min) are shown for three sample genes (AT2G43400, AT4G38490, and AT5G04310) ( FIG. 11B ). These data support the notion that a temporal relationship between bZIP1 and the Class IIIA “transient” primary target genes likely mediates an early and transient response to the N-signal. 
     Cis-element context analysis uncovers elements associated with signal×TF interactions. A distinguishing feature of the Class III “transient” bZIP1 primary targets is their significant enrichment in genes responding to a bZIP1×N-signal interaction ( FIG. 10A ). This could be a result of i) the post-translational modification of bZIP1 and/or ii) the transcriptional or post-translational modification of its interactors in response to N-signaling ( FIG. 1B ;  FIG. 12A ). To uncover evidence for possible bZIP1 TF partners, the class-specific enrichment of cis-elements in the promoters of genes in each of the three bZIP1 primary target classes was examined ( FIG. 12B ). The Class III “transient” bZIP1 primary target genes contained the largest number and most highly significant enrichment of cis-motifs, compared to the other classes of bZIP1 targets ( FIG. 12B ;  FIG. 17 ). Specifically, promoters of Class IIIA genes (primary targets activated by bZIP1, but no detectable bZIP1 binding) are significantly enriched with bZIP family TF binding sites (e.g. the TGA1 binding site (Yilmaz et al., 2011, Nucleic Acids Research 39:D1118), ABRE binding site (Yilmaz et al., 2011, Nucleic Acids Research 39:D1118), and GBF1/2/3 binding site (de Vetten et al., 1995, Plant Journal 7:589)). Other significant co-inherited cis-elements were specifically found in Class IIIA bZIP1 targets and include: MYB family TF binding sites (I-box (Yilmaz et al., 2011, Nucleic Acids Research 39:D1118) and CCA1 motif (Yilmaz et al., 2011, Nucleic Acids Research 39:D1118)), GATA promoter motif (Yilmaz et al., 2011, Nucleic Acids Research 39:D1118), and the light responsive motif SORLIP1 (Yilmaz et al., 2011, Nucleic Acids Research 39:D1118). These findings suggest that Class IIIA “transient” TF-target genes may be co-activated by bZIP1 and other TFs, including other bZIP family members, for which there is in vivo evidence of association with bZIP1 (Kang et al., 2010, Molecular Plant 3:361; Ehlert et al., 2006, The Plant Journal 46:890). For the Class IIIB bZIP1 target genes (primary target genes repressed by bZIP1, but no detectable bZIP1 binding), a number of cis-elements implicated in light and temperature signaling were significantly over-represented in their promoters, including T-box, SORLREP1, LTRE, and HSE binding site (Yilmaz et al., 2011, Nucleic Acids Research 39:D1118). Combined, the significant enrichment in Class III “transient” bZIP1 primary targets of genes i) early and ii) transiently regulated in response to a N-signal, iii) whose expression depends on a N x TF interaction, and iv) whose promoters are enriched in co-inherited cis-elements, support a model of temporal bZIP1-target association in response to the N-signal and/or a N-responsive interaction of bZIP1 with other TFs, as depicted in  FIG. 12A . 
     7.4. Discussion and Concluding Remarks 
     A previously unrecognized “transient” mode of TF action was uncovered by a conceptual innovation in the experimental design to temporally perturb both a TF and signal, and in the integration and interpretation of TF-binding and TF-regulation data. This allowed for identification of primary TF targets based on either gene regulation or TF-binding, and the association of this regulation with a signal. This contrasts with previous studies of TFs in both plants and animals, where the identification of primary targets has been limited to TF-binding and/or the overlap between TF-regulation and TF-binding (Reeves et al., 2011, Plant Molecular Biology 75:347; Gorski et al., 2011, Nucleic Acids Research 39:9536; Hull et al., 2013, BMC Genomics 14:92; Fujisawa et al., 2011, Planta 235:1107; Wagner et al., 2004, The Plant Journal: for cellular and molecular biology 39:273). The approach enabled discovery of a new class of “transient” TF targets that are regulated by the TF but not detectably bound by it, because of three complementary features of the system: i) the ability to temporally induce the nuclear import of the TF bZIP1 in the presence or absence of a signal; ii) the use of a protein synthesis inhibitor (CHX) to identify primary TF-targets based solely on gene regulation; and iii) the ability to perform transcriptome analysis and ChIP-Seq on the same samples which allowed direct data comparison. Combining these features enabled the distinction between three temporal modes of bZIP1 action in regulating primary TF-target genes: “poised”, “active” and “transient”. By examining the TF modes of action in the presence or absence of a signal it transduces (N), it was found that Class III “transient” gene targets (TF-regulated but not bound) were most relevant to the N-signal provided, as they show unique and significant: i) enrichment in N-responsive genes ( FIG. 11A ), ii) early and iii) transient induction by a N-signal ( FIG. 11B ), iv) regulation by TF×N-signal interactions ( FIG. 11A ), and v) GO-term enrichment in N-related processes ( FIG. 11A ). These features distinguish the Class III “transient” TF-target genes, compared to the other two classes of primary TF targets: “poised” and “active”. It is noteworthy that the Class III “transient” TF-targets identified in the cell-based system also play an important role in vivo—based on significant overlap with in planta data ( FIG. 11B ). However, they would have been dismissed as secondary TF-targets in those in planta studies, and their role in mediating a dynamic GRN would have been missed. 
     This discovery suggests that the Class III “transient” TF-target genes are likely the result of a temporal association between bZIP1 with these targets, acting either directly on the primary target DNA and/or through TF partner interactions ( FIG. 12A ). In support of the role of TF partners in this temporal, N-signal mediated regulation, cis-element analysis revealed that the Class III “transient” bZIP1 target genes had the highest enrichment, both in number and in significance, of cis-elements that co-occurred with the bZIP1 binding site, compared to the inactive “poised” Class I genes and the constitutively “active” Class II genes ( FIG. 12B ). TFs associated with these co-occurring cis-elements include other bZIP family members and TFs belonging to the MYB family. Querying a protein-protein interaction database (Katari et al., 2010, Plant physiology 152:500) revealed that bZIP1 interacts with 11 other members of the bZIP family (Table 7). Interestingly, 3 out of these 11 bZIP TFs shown to interact with bZIP1 in vitro (Katari et al., 2010, Plant physiology 152:500), were also determined to be primary targets of bZIP1 in this study (bZIP25, bZIP53, bZIP9), suggesting that bZIP1 regulates and activates some of its protein-interaction TF partners. The interactions between bZIP1 with bZIP25/53/9 have also been independently experimentally validated in vivo (Baena-Gonzalez et al., 2007, Nature 448:938; Kang et al., 2010, Molecular Plant 3:361; Ehlert et al., 2006, The Plant Journal 46:890). These data support the hypothesis that bZIP1 may be a master response gene that activates and interacts with specific bZIP family members, and/or potentially with members of the MYB family, to “temporally” co-regulate downstream genes in response to a N-signal. 
     
       
         
           
               
             
               
                 TABLE 7 
               
               
                   
               
               
                 bZIP1 protein-protein interaction partners. 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                 At5g37780 
                 ACAM-1, CAM1, TCH1, calmodulin 1 
               
               
                 At1g66410 
                 ACAM-4, CAM4, calmodulin 4 
               
               
                 At5g21274 
                 ACAM-6, CAM6, calmodulin 6 
               
               
                 At2g41100 
                 ATCAL4, TCH3, Calcium-binding EF hand family 
               
               
                   
                 protein 
               
               
                 At3g51920 
                 ATCML9, CAM9, CML9, calmodulin 9 
               
               
                 At2g41090 
                 Calcium-binding EF-hand family protein 
               
               
                 At3g43810 
                 CAM7, calmodulin 7 
               
               
                 At4g14640 
                 CAM8, calmodulin 8 
               
               
                 At5g41910 
                 MED10A, Mediator complex, subunit Med10 
               
               
                 At4g34590 
                 ATB2, AtbZIP11, BZIP11, GBF6, G-box binding 
               
               
                   
                 factor 6 
               
               
                 At5g49450 
                 AtbZIP1, bZIP1, basic leucine-zipper 1 
               
               
                 At4g02640 
                 ATBZIP10, BZO2H1, bZIP transcription factor 
               
               
                   
                 family protein 
               
               
                 At2g18160 
                 ATBZIP2, bZIP2, GBF5, basic leucine-zipper 2 
               
               
                 At3g54620 
                 ATBZIP25, BZIP25, BZO2H4, basic leucine 
               
               
                   
                 zipper 25 
               
               
                 At1g59530 
                 ATBZIP4, bZIP4, basic leucine-zipper 4 
               
               
                 At3g30530 
                 ATBZIP42, bZIP42, basic leucine-zipper 42 
               
               
                 At1g75390 
                 AtbZIP44, bZIP44, basic leucine-zipper 44 
               
               
                 At3g62420 
                 ATBZIP53, BZIP53, basic region/leucine zipper 
               
               
                   
                 motif 53 
               
               
                 At1g13600 
                 AtbZIP58, bZIP58, basic leucine-zipper 58 
               
               
                 At5g28770 
                 AtbZIP63, BZO2H3, bZIP transcription factor 
               
               
                   
                 family protein 
               
               
                 At5g24800 
                 ATBZIP9, BZIP9, BZO2H2, basic leucine zipper 9 
               
               
                   
               
            
           
         
       
     
     To place these findings in perspective, the general field of GRN validation has focused on determining when and how TF binding does, or does not, result in gene activation (Reeves et al., 2011, Plant Molecular Biology 75:347; Gorski et al, 2011, Nucleic Acids Research 39:9536). This focus has limited the field to studying the more stable and static “gold standard” interactions exemplified by the bZIP1 Class II genes (TF-bound and regulated). The discovery of the Class III “transient” TF-targets (TF-regulated, no binding) now opens the opposite question/perspective in the general field of transcriptional control: How and why can TF-induced changes in mRNA occur in the absence of stable TF binding? The simple explanation that the Class IIIA mRNA is stabilized by CHX or bZIP1 is not supported by the data, as +/-CHX results are comparable ( FIG. 16 ), and there was no evidence for either bZIP1 regulated small RNAs or 3′ UTR elements that could affect RNA stability in Class III genes. Therefore, these transient TF-target interactions may be conceptualized as the “hit-and-run” model of transcription, which posits that a TF can act as a trigger to organize a stable transcriptional complex, after which transcription by RNA polymerase II can continue without the TF being bound to the DNA (Schaffner, 1988, Nature 336:427-428). 
     In support of this “hit-and-run” model, the Class III “transient” genes are enriched in mRNAs with short half-lives (&lt;2 hour) (Chiba et al., 2013, Plant &amp; cell physiology 54:180) indicating that they are actively transcribed at the 5 hour time-point when the gene is induced by the TF but is not stably bound to it ( FIG. 18 ). This “hit-and-run” model of TF action suggests a general mechanism for the deployment of an acute response to nutrient level change, in which a master regulatory TF transiently and rapidly activates a large set of genes in response to a signal. This “pioneer” TF responds to N-signals possibly by recruiting TF partners, as supported by the finding that Class III targets are most significantly enriched with cis-regulatory elements of known bZIP1 interactors. 
     The “transient”, signal-induced association of a target with a TF can be analaogized to a “touch-and-go” (hit-and-run) landing or circuit maneuver used in aviation. This involves landing a plane on a runway and taking off again without coming to a full stop, allowing many landings in a short time. This maneuver also allows pilots to rapidly detect or avoid another plane or object on the runway, and could serve an analogous role for bZIP1 and its TF partners. The “touch-and-go” (hit-and-run) mode may enable bZIP1 to “direct”, “detect” or “avoid” TFs on a gene target, or alternatively to rapidly activate and leave the promoter “empty” for its TF partners to occupy. By contrast, the more traditional “stop-and-go” action requiring a full stop before taking off again, is a more stable maneuver which can be analogized to the classic Class II “gold standard” set, in which the TF lands (stably binds) and regulates a gene. While these more stable and static interactions have been the focus of most TF studies, the discovery of this new “touch-and-go” (hit-and-run) mode of TF action opens a new concept and field of inquiry in the study of dynamic GRNs in plants and animals. 
     8. EXAMPLE 3 
     8.1. Plant Growth and Treatment 
     Rice seeds ( Oryza sativa  ssp.  japonica ) were kindly provided by Dale Bumpers of the National Rice Research Center (AR, USA). Seeds were surface-sterilized and vernalized on 1× Murashige and Skoog (MS) basal salts (custom-made; GIBCO) with 0.5 mM ammonium succinate and 3 mM sucrose, 0.8% BactoAgar at pH 5.5 for 3 days in dark conditions at 27° C. Germinated seeds were transferred to a hydroponic system (Phytatray II, Sigma Aldrich) containing basal MS salts (custom-made; GIBCO) with 0.5 mM ammonium succinate and 3 mM sucrose at pH 5.5 to grow for 12 days under long-day (16 h light: 8 h dark) at 27° C., at light intensity of 180 μE·s −1 ·m −2 . Media was replaced every 3 days and the plants were transferred to fresh media containing basal MS salts for 24 h prior treatment. On day 13, plants were transiently treated for 2 h at the start of their light cycle by adding Nitrogen (N) at a final concentration of 20 mM KNO 3  and 20 mM NH 4 NO 3  (referred here as 1×N). Control plants were treated with KCl at a final concentration of 20 mM. After treatment, roots and shoots were harvested separately using a blade, and immediately submerged into liquid nitrogen and stored at −80° C. prior to RNA extraction. 
       Arabidopsis  seeds were placed for 2 days in the dark at 4° C. to synchronize germination. Seeds were surface-sterilized and then transferred to a hydroponic system (Phytatray I, Sigma Aldrich) containing the same media previously described for rice (pH 5.7). Growth conditions were the same as in rice, except that plants were under 50 μE s−1·m−2 light intensity at 22° C. N-starvation and treatments were done as described above ( FIG. 19 ). RNA was isolated using TRIzol reagent following manufacturer&#39;s protocols. 
     8.2. Microarray Experiments and Analysis 
     cDNA synthesis, array hybridization and normalization of the signal intensities were performed according to the instructions provided by Affymetrix. Affymetrix  Arabidopsis  ATH1 Genome Array Chip and Rice Genome Array Chip were used for respective species. Data normalization was performed using the RMA (Robust Microarray Analysis) method in the Bioconductor package in R statistical environment. A two-way Analysis of Variance (ANOVA) was performed using custom-made function in R to identify probes that were differentially expressed following N treatment. The p-values for the model were corrected for multiple hypotheses testing using FDR correction at 5% (Benjamini and Hochberg, 1995, Journal of the Royal Statistical Society 57:289). The probes passing the cut-off (p≤0.05) for the model and, N treatment or interaction of N treatment and tissue, were deemed significant. A Tukey&#39;s HSD post-hoc analysis was performed on significant probes to determine the tissue specificity of N-regulation at p-value cut-off ≤0.05 and fold-change ≥1.5-fold ( FIG. 19 ). Affy probes mapping to more than one gene were disregarded resulting in a significant set of N-regulated 1417  Arabidopsis  genes and 451 Rice genes ( FIG. 20 ). 
     Orthologous N-regulated genes between Rice and  Arabidopsis  were obtained using reverse Blast (Camacho et al., 2008, BMC Bioinformatics 10:421) with an e-value≤1e −20 , thereby allowing for multiple ortholog hits ( FIG. 20 ). 
     8.3. Network Analysis 
     A Rice Multinetwork was generated using the following interactions ( FIG. 21 ): 
     Metabolic interactions were obtained from RiceCyc (Dharmawardhana et al., 2013, Rice 6:15). 
     Protein-Protein interactions were obtained from the PRIN database (Gu et al., 2011, BMC Bioinformatics 12:161), and published work, which include experimentally determined and computationally predicted interactions (Ding et al., 2009, Plant Physiology 149(3):1478; Rohila et al., 2006, The Plant Journal 46:1; Ho et al., 2012, The Rice Journal 5:15). 
     Predicted Regulatory interactions were created between a Transcription Factor (TF) and its putative target using TF family membership obtained from Grassius (Yilmaz et al., 2009, Plant Physiology 149:171) and identification of cis-regulatory motifs, obtained from AGRIS (Palaniswamy et al., 2006, Plant Physioloy 140:818), in 1000 bp upstream of promoter sequence of Target genes. Motifs were searched using the DNA pattern search tool from the RSA tools server with default parameters (van Helden, 2003, Nucleic Acids Research 31:3593). 
     The 451 N-regulated rice genes were queried against the Rice Multinetwork to create a N-regulated gene network in Rice. Additionally, conserved correlation edges between two N-regulated Rice genes were proposed if the respective  Arabidopsis  N-regulated orthologs were also correlated significantly in the same direction (both positively or negatively) with Pearson correlation coefficient ≥0.8. Predicted regulatory interactions were further restricted to those TF and Target pairs where the two were also significantly correlated (Pearson correlation coefficient ≥0.8 and p-value ≤0.01), which resulted in a network of 206 Rice genes, of which 21 are transcription factors, with 6,818 edges ( FIG. 21 ). 
     The network was further refined by removing conserved correlation edges that are not supported with predicted regulatory edges which resulted in a “N-regulated correlated network” containing 151 Rice genes, of which 16 were TFs (Table 8). All network visualizations were created using Cytoscape (v2.8.3) software (Shannon et al., 2003, Genome Research 13:2498). 
     
       
         
           
               
             
               
                 TABLE 8 
               
             
            
               
                   
               
               
                 Number of targets of transcription factors at each step in the network creation process. 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                   
                   
                 Rice Core 
               
               
                   
                   
                 Rice Homology 
                 Rice Core 
                 Correlated 
               
               
                   
                   
                 Network 
                 Network 
                 Network 
               
               
                 Gene Locus ID 
                 Gene Description 
                 # of targets 
                 # of targets 
                 # of targets 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 LOC_OS01G54020 
                 transcription factor HBP-1b, putative, expressed 
                 210 
                 114 
                 41 
               
               
                 LOC_OS01G64000 
                 ABA response element binding factor, putative, expressed 
                 136 
                 79 
                 34 
               
               
                 LOC_OS06G41100 
                 TGA10 transciption factor, putative, expressed 
                 114 
                 48 
                 5 
               
               
                 LOC_OS09G35030 
                 sbC8F6, putative, expressed 
                 108 
                 64 
                 1 
               
               
                 LOC_OS01G06640 
                 DNA binding protein, putative, expressed 
                 106 
                 58 
                 20 
               
               
                 LOC_OS05G37170 
                 transcription factor TGA6, putative, expressed 
                 86 
                 51 
                 9 
               
               
                 LOC_OS04G42950 
                 DNA binding factor 6, putative, expressed 
                 84 
                 36 
                 6 
               
               
                 LOC_OS02G06910 
                 auxin response factor 6, putative, expressed 
                 68 
               
               
                 LOC_OS04G55970 
                 DNA binding protein, putative, expressed 
                 63 
                 30 
                 4 
               
               
                 LOC_OS03G04310 
                 DNA binding protein, putative, expressed 
                 52 
                 20 
                 4 
               
               
                 LOC_OS06G07030 
                 dehydration responsive element binding protein, putative, expressed 
                 45 
               
               
                 LOC_OS09G26420 
                 ethylene response factor, putative, expressed 
                 30 
               
               
                 LOC_OS08G42550 
                 AP2 domain containing protein, expressed 
                 26 
                 9 
                 1 
               
               
                 LOC_OS01G34060 
                 DNA binding protein, putative, expressed 
                 14 
                 5 
                 2 
               
               
                 LOC_OS05G38140 
                 bHLH transcription factor, putative, expressed 
                 6 
               
               
                 LOC_OS03G47730 
                 knotted1-interacting protein, putative, expressed 
                 3 
               
               
                   
               
            
           
         
       
     
     A comparison of the number of TF targets at various network building steps as shown in  FIG. 21 , demonstrates that TFs with the most targets are more likely to be conserved between  Arabidopsis  and Rice and therefore are candidates for further translational studies (Table 9). BioMaps (GO-term enrichment analysis) of the targets of all TFs present in the “N-regulated core network” revealed that targets of only two TFs, LOC_Os01g64000 and LOC_Os01g64020, are enriched for “nitrate assimilation” and “nitrate metabolic process” (Table 10). A closer look at the N-assimilation pathway in the N-regulated Core Network revealed a set of 7 Rice transcription factors, which are directly targeting the genes in the N-assimilation pathway (Table 11). Three of the 7 TFs were also present in the correlated core N-regulated network, which implies that these TF-target gene pairs have conserved N-response in both  Arabidopsis  and Rice (Table 11). 
     
       
         
           
               
             
               
                 TABLE 9 
               
             
            
               
                   
               
               
                 Rice and  Arabidopsis  orthologous transcription factors in the “N-regulated core network.” 
               
            
           
           
               
               
            
               
                   
                   Arabidopsis  Orthologs 
               
            
           
           
               
               
            
               
                 Rice Core Network 
                 Orthologs 
               
            
           
           
               
               
               
               
               
               
            
               
                 Gene Locus ID 
                 Hubs 
                 Rank 
                 Gene Description 
                 Gene ID 
                 Orthologs Gene Description 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 LOC_OS01G64020 
                 114 
                 1 
                 transciption factor HBP-1b, 
                 AT1G22070 
                 TGA3, TGA1A-related gene 3 
               
               
                   
                   
                   
                 putative, expressed 
                 AT1G77920 
                 bZIP transcription factor family protein 
               
               
                   
                   
                   
                   
                 AT5G10030 
                 OBF4, TGA4, TGACG motif binding factor 4 
               
               
                   
                   
                   
                   
                 AT5G65210 
                 TGA1, bZIP transcription factor family protein 
               
               
                 LOC_OS01G64000 
                 79 
                 2 
                 ABA response element binding 
                 AT3G56850 
                 AREB3, DPBF3, ABA-responsive element binding protein 3 
               
               
                   
                   
                   
                 factor, putative, expressed 
               
               
                 LOC_OS09G35030 
                 64 
                 3 
                 sbCBF6, putative, expressed 
                 AT1G63030 
                 ddf2, Integrase-type DNA-binding superfamily protein 
               
               
                 LOC_OS01G06640 
                 58 
                 4 
                 DNA binding protein, putative, 
                 AT3G25710 
                 ATAIG1, BHLH32, TMOS, basic helix-loop helix 32 
               
               
                   
                   
                   
                 expressed 
               
               
                 LOC_OS05G37170 
                 51 
                 5 
                 transcription factor TGA6, 
                 AT1G22070 
                 TGA3, TGA1A-related gene 3 
               
               
                   
                   
                   
                 putative, expressed 
                 AT3G77920 
                 bZIP transcription factor family protein 
               
               
                   
                   
                   
                   
                 AT5G10030 
                 OBF4, TGA4, TGAG motif-binding factor 4 
               
               
                   
                   
                   
                   
                 AT5G65210 
                 TGA1, bZIP transcription factor family protein 
               
               
                 LOC_OS06G41100 
                 48 
                 6 
                 TGA10 transciption factor, 
                 AT1G22070 
                 TGA3, TGA1A-related gene 3 
               
               
                   
                   
                   
                 putative, expressed 
                 AT1G77920 
                 bZIP transcription factor family protein 
               
               
                   
                   
                   
                   
                 AT5G10030 
                 OBF4, TGA4, TGAG motif-binding factor 4 
               
               
                   
                   
                   
                   
                 AT5G65210 
                 TGA1, bZIP transcription factor family protein 
               
               
                 LOC_OS04G42950 
                 36 
                 7 
                 DNA binding protein, putative, 
                 AT5G26660 
                 ATMYB86, MYB86, myb domain protein 86 
               
               
                   
                   
                   
                 expressed 
                 AT5G60890 
                 ATMB34, ATR1, MYB34, myb domain protein 34 
               
               
                   
                   
                   
                   
                 AT5G61420 
                 AtMYB28, HAG1, MYB28, PMG1, myb domain protein 28 
               
               
                 LOC_OS04G55970 
                 30 
                 8 
                 DNA binding protein, putative, 
                 AT1G79700 
                 Integrase-type DNA-binding superfamily 
               
               
                   
                   
                   
                 expressed 
                   
                 proteinAINTEGUMENTA-like 6 
               
               
                   
                   
                   
                   
                 AT2G28550 
                 RAP2.7, TOE1, related to AP2.7 
               
               
                   
                   
                   
                   
                 AT3G20840 
                 PLT1, integrase-type DNA binding superfamily protein 
               
               
                   
                   
                   
                   
                 AT3G54320 
                 ASML1, ATWRI1, WRI, WRI1, integrase-type DNA- 
               
               
                   
                   
                   
                   
                   
                 binding superfamily protein 
               
               
                   
                   
                   
                   
                 AT5G10510 
                 AIL6, PLT3, AINTEGUMENTA-like 6 
               
               
                 LOC_OS03G04310 
                 20 
                 9 
                 DNA binding protein, putative, 
                 AT3G26744 
                 ATICE1, ICE1, SCRM, basic helix-loop-helix (bHLH) 
               
               
                   
                   
                   
                 expressed 
                   
                 DNA-binding superfamily protein 
               
               
                 LOC_OS08G42550 
                 9 
                 10 
                 AP2 domain containing protein, 
                 AT1G29200 
                 O-fucosyltransferase family protein 
               
               
                   
                   
                   
                 expressed 
               
               
                 LOC_OS01G34060 
                 5 
                 11 
                 DNA binding protein, putative, 
                 AT1G49010 
                 Duplicated homeodomain-like superfamily protein 
               
               
                   
                   
                   
                 expressed 
                 AT3G16350 
                 Homeodomain-like superfamily protein 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 10 
               
             
            
               
                   
               
               
                 BioMaps (Gene Ontology Enrichment Analysis) of N-regulated TF targets in the “N-regulated 
               
               
                 Core Network.” Only LOC_OS01G64020 and LOC_OS01G64000 targets had over-represented 
               
               
                 GO-terms (“nitrate metabolic process” and “nitrate assimilation”) (p-value cutoff ≤ 0.05). 
               
            
           
           
               
               
               
               
            
               
                   
                   
                 # of Targets in Rice 
                   
               
               
                   
                   
                 Core Network (N- 
                 Over-represented 
               
               
                 Gene Locus ID 
                 Gene Description 
                 assimilation pathway) 
                 GO:Terms for targets 
               
               
                   
               
               
                 LOC_OS01G64020 
                 transcription factor HBP-1b, 
                 114 (5) 
                 nitrate metabolic process 
               
               
                   
                 putative, expressed 
                   
                 (GO:0042126), nitrate 
               
               
                   
                   
                   
                 assimilation (GO:0042128) 
               
               
                 LOC_OS01G64000 
                 ABA response element 
                  79 (4) 
                 nitrate metabolic process 
               
               
                   
                 binding factor, putative, 
                   
                 (GO:0042126), nitrate 
               
               
                   
                 expressed 
                   
                 assimilation (GO:0042128) 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 11 
               
             
            
               
                   
               
               
                 Rice and  Arabidopsis  orthologous transcription factors targeting the “N-assimilation pathway.” 
               
            
           
           
               
               
               
            
               
                 Rice TF Targets 
                 Rice TFs 
                   Arabidopsis  Orthologs of Rice TF 
               
            
           
           
               
               
               
               
               
               
            
               
                 ID 
                 Description 
                 ID 
                 Description 
                 ID 
                 Description 
               
               
                   
               
               
                 LOC_OS01G25484 
                 ferredoxin-nitrite reductase, 
                 LOC_OS01G64020 
                 transcription 
                 AT1G22070 
                 TGA3, TGA1A-related gene 3 
               
               
                   
                 chloroplast precursor, putative, 
                   
                 factor HBP-1b, 
               
               
                   
                 expressed 
                   
                 putative, 
               
               
                 LOC_OS01G48960 
                 glutamate synthase, chloroplast 
                   
                 expressed 
                 AT1G77920 
                 bZIP transcription factor family 
               
               
                   
                 precursor, putative, expressed 
                   
                   
                   
                 protein 
               
               
                 LOC_OS02G53130 
                 nitrate reductase, putative, expressed 
                   
                   
                 AT5G10030 
                 OBF4, TGA4, TGACG motif- 
               
               
                   
                   
                   
                   
                   
                 binding factor 4 
               
               
                 LOC_OS03G13250 
                 peptide transporter PTR2, 
               
               
                   
                 putative, expressed 
               
               
                 LOC_OS06G15370 
                 peptide transporter PTR2, putative, 
                   
                   
                 AT5G65210 
                 TGA1, bZIP transcription factor 
               
               
                   
                 expressed 
                   
                   
                   
                 family protein 
               
               
                 LOC_OS06G15370 
                 peptide transporter PTR2, 
                 LOC_OS01G64000 
                 ABA respone 
                 AT3G56850 
                 AREB3, DPBF3, ABA- 
               
               
                   
                 putative, expressed 
                   
                 element binding 
                   
                 responseive element binding 
               
               
                 LOC_OS01G25484 
                 ferredoxin-nitrite reductase, 
                   
                 factor, putative, 
                   
                 protein 3 
               
               
                   
                 chloroplast precursor, putative, 
                   
                 expressed 
               
               
                   
                 expressed 
               
               
                 LOC_OS01G48960 
                 glutamate synthase, chloroplase 
               
               
                   
                 precursor, putative, expressed 
               
               
                 LOC_OS02G53130 
                 nitrate reductase, putative, 
               
               
                   
                 expressed 
               
               
                 LOC_OS01G25484 
                 ferredoxin-nitrite reductase, 
                 LOC_OS09G35030 
                 sbCBF6, 
                 AT1G63030 
                 ddf2, Integrase-type DNA- 
               
               
                   
                 chloroplast precursor, putative, 
                   
                 putative, 
                   
                 binding superfamiy protein 
               
               
                   
                 expressed 
                   
                 expressed 
               
               
                 LOC_OS01G48960 
                 glutamate synthase, chloroplast 
               
               
                   
                 precursor, putative, expressed 
               
               
                 LOC_OS03G13250 
                 peptide transporter PTR2, putative, 
               
               
                   
                 expressed 
               
               
                 LOC_OS06G15370 
                 peptide transporter PTR2, 
                 LOC_OS01G06440 
                 DNA binding 
                 AT3G25710 
                 ATAIG1, BHLH32, TMO5, 
               
               
                   
                 putative, expressed 
                   
                 protein, 
                   
                 basic helix-loop-helix 32 
               
               
                 LOC_OS01G48960 
                 glutamate synthase, chloroplast 
                   
                 putative, 
               
               
                   
                 precursor, putative, expressed 
                   
                 expressed 
               
               
                 LOC_OS01G48960 
                 glutamate synthase, chloroplast 
                 LOC_OS05G37170 
                 transcription 
                 AT1G22070 
                 TGA3, TGA1A-related gene 3 
               
               
                   
                 precursor, putative, expressed 
                   
                 factor TGA6, 
               
               
                   
                   
                   
                 putative, 
                 AT1G77920 
                 bZIP transcription factor family 
               
               
                   
                   
                   
                 expressed 
                   
                 protein 
               
               
                 LOC_OS03G13250 
                 peptide transporter PTR2, putative, 
                   
                   
                 AT5G10030 
                 OBF4, TGA4, TGACG motif- 
               
               
                   
                 expressed 
                   
                   
                   
                 binding factor 4 
               
               
                   
                   
                   
                   
                 AT5G65210 
                 TGA1, bZIP transcription factor 
               
               
                   
                   
                   
                   
                   
                 family protein 
               
               
                 LOC_OS02G20360 
                 tyrosine aminotransferase, putative, 
                 LOC_OS03G04310 
                 DNA binding 
                 AT3G26744 
                 ATICE1, ICE1, SCRM, basic 
               
               
                   
                 expressed 
                   
                 protein, putative, 
                   
                 helix-loop-helix (bHLH) DNA- 
               
               
                   
                   
                   
                 expressed 
                   
                 binding superfamily protein 
               
               
                 LOC_OS02G20360 
                 tyrosine aminotransferase, putative, 
                 LOC_OS01G34060 
                 DNA binding 
                 AT1G49010 
                 Duplicated homeodomain-like 
               
               
                   
                 expressed 
                   
                 protein, putative, 
                   
                 superfamily protein 
               
               
                   
                   
                   
                 expressed 
                 AT3G16350 
                 Homeodomain-like superfamiy 
               
               
                   
                   
                   
                   
                   
                 protein 
               
               
                   
               
            
           
         
       
     
     9. EXAMPLE 4 
     9.1. Building Crop Networks 
     Network analysis and tools can be used to translate knowledge from models-to-crops to aid in translation to agriculture. By using a publicly available microarray N-treatment dataset of maize that discovered biomarkers nitrogen status in the field, a step-by-step analysis incorporating  Arabidopsis  network knowledge results in networks that enable focused hypothesis generation with translational value. 
     5,057 N-responsive genes were identified using functions in VirtualPlant maize, which form a correlation network of 4,278 maize genes. This network is too large to enable focused translational targets, and more than 50% of the maize genes are unannotated. This maize transcriptome data may be interpreted in the context of the  Arabidopsis  network to derive networks and focused translational targets. 
     First, the 5,057 maize genes were mapped to 3,756  arabidopsis  homologs using VirtualPlant maize, which uses the maize “best-hit” to  Arabidopsis  data provided by Phytozyme (www.phytozyme.net). 
     Next, the “gene network” function in VirtualPlant (protein:protein, metabolic, cis-binding, and text-mining edges) was used to obtain a network of 2,262 connected maize genes. A GO term over-representation test on this network identifies Nitrogen metabolic process (p&lt;1e −33 ) and sulfur metabolic process (p&lt;0.005) among the significant terms. Hyoptheses were focused for translational studies using conserved N-networks, and the maize translational network was refined by selecting genes that are N-regulated in both maize and  Arabidopsis  in Step 3. 
     Subsequently, an  Arabidopsis  nitrogen response gene set (1,254 genes) was created as a union of genes responsive in shoots (Gutierrez et al., 2008, Proc Natl Acad Sci USA, 105(12):4939) and roots (Schena and Yamamoto, 1988, Science 241(4868):965). These  Arabidopsis  genes and the 2,262 maize genes were intersected to produce a highly significant (p&lt;0.001) overlapping gene list of 223 N-regulated genes. The regulatory edges in this conserved network were required to have a correlation of &gt;0.7 or &lt;−0.7 (within maize), as described in (Gutierrez et al., 2008, Proc Natl Acad Sci USA, 105(12):4939) and (Sheen, 2001, Plant physiology 149(3):1231). BioMaps analysis in Virtual plant uncovered significant GO terms including photoperiodism (p-val&lt;0.005) and nitrate transport (p-val&lt;0.01) and 15 TF hubs for focused generation of translational targets. 
     Using the VirtualPlant-meets-Cytoscape function, a “hubbiness” table was generated to identify the master regulatory nodes in the core N-regulatory network conserved between maize and  Arabidopsis.  Remarkably, the 5 top TF hubs include TFs (CCA1, GLK1 and bZIP9) ( FIG. 22 ) previously validated in  Arabidopsis  as major regulators of an organic N-response network to regulate genes involved in N-assimilation, including ASN1 (Gutierrez et al., 2008, Proc Natl Acad Sci USA, 105(12):4939; Baena-Gonzalez, 2010, Mol Plant 3(2):300). Components of this network-including AS and a bZIP TF have also been implicated in NUE studies of maize by QTL analysis and Q-PCR. 
     The TF hubs of this N-regulatory network between maize and  Arabidopsis  ( FIG. 22 ) provide a focus for network module identification and translational targeting. For example, a conserved network module ( FIG. 23 ) shows several TF hubs previously validated to regulate genes involved in N-assimilation in  Arabidopsis  (Gutierrez et al., 2008, Proc Natl Acad Sci USA, 105(12):4939). Additionally, the likely maize ortholog of  Arabidopsis  bZIP1 lies within a strong QTL for NUE in maize (Moose lab, unpublished). This netork module also reinforces the discovery that nitrogen-regulation of CCA1 imparts nutrient regulation of N-assimilation and the circadian clock in  Arabidopsis  (Gutierrez et al., 2008, Proc Natl Acad Sci USA, 105(12):4939) and now in maize. This conserved network also suggests nitrogen influences sulfure uptake (e.g. sulfur transporter gene). 
     10. EXAMPLE 5 
     10.1. Introduction 
     Signal propagation through gene regulatory networks (GRNs) enables organisms to rapidly respond to changes in environmental signals. For example, dynamic GRN studies in plants have uncovered genome-wide responses that occur within as little as three minutes following a nitrogen (N) nutrient signal perturbation (Kouk et al., 2010, Genome Biology 11:R123). Yet, many of the underlying rapid and temporal network connections between transcription factors (TFs) and their targets elude detection even in fine-scale time-course studies (Ni et al., 2009,  Gene Dev  23(11):1351-1363; Chang et al., 2013,  Elife  2:e00675), as current methods used (e.g. chromatin immunoprecipitation, ChIP) require stable TF-binding in at least one time-point to identify primary targets (Gorski et al, 2011, Nucleic Acids Research 39(22):9536-9548; Hughes et al., 2013, Genetics 195(1):9-36; Marchive et al., 2013, Nature Communications 4). However, recent models suggest that GRNs built solely on TF-binding data are insufficient to recapture transcriptional regulation (Biggin MD, 2011, Dev Cell 21(4):611-626; Walhout A J M, 2011, Genome Biol 12(4); Lickwar et al., 2012, Nature 484(7393):251-255). Compounding this dilemma, TFs have been found to stably bind to only a small percentage (5-32%) of the TF-regulated genes across eukaryotes (Gorski et al, 2011, Nucleic Acids Research 39(22):9536-9548; Hughes et al., 2013, Genetics 195(1):9-36; Marchive et al., 2013, Nature Communications 4; Monke et al., 2012, Nucleic Acids Research 40:82401; Arenhart et al., 2014, Molecular plant 7(4):709-721; Bolduc et al., 2012, Gene Dev 26(15):1685-1690; Bianco et al., 2014, Cancer research 74(7):2015-2025). Since TF-binding is required to define the primary targets in current GRN studies, the large set of TF-regulated, but not TF-bound genes must be categorically dismissed as indirect or secondary targets (Gorski et al, 2011, Nucleic Acids Research 39(22):9536-9548; Hughes et al., 2013, Genetics 195(1):9-36; Arenhart et al., 2014, Molecular plant 7(4):709-721; Bolduc et al., 2012, Gene Dev 26(15):1685-1690; Bianco et al., 2014, Cancer research 74(7):2015-2025). Provided herein is an alternative—and more intriguing conclusion—that these typically dismissed targets comprise the “dark matter” of rapid and transient signal transduction that has previously eluded detection across eukaryotes. 
     To capture these rapid and dynamic network connections that elude detection by biochemical TF-binding assays, an approach was developed that can identify primary targets based on a functional read out—TF-induced gene regulation—even in the absence of detectable TF-binding. This study focuses on the master TF bZIP1 (BASIC LEUCINE ZIPPER 1), a central integrator of metabolic signaling including sugar (Baena-Gonzalez et al., 2007, Nature 448:938; Kang et al., 2010, Molecular Plant 3:361-373; Dietrich et al., 2011, The Plant Cell 23:381-395) and N nutrient signals (Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939; Obertello et al., 2010, BMC Systems Biology 4:111). To uncover the underlying dynamic GRNs, both bZIP1 and the N-signal it transduces were temporally perturbed in a cell-based system designed for temporal TF perturbation. This cell-based system named TARGET (Transient Assay Reporting Genome-wide Effects of Transcription factors), which involves inducible TF nuclear localization, is able to identify primary TF targets based solely on TF-induced gene regulation, as shown for a well-studied TF involved in plant hormone signaling—ABI3 (Bargmann et al., 2013, Molecular Plant 6(3):978). In this study, by adapting a micro-ChIP protocol (Dahl et al., 2008, Nucleic Acids Research, 36:e15) to the cell-based TARGET system, primary targets were monitored based on either TF-induced gene regulation or TF-binding quantified in the same cell samples, enabling a direct comparison. The use of isolated cells allowed the capture of rapid and transient regulatory events including the formation of TF-DNA complexes within 1-5 min from the onset of TF translocation to the nucleus. Such a short-lived interaction would likely be missed in planta, as effective protein-DNA cross-linking in intact plant tissues requires prolonged (for a minimum of 15 minutes) infiltration under vacuum. Unexpectedly, the primary TF targets that are regulated by, but not stably bound to bZIP1—termed “transient”—were the most biologically relevant to rapid transduction of the N-signal. These transient TF-targets include first-responder genes, induced as early as 3-6 minutes after N-signal perturbation in planta (Kouk et al., 2010, Genome Biology 11:R123). This discovery suggests that the current “gold-standard” of GRNs built solely on the intersection of TF-binding and TF-regulation data miss a large and important class of transient TF targets, which are at the heart of dynamic networks. Moreover, the shared features of these transient bZIP1 targets and their role in rapid N-signaling provides genome-wide support for a classic, but largely forgotten model of “hit-and-run” transcription (Schaffner, 1988, Nature 336:427-428). This transient mode-of-action can enable a master TF to catalytically and rapidly activate a large set of genes in response to a signal. 
     10.2. Materials and Methods 
     Plant Materials and DNA Constructs. Wild-type  Arabidopsis thaliana  seeds [Columbia ecotype (Col-0)] were vapor-phase sterilized, vernalized for 3 days, then 1 ml of seed were sown on agar plates containing 2.2 g/l custom made Murashige and Skoog salts without N or sucrose (Sigma-Aldrich), 1% [w/v] sucrose, 0.5 g/l MES hydrate (Sigma-Aldrich), 1 mM KNO3 and 2% [w/v] agar. Plants were grown vertically on plates in an Intellus environment controller (Percival Scientific, Perry, Iowa), whose light regime was set to 50 μmol m −2  s −1  and 16 h-light/8 h-dark at constant temp of 22° C. The bZIP1 (At5g49450) cDNA in pENTR was obtained from the REGIA collection (Paz-Ares et al., 2002  Comp Funct Genomics  3(2):102-108) and was then cloned into the destination vector pBeaconRFP_GR used in the protoplast expression system (Bargmann et al., 2009, Plant physiology 149:1231) by LR recombination (Life Technologies). The pBeaconRFP_GR vector is available through the VIB website (http://gateway.psb.ugent.be/). 
     Protoplast Preparation, Transfection, Treatments and Cell Sorting. Root protoplasts were prepared, transfected and sorted as previously described (Bargmann et al., 2013, Molecular Plant 6(3):978; Yoo et al., 2007, Nature Protocols 2:1565; Bargmann et al., 2009, Plant physiology 149:1231). Briefly, roots of 10-day-old seedlings were harvested and treated with cell wall digesting enzymes (Cellulase and Macerozyme; Yakult, Japan) for 4 h. Cells were filtered and washed then transfected with 40 μg of pBeaconRFP_GR::bZIP1 plasmid DNA per 1×106 cells facilitated by polyethylene glycol treatment (PEG; Fluka 81242) for 25 minutes (Bargmann et al., 2009, Plant physiology 149:1231). Cells were washed drop-wise, concentrated by centrifugation, then resuspended in wash solution W5 (154 mM NaCl, 125 mM CaCl 2 , 5 mM KCl, 5 mM IViES, 1 mM Glucose) for overnight incubation at room temperature. Protoplast suspensions were treated sequentially with: 1) a N-signal treatment of either a 20 mM KNO3 and 20 mM NH4NO3 solution (N) or 20 mM KCl (control) for 2 h, 2) either CHX (35 μM in DMSO, Sigma-Aldrich) or solvent alone as mock for 20 min, and then 3) with either DEX (10 μM in EtOH, Sigma-Aldrich) or solvent alone as mock for 5 h at room temperature. Treated protoplast suspensions were FACS sorted as in (13): approximately 10,000 RFP-positive cells were FACS sorted directly into RLT buffer (QIAGEN) for RNA extraction. 
     RNA Extraction and Microarray. RNA from 6 replicates (3 treatment replicates and 2 biological replicates) was extracted from protoplasts using an RNeasy Micro Kit with RNase-free DNaseI Set (QIAGEN and quantified on a Bioanalyzer RNA Pico Chip (Agilent Technologies). RNA was then converted into cDNA, amplified and labeled with Ovation Pico WTA System V2 (NuGEN) and Encore Biotin Module (NuGEN), respectively. The labeled cDNA was hybridized, washed and stained on an ATH1-121501  Arabidopsis  Genome Array (Affymetrix) using a Hybridization Control Kit (Affymetrix), a GeneChip Hybridization, Wash, and Stain Kit (Affymetrix), a GeneChip Fluidics Station 450 and a GeneChip Scanner (Affymetrix). 
     Analysis of microarray data with CHX treatment. Microarray intensities were normalized using the GCRMA (http://www.bioconductor.org/packages/2.11/bioc/html/gcrma.html) package. Differentially expressed genes were then determined by a 3-way ANOVA with N, DEX and biological replicates as factors. The raw p-value from ANOVA was adjusted by False Discovery Rate (FDR) to control for multiple testing (Benjamini et al., 2005, Genetics 171:783). Genes significantly regulated by the N-signal and/or DEX-induced bZIP1 nuclear localization were then selected with a FDR cutoff of 5%. Genes significantly regulated by the interaction of the N-signal and bZIP1 (N-signal×bZIP1) were selected with a p-val (ANOVA) cutoff of 0.01. Only unambiguous probes were included. Heat maps were created using Multiple Experiment Viewer software (TIGR; http://www.tm4.org/mev/). The significance of overlaps of gene sets were calculated using the GeneSect (R)script (Katari et al., 2010, Plant physiology 152:500) using the microarray as background. Hypergeometric distribution was used in one case (specified in the manuscript) to evaluate the enrichment of gene sets, when a specific background—N-responsive genes identified in different root cell types (Gifford et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:803-808)—was needed. 
     Filtering bZIP1 targets for the effects of protoplasting, and response to CHX or DEX. In this step, genes were filtered out whose expression states responded to protoplasting, or to treatments of DEX or CHX that were not related to the bZIP1 mediated regulation, in the following three steps: Filter 1: DEX-response filter: Genes responding to DEX independent of TF. Genes significantly induced/repressed by DEX-treatment in protoplasts transfected with the empty pBeanconRFP GR_plasmid (ANOVA analysis; FDR&lt;0.05), were excluded from analysis (1.6% genes filtered). Filter 2: Protoplast-response filter: Genes induced by protoplasting. Genes that are induced by root protoplasting (Birnbaum K, et al., 2003,  Science  302(5652):1956-1960) were removed from the list of bZIP1 targets (12.3% genes filtered). Filter 3: DEX×CHX interaction filter. Genes whose DEX-regulation is modified by CHX. This filter removes genes from the analysis in cases where the effects of DEX-induced TF nuclear import on gene regulation are affected by CHX treatment. To do this, a 3-way ANOVA was performed (Factors Nitrogen, DEX, and CHX) and bZIP1 primary targets were identified whose gene expression regulation by the DEX-induced nuclear import of bZIP1 is different between +CHX and −CHX conditions (FDR cutoff of interaction term CHX*DEX&lt;0.05). This eliminated genes that are regulated by bZIP1 in the presence of CHX, but not in the absence of CHX. This gene set may contain bZIP1 targets under a self-control negative feedback loop, and bZIP1 targets for which the half-lives of the transcripts affected by CHX. While the first case is potentially interesting, the second case represents the CHX artifact to be removed. Since it is difficult to differentiate between the two outcomes, these CHX-sensitive DEX-responsive genes dependent on bZIP1 were eliminated from the list of bZIP1 target genes (17.4% genes filtered), thus increasing precision over recall. 
     Micro-Chromatin Immunoprecipitation. For each combination of protoplast treatments (see above), an unsorted suspension of protoplasts containing approximately 5,000-10,000 GR::bZIP1 transfected cells was fixed for ChIP analysis, using an adapted version of the micro-ChIP protocol by Dahl et al (Dahl et al., 2008, Nucleic Acids Research 36:e15). The advantage in a ChIP analysis from protoplasts is that short-lived interactions would likely be missed in planta assays, as effective protein-DNA cross-linking in intact plant tissues requires prolonged (for a minimum of 15 minutes) infiltration under vacuum (Gendrel et al., 2005, Nat Methods 2(3):213-218). Cells were incubated with gentle rotation in 1% formaldehyde in W5 buffer for 7 minutes, then washed with W5 buffer and frozen in liquid N2. μChIP was performed according to Dahl et al. (2008, Nucleic Acids Research 36:e15) with a few modifications below. The GR::bZIP1-DNA complexes were captured using anti-GR antibody [GR (P-20) (Santa Cruz biotech) bound to Protein-A beads (Life Biotechnologies)]. A washing step with LiCl buffer [0.25M LiCl, 1% Na deoxycholate, 10 mM Tris-HCl (pH8), 1% NP-40] was added in between the wash with RIPA buffer and TE (Dahl et al., 2008, Nucleic Acids Research 36:e15). After elution from the beads, the ChIP material and the Input DNA were cleaned and concentrated using QIAGEN MiniElute Kit (QIAGEN). The protoplast suspension used for micro-ChIP was not FACS sorted in order to maintain a comparable incubation time between the samples that were used for microarray analyses and for micro ChIP. Importantly, while FACS sorting of transformed cells is required for microarray studies, it was not required to identify DNA targets using ChIP-seq. 
     ChIP-Seq library preparation. The ChIP DNA and Input DNA were prepared for Illumina HiSeq sequencing platform following the Illumina ChIP-Seq protocol (Illumina, San Diego, Calif.) with modifications. Barcoded adaptors and enrichment primers (BiOO Scientific, TX, USA) were used according to the manufacturer&#39;s protocol. The concentration and the quality of the libraries was determined by the Qubit Fluorometric DNA Assay (InVitrogen, NY, USA), DNA 12000 Bioanalzyer chip (Agilent, CA, USA) and KAPA Quant Library Kit for Illumina (KAPA Biosystems, MA, USA). A total of 8 libraries were then pooled in equimolar amounts and sequenced on two lanes of an Illumina HiSeq platform for 100 cycles in paired-end configuration (Cold Spring Harbor Lab, N.Y.). 
     ChIP-Seq Analysis. Reads obtained from the four treatments (with DEX and N in the presence of CHX) were filtered and aligned to the  Arabidopsis thaliana  genome (TAIR10) and clonal reads were removed. The ChIP alignment data was compared to its partner Input DNA and peaks were called using the QuEST package (20) with a ChIP seeding enrichment ≥3, and extension and background enrichments ≥2. These regions were overlapped with the genome annotation to identify genes within 500 bp downstream of the peak. The gene lists from multiple treatments were largely overlapping sets, and hence were pooled to generate a single list of genes that show significant binding of bZIP1. Due to technical issues, the experimental design used for ChIP-Seq precludes the observation of significant differences between the genes bound by bZIP1 under the different treatment conditions. This is because the samples fixed for ChIP included a variable number of transfected cells that were not sorted by FACS. 
     The ChIP-seq studies were performed using a micro-ChIP protocol on ˜10,000 cells, which result in a low DNA input, compared to standard ChIP studies. It has been shown that peak discovery from ChIP data becomes more challenging as the number of cells goes down ( FIG. 3  in Gilfillan et al., 2012, Bmc Genomics, 13). Therefore, ChIP libraries made from these very low input-DNA samples have a higher level of background noise, necessitating lower peak calling thresholds. However, even with this caveat for micro-ChIP studies, we were able to recover 850 targets including several previously validated bZIP1 targets (ASN1 and ProDH) (Dietrich et al., 2011, The Plant Cell 23:381-395). 
     Time-series ChIP-seq. The ChIP time-series samples were pre-treated with a N-signal treatment of 20 mM KNO3 and 20 mM NH4NO3 solution (N) for 2 h, followed by CHX (35 μM in DMSO, Sigma-Aldrich) for 20 min. Protoplasts were then treated with DEX (10 μM in Ethanol, Sigma-Aldrich) and samples were harvested at 1, 5, 30 and 60 min after the start of the DEX-induced bZIP1 nuclear localization. 
     Cis-element Motif Analysis. 1 Kb regions upstream of the TSS (Transcription Start Site) for target genes were extracted based on TAIR10 annotation and submitted to the Elefinder program (all promoters from the genome as background) (Li et al., 2011, Plant physiology 156:2124-2140) or MEME (against a randomized dinucleotide background) (Bailey et al., 2009, Nucleic Acids Research 37:W202-208) to determine over-representation of known cis-element binding sites (different parameters used in specific cases were notified in the paper if applicable). The E-value of significance for each motif was used to cluster the occurrence of motifs in the various subsets using the HCL algorithm in MeV (Saeed et al., 2006, Methods in Enzymology 411:134-193). Motifs that show a higher specificity to a particular category or a sub-group were identified with the PTM algorithm in MeV. De novo motif identification was performed on 1 Kb upstream sequence of the genes regulated by bZIP1 from microarray and ChIP-Seq data separately using the MEME suite (Bailey et al., 2009, Nucleic Acids Research 37:W202-208). 
     Accession numbers. The raw data from all Microarray assays, were submitted to NCBI GEO and is available under the accession number GSE54049. The raw sequencing data from ChIP-Seq assays is available from NCBI SRA under the accession SRX425878. 
     10.3. Results 
     Temporal perturbation of both bZIP1 and the N-signal it transduces. To identify how bZIP1 mediates the rapid propagation of a N-signal in a GRN, both bZIP1 and the N-signal it transduces were temporally perturbed in the cell-based TARGET system ( FIG. 24  A&amp;B) (Bargmann et al., 2013, Molecular Plant 6(3):978). bZIP1, which is ubiquitously expressed across all root cell-types (Birnbaum K, et al., 2003,  Science  302(5652):1956-1960), was transiently overexpressed in root protoplasts as a GR::bZIP1 fusion protein, enabling temporal induction of nuclear localization by dexamethasone (DEX) ( FIG. 24A ) (Bargmann et al., 2013, Molecular Plant 6(3):978). Transfected root cells expressing the GR::bZIP1 fusion protein were sequentially treated with: 1) inorganic nitrogen (+/−N), 2) cycloheximide (+/−CHX) and 3) dexamethasone (+/−DEX) ( FIG. 24C ). The N-treatment can induce post-translational modifications of bZIP1 (Baena-Gonzalez et al., 2007, Nature 448:938-942), or influence bZIP1 partners by transcriptional or post-transcriptional mechanisms ( FIG. 24B ). DEX-treatment induces TF nuclear import ( FIG. 24A ) (Bargmann et al., 2013, Molecular Plant 6(3):978). Further, genes regulated by DEX-induced TF import are deemed primary targets, as a CHX pre-treatment blocks translation of downstream regulators, as previously shown in the TARGET system (Bargmann et al., 2013, Molecular Plant 6(3):978) and in planta (Eklund et al., 2010, Plant Cell 22:349-363) ( FIG. 24A ). Importantly, to eliminate any side effects caused by CHX pre-treatment, only genes whose transcriptome response to DEX-induced TF nuclear import is the same in either the presence or absence of CHX were considered. Such bZIP1 primary targets identified based on gene regulation following DEX-induced TF import, were identified using Affymetrix ATH1 microarrays. In parallel, primary targets identified by TF-binding were identified in a micro-ChIP-Seq assay (Dahl et al., 2008, Nucleic Acids Research 36:e15) using anti-GR antibodies. Both transcriptome and ChIP-seq data were obtained 5 hours after the DEX-induced nuclear import of bZIP1, from the same cell samples, enabling a direct comparison ( FIG. 24  C&amp;D). Regarding the N-signal, 328 N-responsive genes were identified in the cell-based experiments ( FIG. 25 ; Table 12). These N-responsive genes significantly overlap with the N-responsive genes identified in whole seedlings exposed to a similar N-treatment (NH 4 NO 3 ) (Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939-4944), and from roots treated with nitrate (Wang et al., 2003, Plant Physiol. 132(2):556-567; Wang et al., 2004, Plant physiology 136(1):2512-2522), including a dynamic study (Krouk et al., 2010, Genome Biology 11:R123) (121/328, p-val&lt;0.001) ( FIG. 26 ; Table 13). The N-responsive genes in the cell-based experiments are enriched with genes that respond to N-treatment across all root cell-types in planta (p-val=8.8E−13, hypergeometric distribution) (Gifford et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:803-808). 
     
       
         
           
               
             
               
                 TABLE 12 
               
             
            
               
                   
               
               
                 N-responsive genes (FDR &lt; 0.05) in root protoplasts used in the TARGET system. 
               
            
           
           
               
               
               
            
               
                 Locus 
                 Symbol 
                 FullName 
               
               
                   
               
            
           
           
               
            
               
                 A. Genes that are up-regulated by N-treatment (FDR &lt; 0.05) 
               
            
           
           
               
               
               
            
               
                 AT3G17790 
                 ATACP5 
                   
               
               
                 AT4G39260 
                 ATGRP8 
                 GLYCINE-RICH PROTEIN 8 
               
               
                 AT3G20770 
                 AtEIN3 
               
               
                 AT2G38530 
                 cdf3 
                 cell growth defect factor-3 
               
               
                 AT3G47420 
                 AtG3Pp1 
                 Glycerol-3-phosphate permease 1 
               
               
                 AT3G61860 
                 At-RS31 
                 arginine/serine-rich splicing factor 31 
               
               
                 AT4G13250 
                 NYC1 
                 NON-YELLOW COLORING 1 
               
               
                 AT4G24620 
                 PGI 
               
               
                 AT5G19430 
               
               
                 AT4G11560 
               
               
                 AT5G24870 
               
               
                 AT1G20110 
               
               
                 AT2G01850 
                 ATXTH27 
               
               
                 AT4G14930 
               
               
                 AT1G19730 
                 ATH4 
                 thioredoxin H-type 4 
               
               
                 AT3G60750 
               
               
                 AT5G01340 
                 AtmSFC1 
               
               
                 AT5G04540 
                 AtMTM2 
               
               
                 AT3G56150 
                 ATEIF3C-1 
               
               
                 AT5G48180 
                 AtNSP5 
               
               
                 AT4G00940 
               
               
                 AT5G53460 
                 GLT1 
                 NADH-dependent glutamate synthase 1 
               
               
                 AT1G25550 
               
               
                 AT4G36760 
                 APP1 
                 aminopeptidase P1 
               
               
                 AT1G23820 
                 SPDS1 
                 spermidine synthase 1 
               
               
                 AT3G10740 
                 ARAF 
                 ALPHA-L-ARABINOFURANOSIDASE 
               
               
                 AT4G32070 
                 Phox4 
                 Phox4 
               
               
                 AT2G21290 
               
               
                 AT5G07890 
               
               
                 AT3G62140 
               
               
                 AT3G19030 
               
               
                 AT5G11470 
               
               
                 AT4G17340 
                 DELTA-TIP2 
               
               
                 AT1G04400 
                 AT-PHH1 
               
               
                 AT3G49620 
                 DIN11 
                 DARK INDUCIBLE 11 
               
               
                 AT2G26150 
                 ATHSFA2 
                 heat shock transcription factor A2 
               
               
                 AT3G58610 
               
               
                 AT1G64190 
               
               
                 AT1G74310 
                 ATHSP101 
                 heat shock protein 11 
               
               
                 AT2G26980 
                 CIPK3 
                 CBL-interacting protein kinase 3 
               
               
                 AT4G12400 
                 Hop3 
                 Hop3 
               
               
                 AT1G68720 
                 ATTADA 
                   ARABIDOPSIS THALIANA  TRNA ADENOSINE DEAMINASE A 
               
               
                 AT1G27300 
               
               
                 AT2G18550 
                 ATHB21 
                 homeobox protein 21 
               
               
                 AT1G78050 
                 PGM 
                 phosphoglycerate/bisphosphoglycerate mutase 
               
               
                 AT3G19290 
                 ABF4 
                 ABRE binding factor 4 
               
               
                 AT4G27910 
                 ATX4 
               
               
                 AT2G18050 
                 HIS1-3 
                 histone H1-3 
               
               
                 AT5G12860 
                 DiT1 
                 dicarboxylate transporter 1 
               
               
                 AT5G41670 
               
               
                 AT3G49630 
               
               
                 AT4G09620 
               
               
                 AT1G54050 
               
               
                 AT2G03270 
               
               
                 AT5G48570 
                 ATFKBP65 
               
               
                 AT4G24000 
                 ATCSLG2 
                   ARABIDOPSIS THALIANA  CELLULOSE SYNTHASE LIKE G2 
               
               
                 AT1G65540 
                 AtLETM2 
               
               
                 AT4G23440 
               
               
                 AT5G12030 
                 AT-HSP17.6A 
                 heat shock protein 17.6A 
               
               
                 AT5G62900 
               
               
                 AT1G53540 
               
               
                 AT1G37130 
                 ATNR2 
                   ARABIDOPSIS  NITRATE REDUCTASE 2 
               
               
                 AT3G16050 
                 A37 
               
               
                 AT1G58360 
                 AAP1 
                 amino acid permease 1 
               
               
                 AT3G52340 
                 ATSPP2 
                 SUCROSE-PHOSPHATASE 2 
               
               
                 AT2G16060 
                 AHB1 
                 hemoglobin 1 
               
               
                 AT5G49470 
               
               
                 AT1G58080 
                 ATATP-PRT1 
                 ATP phosphoribosyl transferase 1 
               
               
                 AT1G13300 
                 HRS1 
                 HYPERSENSITIVITY TO LOW PI-ELICITED PRIMARY ROOT 
               
               
                   
                   
                 SHORTENING 1 
               
               
                 AT5G20790 
               
               
                 AT5G13180 
                 ANAC083 
                 NAC domain containing protein 83 
               
               
                 AT5G49000 
               
               
                 AT5G63680 
               
               
                 AT1G06570 
                 HPD 
                 4-hydroxyphenylpyruvate dioxygenase 
               
               
                 AT1G55510 
                 BCDH BETA1 
                 branched-chain alpha-keto acid decarboxylase E1 beta subunit 
               
               
                 AT3G52490 
               
               
                 AT3G60690 
               
               
                 AT2G38400 
                 AGT3 
                 alanine:glyoxylate aminotransferase 3 
               
               
                 AT4G23100 
                 ATECS1 
               
               
                 AT1G09460 
               
               
                 AT4G38470 
                 STY46 
                 serine/threonine/tyrosine kinase 46 
               
               
                 AT2G41190 
               
               
                 AT5G07010 
                 ATST2A 
                   ARABIDOPSIS THALIANA  SULFOTRANSFERASE 2A 
               
               
                 AT1G23190 
                 PGM3 
                 phosphoglucomutase 3 
               
               
                 AT5G04630 
                 CYP77A9 
                 cytochrome P45, family 77, subfamily A, polypeptide 9 
               
               
                 AT3G48360 
                 ATBT2 
               
               
                 AT4G37540 
                 LBD39 
                 LOB domain-containing protein 39 
               
               
                 AT1G49500 
               
               
                 AT1G80160 
                 GLYI7 
                 glyoxylase I 7 
               
               
                 AT5G47560 
                 ATSDAT 
               
               
                 AT1G53580 
                 ETHE1 
                 ETHE1-LIKE 
               
               
                 AT4G34030 
                 MCCB 
                 3-methylcrotonyl-CoA carboxylase 
               
               
                 AT3G49940 
                 LBD38 
                 LOB domain-containing protein 38 
               
               
                 AT5G10210 
               
               
                 AT2G33150 
                 KAT2 
                 3-KETOACYL-COA THIOLASE 2 
               
               
                 AT1G03790 
                 SOM 
                 SOMNUS 
               
               
                 AT4G31240 
               
               
                 AT1G04410 
                 c-NAD-MDH1 
                 cytosolic-NAD-dependent malate dehydrogenase 1 
               
               
                 AT3G13750 
                 BGAL1 
                 beta galactosidase 1 
               
               
                 AT1G23870 
                 ATTPS9 
                 trehalose-phosphatase/synthase 9 
               
               
                 AT1G62660 
               
               
                 AT5G54080 
                 AtHGO 
               
               
                 AT4G09760 
               
               
                 AT4G38340 
               
               
                 AT5G52300 
                 LTI65 
                 LOW-TEMPERATURE-INDUCED 65 
               
               
                 AT1G08190 
                 ATVAM2 
               
               
                 AT1G14340 
               
               
                 AT2G45960 
                 ATHH2 
               
               
                 AT1G23800 
                 ALDH2B 
                 aldehyde dehydrogenase 2B 
               
               
                 AT3G01420 
                 ALPHA-DOX1 
                 alpha-dioxygenase 1 
               
               
                 AT3G16240 
                 AQP1 
               
               
                 AT5G04250 
               
               
                 AT4G33080 
               
               
                 AT2G42560 
               
               
                 AT5G13110 
                 G6PD2 
                 glucose-6-phosphate dehydrogenase 2 
               
               
                 AT1G16170 
               
               
                 AT5G20885 
               
               
                 AT5G66400 
                 ATDI8 
                   ARABIDOPSIS THALIANA  DROUGHT-INDUCED 8 
               
               
                 AT3G45060 
                 ATNRT2.6 
                   ARABIDOPSIS THALIANA  HIGH AFFINITY NITRATE TRANSPORTER 2.6 
               
               
                 AT2G42750 
               
               
                 AT3G45300 
                 ATIVD 
               
               
                 AT5G40450 
               
               
                 AT2G38800 
               
               
                 AT1G52320 
               
               
                 AT2G23030 
                 SNRK2-9 
                 SUCROSE NONFERMENTING 1-RELATED PROTEIN KINASE 2-9 
               
               
                 AT4G35090 
                 CAT2 
                 catalase 2 
               
               
                 AT3G42860 
               
               
                 AT3G53540 
                 TRM19 
                 TON1 Recruiting Motif 19 
               
               
                 AT4G34000 
                 ABF3 
                 abscisic acid responsive elements-binding factor 3 
               
               
                 AT3G27820 
                 ATMDAR4 
                 MONODEHYDROASCORBATE REDUCTASE 4 
               
               
                 AT5G48250 
                 BBX8 
                 B-box domain protein 8 
               
               
                 AT5G50850 
                 MAB1 
                 MACCI-BOU 
               
               
                 AT1G30510 
                 ATRFNR2 
                 root FNR 2 
               
               
                 AT1G63940 
                 MDAR6 
                 monodehydroascorbate reductase 6 
               
               
                 AT3G26100 
               
               
                 AT5G65210 
                 TGA1 
                 TGACG sequence-specific binding protein 1 
               
               
                 AT1G73920 
               
               
                 AT1G60710 
                 ATB2 
               
               
                 AT5G15450 
                 APG6 
                 ALBINO AND PALE GREEN 6 
               
               
                 AT3G48990 
                 AAE3 
                 ACYL-ACTIVATING ENZYME 3 
               
               
                 AT2G15620 
                 ATHNIR 
                   ARABIDOPSIS THALIANA  NITRITE REDUCTASE 
               
               
                 AT5G39590 
               
               
                 AT1G68670 
               
               
                 AT5G65660 
               
               
                 AT3G61430 
                 ATPIP1 
                   ARABIDOPSIS THALIANA  PLASMA MEMBRANE INTRINSIC PROTEIN 1 
               
               
                 AT4G12340 
               
               
                 AT5G67420 
                 ASL39 
                 ASYMMETRIC LEAVES2-LIKE 39 
               
            
           
           
               
            
               
                 B. genes that are down-regulated by N-treatment (FDR &lt; 0.05) 
               
            
           
           
               
               
               
            
               
                 AT1G56060 
                   
                   
               
               
                 AT1G53430 
               
               
                 AT3G21230 
                 4CL5 
                 4-coumarate:CoA ligase 5 
               
               
                 AT4G02330 
                 AtPME41 
               
               
                 AT4G01850 
                 AtSAM2 
               
               
                 AT1G52200 
               
               
                 AT2G23270 
               
               
                 AT5G59480 
               
               
                 AT2G17220 
                 Kin3 
                 kinase 3 
               
               
                 AT3G10640 
                 VPS60.1 
               
               
                 AT5G58120 
               
               
                 AT5G61210 
                 ATSNAP33 
               
               
                 AT1G10160 
               
               
                 AT3G15520 
               
               
                 AT4G19960 
                 ATKUP9 
               
               
                 AT4G28940 
               
               
                 AT4G30560 
                 ATCNGC9 
                 cyclic nucleotide gated channel 9 
               
               
                 AT2G38120 
                 AtAUX1 
               
               
                 AT3G59900 
                 ARGOS 
                 AUXIN-REGULATED GENE INVOLVED IN ORGAN SIZE 
               
               
                 AT4G28850 
                 ATXTH26 
               
               
                 AT4G39720 
               
               
                 AT1G09920 
               
               
                 AT4G24580 
                 REN1 
                 ROP1 ENHANCER 1 
               
               
                 AT4G39940 
                 AKN2 
                 APS-kinase 2 
               
               
                 AT1G54690 
                 G-H2AX 
                 GAMMA H2AX 
               
               
                 AT3G10940 
                 LSF2 
                 LIKE SEX4 2 
               
               
                 AT5G01490 
                 ATCAX4 
               
               
                 AT1G73530 
               
               
                 AT4G24350 
               
               
                 AT3G55630 
                 ATDFD 
                 DHFS-FPGS homolog D 
               
               
                 AT5G43520 
               
               
                 AT1G74870 
               
               
                 AT2G35990 
                 LOG2 
                 LONELY GUY 2 
               
               
                 AT1G32350 
                 AOX1D 
                 alternative oxidase 1D 
               
               
                 AT3G56400 
                 ATWRKY70 
                   ARABIDOPSIS THALIANA  WRKY DNA-BINDING PROTEIN 7 
               
               
                 AT2G47140 
                 AtSDR5 
               
               
                 AT4G26470 
               
               
                 AT1G73066 
               
               
                 AT2G43000 
                 ANAC042 
                 NAC domain containing protein 42 
               
               
                 AT5G06720 
                 ATPA2 
                 peroxidase 2 
               
               
                 AT1G09930 
                 ATOPT2 
                 oligopeptide transporter 2 
               
               
                 AT1G09520 
               
               
                 AT4G25030 
               
               
                 AT1G18860 
                 ATWRKY61 
                 WRKY DNA-BINDING PROTEIN 61 
               
               
                 AT2G39530 
               
               
                 AT3G02850 
                 SKOR 
                 STELAR K+ outward rectifier 
               
               
                 AT5G24540 
                 BGLU31 
                 beta glucosidase 31 
               
               
                 AT5G39680 
                 EMB2744 
                 EMBRYO DEFECTIVE 2744 
               
               
                 AT1G16380 
                 ATCHX1 
               
               
                 AT4G11170 
               
               
                 AT3G07390 
                 AIR12 
                 Auxin-Induced in Root cultures 12 
               
               
                 AT5G44060 
               
               
                 AT1G35200 
               
               
                 AT1G72070 
               
               
                 AT2G25735 
               
               
                 AT2G32020 
               
               
                 AT3G10630 
               
               
                 AT1G53920 
                 GLIP5 
                 GDSL-motif lipase 5 
               
               
                 AT1G18570 
                 AtMYB51 
                 myb domain protein 51 
               
               
                 AT2G19570 
                 AT-CDA1 
               
               
                 AT3G08750 
               
               
                 AT1G30370 
                 DLAH 
                 DAD1-like acylhydrolase 
               
               
                 AT3G08730 
                 ATPK1 
                   ARABIDOPSIS THALIANA  PROTEIN-SERINE KINASE 1 
               
               
                 AT1G14540 
                 PER4 
                 peroxidase 4 
               
               
                 AT5G15130 
                 ATWRKY72 
                   ARABIDOPSIS THALIANA  WRKY DNA-BINDING PROTEIN 72 
               
               
                 AT1G14550 
               
               
                 AT4G22720 
               
               
                 AT5G60250 
               
               
                 AT1G73510 
               
               
                 AT4G14368 
               
               
                 AT2G33710 
               
               
                 AT4G37900 
               
               
                 AT1G33590 
               
               
                 AT4G08770 
                 Prx37 
                 peroxidase 37 
               
               
                 AT3G50790 
               
               
                 AT4G23570 
                 SGT1A 
               
               
                 AT1G18390 
               
               
                 AT5G26920 
                 CBP60G 
                 Cam-binding protein 6-like G 
               
               
                 AT1G05575 
               
               
                 AT3G01500 
                 ATBCA1 
                 BETA CARBONIC ANHYDRASE 1 
               
               
                 AT1G68765 
                 IDA 
                 INFLORESCENCE DEFICIENT IN ABSCISSION 
               
               
                 AT5G64650 
               
               
                 AT3G55090 
                 ABCG16 
                 ATP-binding cassette G16 
               
               
                 AT4G17785 
                 MYB39 
                 myb domain protein 39 
               
               
                 AT1G02900 
                 ATRALF1 
                 RAPID ALKALINIZATION FACTOR 1 
               
               
                 AT3G57080 
                 NRPE5 
               
               
                 AT5G05220 
               
               
                 AT3G22900 
                 NRPD7 
               
               
                 AT1G03990 
               
               
                 AT4G04490 
                 CRK36 
                 cysteine-rich RLK (RECEPTOR-like protein kinase) 36 
               
               
                 AT5G14740 
                 BETA CA2 
                 BETA CARBONIC ANHYDRASE 2 
               
               
                 AT1G76550 
               
               
                 AT2G29330 
                 TRI 
                 tropinone reductase 
               
               
                 AT5G45280 
               
               
                 AT5G64860 
                 DPE1 
                 disproportionating enzyme 
               
               
                 AT1G54890 
               
               
                 AT4G18950 
               
               
                 AT1G02360 
               
               
                 AT1G10330 
               
               
                 AT1G76570 
               
               
                 AT2G44790 
                 UCC2 
                 uclacyanin 2 
               
               
                 AT2G22870 
                 EMB2001 
                 embryo defective 21 
               
               
                 AT2G42880 
                 ATMPK20 
                 MAP kinase 2 
               
               
                 AT1G51680 
                 4CL.1 
                 4-COUMARATE:COA LIGASE 1 
               
               
                 AT1G75960 
               
               
                 AT1G05670 
               
               
                 AT2G18190 
               
               
                 AT1G80240 
                 DGR1 
                 DUF642 L-GalL responsive gene 1 
               
               
                 AT5G11910 
               
               
                 AT5G16770 
                 AtMYB9 
                 myb domain protein 9 
               
               
                 AT1G17300 
               
               
                 AT5G40770 
                 ATPHB3 
                 prohibitin 3 
               
               
                 AT1G22890 
               
               
                 AT5G65930 
                 KCBP 
                 KINESIN-LIKE CALMODULIN-BINDING PROTEIN 
               
               
                 AT1G72280 
                 AERO1 
                 endoplasmic reticulum oxidoreductins 1 
               
               
                 AT5G03620 
               
               
                 AT2G18180 
               
               
                 AT1G71400 
                 AtRLP12 
                 receptor like protein 12 
               
               
                 AT3G29250 
                 AtSDR4 
               
               
                 AT3G63220 
               
               
                 AT1G80850 
               
               
                 AT5G22270 
               
               
                 AT4G17486 
               
               
                 AT2G33820 
                 ATMBAC1 
               
               
                 AT4G23690 
                 AtDIR6 
                   Arabidopsis thaliana  dirigent protein 6 
               
               
                 AT4G09650 
                 ATPD 
                 ATP synthase delta-subunit gene 
               
               
                 AT1G03920 
               
               
                 AT2G43610 
               
               
                 AT3G22800 
               
               
                 AT1G13210 
                 ACA.1 
                 autoinhibited Ca2+/ATPase II 
               
               
                 AT1G30750 
               
               
                 AT1G50590 
               
               
                 AT5G63040 
               
               
                 AT5G07110 
                 PRA1.B6 
                 prenylated RAB acceptor 1.B6 
               
               
                 AT5G63780 
                 SHA1 
                 shoot apical meristem arrest 1 
               
               
                 AT5G66390 
               
               
                 AT3G01280 
                 ATVDAC1 
                   ARABIDOPSIS THALIANA  VOLTAGE DEPENDENT ANION CHANNEL 1 
               
               
                 AT2G34610 
               
               
                 AT2G44380 
               
               
                 AT3G55150 
                 ATEXO70H1 
                 exocyst subunit exo7 family protein H1 
               
               
                 AT3G49130 
               
               
                 AT5G41610 
                 ATCHX18 
                   ARABIDOPSIS THALIANA  CATION/H+ EXCHANGER 18 
               
               
                 AT1G10090 
               
               
                 AT1G64160 
                 AtDIR5 
               
               
                 AT3G48650 
               
               
                 AT5G61440 
                 ACHT5 
                 atypical CYS HIS rich thioredoxin 5 
               
               
                 AT4G37240 
               
               
                 AT5G64100 
               
               
                 AT3G46280 
               
               
                 AT5G24030 
                 SLAH3 
                 SLAC1 homologue 3 
               
               
                 AT1G13280 
                 AOC4 
                 allene oxide cyclase 4 
               
               
                 AT2G10640 
               
               
                 AT1G02450 
                 NIMIN-1 
               
               
                 AT3G22920 
               
               
                 AT1G65840 
                 ATPAO4 
                 polyamine oxidase 4 
               
               
                 AT3G30396 
               
               
                 AT3G05210 
                 ERCC1 
               
               
                 AT5G58630 
                 TRM31 
                 TON1 Recruiting Motif 31 
               
               
                 AT2G44370 
               
               
                 AT4G20870 
                 ATFAH2 
                   ARABIDOPSIS  FATTY ACID HYDROXYLASE 2 
               
               
                 AT5G02780 
                 GSTL1 
                 glutathione transferase lambda 1 
               
               
                 AT1G16150 
                 WAKL4 
                 wall associated kinase-like 4 
               
               
                 AT3G01175 
               
               
                 AT5G64120 
               
               
                 AT2G31380 
                 BBX25 
                 B-box domain protein 25 
               
               
                 AT4G33420 
               
               
                 AT1G56150 
               
               
                 AT2G43620 
               
               
                 AT1G32930 
               
               
                 AT3G23230 
                 AtERF98 
               
               
                 AT3G22890 
                 APS1 
                 ATP sulfurylase 1 
               
               
                 AT1G68850 
               
               
                 AT3G23240 
                 ATERF1 
                 ETHYLENE RESPONSE FACTOR 1 
               
               
                 AT1G71530 
               
               
                 AT4G26690 
                 GDPDL3 
                 Glycerophosphodiester phosphodiesterase (GDPD) like 3 
               
               
                 AT5G17990 
                 pat1 
                 PHOSPHORIBOSYLANTHRANILATE TRANSFERASE 1 
               
               
                 AT2G04500 
               
               
                 AT5G14470 
               
               
                 AT2G02180 
                 TOM3 
                 tobamovirus multiplication protein 3 
               
               
                 AT5G48430 
               
               
                 AT5G67450 
                 AZF1 
                 zinc-finger protein 1 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 13 
               
               
                   
               
               
                 Overlap of N-responsive genes in protoplasts vs. N-response studies performed in planta 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                 At4g24620 
                 PGI, PGI1, phosphoglucose isomerase 1 
               
               
                 At3g49940 
                 LBD38, LOB domain-containing protein 38 
               
               
                 At1g52200 
                 PLAC8 family protein 
               
               
                 At3g61430 
                 ATPIP1, PIP1, PIP1; 1, PIP1A, plasma membrane intrinsic protein 1A 
               
               
                 At3g58610 
                 ketol-acid reductoisomerase 
               
               
                 At3g21230 
                 4CL5, 4-coumarate:CoA ligase 5 
               
               
                 At1g73920 
                 alpha/beta-Hydrolases superfamily protein 
               
               
                 At5g15130 
                 ATWRKY72, WRKY72, WRKY DNA-binding protein 72 
               
               
                 At5g48180 
                 NSP5, nitrile specifier protein 5 
               
               
                 At4g35090 
                 CAT2, catalase 2 
               
               
                 At5g39590 
                 TLD-domain containing nucleolar protein 
               
               
                 At1g23870 
                 ATTPS9, TPS9, TPS9, trehalose-phosphatase/synthase 9 
               
               
                 At4g09620 
                 Mitochondrial transcription termination factor family protein 
               
               
                 At2g19570 
                 AT-CDA1, CDA1, DESZ, cytidine deaminase 1 
               
               
                 At5g43520 
                 Cysteine/Histidine-rich C1 domain family protein 
               
               
                 At1g05575 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: anaerobic 
               
               
                   
                 respiration; LOCATED IN: endomembrane system; EXPRESSED IN: 17 plant structures; 
               
               
                   
                 EXPRESSED DURING: 9 growth stages; BEST  Arabidopsis thaliana  protein match is: unknown 
               
               
                   
                 protein (TAIR: AT2G31945.1); Has 63 Blast hits to 63 proteins in 10 species: Archae - 0; Bacteria - 0; 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 63; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At1g37130 
                 ATNR2, B29, CHL3, NIA2, NIA2-1, NR, NR2, nitrate reductase 2 
               
               
                 At5g22270 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
               
               
                   
                 (TAIR: AT3G11600.1); Has 136 Blast hits to 136 proteins in 15 species: Archae - 0; Bacteria - 0; 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 136; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g04540 
                 Myotubularin-like phosphatases II superfamily 
               
               
                 At1g56150 
                 SAUR-like auxin-responsive protein family 
               
               
                 At5g67420 
                 A5L39, LBD37, LOB domain-containing protein 37 
               
               
                 At5g64100 
                 Peroxidase superfamily protein 
               
               
                 At3g19030 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: pyridoxine 
               
               
                   
                 biosynthetic process, homoserine biosynthetic process; LOCATED IN: endomembrane system; 
               
               
                   
                 EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 9 growth stages; BEST  Arabidopsis   
               
               
                   
                   thaliana  protein match is: unknown protein (TAIR: AT1G49500.1); Has 22 Blast hits to 22 proteins in 2 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 22; Viruses - 0; Other Eukaryotes - 0 
               
               
                   
                 (source: NCBI BLink). 
               
               
                 At5g20885 
                 RING/U-box superfamily protein 
               
               
                 At1g06570 
                 HPD, PDS1, phytoene desaturation 1 
               
               
                 At5g24870 
                 RING/U-box superfamily protein 
               
               
                 At5g04250 
                 Cysteine proteinases superfamily protein 
               
               
                 At2g01850 
                 ATXTH27, EXGT-A3, XTH27, endoxyloglucan transferase A3 
               
               
                 At3g07390 
                 AIR12, auxin-responsive family protein 
               
               
                 At1g02900 
                 ATRALF1, RALF1, RALFL1, rapid alkalinization factor 1 
               
               
                 At5g01340 
                 Mitochondrial substrate carrier family protein 
               
               
                 At1g60710 
                 ATB2, NAD(P)-linked oxidoreductase superfamily protein 
               
               
                 At4g00940 
                 Dof-type zinc finger DNA-binding family protein 
               
               
                 At2g02180 
                 TOM3, tobamovirus multiplication protein 3 
               
               
                 At1g68720 
                 ATTADA, TADA, tRNA arginine adenosine deaminase 
               
               
                 At4g39940 
                 AKN2, APK2, APS-kinase 2 
               
               
                 At3g48360 
                 ATBT2, BT2, BTB and TAZ domain protein 2 
               
               
                 At3g47420 
                 ATPS3, PS3, phosphate starvation-induced gene 3 
               
               
                 At5g12860 
                 DiT1, dicarboxylate transporter 1 
               
               
                 At5g10210 
                 CONTAINS InterPro DOMAIN/s: C2 calcium-dependent membrane targeting (InterPro: IPR000008); 
               
               
                   
                 BEST  Arabidopsis thaliana  protein match is: unknown protein (TAIR: AT5G65030.1); Has 1807 Blast 
               
               
                   
                 hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; 
               
               
                   
                 Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink). 
               
               
                 At4g19960 
                 ATKUP9, HAK9, KT9, KUP9, K+ uptake permease 9 
               
               
                 At1g13280 
                 AOC4, allene oxide cyclase 4 
               
               
                 At3g60750 
                 Transketolase 
               
               
                 At2g15620 
                 ATHNIR, NIR, NIR1, nitrite reductase 1 
               
               
                 At1g65840 
                 ATPAO4, PAO4, polyamine oxidase 4 
               
               
                 At5g24030 
                 SLAH3, SLAC1 homologue 3 
               
               
                 At2g16060 
                 AHB1, ARATH GLB1, ATGLB1, GLB1, HB1, NSHB1, hemoglobin 1 
               
               
                 At3g55150 
                 ATEXO70H1, EXO70H1, exocyst subunit exo70 family protein H1 
               
               
                 At2g23030 
                 SNRK2-9, SNRK2.9, SNF1-related protein kinase 2.9 
               
               
                 At1g58360 
                 AAP1, NAT2, amino acid permease 1 
               
               
                 At4g38340 
                 Plant regulator RWP-RK family protein 
               
               
                 At2g32020 
                 Acyl-CoA N-acyltransferases (NAT) superfamily protein 
               
               
                 At5g48570 
                 ATFKBP65, FKBP65, ROF2, FKBP-type peptidyl-prolyl cis-trans isomerase family protein 
               
               
                 At1g62660 
                 Glycosyl hydrolases family 32 protein 
               
               
                 At2g34610 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
               
               
                   
                 (TAIR: AT1G30190.1); Has 342 Blast hits to 279 proteins in 74 species: Archae - 0; Bacteria - 7; 
               
               
                   
                 Metazoa - 76; Fungi - 18; Plants - 51; Viruses - 0; Other Eukaryotes - 190 (source: NCBI BLink). 
               
               
                 At1g49500 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 19 plant 
               
               
                   
                 structures; EXPRESSED DURING: 10 growth stages; BEST  Arabidopsis thaliana  protein match is: 
               
               
                   
                 unknown protein (TAIR: AT3G19030.1); Has 24 Blast hits to 24 proteins in 2 species: Archae - 0; 
               
               
                   
                 Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 24; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At1g54690 
                 G-H2AX, GAMMA-H2AX, H2AXB, HTA3, gamma histone variant H2AX 
               
               
                 At2g33710 
                 Integrase-type DNA-binding superfamily protein 
               
               
                 At3g22890 
                 APS1, ATP sulfulylase 1 
               
               
                 At3g23240 
                 ATERF1, ERF1, ethylene response factor 1 
               
               
                 At1g54050 
                 HSP20-like chaperones superfamily protein 
               
               
                 At4g37540 
                 LBD39, LOB domain-containing protein 39 
               
               
                 At1g58080 
                 ATATP-PRT1, ATP-PRT1, HISN1A, ATP phosphoribosyl transferase 1 
               
               
                 At5g50850 
                 MAB1, Transketolase family protein 
               
               
                 At5g12030 
                 AT-HSP17.6A, HSP17.6, HSP17.6A, heat shock protein 17.6A 
               
               
                 At1g13300 
                 HRS1, myb-like transcription factor family protein 
               
               
                 At1g14340 
                 RNA-binding (RRM/RBD/RNP motifs) family protein 
               
               
                 At3g60690 
                 SAUR-like auxin-responsive protein family 
               
               
                 At2g43620 
                 Chitinase family protein 
               
               
                 At5g63780 
                 SHA1, RING/FYVE/PHD zinc finger superfamily protein 
               
               
                 At5g59480 
                 Haloacid dehalogenase-like hydrolase (HAD) superfamily protein 
               
               
                 At1g09460 
                 Carbohydrate-binding X8 domain superfamily protein 
               
               
                 At5g13180 
                 ANAC083, NAC083, VNI2, NAC domain containing protein 83 
               
               
                 At5g62900 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: N-terminal protein 
               
               
                   
                 myristoylation; LOCATED IN: cellular_component unknown; EXPRESSED IN: 22 plant structures; 
               
               
                   
                 EXPRESSED DURING: 12 growth stages; BEST  Arabidopsis thaliana  protein match is: unknown 
               
               
                   
                 protein (TAIR: AT5G50090.1); Has 157 Blast hits to 157 proteins in 14 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 0; Fungi - 0; Plants - 157; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At4g34000 
                 ABF3, DPBF5, abscisic acid responsive elements-binding factor 3 
               
               
                 At2g39530 
                 Uncharacterised protein family (UPF0497) 
               
               
                 At2g17220 
                 Protein kinase superfamily protein 
               
               
                 At1g64190 
                 6-phosphogluconate dehydrogenase family protein 
               
               
                 At1g14540 
                 Peroxidase superfamily protein 
               
               
                 At1g33590 
                 Leucine-rich repeat (LRR) family protein 
               
               
                 At1g78050 
                 PGM, phosphoglycerate/bisphosphoglycerate mutase 
               
               
                 At1g63940 
                 MDAR6, monodehydroascothate reductase 6 
               
               
                 At3g59900 
                 ARGOS, auxin-regulated gene involved in organ size 
               
               
                 At4g37900 
                 Protein of unknown function (duplicated DUF1399) 
               
               
                 At2g26980 
                 CIPK3, SnRK3.17, CBL-interacting protein kinase 3 
               
               
                 At1g50590 
                 RmlC-like cupins superfamily protein 
               
               
                 At5g26920 
                 CBP60G, Cam-binding protein 60-like G 
               
               
                 At4g34030 
                 MCCB, 3-methylcrotonyl-CoA carboxylase 
               
               
                 At5g64120 
                 Peroxidase superfamily protein 
               
               
                 At5g65210 
                 TGA1, bZIP transcription factor family protein 
               
               
                 At1g18390 
                 Protein kinase superfamily protein 
               
               
                 At1g14550 
                 Peroxidase superfamily protein 
               
               
                 At5g13110 
                 G6PD2, glucose-6-phosphate dehydrogenase 2 
               
               
                 At2g42880 
                 ATMPK20, MPK20, MAP kinase 20 
               
               
                 At3g10740 
                 ARAF, ARAF1, ASD1, ATASD1, alpha-L-arabinofuranosidase 1 
               
               
                 At2g44380 
                 Cysteine/Histidine-rich C1 domain family protein 
               
               
                 At5g53460 
                 GLT1, NADH-dependent glutamate synthase 1 
               
               
                 At5g16770 
                 AtMYB9, MYB9, myb domain protein 9 
               
               
                 At1g23190 
                 Phosphoglucomutase/phosphomannomutase family protein 
               
               
                 At3g48990 
                 AMP-dependent synthetase and ligase family protein 
               
               
                 At5g47560 
                 ATSDAT, ATTDT, TDT, tonoplast dicarboxylate transporter 
               
               
                 At1g76550 
                 Phosphofructokinase family protein 
               
               
                 At5g07010 
                 ATST2A, ST2A, sulfotransferase 2A 
               
               
                 At1g30510 
                 ATRFNR2, RFNR2, root FNR 2 
               
               
                 At1g30370 
                 alpha/beta-Hydrolases superfamily protein 
               
               
                 At1g68670 
                 myb-like transcription factor family protein 
               
               
                 At5g45280 
                 Pectinacetylestemse family protein 
               
               
                 At4g38470 
                 ACT-like protein tyrosine kinase family protein 
               
               
                 At1g16170 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
               
               
                   
                 biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 24 
               
               
                   
                 plant structures; EXPRESSED DURING: 15 growth stages; BEST  Arabidopsis thaliana  protein match 
               
               
                   
                 is: unknown protein (TAIR: AT1G79660.1); Has 55 Blast hits to 55 proteins in 13 species: Archae - 0; 
               
               
                   
                 Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 55; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At5g41670 
                 6-phosphogluconate dehydrogenase family protein 
               
               
                 At2g43000 
                 anac042, NAC042, NAC domain containing protein 42 
               
               
                 At4g39720 
                 VQ motif-containing protein 
               
               
                 At1g51680 
                 4CL.1, 4CL1, AT4CL1, 4-coumarate:CoA ligase 1 
               
               
                 At3g55090 
                 ABC-2 type transporter family protein 
               
               
                 At5g15450 
                 APG6, CLPB-P, CLPB3, casein lytic proteinase B3 
               
               
                 At1g53920 
                 GLIP5, GDSL-motif lipase 5 
               
               
                 At5g07890 
                 myosin heavy chain-related 
               
               
                 At3g29250 
                 NAD(P)-binding Rossmann-fold superfamily protein 
               
               
                 At1g25550 
                 myb-like transcription factor family protein 
               
               
                 At5g48430 
                 Eukaryotic aspartyl protease family protein 
               
               
                 At4g37240 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: N-terminal protein 
               
               
                   
                 myristoylation; LOCATED IN: cellular_component unknown; EXPRESSED IN: 22 plant structures; 
               
               
                   
                 EXPRESSED DURING: 13 growth stages; BEST  Arabidopsis thaliana  protein match is: unknown 
               
               
                   
                 protein (TAIR: AT2G23690.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 
               
               
                   
                 (source: NCBI BLink). 
               
               
                   
               
            
           
         
       
     
     Primary targets of bZIP1 can be identified by either TF-regulation or TF-binding. bZIP1 primary targets were first identified based solely on TF-induced gene regulation. A total of 901 genes were identified as primary bZIP1 targets based on significant regulation in response to DEX-induced TF nuclear import, compared to minus DEX controls (ANOVA analysis; FDR adjusted p-value&lt;0.05) ( FIG. 27A ;  FIG. 24D ; Tables 14-16). These DEX-responsive genes are deemed to be primary targets of bZIP1, as pre-treatment of the samples with CHX (prior to DEX-induced TF nuclear import) blocks translation of mRNAs of primary bZIP1 targets, thus preventing changes in the mRNA levels of secondary targets in the GRN. To control for the potential side effects of CHX, this list of bZIP1 primary targets excluded genes whose DEX-induced mRNA response was altered by CHX treatment. With regard to the N-signal, 28 out of the 901 bZIP1 primary targets were regulated in response to a significant N-treatment×TF interaction (p-val&lt;0.01) ( FIG. 28 ; Table 17). This could reflect a post-translational modification of bZIP1 by the N-signal, or the N-induced modification of bZIP1 partners at the transcriptional and/or post-translational level ( FIG. 24B ). 
     bZIP1 primary targets were next identified based solely on TF-DNA binding. Genes bound by bZIP1 were identified as genic regions enriched in the ChIP DNA, compared to the background (input DNA), using the QuEST peak-calling algorithm ( FIG. 27C ) (Valouev et al., 2008, Nature Methods 5:829-834). This identified 850 genes with significant bZIP1 binding (FDR&lt;0.05) ( FIG. 24D ; Table 18), which included validated bZIP1 targets identified by single gene studies (e.g. ASN1 and ProDH) (Dietrich et al., 2011, The Plant Cell 23:381-395). It is noted that ChIP-seq can potentially detect genes directly bound to bZIP1, as well as genes indirectly bound by bZIP1 through bridging interactors. Thus, to independently assess whether primary targets identified either by TF-binding or TF-regulation were due to direct binding of bZIP1, cis-element analysis was performed ( FIG. 27  B&amp;D). The bZIP1-bound genes and the bZIP1 regulated genes, are each highly significantly enriched in known bZIP1 binding sites, based on analysis of de novo cis-motifs using MEME (Bailey et al., 2009, Nucleic Acids Research 37:W202-208) or known cis-motif enrichment using Elefinder (Li et al., 2011, Plant physiology 156:2124-2140) ( FIG. 27  B&amp;D). 
     
       
         
           
               
             
               
                 TABLE 14 
               
             
            
               
                   
               
               
                 Genes identified to be ZIP1 targets based on ANOVA analysis of  
               
               
                 transcriptome and/or by ChIP-Seq analysis. 
               
            
           
           
               
               
            
               
                 Category of Genes 
                 Number of Genes 
               
               
                   
               
            
           
           
               
            
               
                 Microarray Analysis 
               
            
           
           
               
               
               
            
               
                 Significantly regulated  
                 Nitrogen (FDR &lt; 0.05) 
                 328 
               
               
                 by ANOVA factor 
                   bZIP1  ( FDR  &lt;  0.05 ) 
                 901 
               
               
                   
                 NitrogenXbZIP1 
                 82 
               
               
                   
                 (pval &lt; 0.01) 
                   
               
               
                   
                   bZIP1  ( FDR  &lt;  0.05 )  AND   
                 28 
               
               
                   
                 
                   NitrogenXbZIP1 
                 
                   
               
               
                   
                 ( pval  &lt;  0.01 ) 
                   
               
            
           
           
               
            
               
                 ChIP-SEQ Analysis 
               
            
           
           
               
               
            
               
                 
                   bZIP1 bound genes 
                 
                 850 
               
               
                   
               
               
                 In italic: genes considered as TF primary targets in this study. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 15 
               
             
            
               
                   
               
               
                 bZIP1 primary targets identified as genes up-regulated or down-regulated  
               
               
                 by DEX-induced nuclear import of bZIP1 (FDR &lt; 0.05). 
               
            
           
           
               
               
               
               
               
            
               
                   
                 mean  
                 mean  
                 mean  
                 mean  
               
               
                   
                 expression 
                 expression 
                 expression 
                 expression 
               
               
                   
                 level  
                 level  
                 level  
                 level  
               
               
                   
                 (−N/−Dex) 
                 (−N/+Dex) 
                 (+N/−Dex) 
                 (+N/+Dex) 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 A. Genes that are up- 
                   
                   
                   
                   
               
               
                 regulated by DEX 
                   
                   
                   
                   
               
               
                 (FDR &lt; 0.05) 
                   
                   
                   
                   
               
               
                 AT3G01290 
                 10184.42 
                 11470.63 
                 9717.07 
                 11446.96 
               
               
                 AT5G07440 
                 7205.35 
                 10345.22 
                 7677.83 
                 10608.98 
               
               
                 AT1G73260 
                 8932.55 
                 9699.11 
                 9311.45 
                 10476.40 
               
               
                 AT5G52050 
                 8413.93 
                 9799.60 
                 8527.51 
                 10023.89 
               
               
                 AT3G30775 
                 5957.48 
                 9395.19 
                 5816.87 
                 9054.40 
               
               
                 AT5G01600 
                 4784.75 
                 7836.06 
                 5315.54 
                 7812.26 
               
               
                 AT3G60140 
                 4631.95 
                 7436.68 
                 5268.33 
                 7486.52 
               
               
                 AT5G40780 
                 6351.57 
                 7390.86 
                 6651.01 
                 7327.18 
               
               
                 AT5G12340 
                 6655.56 
                 7648.56 
                 6683.99 
                 7311.89 
               
               
                 AT1G69490 
                 4711.22 
                 7387.64 
                 4805.96 
                 7198.73 
               
               
                 AT3G45970 
                 4244.45 
                 6891.99 
                 4430.99 
                 6987.22 
               
               
                 AT5G03380 
                 5921.87 
                 6920.93 
                 6001.52 
                 6778.08 
               
               
                 AT5G28050 
                 2746.82 
                 7454.05 
                 2832.16 
                 6293.82 
               
               
                 AT2G34600 
                 5129.64 
                 6443.44 
                 5192.91 
                 6111.11 
               
               
                 AT5G64120 
                 5699.56 
                 7021.79 
                 5052.95 
                 6031.23 
               
               
                 AT4G15610 
                 5307.80 
                 6201.30 
                 5323.19 
                 5859.60 
               
               
                 AT1G80380 
                 3193.36 
                 5593.63 
                 3482.22 
                 5681.45 
               
               
                 AT2G39200 
                 5179.32 
                 5821.64 
                 5037.85 
                 5665.74 
               
               
                 AT3G56360 
                 3523.14 
                 5696.51 
                 3522.84 
                 5602.26 
               
               
                 AT1G15040 
                 2677.05 
                 5590.67 
                 2974.84 
                 5585.75 
               
               
                 AT5G66400 
                 3990.79 
                 4256.05 
                 4625.69 
                 5544.75 
               
               
                 AT4G01870 
                 4589.86 
                 5531.82 
                 4415.21 
                 5483.60 
               
               
                 AT5G56870 
                 3710.66 
                 5064.44 
                 3959.70 
                 5090.22 
               
               
                 AT3G19390 
                 2282.54 
                 5063.88 
                 2733.05 
                 5028.37 
               
               
                 AT5G06300 
                 4016.04 
                 4502.49 
                 4312.07 
                 4779.59 
               
               
                 AT1G68440 
                 2879.57 
                 4408.78 
                 3220.60 
                 4635.18 
               
               
                 AT1G10070 
                 1991.74 
                 4673.62 
                 2354.02 
                 4455.75 
               
               
                 AT5G20150 
                 2916.04 
                 3829.24 
                 3543.14 
                 4451.22 
               
               
                 AT1G23870 
                 2774.60 
                 3629.67 
                 3635.51 
                 4415.35 
               
               
                 AT3G47960 
                 2989.02 
                 3938.43 
                 3321.11 
                 4262.19 
               
               
                 AT5G47740 
                 3367.67 
                 3947.58 
                 3614.82 
                 4217.10 
               
               
                 AT2G23170 
                 3558.08 
                 4503.52 
                 3485.93 
                 4165.23 
               
               
                 AT4G38470 
                 1408.69 
                 3152.12 
                 2007.53 
                 4099.55 
               
               
                 AT2G19800 
                 2246.77 
                 4333.96 
                 2200.99 
                 3882.93 
               
               
                 AT5G67300 
                 3211.67 
                 3812.88 
                 3290.90 
                 3832.21 
               
               
                 AT3G61260 
                 2826.59 
                 4226.43 
                 2752.02 
                 3824.18 
               
               
                 AT2G38400 
                 1970.17 
                 3129.70 
                 2516.19 
                 3716.21 
               
               
                 AT1G54100 
                 2555.41 
                 3120.81 
                 3004.69 
                 3689.79 
               
               
                 AT5G49440 
                 2727.51 
                 3759.00 
                 2516.28 
                 3613.92 
               
               
                 AT1G67480 
                 1002.02 
                 3773.82 
                 1059.32 
                 3525.08 
               
               
                 AT1G64660 
                 1905.16 
                 3536.41 
                 2134.11 
                 3434.33 
               
               
                 AT1G25275 
                 2905.62 
                 3755.00 
                 2568.03 
                 3299.31 
               
               
                 AT4G33150 
                 1814.47 
                 2840.47 
                 2230.03 
                 3288.96 
               
               
                 AT3G04070 
                 2724.93 
                 3390.50 
                 2797.02 
                 3266.73 
               
               
                 AT5G57655 
                 2290.70 
                 2911.98 
                 2555.48 
                 3247.33 
               
               
                 AT5G43580 
                 2427.72 
                 3256.69 
                 2635.41 
                 3222.34 
               
               
                 AT4G35770 
                 948.38 
                 3140.55 
                 1314.57 
                 3177.19 
               
               
                 AT5G11090 
                 2078.24 
                 2784.47 
                 2283.94 
                 3085.78 
               
               
                 AT1G08830 
                 2441.65 
                 2922.21 
                 2469.18 
                 2780.36 
               
               
                 AT3G56240 
                 2353.08 
                 2907.75 
                 2327.40 
                 2728.18 
               
               
                 AT1G79340 
                 2204.62 
                 2609.32 
                 2337.77 
                 2721.73 
               
               
                 AT5G54500 
                 2372.67 
                 3095.73 
                 2004.25 
                 2690.71 
               
               
                 AT3G05200 
                 1793.81 
                 2231.06 
                 1938.52 
                 2553.69 
               
               
                 AT4G36040 
                 1903.75 
                 2772.28 
                 1948.94 
                 2551.54 
               
               
                 AT1G68620 
                 1757.50 
                 2432.63 
                 1713.98 
                 2503.30 
               
               
                 AT1G11260 
                 1818.65 
                 2621.83 
                 1712.04 
                 2398.40 
               
               
                 AT4G32950 
                 481.13 
                 2304.42 
                 619.27 
                 2368.04 
               
               
                 AT4G20860 
                 1743.34 
                 2314.59 
                 1847.07 
                 2193.24 
               
               
                 AT1G14330 
                 1769.07 
                 2184.54 
                 1787.45 
                 2156.24 
               
               
                 AT3G14990 
                 1486.66 
                 2353.45 
                 1600.26 
                 2108.65 
               
               
                 AT4G15550 
                 1482.06 
                 1895.48 
                 1505.45 
                 2052.15 
               
               
                 AT5G50200 
                 1702.01 
                 2185.46 
                 1724.26 
                 2040.88 
               
               
                 AT4G37790 
                 1516.07 
                 2019.80 
                 1563.38 
                 2034.09 
               
               
                 AT1G03090 
                 1196.37 
                 1905.17 
                 1458.24 
                 2014.86 
               
               
                 AT2G33150 
                 1467.96 
                 1678.65 
                 1719.03 
                 2011.98 
               
               
                 AT1G43160 
                 1640.78 
                 2089.38 
                 1677.85 
                 2004.44 
               
               
                 AT5G05340 
                 1990.71 
                 2455.06 
                 1675.36 
                 1997.69 
               
               
                 AT1G22360 
                 1435.43 
                 1834.51 
                 1651.79 
                 1940.94 
               
               
                 AT5G64260 
                 1833.49 
                 2167.71 
                 1692.73 
                 1935.14 
               
               
                 AT1G32460 
                 1457.27 
                 2439.73 
                 1366.24 
                 1929.38 
               
               
                 AT1G29400 
                 1732.04 
                 2012.76 
                 1657.37 
                 1917.29 
               
               
                 AT5G11520 
                 1366.90 
                 1831.79 
                 1466.17 
                 1910.76 
               
               
                 AT4G39780 
                 1312.50 
                 1899.95 
                 1496.49 
                 1897.93 
               
               
                 AT5G67310 
                 1827.99 
                 2284.68 
                 1585.68 
                 1860.24 
               
               
                 AT5G08350 
                 73.19 
                 1944.64 
                 79.08 
                 1798.98 
               
               
                 AT3G15450 
                 1476.21 
                 1901.72 
                 1501.24 
                 1773.58 
               
               
                 AT5G28610 
                 1341.26 
                 1888.26 
                 1387.43 
                 1761.45 
               
               
                 AT4G03510 
                 953.82 
                 1726.31 
                 968.89 
                 1759.19 
               
               
                 AT2G38750 
                 1213.34 
                 1600.58 
                 1313.42 
                 1695.27 
               
               
                 AT5G67320 
                 1596.01 
                 2100.45 
                 1420.94 
                 1678.29 
               
               
                 AT3G14770 
                 643.54 
                 1627.16 
                 767.40 
                 1620.43 
               
               
                 AT1G27100 
                 1301.70 
                 1680.26 
                 1281.77 
                 1598.90 
               
               
                 AT1G69890 
                 1143.76 
                 1882.02 
                 1024.97 
                 1556.08 
               
               
                 AT5G61600 
                 1383.51 
                 1762.18 
                 1271.92 
                 1552.54 
               
               
                 AT1G80460 
                 1202.78 
                 1535.00 
                 1168.86 
                 1548.39 
               
               
                 AT5G48430 
                 1757.39 
                 2322.30 
                 1372.87 
                 1508.49 
               
               
                 AT3G11410 
                 1189.35 
                 1363.58 
                 1210.84 
                 1479.68 
               
               
                 AT4G27260 
                 1018.07 
                 1484.79 
                 1009.82 
                 1464.57 
               
               
                 AT3G51730 
                 907.42 
                 1308.15 
                 1001.97 
                 1457.17 
               
               
                 AT1G04410 
                 946.12 
                 1162.96 
                 1212.68 
                 1441.19 
               
               
                 AT2G02800 
                 1173.58 
                 1632.63 
                 1183.50 
                 1407.36 
               
               
                 AT2G32660 
                 1135.17 
                 1410.73 
                 1132.61 
                 1400.63 
               
               
                 AT3G43430 
                 905.85 
                 1670.63 
                 819.65 
                 1400.22 
               
               
                 AT3G55450 
                 1238.32 
                 1609.73 
                 1068.06 
                 1354.31 
               
               
                 AT1G08930 
                 1194.49 
                 1381.44 
                 1091.15 
                 1306.69 
               
               
                 AT5G44380 
                 1054.14 
                 1584.83 
                 983.22 
                 1289.14 
               
               
                 AT3G52060 
                 867.54 
                 1171.26 
                 825.77 
                 1284.28 
               
               
                 AT3G15630 
                 970.70 
                 1691.80 
                 902.42 
                 1237.34 
               
               
                 AT1G08920 
                 843.98 
                 1132.36 
                 964.58 
                 1195.78 
               
               
                 AT1G30820 
                 610.39 
                 1245.12 
                 725.50 
                 1164.67 
               
               
                 AT4G34350 
                 630.77 
                 988.61 
                 876.35 
                 1164.52 
               
               
                 AT5G16110 
                 798.11 
                 1210.43 
                 756.99 
                 1139.91 
               
               
                 AT4G38060 
                 885.30 
                 1080.25 
                 916.81 
                 1109.34 
               
               
                 AT3G19930 
                 669.32 
                 1349.89 
                 603.66 
                 1089.31 
               
               
                 AT3G06850 
                 705.39 
                 1259.52 
                 746.19 
                 1072.72 
               
               
                 AT1G68410 
                 917.29 
                 1179.01 
                 921.44 
                 1054.98 
               
               
                 AT3G12320 
                 768.10 
                 957.25 
                 887.47 
                 1030.97 
               
               
                 AT1G18270 
                 554.66 
                 1117.09 
                 589.44 
                 1007.85 
               
               
                 AT4G15630 
                 660.42 
                 1000.90 
                 631.83 
                 1003.19 
               
               
                 AT1G15380 
                 677.06 
                 949.20 
                 711.13 
                 1002.44 
               
               
                 AT4G30490 
                 790.90 
                 982.97 
                 819.52 
                 992.49 
               
               
                 AT5G20250 
                 295.01 
                 1063.61 
                 377.67 
                 976.27 
               
               
                 AT3G45300 
                 527.47 
                 768.10 
                 788.61 
                 968.78 
               
               
                 AT3G15950 
                 637.26 
                 1011.75 
                 601.23 
                 948.72 
               
               
                 AT5G65110 
                 645.46 
                 1043.94 
                 629.59 
                 925.59 
               
               
                 AT3G46690 
                 512.82 
                 889.96 
                 495.74 
                 921.56 
               
               
                 AT2G39210 
                 530.68 
                 850.67 
                 614.41 
                 890.85 
               
               
                 AT5G41610 
                 493.04 
                 1077.30 
                 399.49 
                 882.34 
               
               
                 AT4G24220 
                 595.64 
                 978.37 
                 543.62 
                 877.62 
               
               
                 AT5G04040 
                 492.68 
                 886.80 
                 594.52 
                 877.26 
               
               
                 AT1G28130 
                 569.60 
                 844.63 
                 506.85 
                 876.67 
               
               
                 AT5G67420 
                 206.65 
                 326.20 
                 733.39 
                 876.59 
               
               
                 AT1G76990 
                 511.46 
                 794.92 
                 531.69 
                 869.96 
               
               
                 AT5G24530 
                 533.88 
                 826.44 
                 559.74 
                 845.58 
               
               
                 AT4G18340 
                 257.55 
                 1111.63 
                 246.45 
                 834.12 
               
               
                 AT5G10450 
                 700.33 
                 846.43 
                 688.08 
                 822.06 
               
               
                 AT3G17110 
                 530.43 
                 585.81 
                 570.25 
                 819.94 
               
               
                 AT2G32510 
                 497.35 
                 774.09 
                 529.25 
                 811.11 
               
               
                 AT1G29760 
                 610.06 
                 780.86 
                 724.85 
                 788.34 
               
               
                 AT1G22830 
                 535.37 
                 873.50 
                 565.71 
                 787.30 
               
               
                 AT2G30600 
                 358.04 
                 829.99 
                 331.61 
                 780.48 
               
               
                 AT1G22190 
                 620.74 
                 786.03 
                 592.52 
                 768.94 
               
               
                 AT1G58180 
                 440.02 
                 836.01 
                 428.79 
                 761.66 
               
               
                 AT2G31390 
                 481.43 
                 580.20 
                 596.80 
                 761.61 
               
               
                 AT3G29240 
                 326.16 
                 792.83 
                 352.29 
                 756.15 
               
               
                 AT3G49790 
                 474.90 
                 852.12 
                 449.07 
                 731.71 
               
               
                 AT2G38820 
                 295.83 
                 728.53 
                 332.08 
                 715.79 
               
               
                 AT1G08720 
                 633.75 
                 805.71 
                 610.86 
                 709.33 
               
               
                 AT4G01026 
                 499.36 
                 799.47 
                 501.33 
                 689.90 
               
               
                 AT1G26270 
                 437.10 
                 749.41 
                 455.57 
                 684.98 
               
               
                 AT4G21440 
                 518.10 
                 847.63 
                 390.31 
                 677.20 
               
               
                 AT5G54080 
                 466.34 
                 563.21 
                 571.81 
                 670.32 
               
               
                 AT1G62570 
                 480.50 
                 653.30 
                 563.75 
                 668.93 
               
               
                 AT1G76410 
                 477.22 
                 685.02 
                 530.84 
                 665.41 
               
               
                 AT4G32870 
                 600.84 
                 739.01 
                 436.98 
                 652.54 
               
               
                 AT5G45630 
                 293.64 
                 851.38 
                 248.54 
                 650.24 
               
               
                 AT3G51840 
                 456.42 
                 561.01 
                 539.55 
                 649.19 
               
               
                 AT1G55510 
                 359.48 
                 505.19 
                 438.72 
                 632.62 
               
               
                 AT1G76240 
                 416.87 
                 627.84 
                 476.67 
                 628.97 
               
               
                 AT3G16150 
                 73.84 
                 851.91 
                 77.41 
                 622.58 
               
               
                 AT5G40450 
                 425.44 
                 515.17 
                 539.91 
                 610.18 
               
               
                 AT2G23450 
                 477.27 
                 663.73 
                 456.64 
                 608.98 
               
               
                 AT5G49360 
                 100.52 
                 564.27 
                 138.45 
                 583.56 
               
               
                 AT4G10840 
                 411.43 
                 503.25 
                 459.63 
                 553.75 
               
               
                 AT5G15190 
                 245.58 
                 502.01 
                 320.39 
                 540.57 
               
               
                 AT2G44670 
                 312.67 
                 631.34 
                 285.27 
                 535.16 
               
               
                 AT3G61060 
                 163.22 
                 600.33 
                 208.76 
                 531.13 
               
               
                 AT2G12400 
                 323.07 
                 500.47 
                 366.46 
                 529.50 
               
               
                 AT3G13460 
                 433.42 
                 520.52 
                 408.87 
                 525.71 
               
               
                 AT1G06570 
                 263.25 
                 395.08 
                 327.78 
                 518.78 
               
               
                 AT2G26280 
                 431.35 
                 509.69 
                 443.22 
                 516.43 
               
               
                 AT5G04740 
                 413.67 
                 480.88 
                 418.89 
                 506.93 
               
               
                 AT2G14170 
                 302.99 
                 514.20 
                 317.60 
                 505.01 
               
               
                 AT1G02860 
                 290.17 
                 632.44 
                 310.74 
                 504.02 
               
               
                 AT4G13430 
                 356.83 
                 440.33 
                 378.32 
                 502.99 
               
               
                 AT1G72770 
                 250.42 
                 475.96 
                 359.01 
                 501.13 
               
               
                 AT1G55020 
                 222.81 
                 510.73 
                 247.00 
                 500.39 
               
               
                 AT3G54620 
                 384.47 
                 486.84 
                 414.77 
                 496.60 
               
               
                 AT1G65840 
                 487.99 
                 619.99 
                 440.66 
                 490.79 
               
               
                 AT3G54140 
                 301.69 
                 421.20 
                 364.28 
                 486.97 
               
               
                 AT4G39730 
                 304.20 
                 457.54 
                 298.99 
                 467.18 
               
               
                 AT4G17950 
                 378.17 
                 463.37 
                 417.61 
                 466.59 
               
               
                 AT4G01120 
                 171.46 
                 448.16 
                 195.47 
                 455.26 
               
               
                 AT1G01490 
                 296.79 
                 504.22 
                 354.46 
                 455.22 
               
               
                 AT1G16150 
                 389.48 
                 664.54 
                 258.23 
                 451.86 
               
               
                 AT3G57890 
                 359.52 
                 398.76 
                 365.14 
                 448.61 
               
               
                 AT3G23230 
                 477.73 
                 720.03 
                 284.96 
                 446.59 
               
               
                 AT3G51860 
                 359.25 
                 406.42 
                 347.34 
                 439.13 
               
               
                 AT1G61660 
                 376.46 
                 482.03 
                 340.63 
                 433.51 
               
               
                 AT2G39570 
                 147.42 
                 576.87 
                 162.97 
                 427.86 
               
               
                 AT1G67810 
                 258.42 
                 466.67 
                 261.45 
                 418.71 
               
               
                 AT1G63180 
                 293.52 
                 504.12 
                 298.99 
                 418.36 
               
               
                 AT5G16970 
                 274.42 
                 361.16 
                 293.68 
                 417.10 
               
               
                 AT5G63620 
                 321.59 
                 383.09 
                 361.31 
                 415.60 
               
               
                 AT4G29950 
                 248.77 
                 424.65 
                 265.88 
                 410.83 
               
               
                 AT3G46440 
                 296.17 
                 388.65 
                 320.64 
                 407.40 
               
               
                 AT3G01175 
                 360.83 
                 535.86 
                 283.40 
                 405.06 
               
               
                 AT3G17420 
                 277.61 
                 422.27 
                 317.09 
                 397.44 
               
               
                 AT1G66470 
                 226.02 
                 346.31 
                 299.54 
                 391.92 
               
               
                 AT3G46280 
                 386.23 
                 572.31 
                 286.47 
                 390.51 
               
               
                 AT3G57540 
                 246.02 
                 338.91 
                 315.59 
                 386.72 
               
               
                 AT3G53150 
                 309.42 
                 429.81 
                 287.16 
                 383.79 
               
               
                 AT1G03790 
                 223.72 
                 293.00 
                 296.24 
                 383.24 
               
               
                 AT1G61740 
                 204.52 
                 373.13 
                 248.24 
                 382.22 
               
               
                 AT5G61590 
                 169.36 
                 322.75 
                 217.79 
                 369.15 
               
               
                 AT4G23880 
                 246.89 
                 339.77 
                 230.07 
                 368.41 
               
               
                 AT4G15620 
                 220.23 
                 431.88 
                 163.64 
                 360.52 
               
               
                 AT5G64460 
                 232.76 
                 344.86 
                 270.38 
                 357.94 
               
               
                 AT1G75450 
                 201.99 
                 431.13 
                 186.76 
                 355.21 
               
               
                 AT2G15695 
                 223.60 
                 335.08 
                 210.60 
                 354.64 
               
               
                 AT3G17440 
                 235.08 
                 325.79 
                 244.52 
                 350.48 
               
               
                 AT3G20410 
                 260.99 
                 397.46 
                 248.52 
                 347.30 
               
               
                 AT3G19920 
                 181.43 
                 297.01 
                 181.99 
                 347.01 
               
               
                 AT2G27490 
                 265.83 
                 366.46 
                 281.46 
                 346.25 
               
               
                 AT1G75230 
                 298.68 
                 362.99 
                 303.28 
                 344.29 
               
               
                 AT5G37260 
                 183.58 
                 323.24 
                 191.07 
                 338.89 
               
               
                 AT3G48690 
                 136.33 
                 376.40 
                 124.31 
                 333.70 
               
               
                 AT5G06980 
                 229.34 
                 369.71 
                 276.34 
                 328.19 
               
               
                 AT4G28040 
                 126.83 
                 311.27 
                 164.96 
                 326.75 
               
               
                 AT1G35580 
                 249.68 
                 388.17 
                 229.39 
                 326.38 
               
               
                 AT5G24470 
                 237.51 
                 330.86 
                 230.82 
                 321.05 
               
               
                 AT4G14420 
                 278.60 
                 365.61 
                 218.88 
                 314.73 
               
               
                 AT2G25900 
                 230.39 
                 321.40 
                 271.91 
                 312.60 
               
               
                 AT5G18630 
                 212.25 
                 282.12 
                 248.33 
                 301.33 
               
               
                 AT5G13740 
                 148.46 
                 287.89 
                 167.62 
                 297.04 
               
               
                 AT1G03100 
                 184.63 
                 398.39 
                 169.38 
                 294.96 
               
               
                 AT1G49670 
                 246.84 
                 272.38 
                 248.68 
                 292.52 
               
               
                 AT1G54740 
                 50.65 
                 279.25 
                 63.67 
                 287.90 
               
               
                 AT3G03170 
                 188.22 
                 240.68 
                 195.94 
                 280.19 
               
               
                 AT1G67470 
                 233.81 
                 347.51 
                 219.61 
                 279.31 
               
               
                 AT1G06520 
                 246.49 
                 338.83 
                 194.75 
                 277.92 
               
               
                 AT1G56700 
                 173.77 
                 270.96 
                 225.74 
                 276.90 
               
               
                 AT3G13450 
                 115.41 
                 292.52 
                 112.43 
                 273.07 
               
               
                 AT1G03610 
                 176.69 
                 299.85 
                 197.11 
                 271.81 
               
               
                 AT3G14050 
                 184.59 
                 249.89 
                 184.11 
                 269.92 
               
               
                 AT5G46590 
                 54.42 
                 277.55 
                 61.46 
                 267.30 
               
               
                 AT1G11380 
                 112.85 
                 259.85 
                 131.99 
                 263.86 
               
               
                 AT5G66030 
                 210.45 
                 277.21 
                 211.28 
                 262.39 
               
               
                 AT2G43060 
                 121.21 
                 237.36 
                 133.52 
                 261.39 
               
               
                 AT4G30550 
                 176.17 
                 235.71 
                 202.63 
                 257.78 
               
               
                 AT1G56145 
                 153.41 
                 292.27 
                 152.77 
                 256.92 
               
               
                 AT1G19700 
                 210.69 
                 250.61 
                 214.73 
                 256.72 
               
               
                 AT2G17500 
                 213.62 
                 274.99 
                 194.47 
                 253.08 
               
               
                 AT4G03080 
                 218.91 
                 264.94 
                 211.69 
                 252.74 
               
               
                 AT4G24330 
                 166.59 
                 259.57 
                 205.16 
                 252.10 
               
               
                 AT5G18610 
                 137.12 
                 200.94 
                 163.91 
                 244.41 
               
               
                 AT5G43190 
                 173.58 
                 276.27 
                 162.71 
                 243.92 
               
               
                 AT3G11340 
                 103.93 
                 253.84 
                 95.09 
                 242.44 
               
               
                 AT1G69570 
                 53.47 
                 280.68 
                 66.82 
                 240.47 
               
               
                 AT5G16120 
                 166.52 
                 193.99 
                 185.28 
                 239.74 
               
               
                 AT1G03080 
                 141.88 
                 212.23 
                 177.46 
                 237.30 
               
               
                 AT5G47390 
                 214.99 
                 261.98 
                 197.83 
                 237.13 
               
               
                 AT5G02780 
                 208.46 
                 325.07 
                 147.70 
                 230.92 
               
               
                 AT1G08630 
                 86.59 
                 305.91 
                 81.73 
                 227.16 
               
               
                 AT2G22080 
                 167.39 
                 214.32 
                 161.86 
                 226.72 
               
               
                 AT3G61070 
                 159.27 
                 230.78 
                 167.05 
                 222.96 
               
               
                 AT5G49690 
                 134.05 
                 194.00 
                 132.84 
                 222.19 
               
               
                 AT4G15280 
                 162.18 
                 216.41 
                 177.44 
                 221.97 
               
               
                 AT1G48840 
                 138.48 
                 191.27 
                 166.86 
                 220.61 
               
               
                 AT1G23550 
                 115.16 
                 205.81 
                 126.48 
                 219.78 
               
               
                 AT3G52710 
                 185.70 
                 224.55 
                 173.68 
                 219.41 
               
               
                 AT4G26290 
                 100.09 
                 204.28 
                 99.72 
                 217.88 
               
               
                 AT1G66070 
                 187.56 
                 241.42 
                 186.15 
                 214.37 
               
               
                 AT1G71980 
                 87.74 
                 200.94 
                 104.80 
                 211.66 
               
               
                 AT5G27350 
                 169.81 
                 217.50 
                 181.09 
                 209.46 
               
               
                 AT4G30170 
                 81.34 
                 235.80 
                 82.59 
                 204.62 
               
               
                 AT1G76160 
                 149.85 
                 241.80 
                 165.87 
                 203.41 
               
               
                 AT3G16800 
                 136.82 
                 188.05 
                 163.34 
                 203.20 
               
               
                 AT4G15545 
                 156.88 
                 210.11 
                 145.84 
                 202.89 
               
               
                 AT2G29380 
                 133.78 
                 205.70 
                 133.94 
                 195.73 
               
               
                 AT3G05390 
                 162.24 
                 261.87 
                 157.21 
                 195.25 
               
               
                 AT4G32320 
                 139.86 
                 219.65 
                 135.38 
                 194.46 
               
               
                 AT1G23880 
                 108.11 
                 207.96 
                 154.52 
                 193.41 
               
               
                 AT5G43430 
                 167.02 
                 202.42 
                 152.23 
                 192.88 
               
               
                 AT5G02810 
                 115.69 
                 171.62 
                 147.36 
                 191.61 
               
               
                 AT4G33910 
                 133.44 
                 231.40 
                 133.01 
                 188.06 
               
               
                 AT3G16910 
                 132.96 
                 200.97 
                 129.81 
                 187.98 
               
               
                 AT4G37540 
                 23.62 
                 63.65 
                 56.50 
                 187.59 
               
               
                 AT5G07080 
                 174.68 
                 247.22 
                 134.82 
                 185.93 
               
               
                 AT5G24030 
                 177.37 
                 240.76 
                 142.93 
                 183.54 
               
               
                 AT3G57020 
                 115.75 
                 152.78 
                 139.84 
                 183.40 
               
               
                 AT1G17190 
                 92.87 
                 188.86 
                 111.21 
                 180.24 
               
               
                 AT3G14780 
                 137.88 
                 158.41 
                 144.07 
                 179.84 
               
               
                 AT4G14500 
                 124.89 
                 193.26 
                 132.77 
                 179.33 
               
               
                 AT1G08090 
                 90.27 
                 189.04 
                 104.52 
                 177.75 
               
               
                 AT3G60690 
                 63.78 
                 115.19 
                 80.58 
                 175.69 
               
               
                 AT3G55150 
                 68.56 
                 258.96 
                 42.22 
                 174.54 
               
               
                 AT5G16960 
                 123.23 
                 167.73 
                 131.78 
                 171.56 
               
               
                 AT2G46270 
                 77.59 
                 150.29 
                 99.41 
                 171.54 
               
               
                 AT5G17640 
                 107.49 
                 190.13 
                 121.67 
                 171.17 
               
               
                 AT3G20860 
                 102.93 
                 177.80 
                 86.02 
                 170.02 
               
               
                 AT3G45060 
                 88.06 
                 139.17 
                 146.70 
                 169.39 
               
               
                 AT1G67880 
                 141.83 
                 194.88 
                 147.45 
                 169.14 
               
               
                 AT5G26740 
                 88.42 
                 165.00 
                 91.06 
                 165.11 
               
               
                 AT5G43830 
                 124.16 
                 213.01 
                 108.34 
                 164.50 
               
               
                 AT1G32200 
                 94.05 
                 141.29 
                 96.44 
                 163.07 
               
               
                 AT5G04770 
                 106.01 
                 197.32 
                 98.70 
                 162.60 
               
               
                 AT5G18850 
                 87.29 
                 173.24 
                 106.32 
                 161.22 
               
               
                 AT4G17140 
                 125.32 
                 158.91 
                 129.87 
                 160.87 
               
               
                 AT3G15610 
                 127.30 
                 184.88 
                 138.02 
                 159.29 
               
               
                 AT1G18260 
                 121.01 
                 130.77 
                 129.39 
                 157.84 
               
               
                 AT4G39070 
                 81.16 
                 197.76 
                 78.43 
                 157.28 
               
               
                 AT1G13080 
                 56.39 
                 132.02 
                 56.78 
                 155.59 
               
               
                 AT4G27657 
                 89.63 
                 155.91 
                 96.74 
                 153.67 
               
               
                 AT1G68850 
                 191.27 
                 332.59 
                 80.41 
                 153.54 
               
               
                 AT3G22930 
                 120.29 
                 248.25 
                 108.40 
                 152.64 
               
               
                 AT4G37590 
                 107.97 
                 167.29 
                 121.12 
                 152.57 
               
               
                 AT5G59220 
                 121.92 
                 147.72 
                 123.64 
                 151.98 
               
               
                 AT4G35780 
                 101.85 
                 146.06 
                 104.35 
                 151.98 
               
               
                 AT1G31480 
                 103.91 
                 150.30 
                 117.73 
                 151.70 
               
               
                 AT5G57630 
                 99.77 
                 156.71 
                 119.20 
                 151.17 
               
               
                 AT1G21310 
                 110.32 
                 184.92 
                 105.96 
                 143.26 
               
               
                 AT4G32300 
                 84.23 
                 150.08 
                 79.46 
                 142.38 
               
               
                 AT1G66170 
                 143.51 
                 216.29 
                 88.76 
                 141.44 
               
               
                 AT5G27920 
                 51.23 
                 141.94 
                 55.44 
                 140.96 
               
               
                 AT2G40170 
                 66.43 
                 140.44 
                 63.41 
                 139.40 
               
               
                 AT5G13750 
                 79.95 
                 151.37 
                 81.87 
                 139.08 
               
               
                 AT5G65630 
                 109.66 
                 146.68 
                 116.75 
                 138.71 
               
               
                 AT4G32960 
                 108.46 
                 144.34 
                 116.28 
                 138.12 
               
               
                 AT3G47500 
                 103.77 
                 139.68 
                 110.41 
                 137.67 
               
               
                 AT5G03720 
                 74.31 
                 137.22 
                 89.23 
                 137.53 
               
               
                 AT4G36670 
                 93.16 
                 179.25 
                 91.44 
                 133.77 
               
               
                 AT4G20870 
                 109.56 
                 213.99 
                 77.04 
                 133.70 
               
               
                 AT5G56100 
                 95.00 
                 127.73 
                 90.07 
                 133.47 
               
               
                 AT5G18170 
                 58.10 
                 106.68 
                 83.00 
                 132.91 
               
               
                 AT2G44360 
                 111.72 
                 152.31 
                 114.74 
                 131.90 
               
               
                 AT5G61510 
                 97.58 
                 121.52 
                 105.48 
                 131.82 
               
               
                 AT3G14067 
                 84.56 
                 132.94 
                 109.50 
                 131.21 
               
               
                 AT5G23050 
                 79.96 
                 112.81 
                 85.27 
                 128.37 
               
               
                 AT1G09460 
                 51.78 
                 96.15 
                 68.09 
                 128.23 
               
               
                 AT5G60200 
                 57.29 
                 113.64 
                 51.11 
                 127.35 
               
               
                 AT3G62650 
                 83.14 
                 114.05 
                 100.20 
                 127.07 
               
               
                 AT5G56180 
                 93.37 
                 125.51 
                 108.00 
                 126.69 
               
               
                 AT1G61810 
                 55.96 
                 171.39 
                 50.57 
                 126.49 
               
               
                 AT4G36790 
                 93.30 
                 121.16 
                 92.98 
                 124.48 
               
               
                 AT2G28200 
                 80.09 
                 107.22 
                 66.42 
                 122.50 
               
               
                 AT5G18650 
                 80.20 
                 119.46 
                 94.34 
                 121.87 
               
               
                 AT1G66550 
                 16.87 
                 178.52 
                 8.85 
                 121.01 
               
               
                 AT2G43400 
                 80.72 
                 117.84 
                 102.26 
                 120.82 
               
               
                 AT4G24060 
                 74.58 
                 116.88 
                 79.81 
                 120.75 
               
               
                 AT1G60940 
                 89.47 
                 114.81 
                 94.79 
                 120.19 
               
               
                 AT5G13110 
                 50.81 
                 55.50 
                 85.60 
                 117.80 
               
               
                 AT1G73240 
                 84.91 
                 120.96 
                 82.12 
                 115.06 
               
               
                 AT3G47640 
                 88.22 
                 124.31 
                 95.33 
                 113.52 
               
               
                 AT1G79700 
                 99.25 
                 144.06 
                 84.18 
                 110.96 
               
               
                 AT5G67450 
                 137.07 
                 197.99 
                 91.95 
                 108.74 
               
               
                 AT4G01030 
                 80.36 
                 134.69 
                 62.12 
                 108.14 
               
               
                 AT5G07070 
                 79.82 
                 107.17 
                 83.36 
                 107.96 
               
               
                 AT3G54630 
                 35.72 
                 138.03 
                 32.62 
                 106.41 
               
               
                 AT5G57660 
                 57.73 
                 90.98 
                 77.73 
                 105.82 
               
               
                 AT5G10210 
                 21.30 
                 48.72 
                 64.20 
                 102.49 
               
               
                 AT3G29160 
                 78.64 
                 120.24 
                 79.77 
                 98.18 
               
               
                 AT1G63700 
                 78.58 
                 105.41 
                 68.50 
                 95.18 
               
               
                 AT4G37220 
                 49.77 
                 108.81 
                 49.51 
                 94.74 
               
               
                 AT5G05440 
                 83.03 
                 131.52 
                 73.58 
                 93.44 
               
               
                 AT3G56000 
                 72.31 
                 96.23 
                 66.14 
                 92.92 
               
               
                 AT2G19350 
                 68.37 
                 78.86 
                 72.52 
                 92.41 
               
               
                 AT4G31240 
                 52.21 
                 69.75 
                 70.95 
                 92.27 
               
               
                 AT4G38500 
                 32.40 
                 67.18 
                 48.08 
                 88.95 
               
               
                 AT1G75220 
                 77.58 
                 101.05 
                 73.89 
                 87.30 
               
               
                 AT2G19810 
                 66.83 
                 96.10 
                 60.49 
                 87.19 
               
               
                 AT3G49060 
                 71.49 
                 102.76 
                 76.53 
                 86.88 
               
               
                 AT4G36730 
                 70.75 
                 99.16 
                 72.19 
                 86.62 
               
               
                 AT1G57680 
                 80.22 
                 119.55 
                 70.72 
                 85.92 
               
               
                 AT1G52240 
                 24.19 
                 113.85 
                 24.24 
                 84.31 
               
               
                 AT2G39130 
                 60.17 
                 77.61 
                 62.96 
                 83.54 
               
               
                 AT1G15050 
                 26.09 
                 148.94 
                 25.21 
                 82.55 
               
               
                 AT1G07250 
                 65.31 
                 70.10 
                 59.97 
                 80.93 
               
               
                 AT1G28260 
                 38.14 
                 59.37 
                 53.22 
                 80.56 
               
               
                 AT3G06780 
                 69.06 
                 95.10 
                 65.59 
                 80.51 
               
               
                 AT1G79350 
                 77.83 
                 99.11 
                 70.96 
                 80.08 
               
               
                 AT1G14340 
                 44.89 
                 51.11 
                 62.44 
                 78.79 
               
               
                 AT5G49650 
                 58.97 
                 83.31 
                 69.58 
                 76.81 
               
               
                 AT1G20300 
                 42.65 
                 75.93 
                 44.46 
                 76.36 
               
               
                 AT2G39980 
                 43.88 
                 88.55 
                 40.86 
                 74.51 
               
               
                 AT5G58620 
                 64.50 
                 88.80 
                 63.60 
                 72.85 
               
               
                 AT2G22870 
                 88.47 
                 110.12 
                 61.46 
                 70.40 
               
               
                 AT3G15260 
                 52.85 
                 64.15 
                 55.86 
                 70.34 
               
               
                 AT1G75800 
                 35.21 
                 55.46 
                 43.50 
                 69.04 
               
               
                 AT3G02550 
                 42.17 
                 91.77 
                 38.20 
                 67.55 
               
               
                 AT1G18460 
                 37.13 
                 60.92 
                 42.38 
                 66.81 
               
               
                 AT5G13760 
                 47.74 
                 66.43 
                 54.92 
                 66.73 
               
               
                 AT1G26730 
                 49.92 
                 91.39 
                 52.09 
                 66.01 
               
               
                 AT2G35230 
                 55.94 
                 73.72 
                 45.53 
                 65.92 
               
               
                 AT3G14760 
                 30.68 
                 107.79 
                 22.41 
                 65.15 
               
               
                 AT3G50780 
                 50.65 
                 62.62 
                 44.75 
                 64.77 
               
               
                 AT1G69910 
                 54.48 
                 71.77 
                 51.52 
                 64.24 
               
               
                 AT5G39040 
                 48.05 
                 70.13 
                 45.72 
                 64.19 
               
               
                 AT3G51540 
                 38.50 
                 68.02 
                 37.25 
                 63.50 
               
               
                 AT2G41190 
                 6.86 
                 45.71 
                 15.34 
                 62.77 
               
               
                 AT5G20050 
                 51.77 
                 72.19 
                 47.39 
                 62.08 
               
               
                 AT1G32930 
                 63.44 
                 86.24 
                 44.68 
                 61.75 
               
               
                 AT2G01570 
                 46.85 
                 71.90 
                 51.08 
                 61.62 
               
               
                 AT3G14740 
                 26.43 
                 87.61 
                 24.95 
                 58.46 
               
               
                 AT3G24520 
                 35.14 
                 63.23 
                 34.03 
                 58.25 
               
               
                 AT2G40420 
                 40.27 
                 53.19 
                 45.52 
                 58.14 
               
               
                 AT1G18330 
                 26.34 
                 54.45 
                 37.77 
                 57.86 
               
               
                 AT3G49940 
                 23.55 
                 32.95 
                 38.48 
                 52.17 
               
               
                 AT3G57420 
                 29.77 
                 51.55 
                 31.01 
                 50.89 
               
               
                 AT3G16170 
                 38.77 
                 48.49 
                 44.68 
                 50.20 
               
               
                 AT5G47560 
                 17.64 
                 31.89 
                 28.49 
                 49.55 
               
               
                 AT3G27690 
                 14.62 
                 72.47 
                 13.43 
                 49.52 
               
               
                 AT4G33420 
                 47.88 
                 90.04 
                 43.70 
                 48.00 
               
               
                 AT2G19320 
                 24.44 
                 42.04 
                 20.39 
                 47.63 
               
               
                 AT1G66890 
                 11.36 
                 50.55 
                 10.69 
                 46.58 
               
               
                 AT3G14750 
                 32.16 
                 55.23 
                 29.39 
                 45.87 
               
               
                 AT4G38490 
                 23.46 
                 40.16 
                 28.81 
                 45.63 
               
               
                 AT2G26600 
                 34.19 
                 45.31 
                 33.79 
                 44.77 
               
               
                 AT3G54960 
                 24.86 
                 44.56 
                 25.62 
                 43.05 
               
               
                 AT1G08980 
                 34.96 
                 47.23 
                 25.50 
                 42.02 
               
               
                 AT3G13965 
                 35.28 
                 45.80 
                 27.62 
                 41.19 
               
               
                 AT2G02040 
                 31.00 
                 37.83 
                 30.63 
                 40.12 
               
               
                 AT1G67070 
                 21.84 
                 44.07 
                 19.20 
                 38.23 
               
               
                 AT5G47240 
                 8.75 
                 37.13 
                 10.66 
                 37.97 
               
               
                 AT1G67510 
                 31.53 
                 52.76 
                 20.67 
                 37.92 
               
               
                 AT5G06690 
                 32.61 
                 57.90 
                 29.49 
                 36.67 
               
               
                 AT1G06560 
                 27.24 
                 35.93 
                 28.73 
                 34.64 
               
               
                 AT5G19090 
                 19.12 
                 32.24 
                 22.01 
                 34.38 
               
               
                 AT1G64670 
                 13.42 
                 38.93 
                 13.04 
                 33.64 
               
               
                 AT4G01330 
                 23.71 
                 37.06 
                 27.66 
                 33.62 
               
               
                 AT5G59590 
                 26.63 
                 34.86 
                 25.22 
                 33.14 
               
               
                 AT3G22920 
                 27.78 
                 61.59 
                 17.92 
                 32.41 
               
               
                 AT4G38340 
                 14.34 
                 15.20 
                 19.22 
                 30.49 
               
               
                 AT4G38480 
                 10.86 
                 22.11 
                 13.01 
                 30.31 
               
               
                 AT1G15060 
                 21.88 
                 31.42 
                 23.75 
                 29.48 
               
               
                 AT2G03220 
                 18.19 
                 29.62 
                 19.33 
                 27.68 
               
               
                 AT1G10060 
                 6.06 
                 19.90 
                 6.33 
                 26.91 
               
               
                 AT1G22400 
                 19.68 
                 27.72 
                 19.28 
                 25.25 
               
               
                 AT3G15440 
                 17.92 
                 24.49 
                 18.42 
                 24.07 
               
               
                 AT4G23870 
                 10.43 
                 19.24 
                 9.65 
                 23.39 
               
               
                 AT3G15620 
                 15.25 
                 34.17 
                 11.40 
                 22.99 
               
               
                 AT2G02700 
                 18.77 
                 35.42 
                 22.59 
                 22.72 
               
               
                 AT5G52250 
                 13.84 
                 20.92 
                 14.12 
                 22.51 
               
               
                 AT1G64010 
                 13.47 
                 26.14 
                 14.03 
                 22.13 
               
               
                 AT5G67440 
                 12.57 
                 24.98 
                 12.56 
                 22.07 
               
               
                 AT5G03550 
                 15.43 
                 19.74 
                 13.92 
                 21.98 
               
               
                 AT2G37440 
                 10.35 
                 21.93 
                 11.17 
                 21.62 
               
               
                 AT1G42480 
                 17.86 
                 25.22 
                 17.67 
                 21.38 
               
               
                 AT4G27480 
                 11.87 
                 20.41 
                 11.65 
                 21.02 
               
               
                 AT1G03870 
                 6.85 
                 36.12 
                 6.04 
                 21.00 
               
               
                 AT3G15650 
                 11.63 
                 25.13 
                 9.63 
                 20.65 
               
               
                 AT3G02150 
                 16.33 
                 22.41 
                 16.55 
                 20.49 
               
               
                 AT1G10560 
                 13.15 
                 18.66 
                 15.05 
                 20.25 
               
               
                 AT5G20885 
                 8.36 
                 11.31 
                 13.58 
                 20.01 
               
               
                 AT1G30900 
                 14.17 
                 22.25 
                 14.04 
                 18.91 
               
               
                 AT5G51850 
                 10.59 
                 15.80 
                 13.04 
                 17.91 
               
               
                 AT1G76185 
                 9.06 
                 12.95 
                 9.57 
                 17.54 
               
               
                 AT1G51820 
                 14.48 
                 29.13 
                 11.64 
                 17.32 
               
               
                 AT3G19400 
                 11.02 
                 21.42 
                 10.14 
                 17.18 
               
               
                 AT5G63800 
                 13.42 
                 20.95 
                 14.00 
                 16.50 
               
               
                 AT3G52490 
                 9.07 
                 12.77 
                 10.98 
                 15.69 
               
               
                 AT2G03740 
                 7.17 
                 24.53 
                 5.19 
                 15.60 
               
               
                 AT2G28120 
                 7.11 
                 14.95 
                 6.95 
                 15.21 
               
               
                 AT3G03470 
                 10.74 
                 11.23 
                 11.17 
                 13.91 
               
               
                 AT3G60510 
                 9.09 
                 17.53 
                 10.61 
                 13.77 
               
               
                 AT1G68400 
                 11.34 
                 20.12 
                 10.76 
                 13.07 
               
               
                 AT5G01590 
                 8.10 
                 15.68 
                 7.19 
                 11.21 
               
               
                 AT1G12080 
                 5.10 
                 19.09 
                 5.14 
                 10.96 
               
               
                 AT2G31380 
                 10.73 
                 17.66 
                 9.54 
                 10.27 
               
               
                 AT1G11780 
                 7.50 
                 8.31 
                 7.75 
                 10.21 
               
               
                 AT1G63710 
                 6.48 
                 11.95 
                 6.23 
                 9.70 
               
               
                 AT4G16690 
                 6.14 
                 8.67 
                 6.33 
                 9.51 
               
               
                 AT3G01270 
                 7.93 
                 13.97 
                 6.75 
                 9.12 
               
               
                 AT2G01860 
                 6.16 
                 8.89 
                 6.91 
                 9.11 
               
               
                 AT5G03350 
                 6.09 
                 8.50 
                 5.72 
                 8.74 
               
               
                 AT2G10640 
                 7.04 
                 14.98 
                 5.78 
                 8.73 
               
               
                 AT4G01110 
                 7.63 
                 8.89 
                 7.20 
                 8.58 
               
               
                 AT3G30396 
                 7.82 
                 14.39 
                 6.03 
                 8.50 
               
               
                 AT3G18980 
                 7.17 
                 8.50 
                 7.11 
                 8.38 
               
               
                 AT5G04310 
                 5.80 
                 7.82 
                 5.66 
                 8.19 
               
               
                 AT1G20340 
                 4.92 
                 16.33 
                 4.92 
                 8.19 
               
               
                 AT4G19810 
                 6.62 
                 7.83 
                 6.37 
                 7.42 
               
               
                 AT1G03600 
                 5.81 
                 7.32 
                 5.90 
                 6.94 
               
               
                 AT2G28630 
                 6.31 
                 12.16 
                 5.64 
                 6.79 
               
               
                 AT4G38200 
                 5.45 
                 5.78 
                 5.70 
                 6.77 
               
               
                 AT3G28510 
                 5.31 
                 6.30 
                 5.30 
                 6.55 
               
               
                 AT1G02670 
                 4.97 
                 7.19 
                 5.44 
                 6.53 
               
               
                 AT5G04630 
                 5.19 
                 5.07 
                 5.16 
                 6.43 
               
               
                 AT3G24310 
                 5.10 
                 5.34 
                 5.26 
                 6.31 
               
               
                 AT2G41200 
                 5.07 
                 5.59 
                 4.99 
                 5.81 
               
               
                 B. Genes that are 
                   
                   
                   
                   
               
               
                 down-regulated by 
                   
                   
                   
                   
               
               
                 DEX (FDR &lt; 0.05) 
                   
                   
                   
                   
               
               
                 AT2G38470 
                 10594.94 
                 9805.00 
                 10690.91 
                 9439.25 
               
               
                 AT3G57450 
                 10275.67 
                 9151.09 
                 9958.55 
                 8270.15 
               
               
                 AT3G45640 
                 8895.22 
                 8082.87 
                 8991.34 
                 7649.50 
               
               
                 AT2G41730 
                 7745.15 
                 7011.42 
                 7278.40 
                 6457.43 
               
               
                 AT4G30280 
                 7638.56 
                 7227.50 
                 7735.48 
                 6672.97 
               
               
                 AT2G38870 
                 7550.52 
                 5944.54 
                 6578.59 
                 5449.26 
               
               
                 AT5G64310 
                 7247.82 
                 6331.15 
                 7483.09 
                 6501.53 
               
               
                 AT5G02230 
                 7230.54 
                 6000.23 
                 7098.06 
                 5757.55 
               
               
                 AT1G30370 
                 7198.83 
                 6096.88 
                 6392.67 
                 4996.87 
               
               
                 AT2G35980 
                 6887.25 
                 5915.12 
                 6900.24 
                 6080.70 
               
               
                 AT2G17660 
                 6519.25 
                 6035.21 
                 7218.16 
                 6322.89 
               
               
                 AT1G14540 
                 6503.27 
                 5600.91 
                 5905.89 
                 4876.12 
               
               
                 AT5G13190 
                 6327.96 
                 5777.02 
                 6277.25 
                 5641.66 
               
               
                 AT4G12720 
                 5417.69 
                 4831.47 
                 5626.66 
                 4720.71 
               
               
                 AT3G06490 
                 5298.66 
                 4516.36 
                 5209.36 
                 4230.12 
               
               
                 AT5G19240 
                 5206.39 
                 4093.63 
                 4888.19 
                 3710.43 
               
               
                 AT1G14550 
                 5125.17 
                 3201.22 
                 3718.19 
                 2242.62 
               
               
                 AT1G78100 
                 4689.46 
                 3678.75 
                 4742.38 
                 3865.18 
               
               
                 AT4G34150 
                 4607.37 
                 4291.35 
                 4572.67 
                 3996.05 
               
               
                 AT2G27390 
                 4566.43 
                 3837.18 
                 4464.66 
                 3801.81 
               
               
                 AT4G08850 
                 4428.08 
                 4007.17 
                 4267.77 
                 3829.57 
               
               
                 AT1G56060 
                 4412.46 
                 3059.50 
                 3859.42 
                 2460.41 
               
               
                 AT3G52400 
                 4286.43 
                 3807.93 
                 4148.80 
                 3653.63 
               
               
                 AT4G40040 
                 4135.05 
                 3616.24 
                 3965.38 
                 3614.05 
               
               
                 AT4G32020 
                 3994.28 
                 3119.61 
                 3736.47 
                 3114.00 
               
               
                 AT3G53730 
                 3945.81 
                 3259.21 
                 4221.20 
                 3631.17 
               
               
                 AT5G08240 
                 3875.35 
                 3274.32 
                 3788.89 
                 3294.04 
               
               
                 AT3G62720 
                 3800.72 
                 3410.65 
                 3918.77 
                 3158.22 
               
               
                 AT1G73010 
                 3512.54 
                 2948.47 
                 4400.95 
                 3492.79 
               
               
                 AT1G70130 
                 3413.86 
                 2346.61 
                 3432.51 
                 2378.90 
               
               
                 AT5G47910 
                 3328.40 
                 3079.49 
                 3463.66 
                 2840.76 
               
               
                 AT4G02380 
                 3292.06 
                 2079.41 
                 3198.37 
                 2088.63 
               
               
                 AT2G23270 
                 3149.67 
                 1677.37 
                 2305.40 
                 1208.21 
               
               
                 AT5G41810 
                 3111.61 
                 2679.01 
                 3039.98 
                 2659.79 
               
               
                 AT4G17230 
                 3054.74 
                 2738.50 
                 3105.45 
                 2656.17 
               
               
                 AT2G30130 
                 2997.40 
                 2304.29 
                 3366.78 
                 2457.53 
               
               
                 AT2G22500 
                 2981.76 
                 2536.55 
                 3104.64 
                 2641.18 
               
               
                 AT3G02800 
                 2956.62 
                 2435.58 
                 2501.23 
                 2086.28 
               
               
                 AT2G31880 
                 2880.46 
                 2387.48 
                 2754.07 
                 2290.80 
               
               
                 AT4G11360 
                 2822.28 
                 2152.72 
                 2401.20 
                 1756.26 
               
               
                 AT3G21070 
                 2814.10 
                 2300.53 
                 2588.43 
                 2215.90 
               
               
                 AT1G06760 
                 2776.71 
                 2378.31 
                 2853.96 
                 2519.50 
               
               
                 AT1G51920 
                 2773.17 
                 1979.42 
                 2214.57 
                 1517.34 
               
               
                 AT3G24550 
                 2722.50 
                 2655.04 
                 2851.78 
                 2564.13 
               
               
                 AT3G02880 
                 2715.25 
                 2563.73 
                 2713.98 
                 2352.20 
               
               
                 AT5G51190 
                 2664.80 
                 2220.62 
                 2418.21 
                 1944.26 
               
               
                 AT1G11210 
                 2645.36 
                 2160.38 
                 3164.87 
                 2356.86 
               
               
                 AT2G06050 
                 2616.60 
                 2165.16 
                 2711.72 
                 2128.88 
               
               
                 AT2G01450 
                 2579.51 
                 2177.06 
                 2716.31 
                 2140.39 
               
               
                 AT5G44610 
                 2554.63 
                 2138.70 
                 2434.61 
                 1936.00 
               
               
                 AT5G62350 
                 2356.45 
                 1655.92 
                 2504.33 
                 1559.98 
               
               
                 AT4G22470 
                 2292.25 
                 1969.35 
                 2081.97 
                 1738.58 
               
               
                 AT2G22470 
                 2273.65 
                 1776.05 
                 2061.53 
                 1672.60 
               
               
                 AT1G52200 
                 2223.03 
                 1509.49 
                 1794.15 
                 1240.12 
               
               
                 AT4G39260 
                 2222.20 
                 1848.46 
                 2425.54 
                 2171.34 
               
               
                 AT5G66070 
                 2187.98 
                 1822.99 
                 2143.00 
                 1836.79 
               
               
                 AT4G01850 
                 2159.94 
                 1177.09 
                 1656.44 
                 936.20 
               
               
                 AT4G37910 
                 2039.79 
                 1589.72 
                 1708.63 
                 1426.12 
               
               
                 AT4G24160 
                 1998.33 
                 1756.43 
                 1899.18 
                 1586.29 
               
               
                 AT4G32060 
                 1969.28 
                 1557.50 
                 1840.41 
                 1513.36 
               
               
                 AT2G19570 
                 1967.42 
                 1602.44 
                 1658.96 
                 1249.48 
               
               
                 AT5G61210 
                 1920.02 
                 1836.03 
                 1854.71 
                 1498.34 
               
               
                 AT5G07310 
                 1917.88 
                 1485.37 
                 2045.93 
                 1539.41 
               
               
                 AT1G13340 
                 1867.19 
                 1491.57 
                 1944.69 
                 1536.05 
               
               
                 AT2G17220 
                 1821.13 
                 1578.15 
                 1680.18 
                 1256.00 
               
               
                 AT1G80820 
                 1802.73 
                 1554.35 
                 1839.63 
                 1563.73 
               
               
                 AT3G13650 
                 1722.32 
                 901.05 
                 1328.90 
                 762.96 
               
               
                 AT5G48540 
                 1708.97 
                 1409.01 
                 1678.11 
                 1375.50 
               
               
                 AT1G04440 
                 1701.41 
                 1560.40 
                 1762.71 
                 1487.92 
               
               
                 AT3G55960 
                 1694.09 
                 1446.07 
                 1693.87 
                 1399.27 
               
               
                 AT4G30290 
                 1653.42 
                 1210.90 
                 2032.78 
                 1267.09 
               
               
                 AT4G28350 
                 1653.13 
                 1171.60 
                 1439.88 
                 1176.22 
               
               
                 AT3G11820 
                 1600.50 
                 1325.60 
                 1566.12 
                 1278.85 
               
               
                 AT1G59910 
                 1591.72 
                 1364.44 
                 1646.71 
                 1393.59 
               
               
                 AT5G07620 
                 1569.64 
                 1126.48 
                 1339.31 
                 1038.34 
               
               
                 AT5G44070 
                 1567.49 
                 1174.12 
                 1195.05 
                 1001.80 
               
               
                 AT3G17020 
                 1555.88 
                 1411.42 
                 1574.25 
                 1369.51 
               
               
                 AT3G59080 
                 1536.13 
                 1236.25 
                 1350.16 
                 1102.62 
               
               
                 AT3G61390 
                 1524.35 
                 1139.96 
                 1463.77 
                 830.00 
               
               
                 AT5G60680 
                 1522.99 
                 1052.96 
                 1329.86 
                 1009.48 
               
               
                 AT4G22820 
                 1520.78 
                 1316.01 
                 1544.71 
                 1311.00 
               
               
                 AT4G40030 
                 1509.28 
                 1144.40 
                 1388.30 
                 1028.36 
               
               
                 AT2G28570 
                 1453.74 
                 1102.83 
                 1338.15 
                 1081.58 
               
               
                 AT1G16670 
                 1432.88 
                 1244.29 
                 1390.31 
                 1188.06 
               
               
                 AT1G55920 
                 1416.03 
                 1028.24 
                 1171.04 
                 960.14 
               
               
                 AT5G39670 
                 1332.60 
                 1026.04 
                 1354.50 
                 999.29 
               
               
                 AT2G25735 
                 1322.34 
                 1095.95 
                 1075.97 
                 794.10 
               
               
                 AT1G28190 
                 1320.00 
                 1083.64 
                 1321.61 
                 1112.49 
               
               
                 AT1G72060 
                 1292.51 
                 1074.21 
                 1075.49 
                 836.87 
               
               
                 AT5G62390 
                 1283.87 
                 1092.32 
                 1285.84 
                 1090.86 
               
               
                 AT3G18250 
                 1276.11 
                 843.37 
                 941.65 
                 678.63 
               
               
                 AT4G18880 
                 1273.25 
                 1066.78 
                 1254.86 
                 948.83 
               
               
                 AT3G49720 
                 1223.58 
                 1045.45 
                 1140.05 
                 960.26 
               
               
                 AT2G25250 
                 1156.23 
                 798.81 
                 1091.29 
                 789.02 
               
               
                 AT1G02400 
                 1125.76 
                 824.28 
                 1042.52 
                 815.59 
               
               
                 AT3G50900 
                 1123.55 
                 910.84 
                 1304.73 
                 953.10 
               
               
                 AT1G17370 
                 1117.83 
                 820.42 
                 998.40 
                 784.41 
               
               
                 AT5G65020 
                 1116.90 
                 955.98 
                 1226.70 
                 1082.21 
               
               
                 AT4G25030 
                 1106.98 
                 910.25 
                 898.93 
                 760.64 
               
               
                 AT5G49620 
                 1094.51 
                 923.27 
                 1155.71 
                 887.29 
               
               
                 AT5G66880 
                 1075.21 
                 846.26 
                 1061.06 
                 939.67 
               
               
                 AT4G34180 
                 1054.26 
                 916.35 
                 957.82 
                 882.79 
               
               
                 AT3G22160 
                 1027.28 
                 773.11 
                 897.50 
                 660.04 
               
               
                 AT3G10640 
                 1011.64 
                 891.22 
                 960.27 
                 772.48 
               
               
                 AT5G58110 
                 1009.27 
                 882.17 
                 1068.85 
                 822.53 
               
               
                 AT1G72070 
                 991.01 
                 759.65 
                 756.53 
                 543.38 
               
               
                 AT2G26380 
                 986.98 
                 727.38 
                 841.17 
                 548.62 
               
               
                 AT5G06720 
                 979.96 
                 470.49 
                 598.64 
                 278.98 
               
               
                 AT3G52360 
                 912.90 
                 699.55 
                 1017.10 
                 882.60 
               
               
                 AT4G30470 
                 894.34 
                 752.07 
                 1057.46 
                 688.34 
               
               
                 AT4G37180 
                 889.54 
                 672.72 
                 918.95 
                 755.82 
               
               
                 AT5G57340 
                 881.06 
                 713.57 
                 951.94 
                 693.08 
               
               
                 AT3G44720 
                 874.87 
                 704.84 
                 803.58 
                 638.68 
               
               
                 AT1G18210 
                 865.92 
                 721.87 
                 841.77 
                 668.69 
               
               
                 AT4G37900 
                 847.54 
                 719.50 
                 577.15 
                 462.63 
               
               
                 AT4G38420 
                 832.76 
                 469.66 
                 572.49 
                 293.99 
               
               
                 AT3G09020 
                 817.18 
                 715.83 
                 739.90 
                 575.96 
               
               
                 AT5G26030 
                 800.07 
                 590.54 
                 678.60 
                 552.31 
               
               
                 AT3G08760 
                 796.60 
                 564.43 
                 743.38 
                 551.95 
               
               
                 AT3G21230 
                 790.87 
                 554.21 
                 669.69 
                 431.90 
               
               
                 AT1G32350 
                 774.03 
                 454.60 
                 499.64 
                 344.20 
               
               
                 AT2G32030 
                 770.33 
                 558.70 
                 609.13 
                 426.36 
               
               
                 AT5G60350 
                 757.40 
                 531.49 
                 814.90 
                 509.35 
               
               
                 AT1G51915 
                 752.57 
                 369.57 
                 551.41 
                 272.93 
               
               
                 AT1G09920 
                 750.89 
                 629.51 
                 570.88 
                 531.45 
               
               
                 AT2G39660 
                 749.80 
                 565.80 
                 707.07 
                 492.75 
               
               
                 AT1G78340 
                 729.18 
                 554.44 
                 642.19 
                 535.97 
               
               
                 AT3G54150 
                 727.23 
                 552.33 
                 660.76 
                 486.37 
               
               
                 AT5G37770 
                 718.69 
                 580.26 
                 685.02 
                 541.13 
               
               
                 AT1G20510 
                 706.29 
                 597.83 
                 783.87 
                 542.51 
               
               
                 AT2G19190 
                 685.28 
                 400.28 
                 553.52 
                 376.68 
               
               
                 AT1G18890 
                 678.67 
                 590.44 
                 785.53 
                 608.15 
               
               
                 AT5G14930 
                 677.86 
                 497.36 
                 720.33 
                 477.00 
               
               
                 AT3G54200 
                 669.01 
                 578.02 
                 677.09 
                 506.17 
               
               
                 AT1G73510 
                 666.96 
                 518.32 
                 417.74 
                 307.73 
               
               
                 AT4G31780 
                 661.82 
                 508.60 
                 656.34 
                 477.88 
               
               
                 AT3G05490 
                 657.57 
                 387.27 
                 502.10 
                 374.36 
               
               
                 AT1G63830 
                 650.19 
                 546.39 
                 642.66 
                 480.94 
               
               
                 AT3G28580 
                 647.41 
                 558.14 
                 727.50 
                 526.40 
               
               
                 AT5G39680 
                 642.29 
                 368.12 
                 352.34 
                 206.80 
               
               
                 AT4G24390 
                 636.82 
                 379.19 
                 424.50 
                 269.58 
               
               
                 AT5G42830 
                 630.34 
                 319.86 
                 363.41 
                 229.22 
               
               
                 AT4G28085 
                 624.10 
                 500.53 
                 545.49 
                 449.97 
               
               
                 AT1G09940 
                 619.64 
                 520.36 
                 623.27 
                 495.64 
               
               
                 AT2G24180 
                 614.05 
                 486.07 
                 674.28 
                 520.77 
               
               
                 AT2G26290 
                 611.67 
                 428.70 
                 605.78 
                 441.57 
               
               
                 AT3G04120 
                 598.45 
                 487.62 
                 571.67 
                 505.88 
               
               
                 AT4G37730 
                 590.41 
                 387.61 
                 477.88 
                 298.68 
               
               
                 AT1G51620 
                 589.71 
                 397.80 
                 544.85 
                 392.83 
               
               
                 AT4G30530 
                 586.26 
                 446.12 
                 544.76 
                 414.90 
               
               
                 AT2G20960 
                 582.08 
                 455.39 
                 507.30 
                 397.68 
               
               
                 AT4G33300 
                 577.05 
                 444.58 
                 530.56 
                 412.41 
               
               
                 AT3G10630 
                 572.60 
                 447.96 
                 428.14 
                 305.24 
               
               
                 AT1G19220 
                 567.55 
                 359.63 
                 469.34 
                 391.68 
               
               
                 AT1G74590 
                 566.35 
                 322.51 
                 478.94 
                 298.72 
               
               
                 AT2G42350 
                 552.15 
                 400.88 
                 505.70 
                 405.11 
               
               
                 AT2G26190 
                 540.73 
                 404.79 
                 481.87 
                 356.94 
               
               
                 AT2G39110 
                 538.72 
                 429.26 
                 558.14 
                 369.80 
               
               
                 AT1G11310 
                 537.13 
                 491.58 
                 514.83 
                 415.15 
               
               
                 AT2G41630 
                 535.84 
                 443.16 
                 541.46 
                 421.65 
               
               
                 AT3G47550 
                 527.25 
                 450.86 
                 543.54 
                 436.06 
               
               
                 AT4G00330 
                 517.44 
                 441.24 
                 499.60 
                 354.96 
               
               
                 AT2G38830 
                 513.49 
                 403.57 
                 440.46 
                 328.92 
               
               
                 AT4G37940 
                 506.95 
                 427.75 
                 507.13 
                 447.15 
               
               
                 AT3G08710 
                 506.90 
                 409.13 
                 464.95 
                 366.87 
               
               
                 AT5G62630 
                 505.16 
                 417.40 
                 449.98 
                 328.76 
               
               
                 AT5G51390 
                 500.46 
                 316.95 
                 473.91 
                 283.61 
               
               
                 AT2G21120 
                 490.38 
                 428.08 
                 506.41 
                 417.25 
               
               
                 AT3G55630 
                 480.92 
                 339.84 
                 277.84 
                 198.71 
               
               
                 AT5G41100 
                 479.59 
                 388.13 
                 397.73 
                 320.80 
               
               
                 AT2G43000 
                 476.73 
                 217.41 
                 281.93 
                 127.29 
               
               
                 AT4G11350 
                 473.60 
                 370.33 
                 422.41 
                 394.08 
               
               
                 AT4G16780 
                 469.56 
                 300.33 
                 378.03 
                 236.91 
               
               
                 AT5G04720 
                 448.61 
                 368.00 
                 406.96 
                 337.63 
               
               
                 AT2G46140 
                 439.56 
                 347.42 
                 407.54 
                 279.81 
               
               
                 AT4G36900 
                 437.23 
                 362.76 
                 496.33 
                 369.50 
               
               
                 AT2G42430 
                 436.12 
                 313.08 
                 401.95 
                 295.15 
               
               
                 AT5G59510 
                 427.55 
                 250.69 
                 417.49 
                 218.37 
               
               
                 AT2G47130 
                 418.63 
                 310.91 
                 388.64 
                 238.18 
               
               
                 AT3G48090 
                 417.97 
                 371.87 
                 453.22 
                 357.78 
               
               
                 AT4G18890 
                 417.22 
                 378.73 
                 425.34 
                 345.77 
               
               
                 AT3G61850 
                 416.47 
                 307.85 
                 502.52 
                 311.56 
               
               
                 AT2G39700 
                 415.94 
                 312.42 
                 314.64 
                 262.48 
               
               
                 AT4G39890 
                 413.32 
                 343.49 
                 419.01 
                 295.70 
               
               
                 AT5G59480 
                 408.82 
                 251.29 
                 324.14 
                 202.63 
               
               
                 AT5G45750 
                 402.86 
                 343.76 
                 360.93 
                 285.44 
               
               
                 AT5G60250 
                 401.41 
                 302.26 
                 322.78 
                 233.26 
               
               
                 AT3G09270 
                 395.41 
                 298.12 
                 336.49 
                 238.53 
               
               
                 AT1G71450 
                 394.30 
                 191.87 
                 215.77 
                 136.56 
               
               
                 AT1G10160 
                 384.80 
                 242.75 
                 234.68 
                 206.77 
               
               
                 AT1G65690 
                 384.45 
                 291.73 
                 338.94 
                 280.36 
               
               
                 AT1G24140 
                 376.60 
                 282.18 
                 369.70 
                 244.70 
               
               
                 AT4G02200 
                 375.43 
                 306.60 
                 344.27 
                 252.99 
               
               
                 AT4G29670 
                 374.13 
                 285.58 
                 360.31 
                 292.47 
               
               
                 AT4G14368 
                 372.74 
                 299.65 
                 250.04 
                 185.77 
               
               
                 AT1G34750 
                 371.50 
                 331.40 
                 383.80 
                 302.44 
               
               
                 AT5G54170 
                 368.19 
                 277.24 
                 379.24 
                 282.00 
               
               
                 AT4G31000 
                 366.31 
                 244.84 
                 283.94 
                 217.10 
               
               
                 AT5G12880 
                 364.45 
                 296.84 
                 344.63 
                 228.53 
               
               
                 AT1G79160 
                 359.73 
                 250.73 
                 377.09 
                 258.36 
               
               
                 AT1G18860 
                 355.43 
                 239.05 
                 237.25 
                 162.56 
               
               
                 AT2G17120 
                 354.39 
                 243.88 
                 280.12 
                 224.50 
               
               
                 AT5G66640 
                 352.37 
                 224.36 
                 297.84 
                 170.23 
               
               
                 AT3G54040 
                 352.28 
                 235.31 
                 288.67 
                 169.22 
               
               
                 AT5G24620 
                 349.85 
                 279.62 
                 286.06 
                 257.58 
               
               
                 AT4G23010 
                 346.37 
                 284.66 
                 326.72 
                 216.42 
               
               
                 AT1G70530 
                 330.15 
                 264.52 
                 340.91 
                 262.10 
               
               
                 AT4G01720 
                 329.46 
                 195.87 
                 290.78 
                 169.55 
               
               
                 AT2G26560 
                 328.67 
                 217.69 
                 238.05 
                 148.38 
               
               
                 AT2G19710 
                 321.11 
                 275.00 
                 305.59 
                 252.88 
               
               
                 AT3G28740 
                 320.29 
                 195.94 
                 326.46 
                 209.90 
               
               
                 AT4G21390 
                 318.39 
                 254.61 
                 322.11 
                 249.73 
               
               
                 AT3G55950 
                 314.00 
                 208.52 
                 276.03 
                 198.12 
               
               
                 AT5G65870 
                 313.09 
                 207.66 
                 295.96 
                 209.03 
               
               
                 AT1G53430 
                 311.41 
                 218.88 
                 263.74 
                 162.28 
               
               
                 AT1G57630 
                 301.78 
                 179.80 
                 292.68 
                 189.47 
               
               
                 AT5G01540 
                 296.89 
                 218.77 
                 286.07 
                 206.48 
               
               
                 AT5G53130 
                 290.17 
                 253.21 
                 273.00 
                 217.14 
               
               
                 AT1G75540 
                 289.25 
                 229.29 
                 284.86 
                 267.65 
               
               
                 AT2G16430 
                 288.37 
                 242.09 
                 340.20 
                 274.37 
               
               
                 AT2G24240 
                 285.10 
                 179.59 
                 310.84 
                 197.68 
               
               
                 AT2G47140 
                 274.18 
                 144.79 
                 162.65 
                 85.14 
               
               
                 AT4G30210 
                 271.35 
                 213.19 
                 253.06 
                 190.97 
               
               
                 AT4G39940 
                 263.87 
                 201.21 
                 161.80 
                 131.95 
               
               
                 AT3G21080 
                 263.37 
                 158.47 
                 191.66 
                 96.73 
               
               
                 AT3G25070 
                 260.11 
                 185.94 
                 248.21 
                 168.51 
               
               
                 AT1G17310 
                 259.77 
                 180.69 
                 208.28 
                 171.07 
               
               
                 AT3G52430 
                 259.01 
                 182.07 
                 316.62 
                 174.16 
               
               
                 AT3G05510 
                 254.46 
                 156.80 
                 167.87 
                 152.16 
               
               
                 AT1G07130 
                 252.68 
                 188.29 
                 259.23 
                 185.23 
               
               
                 AT4G12070 
                 251.34 
                 182.24 
                 238.72 
                 212.56 
               
               
                 AT3G29670 
                 245.29 
                 195.88 
                 260.11 
                 214.41 
               
               
                 AT5G24430 
                 242.79 
                 172.19 
                 249.47 
                 172.19 
               
               
                 AT5G44350 
                 237.68 
                 182.15 
                 249.92 
                 175.38 
               
               
                 AT3G02790 
                 237.46 
                 154.39 
                 218.06 
                 166.72 
               
               
                 AT3G03020 
                 235.62 
                 167.21 
                 208.94 
                 173.60 
               
               
                 AT4G40020 
                 233.07 
                 172.14 
                 187.39 
                 145.78 
               
               
                 AT3G43250 
                 230.33 
                 168.91 
                 216.98 
                 138.94 
               
               
                 AT5G22530 
                 227.62 
                 149.07 
                 210.52 
                 102.89 
               
               
                 AT2G01150 
                 226.39 
                 183.45 
                 300.00 
                 200.26 
               
               
                 AT3G59900 
                 224.19 
                 143.94 
                 119.47 
                 108.04 
               
               
                 AT2G27690 
                 223.63 
                 173.37 
                 229.40 
                 140.60 
               
               
                 AT5G40010 
                 223.44 
                 149.11 
                 179.26 
                 112.00 
               
               
                 AT3G20510 
                 220.97 
                 185.82 
                 197.76 
                 157.64 
               
               
                 AT1G18570 
                 215.25 
                 167.37 
                 173.04 
                 121.02 
               
               
                 AT1G07000 
                 212.12 
                 189.78 
                 224.52 
                 166.21 
               
               
                 AT1G61560 
                 206.08 
                 111.67 
                 134.07 
                 78.72 
               
               
                 AT5G46710 
                 204.13 
                 115.24 
                 178.68 
                 98.07 
               
               
                 AT1G08510 
                 202.66 
                 158.09 
                 182.44 
                 166.13 
               
               
                 AT3G11840 
                 200.71 
                 146.58 
                 164.44 
                 123.71 
               
               
                 AT4G00080 
                 200.58 
                 139.69 
                 241.23 
                 160.09 
               
               
                 AT1G61370 
                 198.89 
                 161.66 
                 184.72 
                 130.95 
               
               
                 AT5G43520 
                 196.01 
                 137.87 
                 113.86 
                 85.56 
               
               
                 AT3G07390 
                 194.86 
                 130.69 
                 122.34 
                 91.62 
               
               
                 AT3G23090 
                 187.47 
                 130.73 
                 152.74 
                 118.35 
               
               
                 AT2G44090 
                 187.45 
                 138.06 
                 158.65 
                 115.52 
               
               
                 AT3G47380 
                 184.44 
                 82.64 
                 149.15 
                 70.09 
               
               
                 AT4G11850 
                 175.57 
                 124.51 
                 143.86 
                 117.19 
               
               
                 AT3G19630 
                 175.34 
                 126.04 
                 183.13 
                 146.21 
               
               
                 AT2G41890 
                 172.57 
                 103.33 
                 202.75 
                 115.01 
               
               
                 AT3G16030 
                 172.35 
                 117.74 
                 137.15 
                 97.15 
               
               
                 AT5G22690 
                 170.36 
                 144.46 
                 158.94 
                 116.55 
               
               
                 AT1G74870 
                 166.63 
                 95.53 
                 99.13 
                 70.00 
               
               
                 AT1G73066 
                 165.80 
                 111.21 
                 123.41 
                 95.52 
               
               
                 AT1G05060 
                 165.30 
                 80.42 
                 131.75 
                 65.50 
               
               
                 AT1G44830 
                 163.47 
                 72.94 
                 126.20 
                 56.04 
               
               
                 AT3G14360 
                 159.92 
                 70.48 
                 109.23 
                 66.97 
               
               
                 AT1G07520 
                 159.28 
                 135.21 
                 149.96 
                 112.75 
               
               
                 AT4G01700 
                 158.84 
                 88.10 
                 131.39 
                 73.00 
               
               
                 AT5G10400 
                 158.79 
                 103.88 
                 124.58 
                 86.10 
               
               
                 AT3G63390 
                 157.00 
                 98.40 
                 107.62 
                 104.12 
               
               
                 AT2G11520 
                 148.26 
                 116.99 
                 126.40 
                 105.06 
               
               
                 AT3G53130 
                 146.81 
                 130.51 
                 175.82 
                 112.17 
               
               
                 AT2G34930 
                 144.25 
                 81.36 
                 130.87 
                 61.45 
               
               
                 AT1G29250 
                 140.47 
                 89.92 
                 101.42 
                 95.01 
               
               
                 AT1G30040 
                 140.10 
                 84.66 
                 120.28 
                 64.56 
               
               
                 AT2G39530 
                 137.58 
                 83.44 
                 84.55 
                 50.39 
               
               
                 AT1G32690 
                 137.33 
                 97.19 
                 110.85 
                 84.09 
               
               
                 AT2G42360 
                 137.30 
                 82.50 
                 142.29 
                 78.23 
               
               
                 AT2G22680 
                 134.47 
                 104.98 
                 141.50 
                 109.21 
               
               
                 AT3G02770 
                 133.37 
                 110.31 
                 139.56 
                 90.55 
               
               
                 AT5G57500 
                 132.87 
                 62.88 
                 78.12 
                 45.79 
               
               
                 AT2G37940 
                 132.34 
                 112.90 
                 132.46 
                 114.85 
               
               
                 AT4G21780 
                 128.86 
                 99.03 
                 110.50 
                 78.21 
               
               
                 AT1G80530 
                 127.35 
                 88.43 
                 128.13 
                 70.73 
               
               
                 AT5G62680 
                 127.34 
                 88.09 
                 107.42 
                 78.22 
               
               
                 AT1G66090 
                 124.24 
                 84.29 
                 110.97 
                 71.78 
               
               
                 AT1G48320 
                 123.74 
                 65.39 
                 90.36 
                 48.64 
               
               
                 AT3G27110 
                 120.14 
                 98.59 
                 116.86 
                 95.35 
               
               
                 AT3G23820 
                 119.79 
                 114.87 
                 144.10 
                 108.77 
               
               
                 AT1G74710 
                 119.70 
                 78.43 
                 128.49 
                 75.38 
               
               
                 AT2G37840 
                 119.50 
                 93.26 
                 118.62 
                 92.18 
               
               
                 AT5G48175 
                 115.84 
                 87.46 
                 96.02 
                 69.89 
               
               
                 AT3G09405 
                 115.62 
                 72.35 
                 102.70 
                 47.74 
               
               
                 AT1G07750 
                 113.10 
                 83.54 
                 125.44 
                 86.83 
               
               
                 AT5G09980 
                 110.04 
                 75.78 
                 106.56 
                 64.75 
               
               
                 AT3G53280 
                 109.25 
                 49.15 
                 81.72 
                 45.51 
               
               
                 AT3G01820 
                 108.90 
                 78.79 
                 97.13 
                 73.82 
               
               
                 AT2G44450 
                 107.93 
                 81.49 
                 100.31 
                 62.24 
               
               
                 AT3G44735 
                 105.44 
                 70.03 
                 84.11 
                 62.64 
               
               
                 AT1G53980 
                 103.44 
                 57.11 
                 81.68 
                 40.82 
               
               
                 AT3G17700 
                 102.91 
                 70.63 
                 83.73 
                 57.39 
               
               
                 AT2G16500 
                 102.35 
                 70.20 
                 91.71 
                 74.38 
               
               
                 AT5G10750 
                 101.55 
                 65.81 
                 97.39 
                 74.41 
               
               
                 AT5G60800 
                 101.43 
                 63.70 
                 94.64 
                 66.92 
               
               
                 AT1G10650 
                 100.69 
                 70.18 
                 116.03 
                 74.97 
               
               
                 AT1G53440 
                 99.13 
                 61.54 
                 86.87 
                 42.22 
               
               
                 AT1G16380 
                 98.90 
                 59.21 
                 53.67 
                 40.07 
               
               
                 AT3G04630 
                 98.30 
                 65.67 
                 67.35 
                 58.42 
               
               
                 AT2G40180 
                 97.56 
                 49.67 
                 70.53 
                 32.23 
               
               
                 AT5G25190 
                 96.39 
                 53.81 
                 96.36 
                 55.40 
               
               
                 AT2G45080 
                 93.74 
                 49.21 
                 97.93 
                 49.04 
               
               
                 AT3G08750 
                 93.07 
                 65.98 
                 71.04 
                 38.94 
               
               
                 AT5G63770 
                 92.87 
                 79.12 
                 115.58 
                 71.90 
               
               
                 AT3G49350 
                 92.15 
                 88.09 
                 128.98 
                 90.92 
               
               
                 AT4G09570 
                 90.60 
                 69.84 
                 86.66 
                 60.25 
               
               
                 AT2G20150 
                 89.57 
                 49.56 
                 48.52 
                 33.97 
               
               
                 AT4G37400 
                 88.98 
                 75.23 
                 94.82 
                 56.32 
               
               
                 AT2G04160 
                 88.96 
                 69.59 
                 92.04 
                 59.41 
               
               
                 AT5G52240 
                 88.72 
                 69.14 
                 68.60 
                 63.23 
               
               
                 AT1G24150 
                 82.18 
                 49.97 
                 88.44 
                 50.10 
               
               
                 AT3G03660 
                 78.51 
                 35.64 
                 51.51 
                 26.41 
               
               
                 AT1G05710 
                 78.04 
                 50.95 
                 65.42 
                 45.80 
               
               
                 AT1G28390 
                 77.59 
                 49.23 
                 62.11 
                 56.64 
               
               
                 AT4G02330 
                 76.52 
                 32.55 
                 59.17 
                 21.47 
               
               
                 AT5G41680 
                 76.34 
                 44.71 
                 85.15 
                 58.78 
               
               
                 AT3G48850 
                 76.26 
                 26.22 
                 41.82 
                 26.39 
               
               
                 AT1G05800 
                 76.23 
                 22.18 
                 76.25 
                 18.98 
               
               
                 AT1G53920 
                 75.05 
                 52.32 
                 55.22 
                 33.42 
               
               
                 AT2G32220 
                 74.40 
                 47.77 
                 60.82 
                 33.68 
               
               
                 AT4G39840 
                 73.11 
                 51.49 
                 70.31 
                 38.51 
               
               
                 AT2G37810 
                 73.02 
                 34.00 
                 50.68 
                 24.68 
               
               
                 AT2G22750 
                 72.42 
                 54.77 
                 62.63 
                 40.93 
               
               
                 AT2G01880 
                 70.53 
                 60.05 
                 73.81 
                 53.64 
               
               
                 AT4G19960 
                 69.95 
                 45.98 
                 45.27 
                 38.32 
               
               
                 AT4G11370 
                 69.74 
                 49.88 
                 67.25 
                 47.44 
               
               
                 AT1G05055 
                 68.76 
                 48.32 
                 57.59 
                 42.69 
               
               
                 AT4G15120 
                 68.53 
                 43.90 
                 50.95 
                 39.99 
               
               
                 AT1G52560 
                 67.76 
                 28.42 
                 83.14 
                 34.54 
               
               
                 AT4G30080 
                 66.84 
                 52.74 
                 80.29 
                 50.25 
               
               
                 AT1G29860 
                 66.78 
                 36.25 
                 46.75 
                 30.49 
               
               
                 AT4G14630 
                 64.86 
                 37.68 
                 52.74 
                 35.81 
               
               
                 AT5G38210 
                 63.74 
                 41.46 
                 55.84 
                 32.01 
               
               
                 AT5G66620 
                 63.09 
                 49.06 
                 59.64 
                 47.29 
               
               
                 AT4G38000 
                 62.11 
                 49.69 
                 79.63 
                 58.88 
               
               
                 AT5G65600 
                 61.42 
                 30.17 
                 38.14 
                 21.61 
               
               
                 AT5G07870 
                 60.63 
                 40.51 
                 56.74 
                 26.82 
               
               
                 AT2G24600 
                 60.55 
                 47.27 
                 55.85 
                 38.17 
               
               
                 AT2G26480 
                 59.95 
                 39.35 
                 67.91 
                 40.83 
               
               
                 AT2G38010 
                 59.18 
                 41.36 
                 65.07 
                 46.06 
               
               
                 AT5G58120 
                 58.25 
                 51.88 
                 50.62 
                 35.19 
               
               
                 AT1G21830 
                 58.10 
                 45.98 
                 63.22 
                 37.68 
               
               
                 AT1G77030 
                 56.83 
                 36.04 
                 38.03 
                 31.58 
               
               
                 AT1G63480 
                 56.33 
                 32.70 
                 53.25 
                 34.52 
               
               
                 AT4G28940 
                 55.88 
                 30.46 
                 27.12 
                 24.99 
               
               
                 AT2G46150 
                 55.77 
                 30.19 
                 42.67 
                 25.63 
               
               
                 AT5G41550 
                 54.53 
                 39.88 
                 47.68 
                 34.78 
               
               
                 AT3G49220 
                 54.38 
                 30.24 
                 50.59 
                 30.68 
               
               
                 AT4G17260 
                 51.13 
                 29.62 
                 34.86 
                 24.60 
               
               
                 AT3G09000 
                 50.81 
                 34.37 
                 39.21 
                 31.70 
               
               
                 AT3G27160 
                 49.43 
                 37.26 
                 45.09 
                 38.05 
               
               
                 AT4G11170 
                 44.31 
                 26.55 
                 25.21 
                 17.90 
               
               
                 AT1G44100 
                 43.23 
                 30.10 
                 50.34 
                 31.34 
               
               
                 AT5G56760 
                 43.19 
                 33.63 
                 44.35 
                 37.50 
               
               
                 AT4G34320 
                 43.13 
                 35.74 
                 39.56 
                 29.61 
               
               
                 AT1G17750 
                 42.72 
                 26.80 
                 48.52 
                 22.57 
               
               
                 AT1G70940 
                 42.16 
                 31.28 
                 50.67 
                 34.90 
               
               
                 AT2G35910 
                 41.06 
                 32.08 
                 31.72 
                 23.72 
               
               
                 AT1G59850 
                 40.89 
                 23.62 
                 35.25 
                 22.56 
               
               
                 AT5G62070 
                 39.79 
                 34.81 
                 40.01 
                 33.58 
               
               
                 AT3G50480 
                 38.95 
                 27.53 
                 26.65 
                 14.65 
               
               
                 AT1G53050 
                 35.29 
                 27.77 
                 35.59 
                 25.51 
               
               
                 AT5G13870 
                 34.95 
                 26.45 
                 38.18 
                 25.58 
               
               
                 AT1G63040 
                 33.11 
                 22.87 
                 38.04 
                 23.62 
               
               
                 AT5G67570 
                 32.93 
                 20.46 
                 25.77 
                 21.88 
               
               
                 AT1G58080 
                 32.56 
                 21.90 
                 53.15 
                 40.06 
               
               
                 AT1G73750 
                 31.67 
                 24.34 
                 27.29 
                 20.16 
               
               
                 AT4G02360 
                 31.22 
                 26.07 
                 30.44 
                 22.52 
               
               
                 AT3G10190 
                 30.27 
                 20.52 
                 25.16 
                 19.98 
               
               
                 AT4G26120 
                 30.12 
                 17.27 
                 28.82 
                 15.97 
               
               
                 AT5G58787 
                 30.05 
                 21.31 
                 38.13 
                 26.25 
               
               
                 AT4G36680 
                 28.74 
                 20.86 
                 24.64 
                 20.30 
               
               
                 AT5G22550 
                 28.35 
                 22.42 
                 27.37 
                 20.72 
               
               
                 AT1G67050 
                 25.58 
                 18.34 
                 23.54 
                 13.63 
               
               
                 AT3G60910 
                 24.33 
                 16.11 
                 20.90 
                 16.63 
               
               
                 AT3G05360 
                 24.26 
                 18.61 
                 23.71 
                 17.17 
               
               
                 AT1G57560 
                 24.10 
                 16.49 
                 19.77 
                 12.56 
               
               
                 AT2G34920 
                 23.56 
                 13.89 
                 23.48 
                 12.28 
               
               
                 AT3G20900 
                 23.47 
                 14.59 
                 21.99 
                 15.22 
               
               
                 AT4G39030 
                 23.17 
                 13.34 
                 21.70 
                 12.18 
               
               
                 AT1G68150 
                 23.14 
                 17.01 
                 26.38 
                 17.18 
               
               
                 AT1G51940 
                 22.71 
                 12.54 
                 18.28 
                 9.88 
               
               
                 AT4G40080 
                 22.23 
                 15.63 
                 20.82 
                 15.38 
               
               
                 AT1G18580 
                 21.46 
                 13.98 
                 18.34 
                 16.83 
               
               
                 AT5G07860 
                 21.44 
                 16.18 
                 23.14 
                 14.60 
               
               
                 AT1G32310 
                 21.29 
                 16.66 
                 22.55 
                 14.12 
               
               
                 AT5G24540 
                 21.22 
                 11.80 
                 11.17 
                 6.14 
               
               
                 AT1G74430 
                 20.83 
                 12.64 
                 14.95 
                 10.57 
               
               
                 AT5G52670 
                 19.63 
                 13.72 
                 21.70 
                 12.29 
               
               
                 AT1G44130 
                 19.52 
                 12.57 
                 17.14 
                 10.14 
               
               
                 AT1G24625 
                 18.35 
                 15.12 
                 16.45 
                 13.12 
               
               
                 AT1G19190 
                 17.18 
                 12.74 
                 15.52 
                 11.54 
               
               
                 AT5G44990 
                 16.17 
                 9.98 
                 12.07 
                 8.38 
               
               
                 AT3G63410 
                 15.85 
                 10.19 
                 11.73 
                 9.37 
               
               
                 AT1G60030 
                 14.88 
                 9.35 
                 12.78 
                 8.11 
               
               
                 AT3G54980 
                 14.83 
                 13.99 
                 14.70 
                 13.30 
               
               
                 AT1G35560 
                 14.73 
                 11.88 
                 17.54 
                 12.13 
               
               
                 AT2G41380 
                 14.68 
                 10.15 
                 11.08 
                 9.95 
               
               
                 AT5G38310 
                 13.79 
                 7.34 
                 7.83 
                 6.66 
               
               
                 AT1G15890 
                 13.73 
                 10.78 
                 11.14 
                 9.25 
               
               
                 AT1G09520 
                 12.31 
                 10.95 
                 10.78 
                 9.84 
               
               
                 AT1G56510 
                 11.50 
                 6.85 
                 7.35 
                 6.40 
               
               
                 AT1G36640 
                 11.24 
                 7.31 
                 7.70 
                 5.61 
               
               
                 AT1G35200 
                 11.01 
                 8.27 
                 8.33 
                 5.35 
               
               
                 AT5G40540 
                 10.60 
                 8.85 
                 11.62 
                 8.49 
               
               
                 AT4G27720 
                 10.47 
                 8.94 
                 12.78 
                 8.64 
               
               
                 AT4G33960 
                 10.43 
                 10.34 
                 12.36 
                 9.41 
               
               
                 AT2G46590 
                 10.15 
                 7.44 
                 9.91 
                 6.51 
               
               
                 AT2G21560 
                 10.04 
                 8.09 
                 14.38 
                 9.82 
               
               
                 AT1G14480 
                 9.06 
                 5.96 
                 7.07 
                 5.94 
               
               
                 AT3G50760 
                 8.95 
                 7.09 
                 8.54 
                 7.09 
               
               
                 AT2G17040 
                 8.67 
                 5.06 
                 8.13 
                 4.96 
               
               
                 AT2G19130 
                 8.62 
                 6.93 
                 7.97 
                 7.00 
               
               
                 AT1G11000 
                 8.36 
                 6.90 
                 8.58 
                 5.95 
               
               
                 AT2G16870 
                 7.87 
                 6.66 
                 6.93 
                 5.96 
               
               
                 AT3G61900 
                 6.57 
                 6.11 
                 7.57 
                 6.19 
               
               
                 AT4G23440 
                 5.43 
                 5.36 
                 6.00 
                 5.54 
               
               
                 AT4G30560 
                 5.33 
                 4.99 
                 4.92 
                 4.92 
               
               
                 AT5G39710 
                 5.21 
                 4.99 
                 4.98 
                 4.98 
               
               
                 AT2G39900 
                 5.15 
                 4.95 
                 4.98 
                 4.95 
               
               
                 AT1G55610 
                 5.00 
                 4.96 
                 5.43 
                 4.98 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 16 
               
             
            
               
                   
               
               
                 Significantly over-represented GO terms (FDR &lt; 0.01) identified for genes up- 
               
               
                 regulated or down-regulated by DEX-induced nuclear import of bZIP1 (FDR &lt; 0.05). 
               
            
           
           
               
               
               
               
            
               
                   
                 Term 
                 p-value 
                 Genes 
               
               
                   
               
            
           
           
               
            
               
                 A. Significantly over-represented GO terms in the DEX up-regulated genes 
               
            
           
           
               
               
               
               
            
               
                 GO:0009310 
                 amine catabolic 
                 0.000255 
                 AT4G33150|AT3G30775|AT2G43400|AT1G08630|AT5G43430| 
               
               
                   
                 process 
                   
                 AT1G64660|AT1G03090|AT1G65840|AT5G54080 
               
               
                 GO:0042221 
                 response to 
                 0.000255 
                 AT1G08720|AT1G08920|AT5G66400|AT2G40170|AT2G22080| 
               
               
                   
                 chemical 
                   
                 AT4G13430|AT4G37790|AT2G34600|AT1G54100|AT5G37260| 
               
               
                   
                 stimulus 
                   
                 AT3G51860|AT5G61590|AT5G47390|AT5G16970|AT2G38750| 
               
               
                   
                   
                   
                 AT4G37220|AT5G16960|AT1G04410|AT1G49670|AT3G11410| 
               
               
                   
                   
                   
                 AT4G32320|AT5G67450|AT5G07440|AT1G08090|AT5G54500| 
               
               
                   
                   
                   
                 AT5G50200|AT2G23170|AT1G08830|AT3G56240|AT1G55020| 
               
               
                   
                   
                   
                 AT4G33420|AT1G20340|AT4G27260|AT5G59220|AT1G28130| 
               
               
                   
                   
                   
                 AT2G19810|AT3G05200|AT2G46270|AT5G03720|AT3G23230| 
               
               
                   
                   
                   
                 AT5G01600|AT1G73260|AT1G08930|AT5G39040|AT5G44380| 
               
               
                   
                   
                   
                 AT1G18330|AT5G13740|AT4G30170|AT4G35770|AT1G16150| 
               
               
                   
                   
                   
                 AT1G15050|AT2G14170|AT1G80460|AT5G10450|AT1G43160| 
               
               
                   
                   
                   
                 AT4G39070|AT5G67300|AT3G14050|AT3G14990|AT4G21440| 
               
               
                   
                   
                   
                 AT1G02860|AT3G30775|AT5G18170|AT1G68850|AT4G34350| 
               
               
                   
                   
                   
                 AT2G01570|AT3G60690|AT5G05340|AT1G17190 
               
               
                 GO:0050896 
                 response to 
                 0.000255 
                 AT1G08920|AT2G43400|AT2G33150|AT5G02810|AT2G40170| 
               
               
                   
                 stimulus 
                   
                 AT2G22080|AT4G13430|AT4G37790|AT1G54100|AT1G02670| 
               
               
                   
                   
                   
                 AT5G61590|AT5G47390|AT3G54960|AT2G38750|AT4G37220| 
               
               
                   
                   
                   
                 AT5G16960|AT1G04410|AT1G49670|AT3G11410|AT4G32320| 
               
               
                   
                   
                   
                 AT5G07440|AT1G08090|AT5G54500|AT1G08830|AT1G25275| 
               
               
                   
                   
                   
                 AT3G15950|AT4G33420|AT4G27260|AT5G59220|AT1G28130| 
               
               
                   
                   
                   
                 AT5G24470|AT2G46270|AT5G03720|AT3G23230|AT1G06520| 
               
               
                   
                   
                   
                 AT5G67320|AT1G73260|AT5G39040|AT5G40780|AT4G30170| 
               
               
                   
                   
                   
                 AT4G35770|AT1G16150|AT1G31480|AT1G80460|AT5G24530| 
               
               
                   
                   
                   
                 AT1G75800|AT1G43160|AT2G39980|AT4G39070|AT3G14050| 
               
               
                   
                   
                   
                 AT3G14990|AT1G60940|AT3G15620|AT5G06980|AT1G02860| 
               
               
                   
                   
                   
                 AT3G47640|AT3G30775|AT1G68850|AT2G26280|AT5G13750| 
               
               
                   
                   
                   
                 AT3G45060|AT1G17190|AT5G67440|AT5G27350|AT1G08720| 
               
               
                   
                   
                   
                 AT5G20150|AT5G66400|AT5G47740|AT5G52250|AT4G24220| 
               
               
                   
                   
                   
                 AT2G34600|AT5G37260|AT3G51860|AT5G16970|AT3G61060| 
               
               
                   
                   
                   
                 AT3G27690|AT5G67450|AT5G47240|AT5G50200|AT2G23170| 
               
               
                   
                   
                   
                 AT4G01120|AT5G61510|AT3G56240|AT1G55020|AT1G20340| 
               
               
                   
                   
                   
                 AT5G43580|AT5G04770|AT2G39200|AT2G19810|AT3G05200| 
               
               
                   
                   
                   
                 AT5G01600|AT1G08930|AT4G37590|AT5G44380|AT1G18330| 
               
               
                   
                   
                   
                 AT5G13740|AT4G36040|AT1G15050|AT2G14170|AT1G13080| 
               
               
                   
                   
                   
                 AT5G64120|AT5G10450|AT5G20250|AT5G67300|AT2G32660| 
               
               
                   
                   
                   
                 AT4G21440|AT1G75230|AT5G18170|AT4G34350|AT2G01570| 
               
               
                   
                   
                   
                 AT3G60690|AT5G05340|AT5G61600 
               
               
                 GO:0016054 
                 organic acid 
                 0.000434 
                 AT3G30775|AT2G43400|AT2G33150|AT5G43430|AT1G64660| 
               
               
                   
                 catabolic 
                   
                 AT4G33150|AT3G51840|AT1G08630|AT5G65110|AT1G03090| 
               
               
                   
                 process 
                   
                 AT5G54080 
               
               
                 GO:0046395 
                 carboxylic acid 
                 0.000434 
                 AT3G30775|AT2G43400|AT2G33150|AT5G43430|AT1G64660| 
               
               
                   
                 catabolic 
                   
                 AT4G33150|AT3G51840|AT1G08630|AT5G65110|AT1G03090| 
               
               
                   
                 process 
                   
                 AT5G54080 
               
               
                 GO:0009063 
                 cellular amino 
                 0.000585 
                 AT4G33150|AT3G30775|AT2G43400|AT1G08630|AT5G43430| 
               
               
                   
                 acid catabolic 
                   
                 AT1G64660|AT1G03090|AT5G54080 
               
               
                   
                 process 
                   
                   
               
               
                 GO:0009628 
                 response to 
                 0.00178 
                 AT1G08720|AT1G08920|AT2G43400|AT5G02810|AT5G66400| 
               
               
                   
                 abiotic stimulus 
                   
                 AT5G52250|AT1G54100|AT5G37260|AT5G61590|AT5G47390| 
               
               
                   
                   
                   
                 AT2G38750|AT1G04410|AT3G11410|AT3G27690|AT5G67450| 
               
               
                   
                   
                   
                 AT5G07440|AT4G01120|AT5G61510|AT1G08830|AT1G25275| 
               
               
                   
                   
                   
                 AT3G56240|AT3G15950|AT1G20340|AT5G59220|AT5G24470| 
               
               
                   
                   
                   
                 AT5G03720|AT1G06520|AT5G67320|AT5G01600|AT1G73260| 
               
               
                   
                   
                   
                 AT1G08930|AT5G40780|AT4G37590|AT1G18330|AT1G31480| 
               
               
                   
                   
                   
                 AT1G80460|AT1G13080|AT5G20250|AT1G43160|AT2G39980| 
               
               
                   
                   
                   
                 AT4G39070|AT5G67300|AT1G60940|AT3G15620|AT5G06980| 
               
               
                   
                   
                   
                 AT4G21440|AT5G18170|AT2G01570|AT5G13750|AT3G45060| 
               
               
                   
                   
                   
                 AT1G17190|AT5G67440 
               
               
                 GO:0006950 
                 response to 
                 0.00375 
                 AT1G08920|AT2G33150|AT2G22080|AT1G54100|AT1G02670| 
               
               
                   
                 stress 
                   
                 AT5G61590|AT5G47390|AT3G54960|AT2G38750|AT4G37220| 
               
               
                   
                   
                   
                 AT5G16960|AT1G04410|AT1G49670|AT3G11410|AT4G32320| 
               
               
                   
                   
                   
                 AT5G07440|AT1G08830|AT3G15950|AT4G33420|AT5G59220| 
               
               
                   
                   
                   
                 AT5G03720|AT5G67320|AT1G73260|AT4G30170|AT4G35770| 
               
               
                   
                   
                   
                 AT1G43160|AT3G14050|AT1G60940|AT1G02860|AT3G47640| 
               
               
                   
                   
                   
                 AT3G30775|AT1G68850|AT2G26280|AT1G17190|AT1G08720| 
               
               
                   
                   
                   
                 AT5G20150|AT5G66400|AT5G47740|AT4G24220|AT5G37260| 
               
               
                   
                   
                   
                 AT5G16970|AT3G61060|AT5G67450|AT5G47240|AT5G50200| 
               
               
                   
                   
                   
                 AT3G56240|AT1G55020|AT5G43580|AT2G39200|AT2G19810| 
               
               
                   
                   
                   
                 AT5G01600|AT1G08930|AT5G44380|AT1G18330|AT4G36040| 
               
               
                   
                   
                   
                 AT2G14170|AT1G13080|AT5G64120|AT5G10450|AT5G20250| 
               
               
                   
                   
                   
                 AT5G67300|AT2G32660|AT4G21440|AT1G75230|AT5G18170| 
               
               
                   
                   
                   
                 AT2G01570|AT5G05340|AT5G61600 
               
               
                 GO:0006979 
                 response to 
                 0.00375 
                 AT2G19810|AT2G22080|AT5G01600|AT1G73260|AT1G08830| 
               
               
                   
                 oxidative stress 
                   
                 AT3G56240|AT5G16970|AT3G30775|AT1G68850|AT4G33420| 
               
               
                   
                   
                   
                 AT5G44380|AT4G30170|AT5G16960|AT4G35770|AT5G05340| 
               
               
                   
                   
                   
                 AT2G14170|AT1G49670|AT4G32320 
               
               
                 GO:0009081 
                 branched chain 
                 0.0044 
                 AT1G18270|AT1G10070|AT5G43430|AT1G10060|AT1G03090| 
               
               
                   
                 family amino 
                   
                 AT2G43400 
               
               
                   
                 acid metabolic 
                   
                   
               
               
                   
                 process 
                   
                   
               
               
                 GO:0044282 
                 small molecule 
                 0.00497 
                 AT3G30775|AT2G43400|AT2G33150|AT5G43430|AT3G51840| 
               
               
                   
                 catabolic 
                   
                 AT4G33150|AT5G65110|AT1G03090|AT1G18270|AT1G64660| 
               
               
                   
                 process 
                   
                 AT1G80460|AT1G08630|AT5G54080 
               
               
                 GO:0048878 
                 chemical 
                 0.00601 
                 AT3G47640|AT1G20340|AT5G24030|AT5G13740|AT2G23170| 
               
               
                   
                 homeostasis 
                   
                 AT4G27260|AT5G47560|AT3G51860|AT1G28130|AT5G01600| 
               
               
                   
                   
                   
                 AT3G56240 
               
            
           
           
               
            
               
                 B. Significantly over-represented GO terms in the DEX down-regulated genes 
               
            
           
           
               
               
               
               
            
               
                 GO:0050896 
                 response to 
                 4.68E−09 
                 AT4G23440|AT3G52360|AT4G17230|AT4G16780|AT5G24620| 
               
               
                   
                 stimulus 
                   
                 AT2G35980|AT1G80820|AT4G17260|AT2G46140|AT4G34180| 
               
               
                   
                   
                   
                 AT3G11840|AT5G62390|AT3G02880|AT3G24550|AT1G61560| 
               
               
                   
                   
                   
                 AT1G18890|AT4G02200|AT4G30080|AT5G44070|AT3G61850| 
               
               
                   
                   
                   
                 AT5G01540|AT1G11210|AT4G12720|AT1G09940|AT2G01150| 
               
               
                   
                   
                   
                 AT5G51190|AT1G13340|AT3G44720|AT2G17040|AT4G39260| 
               
               
                   
                   
                   
                 AT1G55920|AT1G20510|AT3G61900|AT4G33300|AT3G45640| 
               
               
                   
                   
                   
                 AT2G38870|AT3G25070|AT1G57630|AT1G07520|AT3G06490| 
               
               
                   
                   
                   
                 AT2G34930|AT3G17020|AT3G50480|AT5G62680|AT1G80530| 
               
               
                   
                   
                   
                 AT5G61210|AT5G44610|AT5G66070|AT2G26560|AT3G07390| 
               
               
                   
                   
                   
                 AT1G73010|AT2G40180|AT4G11360|AT1G56510|AT5G63770| 
               
               
                   
                   
                   
                 AT4G11170|AT2G41380|AT5G25190|AT5G65020|AT3G13650| 
               
               
                   
                   
                   
                 AT2G06050|AT3G52430|AT4G37910|AT1G11000|AT5G06720| 
               
               
                   
                   
                   
                 AT5G66880|AT3G59900|AT5G48540|AT1G18570|AT2G04160| 
               
               
                   
                   
                   
                 AT3G05360|AT2G39660|AT1G72060|AT5G37770|AT1G11310| 
               
               
                   
                   
                   
                 AT1G15890|AT3G48090|AT5G04720|AT4G26120|AT4G34150| 
               
               
                   
                   
                   
                 AT4G39030|AT1G52560|AT1G05710|AT5G24540|AT5G22690| 
               
               
                   
                   
                   
                 AT3G52400|AT2G17660|AT1G05055|AT3G28740|AT4G02380| 
               
               
                   
                   
                   
                 AT2G19190|AT1G52200|AT1G17750|AT1G74430|AT1G05800| 
               
               
                   
                   
                   
                 AT1G66090|AT3G17700|AT1G30040|AT4G14630|AT1G14550| 
               
               
                   
                   
                   
                 AT5G26030|AT4G11850|AT5G09980|AT5G41550|AT5G58120| 
               
               
                   
                   
                   
                 AT3G28580|AT2G38470|AT1G19220|AT4G18880|AT3G11820| 
               
               
                   
                   
                   
                 AT2G26380|AT1G74710|AT2G16870|AT2G16500|AT1G57560| 
               
               
                   
                   
                   
                 AT1G70940|AT5G47910|AT1G02400|AT5G54170|AT2G46590| 
               
               
                   
                   
                   
                 AT1G14540|AT3G09270|AT5G49620 
               
               
                 GO:0006952 
                 defense 
                 3.03E−08 
                 AT2G38870|AT3G52430|AT3G25070|AT4G11850|AT4G23440| 
               
               
                   
                 response 
                   
                 AT1G11000|AT1G57630|AT2G35980|AT1G18570|AT5G41550| 
               
               
                   
                   
                   
                 AT5G58120|AT2G38470|AT2G34930|AT3G05360|AT2G39660| 
               
               
                   
                   
                   
                 AT5G37770|AT3G11840|AT1G11310|AT3G11820|AT2G26380| 
               
               
                   
                   
                   
                 AT1G74710|AT1G61560|AT2G26560|AT1G15890|AT3G48090| 
               
               
                   
                   
                   
                 AT5G04720|AT2G16870|AT4G39030|AT5G44070|AT5G47910| 
               
               
                   
                   
                   
                 AT1G56510|AT4G12720|AT5G22690|AT4G11170|AT3G52400| 
               
               
                   
                   
                   
                 AT3G28740|AT2G19190|AT1G17750|AT4G39260|AT1G05800| 
               
               
                   
                   
                   
                 AT3G13650|AT1G66090|AT4G33300 
               
               
                 GO:0006950 
                 response to 
                 9.90E−08 
                 AT4G23440|AT2G35980|AT1G80820|AT4G17260|AT2G46140| 
               
               
                   
                 stress 
                   
                 AT4G34180|AT3G11840|AT5G62390|AT3G24550|AT1G61560| 
               
               
                   
                   
                   
                 AT4G02200|AT5G44070|AT1G11210|AT4G12720|AT1G09940| 
               
               
                   
                   
                   
                 AT1G13340|AT4G39260|AT1G55920|AT1G20510|AT4G33300| 
               
               
                   
                   
                   
                 AT3G45640|AT2G38870|AT3G25070|AT1G57630|AT3G06490| 
               
               
                   
                   
                   
                 AT2G34930|AT3G17020|AT5G44610|AT2G26560|AT1G73010| 
               
               
                   
                   
                   
                 AT1G56510|AT5G63770|AT4G11170|AT5G65020|AT3G13650| 
               
               
                   
                   
                   
                 AT2G06050|AT3G52430|AT4G37910|AT1G11000|AT5G66880| 
               
               
                   
                   
                   
                 AT5G06720|AT1G18570|AT3G05360|AT2G39660|AT1G72060| 
               
               
                   
                   
                   
                 AT5G37770|AT1G11310|AT1G15890|AT3G48090|AT5G04720| 
               
               
                   
                   
                   
                 AT4G34150|AT4G39030|AT1G52560|AT5G22690|AT3G52400| 
               
               
                   
                   
                   
                 AT1G05055|AT3G28740|AT4G02380|AT2G19190|AT1G52200| 
               
               
                   
                   
                   
                 AT1G17750|AT1G05800|AT1G66090|AT4G14630|AT1G14550| 
               
               
                   
                   
                   
                 AT5G26030|AT4G11850|AT5G41550|AT5G58120|AT2G38470| 
               
               
                   
                   
                   
                 AT3G11820|AT2G26380|AT1G74710|AT2G16870|AT2G16500| 
               
               
                   
                   
                   
                 AT5G47910|AT5G54170|AT2G46590|AT1G14540|AT5G49620 
               
               
                 GO:0051707 
                 response to 
                 1.21E−06 
                 AT3G45640|AT2G06050|AT2G38870|AT3G52430|AT3G25070| 
               
               
                   
                 other 
                   
                 AT4G11850|AT5G24620|AT2G35980|AT1G18570|AT2G38470| 
               
               
                   
                 organism 
                   
                 AT3G06490|AT2G34930|AT3G50480|AT2G39660|AT5G61210| 
               
               
                   
                   
                   
                 AT1G11310|AT3G11820|AT1G74710|AT3G24550|AT1G61560| 
               
               
                   
                   
                   
                 AT2G26560|AT3G48090|AT4G39030|AT5G44070|AT5G47910| 
               
               
                   
                   
                   
                 AT1G56510|AT4G12720|AT5G24540|AT3G52400|AT3G28740| 
               
               
                   
                   
                   
                 AT2G19190|AT1G17750|AT1G05800|AT3G17700 
               
               
                 GO:0009607 
                 response to 
                 2.35E−06 
                 AT3G45640|AT2G06050|AT2G38870|AT3G52430|AT3G25070| 
               
               
                   
                 biotic 
                   
                 AT4G11850|AT5G24620|AT2G35980|AT1G18570|AT2G38470| 
               
               
                   
                 stimulus 
                   
                 AT3G06490|AT2G34930|AT3G50480|AT2G39660|AT5G61210| 
               
               
                   
                   
                   
                 AT5G62390|AT1G11310|AT3G11820|AT1G74710|AT3G24550| 
               
               
                   
                   
                   
                 AT1G61560|AT2G26560|AT3G48090|AT4G39030|AT5G44070| 
               
               
                   
                   
                   
                 AT5G47910|AT1G56510|AT4G12720|AT5G24540|AT3G52400| 
               
               
                   
                   
                   
                 AT3G28740|AT2G19190|AT1G17750|AT1G05800|AT3G17700 
               
               
                 GO:0051704 
                 multi- 
                 2.77E−06 
                 AT3G45640|AT2G06050|AT2G38870|AT3G52430|AT3G25070| 
               
               
                   
                 organism 
                   
                 AT4G11850|AT5G24620|AT2G35980|AT1G18570|AT2G38470| 
               
               
                   
                 process 
                   
                 AT3G06490|AT2G34930|AT3G50480|AT2G39660|AT5G61210| 
               
               
                   
                   
                   
                 AT1G11310|AT3G11820|AT1G74710|AT3G24550|AT1G61560| 
               
               
                   
                   
                   
                 AT2G26560|AT3G48090|AT4G39030|AT5G44070|AT5G47910| 
               
               
                   
                   
                   
                 AT1G56510|AT4G12720|AT5G24540|AT3G52400|AT3G28740| 
               
               
                   
                   
                   
                 AT2G19190|AT1G17750|AT1G05800|AT3G17700 
               
               
                 GO:0002376 
                 immune 
                 1.12E−05 
                 AT3G48090|AT3G52430|AT2G16870|AT3G25070|AT4G11850| 
               
               
                   
                 system 
                   
                 AT4G23440|AT1G57630|AT1G56510|AT2G35980|AT4G12720| 
               
               
                   
                 process 
                   
                 AT5G41550|AT5G58120|AT5G22690|AT3G05360|AT5G37770| 
               
               
                   
                   
                   
                 AT3G11840|AT4G39260|AT1G11310|AT1G74710|AT1G66090| 
               
               
                   
                   
                   
                 AT1G61560|AT2G26560 
               
               
                 GO:0042221 
                 response to 
                 1.18E−05 
                 AT2G06050|AT3G52430|AT4G37910|AT4G17230|AT5G06720| 
               
               
                   
                 chemical 
                   
                 AT5G66880|AT3G59900|AT4G16780|AT1G18570|AT2G04160| 
               
               
                   
                 stimulus 
                   
                 AT4G17260|AT2G46140|AT1G72060|AT5G37770|AT3G11840| 
               
               
                   
                   
                   
                 AT5G62390|AT3G02880|AT3G48090|AT4G26120|AT1G18890| 
               
               
                   
                   
                   
                 AT4G02200|AT4G30080|AT5G44070|AT5G01540|AT1G52560| 
               
               
                   
                   
                   
                 AT1G11210|AT1G05710|AT4G12720|AT1G09940|AT5G51190| 
               
               
                   
                   
                   
                 AT3G52400|AT1G13340|AT2G17660|AT4G02380|AT1G52200| 
               
               
                   
                   
                   
                 AT2G17040|AT1G17750|AT4G39260|AT1G74430|AT3G61900| 
               
               
                   
                   
                   
                 AT3G45640|AT1G14550|AT3G25070|AT5G26030|AT1G07520| 
               
               
                   
                   
                   
                 AT5G09980|AT3G28580|AT2G38470|AT3G06490|AT1G19220| 
               
               
                   
                   
                   
                 AT4G18880|AT5G61210|AT5G44610|AT3G11820|AT5G66070| 
               
               
                   
                   
                   
                 AT2G26560|AT3G07390|AT2G16500|AT1G57560|AT2G40180| 
               
               
                   
                   
                   
                 AT4G11360|AT4G11170|AT2G41380|AT5G25190|AT1G14540| 
               
               
                   
                   
                   
                 AT5G65020|AT3G09270|AT5G49620 
               
               
                 GO:0031348 
                 negative 
                 3.00E−05 
                 AT3G25070|AT1G11310|AT3G52400|AT3G11820|AT4G39030| 
               
               
                   
                 regulation of 
                   
                 AT1G74710|AT3G52430 
               
               
                   
                 defense 
                   
                   
               
               
                   
                 response 
                   
                   
               
               
                 GO:0045087 
                 innate 
                 6.55E−05 
                 AT3G48090|AT3G52430|AT2G16870|AT3G25070|AT4G11850| 
               
               
                   
                 immune 
                   
                 AT4G23440|AT1G57630|AT1G56510|AT4G12720|AT5G41550| 
               
               
                   
                 response 
                   
                 AT5G58120|AT5G22690|AT5G37770|AT4G39260|AT1G11310| 
               
               
                   
                   
                   
                 AT1G74710|AT1G66090|AT1G61560|AT2G26560 
               
               
                 GO:0006955 
                 immune 
                 7.49E−05 
                 AT3G48090|AT3G52430|AT2G16870|AT3G25070|AT4G11850| 
               
               
                   
                 response 
                   
                 AT4G23440|AT1G57630|AT1G56510|AT4G12720|AT5G41550| 
               
               
                   
                   
                   
                 AT5G58120|AT5G22690|AT5G37770|AT4G39260|AT1G11310| 
               
               
                   
                   
                   
                 AT1G74710|AT1G66090|AT1G61560|AT2G26560 
               
               
                 GO:0009620 
                 response to 
                 0.000103 
                 AT2G06050|AT2G38470|AT3G06490|AT2G34930|AT2G38870| 
               
               
                   
                 fungus 
                   
                 AT3G52400|AT2G39660|AT5G47910|AT1G56510|AT1G11310| 
               
               
                   
                   
                   
                 AT3G11820|AT1G05800|AT1G74710|AT3G24550|AT1G61560 
               
               
                 GO:0080134 
                 regulation of 
                 0.000169 
                 AT3G45640|AT1G11310|AT3G11820|AT2G31880|AT3G52430| 
               
               
                   
                 response to 
                   
                 AT4G12720|AT3G25070|AT3G52400|AT4G39030|AT1G74710| 
               
               
                   
                 stress 
                   
                 AT3G05360 
               
               
                 GO:0016310 
                 phosphorylation 
                 0.00018 
                 AT3G45640|AT5G40540|AT3G25070|AT1G55610|AT5G41680| 
               
               
                   
                   
                   
                 AT1G16670|AT2G41890|AT2G17220|AT1G51940|AT4G09570| 
               
               
                   
                   
                   
                 AT2G31880|AT4G28350|AT2G19130|AT5G38210|AT1G70130| 
               
               
                   
                   
                   
                 AT3G55950|AT2G37840|AT3G16030|AT1G51620|AT2G39660| 
               
               
                   
                   
                   
                 AT1G70530|AT3G02880|AT1G53430|AT1G61370|AT3G24550| 
               
               
                   
                   
                   
                 AT3G08760|AT2G11520|AT1G18890|AT4G21390|AT5G07620| 
               
               
                   
                   
                   
                 AT1G53440|AT1G28390|AT5G65600|AT1G04440|AT2G39110| 
               
               
                   
                   
                   
                 AT1G17750|AT4G08850|AT1G53050|AT4G39940 
               
               
                 GO:0031347 
                 regulation of 
                 0.000214 
                 AT1G11310|AT3G11820|AT2G31880|AT3G52430|AT4G12720| 
               
               
                   
                 defense 
                   
                 AT3G25070|AT3G52400|AT4G39030|AT1G74710|AT3G05360 
               
               
                   
                 response 
                   
                   
               
               
                 GO:0010033 
                 response to 
                 0.000224 
                 AT3G52430|AT4G17230|AT5G66880|AT3G59900|AT4G16780| 
               
               
                   
                 organic 
                   
                 AT1G18570|AT2G04160|AT4G17260|AT5G37770|AT3G11840| 
               
               
                   
                 substance 
                   
                 AT5G62390|AT3G02880|AT3G48090|AT4G26120|AT1G18890| 
               
               
                   
                   
                   
                 AT4G30080|AT5G01540|AT1G05710|AT5G51190|AT3G52400| 
               
               
                   
                   
                   
                 AT2G17040|AT1G17750|AT4G39260|AT1G74430|AT3G61900| 
               
               
                   
                   
                   
                 AT3G45640|AT3G25070|AT1G07520|AT5G09980|AT3G28580| 
               
               
                   
                   
                   
                 AT2G38470|AT3G06490|AT1G19220|AT4G18880|AT5G61210| 
               
               
                   
                   
                   
                 AT5G44610|AT3G11820|AT5G66070|AT3G07390|AT1G57560| 
               
               
                   
                   
                   
                 AT2G40180|AT4G11360|AT5G25190|AT5G49620 
               
               
                 GO:0006468 
                 protein 
                 0.000235 
                 AT3G45640|AT5G40540|AT3G25070|AT1G55610|AT5G41680| 
               
               
                   
                 phosphorylation 
                   
                 AT1G16670|AT2G41890|AT2G17220|AT1G51940|AT4G09570| 
               
               
                   
                   
                   
                 AT2G31880|AT4G28350|AT2G19130|AT5G38210|AT1G70130| 
               
               
                   
                   
                   
                 AT3G55950|AT2G37840|AT3G16030|AT1G51620|AT2G39660| 
               
               
                   
                   
                   
                 AT1G70530|AT3G02880|AT1G53430|AT1G61370|AT3G24550| 
               
               
                   
                   
                   
                 AT3G08760|AT2G11520|AT1G18890|AT4G21390|AT5G07620| 
               
               
                   
                   
                   
                 AT1G53440|AT1G28390|AT5G65600|AT1G04440|AT2G39110| 
               
               
                   
                   
                   
                 AT1G17750|AT4G08850|AT1G53050 
               
               
                 GO:0006793 
                 phosphorus 
                 0.000373 
                 AT3G45640|AT5G40540|AT3G25070|AT1G55610|AT5G41680| 
               
               
                   
                 metabolic 
                   
                 AT1G16670|AT2G41890|AT2G17220|AT1G51940|AT4G09570| 
               
               
                   
                 process 
                   
                 AT2G31880|AT4G28350|AT2G19130|AT5G38210|AT1G70130| 
               
               
                   
                   
                   
                 AT3G55950|AT2G37840|AT3G16030|AT1G51620|AT2G39660| 
               
               
                   
                   
                   
                 AT1G70530|AT3G02880|AT1G53430|AT1G61370|AT3G24550| 
               
               
                   
                   
                   
                 AT3G08760|AT2G11520|AT1G18890|AT4G21390|AT5G07620| 
               
               
                   
                   
                   
                 AT1G53440|AT1G28390|AT5G65600|AT1G04440|AT3G02800| 
               
               
                   
                   
                   
                 AT2G39110|AT1G17750|AT4G08850|AT1G53050|AT4G39940 
               
               
                 GO:0006796 
                 phosphate 
                 0.000373 
                 AT3G45640|AT5G40540|AT3G25070|AT1G55610|AT5G41680| 
               
               
                   
                 metabolic 
                   
                 AT1G16670|AT2G41890|AT2G17220|AT1G51940|AT4G09570| 
               
               
                   
                 process 
                   
                 AT2G31880|AT4G28350|AT2G19130|AT5G38210|AT1G70130| 
               
               
                   
                   
                   
                 AT3G55950|AT2G37840|AT3G16030|AT1G51620|AT2G39660| 
               
               
                   
                   
                   
                 AT1G70530|AT3G02880|AT1G53430|AT1G61370|AT3G24550| 
               
               
                   
                   
                   
                 AT3G08760|AT2G11520|AT1G18890|AT4G21390|AT5G07620| 
               
               
                   
                   
                   
                 AT1G53440|AT1G28390|AT5G65600|AT1G04440|AT3G02800| 
               
               
                   
                   
                   
                 AT2G39110|AT1G17750|AT4G08850|AT1G53050|AT4G39940 
               
               
                 GO:0050832 
                 defense 
                 0.00054 
                 AT2G38470|AT2G34930|AT2G38870|AT3G52400|AT2G39660| 
               
               
                   
                 response to 
                   
                 AT5G47910|AT1G56510|AT1G11310|AT3G11820|AT1G05800| 
               
               
                   
                 fungus 
                   
                 AT1G74710|AT1G61560 
               
               
                 GO:0008219 
                 cell death 
                 0.000593 
                 AT5G22690|AT3G48090|AT5G04720|AT2G16870|AT3G25070| 
               
               
                   
                   
                   
                 AT4G23440|AT1G11000|AT1G11310|AT4G12720|AT1G66090| 
               
               
                   
                   
                   
                 AT5G41550|AT1G61560|AT5G58120|AT4G33300|AT2G26560| 
               
               
                   
                   
                   
                 AT1G15890 
               
               
                 GO:0016265 
                 death 
                 0.000593 
                 AT5G22690|AT3G48090|AT5G04720|AT2G16870|AT3G25070| 
               
               
                   
                   
                   
                 AT4G23440|AT1G11000|AT1G11310|AT4G12720|AT1G66090| 
               
               
                   
                   
                   
                 AT5G41550|AT1G61560|AT5G58120|AT4G33300|AT2G26560| 
               
               
                   
                   
                   
                 AT1G15890 
               
               
                 GO:0010200 
                 response to 
                 0.00127 
                 AT3G45640|AT2G17040|AT3G11840|AT1G07520|AT2G38470| 
               
               
                   
                 chitin 
                   
                 AT4G18880|AT5G51190|AT4G26120|AT5G66070|AT4G17230| 
               
               
                   
                   
                   
                 AT4G11360 
               
               
                 GO:0048583 
                 regulation of  
                 0.00199 
                 AT3G45640|AT3G52430|AT3G25070|AT3G52400|AT4G39030| 
               
               
                   
                 response to 
                   
                 AT3G05360|AT5G66880|AT4G09570|AT1G11310|AT3G11820| 
               
               
                   
                 stimulus 
                   
                 AT2G31880|AT4G12720|AT1G74710 
               
               
                 GO:0012501 
                 programmed 
                 0.00424 
                 AT5G22690|AT3G48090|AT5G04720|AT2G16870|AT3G25070| 
               
               
                   
                 cell death 
                   
                 AT4G23440|AT4G12720|AT1G66090|AT5G41550|AT5G58120| 
               
               
                   
                   
                   
                 AT4G33300|AT2G26560|AT1G15890 
               
               
                 GO:0006979 
                 response to 
                 0.0049 
                 AT3G45640|AT3G48090|AT1G14550|AT5G26030|AT2G16500| 
               
               
                   
                 oxidative 
                   
                 AT5G06720|AT1G52560|AT1G11210|AT4G12720|AT1G09940| 
               
               
                   
                 stress 
                   
                 AT1G13340|AT4G02380|AT1G14540|AT1G52200|AT1G72060| 
               
               
                   
                   
                   
                 AT5G37770 
               
               
                 GO:0006464 
                 protein 
                 0.0081 
                 AT5G40540|AT1G55610|AT2G41890|AT2G17220|AT2G19130| 
               
               
                   
                 modification 
                   
                 AT5G38210|AT2G39660|AT3G11840|AT3G02880|AT1G53430| 
               
               
                   
                 process 
                   
                 AT3G24550|AT2G11520|AT1G18890|AT5G57500|AT4G12720| 
               
               
                   
                   
                   
                 AT5G65600|AT1G04440|AT1G17750|AT4G08850|AT3G45640| 
               
               
                   
                   
                   
                 AT3G25070|AT5G41680|AT1G16670|AT3G61390|AT1G51940| 
               
               
                   
                   
                   
                 AT4G09570|AT2G31880|AT4G28350|AT1G70130|AT3G55950| 
               
               
                   
                   
                   
                 AT2G37840|AT3G16030|AT1G51620|AT1G70530|AT1G61370| 
               
               
                   
                   
                   
                 AT3G08760|AT4G21390|AT5G07620|AT1G53440|AT1G28390| 
               
               
                   
                   
                   
                 AT2G38830|AT2G39110|AT1G53050 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 17 
               
               
                   
               
               
                 Genes regulated by DEX-induced nuclear import of bZIP1 
               
               
                 (FDR &lt; 0.05) and by the interaction of N-signal 
               
               
                 and DEX-induced nuclear import of bZIP1 (p-val &lt; 0.01). 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                 Cluster1 
                   
               
               
                 At4g37540 
                 LBD39, LOB domain-containing protein 39 
               
               
                 At5g04630 
                 CYP77A9, cytochrome P450, family 77, subfamily A, 
               
               
                   
                 polypeptide 9 
               
               
                 At3g60690 
                 SAUR-like auxin-responsive protein family 
               
               
                 At4g38340 
                 NLP3; Plant regulator RWP-RK family protein 
               
               
                 Cluster2 
               
               
                 At4g33420 
                 Peroxidase superfamily protein 
               
               
                 At2g31380 
                 STH, salt tolerance homologue 
               
               
                 At3g30396 
                 transposable element gene 
               
               
                 At1g15050 
                 IAA34, indole-3-acetic acid inducible 34 
               
               
                 At5g28050 
                 Cytidine/deoxycytidylate deaminase family protein 
               
               
                 At1g01490 
                 Heavy metal transport/detoxification superfamily protein 
               
               
                 At2g39570 
                 ACT domain-containing protein 
               
               
                 At3g55150 
                 ATEXO70H1, EXO70H1, exocyst subunit exo70 family 
               
               
                   
                 protein H1 
               
               
                 At2g28630 
                 KCS12, 3-ketoacyl-CoA synthase 12 
               
               
                 At2g02700 
                 Cysteine/Histidine-rich C1 domain family protein 
               
               
                 Cluster3 
               
               
                 At1g55610 
                 BRL1, BRI1 like 
               
               
                 At4g33960 
                 unknown protein; 
               
               
                 At3g23820 
                 GAE6, UDP-D-glucuronate 4-epimerase 6 
               
               
                 At3g49350 
                 Ypt/Rab-GAP domain of gyp1p superfamily protein 
               
               
                 Cluster4 
               
               
                 At1g56510 
                 ADR2, WRR4, Disease resistance protein (TIR-NBS-LRR 
               
               
                   
                 class) 
               
               
                 At3g14360 
                 alpha/beta-Hydrolases superfamily protein 
               
               
                 At3g59900 
                 ARGOS, auxin-regulated gene involved in organ size 
               
               
                 At4g30560 
                 ATCNGC9, CNGC9, cyclic nucleotide gated channel 9 
               
               
                 At5g61210 
                 ATSNAP33, ATSNAP33B, SNAP33, SNP33, soluble 
               
               
                   
                 N-ethylmaleimide-sensitive factor adaptor protein 33 
               
               
                 At5g39710 
                 EMB2745, Tetratricopeptide repeat (TPR)-like 
               
               
                   
                 superfamily protein 
               
               
                 At3g63390 
                 unknown protein; 
               
               
                 At4g28940 
                 Phosphorylase superfamily protein 
               
               
                 At2g39900 
                 GATA type zinc finger transcription factor family protein 
               
               
                 At3g53280 
                 CYP71B5, cytochrome p450 71b5 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 18 
               
             
            
               
                   
               
               
                 Genes bound by GR::bZIP1 as detected by ChIP-seq with anti-GR antibody. 
               
            
           
           
               
               
            
               
                   
                 present in 
               
               
                   
                 ATH1 
               
               
                   
                 microarray by 
               
               
                 bZIP1 bound 
                 unambiguous 
               
               
                 genes 
                 probes 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 AT1G01060 
                 YES 
                 LHY 
                 LATE ELONGATED HYPOCOTYL 
               
               
                 AT1G01460 
                 YES 
                 ATPIPK11 
               
               
                 AT1G01470 
                 YES 
                 LEA14 
                 LATE EMBRYOGENESIS ABUNDANT 14 
               
               
                 AT1G01550 
                 YES 
                 BPS1 
                 BYPASS 1 
               
               
                 AT1G01560 
                 YES 
                 ATMPK11 
                 MAP kinase 11 
               
               
                 AT1G01720 
                 YES 
                 ANAC2 
                   Arabidopsis  NAC domain containing protein 2 
               
               
                 AT1G01725 
                 YES 
               
               
                 AT1G03850 
                 YES 
                 ATGRXS13 
                 glutaredoxin 13 
               
               
                 AT1G04530 
                 YES 
                 TPR4 
                 tetratricopeptide repeat 4 
               
               
                 AT1G05330 
                 YES 
               
               
                 AT1G05340 
                 YES 
               
               
                 AT1G05680 
                 YES 
                 UGT74E2 
                 Uridine diphosphate glycosyltransferase 74E2 
               
               
                 AT1G06760 
                 YES 
               
               
                 AT1G08510 
                 YES 
                 FATB 
                 fatty acyl-ACP thioesterases B 
               
               
                 AT1G08940 
                 YES 
               
               
                 AT1G09070 
                 YES 
                 (AT)SRC2 
                 SOYBEAN GENE REGULATED BY COLD-2 
               
               
                 AT1G09080 
                 YES 
                 BIP3 
                 binding protein 3 
               
               
                 AT1G09930 
                 YES 
                 ATOPT2 
                 oligopeptide transporter 2 
               
               
                 AT1G10170 
                 YES 
                 ATNFXL1 
                 NF-X-like 1 
               
               
                 AT1G11560 
                 YES 
               
               
                 AT1G11670 
                 YES 
               
               
                 AT1G12960 
                 YES 
               
               
                 AT1G13210 
                 YES 
                 ACA.1 
                 autoinhibited Ca2+/ATPase II 
               
               
                 AT1G13260 
                 YES 
                 EDF4 
                 ETHYLENE RESPONSE DNA BINDING FACTOR 4 
               
               
                 AT1G13270 
                 YES 
                 MAP1B 
                 METHIONINE AMINOPEPTIDASE 1B 
               
               
                 AT1G14040 
                 YES 
               
               
                 AT1G14530 
                 YES 
                 THH1 
                 TOM THREE HOMOLOG 1 
               
               
                 AT1G14540 
                 YES 
                 PER4 
                 peroxidase 4 
               
               
                 AT1G14550 
                 YES 
               
               
                 AT1G14560 
                 YES 
               
               
                 AT1G15010 
                 YES 
               
               
                 AT1G15040 
                 YES 
                 GAT 
                 glutamine amidotransferase 
               
               
                 AT1G15080 
                 YES 
                 ATLPP2 
                 LIPID PHOSPHATE PHOSPHATASE 2 
               
               
                 AT1G16640 
                 YES 
               
               
                 AT1G16670 
                 YES 
               
               
                 AT1G17180 
                 YES 
                 ATGSTU25 
                 glutathione S-transferase TAU 25 
               
               
                 AT1G17420 
                 YES 
                 ATLOX3 
                   Arabidopsis thaliana  lipoxygenase 3 
               
               
                 AT1G17850 
                 YES 
               
               
                 AT1G17860 
                 YES 
               
               
                 AT1G17870 
                 YES 
                 ATEGY3 
                 ETHYLENE-DEPENDENT GRAVITROPISM-DEFICIENT 
               
               
                   
                   
                   
                 AND YELLOW-GREEN-LIKE 3 
               
               
                 AT1G18210 
                 YES 
               
               
                 AT1G18310 
                 YES 
               
               
                 AT1G18740 
                 YES 
               
               
                 AT1G19020 
                 YES 
               
               
                 AT1G19025 
                 YES 
               
               
                 AT1G19180 
                 YES 
                 JAZ1 
                 jasmonate-zim-domain protein 1 
               
               
                 AT1G19190 
                 YES 
               
               
                 AT1G19210 
                 YES 
               
               
                 AT1G19770 
                 YES 
                 ATPUP14 
                 purine permease 14 
               
               
                 AT1G20440 
                 YES 
                 AtCOR47 
               
               
                 AT1G20450 
                 YES 
                 ERD1 
                 EARLY RESPONSIVE TO DEHYDRATION 1 
               
               
                 AT1G21850 
                 YES 
                 sks8 
                 SKU5 similar 8 
               
               
                 AT1G22070 
                 YES 
                 TGA3 
                 TGA1A-related gene 3 
               
               
                 AT1G22080 
                 YES 
               
               
                 AT1G22190 
                 YES 
                 RAP2.4 
                 related to AP2 4 
               
               
                 AT1G22200 
                 YES 
               
               
                 AT1G22570 
                 YES 
               
               
                 AT1G22830 
                 YES 
               
               
                 AT1G22840 
                 YES 
                 ATCYTC-A 
                 CYTOCHROME C-A 
               
               
                 AT1G23480 
                 YES 
                 ATCSLA3 
                 cellulose synthase-like A3 
               
               
                 AT1G23710 
                 YES 
               
               
                 AT1G25400 
                 YES 
               
               
                 AT1G25550 
                 YES 
               
               
                 AT1G25560 
                 YES 
                 EDF1 
                 ETHYLENE RESPONSE DNA BINDING FACTOR 1 
               
               
                 AT1G27100 
                 YES 
               
               
                 AT1G27720 
                 YES 
                 TAF4 
                 TBP-associated factor 4 
               
               
                 AT1G27730 
                 YES 
                 STZ 
                 salt tolerance zinc finger 
               
               
                 AT1G27760 
                 YES 
                 ATSAT32 
                 SALT-TOLERANCE 32 
               
               
                 AT1G27770 
                 YES 
                 ACA1 
                 autoinhibited Ca2+-ATPase 1 
               
               
                 AT1G28280 
                 YES 
               
               
                 AT1G28480 
                 YES 
                 GRX48 
               
               
                 AT1G29395 
                 YES 
                 COR413-TM1 
                 COLD REGULATED 314 THYLAKOID MEMBRANE 1 
               
               
                 AT1G29400 
                 YES 
                 AML5 
                 MEI2-like protein 5 
               
               
                 AT1G29680 
                 YES 
               
               
                 AT1G29690 
                 YES 
                 CAD1 
                 constitutively activated cell death 1 
               
               
                 AT1G30135 
                 YES 
                 JAZ8 
                 jasmonate-zim-domain protein 8 
               
               
                 AT1G30370 
                 YES 
                 DLAH 
                 DAD1-like acylhydrolase 
               
               
                 AT1G30700 
                 YES 
               
               
                 AT1G30740 
                 YES 
               
               
                 AT1G31820 
                 YES 
                 PUT1 
                 POLYAMINE UPTAKE TRANSPORTER 1 
               
               
                 AT1G32070 
                 YES 
                 ATNSI 
                 nuclear shuttle interacting 
               
               
                 AT1G32640 
                 YES 
                 ATMYC2 
               
               
                 AT1G32920 
                 YES 
               
               
                 AT1G32930 
                 YES 
               
               
                 AT1G33590 
                 YES 
               
               
                 AT1G35140 
                 YES 
                 EXL1 
                 EXORDIUM like 1 
               
               
                 AT1G35910 
                 YES 
                 TPPD 
                 trehalose-6-phosphate phosphatase D 
               
               
                 AT1G42560 
                 YES 
                 ATMLO9 
                   ARABIDOPSIS THALIANA  MILDEW RESISTANCE 
               
               
                   
                   
                   
                 LOCUS O 9 
               
               
                 AT1G42990 
                 YES 
                 ATBZIP6 
                 basic region/leucine zipper motif 6 
               
               
                 AT1G43160 
                 YES 
                 RAP2.6 
                 related to AP2 6 
               
               
                 AT1G43900 
                 YES 
               
               
                 AT1G43910 
                 YES 
               
               
                 AT1G45145 
                 YES 
                 ATH5 
                 THIOREDOXIN H-TYPE 5 
               
               
                 AT1G49520 
                 YES 
               
               
                 AT1G50750 
                 YES 
               
               
                 AT1G52890 
                 YES 
                 ANAC19 
                 NAC domain containing protein 19 
               
               
                 AT1G53720 
                 YES 
                 ATCYP59 
                 CYCLOPHILIN 59 
               
               
                 AT1G53830 
                 YES 
                 ATPME2 
                 pectin methylesterase 2 
               
               
                 AT1G53840 
                 YES 
                 ATPME1 
                 pectin methylesterase 1 
               
               
                 AT1G55450 
                 YES 
               
               
                 AT1G56050 
                 YES 
               
               
                 AT1G56060 
                 YES 
               
               
                 AT1G56590 
                 YES 
                 ZIP4 
                 ZIG SUPPRESSOR 4 
               
               
                 AT1G56660 
                 YES 
               
               
                 AT1G56670 
                 YES 
               
               
                 AT1G58210 
                 YES 
                 EMB1674 
                 EMBRYO DEFECTIVE 1674 
               
               
                 AT1G58420 
                 YES 
               
               
                 AT1G59590 
                 YES 
                 ZCF37 
               
               
                 AT1G59600 
                 YES 
                 ZCW7 
               
               
                 AT1G59870 
                 YES 
                 ABCG36 
                 ATP-binding cassette G36 
               
               
                 AT1G60190 
                 YES 
                 AtPUB19 
               
               
                 AT1G61340 
                 YES 
                 AtFBS1 
               
               
                 AT1G61360 
                 YES 
               
               
                 AT1G61820 
                 YES 
                 BGLU46 
                 beta glucosidase 46 
               
               
                 AT1G61870 
                 YES 
                 PPR336 
                 pentatricopeptide repeat 336 
               
               
                 AT1G61890 
                 YES 
               
               
                 AT1G62300 
                 YES 
                 ATWRKY6 
               
               
                 AT1G62570 
                 YES 
                 FMO GS-OX4 
                 flavin-monooxygenase glucosinolate S-oxygenase 4 
               
               
                 AT1G62790 
                 YES 
               
               
                 AT1G64390 
                 YES 
                 AtGH9C2 
                 glycosyl hydrolase 9C2 
               
               
                 AT1G64660 
                 YES 
                 ATMGL 
                 methionine gamma-lyase 
               
               
                 AT1G64670 
                 YES 
                 BDG1 
                 BODYGUARD1 
               
               
                 AT1G65510 
                 YES 
               
               
                 AT1G65520 
                 YES 
                 ATECI1 
                   ARABIDOPSIS THALIANA  DELTA(3), DELTA(2)-ENOYL 
               
               
                   
                   
                   
                 COA ISOMERASE 1 
               
               
                 AT1G66160 
                 YES 
                 ATCMPG1 
               
               
                 AT1G66170 
                 YES 
                 MMD1 
                 MALE MEIOCYTE DEATH 1 
               
               
                 AT1G68440 
                 YES 
               
               
                 AT1G68670 
                 YES 
               
               
                 AT1G68760 
                 YES 
                 ATNUDT1 
                   ARABIDOPSIS THALIANA  NUDIX HYDROLASE 
               
               
                   
                   
                   
                 HOMOLOG 1 
               
               
                 AT1G68765 
                 YES 
                 IDA 
                 INFLORESCENCE DEFICIENT IN ABSCISSION 
               
               
                 AT1G68840 
                 YES 
                 AtRAV2 
               
               
                 AT1G69220 
                 YES 
                 SIK1 
               
               
                 AT1G69490 
                 YES 
                 ANAC29 
                   Arabidopsis  NAC domain containing protein 29 
               
               
                 AT1G69760 
                 YES 
               
               
                 AT1G69880 
                 YES 
                 ATH8 
                 thioredoxin H-type 8 
               
               
                 AT1G69890 
                 YES 
               
               
                 AT1G69930 
                 YES 
                 ATGSTU11 
                 glutathione S-transferase TAU 11 
               
               
                 AT1G70420 
                 YES 
               
               
                 AT1G71530 
                 YES 
               
               
                 AT1G71697 
                 YES 
                 ATCK1 
                 choline kinase 1 
               
               
                 AT1G72520 
                 YES 
                 ATLOX4 
                   Arabidopsis thaliana  lipoxygenase 4 
               
               
                 AT1G73010 
                 YES 
                 AtPPsPase1 
                 pyrophosphate-specific phosphatase1 
               
               
                 AT1G73080 
                 YES 
                 ATPEPR1 
                 PEP1 RECEPTOR 1 
               
               
                 AT1G73500 
                 YES 
                 ATMKK9 
               
               
                 AT1G73510 
                 YES 
               
               
                 AT1G73530 
                 YES 
               
               
                 AT1G73540 
                 YES 
                 atnudt21 
                 nudix hydrolase homolog 21 
               
               
                 AT1G74310 
                 YES 
                 ATHSP11 
                 heat shock protein 11 
               
               
                 AT1G74450 
                 YES 
               
               
                 AT1G74930 
                 YES 
                 ORA47 
               
               
                 AT1G76170 
                 YES 
               
               
                 AT1G76180 
                 YES 
                 ERD14 
                 EARLY RESPONSE TO DEHYDRATION 14 
               
               
                 AT1G76600 
                 YES 
               
               
                 AT1G76640 
                 YES 
               
               
                 AT1G76650 
                 YES 
                 CML38 
                 calmodulin-like 38 
               
               
                 AT1G78080 
                 YES 
                 RAP2.4 
                 related to AP2 4 
               
               
                 AT1G78290 
                 YES 
                 SNRK2-8 
                 SNF1-RELATED PROTEIN KINASE 2-8 
               
               
                 AT1G78340 
                 YES 
                 ATGSTU22 
                 glutathione S-transferase TAU 22 
               
               
                 AT1G79400 
                 YES 
                 ATCHX2 
                 cation/H+ exchanger 2 
               
               
                 AT1G79990 
                 YES 
               
               
                 AT1G80010 
                 YES 
                 FRS8 
                 FAR1-related sequence 8 
               
               
                 AT1G80380 
                 YES 
               
               
                 AT1G80820 
                 YES 
                 ATCCR2 
               
               
                 AT1G80840 
                 YES 
                 ATWRKY4 
               
               
                 AT1G80850 
                 YES 
               
               
                 AT1G80930 
                 YES 
               
               
                 AT2G01300 
                 YES 
               
               
                 AT2G01670 
                 YES 
                 atnudt17 
                 nudix hydrolase homolog 17 
               
               
                 AT2G03750 
                 YES 
               
               
                 AT2G03760 
                 YES 
                 AtSOT1 
               
               
                 AT2G04040 
                 YES 
                 ATDTX1 
               
               
                 AT2G04050 
                 YES 
               
               
                 AT2G04880 
                 YES 
                 ATWRKY1 
               
               
                 AT2G04890 
                 YES 
                 SCL21 
                 SCARECROW-like 21 
               
               
                 AT2G05710 
                 YES 
                 ACO3 
                 aconitase 3 
               
               
                 AT2G05720 
                 YES 
               
               
                 AT2G05940 
                 YES 
                 RIPK 
                 RPM1-induced protein kinase 
               
               
                 AT2G07050 
                 YES 
                 CAS1 
                 cycloartenol synthase 1 
               
               
                 AT2G17080 
                 YES 
               
               
                 AT2G17660 
                 YES 
               
               
                 AT2G17670 
                 YES 
               
               
                 AT2G17840 
                 YES 
                 ERD7 
                 EARLY-RESPONSIVE TO DEHYDRATION 7 
               
               
                 AT2G18190 
                 YES 
               
               
                 AT2G18210 
                 YES 
               
               
                 AT2G18240 
                 YES 
               
               
                 AT2G18690 
                 YES 
               
               
                 AT2G20560 
                 YES 
               
               
                 AT2G20570 
                 YES 
                 ATGLK1 
                   ARABIDOPSIS  GOLDEN2-LIKE 1 
               
               
                 AT2G22470 
                 YES 
                 AGP2 
                 arabinogalactan protein 2 
               
               
                 AT2G22500 
                 YES 
                 ATPUMP5 
                 PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 5 
               
               
                 AT2G22760 
                 YES 
               
               
                 AT2G22860 
                 YES 
                 ATPSK2 
                 phytosulfokine 2 precursor 
               
               
                 AT2G22870 
                 YES 
                 EMB21 
                 embryo defective 21 
               
               
                 AT2G22880 
                 YES 
               
               
                 AT2G23120 
                 YES 
               
               
                 AT2G23170 
                 YES 
                 GH3.3 
               
               
                 AT2G23320 
                 YES 
                 AtWRKY15 
               
               
                 AT2G23810 
                 YES 
                 TET8 
                 tetraspanin8 
               
            
           
           
               
               
               
            
               
                 AT2G24570 
                 YES 
                 ATWRKY17 
               
            
           
           
               
               
               
               
            
               
                 AT2G24850 
                 YES 
                 TAT 
                 TYROSINE AMINOTRANSFERASE 
               
               
                 AT2G25460 
                 YES 
               
               
                 AT2G25490 
                 YES 
                 EBF1 
                 EIN3-binding F box protein 1 
               
               
                 AT2G25735 
                 YES 
               
               
                 AT2G26530 
                 YES 
                 AR781 
               
               
                 AT2G26690 
                 YES 
               
               
                 AT2G27080 
                 YES 
               
               
                 AT2G27090 
                 YES 
               
               
                 AT2G28400 
                 YES 
               
               
                 AT2G29080 
                 YES 
                 ftsh3 
                 FTSH protease 3 
               
               
                 AT2G29470 
                 YES 
                 ATGSTU3 
                 glutathione S-transferase tau 3 
               
               
                 AT2G29480 
                 YES 
                 ATGSTU2 
                 glutathione S-transferase tau 2 
               
               
                 AT2G29490 
                 YES 
                 ATGSTU1 
                 glutathione S-transferase TAU 1 
               
               
                 AT2G30040 
                 YES 
                 MAPKKK14 
                 mitogen-activated protein kinase kinase kinase 14 
               
               
                 AT2G30240 
                 YES 
                 ATCHX13 
               
            
           
           
               
               
               
            
               
                 AT2G30250 
                 YES 
                 ATWRKY25 
               
            
           
           
               
               
               
               
            
               
                 AT2G31690 
                 YES 
                   
                   
               
               
                 AT2G32020 
                 YES 
               
               
                 AT2G32120 
                 YES 
                 HSP7T-2 
                 heat-shock protein 7T-2 
               
               
                 AT2G32150 
                 YES 
               
               
                 AT2G32220 
                 YES 
               
               
                 AT2G33710 
                 YES 
               
               
                 AT2G34910 
                 YES 
               
               
                 AT2G35410 
                 YES 
               
               
                 AT2G35930 
                 YES 
                 AtPUB23 
               
               
                 AT2G35980 
                 YES 
                 ATNHL1 
                   ARABIDOPSIS  NDR1/HIN1-LIKE 1 
               
               
                 AT2G36220 
                 YES 
               
               
                 AT2G36230 
                 YES 
                 APG1 
                 ALBINO AND PALE GREEN 1 
               
               
                 AT2G36950 
                 YES 
               
               
                 AT2G37430 
                 YES 
                 ZAT11 
                 zinc finger of  Arabidopsis thaliana  11 
               
               
                 AT2G37975 
                 YES 
               
               
                 AT2G38240 
                 YES 
               
               
                 AT2G38470 
                 YES 
                 ATWRKY33 
                 WRKY DNA-BINDING PROTEIN 33 
               
               
                 AT2G38480 
                 YES 
               
               
                 AT2G38830 
                 YES 
               
               
                 AT2G39190 
                 YES 
                 ATATH8 
               
               
                 AT2G39200 
                 YES 
                 ATMLO12 
                 MILDEW RESISTANCE LOCUS O 12 
               
               
                 AT2G39660 
                 YES 
                 BIK1 
                 botrytis-induced kinase1 
               
               
                 AT2G39670 
                 YES 
               
               
                 AT2G39990 
                 YES 
                 AteIF3f 
                   Arabidopsis thaliana  eukaryotic translation initiation factor 3 
               
               
                   
                   
                   
                 subunit F 
               
               
                 AT2G40000 
                 YES 
                 ATHSPRO2 
                   ARABIDOPSIS  ORTHOLOG OF SUGAR BEET HS1 PRO-1 2 
               
               
                 AT2G40140 
                 YES 
                 ATSZF2 
               
               
                 AT2G41000 
                 YES 
               
               
                 AT2G41010 
                 YES 
                 ATCAMBP25 
                 calmodulin (CAM)-binding protein of 25 kDa 
               
               
                 AT2G41100 
                 YES 
                 ATCAL4 
                   ARABIDOPSIS THALIANA  CALMODULIN LIKE 4 
               
               
                 AT2G41110 
                 YES 
                 ATCAL5 
               
               
                 AT2G41410 
                 YES 
               
               
                 AT2G41430 
                 YES 
                 CID1 
                 CTC-Interacting Domain 1 
               
               
                 AT2G41620 
                 YES 
               
               
                 AT2G41630 
                 YES 
                 TFIIB 
                 transcription factor IIB 
               
               
                 AT2G41640 
                 YES 
               
               
                 AT2G41730 
                 YES 
               
               
                 AT2G41740 
                 YES 
                 ATVLN2 
               
               
                 AT2G41790 
                 YES 
               
               
                 AT2G41800 
                 YES 
               
               
                 AT2G41890 
                 YES 
               
               
                 AT2G43130 
                 YES 
                 ARA-4 
               
               
                 AT2G43290 
                 YES 
                 MSS3 
                 multicopy suppressors of snf4 deficiency in yeast 3 
               
               
                 AT2G44790 
                 YES 
                 UCC2 
                 uclacyanin 2 
               
               
                 AT2G44840 
                 YES 
                 ATERF13 
                 ETHYLENE-RESPONSIVE ELEMENT BINDING FACTOR 
               
               
                   
                   
                   
                 13 
               
               
                 AT2G45400 
                 YES 
                 BEN1 
               
               
                 AT2G45810 
                 YES 
               
               
                 AT2G45820 
                 YES 
               
               
                 AT2G46140 
                 YES 
               
               
                 AT2G46260 
                 YES 
                 LRB1 
                 light-response BTB 1 
               
               
                 AT2G46390 
                 YES 
                 SDH8 
                 succinate dehydrogenase 8 
               
               
                 AT2G46400 
                 YES 
                 ATWRKY46 
                 WRKY DNA-BINDING PROTEIN 46 
               
               
                 AT2G46420 
                 YES 
               
               
                 AT2G46830 
                 YES 
                 AtCCA1 
               
               
                 AT2G47000 
                 YES 
                 ABCB4 
                 ATP-binding cassette B4 
               
               
                 AT2G47550 
                 YES 
               
               
                 AT2G47950 
                 YES 
               
               
                 AT3G01280 
                 YES 
                 ATVDAC1 
                   ARABIDOPSIS THALIANA  VOLTAGE DEPENDENT 
               
               
                   
                   
                   
                 ANION CHANNEL 1 
               
               
                 AT3G01290 
                 YES 
                 AtHIR2 
               
               
                 AT3G01560 
                 YES 
               
               
                 AT3G01830 
                 YES 
               
               
                 AT3G01840 
                 YES 
                 LYK2 
                 LysM-containing receptor-like kinase 2 
               
               
                 AT3G02040 
                 YES 
                 AtGDPD1 
               
               
                 AT3G02480 
                 YES 
               
               
                 AT3G02840 
                 YES 
               
               
                 AT3G02850 
                 YES 
                 SKOR 
                 STELAR K+ outward rectifier 
               
               
                 AT3G02880 
                 YES 
               
               
                 AT3G03810 
                 YES 
                 EDA3 
                 embryo sac development arrest 3 
               
               
                 AT3G03890 
                 YES 
               
               
                 AT3G04070 
                 YES 
                 anac47 
                 NAC domain containing protein 47 
               
               
                 AT3G04120 
                 YES 
                 GAPC 
                 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 
               
               
                   
                   
                   
                 C SUBUNIT 
               
               
                 AT3G04130 
                 YES 
               
               
                 AT3G04730 
                 YES 
                 IAA16 
                 indoleacetic acid-induced protein 16 
               
               
                 AT3G05310 
                 YES 
                 MIRO3 
                 MIRO-related GTP-ase 3 
               
               
                 AT3G06490 
                 YES 
                 AtMYB18 
                 myb domain protein 18 
               
               
                 AT3G06500 
                 YES 
                 A/N-InvC 
                 alkaline/neutral invertase C 
               
               
                 AT3G06510 
                 YES 
                 ATSFR2 
                 SENSITIVE TO FREEZING 2 
               
               
                 AT3G08580 
                 YES 
                 AAC1 
                 ADP/ATP carrier 1 
               
               
                 AT3G08590 
                 YES 
                 iPGAM2 
                 2,3-biphosphoglycerate-independent phosphoglycerate mutase 2 
               
               
                 AT3G08610 
                 YES 
               
               
                 AT3G09440 
                 YES 
               
               
                 AT3G09940 
                 YES 
                 ATMDAR3 
                 
                   ARABIDOPSIS THALIANA 
                 
               
               
                   
                   
                   
                 MONODEHYDROASCORBATE REDUCTASE 3 
               
               
                 AT3G10300 
                 YES 
               
               
                 AT3G10920 
                 YES 
                 ATMSD1 
                   ARABIDOPSIS  MANGANESE SUPEROXIDE DISMUTASE 1 
               
               
                 AT3G10930 
                 YES 
               
               
                 AT3G10985 
                 YES 
                 ATWI-12 
                   ARABIDOPSIS THALIANA  WOUND-INDUCED PROTEIN 
               
               
                   
                   
                   
                 12 
               
               
                 AT3G12120 
                 YES 
                 FAD2 
                 fatty acid desaturase 2 
               
               
                 AT3G12320 
                 YES 
               
               
                 AT3G13310 
                 YES 
               
               
                 AT3G13320 
                 YES 
                 atcax2 
               
            
           
           
               
               
               
            
               
                 AT3G13790 
                 YES 
                 ATBFRUCT1 
               
            
           
           
               
               
               
               
            
               
                 AT3G13920 
                 YES 
                 EIF4A1 
                 eukaryotic translation initiation factor 4A1 
               
               
                 AT3G14940 
                 YES 
                 ATPPC3 
                 phosphoenolpyruvate carboxylase 3 
               
               
                 AT3G14990 
                 YES 
                 AtDJ1A 
                 DJ-1 homolog A 
               
               
                 AT3G15210 
                 YES 
                 ATERF-4 
                 ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 4 
               
               
                 AT3G15450 
                 YES 
               
               
                 AT3G15460 
                 YES 
               
               
                 AT3G15500 
                 YES 
                 ANAC55 
                 NAC domain containing protein 55 
               
               
                 AT3G15620 
                 YES 
                 UVR3 
                 UV REPAIR DEFECTIVE 3 
               
               
                 AT3G15630 
                 YES 
               
               
                 AT3G16857 
                 YES 
                 ARR1 
                 response regulator 1 
               
               
                 AT3G16860 
                 YES 
                 COBL8 
                 COBRA-like protein 8 precursor 
               
               
                 AT3G17390 
                 YES 
                 MAT4 
                 METHIONINE ADENOSYLTRANSFERASE 4 
               
               
                 AT3G19020 
                 YES 
               
               
                 AT3G19030 
                 YES 
               
               
                 AT3G19240 
                 YES 
               
               
                 AT3G19570 
                 YES 
                 QWRF1 
                 QWRF domain containing 1 
               
               
                 AT3G19580 
                 YES 
                 AZF2 
                 zinc-finger protein 2 
               
               
                 AT3G19930 
                 YES 
                 ATSTP4 
                 SUGAR TRANSPORTER 4 
               
               
                 AT3G21070 
                 YES 
                 ATNADK-1 
                 NAD KINASE 1 
               
               
                 AT3G21500 
                 YES 
                 DXL1 
                 DXS-like 1 
               
               
                 AT3G22370 
                 YES 
                 AOX1A 
                 alternative oxidase 1A 
               
               
                 AT3G22380 
                 YES 
                 TIC 
                 TIME FOR COFFEE 
               
               
                 AT3G22900 
                 YES 
                 NRPD7 
               
               
                 AT3G22910 
                 YES 
               
               
                 AT3G23170 
                 YES 
               
               
                 AT3G23250 
                 YES 
                 ATMYB15 
                 MYB DOMAIN PROTEIN 15 
               
               
                 AT3G23460 
                 YES 
               
               
                 AT3G24050 
                 YES 
                 GATA1 
                 GATA transcription factor 1 
               
               
                 AT3G24170 
                 YES 
                 ATGR1 
                 glutathione-disulfide reductase 
               
               
                 AT3G24550 
                 YES 
                 ATPERK1 
                 proline-rich extensin-like receptor kinase 1 
               
               
                 AT3G24560 
                 YES 
                 RSY3 
                 RASPBERRY 3 
               
               
                 AT3G25250 
                 YES 
                 AGC2 
               
               
                 AT3G25600 
                 YES 
               
               
                 AT3G25610 
                 YES 
               
               
                 AT3G25650 
                 YES 
                 ASK15 
                 SKP1-like 15 
               
               
                 AT3G25655 
                 YES 
                 IDL1 
                 inflorescence deficient in abscission (IDA)-like 1 
               
               
                 AT3G25780 
                 YES 
                 AOC3 
                 allene oxide cyclase 3 
               
               
                 AT3G27510 
                 YES 
               
               
                 AT3G28690 
                 YES 
               
               
                 AT3G29010 
                 YES 
               
               
                 AT3G29290 
                 YES 
                 emb276 
                 embryo defective 276 
               
               
                 AT3G30775 
                 YES 
                 AT-POX 
               
               
                 AT3G44260 
                 YES 
                 AtCAF1a 
                 CCR4-associated factor 1a 
               
               
                 AT3G45730 
                 YES 
               
               
                 AT3G45740 
                 YES 
               
               
                 AT3G45970 
                 YES 
                 ATEXLA1 
                 expansin-like A1 
               
               
                 AT3G45980 
                 YES 
                 H2B 
                 HISTONE H2B 
               
               
                 AT3G46620 
                 YES 
                 AtRDUF1 
                   Arabidopsis thaliana  RING and Domain of Unknown Function 
               
               
                   
                   
                   
                 1117 1 
               
               
                 AT3G47340 
                 YES 
                 ASN1 
                 glutamine-dependent asparagine synthase 1 
               
               
                 AT3G48520 
                 YES 
                 CYP94B3 
                 cytochrome P45, family 94, subfamily B, polypeptide 3 
               
               
                 AT3G49000 
                 YES 
               
               
                 AT3G49530 
                 YES 
                 ANAC62 
                 NAC domain containing protein 62 
               
            
           
           
               
               
               
            
               
                 AT3G49780 
                 YES 
                 ATPSK3 (FORMER SYMBOL) 
               
            
           
           
               
               
               
               
            
               
                 AT3G49790 
                 YES 
                   
                   
               
               
                 AT3G50900 
                 YES 
               
               
                 AT3G50910 
                 YES 
               
               
                 AT3G50930 
                 YES 
                 BCS1 
                 cytochrome BC1 synthesis 
               
               
                 AT3G50960 
                 YES 
                 PLP3a 
                 phosducin-like protein 3 homolog 
               
               
                 AT3G50970 
                 YES 
                 LTI3 
                 LOW TEMPERATURE-INDUCED 3 
               
               
                 AT3G50980 
                 YES 
                 XERO1 
                 dehydrin xero 1 
               
               
                 AT3G51920 
                 YES 
                 ATCML9 
               
               
                 AT3G52450 
                 YES 
                 AtPUB22 
               
               
                 AT3G52700 
                 YES 
               
               
                 AT3G52710 
                 YES 
               
               
                 AT3G52800 
                 YES 
               
               
                 AT3G52810 
                 YES 
                 ATPAP21 
                 PURPLE ACID PHOSPHATASE 21 
               
               
                 AT3G52930 
                 YES 
                 AtFBA8 
               
               
                 AT3G53480 
                 YES 
                 ABCG37 
                 ATP-binding cassette G37 
               
               
                 AT3G53510 
                 YES 
                 ABCG2 
                 ATP-binding cassette G2 
               
               
                 AT3G53600 
                 YES 
               
               
                 AT3G53610 
                 YES 
                 ATRAB8 
                 RAB GTPase homolog 8 
               
               
                 AT3G53760 
                 YES 
                 ATGCP4 
               
               
                 AT3G54150 
                 YES 
               
               
                 AT3G55440 
                 YES 
                 ATCTIMC 
                 CYTOSOLIC TRIOSE PHOSPHATE ISOMERASE 
               
               
                 AT3G55620 
                 YES 
                 eIF6A 
                 eukaryotic initiation facor 6A 
               
               
                 AT3G55630 
                 YES 
                 ATDFD 
                 DHFS-FPGS homolog D 
               
               
                 AT3G55640 
                 YES 
               
               
                 AT3G55970 
                 YES 
                 ATJRG21 
               
               
                 AT3G55980 
                 YES 
                 ATSZF1 
               
               
                 AT3G56800 
                 YES 
                 ACAM-3 
                 CALMODULIN 3 
               
               
                 AT3G56880 
                 YES 
               
               
                 AT3G57450 
                 YES 
               
               
                 AT3G57460 
                 YES 
               
               
                 AT3G59350 
                 YES 
               
               
                 AT3G59360 
                 YES 
                 ATUTR6 
                 UDP-GALACTOSE TRANSPORTER 6 
               
               
                 AT3G60130 
                 YES 
                 BGLU16 
                 beta glucosidase 16 
               
               
                 AT3G60140 
                 YES 
                 BGLU3 
                 BETA GLUCOSIDASE 3 
               
               
                 AT3G61190 
                 YES 
                 BAP1 
                 BON association protein 1 
               
               
                 AT3G61640 
                 YES 
                 AGP2 
                 arabinogalactan protein 2 
               
               
                 AT3G61890 
                 YES 
                 ATHB-12 
                 homeobox 12 
               
               
                 AT3G62260 
                 YES 
               
               
                 AT3G62410 
                 YES 
                 CP12 
                 CP12 DOMAIN-CONTAINING PROTEIN 1 
               
               
                 AT3G63380 
                 YES 
               
               
                 AT4G00170 
                 YES 
               
               
                 AT4G00690 
                 YES 
                 ULP1B 
                 UB-like protease 1B 
               
               
                 AT4G01370 
                 YES 
                 ATMPK4 
                 MAP kinase 4 
               
               
                 AT4G02380 
                 YES 
                 AtLEA5 
                   Arabidopsis thaliana  late embryogenensis abundant like 5 
               
               
                 AT4G02880 
                 YES 
               
               
                 AT4G04500 
                 YES 
                 CRK37 
                 cysteine-rich RLK (RECEPTOR-like protein kinase) 37 
               
               
                 AT4G05050 
                 YES 
                 UBQ11 
                 ubiquitin 11 
               
               
                 AT4G05100 
                 YES 
                 AtMYB74 
                 myb domain protein 74 
               
               
                 AT4G05320 
                 YES 
                 UBI1 
                 ubiquitin 1 
               
               
                 AT4G08850 
                 YES 
               
               
                 AT4G08950 
                 YES 
                 EXO 
                 EXORDIUM 
               
               
                 AT4G09630 
                 YES 
               
               
                 AT4G11280 
                 YES 
                 ACS6 
                 1-aminocyclopropane-1-carboxylic acid (acc) synthase 6 
               
               
                 AT4G11350 
                 YES 
               
               
                 AT4G11360 
                 YES 
                 RHA1B 
                 RING-H2 finger A1B 
               
               
                 AT4G11560 
                 YES 
               
               
                 AT4G11570 
                 YES 
               
               
                 AT4G11670 
                 YES 
               
               
                 AT4G12720 
                 YES 
                 AtNUDT7 
                   Arabidopsis thaliana  Nudix hydrolase homolog 7 
               
               
                 AT4G12730 
                 YES 
                 FLA2 
                 FASCICLIN-like arabinogalactan 2 
               
               
                 AT4G13390 
                 YES 
                 EXT12 
                 extensin 12 
               
               
                 AT4G15610 
                 YES 
               
               
                 AT4G16670 
                 YES 
               
               
                 AT4G16680 
                 YES 
               
               
                 AT4G16820 
                 YES 
                 PLA-I{beta]2 
                 phospholipase A I beta 2 
               
               
                 AT4G16830 
                 YES 
               
               
                 AT4G17490 
                 YES 
                 ATERF6 
                 ethylene responsive element binding factor 6 
               
               
                 AT4G17500 
                 YES 
                 ATERF-1 
                 ethylene responsive element binding factor 1 
               
               
                 AT4G17520 
                 YES 
               
               
                 AT4G17615 
                 YES 
                 ATCBL1 
                   ARABIDOPSIS THALIANA  CALCINEURIN B-LIKE 
               
               
                   
                   
                   
                 PROTEIN 
               
            
           
           
               
               
               
            
               
                 AT4G18170 
                 YES 
                 ATWRKY28 
               
            
           
           
               
               
               
               
            
               
                 AT4G18880 
                 YES 
                 AT-HSFA4A 
                   ARABIDOPSIS THALIANA  HEAT SHOCK 
               
               
                   
                   
                   
                 TRANSCRIPTION FACTOR A4A 
               
               
                 AT4G19200 
                 YES 
               
               
                 AT4G19210 
                 YES 
                 ABCE2 
                 ATP-binding cassette E2 
               
               
                 AT4G20000 
                 YES 
               
               
                 AT4G20830 
                 YES 
               
               
                 AT4G20840 
                 YES 
               
               
                 AT4G20860 
                 YES 
               
               
                 AT4G20870 
                 YES 
                 ATFAH2 
                   ARABIDOPSIS  FATTY ACID HYDROXYLASE 2 
               
               
                 AT4G21120 
                 YES 
                 AAT1 
                 amino acid transporter 1 
               
               
                 AT4G21490 
                 YES 
                 NDB3 
                 NAD(P)H dehydrogenase B3 
               
               
                 AT4G21820 
                 YES 
               
               
                 AT4G21850 
                 YES 
                 ATMSRB9 
                 methionine sulfoxide reductase B9 
               
               
                 AT4G22720 
                 YES 
               
               
                 AT4G23190 
                 YES 
                 AT-RLK3 
                 RECEPTOR LIKE PROTEIN KINASE 3 
               
               
                 AT4G24390 
                 YES 
                 AFB4 
                 auxin signaling F-box 4 
               
               
                 AT4G24570 
                 YES 
                 DIC2 
                 dicarboxylate carrier 2 
               
               
                 AT4G24580 
                 YES 
                 REN1 
                 ROP1 ENHANCER 1 
               
               
                 AT4G25570 
                 YES 
                 ACYB-2 
               
               
                 AT4G25580 
                 YES 
               
               
                 AT4G25810 
                 YES 
                 XTH23 
                 xyloglucan endotransglucosylase/hydrolase 23 
               
               
                 AT4G25820 
                 YES 
                 ATXTH14 
               
               
                 AT4G26040 
                 YES 
               
               
                 AT4G26180 
                 YES 
               
               
                 AT4G27270 
                 YES 
               
               
                 AT4G27280 
                 YES 
               
               
                 AT4G27580 
                 YES 
               
               
                 AT4G27652 
                 YES 
               
               
                 AT4G27654 
                 YES 
               
               
                 AT4G27657 
                 YES 
               
               
                 AT4G28460 
                 YES 
               
               
                 AT4G29780 
                 YES 
               
               
                 AT4G29790 
                 YES 
               
               
                 AT4G30210 
                 YES 
                 AR2 
               
               
                 AT4G30280 
                 YES 
                 ATXTH18 
                 XYLOGLUCAN 
               
               
                   
                   
                   
                 ENDOTRANSGLUCOSYLASE/HYDROLASE 18 
               
               
                 AT4G30290 
                 YES 
                 ATXTH19 
                 XYLOGLUCAN 
               
               
                   
                   
                   
                 ENDOTRANSGLUCOSYLASE/HYDROLASE 19 
               
               
                 AT4G30430 
                 YES 
                 TET9 
                 tetraspanin9 
               
               
                 AT4G30440 
                 YES 
                 GAE1 
                 UDP-D-glucuronate 4-epimerase 1 
               
               
                 AT4G30530 
                 YES 
                 GGP1 
                 gamma-glutamyl peptidase 1 
               
               
                 AT4G30600 
                 YES 
               
            
           
           
               
               
               
            
               
                 AT4G31550 
                 YES 
                 ATWRKY11 
               
            
           
           
               
               
               
               
            
               
                 AT4G31800 
                 YES 
                 ATWRKY18 
                   ARABIDOPSIS THALIANA  WRKY DNA-BINDING 
               
               
                   
                   
                   
                 PROTEIN 18 
               
               
                 AT4G31805 
                 YES 
               
               
                 AT4G32020 
                 YES 
               
               
                 AT4G32920 
                 YES 
               
               
                 AT4G33666 
                 YES 
               
               
                 AT4G33670 
                 YES 
               
               
                 AT4G33780 
                 YES 
               
               
                 AT4G33920 
                 YES 
               
               
                 AT4G33925 
                 YES 
                 SSN2 
                 suppressor of sni1 2 
               
               
                 AT4G33950 
                 YES 
                 ATOST1 
                 OPEN STOMATA 1 
               
               
                 AT4G34150 
                 YES 
               
               
                 AT4G34160 
                 YES 
                 CYCD3 
               
               
                 AT4G34410 
                 YES 
                 RRTF1 
                 redox responsive transcription factor 1 
               
               
                 AT4G35580 
                 YES 
                 CBNAC 
                 calmodulin-binding NAC protein 
               
               
                 AT4G36010 
                 YES 
               
               
                 AT4G36040 
                 YES 
                 J11 
                 DnaJ11 
               
               
                 AT4G36500 
                 YES 
               
               
                 AT4G36640 
                 YES 
               
               
                 AT4G37010 
                 YES 
                 CEN2 
                 centrin 2 
               
               
                 AT4G37260 
                 YES 
                 ATMYB73 
               
               
                 AT4G37270 
                 YES 
                 ATHMA1 
                   ARABIDOPSIS THALIANA  HEAVY METAL ATPASE 1 
               
               
                 AT4G37370 
                 YES 
                 CYP81D8 
                 cytochrome P45, family 81, subfamily D, polypeptide 8 
               
               
                 AT4G37590 
                 YES 
                 MEL1 
                 MAB4/ENP/NPY1-LIKE 1 
               
               
                 AT4G37610 
                 YES 
                 BT5 
                 BTB and TAZ domain protein 5 
               
               
                 AT4G37770 
                 YES 
                 ACS8 
                 1-amino-cyclopropane-1-carboxylate synthase 8 
               
               
                 AT4G37900 
                 YES 
               
               
                 AT4G37910 
                 YES 
                 mtHsc7-1 
                 mitochondrial heat shock protein 7-1 
               
               
                 AT4G38420 
                 YES 
                 sks9 
                 SKU5 similar 9 
               
               
                 AT4G39080 
                 YES 
                 VHA-A3 
                 vacuolar proton ATPase A3 
               
               
                 AT4G39090 
                 YES 
                 RD19 
                 RESPONSIVE TO DEHYDRATION 19 
               
               
                 AT4G39260 
                 YES 
                 ATGRP8 
                 GLYCINE-RICH PROTEIN 8 
               
               
                 AT4G39640 
                 YES 
                 GGT1 
                 gamma-glutamyl transpeptidase 1 
               
               
                 AT4G40030 
                 YES 
               
               
                 AT4G40040 
                 YES 
               
               
                 AT5G01380 
                 YES 
               
               
                 AT5G01500 
                 YES 
                 TAAC 
                 thylakoid ATP/ADP carrier 
               
               
                 AT5G01510 
                 YES 
                 RUS5 
                 ROOT UV-B SENSITIVE 5 
               
               
                 AT5G01540 
                 YES 
                 LecRK-VI.2 
                 L-type lectin receptor kinase-VI.2 
               
               
                 AT5G01600 
                 YES 
                 ATFER1 
                   ARABIDOPSIS THALIANA  FERRETIN 1 
               
               
                 AT5G01750 
                 YES 
               
               
                 AT5G01820 
                 YES 
                 ATCIPK14 
               
               
                 AT5G01950 
                 YES 
               
               
                 AT5G01960 
                 YES 
               
               
                 AT5G02020 
                 YES 
                 SIS 
                 Salt Induced Serine rich 
               
               
                 AT5G02230 
                 YES 
               
               
                 AT5G02240 
                 YES 
               
               
                 AT5G02810 
                 YES 
                 APRR7 
               
               
                 AT5G02820 
                 YES 
                 BIN5 
                 BRASSINOSTEROID INSENSITIVE 5 
               
               
                 AT5G03210 
                 YES 
                 AtDIP2 
               
               
                 AT5G03380 
                 YES 
               
               
                 AT5G03610 
                 YES 
               
               
                 AT5G04330 
                 YES 
                 CYP84A4 
                 CYTOCHROME P45 84A4 
               
               
                 AT5G04750 
                 YES 
               
               
                 AT5G05410 
                 YES 
                 DREB2 
                 DEHYDRATION-RESPONSIVE ELEMENT BINDING 
               
               
                   
                   
                   
                 PROTEIN 2 
               
               
                 AT5G05420 
                 YES 
               
               
                 AT5G05600 
                 YES 
               
               
                 AT5G05790 
                 YES 
               
               
                 AT5G06290 
                 YES 
                 2-Cys Prx B 
                 2-cysteine peroxiredoxin B 
               
               
                 AT5G06300 
                 YES 
                 LOG7 
                 LONELY GUY 7 
               
               
                 AT5G06320 
                 YES 
                 NHL3 
                 NDR1/HIN1-like 3 
               
               
                 AT5G07440 
                 YES 
                 GDH2 
                 glutamate dehydrogenase 2 
               
               
                 AT5G07450 
                 YES 
                 CYCP4; 3 
                 cyclin p4; 3 
               
               
                 AT5G07730 
                 YES 
               
               
                 AT5G07740 
                 YES 
               
               
                 AT5G08230 
                 YES 
               
               
                 AT5G08240 
                 YES 
               
               
                 AT5G09990 
                 YES 
                 PROPEP5 
                 elicitor peptide 5 precursor 
               
               
                 AT5G10180 
                 YES 
                 AST68 
                   ARABIDOPSIS  SULFATE TRANSPORTER 68 
               
               
                 AT5G10630 
                 YES 
               
               
                 AT5G10690 
                 YES 
               
               
                 AT5G10695 
                 YES 
               
               
                 AT5G10700 
                 YES 
               
               
                 AT5G10710 
                 YES 
               
               
                 AT5G11090 
                 YES 
               
               
                 AT5G11650 
                 YES 
               
               
                 AT5G11670 
                 YES 
                 ATNADP-ME2 
                   Arabidopsis thaliana  NADP-malic enzyme 2 
               
               
                 AT5G11740 
                 YES 
                 AGP15 
                 arabinogalactan protein 15 
               
               
                 AT5G12340 
                 YES 
               
               
                 AT5G13200 
                 YES 
               
               
                 AT5G13220 
                 YES 
                 JAS1 
                 JASMONATE-ASSOCIATED 1 
               
               
                 AT5G13470 
                 YES 
               
               
                 AT5G14730 
                 YES 
               
               
                 AT5G14740 
                 YES 
                 BETA CA2 
                 BETA CARBONIC ANHYDRASE 2 
               
               
                 AT5G15090 
                 YES 
                 ATVDAC3 
                   ARABIDOPSIS THALIANA  VOLTAGE DEPENDENT 
               
               
                   
                   
                   
                 ANION CHANNEL 3 
               
               
                 AT5G15130 
                 YES 
                 ATWRKY72 
                   ARABIDOPSIS THALIANA  WRKY DNA-BINDING 
               
               
                   
                   
                   
                 PROTEIN 72 
               
               
                 AT5G15980 
                 YES 
               
               
                 AT5G17330 
                 YES 
                 GAD 
                 glutamate decarboxylase 
               
               
                 AT5G17350 
                 YES 
               
               
                 AT5G17360 
                 YES 
               
               
                 AT5G17460 
                 YES 
               
               
                 AT5G17650 
                 YES 
               
               
                 AT5G18270 
                 YES 
                 ANAC87 
                   Arabidopsis  NAC domain containing protein 87 
               
               
                 AT5G18310 
                 YES 
               
               
                 AT5G18475 
                 YES 
               
               
                 AT5G19110 
                 YES 
               
               
                 AT5G19240 
                 YES 
               
               
                 AT5G20150 
                 YES 
                 ATSPX1 
                   ARABIDOPSIS THALIANA  SPX DOMAIN GENE 1 
               
               
                 AT5G20230 
                 YES 
                 ATBCB 
                 blue-copper-binding protein 
               
               
                 AT5G20240 
                 YES 
                 PI 
                 PISTILLATA 
               
               
                 AT5G24590 
                 YES 
                 ANAC91 
                   Arabidopsis  NAC domain containing protein 91 
               
               
                 AT5G24650 
                 YES 
               
               
                 AT5G24800 
                 YES 
                 ATBZIP9 
                   ARABIDOPSIS THALIANA  BASIC LEUCINE ZIPPER 9 
               
               
                 AT5G24930 
                 YES 
                 ATCOL4 
               
               
                 AT5G25280 
                 YES 
               
               
                 AT5G25930 
                 YES 
               
               
                 AT5G26030 
                 YES 
                 ATFC-I 
               
               
                 AT5G26340 
                 YES 
                 ATSTP13 
                 SUGAR TRANSPORT PROTEIN 13 
               
               
                 AT5G26360 
                 YES 
               
               
                 AT5G26760 
                 YES 
               
               
                 AT5G27420 
                 YES 
                 ATL31 
                   Arabidopsis  toxicos en levadura 31 
               
               
                 AT5G35735 
                 YES 
               
               
                 AT5G36260 
                 YES 
               
               
                 AT5G37500 
                 YES 
                 GORK 
                 gated outwardly-rectifying K+ channel 
               
               
                 AT5G37770 
                 YES 
                 CML24 
                 CALMODULIN-LIKE 24 
               
               
                 AT5G39580 
                 YES 
               
               
                 AT5G39670 
                 YES 
               
               
                 AT5G39680 
                 YES 
                 EMB2744 
                 EMBRYO DEFECTIVE 2744 
               
               
                 AT5G40690 
                 YES 
               
               
                 AT5G40780 
                 YES 
                 LHT1 
                 lysine histidine transporter 1 
               
               
                 AT5G41080 
                 YES 
                 AtGDPD2 
               
               
                 AT5G41810 
                 YES 
               
               
                 AT5G42050 
                 YES 
               
               
                 AT5G42370 
                 YES 
               
               
                 AT5G42380 
                 YES 
                 CML37 
                 calmodulin like 37 
               
               
                 AT5G42830 
                 YES 
               
               
                 AT5G43440 
                 YES 
               
               
                 AT5G43450 
                 YES 
               
               
                 AT5G43580 
                 YES 
                 UPI 
                 UNUSUAL SERINE PROTEASE INHIBITOR 
               
               
                 AT5G44320 
                 YES 
               
               
                 AT5G44330 
                 YES 
               
               
                 AT5G45110 
                 YES 
                 ATNPR3 
               
               
                 AT5G45140 
                 YES 
                 NRPC2 
                 nuclear RNA polymerase C2 
               
               
                 AT5G45350 
                 YES 
               
               
                 AT5G45630 
                 YES 
               
               
                 AT5G46780 
                 YES 
               
               
                 AT5G47200 
                 YES 
                 ATRAB1A 
                 RAB GTPase homolog 1A 
               
               
                 AT5G47210 
                 YES 
               
               
                 AT5G47220 
                 YES 
                 ATERF-2 
                 ETHYLENE RESPONSE FACTOR-2 
               
               
                 AT5G47230 
                 YES 
                 ATERF-5 
                 ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR-5 
               
               
                 AT5G47910 
                 YES 
                 ATRBOHD 
               
               
                 AT5G47960 
                 YES 
                 ATRABA4C 
                 RAB GTPase homolog A4C 
               
               
                 AT5G47970 
                 YES 
               
               
                 AT5G49030 
                 YES 
                 OVA2 
                 ovule abortion 2 
               
               
                 AT5G49220 
                 YES 
               
               
                 AT5G49480 
                 YES 
                 ATCP1 
                 Ca2+-binding protein 1 
               
               
                 AT5G49520 
                 YES 
                 ATWRKY48 
                   ARABIDOPSIS THALIANA  WRKY DNA-BINDING 
               
               
                   
                   
                   
                 PROTEIN 48 
               
               
                 AT5G50900 
                 YES 
               
               
                 AT5G52050 
                 YES 
               
               
                 AT5G52400 
                 YES 
                 CYP715A1 
                 cytochrome P45, family 715, subfamily A, polypeptide 1 
               
               
                 AT5G52410 
                 YES 
               
               
                 AT5G52750 
                 YES 
               
               
                 AT5G53110 
                 YES 
               
               
                 AT5G54490 
                 YES 
                 PBP1 
                 pinoid-binding protein 1 
               
               
                 AT5G55140 
                 YES 
               
               
                 AT5G55780 
                 YES 
               
               
                 AT5G56340 
                 YES 
                 ATCRT1 
               
               
                 AT5G56980 
                 YES 
               
               
                 AT5G57190 
                 YES 
                 PSD2 
                 phosphatidylserine decarboxylase 2 
               
               
                 AT5G57500 
                 YES 
               
               
                 AT5G57510 
                 YES 
               
               
                 AT5G57550 
                 YES 
                 XTH25 
                 xyloglucan endotransglucosylase/hydrolase 25 
               
               
                 AT5G57560 
                 YES 
                 TCH4 
                 Touch 4 
               
               
                 AT5G57720 
                 YES 
               
               
                 AT5G58060 
                 YES 
                 ATGP1 
               
               
                 AT5G58070 
                 YES 
                 ATTIL 
                 TEMPERATURE-INDUCED LIPOCALIN 
               
               
                 AT5G59450 
                 YES 
               
               
                 AT5G59490 
                 YES 
               
               
                 AT5G59820 
                 YES 
                 AtZAT12 
               
               
                 AT5G59830 
                 YES 
               
               
                 AT5G61520 
                 YES 
               
               
                 AT5G61890 
                 YES 
               
               
                 AT5G61910 
                 YES 
               
               
                 AT5G62520 
                 YES 
                 SRO5 
                 similar to RCD one 5 
               
               
                 AT5G62530 
                 YES 
                 ALDH12A1 
                 aldehyde dehydrogenase 12A1 
               
               
                 AT5G63130 
                 YES 
               
               
                 AT5G63780 
                 YES 
                 SHA1 
                 shoot apical meristem arrest 1 
               
               
                 AT5G63790 
                 YES 
                 ANAC12 
                 NAC domain containing protein 12 
               
               
                 AT5G64120 
                 YES 
               
               
                 AT5G64240 
                 YES 
                 AtMC3 
                 metacaspase 3 
               
               
                 AT5G64310 
                 YES 
                 AGP1 
                 arabinogalactan protein 1 
               
               
                 AT5G64650 
                 YES 
               
               
                 AT5G64660 
                 YES 
                 ATCMPG2 
               
               
                 AT5G64905 
                 YES 
                 PROPEP3 
                 elicitor peptide 3 precursor 
               
               
                 AT5G65205 
                 YES 
               
               
                 AT5G65300 
                 YES 
               
               
                 AT5G65660 
                 YES 
               
               
                 AT5G66055 
                 YES 
                 AKRP 
                 ankyrin repeat protein 
               
               
                 AT5G66060 
                 YES 
               
               
                 AT5G66460 
                 YES 
                 AtMAN7 
               
               
                 AT5G67080 
                 YES 
                 MAPKKK19 
                 mitogen-activated protein kinase kinase kinase 19 
               
               
                 AT5G67300 
                 YES 
                 ATMYB44 
                   ARABIDOPSIS THALIANA  MYB DOMAIN PROTEIN 44 
               
               
                 AT5G67310 
                 YES 
                 CYP81G1 
                 cytochrome P45, family 81, subfamily G, polypeptide 1 
               
               
                 AT5G67420 
                 YES 
                 ASL39 
                 ASYMMETRIC LEAVES2-LIKE 39 
               
               
                 AT5G67560 
                 YES 
                 ARLA1D 
                 ADP-ribosylation factor-like A1D 
               
               
                 AT1G01471 
                 NO 
               
               
                 AT1G02520 
                 NO 
                 ABCB11 
                 ATP-binding cassette B11 
               
               
                 AT1G02530 
                 NO 
                 ABCB12 
                 ATP-binding cassette B12 
               
               
                 AT1G02590 
                 NO 
               
               
                 AT1G02600 
                 NO 
               
               
                 AT1G02920 
                 NO 
                 ATGST11 
                   ARABIDOPSIS  GLUTATHIONE S-TRANSFERASE 11 
               
               
                 AT1G02930 
                 NO 
                 ATGST1 
                   ARABIDOPSIS  GLUTATHIONE S-TRANSFERASE 1 
               
               
                 AT1G03220 
                 NO 
               
               
                 AT1G05320 
                 NO 
               
               
                 AT1G05675 
                 NO 
               
               
                 AT1G07135 
                 NO 
               
               
                 AT1G08950 
                 NO 
               
               
                 AT1G09690 
                 NO 
               
               
                 AT1G09932 
                 NO 
               
               
                 AT1G10155 
                 NO 
                 ATPP2-A1 
                 phloem protein 2-A1 
               
               
                 AT1G11550 
                 NO 
               
               
                 AT1G13350 
                 NO 
               
               
                 AT1G13360 
                 NO 
               
               
                 AT1G14549 
                 NO 
               
               
                 AT1G14870 
                 NO 
                 AtPCR2 
               
               
                 AT1G15015 
                 NO 
               
               
                 AT1G15030 
                 NO 
               
               
                 AT1G15045 
                 NO 
               
               
                 AT1G15090 
                 NO 
               
               
                 AT1G16635 
                 NO 
               
               
                 AT1G17147 
                 NO 
               
               
                 AT1G18200 
                 NO 
                 AtRABA6b 
                 RAB GTPase homolog A6B 
               
               
                 AT1G18300 
                 NO 
                 atnudt4 
                 nudix hydrolase homolog 4 
               
               
                 AT1G18745 
                 NO 
               
               
                 AT1G21395 
                 NO 
               
               
                 AT1G24160 
                 NO 
               
               
                 AT1G27695 
                 NO 
               
               
                 AT1G29640 
                 NO 
               
               
                 AT1G30720 
                 NO 
               
               
                 AT1G30730 
                 NO 
               
               
                 AT1G32928 
                 NO 
               
               
                 AT1G42980 
                 NO 
               
               
                 AT1G49610 
                 NO 
               
               
                 AT1G53625 
                 NO 
               
               
                 AT1G55340 
                 NO 
               
               
                 AT1G56240 
                 NO 
                 AtPP2-B13 
                 phloem protein 2-B13 
               
               
                 AT1G56242 
                 NO 
               
               
                 AT1G57690 
                 NO 
               
               
                 AT1G57980 
                 NO 
               
               
                 AT1G57990 
                 NO 
                 ATPUP18 
                 purine permease 18 
               
               
                 AT1G61880 
                 NO 
               
               
                 AT1G62870 
                 NO 
               
               
                 AT1G68770 
                 NO 
               
               
                 AT1G68845 
                 NO 
               
               
                 AT1G69130 
                 NO 
               
               
                 AT1G69290 
                 NO 
               
               
                 AT1G69300 
                 NO 
               
               
                 AT1G70390 
                 NO 
               
               
                 AT1G70780 
                 NO 
               
               
                 AT1G70782 
                 NO 
                 CPuORF28 
                 conserved peptide upstream open reading frame 28 
               
               
                 AT1G71520 
                 NO 
               
               
                 AT1G71528 
                 NO 
               
               
                 AT1G74929 
                 NO 
               
               
                 AT1G76680 
                 NO 
                 ATOPR1 
                   ARABIDOPSIS  12-OXOPHYTODIENOATE REDUCTASE 1 
               
               
                 AT1G76690 
                 NO 
                 ATOPR2 
                   ARABIDOPSIS  12-OXOPHYTODIENOATE REDUCTASE 2 
               
               
                 AT1G78830 
                 NO 
               
               
                 AT1G78850 
                 NO 
               
               
                 AT1G79240 
                 NO 
               
               
                 AT1G79980 
                 NO 
               
               
                 AT2G07772 
                 NO 
               
               
                 AT2G17190 
                 NO 
               
               
                 AT2G17830 
                 NO 
               
               
                 AT2G18193 
                 NO 
               
               
                 AT2G19260 
                 NO 
               
               
                 AT2G20562 
                 NO 
               
               
                 AT2G23118 
                 NO 
               
               
                 AT2G23321 
                 NO 
               
               
                 AT2G25130 
                 NO 
               
               
                 AT2G30020 
                 NO 
               
               
                 AT2G31030 
                 NO 
                 ORP1B 
                 OSBP(oxysterol binding protein)-related protein 1B 
               
               
                 AT2G31345 
                 NO 
               
               
                 AT2G32190 
                 NO 
               
               
                 AT2G32210 
                 NO 
               
               
                 AT2G36770 
                 NO 
               
               
                 AT2G36800 
                 NO 
                 DOGT1 
                 don-glucosyltransferase 1 
               
               
                 AT2G38230 
                 NO 
                 ATPDX1.1 
                   ARABIDOPSIS THALIANA  PYRIDOXINE BIOSYNTHESIS 
               
               
                   
                   
                   
                 1.1 
               
               
                 AT2G38823 
                 NO 
               
               
                 AT2G41415 
                 NO 
               
               
                 AT2G41440 
                 NO 
               
               
                 AT2G43120 
                 NO 
               
               
                 AT2G45390 
                 NO 
               
               
                 AT2G45950 
                 NO 
                 ASK2 
                 SKP1-like 2 
               
               
                 AT2G46995 
                 NO 
               
               
                 AT3G02030 
                 NO 
               
               
                 AT3G02468 
                 NO 
                 CPuORF9 
                 conserved peptide upstream open reading frame 9 
               
               
                 AT3G02470 
                 NO 
                 SAMDC 
                 S-adenosylmethionine decarboxylase 
               
               
                 AT3G10815 
                 NO 
               
               
                 AT3G10986 
                 NO 
               
               
                 AT3G11950 
                 NO 
               
               
                 AT3G13080 
                 NO 
                 ABCC3 
                 ATP-binding cassette C3 
               
               
                 AT3G13300 
                 NO 
                 VCS 
                 VARICOSE 
               
               
                 AT3G13432 
                 NO 
               
               
                 AT3G13600 
                 NO 
               
               
                 AT3G14362 
                 NO 
                 DVL19 
                 DEVIL 19 
               
               
                 AT3G18950 
                 NO 
               
               
                 AT3G18952 
                 NO 
               
               
                 AT3G23470 
                 NO 
               
               
                 AT3G25597 
                 NO 
               
               
                 AT3G29000 
                 NO 
               
               
                 AT3G30770 
                 NO 
               
               
                 AT3G46080 
                 NO 
               
               
                 AT3G46090 
                 NO 
                 ZAT7 
               
               
                 AT3G47790 
                 NO 
                 ABCA8 
                 ATP-binding cassette A8 
               
               
                 AT3G48515 
                 NO 
               
               
                 AT3G49570 
                 NO 
                 LSU3 
                 RESPONSE TO LOW SULFUR 3 
               
               
                 AT3G49796 
                 NO 
               
               
                 AT3G56790 
                 NO 
               
               
                 AT3G62420 
                 NO 
                 ATBZIP53 
                 basic region/leucine zipper motif 53 
               
               
                 AT3G62422 
                 NO 
                 CPuORF3 
                 conserved peptide upstream open reading frame 3 
               
               
                 AT4G01360 
                 NO 
                 BPS3 
                 BYPASS 3 
               
               
                 AT4G03635 
                 NO 
               
               
                 AT4G05048 
                 NO 
                 U49.1 
               
               
                 AT4G08555 
                 NO 
               
               
                 AT4G09040 
                 NO 
               
               
                 AT4G12731 
                 NO 
               
               
                 AT4G12735 
                 NO 
               
               
                 AT4G13395 
                 NO 
                 DVL1 
                 DEVIL 1 
               
               
                 AT4G15760 
                 NO 
                 MO1 
                 monooxygenase 1 
               
               
                 AT4G17616 
                 NO 
               
               
                 AT4G20920 
                 NO 
               
               
                 AT4G21830 
                 NO 
                 ATMSRB7 
                 methionine sulfoxide reductase B7 
               
               
                 AT4G21910 
                 NO 
               
               
                 AT4G21920 
                 NO 
               
               
                 AT4G22590 
                 NO 
                 TPPG 
                 trehalose-6-phosphate phosphatase G 
               
               
                 AT4G22592 
                 NO 
                 CPuORF27 
                 conserved peptide upstream open reading frame 27 
               
               
                 AT4G22710 
                 NO 
                 CYP76A2 
                 cytochrome P45, family 76, subfamily A, polypeptide 2 
               
            
           
           
               
               
               
            
               
                 AT4G23550 
                 NO 
                 ATWRKY29 
               
            
           
           
               
               
               
               
            
               
                 AT4G23560 
                 NO 
                 AtGH9B15 
                 glycosyl hydrolase 9B15 
               
               
                 AT4G24565 
                 NO 
               
               
                 AT4G27585 
                 NO 
               
               
                 AT4G28470 
                 NO 
                 ATRPN1B 
               
               
                 AT4G32480 
                 NO 
               
               
                 AT4G34131 
                 NO 
                 UGT73B3 
                 UDP-glucosyl transferase 73B3 
               
               
                 AT4G34412 
                 NO 
               
               
                 AT4G36648 
                 NO 
               
               
                 AT4G37390 
                 NO 
                 AUR3 
                 AUXIN UPREGULATED 3 
               
               
                 AT4G37608 
                 NO 
               
               
                 AT5G01542 
                 NO 
               
               
                 AT5G01595 
                 NO 
               
               
                 AT5G02815 
                 NO 
               
               
                 AT5G03204 
                 NO 
               
               
                 AT5G06310 
                 NO 
                 AtPOT1b 
                 protection of telomeres 1b 
               
               
                 AT5G06990 
                 NO 
               
               
                 AT5G08770 
                 NO 
               
               
                 AT5G08780 
                 NO 
               
               
                 AT5G08790 
                 NO 
                 anac81 
                   Arabidopsis  NAC domain containing protein 81 
               
               
                 AT5G13210 
                 NO 
               
               
                 AT5G15960 
                 NO 
                 KIN1 
               
               
                 AT5G15970 
                 NO 
                 AtCor6.6 
               
               
                 AT5G18480 
                 NO 
                 PGSIP6 
                 plant glycogenin-like starch initiation protein 6 
               
               
                 AT5G19230 
                 NO 
               
               
                 AT5G20010 
                 NO 
                 ATRAN1 
                   ARABIDOPSIS THALIANA  RAS-RELATED NUCLEAR 
               
               
                   
                   
                   
                 PROTEIN 
               
               
                 AT5G20225 
                 NO 
               
               
                 AT5G21930 
                 NO 
                 ATHMA8 
                   ARABIDOPSIS  HEAVY METAL ATPASE 8 
               
               
                 AT5G21940 
                 NO 
               
               
                 AT5G24630 
                 NO 
                 BIN4 
                 brassinosteroid-insensitive4 
               
               
                 AT5G24640 
                 NO 
               
               
                 AT5G36920 
                 NO 
               
               
                 AT5G39581 
                 NO 
               
               
                 AT5G40700 
                 NO 
               
               
                 AT5G40880 
                 NO 
               
               
                 AT5G42053 
                 NO 
               
               
                 AT5G43570 
                 NO 
               
               
                 AT5G43620 
                 NO 
               
               
                 AT5G43650 
                 NO 
                 BHLH92 
               
               
                 AT5G47229 
                 NO 
               
               
                 AT5G51730 
                 NO 
               
               
                 AT5G53300 
                 NO 
                 UBC1 
                 ubiquitin-conjugating enzyme 1 
               
               
                 AT5G53588 
                 NO 
                 CPuORF5 
                 conserved peptide upstream open reading frame 5 
               
               
                 AT5G53590 
                 NO 
               
               
                 AT5G53592 
                 NO 
               
               
                 AT5G54100 
                 NO 
               
               
                 AT5G55870 
                 NO 
               
               
                 AT5G56975 
                 NO 
               
               
                 AT5G57010 
                 NO 
               
               
                 AT5G57015 
                 NO 
                 ckl12 
                 casein kinase I-like 12 
               
               
                 AT5G61900 
                 NO 
                 BON 
               
               
                 AT5G64320 
                 NO 
               
               
                 AT5G64401 
                 NO 
               
               
                 AT5G65207 
                 NO 
               
               
                 AT5G65687 
                 NO 
               
               
                 AT5G65690 
                 NO 
                 PCK2 
                 phosphoenolpyruvate carboxykinase 2 
               
               
                   
               
            
           
         
       
     
     Integration of TF-regulation and TF-binding data identifies three modes-of-action for bZIP1 and its primary targets: poised, stable, and transient. To understand the underlying mechanisms by which bZIP1 propagates N-signals through a GRN, primary targets identified either by TF-induced gene regulation or TF-binding were integrated. To enable a direct comparison of transcriptome and TF-binding data, of the 850 genes bound to bZIP1, 187 genes not represented on the ATH1 microarray were omitted. 136 genes that did not pass the stringent filters for effects of protoplasting, DEX, or CHX treatment were also omitted. This resulted in a filtered total of 527 bZIP1 bound genes ( FIG. 29A ). The resulting list of 1,308 high-confidence primary targets of bZIP1 identified either by TF-mediated gene regulation (901 genes) or TF-binding (527 genes) were integrated and analyzed for biological relevance to the N-signal ( FIG. 29 ). The intersection of the TF-regulation and TF-binding data identified three classes of primary targets, representing distinct modes-of-action for bZIP1 in N-signal propagation ( FIG. 29A ; Table 19). Class I targets (407 genes) were deemed “Poised”, as they are bound to bZIP1 but show no significant TF-induced gene regulation. Class II targets (120 genes), are deemed “Stable”, as they are both bound and regulated by bZIP1. Unexpectedly, Class III targets (781 genes)—the largest class of bZIP1 primary target genes—were deemed “Transient” as they are regulated by bZIP1 perturbation, but not detectably bound to it. We note that these are not indirect TF targets, as ChIP-seq is able to detect direct or indirect binding by bZIP1, i.e., as part of a protein complex. They also cannot be dismissed as secondary targets of bZIP1, as they are regulated in response to DEX-induced bZIP1 perturbation performed in the presence of CHX, which blocks the regulation of secondary targets. 
     
       
         
           
               
             
               
                 TABLE 19 
               
               
                   
               
               
                 Classes of bZIP1 primary targets: Class I, Poised; Class II Stable (IIA induced; IIB repressed); and Class 
               
               
                 III transient (IIIA induced, IIIB repressed) listed as 5 subclasses. Gene annotations are from TAIR10. 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                 Class I. BN: Bind but no regulation 
                   
               
            
           
           
               
               
               
            
               
                 At1g14560 
                 Mitochondrial substrate carrier family protein 
                 Class I 
               
               
                 At2g23120 
                 Late embryogenesis abundant protein, group 6 
                 Class I 
               
               
                 At5g57720 
                 AP2/B3-like transcriptional factor family protein 
                 Class I 
               
               
                 At5g02820 
                 BIN5, RHL2, Spo11/DNA topoisomerase VI, subunit A protein 
                 Class I 
               
               
                 At4g09630 
                 Protein of unknown function (DUF616) 
                 Class I 
               
               
                 At3g52700 
                 unknown protein; Has 6 Blast hits to 6 proteins in 2 species: Archae - 0; Bacteria - 0; Metazoa - 
                 Class I 
               
               
                   
                 0; Fungi - 0; Plants - 6; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At1g16640 
                 AP2/B3-like transcriptional factor family protein 
                 Class I 
               
               
                 At3g10920 
                 ATMSD1, MEE33, MSD1, manganese superoxide dismutase 1 
                 Class I 
               
               
                 At1g61820 
                 BGLU46, beta glucosidase 46 
                 Class I 
               
               
                 At4g39080 
                 VHA-A3, vacuolar proton ATPase A3 
                 Class I 
               
               
                 At1g53720 
                 ATCYP59, CYP59, cyclophilin 59 
                 Class I 
               
               
                 At3g29290 
                 emb2076, Pentatricopeptide repeat (PPR) superfamily protein 
                 Class I 
               
               
                 At1g64390 
                 AtGH9C2, GH9C2, glycosyl hydrolase 9C2 
                 Class I 
               
               
                 At5g01500 
                 TAAC, thylakoid ATP/ADP carrier 
                 Class I 
               
               
                 At3g45980 
                 H2B, HTB9, Histone superfamily protein 
                 Class I 
               
               
                 At1g32920 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: response 
                 Class I 
               
               
                   
                 to wounding; LOCATED IN: endomembrane system; EXPRESSED IN: 23 plant structures; 
               
               
                   
                 EXPRESSED DURING: 13 growth stages; BEST  Arabidopsis thaliana  protein match is: 
               
               
                   
                 unknown protein (TAIR: AT1G32928.1); Has 42 Blast hits to 42 proteins in 8 species: Archae - 
               
               
                   
                 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 42; Viruses - 0; Other Eukaryotes - 0 (source: 
               
               
                   
                 NCBI BLink). 
               
               
                 At4g23190 
                 AT-RLK3, CRK11, cysteine-rich RLK (RECEPTOR-like protein kinase) 11 
                 Class I 
               
               
                 At2g36230 
                 APG10, HISN3, Aldolase-type TIM barrel family protein 
                 Class I 
               
               
                 At2g26690 
                 Major facilitator superfamily protein 
                 Class I 
               
               
                 At1g73080 
                 ATPEPR1, PEPR1, PEP1 receptor 1 
                 Class I 
               
               
                 At4g35580 
                 NTL9, NAC transcription factor-like 9 
                 Class I 
               
               
                 At4g33950 
                 ATOST1, OST1, P44, SNRK2-6, SNRK2.6, SRK2E, Protein kinase superfamily protein 
                 Class I 
               
               
                 At5g67560 
                 ARLA1D, ATARLA1D, ADP-ribosylation factor-like A1D 
                 Class I 
               
               
                 At5g10180 
                 AST68, SULTR2; 1, slufate transporter 2; 1 
                 Class I 
               
               
                 At5g42370 
                 Calcineurin-like metallo-phosphoesterase superfamily protein 
                 Class I 
               
               
                 At5g26760 
                 unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 
                 Class I 
               
               
                   
                 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 
               
               
                   
                 (source: NCBI BLink). 
               
               
                 At4g17615 
                 ATCBL1, CBL1, SCABP5, calcineurin B-like protein 1 
                 Class I 
               
               
                 At1g29690 
                 CAD1, MAC/Perforin domain-containing protein 
                 Class I 
               
               
                 At3g16857 
                 ARR1, RR1, response regulator 1 
                 Class I 
               
               
                 At3g15500 
                 ANAC055, ATNAC3, NAC055, NAC3, NAC domain containing protein 3 
                 Class I 
               
               
                 At5g64650 
                 Ribosomal protein L17 family protein 
                 Class I 
               
               
                 At3g13790 
                 ATBFRUCT1, ATCWINV1, Glycosyl hydrolases family 32 protein 
                 Class I 
               
               
                 At5g05600 
                 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein 
                 Class I 
               
               
                 At4g01370 
                 ATMPK4, MPK4, MAP kinase 4 
                 Class I 
               
               
                 At2g41430 
                 CID1, ERD15, LSR1, dehydration-induced protein (ERD15) 
                 Class I 
               
               
                 At3g22900 
                 NRPD7, RNA polymerase Rpb7-like, N-terminal domain 
                 Class I 
               
               
                 At1g14040 
                 EXS (ERD1/XPR1/SYG1) family protein 
                 Class I 
               
               
                 At3g52930 
                 Aldolase superfamily protein 
                 Class I 
               
               
                 At2g29080 
                 ftsh3, FTSH protease 3 
                 Class I 
               
               
                 At4g16680 
                 P-loop containing nucleoside triphosphate hydrolases superfamily protein 
                 Class I 
               
               
                 At4g39640 
                 GGT1, gamma-glutamyl transpeptidase 1 
                 Class I 
               
               
                 At2g32120 
                 HSP70T-2, heat-shock protein 70T-2 
                 Class I 
               
               
                 At1g23480 
                 ATCSLA03, ATCSLA3, CSLA03, CSLA03, CSLA3, cellulose synthase-like A3 
                 Class I 
               
               
                 At1g15080 
                 ATLPP2, ATPAP2, LPP2, lipid phosphate phosphatase 2 
                 Class I 
               
               
                 At3g13320 
                 atcax2, CAX2, cation exchanger 2 
                 Class I 
               
               
                 At1g43900 
                 Protein phosphatase 2C family protein 
                 Class I 
               
               
                 At2g04040 
                 ATDTX1, TX1, MATE efflux family protein 
                 Class I 
               
               
                 At3g56800 
                 acam-3, CAM3, calmodulin 3 
                 Class I 
               
               
                 At2g30240 
                 ATCHX13, CHX13, Cation/hydrogen exchanger family protein 
                 Class I 
               
               
                 At4g12730 
                 FLA2, FASCICLIN-like arabinogalactan 2 
                 Class I 
               
               
                 At5g53110 
                 RING/U-box superfamily protein 
                 Class I 
               
               
                 At5g05790 
                 Duplicated homeodomain-like superfamily protein 
                 Class I 
               
               
                 At3g19020 
                 Leucine-rich repeat (LRR) family protein 
                 Class I 
               
               
                 At5g17360 
                 BEST  Arabidopsis thaliana  protein match is: DNA LIGASE 6 (TAIR: AT1G66730.1); Has 
                 Class I 
               
               
                   
                 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 
               
               
                   
                 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink). 
               
               
                 At3g25610 
                 ATPase E1-E2 type family protein/haloacid dehalogenase-like hydrolase family protein 
                 Class I 
               
               
                 At1g61890 
                 MATE efflux family protein 
                 Class I 
               
               
                 At5g56980 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class I 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 18 
               
               
                   
                 plant structures; EXPRESSED DURING: 12 growth stages; BEST  Arabidopsis thaliana   
               
               
                   
                 protein match is: unknown protein (TAIR: AT4G26130.1); Has 30201 Blast hits to 17322 
               
               
                   
                 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 
               
               
                   
                 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink). 
               
               
                 At5g07730 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class I 
               
               
                   
                 (TAIR: AT5G61360.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At3g59360 
                 ATUTR6, UTR6, UDP-galactose transporter 6 
                 Class I 
               
               
                 At5g44320 
                 Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) 
                 Class I 
               
               
                 At4g33666 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class I 
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast; EXPRESSED IN: 19 plant 
               
               
                   
                 structures; EXPRESSED DURING: 11 growth stages; Has 30201 Blast hits to 17322 proteins 
               
               
                   
                 in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; 
               
               
                   
                 Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink). 
               
               
                 At5g42050 
                 DCD (Development and Cell Death) domain protein 
                 Class I 
               
               
                 At4g19210 
                 ATRLI2, RLI2, RNAse 1 inhibitor protein 2 
                 Class I 
               
               
                 At5g43450 
                 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein 
                 Class I 
               
               
                 At2g07050 
                 CAS1, cycloartenol synthase 1 
                 Class I 
               
               
                 At1g60190 
                 ARM repeat superfamily protein 
                 Class I 
               
               
                 At1g68840 
                 EDF2, RAP2.8, RAV2, TEM2, related to ABI3/VP1 2 
                 Class I 
               
               
                 At4g36640 
                 Sec14p-like phosphatidylinositol transfer family protein 
                 Class I 
               
               
                 At3g53480 
                 ABCG37, ATPDR9, PDR9, PIS1, pleiotropic drug resistance 9 
                 Class I 
               
               
                 At2g31690 
                 alpha/beta-Hydrolases superfamily protein 
                 Class I 
               
               
                 At5g61910 
                 DCD (Development and Cell Death) domain protein 
                 Class I 
               
               
                 At1g35140 
                 EXL7, PHI-1, Phosphate-responsive 1 family protein 
                 Class I 
               
               
                 At3g04730 
                 IAA16, indoleacetic acid-induced protein 16 
                 Class I 
               
               
                 At2g45400 
                 BEN1, NAD(P)-binding Rossmann-fold superfamily protein 
                 Class I 
               
               
                 At1g30700 
                 FAD-binding Berberine family protein 
                 Class I 
               
               
                 At4g00170 
                 Plant VAMP (vesicle-associated membrane protein) family protein 
                 Class I 
               
               
                 At4g39090 
                 RD19, RD19A, Papain family cysteine protease 
                 Class I 
               
               
                 At1g05330 
                 unknown protein; Has 6 Blast hits to 6 proteins in 2 species: Archae - 0; Bacteria - 0; Metazoa - 
                 Class I 
               
               
                   
                 0; Fungi - 0; Plants - 6; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g01750 
                 Protein of unknown function (DUF567) 
                 Class I 
               
               
                 At3g10985 
                 ATWI-12, SAG20, WI12, senescence associated gene 20 
                 Class I 
               
               
                 At5g10690 
                 pentatricopeptide (PPR) repeat-containing protein/CBS domain-containing protein 
                 Class I 
               
               
                 At3g17390 
                 MAT4, MTO3, SAMS3, S-adenosylmethionine synthetase family protein 
                 Class I 
               
               
                 At2g18690 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class I 
               
               
                   
                 biological_process unknown; LOCATED IN: membrane; EXPRESSED IN: 17 plant 
               
               
                   
                 structures; EXPRESSED DURING: 9 growth stages; CONTAINS InterPro DOMAIN/s: 
               
               
                   
                 Protein of unknown function DUF975 (InterPro: IPR010380); BEST  Arabidopsis thaliana   
               
               
                   
                 protein match is: unknown protein (TAIR: AT2G18680.1); Has 213 Blast hits to 211 proteins 
               
               
                   
                 in 20 species: Archae - 0; Bacteria - 8; Metazoa - 0; Fungi - 0; Plants - 205; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At3g52800 
                 A20/AN1-like zinc finger family protein 
                 Class I 
               
               
                 At2g38480 
                 Uncharacterised protein family (UPF0497) 
                 Class I 
               
               
                 At5g52750 
                 Heavy metal transport/detoxification superfamily protein 
                 Class I 
               
               
                 At2g18190 
                 P-loop containing nucleoside triphosphate hydrolases superfamily protein 
                 Class I 
               
               
                 At5g52400 
                 CYP715A1, cytochrome P450, family 715, subfamily A, polypeptide 1 
                 Class I 
               
               
                 At1g11670 
                 MATE efflux family protein 
                 Class I 
               
               
                 At4g25570 
                 ACYB-2, Cytochrome b561/ferric reductase transmembrane protein family 
                 Class I 
               
               
                 At4g34160 
                 CYCD3, CYCD3; 1, CYCLIN D3; 1 
                 Class I 
               
               
                 At3g22370 
                 AOX1A, ATAOX1A, alternative oxidase 1A 
                 Class I 
               
               
                 At1g01550 
                 BPS1, Protein of unknown function (DUF793) 
                 Class I 
               
               
                 At3g23250 
                 ATMYB15, ATY19, MYB15, myb domain protein 15 
                 Class I 
               
               
                 At3g53610 
                 ATRAB8, AtRab8B, AtRABE1a, RAB8, RAB GTPase homolog 8 
                 Class I 
               
               
                 At5g45110 
                 ATNPR3, NPR3, NPR1-like protein 3 
                 Class I 
               
               
                 At5g45140 
                 NRPC2, nuclear RNA polymerase C2 
                 Class I 
               
               
                 At3g50980 
                 XERO1, dehydrin xero 1 
                 Class I 
               
               
                 At5g58060 
                 ATGP1, ATYKT61, YKT61, SNARE-like superfamily protein 
                 Class I 
               
               
                 At1g79990 
                 structural molecules 
                 Class I 
               
               
                 At5g03210 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class I 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 11 
               
               
                   
                 plant structures; EXPRESSED DURING: 7 growth stages; Has 6 Blast hits to 6 proteins in 2 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 6; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g57550 
                 XTH25, XTR3, xyloglucan endotransglucosylase/hydrolase 25 
                 Class I 
               
               
                 At1g61360 
                 S-locus lectin protein kinase family protein 
                 Class I 
               
               
                 At3g19240 
                 Vacuolar import/degradation, Vid27-related protein 
                 Class I 
               
               
                 At5g66060 
                 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein 
                 Class I 
               
               
                 At4g04500 
                 CRK37, cysteine-rich RLK (RECEPTOR-like protein kinase) 37 
                 Class I 
               
               
                 At1g32070 
                 ATNSI, NSI, nuclear shuttle interacting 
                 Class I 
               
               
                 At5g49220 
                 Protein of unknown function (DUF789) 
                 Class I 
               
               
                 At2g04050 
                 MATE efflux family protein 
                 Class I 
               
               
                 At1g09070 
                 (AT)SRC2, SRC2, soybean gene regulated by cold-2 
                 Class I 
               
               
                 At5g55780 
                 Cysteine/Histidine-rich C1 domain family protein 
                 Class I 
               
               
                 At5g06290 
                 2-Cys Prx B, 2CPB, 2-cysteine peroxiredoxin B 
                 Class I 
               
               
                 At1g12960 
                 Ribosomal protein L18e/L15 superfamily protein 
                 Class I 
               
               
                 At3g46620 
                 zinc finger (C3HC4-type RING finger) family protein 
                 Class I 
               
               
                 At3g55640 
                 Mitochondrial substrate carrier family protein 
                 Class I 
               
               
                 At5g01960 
                 RING/U-box superfamily protein 
                 Class I 
               
               
                 At1g35910 
                 Haloacid dehalogenase-like hydrolase (HAD) superfamily protein 
                 Class I 
               
               
                 At1g29680 
                 Protein of unknown function (DUF1264) 
                 Class I 
               
               
                 At1g14530 
                 THH1, Protein of unknown function (DUF1084) 
                 Class I 
               
               
                 At5g06320 
                 NHL3, NDR1/HIN1-like 3 
                 Class I 
               
               
                 At1g05680 
                 UGT74E2, Uridine diphosphate glycosyltransferase 74E2 
                 Class I 
               
               
                 At4g27270 
                 Quinone reductase family protein 
                 Class I 
               
               
                 At3g50970 
                 LTI30, XERO2, dehydrin family protein 
                 Class I 
               
               
                 At5g64240 
                 AtMC3, MC3, metacaspase 3 
                 Class I 
               
               
                 At3g02040 
                 SRG3, senescence-related gene 3 
                 Class I 
               
               
                 At4g05320 
                 UBQ10, polyubiquitin 10 
                 Class I 
               
               
                 At3g16860 
                 COBL8, COBRA-like protein 8 precursor 
                 Class I 
               
               
                 At5g04750 
                 F1F0-ATPase inhibitor protein, putative 
                 Class I 
               
               
                 At4g36500 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class I 
               
               
                   
                 biological_process unknown; LOCATED IN: mitochondrion; EXPRESSED IN: 22 plant 
               
               
                   
                 structures; EXPRESSED DURING: 13 growth stages; BEST  Arabidopsis thaliana  protein 
               
               
                   
                 match is: unknown protein (TAIR: AT2G18210.1); Has 50 Blast hits to 50 proteins in 7 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 50; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g17460 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: response 
                 Class I 
               
               
                   
                 to salt stress; LOCATED IN: mitochondrion; Has 30201 Blast hits to 17322 proteins in 780 
               
               
                   
                 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 
               
               
                   
                 0; Other Eukaryotes - 2996 (source: NCBI BLink). 
               
               
                 At3g49530 
                 ANAC062, NAC062, NTL6, NAC domain containing protein 62 
                 Class I 
               
               
                 At1g22080 
                 Cysteine proteinases superfamily protein 
                 Class I 
               
               
                 At4g37260 
                 ATMYB73, MYB73, myb domain protein 73 
                 Class I 
               
               
                 At5g02240 
                 NAD(P)-binding Rossmann-fold superfamily protein 
                 Class I 
               
               
                 At1g01720 
                 ANAC002, ATAF1, NAC (No Apical Meristem) domain transcriptional regulator superfamily 
                 Class I 
               
               
                   
                 protein 
               
               
                 At5g13470 
                 unknown protein; Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; 
                 Class I 
               
               
                   
                 Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At1g59870 
                 ABCG36, ATABCG36, ATPDR8, PDR8, PEN3, ABC-2 and Plant PDR ABC-type transporter 
                 Class I 
               
               
                   
                 family protein 
               
               
                 At3g52450 
                 PUB22, plant U-box 22 
                 Class I 
               
               
                 At1g49520 
                 SWIB complex BAF60b domain-containing protein 
                 Class I 
               
               
                 At1g78290 
                 SNRK2-8, SNRK2.8, SRK2C, Protein kinase superfamily protein 
                 Class I 
               
               
                 At3g63380 
                 ATPase E1-E2 type family protein/haloacid dehalogenase-like hydrolase family protein 
                 Class I 
               
               
                 At5g25930 
                 Protein kinase family protein with leucine-rich repeat domain 
                 Class I 
               
               
                 At4g24580 
                 REN1, Rho GTPase activation protein (RhoGAP) with PH domain 
                 Class I 
               
               
                 At1g80850 
                 DNA glycosylase superfamily protein 
                 Class I 
               
               
                 At5g37500 
                 GORK, gated outwardly-rectifying K+ channel 
                 Class I 
               
               
                 At4g21850 
                 ATMSRB9, MSRB9, methionine sulfoxide reductase B9 
                 Class I 
               
               
                 At3g09440 
                 Heat shock protein 70 (Hsp 70) family protein 
                 Class I 
               
               
                 At3g14940 
                 ATPPC3, PPC3, phosphoenolpyruvate carboxylase 3 
                 Class I 
               
               
                 At2g27090 
                 Protein of unknown function (DUF630 and DUF632) 
                 Class I 
               
               
                 At3g45730 
                 unknown protein; Has 3 Blast hits to 3 proteins in 1 species: Archae - 0; Bacteria - 0; Metazoa - 
                 Class I 
               
               
                   
                 0; Fungi - 0; Plants - 3; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g63780 
                 SHA1, RING/FYVE/PHD zinc finger superfamily protein 
                 Class I 
               
               
                 At3g08590 
                 Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent 
                 Class I 
               
               
                 At2g40000 
                 ATHSPRO2, HSPRO2, ortholog of sugar beet HS1 PRO-1 2 
                 Class I 
               
               
                 At5g66055 
                 AKRP, EMB16, EMB2036, ankyrin repeat protein 
                 Class I 
               
               
                 At1g17870 
                 ATEGY3, EGY3, ethylene-dependent gravitropism-deficient and yellow-green-like 3 
                 Class I 
               
               
                 At1g69220 
                 SIK1, Protein kinase superfamily protein 
                 Class I 
               
               
                 At5g20240 
                 PI, K-box region and MADS-box transcription factor family protein 
                 Class I 
               
               
                 At1g68760 
                 ATNUDT1, ATNUDX1, NUDX1, NUDX1, nudix hydrolase 1 
                 Class I 
               
               
                 At1g20440 
                 AtCOR47, COR47, RD17, cold-regulated 47 
                 Class I 
               
               
                 At1g19180 
                 JAZ1, TIFY10A, jasmonate-zim-domain protein 1 
                 Class I 
               
               
                 At5g52410 
                 CONTAINS InterPro DOMAIN/s: S-layer homology domain (InterPro: IPR001119); BEST 
                 Class I 
               
               
                   
                   Arabidopsis thaliana  protein match is: unknown protein (TAIR: AT5G23890.1); Has 30201 
               
               
                   
                 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; 
               
               
                   
                 Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink). 
               
               
                 At5g39580 
                 Peroxidase superfamily protein 
                 Class I 
               
               
                 At5g15980 
                 Pentatricopeptide repeat (PPR) superfamily protein 
                 Class I 
               
               
                 At3g24050 
                 GATA1, GATA transcription factor 1 
                 Class I 
               
               
                 At1g61870 
                 PPR336, pentatricopeptide repeat 336 
                 Class I 
               
               
                 At5g10710 
                 INVOLVED IN: chromosome segregation, cell division; LOCATED IN: chromosome, 
                 Class I 
               
               
                   
                 centromeric region, nucleus; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 
               
               
                   
                 13 growth stages; CONTAINS InterPro DOMAIN/s: Centromere protein Cenp-O 
               
               
                   
                 (InterPro: IPR018464); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At1g50750 
                 Plant mobile domain protein family 
                 Class I 
               
               
                 At5g05420 
                 FKBP-like peptidyl-prolyl cis-trans isomerase family protein 
                 Class I 
               
               
                 At1g09080 
                 BIP3, Heat shock protein 70 (Hsp 70) family protein 
                 Class I 
               
               
                 At1g58210 
                 EMB1674, kinase interacting family protein 
                 Class I 
               
               
                 At5g02020 
                 Encodes a protein involved in salt tolerance, names SIS (Salt Induced Serine rich). 
                 Class I 
               
               
                 At2g39190 
                 ATATH8, Protein kinase superfamily protein 
                 Class I 
               
               
                 At1g62790 
                 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein 
                 Class I 
               
               
                 At4g26040 
                 unknown protein; Has 2 Blast hits to 2 proteins in 1 species: Archae - 0; Bacteria - 0; Metazoa - 
                 Class I 
               
               
                   
                 0; Fungi - 0; Plants - 2; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At3g23460 
                 S-adenosyl-L-methionine-dependent methyltransferases superfamily protein 
                 Class I 
               
               
                 At2g36950 
                 Heavy metal transport/detoxification superfamily protein 
                 Class I 
               
               
                 At5g04330 
                 Cytochrome P450 superfamily protein 
                 Class I 
               
               
                 At2g23320 
                 WRKY15, WRKY DNA-binding protein 15 
                 Class I 
               
               
                 At2g23810 
                 TET8, tetraspanin8 
                 Class I 
               
               
                 At3g03890 
                 FMN binding 
                 Class I 
               
               
                 At1g17180 
                 ATGSTU25, GSTU25, glutathione S-transferase TAU 25 
                 Class I 
               
               
                 At1g56660 
                 unknown protein; Has 665200 Blast hits to 205811 proteins in 4684 species: Archae - 3320; 
                 Class I 
               
               
                   
                 Bacteria - 107592; Metazoa - 249086; Fungi - 76753; Plants - 38542; Viruses - 3008; Other 
               
               
                   
                 Eukaryotes - 186899 (source: NCBI BLink). 
               
               
                 At4g33670 
                 NAD(P)-linked oxidoreductase superfamily protein 
                 Class I 
               
               
                 At1g05340 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class I 
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast; EXPRESSED IN: 14 plant 
               
               
                   
                 structures; EXPRESSED DURING: 7 growth stages; BEST  Arabidopsis thaliana  protein 
               
               
                   
                 match is: unknown protein (TAIR: AT2G32210.1); Has 189 Blast hits to 189 proteins in 27 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 21; Plants - 168; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At3g55440 
                 ATCTIMC, CYTOTPI, TPI, triosephosphate isomerase 
                 Class I 
               
               
                 At3g49000 
                 RNA polymerase III subunit RPC82 family protein 
                 Class I 
               
               
                 At4g25820 
                 ATXTH14, XTH14, XTR9, xyloglucan endotransglucosylase/hydrolase 14 
                 Class I 
               
               
                 At1g27770 
                 ACA1, PEA1, autoinhibited Ca2+-ATPase 1 
                 Class I 
               
               
                 At5g09990 
                 PROPEP5, elicitor peptide 5 precursor 
                 Class I 
               
               
                 At5g10630 
                 Translation elongation factor EF1A/initiation factor IF2gamma family protein 
                 Class I 
               
               
                 At4g16830 
                 Hyaluronan/mRNA binding family 
                 Class I 
               
               
                 At3g13920 
                 EIF4A1, RH4, TIF4A1, eukaryotic translation initiation factor 4A1 
                 Class I 
               
               
                 At1g25550 
                 myb-like transcription factor family protein 
                 Class I 
               
               
                 At5g24650 
                 Mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family protein 
                 Class I 
               
               
                 At3g59350 
                 Protein kinase superfamily protein 
                 Class I 
               
               
                 At2g29470 
                 ATGSTU3, GST21, GSTU3, glutathione S-transferase tau 3 
                 Class I 
               
               
                 At4g33925 
                 unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 
                 Class I 
               
               
                   
                 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 
               
               
                   
                 (source: NCBI BLink). 
               
               
                 At4g25580 
                 CAP160 protein 
                 Class I 
               
               
                 At2g03750 
                 P-loop containing nucleoside triphosphate hydrolases superfamily protein 
                 Class I 
               
               
                 At1g42990 
                 ATBZIP60, BZIP60, BZIP60, basic region/leucine zipper motif 60 
                 Class I 
               
               
                 At5g36260 
                 Eukaryotic aspartyl protease family protein 
                 Class I 
               
               
                 At1g78080 
                 RAP2.4, related to AP2 4 
                 Class I 
               
               
                 At2g37975 
                 Yos1-like protein 
                 Class I 
               
               
                 At5g55140 
                 ribosomal protein L30 family protein 
                 Class I 
               
               
                 At3g08610 
                 unknown protein; Has 40 Blast hits to 40 proteins in 15 species: Archae - 0; Bacteria - 0; 
                 Class I 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 40; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g57190 
                 PSD2, phosphatidylserine decarboxylase 2 
                 Class I 
               
               
                 At1g27720 
                 TAF4, TAF4B, TBP-associated factor 4B 
                 Class I 
               
               
                 At1g30740 
                 FAD-binding Berberine family protein 
                 Class I 
               
               
                 At2g24570 
                 ATWRKY17, WRKY17, WRKY DNA-binding protein 17 
                 Class I 
               
               
                 At2g44790 
                 UCC2, uclacyanin 2 
                 Class I 
               
               
                 At3g49780 
                 ATPSK3 (FORMER SYMBOL), ATPSK4, PSK4, phytosulfokine 4 precursor 
                 Class I 
               
               
                 At3g51920 
                 ATCML9, CAM9, CML9, calmodulin 9 
                 Class I 
               
               
                 At5g65660 
                 hydroxyproline-rich glycoprotein family protein 
                 Class I 
               
               
                 At3g19030 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class I 
               
               
                   
                 pyridoxine biosynthetic process, homoserine biosynthetic process; LOCATED IN: 
               
               
                   
                 endomembrane system; EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 9 
               
               
                   
                 growth stages; BEST  Arabidopsis thaliana  protein match is: unknown protein 
               
               
                   
                 (TAIR: AT1G49500.1); Has 22 Blast hits to 22 proteins in 2 species: Archae - 0; Bacteria - 0; 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 22; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At4g11570 
                 Haloacid dehalogenase-like hydrolase (HAD) superfamily protein 
                 Class I 
               
               
                 At4g11560 
                 bromo-adjacent homology (BAH) domain-containing protein 
                 Class I 
               
               
                 At3g19580 
                 AZF2, ZF2, zinc-finger protein 2 
                 Class I 
               
               
                 At5g44330 
                 Tetratricopeptide repeat (TPR)-like superfamily protein 
                 Class I 
               
               
                 At4g21820 
                 binding; calmodulin binding 
                 Class I 
               
               
                 At3g08580 
                 AAC1, ADP/ATP carrier 1 
                 Class I 
               
               
                 At5g66460 
                 Glycosyl hydrolase superfamily protein 
                 Class I 
               
               
                 At1g74450 
                 Protein of unknown function (DUF793) 
                 Class I 
               
               
                 At2g41110 
                 ATCAL5, CAM2, calmodulin 2 
                 Class I 
               
               
                 At4g37270 
                 ATHMA1, HMA1, heavy metal atpase 1 
                 Class I 
               
               
                 At1g29395 
                 COR413-TM1, COR413IM1, COR414-TM1, COLD REGULATED 314 INNER 
                 Class I 
               
               
                   
                 MEMBRANE 1 
               
               
                 At1g20450 
                 ERD10, LTI29, LTI45, Dehydrin family protein 
                 Class I 
               
               
                 At1g32640 
                 ATMYC2, JAI1, JIN1, MYC2, RD22BP1, ZBF1, Basic helix-loop-helix (bHLH) DNA- 
                 Class I 
               
               
                   
                 binding family protein 
               
               
                 At5g47960 
                 ATRABA4C, RABA4C, SMG1, RAB GTPase homolog A4C 
                 Class I 
               
               
                 At3g03810 
                 EDA30, O-fucosyltransferase family protein 
                 Class I 
               
               
                 At1g62300 
                 ATWRKY6, WRKY6, WRKY family transcription factor 
                 Class I 
               
               
                 At4g13390 
                 Proline-rich extensin-like family protein 
                 Class I 
               
               
                 At2g39990 
                 AteIF3f, EIF2, eIF3F, eukaryotic translation initiation factor 2 
                 Class I 
               
               
                 At5g59450 
                 GRAS family transcription factor 
                 Class I 
               
               
                 At5g01380 
                 Homeodomain-like superfamily protein 
                 Class I 
               
               
                 At4g37370 
                 CYP81D8, cytochrome P450, family 81, subfamily D, polypeptide 8 
                 Class I 
               
               
                 At1g13210 
                 ACA.1, autoinhibited Ca2+/ATPase II 
                 Class I 
               
               
                 At2g41620 
                 Nucleoporin interacting component (Nup93/Nic96-like) family protein 
                 Class I 
               
               
                 At2g41740 
                 ATVLN2, VLN2, villin 2 
                 Class I 
               
               
                 At5g18475 
                 Pentatricopeptide repeat (PPR) superfamily protein 
                 Class I 
               
               
                 At2g17840 
                 ERD7, Senescence/dehydration-associated protein-related 
                 Class I 
               
               
                 At2g25490 
                 EBF1, FBL6, EIN3-binding F box protein 1 
                 Class I 
               
               
                 At4g20840 
                 FAD-binding Berberine family protein 
                 Class I 
               
               
                 At1g53830 
                 ATPME2, PME2, pectin methylesterase 2 
                 Class I 
               
               
                 At5g59830 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class I 
               
               
                   
                 (TAIR: AT5G13660.2); Has 174 Blast hits to 139 proteins in 16 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 0; Fungi - 0; Plants - 172; Viruses - 0; Other Eukaryotes - 2 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At1g01060 
                 LHY, LHY1, Homeodomain-like superfamily protein 
                 Class I 
               
               
                 At1g31820 
                 Amino acid permease family protein 
                 Class I 
               
               
                 At1g80010 
                 FRS8, FAR1-related sequence 8 
                 Class I 
               
               
                 At2g45810 
                 DEA(D/H)-box RNA helicase family protein 
                 Class I 
               
               
                 At1g55450 
                 S-adenosyl-L-methionine-dependent methyltransferases superfamily protein 
                 Class I 
               
               
                 At1g21850 
                 sks8, SKU5 similar 8 
                 Class I 
               
               
                 At5g50900 
                 ARM repeat superfamily protein 
                 Class I 
               
               
                 At3g56880 
                 VQ motif-containing protein 
                 Class I 
               
               
                 At1g76180 
                 ERD14, Dehydrin family protein 
                 Class I 
               
               
                 At4g25810 
                 XTH23, XTR6, xyloglucan endotransglycosylase 6 
                 Class I 
               
               
                 At3g24170 
                 ATGR1, GR1, glutathione-disulfide reductase 
                 Class I 
               
               
                 At5g47210 
                 Hyaluronan/mRNA binding family 
                 Class I 
               
               
                 At5g07450 
                 CYCP4; 3, cyclin p4; 3 
                 Class I 
               
               
                 At2g39670 
                 Radical SAM superfamily protein 
                 Class I 
               
               
                 At1g56670 
                 GDSL-like Lipase/Acylhydrolase superfamily protein 
                 Class I 
               
               
                 At5g08230 
                 Tudor/PWWP/MBT domain-containing protein 
                 Class I 
               
               
                 At3g24560 
                 RSY3, Adenine nucleotide alpha hydrolases-like superfamily protein 
                 Class I 
               
               
                 At1g17860 
                 Kunitz family trypsin and protease inhibitor protein 
                 Class I 
               
               
                 At3g57460 
                 catalytics; metal ion binding 
                 Class I 
               
               
                 At2g20570 
                 ATGLK1, GLK1, GPRI1, GBF&#39;s pro-rich region-interacting factor 1 
                 Class I 
               
               
                 At3g21500 
                 DXPS1, 1-deoxy-D-xylulose 5-phosphate synthase 1 
                 Class I 
               
               
                 At3g25650 
                 ASK15, SK15, SKP1-like 15 
                 Class I 
               
               
                 At5g46780 
                 VQ motif-containing protein 
                 Class I 
               
               
                 At5g43440 
                 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein 
                 Class I 
               
               
                 At3g50910 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class I 
               
               
                   
                 (TAIR: AT5G66480.1); Has 76 Blast hits to 75 proteins in 28 species: Archae - 0; Bacteria - 
               
               
                   
                 10; Metazoa - 7; Fungi - 2; Plants - 49; Viruses - 0; Other Eukaryotes - 8 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At4g26180 
                 Mitochondrial substrate carrier family protein 
                 Class I 
               
               
                 At3g25250 
                 AGC2, AGC2-1, AtOXI1, OXI1, AGC (cAMP-dependent, cGMP-dependent and protein 
                 Class I 
               
               
                   
                 kinase C) kinase family protein 
               
               
                 At1g59600 
                 ZCW7, ZCW7 
                 Class I 
               
               
                 At2g05720 
                 Transducin/WD40 repeat-like superfamily protein 
                 Class I 
               
               
                 At2g43290 
                 MSS3, Calcium-binding EF-hand family protein 
                 Class I 
               
               
                 At3g53760 
                 ATGCP4, GCP4, GAMMA-TUBULIN COMPLEX PROTEIN 4 
                 Class I 
               
               
                 At5g11670 
                 ATNADP-ME2, NADP-ME2, NADP-malic enzyme 2 
                 Class I 
               
               
                 At5g07740 
                 actin binding 
                 Class I 
               
               
                 At5g27420 
                 ATL31, CNI1, carbon/nitrogen insensitive 1 
                 Class I 
               
               
                 At3g15460 
                 Ribosomal RNA processing Brix domain protein 
                 Class I 
               
               
                 At5g47230 
                 ATERF-5, ATERF5, ERF5, ethylene responsive element binding factor 5 
                 Class I 
               
               
                 At3g62410 
                 CP12, CP12-2, CP12 domain-containing protein 2 
                 Class I 
               
               
                 At5g03610 
                 GDSL-like Lipase/Acylhydrolase superfamily protein 
                 Class I 
               
               
                 At4g05050 
                 UBQ11, ubiquitin 11 
                 Class I 
               
               
                 At1g22200 
                 Endoplasmic reticulum vesicle transporter protein 
                 Class I 
               
               
                 At4g32920 
                 glycine-rich protein 
                 Class I 
               
               
                 At5g59820 
                 RHL41, ZAT12, C2H2-type zinc finger family protein 
                 Class I 
               
               
                 At5g49030 
                 OVA2, tRNA synthetase class I (I, L, M and V) family protein 
                 Class I 
               
               
                 At1g68670 
                 myb-like transcription factor family protein 
                 Class I 
               
               
                 At5g26360 
                 TCP-1/cpn60 chaperonin family protein 
                 Class I 
               
               
                 At5g24800 
                 ATBZIP9, BZIP9, BZO2H2, basic leucine zipper 9 
                 Class I 
               
               
                 At4g00690 
                 ULP1B, UB-like protease 1B 
                 Class I 
               
               
                 At3g06500 
                 Plant neutral invertase family protein 
                 Class I 
               
               
                 At1g80930 
                 MIF4G domain-containing protein/MA3 domain-containing protein 
                 Class I 
               
               
                 At1g69880 
                 ATH8, TH8, thioredoxin H-type 8 
                 Class I 
               
               
                 At5g24930 
                 ATCOL4, COL4, CONSTANS-like 4 
                 Class I 
               
               
                 At2g46260 
                 BTB/POZ/Kelch-associated protein 
                 Class I 
               
               
                 At1g19020 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class I 
               
               
                   
                 (TAIR: AT3G48180.1); Has 88 Blast hits to 88 proteins in 15 species: Archae - 0; Bacteria - 0; 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 88; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At1g68765 
                 IDA, Putative membrane lipoprotein 
                 Class I 
               
               
                 At1g56590 
                 ZIP4, Clathrin adaptor complexes medium subunit family protein 
                 Class I 
               
               
                 At5g01820 
                 ATCIPK14, ATSR1, CIPK14, SnRK3.15, SR1, serine/threonine protein kinase 1 
                 Class I 
               
               
                 At4g05100 
                 AtMYB74, MYB74, myb domain protein 74 
                 Class I 
               
               
                 At5g58070 
                 ATTIL, TIL, temperature-induced lipocalin 
                 Class I 
               
               
                 At5g15090 
                 ATVDAC3, VDAC3, voltage dependent anion channel 3 
                 Class I 
               
               
                 At3g06510 
                 ATSFR2, SFR2, Glycosyl hydrolase superfamily protein 
                 Class I 
               
               
                 At2g40140 
                 ATSZF2, CZF1, SZF2, ZFAR1, zinc finger (CCCH-type) family protein 
                 Class I 
               
               
                 At3g50960 
                 PLP3a, phosducin-like protein 3 homolog 
                 Class I 
               
               
                 At1g17850 
                 Rhodanese/Cell cycle control phosphatase superfamily protein 
                 Class I 
               
               
                 At1g28280 
                 VQ motif-containing protein 
                 Class I 
               
               
                 At4g36010 
                 Pathogenesis-related thaumatin superfamily protein 
                 Class I 
               
               
                 At3g44260 
                 Polynucleotidyl transferase, ribonuclease H-like superfamily protein 
                 Class I 
               
               
                 At5g35735 
                 Auxin-responsive family protein 
                 Class I 
               
               
                 At1g01725 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class I 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 23 
               
               
                   
                 plant structures; EXPRESSED DURING: 14 growth stages; BEST  Arabidopsis thaliana   
               
               
                   
                 protein match is: unknown protein (TAIR: AT4G00530.1); Has 20 Blast hits to 20 proteins in 7 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 20; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At3g45740 
                 hydrolase family protein/HAD-superfamily protein 
                 Class I 
               
               
                 At3g55620 
                 emb1624, Translation initiation factor IF6 
                 Class I 
               
               
                 At5g63790 
                 ANAC102, NAC102, NAC domain containing protein 102 
                 Class I 
               
               
                 At2g34910 
                 BEST  Arabidopsis thaliana  protein match is: root hair specific 4 (TAIR: AT1G30850.1); Has 
                 Class I 
               
               
                   
                 43 Blast hits to 43 proteins in 9 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; 
               
               
                   
                 Plants - 43; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g01510 
                 RUS5, Protein of unknown function, DUF647 
                 Class I 
               
               
                 At2g43130 
                 ARA-4, ARA4, ATRAB11F, ATRABA5C, RABA5C, P-loop containing nucleoside 
                 Class I 
               
               
                   
                 triphosphate hydrolases superfamily protein 
               
               
                 At3g22380 
                 TIC, time for coffee 
                 Class I 
               
               
                 At1g45145 
                 ATH5, ATTRX5, LIV1, TRX5, thioredoxin H-type 5 
                 Class I 
               
               
                 At1g22070 
                 TGA3, TGA1A-related gene 3 
                 Class I 
               
               
                 At5g14740 
                 BETA CA2, CA18, CA2, carbonic anhydrase 2 
                 Class I 
               
               
                 At2g18240 
                 Rer1 family protein 
                 Class I 
               
               
                 At2g46420 
                 Plant protein 1589 of unknown function 
                 Class I 
               
               
                 At5g56340 
                 ATCRT1, RING/U-box superfamily protein 
                 Class I 
               
               
                 At5g18310 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class I 
               
               
                   
                 biological_process unknown; LOCATED IN: plasma membrane; EXPRESSED IN: 22 plant 
               
               
                   
                 structures; EXPRESSED DURING: 13 growth stages; BEST  Arabidopsis thaliana  protein 
               
               
                   
                 match is: unknown protein (TAIR: AT5G48500.1); Has 30201 Blast hits to 17322 proteins in 
               
               
                   
                 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; 
               
               
                   
                 Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink). 
               
               
                 At3g28690 
                 Protein kinase superfamily protein 
                 Class I 
               
               
                 At3g15210 
                 ATERF-4, ATERF4, ERF4, RAP2.5, ethylene responsive element binding factor 4 
                 Class I 
               
               
                 At1g69760 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class I 
               
               
                   
                 (TAIR: AT1G26920.1); Has 51 Blast hits to 51 proteins in 15 species: Archae - 0; Bacteria - 2; 
               
               
                   
                 Metazoa - 2; Fungi - 7; Plants - 29; Viruses - 0; Other Eukaryotes - 11 (source: NCBI BLink). 
               
               
                 At2g46390 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class I 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 24 
               
               
                   
                 plant structures; EXPRESSED DURING: 15 growth stages; Has 4 Blast hits to 4 proteins in 2 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 4; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At2g17080 
                   Arabidopsis  protein of unknown function (DUF241) 
                 Class I 
               
               
                 At1g76170 
                 2-thiocytidine tRNA biosynthesis protein, TtcA 
                 Class I 
               
               
                 At5g61890 
                 Integrase-type DNA-binding superfamily protein 
                 Class I 
               
               
                 At2g20560 
                 DNAJ heat shock family protein 
                 Class I 
               
               
                 At4g30600 
                 signal recognition particle receptor alpha subunit family protein 
                 Class I 
               
               
                 At3g19570 
                 Family of unknown function (DUF566) 
                 Class I 
               
               
                 At5g11740 
                 AGP15, ATAGP15, arabinogalactan protein 15 
                 Class I 
               
               
                 At1g04530 
                 Tetratricopeptide repeat (TPR)-like superfamily protein 
                 Class I 
               
               
                 At2g29490 
                 ATGSTU1, GST19, GSTU1, glutathione S-transferase TAU 1 
                 Class I 
               
               
                 At5g61520 
                 Major facilitator superfamily protein 
                 Class I 
               
               
                 At4g02880 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class I 
               
               
                   
                 (TAIR: AT1G03290.2); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At1g43910 
                 P-loop containing nucleoside triphosphate hydrolases superfamily protein 
                 Class I 
               
               
                 At2g30250 
                 ATWRKY25, WRKY25, WRKY DNA-binding protein 25 
                 Class I 
               
               
                 At4g08950 
                 EXO, Phosphate-responsive 1 family protein 
                 Class I 
               
               
                 At4g20830 
                 FAD-binding Berberine family protein 
                 Class I 
               
               
                 At1g18740 
                 Protein of unknown function (DUF793) 
                 Class I 
               
               
                 At3g01560 
                 Protein of unknown function (DUF1421) 
                 Class I 
               
               
                 At5g10700 
                 Peptidyl-tRNA hydrolase II (PTH2) family protein 
                 Class I 
               
               
                 At2g41410 
                 Calcium-binding EF-hand family protein 
                 Class I 
               
               
                 At4g33780 
                 FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process 
                 Class I 
               
               
                   
                 unknown; LOCATED IN: chloroplast; EXPRESSED IN: 24 plant structures; EXPRESSED 
               
               
                   
                 DURING: 15 growth stages; BEST  Arabidopsis thaliana  protein match is: short hypocotyl in 
               
               
                   
                 white light1 (TAIR: AT1G69935.1); Has 40 Blast hits to 40 proteins in 10 species: Archae - 0; 
               
               
                   
                 Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 40; Viruses - 0; Other Eukaryotes - 0 (source: 
               
               
                   
                 NCBI BLink). 
               
               
                 At3g60130 
                 BGLU16, beta glucosidase 16 
                 Class I 
               
               
                 At1g42560 
                 ATMLO9, MLO9, Seven transmembrane MLO family protein 
                 Class I 
               
               
                 At2g35930 
                 PUB23, plant U-box 23 
                 Class I 
               
               
                 At3g04130 
                 Tetratricopeptide repeat (TPR)-like superfamily protein 
                 Class I 
               
               
                 At5g49480 
                 ATCP1, CP1, Ca2+-binding protein 1 
                 Class I 
               
               
                 At4g37010 
                 CEN2, centrin 2 
                 Class I 
               
               
                 At3g52810 
                 ATPAP21, PAP21, purple acid phosphatase 21 
                 Class I 
               
               
                 At1g10170 
                 ATNFXL1, NFXL1, NF-X-like 1 
                 Class I 
               
               
                 At2g41000 
                 Chaperone DnaJ-domain superfamily protein 
                 Class I 
               
               
                 At1g33590 
                 Leucine-rich repeat (LRR) family protein 
                 Class I 
               
               
                 At5g64905 
                 PROPEP3, elicitor peptide 3 precursor 
                 Class I 
               
               
                 At5g62530 
                 ALDH12A1, ATP5CDH, P5CDH, aldehyde dehydrogenase 12A1 
                 Class I 
               
               
                 At1g79400 
                 ATCHX2, CHX2, cation/H+ exchanger 2 
                 Class I 
               
               
                 At4g16670 
                 Plant protein of unknown function (DUF828) with plant pleckstrin homology-like region 
                 Class I 
               
               
                 At4g27652 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class I 
               
               
                   
                 (TAIR: AT4G27657.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At5g25280 
                 serine-rich protein-related 
                 Class I 
               
               
                 At2g03760 
                 AtSOT1, AtSOT12, ATST1, RAR047, SOT12, ST, ST1, sulphotransferase 12 
                 Class I 
               
               
                 At1g01460 
                 ATPIPK11, PIPK11, Phosphatidylinositol-4-phosphate 5-kinase, core 
                 Class I 
               
               
                 At4g11670 
                 Protein of unknown function (DUF810) 
                 Class I 
               
               
                 At4g27580 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class I 
               
               
                   
                 biological_process unknown; LOCATED IN: mitochondrion, cell wall; EXPRESSED IN: 9 
               
               
                   
                 plant structures; EXPRESSED DURING: 6 growth stages; Has 30201 Blast hits to 17322 
               
               
                   
                 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 
               
               
                   
                 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink). 
               
               
                 At3g05310 
                 MIRO3, MIRO-related GTP-ase 3 
                 Class I 
               
               
                 At3g12120 
                 FAD2, fatty acid desaturase 2 
                 Class I 
               
               
                 At4g28460 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class I 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 10 
               
               
                   
                 plant structures; EXPRESSED DURING: LP.04 four leaves visible, 4 anthesis, petal 
               
               
                   
                 differentiation and expansion stage; Has 8 Blast hits to 8 proteins in 3 species: Archae - 0; 
               
               
                   
                 Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 8; Viruses - 0; Other Eukaryotes - 0 (source: 
               
               
                   
                 NCBI BLink). 
               
               
                 At2g17670 
                 Tetratricopeptide repeat (TPR)-like superfamily protein 
                 Class I 
               
               
                 At3g61640 
                 AGP20, AtAGP20, arabinogalactan protein 20 
                 Class I 
               
               
                 At4g18170 
                 ATWRKY28, WRKY28, WRKY DNA-binding protein 28 
                 Class I 
               
               
                 At4g31805 
                 WRKY family transcription factor 
                 Class I 
               
               
                 At1g76600 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: N- 
                 Class I 
               
               
                   
                 terminal protein myristoylation; LOCATED IN: nucleolus, nucleus; EXPRESSED IN: 24 
               
               
                   
                 plant structures; EXPRESSED DURING: 15 growth stages; BEST  Arabidopsis thaliana   
               
               
                   
                 protein match is: unknown protein (TAIR: AT1G21010.1); Has 220 Blast hits to 220 proteins 
               
               
                   
                 in 14 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 220; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At1g65510 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: N- 
                 Class I 
               
               
                   
                 terminal protein myristoylation; LOCATED IN: endomembrane system; EXPRESSED IN: 9 
               
               
                   
                 plant structures; EXPRESSED DURING: LP.06 six leaves visible, LP.04 four leaves visible, 4 
               
               
                   
                 anthesis, petal differentiation and expansion stage, LP.08 eight leaves visible; BEST 
               
               
                   
                   Arabidopsis thaliana  protein match is: unknown protein (TAIR: AT1G65486.1); Has 22 Blast 
               
               
                   
                 hits to 22 proteins in 2 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 22; 
               
               
                   
                 Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At2g46830 
                 CCA1, circadian clock associated 1 
                 Class I 
               
               
                 At4g30440 
                 GAE1, UDP-D-glucuronate 4-epimerase 1 
                 Class I 
               
               
                 At5g65205 
                 NAD(P)-binding Rossmann-fold superfamily protein 
                 Class I 
               
               
                 At5g40690 
                 CONTAINS InterPro DOMAIN/s: EF-Hand 1, calcium-binding site (InterPro: IPR018247); 
                 Class I 
               
               
                   
                 BEST  Arabidopsis thaliana  protein match is: unknown protein (TAIR: AT2G41730.1); Has 
               
               
                   
                 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 
               
               
                   
                 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink). 
               
               
                 At1g74310 
                 ATHSP101, HOT1, HSP101, heat shock protein 101 
                 Class I 
               
               
                 At5g01950 
                 Leucine-rich repeat protein kinase family protein 
                 Class I 
               
               
                 At1g56050 
                 GTP-binding protein-related 
                 Class I 
               
               
                 At1g22840 
                 ATCYTC-A, CYTC-1, CYTOCHROME C-1 
                 Class I 
               
               
                 At4g19200 
                 proline-rich family protein 
                 Class I 
               
               
                 At1g19025 
                 DNA repair metallo-beta-lactamase family protein 
                 Class I 
               
               
                 At2g05710 
                 ACO3, aconitase 3 
                 Class I 
               
               
                 At1g08940 
                 Phosphoglycerate mutase family protein 
                 Class I 
               
               
                 At2g47000 
                 ABCB4, ATPGP4, MDR4, PGP4, ATP binding cassette subfamily B4 
                 Class I 
               
               
                 At3g27510 
                 Cysteine/Histidine-rich C1 domain family protein 
                 Class I 
               
               
                 At4g27280 
                 Calcium-binding EF-hand family protein 
                 Class I 
               
               
                 At1g71697 
                 ATCK1, CK, CK1, choline kinase 1 
                 Class I 
               
               
                 At4g21490 
                 NDB3, NAD(P)H dehydrogenase B3 
                 Class I 
               
               
                 At5g47970 
                 Aldolase-type TIM barrel family protein 
                 Class I 
               
               
                 At1g18310 
                 glycosyl hydrolase family 81 protein 
                 Class I 
               
               
                 At1g71530 
                 Protein kinase superfamily protein 
                 Class I 
               
               
                 At2g32150 
                 Haloacid dehalogenase-like hydrolase (HAD) superfamily protein 
                 Class I 
               
               
                 At1g59590 
                 ZCF37, ZCF37 
                 Class I 
               
               
                 At1g19770 
                 ATPUP14, PUP14, purine permease 14 
                 Class I 
               
               
                 At4g29790 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class I 
               
               
                   
                 (TAIR: AT2G19390.1); Has 538 Blast hits to 357 proteins in 124 species: Archae - 0; Bacteria - 
               
               
                   
                 74; Metazoa - 109; Fungi - 58; Plants - 105; Viruses - 2; Other Eukaryotes - 190 (source: 
               
               
                   
                 NCBI BLink). 
               
               
                 At1g27760 
                 ATSAT32, SAT32, interferon-related developmental regulator family protein/IFRD protein 
                 Class I 
               
               
                   
                 family 
               
               
                 At1g11560 
                 Oligosaccharyltransferase complex/magnesium transporter family protein 
                 Class I 
               
               
                 At2g04880 
                 ATWRKY1, WRKY1, ZAP1, zinc-dependent activator protein-1 
                 Class I 
               
               
                 At1g53840 
                 ATPME1, PME1, pectin methylesterase 1 
                 Class I 
               
            
           
           
               
               
            
               
                 ClassIIA. BA: bind and activate 
                   
               
            
           
           
               
               
               
            
               
                 At1g69490 
                 ANAC029, ATNAP, NAP, NAC-like, activated by AP3/PI 
                 Class IIA 
               
               
                 At5g03380 
                 Heavy metal transport/detoxification superfamily protein 
                 Class IIA 
               
               
                 At2g23170 
                 GH3.3, Auxin-responsive GH3 family protein 
                 Class IIA 
               
               
                 At1g66170 
                 MMD1, RING/FYVE/PHD zinc finger superfamily protein 
                 Class IIA 
               
               
                 At4g20860 
                 FAD-binding Berberine family protein 
                 Class IIA 
               
               
                 At3g12320 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class IIA 
               
               
                   
                 (TAIR: AT5G06980.4); Has 102 Blast hits to 102 proteins in 16 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 0; Fungi - 0; Plants - 98; Viruses - 0; Other Eukaryotes - 4 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At5g06300 
                 Putative lysine decarboxylase family protein 
                 Class IIA 
               
               
                 At3g15630 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class IIA 
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast; EXPRESSED IN: 24 plant 
               
               
                   
                 structures; EXPRESSED DURING: 15 growth stages; BEST  Arabidopsis thaliana  protein 
               
               
                   
                 match is: unknown protein (TAIR: AT1G52720.1); Has 61 Blast hits to 61 proteins in 13 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 61; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At3g19930 
                 ATSTP4, STP4, sugar transporter 4 
                 Class IIA 
               
               
                 At1g43160 
                 RAP2.6, related to AP2 6 
                 Class IIA 
               
               
                 At3g01290 
                 SPFH/Band 7/PHB domain-containing membrane-associated protein family 
                 Class IIA 
               
               
                 At2g39200 
                 ATMLO12, MLO12, Seven transmembrane MLO family protein 
                 Class IIA 
               
               
                 At3g14990 
                 Class I glutamine amidotransferase-like superfamily protein 
                 Class IIA 
               
               
                 At1g69890 
                 Protein of unknown function (DUF569) 
                 Class IIA 
               
               
                 At4g15610 
                 Uncharacterised protein family (UPF0497) 
                 Class IIA 
               
               
                 At3g15450 
                 Aluminium induced protein with YGL and LRDR motifs 
                 Class IIA 
               
               
                 At1g62570 
                 FMO GS-OX4, flavin-monooxygenase glucosinolate S-oxygenase 4 
                 Class IIA 
               
               
                 At1g29400 
                 AML5, ML5, MEI2-like protein 5 
                 Class IIA 
               
               
                 At1g32930 
                 Galactosyltransferase family protein 
                 Class IIA 
               
               
                 At5g67420 
                 ASL39, LBD37, LOB domain-containing protein 37 
                 Class IIA 
               
               
                 At5g64120 
                 Peroxidase superfamily protein 
                 Class IIA 
               
               
                 At3g30775 
                 AT-POX, ATPDH, ATPOX, ERD5, PRO1, PRODH, Methylenetetrahydrofolate reductase 
                 Class IIA 
               
               
                   
                 family protein 
               
               
                 At1g22830 
                 Tetratricopeptide repeat (TPR)-like superfamily protein 
                 Class IIA 
               
               
                 At1g22190 
                 Integrase-type DNA-binding superfamily protein 
                 Class IIA 
               
               
                 At2g22870 
                 EMB2001, P-loop containing nucleoside triphosphate hydrolases superfamily protein 
                 Class IIA 
               
               
                 At5g11090 
                 serine-rich protein-related 
                 Class IIA 
               
               
                 At5g07440 
                 GDH2, glutamate dehydrogenase 2 
                 Class IIA 
               
               
                 At5g67310 
                 CYP81G1, cytochrome P450, family 81, subfamily G, polypeptide 1 
                 Class IIA 
               
               
                 At1g68440 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class IIA 
               
               
                   
                 (TAIR: AT1G25400.2); Has 86 Blast hits to 86 proteins in 29 species: Archae - 0; Bacteria - 
               
               
                   
                 6; Metazoa - 27; Fungi - 11; Plants - 24; Viruses - 0; Other Eukaryotes - 18 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At1g15040 
                 Class I glutamine amidotransferase-like superfamily protein 
                 Class IIA 
               
               
                 At5g43580 
                 Serine protease inhibitor, potato inhibitor I-type family protein 
                 Class IIA 
               
               
                 At3g49790 
                 Carbohydrate-binding protein 
                 Class IIA 
               
               
                 At5g52050 
                 MATE efflux family protein 
                 Class IIA 
               
               
                 At5g12340 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class IIA 
               
               
                   
                 (TAIR: AT1G28190.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At4g27657 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class IIA 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 15 
               
               
                   
                 plant structures; EXPRESSED DURING: 9 growth stages; BEST  Arabidopsis thaliana   
               
               
                   
                 protein match is: unknown protein (TAIR: AT5G54145.1); Has 30201 Blast hits to 17322 
               
               
                   
                 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 
               
               
                   
                 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink). 
               
               
                 At5g02810 
                 APRR7, PRR7, pseudo-response regulator 7 
                 Class IIA 
               
               
                 At3g45970 
                 ATEXLA1, ATEXPL1, ATHEXP BETA 2.1, EXLA1, EXPL1, expansin-like A1 
                 Class IIA 
               
               
                 At4g20870 
                 ATFAH2, FAH2, fatty acid hydroxylase 2 
                 Class IIA 
               
               
                 At1g64670 
                 BDG1, alpha/beta-Hydrolases superfamily protein 
                 Class IIA 
               
               
                 At3g60140 
                 BGLU30, DIN2, SRG2, Glycosyl hydrolase superfamily protein 
                 Class IIA 
               
               
                 At1g64660 
                 ATMGL, MGL, methionine gamma-lyase 
                 Class IIA 
               
               
                 At5g67300 
                 ATMYB44, ATMYBR1, MYB44, MYBR1, myb domain protein r1 
                 Class IIA 
               
               
                 At5g20150 
                 ATSPX1, SPX1, SPX domain gene 1 
                 Class IIA 
               
               
                 At4g36040 
                 Chaperone DnaJ-domain superfamily protein 
                 Class IIA 
               
               
                 At5g40780 
                 LHT1, lysine histidine transporter 1 
                 Class IIA 
               
               
                 At1g80380 
                 P-loop containing nucleoside triphosphate hydrolases superfamily protein 
                 Class IIA 
               
               
                 At1g27100 
                 Actin cross-linking protein 
                 Class IIA 
               
               
                 At3g15620 
                 UVR3, DNA photolyase family protein 
                 Class IIA 
               
               
                 At5g01600 
                 ATFER1, FER1, ferretin 1 
                 Class IIA 
               
               
                 At3g52710 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class IIA 
               
               
                   
                 biological_process unknown; LOCATED IN: plasma membrane; EXPRESSED IN: 19 plant 
               
               
                   
                 structures; EXPRESSED DURING: 9 growth stages; BEST  Arabidopsis thaliana  protein 
               
               
                   
                 match is: unknown protein (TAIR: AT2G36220.1); Has 64 Blast hits to 64 proteins in 10 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 64; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At3g04070 
                 anac047, NAC047, NAC domain containing protein 47 
                 Class IIA 
               
               
                 At4g37590 
                 NPY5, Phototropic-responsive NPH3 family protein 
                 Class IIA 
               
               
                 At5g45630 
                 Protein of unknown function, DUF584 
                 Class IIA 
               
            
           
           
               
               
            
               
                 ClassIIB. BR: bind and repress 
                   
               
            
           
           
               
               
               
            
               
                 At3g50900 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class IIB 
               
               
                   
                 (TAIR: AT5G66490.1); Has 45 Blast hits to 45 proteins in 7 species: Archae - 0; Bacteria - 0; 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 45; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g57500 
                 Galactosyltransferase family protein 
                 Class IIB 
               
               
                 At1g19190 
                 alpha/beta-Hydrolases superfamily protein 
                 Class IIB 
               
               
                 At2g25735 
                 unknown protein; Has 31 Blast hits to 31 proteins in 9 species: Archae - 0; Bacteria - 0; 
                 Class IIB 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 31; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At1g56060 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class IIB 
               
               
                   
                 (TAIR: AT2G32210.1); Has 180 Blast hits to 180 proteins in 22 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 0; Fungi - 10; Plants - 170; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At4g08850 
                 Leucine-rich repeat receptor-like protein kinase family protein 
                 Class IIB 
               
               
                 At5g08240 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class IIB 
               
               
                   
                 (TAIR: AT5G23160.1); Has 69 Blast hits to 69 proteins in 10 species: Archae - 0; Bacteria - 
               
               
                   
                 1; Metazoa - 0; Fungi - 0; Plants - 68; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At3g21070 
                 ATNADK-1, NADK1, NAD kinase 1 
                 Class IIB 
               
               
                 At4g37910 
                 mtHsc70-1, mitochondrial heat shock protein 70-1 
                 Class IIB 
               
               
                 At4g12720 
                 AtNUDT7, ATNUDX7, GFG1, NUDT7, MutT/nudix family protein 
                 Class IIB 
               
               
                 At3g02880 
                 Leucine-rich repeat protein kinase family protein 
                 Class IIB 
               
               
                 At3g06490 
                 AtMYB108, BOS1, MYB108, myb domain protein 108 
                 Class IIB 
               
               
                 At1g18210 
                 Calcium-binding EF-hand family protein 
                 Class IIB 
               
               
                 At5g26030 
                 ATFC-I, FC-I, FC1, ferrochelatase 1 
                 Class IIB 
               
               
                 At3g55630 
                 ATDFD, DFD, DHFS-FPGS homolog D 
                 Class IIB 
               
               
                 At4g24390 
                 RNI-like superfamily protein 
                 Class IIB 
               
               
                 At2g41730 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class IIB 
               
               
                   
                 (TAIR: AT5G24640.1); Has 25 Blast hits to 25 proteins in 5 species: Archae - 0; Bacteria - 0; 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 25; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g41810 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 Class IIB 
               
               
                   
                 (TAIR: AT1G64340.1); Has 876 Blast hits to 690 proteins in 132 species: Archae - 0; 
               
               
                   
                 Bacteria - 38; Metazoa - 180; Fungi - 112; Plants - 59; Viruses - 2; Other Eukaryotes - 485 
               
               
                   
                 (source: NCBI BLink). 
               
               
                 At5g02230 
                 Haloacid dehalogenase-like hydrolase (HAD) superfamily protein 
                 Class IIB 
               
               
                 At1g16670 
                 Protein kinase superfamily protein 
                 Class IIB 
               
               
                 At3g04120 
                 GAPC, GAPC-1, GAPC1, glyceraldehyde-3-phosphate dehydrogenase C subunit 1 
                 Class IIB 
               
               
                 At2g32220 
                 Ribosomal L27e protein family 
                 Class IIB 
               
               
                 At5g37770 
                 CML24, TCH2, EF hand calcium-binding protein family 
                 Class IIB 
               
               
                 At2g38470 
                 ATWRKY33, WRKY33, WRKY DNA-binding protein 33 
                 Class IIB 
               
               
                 At4g30290 
                 ATXTH19, XTH19, xyloglucan endotransglucosylase/hydrolase 19 
                 Class IIB 
               
               
                 At5g39670 
                 Calcium-binding EF-hand family protein 
                 Class IIB 
               
               
                 At1g08510 
                 FATB, fatty acyl-ACP thioesterases B 
                 Class IIB 
               
               
                 At3g57450 
                 unknown protein; Has 65 Blast hits to 65 proteins in 11 species: Archae - 0; Bacteria - 0; 
                 Class IIB 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 65; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At2g35980 
                 ATNHL10, NHL10, YLS9, Late embryogenesis abundant (LEA) hydroxyproline-rich 
                 Class IIB 
               
               
                   
                 glycoprotein family 
               
               
                 At3g24550 
                 ATPERK1, PERK1, proline extensin-like receptor kinase 1 
                 Class IIB 
               
               
                 At1g80820 
                 ATCCR2, CCR2, cinnamoyl coa reductase 
                 Class IIB 
               
               
                 At4g34150 
                 Calcium-dependent lipid-binding (CaLB domain) family protein 
                 Class IIB 
               
               
                 At5g01540 
                 LECRKA4.1, lectin receptor kinase a4.1 
                 Class IIB 
               
               
                 At1g14540 
                 Peroxidase superfamily protein 
                 Class IIB 
               
               
                 At2g41630 
                 TFIIB, transcription factor IIB 
                 Class IIB 
               
               
                 At2g38830 
                 Ubiquitin-conjugating enzyme/RWD-like protein 
                 Class IIB 
               
               
                 At3g54150 
                 S-adenosyl-L-methionine-dependent methyltransferases superfamily protein 
                 Class IIB 
               
               
                 At4g11350 
                 Protein of unknown function (DUF604) 
                 Class IIB 
               
               
                 At4g37900 
                 Protein of unknown function (duplicated DUF1399) 
                 Class IIB 
               
               
                 At4g30210 
                 AR2, ATR2, P450 reductase 2 
                 Class IIB 
               
               
                 At4g02380 
                 AtLEA5, SAG21, senescence-associated gene 21 
                 Class IIB 
               
               
                 At1g73510 
                 unknown protein; Has 7 Blast hits to 7 proteins in 2 species: Archae - 0; Bacteria - 0; 
                 Class IIB 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 7; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At2g41890 
                 curculin-like (mannose-binding) lectin family protein/PAN domain-containing protein 
                 Class IIB 
               
               
                 At1g14550 
                 Peroxidase superfamily protein 
                 Class IIB 
               
               
                 At4g30280 
                 ATXTH18, XTH18, xyloglucan endotransglucosylase/hydrolase 18 
                 Class IIB 
               
               
                 At5g39680 
                 EMB2744, Pentatricopeptide repeat (PPR) superfamily protein 
                 Class IIB 
               
               
                 At4g39260 
                 ATGRP8, CCR1, GR-RBP8, GRP8, cold, circadian rhythm, and RNA binding 1 
                 Class IIB 
               
               
                 At4g38420 
                 sks9, SKU5 similar 9 
                 Class IIB 
               
               
                 At2g46140 
                 Late embryogenesis abundant protein 
                 Class IIB 
               
               
                 At1g78340 
                 ATGSTU22, GSTU22, glutathione S-transferase TAU 22 
                 Class IIB 
               
               
                 At2g39660 
                 BIK1, botrytis-induced kinase1 
                 Class IIB 
               
               
                 At4g18880 
                 AT-HSFA4A, HSF A4A, heat shock transcription factor A4A 
                 Class IIB 
               
               
                 At4g40040 
                 Histone superfamily protein 
                 Class IIB 
               
               
                 At4g11360 
                 RHA1B, RING-H2 finger A1B 
                 Class IIB 
               
               
                 At4g30530 
                 Class I glutamine amidotransferase-like superfamily protein 
                 Class IIB 
               
               
                 At1g30370 
                 alpha/beta-Hydrolases superfamily protein 
                 Class IIB 
               
               
                 At4g40030 
                 Histone superfamily protein 
                 Class IIB 
               
               
                 At5g47910 
                 ATRBOHD, RBOHD, respiratory burst oxidase homologue D 
                 Class IIB 
               
               
                 At5g64310 
                 AGP1, ATAGP1, arabinogalactan protein 1 
                 Class IIB 
               
               
                 At5g42830 
                 HXXXD-type acyl-transferase family protein 
                 Class IIB 
               
               
                 At1g73010 
                 ATPS2, PS2, phosphate starvation-induced gene 2 
                 Class IIB 
               
               
                 At5g19240 
                 Glycoprotein membrane precursor GPI-anchored 
                 Class IIB 
               
               
                 At1g06760 
                 winged-helix DNA-binding transcription factor family protein 
                 Class IIB 
               
               
                 At2g22500 
                 ATPUMP5, DIC1, UCP5, uncoupling protein 5 
                 Class IIB 
               
               
                 At4g32020 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 Class IIB 
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast; EXPRESSED IN: 24 plant 
               
               
                   
                 structures; EXPRESSED DURING: 15 growth stages; BEST  Arabidopsis thaliana  protein 
               
               
                   
                 match is: unknown protein (TAIR: AT2G25250.1); Has 65 Blast hits to 65 proteins in 19 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 3; Fungi - 8; Plants - 54; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At2g17660 
                 RPM1-interacting protein 4 (RIN4) family protein 
                 Class IIB 
               
               
                 At2g22470 
                 AGP2, ATAGP2, arabinogalactan protein 2 
                 Class IIB 
               
            
           
           
               
               
            
               
                 ClassIIIA. NA: No binding but activation 
                   
               
            
           
           
               
               
               
            
               
                 At3g15440 
                 BEST  Arabidopsis thaliana  protein match is: RING/U-box superfamily protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT3G15740.1); Has 12 Blast hits to 12 proteins in 2 species: Archae - 0; Bacteria - 0; 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 12; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At4g15280 
                 UGT71B5, UDP-glucosyl transferase 71B5 
                 ClassIIIA 
               
               
                 At3g27690 
                 LHCB2, LHCB2.3, LHCB2.4, photosystem II light harvesting complex gene 2.3 
                 ClassIIIA 
               
               
                 At5g67450 
                 AZF1, ZF1, zinc-finger protein 1 
                 ClassIIIA 
               
               
                 At1g18460 
                 alpha/beta-Hydrolases superfamily protein 
                 ClassIIIA 
               
               
                 At1g03600 
                 PSB27, photosystem II family protein 
                 ClassIIIA 
               
               
                 At5g44380 
                 FAD-binding Berberine family protein 
                 ClassIIIA 
               
               
                 At3g24310 
                 ATMYB71, MYB305, myb domain protein 305 
                 ClassIIIA 
               
               
                 At3g14780 
                 CONTAINS InterPro DOMAIN/s: Transposase, Ptta/En/Spm, plant (InterPro: IPR004252); 
                 ClassIIIA 
               
               
                   
                 BEST  Arabidopsis thaliana  protein match is: glucan synthase-like 4 (TAIR: AT3G14570.2); 
               
               
                   
                 Has 315 Blast hits to 313 proteins in 50 species: Archae - 2; Bacteria - 16; Metazoa - 11; 
               
               
                   
                 Fungi - 7; Plants - 181; Viruses - 2; Other Eukaryotes - 96 (source: NCBI BLink). 
               
               
                 At5g65110 
                 ACX2, ATACX2, acyl-CoA oxidase 2 
                 ClassIIIA 
               
               
                 At1g23870 
                 ATTPS9, TPS9, TPS9, trehalose-phosphatase/synthase 9 
                 ClassIIIA 
               
               
                 At1g08720 
                 ATEDR1, EDR1, Protein kinase superfamily protein 
                 ClassIIIA 
               
               
                 At3g03170 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT5G24890.1); Has 184 Blast hits to 184 proteins in 18 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 0; Fungi - 0; Plants - 184; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At1g02860 
                 BAH1, NLA, SPX (SYG1/Pho81/XPR1) domain-containing protein 
                 ClassIIIA 
               
               
                 At1g08830 
                 CSD1, copper/zinc superoxide dismutase 1 
                 ClassIIIA 
               
               
                 At5g63800 
                 BGAL6, MUM2, Glycosyl hydrolase family 35 protein 
                 ClassIIIA 
               
               
                 At4g37790 
                 HAT22, Homeobox-leucine zipper protein family 
                 ClassIIIA 
               
               
                 At3g02150 
                 PTF1, TCP13, TFPD, plastid transcription factor 1 
                 ClassIIIA 
               
               
                 At5g64460 
                 Phosphoglycerate mutase family protein 
                 ClassIIIA 
               
               
                 At2g33150 
                 KAT2, PED1, PKT3, peroxisomal 3-ketoacyl-CoA thiolase 3 
                 ClassIIIA 
               
               
                 At1g06570 
                 HPD, PDS1, phytoene desaturation 1 
                 ClassIIIA 
               
               
                 At3g14750 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT1G67170.1); Has 4036 Blast hits to 3091 proteins in 519 species: Archae - 61; 
               
               
                   
                 Bacteria - 669; Metazoa - 1503; Fungi - 255; Plants - 421; Viruses - 4; Other Eukaryotes - 
               
               
                   
                 1123 (source: NCBI BLink). 
               
               
                 At1g18330 
                 EPR1, RVE7, Homeodomain-like superfamily protein 
                 ClassIIIA 
               
               
                 At3g49060 
                 U-box domain-containing protein kinase family protein 
                 ClassIIIA 
               
               
                 At3g16800 
                 Protein phosphatase 2C family protein 
                 ClassIIIA 
               
               
                 At1g72770 
                 HAB1, homology to ABI1 
                 ClassIIIA 
               
               
                 At5g20050 
                 Protein kinase superfamily protein 
                 ClassIIIA 
               
               
                 At1g18260 
                 HCP-like superfamily protein 
                 ClassIIIA 
               
               
                 At2g26280 
                 CID7, CTC-interacting domain 7 
                 ClassIIIA 
               
               
                 At5g13760 
                 Plasma-membrane choline transporter family protein 
                 ClassIIIA 
               
               
                 At1g55020 
                 ATLOX1, LOX1, lipoxygenase 1 
                 ClassIIIA 
               
               
                 At5g03720 
                 AT-HSFA3, HSFA3, heat shock transcription factor A3 
                 ClassIIIA 
               
               
                 At1g76240 
                   Arabidopsis  protein of unknown function (DUF241) 
                 ClassIIIA 
               
               
                 At3g11340 
                 UDP-Glycosyltransferase superfamily protein 
                 ClassIIIA 
               
               
                 At3g16150 
                 N-terminal nucleophile aminohydrolases (Ntn hydrolases) superfamily protein 
                 ClassIIIA 
               
               
                 At2g34600 
                 JAZ7, TIFY5B, jasmonate-zim-domain protein 7 
                 ClassIIIA 
               
               
                 At3g43430 
                 RING/U-box superfamily protein 
                 ClassIIIA 
               
               
                 At2g41200 
                 unknown protein; Has 26 Blast hits to 26 proteins in 11 species: Archae - 0; Bacteria - 0; 
                 ClassIIIA 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 26; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At1g75230 
                 DNA glycosylase superfamily protein 
                 ClassIIIA 
               
               
                 At1g52240 
                 ATROPGEF11, PIRF1, ROPGEF11, RHO guanyl-nucleotide exchange factor 11 
                 ClassIIIA 
               
               
                 At1g13080 
                 CYP71B2, cytochrome P450, family 71, subfamily B, polypeptide 2 
                 ClassIIIA 
               
               
                 At1g68400 
                 leucine-rich repeat transmembrane protein kinase family protein 
                 ClassIIIA 
               
               
                 At1g56145 
                 Leucine-rich repeat transmembrane protein kinase 
                 ClassIIIA 
               
               
                 At5g61510 
                 GroES-like zinc-binding alcohol dehydrogenase family protein 
                 ClassIIIA 
               
               
                 At2g26600 
                 Glycosyl hydrolase superfamily protein 
                 ClassIIIA 
               
               
                 At1g02670 
                 P-loop containing nucleoside triphosphate hydrolases superfamily protein 
                 ClassIIIA 
               
               
                 At1g14340 
                 RNA-binding (RRM/RBD/RNP motifs) family protein 
                 ClassIIIA 
               
               
                 At2g41190 
                 Transmembrane amino acid transporter family protein 
                 ClassIIIA 
               
               
                 At1g06520 
                 ATGPAT1, GPAT1, glycerol-3-phosphate acyltransferase 1 
                 ClassIIIA 
               
               
                 At1g23880 
                 NHL domain-containing protein 
                 ClassIIIA 
               
               
                 At3g52060 
                 Core-2/I-branching beta-1,6-N-acetylglucosaminyltransferase family protein 
                 ClassIIIA 
               
               
                 At1g08980 
                 AMI1, ATAMI1, ATTOC64-I, TOC64-I, amidase 1 
                 ClassIIIA 
               
               
                 At5g37260 
                 CIR1, RVE2, Homeodomain-like superfamily protein 
                 ClassIIIA 
               
               
                 At4g23880 
                 unknown protein; Has 73 Blast hits to 69 proteins in 22 species: Archae - 0; Bacteria - 4; 
                 ClassIIIA 
               
               
                   
                 Metazoa - 9; Fungi - 2; Plants - 18; Viruses - 0; Other Eukaryotes - 40 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At4g38200 
                 SEC7-like guanine nucleotide exchange family protein 
                 ClassIIIA 
               
               
                 At5g59590 
                 UGT76E2, UDP-glucosyl transferase 76E2 
                 ClassIIIA 
               
               
                 At1g25275 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIA 
               
               
                   
                 response to karrikin; LOCATED IN: endomembrane system; EXPRESSED IN: 23 plant 
               
               
                   
                 structures; EXPRESSED DURING: 13 growth stages; Has 18 Blast hits to 18 proteins in 4 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 18; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At2g29380 
                 HAI3, highly ABA-induced PP2C gene 3 
                 ClassIIIA 
               
               
                 At1g08090 
                 ACH1, ATNRT2.1, ATNRT2:1, LIN1, NRT2, NRT2.1, NRT2:1, NRT2;1AT, nitrate 
                 ClassIIIA 
               
               
                   
                 transporter 2:1 
               
               
                 At5g57655 
                 xylose isomerase family protein 
                 ClassIIIA 
               
               
                 At4g01110 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT1G01453.1); Has 273 Blast hits to 272 proteins in 18 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 0; Fungi - 0; Plants - 273; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At3g54960 
                 ATPDI1, ATPDIL1-3, PDI1, PDIL1-3, PDI-like 1-3 
                 ClassIIIA 
               
               
                 At3g54620 
                 ATBZIP25, BZIP25, BZO2H4, basic leucine zipper 25 
                 ClassIIIA 
               
               
                 At1g03870 
                 FLA9, FASCICLIN-like arabinoogalactan 9 
                 ClassIIIA 
               
               
                 At3g19400 
                 Cysteine proteinases superfamily protein 
                 ClassIIIA 
               
               
                 At3g13965 
                 pseudogene, hypothetical protein 
                 ClassIIIA 
               
               
                 At4g32960 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT4G32970.1); Has 106 Blast hits to 106 proteins in 39 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 62; Fungi - 0; Plants - 37; Viruses - 0; Other Eukaryotes - 7 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At5g51850 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT5G62170.1); Has 384 Blast hits to 375 proteins in 79 species: Archae - 0; Bacteria - 
               
               
                   
                 14; Metazoa - 135; Fungi - 31; Plants - 92; Viruses - 0; Other Eukaryotes - 112 (source: 
               
               
                   
                 NCBI BLink). 
               
               
                 At3g29240 
                 Protein of unknown function (DUF179) 
                 ClassIIIA 
               
               
                 At3g29160 
                 AKIN11, ATKIN11, KIN11, SNRK1.2, SNF1 kinase homolog 11 
                 ClassIIIA 
               
               
                 At5g56100 
                 glycine-rich protein/oleosin 
                 ClassIIIA 
               
               
                 At5g47740 
                 Adenine nucleotide alpha hydrolases-like superfamily protein 
                 ClassIIIA 
               
               
                 At1g03100 
                 Pentatricopeptide repeat (PPR) superfamily protein 
                 ClassIIIA 
               
               
                 At1g67480 
                 Galactose oxidase/kelch repeat superfamily protein 
                 ClassIIIA 
               
               
                 At5g08350 
                 GRAM domain-containing protein/ABA-responsive protein-related 
                 ClassIIIA 
               
               
                 At3g23230 
                 Integrase-type DNA-binding superfamily protein 
                 ClassIIIA 
               
               
                 At4g28040 
                 nodulin MtN21/EamA-like transporter family protein 
                 ClassIIIA 
               
               
                 At5g47560 
                 ATSDAT, ATTDT, TDT, tonoplast dicarboxylate transporter 
                 ClassIIIA 
               
               
                 At5g04040 
                 SDP1, Patatin-like phospholipase family protein 
                 ClassIIIA 
               
               
                 At4g27480 
                 Core-2/I-branching beta-1,6-N-acetylglucosaminyltransferase family protein 
                 ClassIIIA 
               
               
                 At1g08930 
                 ERD6, Major facilitator superfamily protein 
                 ClassIIIA 
               
               
                 At3g15650 
                 alpha/beta-Hydrolases superfamily protein 
                 ClassIIIA 
               
               
                 At1g79700 
                 Integrase-type DNA-binding superfamily protein 
                 ClassIIIA 
               
               
                 At3g24520 
                 AT-HSFC1, HSFC1, heat shock transcription factor C1 
                 ClassIIIA 
               
               
                 At4g36730 
                 GBF1, G-box binding factor 1 
                 ClassIIIA 
               
               
                 At4g01030 
                 pentatricopeptide (PPR) repeat-containing protein 
                 ClassIIIA 
               
               
                 At1g79340 
                 AtMC4, MC4, metacaspase 4 
                 ClassIIIA 
               
               
                 At1g10560 
                 ATPUB18, PUB18, plant U-box 18 
                 ClassIIIA 
               
               
                 At2g43400 
                 ETFQO, electron-transfer flavoprotein: ubiquinone oxidoreductase 
                 ClassIIIA 
               
               
                 At5g56180 
                 ARP8, ARP8, ATARP8, actin-related protein 8 
                 ClassIIIA 
               
               
                 At5g18170 
                 GDH1, glutamate dehydrogenase 1 
                 ClassIIIA 
               
               
                 At4g16690 
                 ATMES16, MES16, methyl esterase 16 
                 ClassIIIA 
               
               
                 At2g32510 
                 MAPKKK17, mitogen-activated protein kinase kinase kinase 17 
                 ClassIIIA 
               
               
                 At1g76185 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT1G20460.1); Has 37 Blast hits to 37 proteins in 11 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 0; Fungi - 0; Plants - 37; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At2g44360 
                 unknown protein; Has 23 Blast hits to 23 proteins in 10 species: Archae - 0; Bacteria - 0; 
                 ClassIIIA 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 23; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At3g45300 
                 ATIVD, IVD, IVDH, isovaleryl-CoA-dehydrogenase 
                 ClassIIIA 
               
               
                 At3g22920 
                 Cyclophilin-like peptidyl-prolyl cis-trans isomerase family protein 
                 ClassIIIA 
               
               
                 At4g39730 
                 Lipase/lipooxygenase, PLAT/LH2 family protein 
                 ClassIIIA 
               
               
                 At4g14500 
                 Polyketide cyclase/dehydrase and lipid transport superfamily protein 
                 ClassIIIA 
               
               
                 At3g14740 
                 RING/FYVE/PHD zinc finger superfamily protein 
                 ClassIIIA 
               
               
                 At3g13450 
                 DIN4, Transketolase family protein 
                 ClassIIIA 
               
               
                 At3g05200 
                 ATL6, RING/U-box superfamily protein 
                 ClassIIIA 
               
               
                 At2g28120 
                 Major facilitator superfamily protein 
                 ClassIIIA 
               
               
                 At2g02700 
                 Cysteine/Histidine-rich C1 domain family protein 
                 ClassIIIA 
               
               
                 At4g26290 
                 unknown protein; Has 9 Blast hits to 9 proteins in 5 species: Archae - 0; Bacteria - 0; 
                 ClassIIIA 
               
               
                   
                 Metazoa - 2; Fungi - 0; Plants - 3; Viruses - 0; Other Eukaryotes - 4 (source: NCBI BLink). 
               
               
                 At4g30170 
                 Peroxidase family protein 
                 ClassIIIA 
               
               
                 At3g11410 
                 AHG3, ATPP2CA, PP2CA, protein phosphatase 2CA 
                 ClassIIIA 
               
               
                 At1g10060 
                 ATBCAT-1, BCAT-1, branched-chain amino acid transaminase 1 
                 ClassIIIA 
               
               
                 At1g63710 
                 CYP86A7, cytochrome P450, family 86, subfamily A, polypeptide 7 
                 ClassIIIA 
               
               
                 At3g49940 
                 LBD38, LOB domain-containing protein 38 
                 ClassIIIA 
               
               
                 At3g22930 
                 CML11, calmodulin-like 11 
                 ClassIIIA 
               
               
                 At2g19320 
                 unknown protein; Has 9 Blast hits to 9 proteins in 4 species: Archae - 0; Bacteria - 0; 
                 ClassIIIA 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 9; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At4g34350 
                 CLB6, HDR, ISPH, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 
                 ClassIIIA 
               
               
                 At5g61590 
                 Integrase-type DNA-binding superfamily protein 
                 ClassIIIA 
               
               
                 At2g28630 
                 KCS12, 3-ketoacyl-CoA synthase 12 
                 ClassIIIA 
               
               
                 At2g19800 
                 MIOX2, myo-inositol oxygenase 2 
                 ClassIIIA 
               
               
                 At3g56240 
                 CCH, copper chaperone 
                 ClassIIIA 
               
               
                 At1g56700 
                 Peptidase C15, pyroglutamyl peptidase I-like 
                 ClassIIIA 
               
               
                 At5g67440 
                 NPY3, Phototropic-responsive NPH3 family protein 
                 ClassIIIA 
               
               
                 At5g43190 
                 Galactose oxidase/kelch repeat superfamily protein 
                 ClassIIIA 
               
               
                 At2g15695 
                 Protein of unknown function DUF829, transmembrane 53 
                 ClassIIIA 
               
               
                 At5g16110 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIA 
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast; EXPRESSED IN: 24 plant 
               
               
                   
                 structures; EXPRESSED DURING: 15 growth stages; BEST  Arabidopsis thaliana  protein 
               
               
                   
                 match is: unknown protein (TAIR: AT3G02555.1); Has 133 Blast hits to 133 proteins in 18 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 133; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At1g66890 
                 FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process 
                 ClassIIIA 
               
               
                   
                 unknown; LOCATED IN: chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED 
               
               
                   
                 DURING: 13 growth stages; BEST  Arabidopsis thaliana  protein match is: 50S ribosomal 
               
               
                   
                 protein-related (TAIR: AT5G16200.1); Has 36 Blast hits to 36 proteins in 7 species: Archae - 
               
               
                   
                 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 36; Viruses - 0; Other Eukaryotes - 0 (source: 
               
               
                   
                 NCBI BLink). 
               
               
                 At3g57540 
                 Remorin family protein 
                 ClassIIIA 
               
               
                 At1g61740 
                 Sulfite exporter TauE/SafE family protein 
                 ClassIIIA 
               
               
                 At1g67470 
                 Protein kinase superfamily protein 
                 ClassIIIA 
               
               
                 At5g49440 
                 unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
                 ClassIIIA 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At4g01870 
                 tolB protein-related 
                 ClassIIIA 
               
               
                 At4g21440 
                 ATM4, ATMYB102, MYB102, MYB102, MYB-like 102 
                 ClassIIIA 
               
               
                 At4g29950 
                 Ypt/Rab-GAP domain of gyp1p superfamily protein 
                 ClassIIIA 
               
               
                 At3g51860 
                 ATCAX3, ATHCX1, CAX1-LIKE, CAX3, cation exchanger 3 
                 ClassIIIA 
               
               
                 At1g16150 
                 WAKL4, wall associated kinase-like 4 
                 ClassIIIA 
               
               
                 At1g67880 
                 beta-1,4-N-acetylglucosaminyltransferase family protein 
                 ClassIIIA 
               
               
                 At1g08630 
                 THA1, threonine aldolase 1 
                 ClassIIIA 
               
               
                 At1g28130 
                 GH3.17, Auxin-responsive GH3 family protein 
                 ClassIIIA 
               
               
                 At3g55150 
                 ATEXO70H1, EXO70H1, exocyst subunit exo70 family protein H1 
                 ClassIIIA 
               
               
                 At1g76160 
                 sks5, SKU5 similar 5 
                 ClassIIIA 
               
               
                 At4g37220 
                 Cold acclimation protein WCOR413 family 
                 ClassIIIA 
               
               
                 At2g31380 
                 STH, salt tolerance homologue 
                 ClassIIIA 
               
               
                 At3g14050 
                 AT-RSH2, ATRSH2, RSH2, RELA/SPOT homolog 2 
                 ClassIIIA 
               
               
                 At3g14770 
                 Nodulin MtN3 family protein 
                 ClassIIIA 
               
               
                 At5g57630 
                 CIPK21, SnRK3.4, CBL-interacting protein kinase 21 
                 ClassIIIA 
               
               
                 At5g24530 
                 DMR6, 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein 
                 ClassIIIA 
               
               
                 At3g56000 
                 ATCSLA14, CSLA14, cellulose synthase like A14 
                 ClassIIIA 
               
               
                 At1g15060 
                 Uncharacterised conserved protein UCP031088, alpha/beta hydrolase 
                 ClassIIIA 
               
               
                 At2g28200 
                 C2H2-type zinc finger family protein 
                 ClassIIIA 
               
               
                 At4g33420 
                 Peroxidase superfamily protein 
                 ClassIIIA 
               
               
                 At5g18650 
                 CHY-type/CTCHY-type/RING-type Zinc finger protein 
                 ClassIIIA 
               
               
                 At1g66070 
                 Translation initiation factor eIF3 subunit 
                 ClassIIIA 
               
               
                 At2g10640 
                 transposable element gene 
                 ClassIIIA 
               
               
                 At5g18610 
                 Protein kinase superfamily protein 
                 ClassIIIA 
               
               
                 At4g15620 
                 Uncharacterised protein family (UPF0497) 
                 ClassIIIA 
               
               
                 At5g50200 
                 ATNRT3.1, NRT3.1, WR3, nitrate transmembrane transporters 
                 ClassIIIA 
               
               
                 At4g01330 
                 Protein kinase superfamily protein 
                 ClassIIIA 
               
               
                 At5g46590 
                 anac096, NAC096, NAC domain containing protein 96 
                 ClassIIIA 
               
               
                 At2g39570 
                 ACT domain-containing protein 
                 ClassIIIA 
               
               
                 At5g04740 
                 ACT domain-containing protein 
                 ClassIIIA 
               
               
                 At1g08920 
                 ESL1, ERD (early response to dehydration) six-like 1 
                 ClassIIIA 
               
               
                 At1g09460 
                 Carbohydrate-binding X8 domain superfamily protein 
                 ClassIIIA 
               
               
                 At4g38060 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT5G65480.1); Has 63 Blast hits to 63 proteins in 13 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 0; Fungi - 0; Plants - 63; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At3g57420 
                 Protein of unknown function (DUF288) 
                 ClassIIIA 
               
               
                 At5g54080 
                 HGO, homogentisate 1,2-dioxygenase 
                 ClassIIIA 
               
               
                 At3g06780 
                 glycine-rich protein 
                 ClassIIIA 
               
               
                 At2g22080 
                 unknown protein; Has 96314 Blast hits to 34847 proteins in 1702 species: Archae - 612; 
                 ClassIIIA 
               
               
                   
                 Bacteria - 27969; Metazoa - 24311; Fungi - 12153; Plants - 4409; Viruses - 1572; Other 
               
               
                   
                 Eukaryotes - 25288 (source: NCBI BLink). 
               
               
                 At1g49670 
                 NQR, ARP protein (REF) 
                 ClassIIIA 
               
               
                 At2g03740 
                 late embryogenesis abundant domain-containing protein/LEA domain-containing protein 
                 ClassIIIA 
               
               
                 At5g56870 
                 BGAL4, beta-galactosidase 4 
                 ClassIIIA 
               
               
                 At4g33150 
                 LKR, LKR/SDH, SDH, lysine-ketoglutarate reductase/saccharopine dehydrogenase 
                 ClassIIIA 
               
               
                   
                 bifunctional enzyme 
               
               
                 At1g23550 
                 SRO2, similar to RCD one 2 
                 ClassIIIA 
               
               
                 At2g12400 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIA 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 25 
               
               
                   
                 plant structures; EXPRESSED DURING: 13 growth stages; BEST  Arabidopsis thaliana   
               
               
                   
                 protein match is: unknown protein (TAIR: AT2G25270.1); Has 177 Blast hits to 172 proteins 
               
               
                   
                 in 23 species: Archae - 0; Bacteria - 2; Metazoa - 3; Fungi - 0; Plants - 164; Viruses - 0; 
               
               
                   
                 Other Eukaryotes - 8 (source: NCBI BLink). 
               
               
                 At1g12080 
                 Vacuolar calcium-binding protein-related 
                 ClassIIIA 
               
               
                 At5g01590 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIA 
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast, chloroplast envelope; 
               
               
                   
                 EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; Has 60 
               
               
                   
                 Blast hits to 59 proteins in 31 species: Archae - 0; Bacteria - 20; Metazoa - 1; Fungi - 2; 
               
               
                   
                 Plants - 33; Viruses - 0; Other Eukaryotes - 4 (source: NCBI BLink). 
               
               
                 At4g19810 
                 Glycosyl hydrolase family protein with chitinase insertion domain 
                 ClassIIIA 
               
               
                 At3g17440 
                 ATNPSN13, NPSN13, novel plant snare 13 
                 ClassIIIA 
               
               
                 At5g03350 
                 Legume lectin family protein 
                 ClassIIIA 
               
               
                 At2g44670 
                 Protein of unknown function (DUF581) 
                 ClassIIIA 
               
               
                 At5g28050 
                 Cytidine/deoxycytidylate deaminase family protein 
                 ClassIIIA 
               
               
                 At5g10450 
                 14-3-3lambda, AFT1, GRF6, G-box regulating factor 6 
                 ClassIIIA 
               
               
                 At4g23870 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT4G11020.1); Has 12 Blast hits to 12 proteins in 4 species: Archae - 0; Bacteria - 0; 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 12; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At1g69910 
                 Protein kinase superfamily protein 
                 ClassIIIA 
               
               
                 At5g13110 
                 G6PD2, glucose-6-phosphate dehydrogenase 2 
                 ClassIIIA 
               
               
                 At1g14330 
                 Galactose oxidase/kelch repeat superfamily protein 
                 ClassIIIA 
               
               
                 At1g06560 
                 NOL1/NOP2/sun family protein 
                 ClassIIIA 
               
               
                 At3g16170 
                 AMP-dependent synthetase and ligase family protein 
                 ClassIIIA 
               
               
                 At5g20250 
                 DIN10, Raffinose synthase family protein 
                 ClassIIIA 
               
               
                 At5g49690 
                 UDP-Glycosyltransferase superfamily protein 
                 ClassIIIA 
               
               
                 At1g07250 
                 UGT71C4, UDP-glucosyl transferase 71C4 
                 ClassIIIA 
               
               
                 At3g51540 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT3G08670.1); Has 22744 Blast hits to 9965 proteins in 783 species: Archae - 64; 
               
               
                   
                 Bacteria - 2760; Metazoa - 8515; Fungi - 3864; Plants - 499; Viruses - 702; Other Eukaryotes - 
               
               
                   
                 6340 (source: NCBI BLink). 
               
               
                 At3g30396 
                 transposable element gene 
                 ClassIIIA 
               
               
                 At1g67510 
                 Leucine-rich repeat protein kinase family protein 
                 ClassIIIA 
               
               
                 At2g39130 
                 Transmembrane amino acid transporter family protein 
                 ClassIIIA 
               
               
                 At5g23050 
                 AAE17, acyl-activating enzyme 17 
                 ClassIIIA 
               
               
                 At1g22360 
                 AtUGT85A2, UGT85A2, UDP-glucosyl transferase 85A2 
                 ClassIIIA 
               
               
                 At2g32660 
                 AtRLP22, RLP22, receptor like protein 22 
                 ClassIIIA 
               
               
                 At1g54740 
                 Protein of unknown function (DUF3049) 
                 ClassIIIA 
               
               
                 At1g03080 
                 kinase interacting (KIP1-like) family protein 
                 ClassIIIA 
               
               
                 At4g38490 
                 unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
                 ClassIIIA 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At4g36790 
                 Major facilitator superfamily protein 
                 ClassIIIA 
               
               
                 At4g38480 
                 Transducin/WD40 repeat-like superfamily protein 
                 ClassIIIA 
               
               
                 At3g61070 
                 PEX11E, peroxin 11E 
                 ClassIIIA 
               
               
                 At3g45060 
                 ATNRT2.6, NRT2.6, high affinity nitrate transporter 2.6 
                 ClassIIIA 
               
               
                 At4g33910 
                 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein 
                 ClassIIIA 
               
               
                 At1g58180 
                 ATBCA6, BCA6, beta carbonic anhydrase 6 
                 ClassIIIA 
               
               
                 At1g71980 
                 Protease-associated (PA) RING/U-box zinc finger family protein 
                 ClassIIIA 
               
               
                 At1g57680 
                 FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process 
                 ClassIIIA 
               
               
                   
                 unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 24 plant structures; 
               
               
                   
                 EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: 
               
               
                   
                 Uncharacterised conserved protein UCP031277 (InterPro: IPR016971); Has 70 Blast hits to 
               
               
                   
                 70 proteins in 19 species: Archae - 0; Bacteria - 0; Metazoa - 1; Fungi - 0; Plants - 66; 
               
               
                   
                 Viruses - 0; Other Eukaryotes - 3 (source: NCBI BLink). 
               
               
                 At3g46280 
                 protein kinase-related 
                 ClassIIIA 
               
               
                 At1g30820 
                 CTP synthase family protein 
                 ClassIIIA 
               
               
                 At3g13460 
                 ECT2, evolutionarily conserved C-terminal region 2 
                 ClassIIIA 
               
               
                 At4g17140 
                 pleckstrin homology (PH) domain-containing protein 
                 ClassIIIA 
               
               
                 At5g16120 
                 alpha/beta-Hydrolases superfamily protein 
                 ClassIIIA 
               
               
                 At1g04410 
                 Lactate/malate dehydrogenase family protein 
                 ClassIIIA 
               
               
                 At4g27260 
                 GH3.5, WES1, Auxin-responsive GH3 family protein 
                 ClassIIIA 
               
               
                 At1g66470 
                 RHD6, ROOT HAIR DEFECTIVE6 
                 ClassIIIA 
               
               
                 At2g02040 
                 ATPTR2, ATPTR2-B, NTR1, PTR2, PTR2-B, peptide transporter 2 
                 ClassIIIA 
               
               
                 At3g05390 
                 FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process 
                 ClassIIIA 
               
               
                   
                 unknown; LOCATED IN: mitochondrion; EXPRESSED IN: 15 plant structures; 
               
               
                   
                 EXPRESSED DURING: 7 growth stages; CONTAINS InterPro DOMAIN/s: Protein of 
               
               
                   
                 unknown function DUF248, methyltransferase putative (InterPro: IPR004159); BEST 
               
               
                   
                   Arabidopsis thaliana  protein match is: S-adenosyl-L-methionine-dependent 
               
               
                   
                 methyltransferases superfamily protein (TAIR: AT4G01240.1); Has 507 Blast hits to 498 
               
               
                   
                 proteins in 33 species: Archae - 4; Bacteria - 8; Metazoa - 0; Fungi - 0; Plants - 493; Viruses - 
               
               
                   
                 0; Other Eukaryotes - 2 (source: NCBI BLink). 
               
               
                 At4g03510 
                 ATRMA1, RMA1, RING membrane-anchor 1 
                 ClassIIIA 
               
               
                 At3g20860 
                 ATNEK5, NEK5, NIMA-related kinase 5 
                 ClassIIIA 
               
               
                 At3g62650 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT2G47485.1); Has 57 Blast hits to 57 proteins in 13 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 0; Fungi - 0; Plants - 57; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At1g54100 
                 ALDH7B4, aldehyde dehydrogenase 7B4 
                 ClassIIIA 
               
               
                 At3g47500 
                 CDF3, cycling DOF factor 3 
                 ClassIIIA 
               
               
                 At5g13750 
                 ZIFL1, zinc induced facilitator-like 1 
                 ClassIIIA 
               
               
                 At3g51730 
                 saposin B domain-containing protein 
                 ClassIIIA 
               
               
                 At1g67810 
                 SUFE2, sulfur E2 
                 ClassIIIA 
               
               
                 At3g52490 
                 Double Clp-N motif-containing P-loop nucleoside triphosphate hydrolases superfamily 
                 ClassIIIA 
               
               
                   
                 protein 
               
               
                 At3g48690 
                 ATCXE12, CXE12, alpha/beta-Hydrolases superfamily protein 
                 ClassIIIA 
               
               
                 At3g55450 
                 PBL1, PBS1-like 1 
                 ClassIIIA 
               
               
                 At1g68620 
                 alpha/beta-Hydrolases superfamily protein 
                 ClassIIIA 
               
               
                 At3g54140 
                 ATPTR1, PTR1, peptide transporter 1 
                 ClassIIIA 
               
               
                 At4g24330 
                 Protein of unknown function (DUF1682) 
                 ClassIIIA 
               
               
                 At1g64010 
                 Serine protease inhibitor (SERPIN) family protein 
                 ClassIIIA 
               
               
                 At2g46270 
                 GBF3, G-box binding factor 3 
                 ClassIIIA 
               
               
                 At5g10210 
                 CONTAINS InterPro DOMAIN/s: C2 calcium-dependent membrane targeting 
                 ClassIIIA 
               
               
                   
                 (InterPro: IPR000008); BEST  Arabidopsis thaliana  protein match is: unknown protein 
               
               
                   
                 (TAIR: AT5G65030.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; 
               
               
                   
                 Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 
               
               
                   
                 (source: NCBI BLink). 
               
               
                 At1g73260 
                 ATKTI1, KTI1, kunitz trypsin inhibitor 1 
                 ClassIIIA 
               
               
                 At1g75800 
                 Pathogenesis-related thaumatin superfamily protein 
                 ClassIIIA 
               
               
                 At5g07080 
                 HXXXD-type acyl-transferase family protein 
                 ClassIIIA 
               
               
                 At1g21310 
                 ATEXT3, EXT3, RSH, extensin 3 
                 ClassIIIA 
               
               
                 At1g61810 
                 BGLU45, beta-glucosidase 45 
                 ClassIIIA 
               
               
                 At4g32300 
                 SD2-5, S-domain-2 5 
                 ClassIIIA 
               
               
                 At1g65840 
                 ATPAO4, PAO4, polyamine oxidase 4 
                 ClassIIIA 
               
               
                 At5g47390 
                 myb-like transcription factor family protein 
                 ClassIIIA 
               
               
                 At5g61600 
                 ERF104, ethylene response factor 104 
                 ClassIIIA 
               
               
                 At5g24030 
                 SLAH3, SLAC1 homologue 3 
                 ClassIIIA 
               
               
                 At5g15190 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIA 
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast; EXPRESSED IN: 17 plant 
               
               
                   
                 structures; EXPRESSED DURING: LP.04 four leaves visible, 4 anthesis, petal 
               
               
                   
                 differentiation and expansion stage, E expanded cotyledon stage, D bilateral stage; Has 7 
               
               
                   
                 Blast hits to 7 proteins in 3 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 
               
               
                   
                 7; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At4g38340 
                 NLP3; Plant regulator RWP-RK family protein 
                 ClassIIIA 
               
               
                 At1g10070 
                 ATBCAT-2, BCAT-2, branched-chain amino acid transaminase 2 
                 ClassIIIA 
               
               
                 At2g19350 
                 Eukaryotic protein of unknown function (DUF872) 
                 ClassIIIA 
               
               
                 At4g31240 
                 protein kinase C-like zinc finger protein 
                 ClassIIIA 
               
               
                 At5g40450 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIA 
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast, plasma membrane; EXPRESSED 
               
               
                   
                 IN: 24 plant structures; EXPRESSED DURING: 13 growth stages; Has 30201 Blast hits to 
               
               
                   
                 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; 
               
               
                   
                 Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink). 
               
               
                 At1g69570 
                 Dof-type zinc finger DNA-binding family protein 
                 ClassIIIA 
               
               
                 At1g11260 
                 ATSTP1, STP1, sugar transporter 1 
                 ClassIIIA 
               
               
                 At4g37540 
                 LBD39, LOB domain-containing protein 39 
                 ClassIIIA 
               
               
                 At3g20410 
                 CPK9, calmodulin-domain protein kinase 9 
                 ClassIIIA 
               
               
                 At5g27920 
                 F-box family protein 
                 ClassIIIA 
               
               
                 At4g01026 
                 PYL7, RCAR2, PYR1-like 7 
                 ClassIIIA 
               
               
                 At4g35780 
                 ACT-like protein tyrosine kinase family protein 
                 ClassIIIA 
               
               
                 At3g06850 
                 BCE2, DIN3, LTA1, 2-oxoacid dehydrogenases acyltransferase family protein 
                 ClassIIIA 
               
               
                 At1g76410 
                 ATL8, RING/U-box superfamily protein 
                 ClassIIIA 
               
               
                 At1g20340 
                 DRT112, PETE2, Cupredoxin superfamily protein 
                 ClassIIIA 
               
               
                 At1g55510 
                 BCDH BETA1, branched-chain alpha-keto acid decarboxylase E1 beta subunit 
                 ClassIIIA 
               
               
                 At4g35770 
                 ATSEN1, DIN1, SEN1, SEN1, Rhodanese/Cell cycle control phosphatase superfamily 
                 ClassIIIA 
               
               
                   
                 protein 
               
               
                 At5g47240 
                 atnudt8, NUDT8, nudix hydrolase homolog 8 
                 ClassIIIA 
               
               
                 At3g14760 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIA 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 6 
               
               
                   
                 plant structures; EXPRESSED DURING: LP.04 four leaves visible, LP.02 two leaves visible; 
               
               
                   
                 Has 63 Blast hits to 63 proteins in 13 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 
               
               
                   
                 0; Plants - 63; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At3g60690 
                 SAUR-like auxin-responsive protein family 
                 ClassIIIA 
               
               
                 At1g32460 
                 unknown protein; Has 19 Blast hits to 19 proteins in 8 species: Archae - 0; Bacteria - 0; 
                 ClassIIIA 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 19; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At2g35230 
                 IKU1, IKU1, VQ motif-containing protein 
                 ClassIIIA 
               
               
                 At5g54500 
                 FQR1, flavodoxin-like quinone reductase 1 
                 ClassIIIA 
               
               
                 At5g43830 
                 Aluminium induced protein with YGL and LRDR motifs 
                 ClassIIIA 
               
               
                 At1g51820 
                 Leucine-rich repeat protein kinase family protein 
                 ClassIIIA 
               
               
                 At1g63180 
                 UGE3, UDP-D-glucose/UDP-D-galactose 4-epimerase 3 
                 ClassIIIA 
               
               
                 At3g61260 
                 Remorin family protein 
                 ClassIIIA 
               
               
                 At2g38750 
                 ANNAT4, annexin 4 
                 ClassIIIA 
               
               
                 At4g32870 
                 Polyketide cyclase/dehydrase and lipid transport superfamily protein 
                 ClassIIIA 
               
               
                 At3g47960 
                 Major facilitator superfamily protein 
                 ClassIIIA 
               
               
                 At5g05340 
                 Peroxidase superfamily protein 
                 ClassIIIA 
               
               
                 At2g38400 
                 AGT3, alanine: glyoxylate aminotransferase 3 
                 ClassIIIA 
               
               
                 At5g66030 
                 ATGRIP, GRIP, Golgi-localized GRIP domain-containing protein 
                 ClassIIIA 
               
               
                 At3g56360 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIA 
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast; EXPRESSED IN: 24 plant 
               
               
                   
                 structures; EXPRESSED DURING: 15 growth stages; BEST  Arabidopsis thaliana  protein 
               
               
                   
                 match is: unknown protein (TAIR: AT5G05250.1); Has 45 Blast hits to 45 proteins in 13 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 45; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g18850 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIA 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 23 
               
               
                   
                 plant structures; EXPRESSED DURING: 13 growth stages; Has 1807 Blast hits to 1807 
               
               
                   
                 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; 
               
               
                   
                 Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink). 
               
               
                 At2g31390 
                 pfkB-like carbohydrate kinase family protein 
                 ClassIIIA 
               
               
                 At5g03550 
                 BEST  Arabidopsis thaliana  protein match is: TRAF-like family protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT2G42460.1); Has 137 Blast hits to 125 proteins in 2 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 0; Fungi - 0; Plants - 137; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At1g42480 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIA 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 24 
               
               
                   
                 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro 
               
               
                   
                 DOMAIN/s: Protein of unknown function DUF3456 (InterPro: IPR021852); Has 177 Blast 
               
               
                   
                 hits to 177 proteins in 59 species: Archae - 0; Bacteria - 0; Metazoa - 140; Fungi - 0; Plants - 
               
               
                   
                 35; Viruses - 0; Other Eukaryotes - 2 (source: NCBI BLink). 
               
               
                 At4g30490 
                 AFG1-like ATPase family protein 
                 ClassIIIA 
               
               
                 At2g25900 
                 ATCTH, ATTZF1, Zinc finger C-x8-C-x5-C-x3-H type family protein 
                 ClassIIIA 
               
               
                 At3g54630 
                 CONTAINS InterPro DOMAIN/s: Kinetochore protein Ndc80 (InterPro: IPR005550); Has 
                 ClassIIIA 
               
               
                   
                 24780 Blast hits to 15608 proteins in 1321 species: Archae - 545; Bacteria - 2969; Metazoa - 
               
               
                   
                 12597; Fungi - 2181; Plants - 1581; Viruses - 39; Other Eukaryotes - 4868 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At1g66550 
                 ATWRKY67, WRKY67, WRKY DNA-binding protein 67 
                 ClassIIIA 
               
               
                 At4g39780 
                 Integrase-type DNA-binding superfamily protein 
                 ClassIIIA 
               
               
                 At1g75450 
                 ATCKX5, ATCKX6, CKX5, cytokinin oxidase 5 
                 ClassIIIA 
               
               
                 At2g01570 
                 RGA, RGA1, GRAS family transcription factor family protein 
                 ClassIIIA 
               
               
                 At4g38470 
                 ACT-like protein tyrosine kinase family protein 
                 ClassIIIA 
               
               
                 At1g35580 
                 CINV1, cytosolic invertase 1 
                 ClassIIIA 
               
               
                 At1g11380 
                 PLAC8 family protein 
                 ClassIIIA 
               
               
                 At1g48840 
                 Plant protein of unknown function (DUF639) 
                 ClassIIIA 
               
               
                 At1g60940 
                 SNRK2-10, SNRK2.10, SRK2B, SNF1-related protein kinase 2.10 
                 ClassIIIA 
               
               
                 At1g31480 
                 SGR2, shoot gravitropism 2 (SGR2) 
                 ClassIIIA 
               
               
                 At3g19390 
                 Granulin repeat cysteine protease family protein 
                 ClassIIIA 
               
               
                 At4g15545 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT1G16520.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At1g32200 
                 ACT1, ATS1, phospholipid/glycerol acyltransferase family protein 
                 ClassIIIA 
               
               
                 At1g61660 
                 basic helix-loop-helix (bHLH) DNA-binding superfamily protein 
                 ClassIIIA 
               
               
                 At1g18270 
                 ketose-bisphosphate aldolase class-II family protein 
                 ClassIIIA 
               
               
                 At5g59220 
                 HAI1, highly ABA-induced PP2C gene 1 
                 ClassIIIA 
               
               
                 At5g48430 
                 Eukaryotic aspartyl protease family protein 
                 ClassIIIA 
               
               
                 At5g06690 
                 WCRKC1, WCRKC thioredoxin 1 
                 ClassIIIA 
               
               
                 At2g40170 
                 ATEM6, EM6, GEA6, Stress induced protein 
                 ClassIIIA 
               
               
                 At5g06980 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT3G12320.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At3g03470 
                 CYP89A9, cytochrome P450, family 87, subfamily A, polypeptide 9 
                 ClassIIIA 
               
               
                 At1g67070 
                 DIN9, PMI2, Mannose-6-phosphate isomerase, type I 
                 ClassIIIA 
               
               
                 At5g05440 
                 PYL5, RCAR8, Polyketide cyclase/dehydrase and lipid transport superfamily protein 
                 ClassIIIA 
               
               
                 At1g80460 
                 GLI1, NHO1, Actin-like ATPase superfamily protein 
                 ClassIIIA 
               
               
                 At2g39210 
                 Major facilitator superfamily protein 
                 ClassIIIA 
               
               
                 At5g63620 
                 GroES-like zinc-binding alcohol dehydrogenase family protein 
                 ClassIIIA 
               
               
                 At1g73240 
                 CONTAINS InterPro DOMAIN/s: Nucleoporin protein Ndc1-Nup (InterPro: IPR019049); 
                 ClassIIIA 
               
               
                   
                 Has 36 Blast hits to 36 proteins in 17 species: Archae - 0; Bacteria - 0; Metazoa - 1; Fungi - 
               
               
                   
                 0; Plants - 35; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At2g30600 
                 BTB/POZ domain-containing protein 
                 ClassIIIA 
               
               
                 At5g04310 
                 Pectin lyase-like superfamily protein 
                 ClassIIIA 
               
               
                 At4g18340 
                 Glycosyl hydrolase superfamily protein 
                 ClassIIIA 
               
               
                 At5g16960 
                 Zinc-binding dehydrogenase family protein 
                 ClassIIIA 
               
               
                 At4g15630 
                 Uncharacterised protein family (UPF0497) 
                 ClassIIIA 
               
               
                 At2g03220 
                 ATFT1, ATFUT1, FT1, MUR2, fucosyltransferase 1 
                 ClassIIIA 
               
               
                 At3g50780 
                 BEST  Arabidopsis thaliana  protein match is: BTB/POZ domain-containing protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT1G63850.1); Has 298 Blast hits to 298 proteins in 22 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 10; Fungi - 0; Plants - 287; Viruses - 0; Other Eukaryotes - 1 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At5g65630 
                 GTE7, global transcription factor group E7 
                 ClassIIIA 
               
               
                 At1g28260 
                 Telomerase activating protein Est1 
                 ClassIIIA 
               
               
                 At3g02550 
                 LBD41, LOB domain-containing protein 41 
                 ClassIIIA 
               
               
                 At3g14067 
                 Subtilase family protein 
                 ClassIIIA 
               
               
                 At5g26740 
                 Protein of unknown function (DUF300) 
                 ClassIIIA 
               
               
                 At4g36670 
                 Major facilitator superfamily protein 
                 ClassIIIA 
               
               
                 At1g19700 
                 BEL10, BLH10, BEL1-like homeodomain 10 
                 ClassIIIA 
               
               
                 At5g64260 
                 EXL2, EXORDIUM like 2 
                 ClassIIIA 
               
               
                 At1g75220 
                 Major facilitator superfamily protein 
                 ClassIIIA 
               
               
                 At2g40420 
                 Transmembrane amino acid transporter family protein 
                 ClassIIIA 
               
               
                 At1g30900 
                 BP80-3; 3, VSR3; 3, VSR6, VACUOLAR SORTING RECEPTOR 6 
                 ClassIIIA 
               
               
                 At5g20885 
                 RING/U-box superfamily protein 
                 ClassIIIA 
               
               
                 At5g52250 
                 Transducin/WD40 repeat-like superfamily protein 
                 ClassIIIA 
               
               
                 At3g46440 
                 UXS5, UDP-XYL synthase 5 
                 ClassIIIA 
               
               
                 At5g13740 
                 ZIF1, zinc induced facilitator 1 
                 ClassIIIA 
               
               
                 At1g11780 
                 oxidoreductase, 2OG-Fe(II) oxygenase family protein 
                 ClassIIIA 
               
               
                 At5g43430 
                 ETFBETA, electron transfer flavoprotein beta 
                 ClassIIIA 
               
               
                 At5g60200 
                 TMO6, TARGET OF MONOPTEROS 6 
                 ClassIIIA 
               
               
                 At5g16970 
                 AER, AT-AER, alkenal reductase 
                 ClassIIIA 
               
               
                 At3g57020 
                 Calcium-dependent phosphotriesterase superfamily protein 
                 ClassIIIA 
               
               
                 At5g02780 
                 GSTL1, glutathione transferase lambda 1 
                 ClassIIIA 
               
               
                 At5g39040 
                 ALS1, ATTAP2, TAP2, transporter associated with antigen processing protein 2 
                 ClassIIIA 
               
               
                 At5g19090 
                 Heavy metal transport/detoxification superfamily protein 
                 ClassIIIA 
               
               
                 At4g24220 
                 AWI31, VEP1, NAD(P)-binding Rossmann-fold superfamily protein 
                 ClassIIIA 
               
               
                 At1g03790 
                 SOM, Zinc finger C-x8-C-x5-C-x3-H type family protein 
                 ClassIIIA 
               
               
                 At2g38820 
                 Protein of unknown function (DUF506) 
                 ClassIIIA 
               
               
                 At1g20300 
                 Pentatricopeptide repeat (PPR) superfamily protein 
                 ClassIIIA 
               
               
                 At3g46690 
                 UDP-Glycosyltransferase superfamily protein 
                 ClassIIIA 
               
               
                 At3g15610 
                 Transducin/WD40 repeat-like superfamily protein 
                 ClassIIIA 
               
               
                 At3g01175 
                 Protein of unknown function (DUF1666) 
                 ClassIIIA 
               
               
                 At1g76990 
                 ACR3, ACT domain repeat 3 
                 ClassIIIA 
               
               
                 At1g68410 
                 Protein phosphatase 2C family protein 
                 ClassIIIA 
               
               
                 At5g27350 
                 SFP1, Major facilitator superfamily protein 
                 ClassIIIA 
               
               
                 At4g32320 
                 APX6, ascorbate peroxidase 6 
                 ClassIIIA 
               
               
                 At5g11520 
                 ASP3, YLS4, aspartate aminotransferase 3 
                 ClassIIIA 
               
               
                 At2g14170 
                 ALDH6B2, aldehyde dehydrogenase 6B2 
                 ClassIIIA 
               
               
                 At1g63700 
                 EMB71, MAPKKK4, YDA, Protein kinase superfamily protein 
                 ClassIIIA 
               
               
                 At1g68850 
                 Peroxidase superfamily protein 
                 ClassIIIA 
               
               
                 At3g15260 
                 Protein phosphatase 2C family protein 
                 ClassIIIA 
               
               
                 At5g04630 
                 CYP77A9, cytochrome P450, family 77, subfamily A, polypeptide 9 
                 ClassIIIA 
               
               
                 At3g01270 
                 Pectate lyase family protein 
                 ClassIIIA 
               
               
                 At1g26730 
                 EXS (ERD1/XPR1/SYG1) family protein 
                 ClassIIIA 
               
               
                 At2g37440 
                 DNAse I-like superfamily protein 
                 ClassIIIA 
               
               
                 At5g49650 
                 XK-2, XK2, xylulose kinase-2 
                 ClassIIIA 
               
               
                 At1g26270 
                 Phosphatidylinositol 3- and 4-kinase family protein 
                 ClassIIIA 
               
               
                 At5g28610 
                 BEST  Arabidopsis thaliana  protein match is: glycine-rich protein (TAIR: AT5G28630.1); Has 
                 ClassIIIA 
               
               
                   
                 1536 Blast hits to 1202 proteins in 136 species: Archae - 0; Bacteria - 8; Metazoa - 888; 
               
               
                   
                 Fungi - 120; Plants - 71; Viruses - 39; Other Eukaryotes - 410 (source: NCBI BLink). 
               
               
                 At5g04770 
                 ATCAT6, CAT6, cationic amino acid transporter 6 
                 ClassIIIA 
               
               
                 At4g10840 
                 Tetratricopeptide repeat (TPR)-like superfamily protein 
                 ClassIIIA 
               
               
                 At2g43060 
                 IBH1, ILI1 binding bHLH 1 
                 ClassIIIA 
               
               
                 At4g03080 
                 BSL1, BRI1 suppressor 1 (BSU1)-like 1 
                 ClassIIIA 
               
               
                 At5g57660 
                 ATCOL5, COL5, CONSTANS-like 5 
                 ClassIIIA 
               
               
                 At5g07070 
                 CIPK2, SnRK3.2, CBL-interacting protein kinase 2 
                 ClassIIIA 
               
               
                 At4g15550 
                 IAGLU, indole-3-acetate beta-D-glucosyltransferase 
                 ClassIIIA 
               
               
                 At2g01860 
                 EMB975, Tetratricopeptide repeat (TPR)-like superfamily protein 
                 ClassIIIA 
               
               
                 At5g58620 
                 zinc finger (CCCH-type) family protein 
                 ClassIIIA 
               
               
                 At1g15050 
                 IAA34, indole-3-acetic acid inducible 34 
                 ClassIIIA 
               
               
                 At5g66400 
                 ATDI8, RAB18, Dehydrin family protein 
                 ClassIIIA 
               
               
                 At2g19810 
                 CCCH-type zinc finger family protein 
                 ClassIIIA 
               
               
                 At3g17420 
                 GPK1, glyoxysomal protein kinase 1 
                 ClassIIIA 
               
               
                 At3g47640 
                 PYE, basic helix-loop-helix (bHLH) DNA-binding superfamily protein 
                 ClassIIIA 
               
               
                 At3g53150 
                 UGT73D1, UDP-glucosyl transferase 73D1 
                 ClassIIIA 
               
               
                 At5g67320 
                 HOS15, WD-40 repeat family protein 
                 ClassIIIA 
               
               
                 At3g17110 
                 pseudogene, glycine-rich protein 
                 ClassIIIA 
               
               
                 At3g61060 
                 AtPP2-A13, PP2-A13, phloem protein 2-A13 
                 ClassIIIA 
               
               
                 At1g01490 
                 Heavy metal transport/detoxification superfamily protein 
                 ClassIIIA 
               
               
                 At5g41610 
                 ATCHX18, CHX18, cation/H+ exchanger 18 
                 ClassIIIA 
               
               
                 At3g57890 
                 Tubulin binding cofactor C domain-containing protein 
                 ClassIIIA 
               
               
                 At4g17950 
                 AT hook motif DNA-binding family protein 
                 ClassIIIA 
               
               
                 At4g01120 
                 ATBZIP54, GBF2, G-box binding factor 2 
                 ClassIIIA 
               
               
                 At3g51840 
                 ACX4, ATG6, ATSCX, acyl-CoA oxidase 4 
                 ClassIIIA 
               
               
                 At4g32950 
                 Protein phosphatase 2C family protein 
                 ClassIIIA 
               
               
                 At4g24060 
                 Dof-type zinc finger DNA-binding family protein 
                 ClassIIIA 
               
               
                 At1g79350 
                 EMB1135, RING/FYVE/PHD zinc finger superfamily protein 
                 ClassIIIA 
               
               
                 At2g39980 
                 HXXXD-type acyl-transferase family protein 
                 ClassIIIA 
               
               
                 At3g15950 
                 NAI2, DNA topoisomerase-related 
                 ClassIIIA 
               
               
                 At2g27490 
                 ATCOAE, dephospho-CoA kinase family 
                 ClassIIIA 
               
               
                 At3g60510 
                 ATP-dependent caseinolytic (Clp) protease/crotonase family protein 
                 ClassIIIA 
               
               
                 At3g28510 
                 P-loop containing nucleoside triphosphate hydrolases superfamily protein 
                 ClassIIIA 
               
               
                 At4g39070 
                 B-box zinc finger family protein 
                 ClassIIIA 
               
               
                 At1g22400 
                 ATUGT85A1, UGT85A1, UDP-Glycosyltransferase superfamily protein 
                 ClassIIIA 
               
               
                 At2g02800 
                 APK2B, protein kinase 2B 
                 ClassIIIA 
               
               
                 At4g14420 
                 HR-like lesion-inducing protein-related 
                 ClassIIIA 
               
               
                 At4g30550 
                 Class I glutamine amidotransferase-like superfamily protein 
                 ClassIIIA 
               
               
                 At1g03610 
                 Protein of unknown function (DUF789) 
                 ClassIIIA 
               
               
                 At2g23450 
                 Protein kinase superfamily protein 
                 ClassIIIA 
               
               
                 At4g13430 
                 ATLEUC1, IIL1, isopropyl malate isomerase large subunit 1 
                 ClassIIIA 
               
               
                 At3g19920 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIA 
               
               
                   
                 (TAIR: AT5G64230.1); Has 217 Blast hits to 217 proteins in 16 species: Archae - 0; Bacteria - 
               
               
                   
                 2; Metazoa - 0; Fungi - 0; Plants - 215; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At5g49360 
                 ATBXL1, BXL1, beta-xylosidase 1 
                 ClassIIIA 
               
               
                 At1g29760 
                 Putative adipose-regulatory protein (Seipin) 
                 ClassIIIA 
               
               
                 At4g38500 
                 Protein of unknown function (DUF616) 
                 ClassIIIA 
               
               
                 At1g15380 
                 Lactoylglutathione lyase/glyoxalase I family protein 
                 ClassIIIA 
               
               
                 At2g17500 
                 Auxin efflux carrier family protein 
                 ClassIIIA 
               
               
                 At5g24470 
                 APRR5, PRR5, pseudo-response regulator 5 
                 ClassIIIA 
               
               
                 At1g03090 
                 MCCA, methylcrotonyl-CoA carboxylase alpha chain, mitochondrial/3-methylcrotonyl- 
                 ClassIIIA 
               
               
                   
                 CoA carboxylase 1 (MCCA) 
               
               
                 At3g18980 
                 ETP1, EIN2 targeting protein1 
                 ClassIIIA 
               
               
                 At3g16910 
                 AAE7, ACN1, acyl-activating enzyme 7 
                 ClassIIIA 
               
               
                 At1g17190 
                 ATGSTU26, GSTU26, glutathione S-transferase tau 26 
                 ClassIIIA 
               
               
                 At5g18630 
                 alpha/beta-Hydrolases superfamily protein 
                 ClassIIIA 
               
               
                 At5g17640 
                 Protein of unknown function (DUF1005) 
                 ClassIIIA 
               
            
           
           
               
               
            
               
                 ClassIIIB. NR: no binding but repression 
                   
               
            
           
           
               
               
               
            
               
                 At1g56510 
                 ADR2, WRR4, Disease resistance protein (TIR-NBS-LRR class) 
                 ClassIIIB 
               
               
                 At1g74710 
                 ATICS1, EDS16, ICS1, SID2, ADC synthase superfamily protein 
                 ClassIIIB 
               
               
                 At2g17040 
                 anac036, NAC036, NAC domain containing protein 36 
                 ClassIIIB 
               
               
                 At1g57630 
                 Toll-Interleukin-Resistance (TIR) domain family protein 
                 ClassIIIB 
               
               
                 At3g63390 
                 unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
                 ClassIIIB 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At1g67050 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIB 
               
               
                   
                 (TAIR: AT5G38320.1); Has 617 Blast hits to 318 proteins in 80 species: Archae - 0; Bacteria - 
               
               
                   
                 16; Metazoa - 141; Fungi - 62; Plants - 128; Viruses - 2; Other Eukaryotes - 268 (source: 
               
               
                   
                 NCBI BLink). 
               
               
                 At1g73750 
                 Uncharacterised conserved protein UCP031088, alpha/beta hydrolase 
                 ClassIIIB 
               
               
                 At3g05490 
                 RALFL22, ralf-like 22 
                 ClassIIIB 
               
               
                 At1g15890 
                 Disease resistance protein (CC-NBS-LRR class) family 
                 ClassIIIB 
               
               
                 At2g46590 
                 DAG2, Dof-type zinc finger DNA-binding family protein 
                 ClassIIIB 
               
               
                 At2g44450 
                 BGLU15, beta glucosidase 15 
                 ClassIIIB 
               
               
                 At1g05800 
                 DGL, alpha/beta-Hydrolases superfamily protein 
                 ClassIIIB 
               
               
                 At1g32690 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIB 
               
               
                   
                 biological_process unknown; LOCATED IN: plasma membrane; EXPRESSED IN: 21 plant 
               
               
                   
                 structures; EXPRESSED DURING: 11 growth stages; BEST  Arabidopsis thaliana  protein 
               
               
                   
                 match is: unknown protein (TAIR: AT2G35200.1); Has 45 Blast hits to 45 proteins in 8 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 45; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g44350 
                 ethylene-responsive nuclear protein-related 
                 ClassIIIB 
               
               
                 At4g30560 
                 ATCNGC9, CNGC9, cyclic nucleotide gated channel 9 
                 ClassIIIB 
               
               
                 At4g26120 
                 Ankyrin repeat family protein/BTB/POZ domain-containing protein 
                 ClassIIIB 
               
               
                 At3g10630 
                 UDP-Glycosyltransferase superfamily protein 
                 ClassIIIB 
               
               
                 At4g39890 
                 AtRABH1c, RABH1c, RAB GTPase homolog H1C 
                 ClassIIIB 
               
               
                 At3g61390 
                 RING/U-box superfamily protein 
                 ClassIIIB 
               
               
                 At3g07390 
                 AIR12, auxin-responsive family protein 
                 ClassIIIB 
               
               
                 At2g23270 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIB 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 
               
               
                   
                 stem, sperm cell, root, stamen; EXPRESSED DURING: 4 anthesis; BEST  Arabidopsis   
               
               
                   
                   thaliana  protein match is: unknown protein (TAIR: AT4G37290.1); Has 36 Blast hits to 35 
               
               
                   
                 proteins in 6 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 36; Viruses - 
               
               
                   
                 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At4g22820 
                 A20/AN1-like zinc finger family protein 
                 ClassIIIB 
               
               
                 At1g51620 
                 Protein kinase superfamily protein 
                 ClassIIIB 
               
               
                 At4g39940 
                 AKN2, APK2, APS-kinase 2 
                 ClassIIIB 
               
               
                 At1g10160 
                 transposable element gene 
                 ClassIIIB 
               
               
                 At3g19630 
                 Radical SAM superfamily protein 
                 ClassIIIB 
               
               
                 At2g44090 
                 Ankyrin repeat family protein 
                 ClassIIIB 
               
               
                 At1g58080 
                 ATATP-PRT1, ATP-PRT1, HISN1A, ATP phosphoribosyl transferase 1 
                 ClassIIIB 
               
               
                 At3g55960 
                 Haloacid dehalogenase-like hydrolase (HAD) superfamily protein 
                 ClassIIIB 
               
               
                 At3g48850 
                 PHT3; 2, phosphate transporter 3; 2 
                 ClassIIIB 
               
               
                 At1g53980 
                 Ubiquitin-like superfamily protein 
                 ClassIIIB 
               
               
                 At1g74430 
                 ATMYB95, ATMYBCP66, MYB95, myb domain protein 95 
                 ClassIIIB 
               
               
                 At5g40540 
                 Protein kinase superfamily protein 
                 ClassIIIB 
               
               
                 At4g14368 
                 Regulator of chromosome condensation (RCC1) family protein 
                 ClassIIIB 
               
               
                 At2g16500 
                 ADC1, ARGDC, ARGDC1, SPE1, arginine decarboxylase 1 
                 ClassIIIB 
               
               
                 At3g05360 
                 AtRLP30, RLP30, receptor like protein 30 
                 ClassIIIB 
               
               
                 At1g20510 
                 OPCL1, OPC-8:0 CoA ligase1 
                 ClassIIIB 
               
               
                 At3g17020 
                 Adenine nucleotide alpha hydrolases-like superfamily protein 
                 ClassIIIB 
               
               
                 At2g42360 
                 RING/U-box superfamily protein 
                 ClassIIIB 
               
               
                 At1g24625 
                 ZFP7, zinc finger protein 7 
                 ClassIIIB 
               
               
                 At5g41550 
                 Disease resistance protein (TIR-NBS-LRR class) family 
                 ClassIIIB 
               
               
                 At2g41380 
                 S-adenosyl-L-methionine-dependent methyltransferases superfamily protein 
                 ClassIIIB 
               
               
                 At5g65870 
                 ATPSK5, PSK5, PSK5, phytosulfokine 5 precursor 
                 ClassIIIB 
               
               
                 At4g11850 
                 MEE54, PLDGAMMA1, phospholipase D gamma 1 
                 ClassIIIB 
               
               
                 At3g13650 
                 Disease resistance-responsive (dirigent-like protein) family protein 
                 ClassIIIB 
               
               
                 At5g56760 
                 ATSERAT1; 1, SAT-52, SAT5, SERAT1; 1, serine acetyltransferase 1; 1 
                 ClassIIIB 
               
               
                 At1g75540 
                 STH2, salt tolerance homolog2 
                 ClassIIIB 
               
               
                 At1g53430 
                 Leucine-rich repeat transmembrane protein kinase 
                 ClassIIIB 
               
               
                 At1g74590 
                 ATGSTU10, GSTU10, glutathione S-transferase TAU 10 
                 ClassIIIB 
               
               
                 At5g52670 
                 Copper transport protein family 
                 ClassIIIB 
               
               
                 At3g44735 
                 ATPSK3, PSK1, PSK3, PHYTOSULFOKINE 3 PRECURSOR 
                 ClassIIIB 
               
               
                 At3g18250 
                 Putative membrane lipoprotein 
                 ClassIIIB 
               
               
                 At1g28190 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIB 
               
               
                   
                 (TAIR: AT5G12340.1); Has 166 Blast hits to 162 proteins in 36 species: Archae - 0; Bacteria - 
               
               
                   
                 2; Metazoa - 15; Fungi - 5; Plants - 124; Viruses - 0; Other Eukaryotes - 20 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At3g02770 
                 Ribonuclease E inhibitor RraA/Dimethylmenaquinone methyltransferase 
                 ClassIIIB 
               
               
                 At5g25190 
                 Integrase-type DNA-binding superfamily protein 
                 ClassIIIB 
               
               
                 At4g00330 
                 CRCK2, calmodulin-binding receptor-like cytoplasmic kinase 2 
                 ClassIIIB 
               
               
                 At1g53050 
                 Protein kinase superfamily protein 
                 ClassIIIB 
               
               
                 At1g05060 
                 unknown protein; Has 34 Blast hits to 34 proteins in 13 species: Archae - 0; Bacteria - 0; 
                 ClassIIIB 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 34; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At3g09020 
                 alpha 1,4-glycosyltransferase family protein 
                 ClassIIIB 
               
               
                 At1g30040 
                 ATGA2OX2, GA2OX2, GA2OX2, gibberellin 2-oxidase 
                 ClassIIIB 
               
               
                 At5g24430 
                 Calcium-dependent protein kinase (CDPK) family protein 
                 ClassIIIB 
               
               
                 At4g21390 
                 B120, S-locus lectin protein kinase family protein 
                 ClassIIIB 
               
               
                 At1g70130 
                 Concanavalin A-like lectin protein kinase family protein 
                 ClassIIIB 
               
               
                 At2g04160 
                 AIR3, Subtilisin-like serine endopeptidase family protein 
                 ClassIIIB 
               
               
                 At3g20510 
                 Transmembrane proteins 14C 
                 ClassIIIB 
               
               
                 At3g10640 
                 VPS60.1, SNF7 family protein 
                 ClassIIIB 
               
               
                 At5g58787 
                 RING/U-box superfamily protein 
                 ClassIIIB 
               
               
                 At2g34920 
                 EDA18, RING/U-box superfamily protein 
                 ClassIIIB 
               
               
                 At1g44130 
                 Eukaryotic aspartyl protease family protein 
                 ClassIIIB 
               
               
                 At4g37940 
                 AGL21, AGAMOUS-like 21 
                 ClassIIIB 
               
               
                 At4g27720 
                 Major facilitator superfamily protein 
                 ClassIIIB 
               
               
                 At5g22530 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIB 
               
               
                   
                 (TAIR: AT5G22520.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At1g17310 
                 MADS-box transcription factor family protein 
                 ClassIIIB 
               
               
                 At1g35560 
                 TCP family transcription factor 
                 ClassIIIB 
               
               
                 At4g40020 
                 Myosin heavy chain-related protein 
                 ClassIIIB 
               
               
                 At1g24140 
                 Matrixin family protein 
                 ClassIIIB 
               
               
                 At1g11210 
                 Protein of unknown function (DUF761) 
                 ClassIIIB 
               
               
                 At1g48320 
                 Thioesterase superfamily protein 
                 ClassIIIB 
               
               
                 At5g12880 
                 proline-rich family protein 
                 ClassIIIB 
               
               
                 At1g10650 
                 SBP (S-ribonuclease binding protein) family protein 
                 ClassIIIB 
               
               
                 At3g09270 
                 ATGSTU8, GSTU8, glutathione S-transferase TAU 8 
                 ClassIIIB 
               
               
                 At1g29250 
                 Alba DNA/RNA-binding protein 
                 ClassIIIB 
               
               
                 At3g61850 
                 DAG1, Dof-type zinc finger DNA-binding family protein 
                 ClassIIIB 
               
               
                 At1g78100 
                 F-box family protein 
                 ClassIIIB 
               
               
                 At4g00080 
                 UNE11, Plant invertase/pectin methylesterase inhibitor superfamily protein 
                 ClassIIIB 
               
               
                 At1g32350 
                 AOX1D, alternative oxidase 1D 
                 ClassIIIB 
               
               
                 At3g49350 
                 Ypt/Rab-GAP domain of gyp1p superfamily protein 
                 ClassIIIB 
               
               
                 At1g80530 
                 Major facilitator superfamily protein 
                 ClassIIIB 
               
               
                 At1g55610 
                 BRL1, BRI1 like 
                 ClassIIIB 
               
               
                 At5g13870 
                 EXGT-A4, XTH5, xyloglucan endotransglucosylase/hydrolase 5 
                 ClassIIIB 
               
               
                 At4g28085 
                 unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
                 ClassIIIB 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At1g07750 
                 RmlC-like cupins superfamily protein 
                 ClassIIIB 
               
               
                 At3g50480 
                 HR4, homolog of RPW8 4 
                 ClassIIIB 
               
               
                 At3g21230 
                 4CL5, 4-coumarate: CoA ligase 5 
                 ClassIIIB 
               
               
                 At5g60350 
                 unknown protein; Has 110 Blast hits to 97 proteins in 36 species: Archae - 0; Bacteria - 10; 
                 ClassIIIB 
               
               
                   
                 Metazoa - 39; Fungi - 2; Plants - 5; Viruses - 0; Other Eukaryotes - 54 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At3g09000 
                 proline-rich family protein 
                 ClassIIIB 
               
               
                 At3g25070 
                 RIN4, RPM1 interacting protein 4 
                 ClassIIIB 
               
               
                 At3g11840 
                 PUB24, plant U-box 24 
                 ClassIIIB 
               
               
                 At2g11520 
                 CRCK3, calmodulin-binding receptor-like cytoplasmic kinase 3 
                 ClassIIIB 
               
               
                 At5g24540 
                 BGLU31, beta glucosidase 31 
                 ClassIIIB 
               
               
                 At2g19130 
                 S-locus lectin protein kinase family protein 
                 ClassIIIB 
               
               
                 At5g48540 
                 receptor-like protein kinase-related family protein 
                 ClassIIIB 
               
               
                 At4g24160 
                 alpha/beta-Hydrolases superfamily protein 
                 ClassIIIB 
               
               
                 At1g09940 
                 HEMA2, Glutamyl-tRNA reductase family protein 
                 ClassIIIB 
               
               
                 At3g59080 
                 Eukaryotic aspartyl protease family protein 
                 ClassIIIB 
               
               
                 At3g27110 
                 Peptidase family M48 family protein 
                 ClassIIIB 
               
               
                 At4g16780 
                 ATHB-2, ATHB2, HAT4, HB-2, homeobox protein 2 
                 ClassIIIB 
               
               
                 At5g44070 
                 ARA8, ATPCS1, CAD1, PCS1, phytochelatin synthase 1 (PCS1) 
                 ClassIIIB 
               
               
                 At5g66880 
                 SNRK2-3, SNRK2.3, SRK2I, sucrose nonfermenting 1(SNF1)-related protein kinase 2.3 
                 ClassIIIB 
               
               
                 At5g49620 
                 AtMYB78, MYB78, myb domain protein 78 
                 ClassIIIB 
               
               
                 At5g22550 
                 Plant protein of unknown function (DUF247) 
                 ClassIIIB 
               
               
                 At3g21080 
                 ABC transporter-related 
                 ClassIIIB 
               
               
                 At3g03020 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIB 
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast; EXPRESSED IN: 21 plant 
               
               
                   
                 structures; EXPRESSED DURING: 13 growth stages; Has 5 Blast hits to 5 proteins in 1 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 5; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g59510 
                 DVL18, RTFL5, ROTUNDIFOLIA like 5 
                 ClassIIIB 
               
               
                 At3g53730 
                 Histone superfamily protein 
                 ClassIIIB 
               
               
                 At1g19220 
                 ARF11, ARF19, IAA22, auxin response factor 19 
                 ClassIIIB 
               
               
                 At1g18890 
                 ATCDPK1, CDPK1, CPK10, calcium-dependent protein kinase 1 
                 ClassIIIB 
               
               
                 At3g44720 
                 ADT4, arogenate dehydratase 4 
                 ClassIIIB 
               
               
                 At4g11170 
                 Disease resistance protein (TIR-NBS-LRR class) family 
                 ClassIIIB 
               
               
                 At5g07620 
                 Protein kinase superfamily protein 
                 ClassIIIB 
               
               
                 At3g54980 
                 Pentatricopeptide repeat (PPR) superfamily protein 
                 ClassIIIB 
               
               
                 At5g06720 
                 ATPA2, PA2, peroxidase 2 
                 ClassIIIB 
               
               
                 At5g41100 
                 FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process 
                 ClassIIIB 
               
               
                   
                 unknown; LOCATED IN: plasma membrane; EXPRESSED IN: 23 plant structures; 
               
               
                   
                 EXPRESSED DURING: 13 growth stages; BEST  Arabidopsis thaliana  protein match is: 
               
               
                   
                 hydroxyproline-rich glycoprotein family protein (TAIR: AT3G26910.2); Has 1503 Blast hits 
               
               
                   
                 to 1197 proteins in 220 species: Archae - 4; Bacteria - 108; Metazoa - 481; Fungi - 318; 
               
               
                   
                 Plants - 186; Viruses - 39; Other Eukaryotes - 367 (source: NCBI BLink). 
               
               
                 At4g02360 
                 Protein of unknown function, DUF538 
                 ClassIIIB 
               
               
                 At4g09570 
                 ATCPK4, CPK4, calcium-dependent protein kinase 4 
                 ClassIIIB 
               
               
                 At1g51940 
                 protein kinase family protein/peptidoglycan-binding LysM domain-containing protein 
                 ClassIIIB 
               
               
                 At5g65020 
                 ANNAT2, annexin 2 
                 ClassIIIB 
               
               
                 At3g48090 
                 ATEDS1, EDS1, alpha/beta-Hydrolases superfamily protein 
                 ClassIIIB 
               
               
                 At1g70530 
                 CRK3, cysteine-rich RLK (RECEPTOR-like protein kinase) 3 
                 ClassIIIB 
               
               
                 At4g12070 
                 unknown protein; INVOLVED IN: biological_process unknown; LOCATED IN: plasma 
                 ClassIIIB 
               
               
                   
                 membrane; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; 
               
               
                   
                 Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 
               
               
                   
                 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At1g63040 
                 a pseudogene member of the DREB subfamily A-4 of ERF/AP2 transcription factor family. 
                 ClassIIIB 
               
               
                   
                 The translated product contains one AP2 domain. There are 17 members in this subfamily 
               
               
                   
                 including TINY. 
               
               
                 At2g01150 
                 RHA2B, RING-H2 finger protein 2B 
                 ClassIIIB 
               
               
                 At4g25030 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIB 
               
               
                   
                 (TAIR: AT5G45410.3); Has 125 Blast hits to 125 proteins in 36 species: Archae - 2; Bacteria - 
               
               
                   
                 31; Metazoa - 0; Fungi - 4; Plants - 88; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At2g32030 
                 Acyl-CoA N-acyltransferases (NAT) superfamily protein 
                 ClassIIIB 
               
               
                 At3g60910 
                 S-adenosyl-L-methionine-dependent methyltransferases superfamily protein 
                 ClassIIIB 
               
               
                 At1g68150 
                 ATWRKY9, WRKY9, WRKY DNA-binding protein 9 
                 ClassIIIB 
               
               
                 At2g06050 
                 DDE1, OPR3, oxophytodienoate-reductase 3 
                 ClassIIIB 
               
               
                 At5g62680 
                 Major facilitator superfamily protein 
                 ClassIIIB 
               
               
                 At5g45750 
                 AtRABA1c, RABA1c, RAB GTPase homolog A1C 
                 ClassIIIB 
               
               
                 At4g18890 
                 BEH3, BES1/BZR1 homolog 3 
                 ClassIIIB 
               
               
                 At2g27390 
                 proline-rich family protein 
                 ClassIIIB 
               
               
                 At4g23440 
                 Disease resistance protein (TIR-NBS class) 
                 ClassIIIB 
               
               
                 At2g22680 
                 Zinc finger (C3HC4-type RING finger) family protein 
                 ClassIIIB 
               
               
                 At3g54040 
                 PAR1 protein 
                 ClassIIIB 
               
               
                 At4g37730 
                 AtbZIP7, bZIP7, basic leucine-zipper 7 
                 ClassIIIB 
               
               
                 At4g30080 
                 ARF16, auxin response factor 16 
                 ClassIIIB 
               
               
                 At3g43250 
                 Family of unknown function (DUF572) 
                 ClassIIIB 
               
               
                 At2g46150 
                 Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family 
                 ClassIIIB 
               
               
                 At5g61210 
                 ATSNAP33, ATSNAP33B, SNAP33, SNP33, soluble N-ethylmaleimide-sensitive factor 
                 ClassIIIB 
               
               
                   
                 adaptor protein 33 
               
               
                 At5g57340 
                 unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
                 ClassIIIB 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At5g07870 
                 HXXXD-type acyl-transferase family protein 
                 ClassIIIB 
               
               
                 At5g54170 
                 Polyketide cyclase/dehydrase and lipid transport superfamily protein 
                 ClassIIIB 
               
               
                 At1g13340 
                 Regulator of Vps4 activity in the MVB pathway protein 
                 ClassIIIB 
               
               
                 At5g48175 
                 FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process 
                 ClassIIIB 
               
               
                   
                 unknown; LOCATED IN: endomembrane system; EXPRESSED IN: hypocotyl, male 
               
               
                   
                 gametophyte, root; BEST  Arabidopsis thaliana  protein match is: Glycosyl hydrolase 
               
               
                   
                 superfamily protein (TAIR: AT3G09260.1); Has 30201 Blast hits to 17322 proteins in 780 
               
               
                   
                 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 
               
               
                   
                 0; Other Eukaryotes - 2996 (source: NCBI BLink). 
               
               
                 At1g07130 
                 ATSTN1, STN1, Nucleic acid-binding, OB-fold-like protein 
                 ClassIIIB 
               
               
                 At2g30130 
                 ASL5, LBD12, PCK1, Lateral organ boundaries (LOB) domain family protein 
                 ClassIIIB 
               
               
                 At4g17230 
                 SCL13, SCARECROW-like 13 
                 ClassIIIB 
               
               
                 At3g05510 
                 Phospholipid/glycerol acyltransferase family protein 
                 ClassIIIB 
               
               
                 At1g18570 
                 AtMYB51, BW51A, BW51B, HIG1, MYB51, myb domain protein 51 
                 ClassIIIB 
               
               
                 At3g27160 
                 GHS1, Ribosomal protein S21 family protein 
                 ClassIIIB 
               
               
                 At2g39700 
                 ATEXP4, ATEXPA4, ATHEXP ALPHA 1.6, EXPA4, expansin A4 
                 ClassIIIB 
               
               
                 At4g40080 
                 ENTH/ANTH/VHS superfamily protein 
                 ClassIIIB 
               
               
                 At1g57560 
                 AtMYB50, MYB50, myb domain protein 50 
                 ClassIIIB 
               
               
                 At2g25250 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIB 
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast; EXPRESSED IN: 23 plant 
               
               
                   
                 structures; EXPRESSED DURING: 14 growth stages; BEST  Arabidopsis thaliana  protein 
               
               
                   
                 match is: unknown protein (TAIR: AT4G32020.1); Has 30 Blast hits to 30 proteins in 7 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 2; Plants - 28; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At2g28570 
                 unknown protein; Has 13 Blast hits to 13 proteins in 6 species: Archae - 0; Bacteria - 0; 
                 ClassIIIB 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 13; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At1g66090 
                 Disease resistance protein (TIR-NBS class) 
                 ClassIIIB 
               
               
                 At1g44100 
                 AAPS, amino acid permease 5 
                 ClassIIIB 
               
               
                 At3g11820 
                 AT-SYR1, ATSYP121, ATSYR1, PEN1, SYP121, SYR1, syntaxin of plants 121 
                 ClassIIIB 
               
               
                 At4g01850 
                 AtSAM2, MAT2, SAM-2, SAM2, S-adenosylmethionine synthetase 2 
                 ClassIIIB 
               
               
                 At2g24240 
                 BTB/POZ domain with WD40/YVTN repeat-like protein 
                 ClassIIIB 
               
               
                 At1g32310 
                 unknown protein; Has 28 Blast hits to 28 proteins in 9 species: Archae - 0; Bacteria - 0; 
                 ClassIIIB 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 28; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g67570 
                 DG1, EMB1408, EMB246, Tetratricopeptide repeat (TPR)-like superfamily protein 
                 ClassIIIB 
               
               
                 At4g11370 
                 RHA1A, RING-H2 finger A1A 
                 ClassIIIB 
               
               
                 At1g60030 
                 ATNAT7, NAT7, nucleobase-ascorbate transporter 7 
                 ClassIIIB 
               
               
                 At1g18860 
                 ATWRKY61, WRKY61, WRKY DNA-binding protein 61 
                 ClassIIIB 
               
               
                 At1g18580 
                 GAUT11, galacturonosyltransferase 11 
                 ClassIIIB 
               
               
                 At1g79160 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIB 
               
               
                   
                 (TAIR: AT1G16500.1); Has 104 Blast hits to 102 proteins in 13 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 0; Fungi - 0; Plants - 104; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At2g19710 
                 Regulator of Vps4 activity in the MVB pathway protein 
                 ClassIIIB 
               
               
                 At4g01720 
                 AtWRKY47, WRKY47, WRKY family transcription factor 
                 ClassIIIB 
               
               
                 At2g37840 
                 Protein kinase superfamily protein 
                 ClassIIIB 
               
               
                 At4g39840 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIB 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 23 
               
               
                   
                 plant structures; EXPRESSED DURING: 13 growth stages; Has 20719 Blast hits to 6096 
               
               
                   
                 proteins in 607 species: Archae - 22; Bacteria - 3243; Metazoa - 4364; Fungi - 2270; Plants - 
               
               
                   
                 237; Viruses - 128; Other Eukaryotes - 10455 (source: NCBI BLink). 
               
               
                 At4g32060 
                 calcium-binding EF hand family protein 
                 ClassIIIB 
               
               
                 At1g70940 
                 ATPIN3, PIN3, Auxin efflux carrier family protein 
                 ClassIIIB 
               
               
                 At2g26290 
                 ARSK1, root-specific kinase 1 
                 ClassIIIB 
               
               
                 At1g44830 
                 Integrase-type DNA-binding superfamily protein 
                 ClassIIIB 
               
               
                 At5g43520 
                 Cysteine/Histidine-rich C1 domain family protein 
                 ClassIIIB 
               
               
                 At4g28350 
                 Concanavalin A-like lectin protein kinase family protein 
                 ClassIIIB 
               
               
                 At2g20960 
                 pEARLI4,  Arabidopsis  phospholipase-like protein (PEARLI 4) family 
                 ClassIIIB 
               
               
                 At3g49220 
                 Plant invertase/pectin methylesterase inhibitor superfamily 
                 ClassIIIB 
               
               
                 At5g52240 
                 AtMAPR5, ATMP1, MSBP1, membrane steroid binding protein 1 
                 ClassIIIB 
               
               
                 At1g09520 
                 LOCATED IN: chloroplast; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 
                 ClassIIIB 
               
               
                   
                 12 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, PHD-type, conserved site 
               
               
                   
                 (InterPro: IPR019786); BEST  Arabidopsis thaliana  protein match is: PHD finger family 
               
               
                   
                 protein (TAIR: AT3G17460.1); Has 56 Blast hits to 56 proteins in 17 species: Archae - 0; 
               
               
                   
                 Bacteria - 2; Metazoa - 0; Fungi - 4; Plants - 46; Viruses - 0; Other Eukaryotes - 4 (source: 
               
               
                   
                 NCBI BLink). 
               
               
                 At1g04440 
                 CKL13, casein kinase like 13 
                 ClassIIIB 
               
               
                 At3g08750 
                 F-box and associated interaction domains-containing protein 
                 ClassIIIB 
               
               
                 At4g17260 
                 Lactate/malate dehydrogenase family protein 
                 ClassIIIB 
               
               
                 At3g63410 
                 APG1, E37, IEP37, VTE3, S-adenosyl-L-methionine-dependent methyltransferases 
                 ClassIIIB 
               
               
                   
                 superfamily protein 
               
               
                 At3g23820 
                 GAE6, UDP-D-glucuronate 4-epimerase 6 
                 ClassIIIB 
               
               
                 At1g51920 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIB 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 
               
               
                   
                 stem, stamen; EXPRESSED DURING: 4 anthesis; Has 22 Blast hits to 22 proteins in 5 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 22; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At4g34180 
                 Cyclase family protein 
                 ClassIIIB 
               
               
                 At1g52560 
                 HSP20-like chaperones superfamily protein 
                 ClassIIIB 
               
               
                 At3g49720 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIB 
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast thylakoid membrane, Golgi 
               
               
                   
                 apparatus, plasma membrane, membrane; EXPRESSED IN: 25 plant structures; 
               
               
                   
                 EXPRESSED DURING: 15 growth stages; BEST  Arabidopsis thaliana  protein match is: 
               
               
                   
                 unknown protein (TAIR: AT5G65810.1); Has 64 Blast hits to 64 proteins in 11 species: 
               
               
                   
                 Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 64; Viruses - 0; Other Eukaryotes - 0 
               
               
                   
                 (source: NCBI BLink). 
               
               
                 At3g28740 
                 CYP81D1, Cytochrome P450 superfamily protein 
                 ClassIIIB 
               
               
                 At3g52360 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIB 
               
               
                   
                 response to karrikin; LOCATED IN: endomembrane system; EXPRESSED IN: 23 plant 
               
               
                   
                 structures; EXPRESSED DURING: 14 growth stages; BEST  Arabidopsis thaliana  protein 
               
               
                   
                 match is: unknown protein (TAIR: AT2G35850.1); Has 34 Blast hits to 34 proteins in 10 
               
               
                   
                 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 34; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At3g17700 
                 ATCNGC20, CNBT1, CNGC20, cyclic nucleotide-binding transporter 1 
                 ClassIIIB 
               
               
                 At4g33300 
                 ADR1-L1, ADR1-like 1 
                 ClassIIIB 
               
               
                 At3g52400 
                 ATSYP122, SYP122, syntaxin of plants 122 
                 ClassIIIB 
               
               
                 At3g20900 
                 unknown protein; Has 2 Blast hits to 2 proteins in 1 species: Archae - 0; Bacteria - 0; 
                 ClassIIIB 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 2; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At5g14930 
                 SAG101, senescence-associated gene 101 
                 ClassIIIB 
               
               
                 At1g35200 
                 60S ribosomal protein L4/L1 (RPL4B), pseudogene, similar to 60S ribosomal protein L4 
                 ClassIIIB 
               
               
                   
                 (fragment) GB: P49691 from ( Arabidopsis thaliana ); blastp match of 50% identity and 6.3e−17 
               
               
                   
                 P-value to SP|Q9XF97|RL4_PRUAR 60S ribosomal protein L4 (L1). (Apricot) { Prunus   
               
               
                   
                   armeniaca } 
               
               
                 At5g38310 
                 unknown protein; Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 
                 ClassIIIB 
               
               
                   
                 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: 
               
               
                   
                 NCBI BLink). 
               
               
                 At3g23090 
                 TPX2 (targeting protein for Xklp2) protein family 
                 ClassIIIB 
               
               
                 At5g63770 
                 ATDGK2, DGK2, diacylglycerol kinase 2 
                 ClassIIIB 
               
               
                 At5g13190 
                 CONTAINS InterPro DOMAIN/s: LPS-induced tumor necrosis factor alpha factor 
                 ClassIIIB 
               
               
                   
                 (InterPro: IPR006629); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At4g30470 
                 NAD(P)-binding Rossmann-fold superfamily protein 
                 ClassIIIB 
               
               
                 At1g29860 
                 ATWRKY71, WRKY71, WRKY DNA-binding protein 71 
                 ClassIIIB 
               
               
                 At4g28940 
                 Phosphorylase superfamily protein 
                 ClassIIIB 
               
               
                 At1g72070 
                 Chaperone DnaJ-domain superfamily protein 
                 ClassIIIB 
               
               
                 At2g45080 
                 cycp3; 1, cyclin p3; 1 
                 ClassIIIB 
               
               
                 At2g01880 
                 ATPAP7, PAP7, purple acid phosphatase 7 
                 ClassIIIB 
               
               
                 At1g34750 
                 Protein phosphatase 2C family protein 
                 ClassIIIB 
               
               
                 At1g09920 
                 TRAF-type zinc finger-related 
                 ClassIIIB 
               
               
                 At2g38010 
                 Neutral/alkaline non-lysosomal ceramidase 
                 ClassIIIB 
               
               
                 At1g21830 
                 unknown protein; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF740 
                 ClassIIIB 
               
               
                   
                 (InterPro: IPR008004); BEST  Arabidopsis thaliana  protein match is: unknown protein 
               
               
                   
                 (TAIR: AT1G44608.1); Has 49 Blast hits to 49 proteins in 12 species: Archae - 0; Bacteria - 
               
               
                   
                 0; Metazoa - 0; Fungi - 0; Plants - 49; Viruses - 0; Other Eukaryotes - 0 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At1g74870 
                 RING/U-box superfamily protein 
                 ClassIIIB 
               
               
                 At3g10190 
                 Calcium-binding EF-hand family protein 
                 ClassIIIB 
               
               
                 At4g37400 
                 CYP81F3, cytochrome P450, family 81, subfamily F, polypeptide 3 
                 ClassIIIB 
               
               
                 At1g07000 
                 ATEXO70B2, EXO70B2, exocyst subunit exo70 family protein B2 
                 ClassIIIB 
               
               
                 At1g73066 
                 Leucine-rich repeat family protein 
                 ClassIIIB 
               
               
                 At2g39530 
                 Uncharacterised protein family (UPF0497) 
                 ClassIIIB 
               
               
                 At5g62070 
                 IQD23, IQ-domain 23 
                 ClassIIIB 
               
               
                 At3g45640 
                 ATMAPK3, ATMPK3, MPK3, mitogen-activated protein kinase 3 
                 ClassIIIB 
               
               
                 At1g11000 
                 ATMLO4, MLO4, Seven transmembrane MLO family protein 
                 ClassIIIB 
               
               
                 At2g26480 
                 UGT76D1, UDP-glucosyl transferase 76D1 
                 ClassIIIB 
               
               
                 At4g02200 
                 Drought-responsive family protein 
                 ClassIIIB 
               
               
                 At5g07310 
                 Integrase-type DNA-binding superfamily protein 
                 ClassIIIB 
               
               
                 At2g16430 
                 ATPAP10, PAP10, purple acid phosphatase 10 
                 ClassIIIB 
               
               
                 At5g44610 
                 MAP18, PCAP2, microtubule-associated protein 18 
                 ClassIIIB 
               
               
                 At4g36680 
                 Tetratricopeptide repeat (TPR)-like superfamily protein 
                 ClassIIIB 
               
               
                 At4g21780 
                 unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
                 ClassIIIB 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At4g22470 
                 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein 
                 ClassIIIB 
               
               
                 At5g60800 
                 Heavy metal transport/detoxification superfamily protein 
                 ClassIIIB 
               
               
                 At4g34320 
                 Protein of unknown function (DUF677) 
                 ClassIIIB 
               
               
                 At2g47130 
                 NAD(P)-binding Rossmann-fold superfamily protein 
                 ClassIIIB 
               
               
                 At5g65600 
                 Concanavalin A-like lectin protein kinase family protein 
                 ClassIIIB 
               
               
                 At1g17370 
                 UBP1B, oligouridylate binding protein 1B 
                 ClassIIIB 
               
               
                 At1g28390 
                 Protein kinase superfamily protein 
                 ClassIIIB 
               
               
                 At4g36900 
                 DEAR4, RAP2.10, related to AP2 10 
                 ClassIIIB 
               
               
                 At2g35910 
                 RING/U-box superfamily protein 
                 ClassIIIB 
               
               
                 At5g44990 
                 Glutathione S-transferase family protein 
                 ClassIIIB 
               
               
                 At4g31780 
                 MGD1, MGDA, monogalactosyl diacylglycerol synthase 1 
                 ClassIIIB 
               
               
                 At5g51190 
                 Integrase-type DNA-binding superfamily protein 
                 ClassIIIB 
               
               
                 At4g23010 
                 ATUTR2, UTR2, UDP-galactose transporter 2 
                 ClassIIIB 
               
               
                 At5g10400 
                 Histone superfamily protein 
                 ClassIIIB 
               
               
                 At4g02330 
                 ATPMEPCRB, Plant invertase/pectin methylesterase inhibitor superfamily 
                 ClassIIIB 
               
               
                 At2g34930 
                 disease resistance family protein/LRR family protein 
                 ClassIIIB 
               
               
                 At2g43000 
                 anac042, NAC042, NAC domain containing protein 42 
                 ClassIIIB 
               
               
                 At5g58110 
                 chaperone binding; ATPase activators 
                 ClassIIIB 
               
               
                 At1g14480 
                 Ankyrin repeat family protein 
                 ClassIIIB 
               
               
                 At1g17750 
                 AtPEPR2, PEPR2, PEP1 receptor 2 
                 ClassIIIB 
               
               
                 At5g62630 
                 HIPL2, hipl2 protein precursor 
                 ClassIIIB 
               
               
                 At5g51390 
                 unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; 
                 ClassIIIB 
               
               
                   
                 Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 
               
               
                   
                 2996 (source: NCBI BLink). 
               
               
                 At5g07860 
                 HXXXD-type acyl-transferase family protein 
                 ClassIIIB 
               
               
                 At4g38000 
                 DOF4.7, DNA binding with one finger 4.7 
                 ClassIIIB 
               
               
                 At2g39900 
                 GATA type zinc finger transcription factor family protein 
                 ClassIIIB 
               
               
                 At3g29670 
                 HXXXD-type acyl-transferase family protein 
                 ClassIIIB 
               
               
                 At2g17120 
                 LYM2, lysm domain GPI-anchored protein 2 precursor 
                 ClassIIIB 
               
               
                 At1g52200 
                 PLAC8 family protein 
                 ClassIIIB 
               
               
                 At2g39110 
                 Protein kinase superfamily protein 
                 ClassIIIB 
               
               
                 At1g55920 
                 ATSERAT2; 1, SAT1, SAT5, SERAT2; 1, serine acetyltransferase 2; 1 
                 ClassIIIB 
               
               
                 At4g01700 
                 Chitinase family protein 
                 ClassIIIB 
               
               
                 At2g31880 
                 EVR, SOBIR1, Leucine-rich repeat protein kinase family protein 
                 ClassIIIB 
               
               
                 At3g62720 
                 ATXT1, XT1, XXT1, xylosyltransferase 1 
                 ClassIIIB 
               
               
                 At2g26380 
                 Leucine-rich repeat (LRR) family protein 
                 ClassIIIB 
               
               
                 At2g47140 
                 NAD(P)-binding Rossmann-fold superfamily protein 
                 ClassIIIB 
               
               
                 At2g19570 
                 AT-CDA1, CDA1, DESZ, cytidine deaminase 1 
                 ClassIIIB 
               
               
                 At3g14360 
                 alpha/beta-Hydrolases superfamily protein 
                 ClassIIIB 
               
               
                 At2g37940 
                 AtIPCS2,  Arabidopsis  Inositol phosphorylceramide synthase 2 
                 ClassIIIB 
               
               
                 At5g60680 
                 Protein of unknown function, DUF584 
                 ClassIIIB 
               
               
                 At5g41680 
                 Protein kinase superfamily protein 
                 ClassIIIB 
               
               
                 At3g47380 
                 Plant invertase/pectin methylesterase inhibitor superfamily protein 
                 ClassIIIB 
               
               
                 At5g62390 
                 ATBAG7, BAG7, BCL-2-associated athanogene 7 
                 ClassIIIB 
               
               
                 At1g07520 
                 GRAS family transcription factor 
                 ClassIIIB 
               
               
                 At4g39030 
                 EDS5, SID1, MATE efflux family protein 
                 ClassIIIB 
               
               
                 At3g53130 
                 CYP97C1, LUT1, Cytochrome P450 superfamily protein 
                 ClassIIIB 
               
               
                 At1g77030 
                 hydrolases, acting on acid anhydrides, in phosphorus-containing anhydrides; ATP-dependent 
                 ClassIIIB 
               
               
                   
                 helicases; nucleic acid binding; ATP binding; RNA binding; helicases 
               
               
                 At3g22160 
                 VQ motif-containing protein 
                 ClassIIIB 
               
               
                 At2g42430 
                 ASL18, LBD16, lateral organ boundaries-domain 16 
                 ClassIIIB 
               
               
                 At3g61900 
                 SAUR-like auxin-responsive protein family 
                 ClassIIIB 
               
               
                 At5g66070 
                 RING/U-box superfamily protein 
                 ClassIIIB 
               
               
                 At2g22750 
                 basic helix-loop-helix (bHLH) DNA-binding superfamily protein 
                 ClassIIIB 
               
               
                 At1g02400 
                 ATGA2OX4, ATGA2OX6, DTA1, GA2OX6, gibberellin 2-oxidase 6 
                 ClassIIIB 
               
               
                 At1g51915 
                 cryptdin protein-related 
                 ClassIIIB 
               
               
                 At4g19960 
                 ATKUP9, HAK9, KT9, KUP9, K+ uptake permease 9 
                 ClassIIIB 
               
               
                 At4g31000 
                 Calmodulin-binding protein 
                 ClassIIIB 
               
               
                 At2g26560 
                 PLA IIA, PLA2A, PLP2, PLP2, phospholipase A 2A 
                 ClassIIIB 
               
               
                 At5g10750 
                 Protein of unknown function (DUF1336) 
                 ClassIIIB 
               
               
                 At3g55950 
                 ATCRR3, CCR3, CRINKLY4 related 3 
                 ClassIIIB 
               
               
                 At3g50760 
                 GATL2, galacturonosyltransferase-like 2 
                 ClassIIIB 
               
               
                 At4g29670 
                 ACHT2, atypical CYS HIS rich thioredoxin 2 
                 ClassIIIB 
               
               
                 At2g37810 
                 Cysteine/Histidine-rich C1 domain family protein 
                 ClassIIIB 
               
               
                 At3g52430 
                 ATPAD4, PAD4, alpha/beta-Hydrolases superfamily protein 
                 ClassIIIB 
               
               
                 At1g36640 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIB 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 
               
               
                   
                 sperm cell, root; BEST  Arabidopsis thaliana  protein match is: unknown protein 
               
               
                   
                 (TAIR: AT1G36622.1); Has 14 Blast hits to 14 proteins in 2 species: Archae - 0; Bacteria - 0; 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 14; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At2g20150 
                 unknown protein; Has 5 Blast hits to 5 proteins in 1 species: Archae - 0; Bacteria - 0; 
                 ClassIIIB 
               
               
                   
                 Metazoa - 0; Fungi - 0; Plants - 5; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At3g08710 
                 ATH9, TH9, TRX H9, thioredoxin H-type 9 
                 ClassIIIB 
               
               
                 At3g02800 
                 Tyrosine phosphatase family protein 
                 ClassIIIB 
               
               
                 At2g24180 
                 CYP71B6, cytochrome p450 71b6 
                 ClassIIIB 
               
               
                 At2g27690 
                 CYP94C1, cytochrome P450, family 94, subfamily C, polypeptide 1 
                 ClassIIIB 
               
               
                 At5g46710 
                 PLATZ transcription factor family protein 
                 ClassIIIB 
               
               
                 At3g02790 
                 zinc finger (C2H2 type) family protein 
                 ClassIIIB 
               
               
                 At3g53280 
                 CYP71B5, cytochrome p450 71b5 
                 ClassIIIB 
               
               
                 At5g62350 
                 Plant invertase/pectin methylesterase inhibitor superfamily protein 
                 ClassIIIB 
               
               
                 At5g40010 
                 AATP1, AAA-ATPase 1 
                 ClassIIIB 
               
               
                 At5g38210 
                 Protein kinase family protein 
                 ClassIIIB 
               
               
                 At2g21560 
                 unknown protein; BEST  Arabidopsis thaliana  protein match is: unknown protein 
                 ClassIIIB 
               
               
                   
                 (TAIR: AT4G39190.1); Has 3685 Blast hits to 2305 proteins in 270 species: Archae - 0; 
               
               
                   
                 Bacteria - 156; Metazoa - 1145; Fungi - 322; Plants - 177; Viruses - 6; Other Eukaryotes - 
               
               
                   
                 1879 (source: NCBI BLink). 
               
               
                 At1g59910 
                 Actin-binding FH2 (formin homology 2) family protein 
                 ClassIIIB 
               
               
                 At5g58120 
                 Disease resistance protein (TIR-NBS-LRR class) family 
                 ClassIIIB 
               
               
                 At5g59480 
                 Haloacid dehalogenase-like hydrolase (HAD) superfamily protein 
                 ClassIIIB 
               
               
                 At3g01820 
                 P-loop containing nucleoside triphosphate hydrolases superfamily protein 
                 ClassIIIB 
               
               
                 At1g63480 
                 AT hook motif DNA-binding family protein 
                 ClassIIIB 
               
               
                 At3g04630 
                 WDL1, WVD2-like 1 
                 ClassIIIB 
               
               
                 At2g17220 
                 Protein kinase superfamily protein 
                 ClassIIIB 
               
               
                 At1g16380 
                 ATCHX1, CHX1, Cation/hydrogen exchanger family protein 
                 ClassIIIB 
               
               
                 At1g61370 
                 S-locus lectin protein kinase family protein 
                 ClassIIIB 
               
               
                 At3g09405 
                 Pectinacetylesterase family protein 
                 ClassIIIB 
               
               
                 At3g47550 
                 RING/FYVE/PHD zinc finger superfamily protein 
                 ClassIIIB 
               
               
                 At3g59900 
                 ARGOS, auxin-regulated gene involved in organ size 
                 ClassIIIB 
               
               
                 At1g24150 
                 ATFH4, FH4, formin homologue 4 
                 ClassIIIB 
               
               
                 At2g16870 
                 Disease resistance protein (TIR-NBS-LRR class) family 
                 ClassIIIB 
               
               
                 At2g42350 
                 RING/U-box superfamily protein 
                 ClassIIIB 
               
               
                 At5g66620 
                 DAR6, DA1-related protein 6 
                 ClassIIIB 
               
               
                 At4g33960 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: 
                 ClassIIIB 
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 20 
               
               
                   
                 plant structures; EXPRESSED DURING: 10 growth stages; BEST  Arabidopsis thaliana   
               
               
                   
                 protein match is: unknown protein (TAIR: AT2G15830.1); Has 32 Blast hits to 32 proteins in 
               
               
                   
                 4 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 32; Viruses - 0; Other 
               
               
                   
                 Eukaryotes - 0 (source: NCBI BLink). 
               
               
                 At3g16030 
                 CES101, lectin protein kinase family protein 
                 ClassIIIB 
               
               
                 At5g22690 
                 Disease resistance protein (TIR-NBS-LRR class) family 
                 ClassIIIB 
               
               
                 At1g11310 
                 ATMLO2, MLO2, PMR2, Seven transmembrane MLO family protein 
                 ClassIIIB 
               
               
                 At1g59850 
                 ARM repeat superfamily protein 
                 ClassIIIB 
               
               
                 At2g21120 
                 Protein of unknown function (DUF803) 
                 ClassIIIB 
               
               
                 At1g05710 
                 basic helix-loop-helix (bHLH) DNA-binding superfamily protein 
                 ClassIIIB 
               
               
                 At1g71450 
                 Integrase-type DNA-binding superfamily protein 
                 ClassIIIB 
               
               
                 At4g37180 
                 Homeodomain-like superfamily protein 
                 ClassIIIB 
               
               
                 At1g61560 
                 ATMLO6, MLO6, Seven transmembrane MLO family protein 
                 ClassIIIB 
               
               
                 At5g39710 
                 EMB2745, Tetratricopeptide repeat (TPR)-like superfamily protein 
                 ClassIIIB 
               
               
                 At1g05055 
                 ATGTF2H2, GTF2H2, general transcription factor II H2 
                 ClassIIIB 
               
               
                 At3g03660 
                 WOX11, WUSCHEL related homeobox 11 
                 ClassIIIB 
               
               
                 At5g09980 
                 PROPEP4, elicitor peptide 4 precursor 
                 ClassIIIB 
               
               
                 At2g26190 
                 calmodulin-binding family protein 
                 ClassIIIB 
               
               
                 At3g54200 
                 Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family 
                 ClassIIIB 
               
               
                 At1g53440 
                 Leucine-rich repeat transmembrane protein kinase 
                 ClassIIIB 
               
               
                 At5g60250 
                 zinc finger (C3HC4-type RING finger) family protein 
                 ClassIIIB 
               
               
                 At1g63830 
                 PLAC8 family protein 
                 ClassIIIB 
               
               
                 At3g08760 
                 ATSIK, Protein kinase superfamily protein 
                 ClassIIIB 
               
               
                 At5g66640 
                 DAR3, DA1-related protein 3 
                 ClassIIIB 
               
               
                 At5g53130 
                 ATCNGC1, CNGC1, cyclic nucleotide gated channel 1 
                 ClassIIIB 
               
               
                 At3g28580 
                 P-loop containing nucleoside triphosphate hydrolases superfamily protein 
                 ClassIIIB 
               
               
                 At4g15120 
                 VQ motif-containing protein 
                 ClassIIIB 
               
               
                 At2g24600 
                 Ankyrin repeat family protein 
                 ClassIIIB 
               
               
                 At2g01450 
                 ATMPK17, MPK17, MAP kinase 17 
                 ClassIIIB 
               
               
                 At1g65690 
                 Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family 
                 ClassIIIB 
               
               
                 At1g53920 
                 GLIP5, GDSL-motif lipase 5 
                 ClassIIIB 
               
               
                 At2g38870 
                 Serine protease inhibitor, potato inhibitor I-type family protein 
                 ClassIIIB 
               
               
                 At2g40180 
                 ATHPP2C5, PP2C5, phosphatase 2C5 
                 ClassIIIB 
               
               
                 At5g04720 
                 ADR1-L2, ADR1-like 2 
                 ClassIIIB 
               
               
                 At1g72060 
                 serine-type endopeptidase inhibitors 
                 ClassIIIB 
               
               
                 At5g24620 
                 Pathogenesis-related thaumatin superfamily protein 
                 ClassIIIB 
               
               
                 At2g19190 
                 FRK1, FLG22-induced receptor-like kinase 1 
                 ClassIIIB 
               
               
                 At4g14630 
                 GLP9, germin-like protein 9 
                 ClassIIIB 
               
               
                   
               
            
           
         
       
     
     To next explore the biological relevance of the three distinct classes of primary bZIP1 targets, the following features were examined: (1) enrichment of cis-regulatory elements ( FIG. 30 ); (2) comparison to bZIP1 regulated genes in planta ( FIG. 29B ), and (3) biological relevance to N-signal transduction in isolated cells ( FIG. 29A &amp; 29C ) and in planta ( FIG. 29C ). This comparative analysis uncovered features common to all three classes of bZIP1 targets, as well as specific features of Class III transient targets that are uniquely relevant to rapid N-signal propagation. The features shared by all three classes of bZIP1 primary targets are: i) bZIP1-binding sites: all three classes of genes deemed to be bZIP1 primary targets share enrichment of known bZIP1 binding sites in their promoters (E&lt;0.01,  FIG. 30 ). ii) In planta relevance to bZIP1: all three classes of bZIP1 primary targets identified in the cell-based TARGET system were validated by their significant overlap with bZIP1-regulated genes identified in transgenic plants, either by comparison to a 35S::bZIP1 overexpression line (100/449 genes; 22% overlap; p-val&lt;0.001) or a T-DNA insertion mutant in bZIP1 (89/488 genes; 18.2% overlap; p-val&lt;0.001) (Kang et al., 2010, Molecular Plant 3:361-373) ( FIG. 29B ). iii) N-regulation in planta: bZIP1 was predicted to be a master regulator in N-response (Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939-4944; Obertello et al., 2010, BMC systems biology 4:111), and in support of this, all three classes of bZIP1 primary targets in protoplasts are significantly enriched with N-responsive genes in planta (Krouk et al., 2010, Genome Biology 11:R123; Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939-4944; Wang et al., 2003, Plant Physiol. 132(2):556-567; Wang et al., 2004, Plant physiology 136(1):2512-2522) (438/1,308 genes, p-val&lt;0.001) ( FIG. 29C ). iv) known bZIP1 functions: all three classes of targets show enrichment of GO-terms associated with other known bZIP1 functions (e.g. Stimulus/Stress) ( FIG. 31 ). Specifically, bZIP1 is reported as a master regulator in response to darkness and sugar starvation (Baena-Gonzalez et al., 2007, Nature 448:938; Kang et al., 2010, Molecular Plant 3:361-373). Consistent with this, all three classes of bZIP1 primary targets share a significant overlap (p-val&lt;0.001) with genes induced by sugar starvation and extended darkness (Krouk et al., 2009, PLoS Comput Biol 5(3):e1000326). 
     In addition to these common features consistent with the role of bZIP1 in planta (Baena-Gonzalez et al., 2007, Nature 448:938; Kang et al., 2010, Molecular Plant 3:361-373; Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939-4944), distinctive features for the Class III transient bZIP1 primary targets specifically relevant to rapid N-signaling were uncovered. These class-specific features are outlined below. 
     Class I “Poised” targets (TF Binding only). Class I bZIP1 primary targets (407 genes) that are bound, but not regulated by bZIP1, are significantly enriched in genes involved in response to biotic/abiotic stimuli, and transport of divalent ions (FDR&lt;0.01) ( FIG. 29A ;  FIG. 31 ). They are also significantly enriched in the known bZIP1 binding site “hybrid ACGT box” (E=3.5e−4), supporting that they are valid primary targets of bZIP1 ( FIG. 30 ). This suggests that bZIP1 is bound to and poised to activate these target genes, possibly in response to a signal or a TF partner not present in the experimental conditions. 
     Class II “Stable” targets (TF Binding and Regulation). Class II targets (120 genes) are regulated and bound by bZIP1. This 23% overlap (p-val&lt;0.001) between transcriptome and ChIP-Seq data ( FIG. 29A ), is comparable to the relatively low overlap observed for other TF perturbation studies performed in planta [23% ABI3 (Monke et al., 2012, Nucleic Acids Research 40:82401); 5% ASRS (Arenhart et al., 2014, Molecular plant 7(4):709-721); KNOTTED1 20%-30% (Bolduc et al., 2012, Gene Dev 26(15):1685-1690)] and in other eukaryotes [8% BRCA1 (Gorski et al, 2011, Nucleic Acids Research 39(22):9536-9548); LRH-1 32% (Bianco et al., 2014, Cancer research 74(7):2015-2025)]. Thus, the Class II “stable” bZIP1 targets correspond to the “gold standard” set typically identified in TF studies across eukaryotes (Gorski et al, 2011, Nucleic Acids Research 39(22):9536-9548; Hughes et al., 2013, Genetics 195(1):9-36; Monke et al., 2012, Nucleic Acids Research 40:82401; Arenhart et al., 2014, Molecular plant 7(4):709-721; Bolduc et al., 2012, Gene Dev 26(15):1685-1690; Bianco et al., 2014, Cancer research 74(7):2015-2025). Further, the cis-element analysis suggests the novel finding that bZIP1 functions to activate or repress target gene expression via two distinct binding sites ( FIG. 30 ). The targets activated by bZIP1 (Class IIA), are significantly enriched with the hybrid ACGT box bZIP1 binding site (E=2.5e−8) ( FIG. 30 ). By contrast, genes repressed by bZIP1 (Class IIB) are enriched with the bZIP binding site GCN4 (E=1.3e−3) ( FIG. 30 ). Interestingly, the GCN4 motif was reported to mediate N and amino acid starvation sensing in yeast (Hill et al., 1986, Science 234:451-457), suggesting a conserved link between bZIPs and nutrient sensing across eukaryotes. Finally, Class II targets share the “Stimulus/Stress” GO terms with other classes, but surprisingly, no significant biological terms unique to Class II targets were identified ( FIG. 29A  and  FIG. 31 ). 
     Class III “Transient” targets (TF Regulation, but no detectable TF binding). Unexpectedly, the largest group of bZIP1 primary targets (781 genes), is represented by the Class III “transient” targets i.e., primary targets regulated by bZIP1 perturbation but not detectably bound by it ( FIG. 29A ). Paradoxically, Class IIIA “transient” targets that are activated by bZIP1 are the most significantly enriched in the known bZIP1 binding site (E=1.3e−52) ( FIG. 30 ), despite their lack of detectable bZIP1 binding. Class IIIB targets repressed by bZIP1 are significantly enriched in a distinct bZIP binding site “GCN4” (E=3.8e−3) ( FIG. 30 ). Intriguingly, both of these known bZIP1-binding sites in the Class III transient genes are also observed in the Class II stable target genes (TF-bound and regulated) ( FIG. 30 ). The lack of detectable TF-binding for Class III targets likely represents a transient or weak interaction of bZIP1 and these primary targets, rather than an indirect interaction, as the ChIP-Seq protocol can also detect indirect binding (e.g. via interacting TF partners). The trivial explanation that the mRNAs for Class IIIA genes are stabilized by CHX or bZIP1 is not supported by the data, as the CHX effect was accounted for by filtering out genes whose response to DEX-induced nuclear localization of bZIP1 is altered by CHX-treatment. Instead, the Class III primary targets likely represent a transient interaction between bZIP1 and its targets. Indeed, 41 genes from Class III transient targets have detectable bZIP1 binding at one or more of the earlier time-points (1, 5, 30, 60 min) measured by ChIP-Seq, following DEX-induced TF nuclear import ( FIG. 29D ; Table 20). These Class III transient genes are uniquely relevant to rapid N-signaling, as described below. 
     
       
         
           
               
             
               
                 TABLE 20 
               
               
                   
               
               
                 Class III bZIP1-regulated genes that show evidence of bZIP1 binding at early (1,  
               
               
                 5, 30 or 60 mm), but not at a 5 hr time point. 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                 At4g14368 
                 Regulator of chromosome condensation (RCC1) family protein 
               
               
                 At1g10060 
                 ATBCAT-1, BCAT-1, branched-chain amino acid transaminase 1 
               
               
                 At1g18460 
                 alpha/beta-Hydrolases superfamily protein 
               
               
                 At3g60690 
                 SAUR-like auxin-responsive protein family 
               
               
                 At2g37840 
                 Protein kinase superfamily protein 
               
               
                 At3g14780 
                 CONTAINS InterPro DOMAIN/s: Transposase, Ptta/En/Spm, plant (InterPro: IPR004252); BEST 
               
               
                   
                   Arabidopsis   thaliana  protein match is: glucan synthase-like 4 (TAIR: AT3G14570.2); Has 315  
               
               
                   
                 Blast hits to 313 proteins in 50 species: Archae-2; Bacteria-16; Metazoa-11; Fungi-7; Plants-181;  
               
               
                   
                 Viruses-2; Other Eukaryotes-96 (source: NCBI BLink). 
               
               
                 At3g01820 
                 P-loop containing nucleoside triphosphate hydrolases superfamily protein 
               
               
                 At1g30820 
                 CTP synthase family protein 
               
               
                 At1g73240 
                 CONTAINS InterPro DOMAIN/s: Nucleoporin protein Ndc1-Nup (InterPro: IPR019049); Has 36  
               
               
                   
                 Blast hits to 36 proteins in 17 species: Archae-0; Bacteria-0; Metazoa-1; Fungi-0; Plants-35;  
               
               
                   
                 Viruses-0; Other Eukaryotes-0 (source: NCBI BLink). 
               
               
                 At4g17140 
                 pleckstrin homology (PH) domain-containing protein 
               
               
                 At1g04410 
                 Lactate/malate dehydrogenase family protein 
               
               
                 At5g59590 
                 UGT76E2, UDP-glucosyl transferase 76E2 
               
               
                 At1g53430 
                 Leucine-rich repeat transmembrane protein kinase 
               
               
                 At1g11000 
                 ATMLO4, MLO4, Seven transmembrane MLO family protein 
               
               
                 At1g08090 
                 ACH1, ATNRT2.1, ATNRT2:1, LIN1, NRT2, NRT2.1, NRT2:1, NRT2; 1AT, nitrate transporter 2:1 
               
               
                 At1g08830 
                 CSD1, copper/zinc superoxide dismutase 1 
               
               
                 At3g02150 
                 PTF1, TCP13, TFPD, plastid transcription factor 1 
               
               
                 At5g24430 
                 Calcium-dependent protein kinase (CDPK) family protein 
               
               
                 At3g51840 
                 ACX4, ATG6, ATSCX, acyl-CoA oxidase 4 
               
               
                 At1g06570 
                 HPD, PDS1, phytoene desaturation 1 
               
               
                 At4g19810 
                 Glycosyl hydrolase family protein with chitinase insertion domain 
               
               
                 At5g01590 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN:  
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast, chloroplast envelope; EXPRESSED IN:  
               
               
                   
                 22 plant structures; EXPRESSED DURING: 13 growth stages; Has 60 Blast hits to 59 proteins in  
               
               
                   
                 31 species: Archae-0; Bacteria-20; Metazoa-1; Fungi-2; Plants-33; Viruses-0; Other Eukaryotes-4 
               
               
                   
                 (source: NCBI BLink). 
               
               
                 At1g77030 
                 hydrolases, acting on acid anhydrides, in phosphorus-containing anhydrides; ATP-dependent 
               
               
                   
                 helicases; nucleic acid binding; ATP binding; RNA binding; helicases 
               
               
                 At3g15950 
                 NAI2, DNA topoisomerase-related 
               
               
                 At5g43430 
                 ETFBETA, electron transfer flavoprotein beta 
               
               
                 At4g34180 
                 Cyclase family protein 
               
               
                 At1g19220 
                 ARF11, ARF19, IAA22, auxin response factor 19 
               
               
                 At1g08630 
                 THA1 threonine aldolase 1 
               
               
                 At1g67510 
                 Leucine-rich repeat protein kinase family protein 
               
               
                 At4g38340 
                 Plant regulator RWP-RK family protein (NLP3) 
               
               
                 At1g57560 
                 AtMYB50, MYB50, myb domain protein 50 
               
               
                 At4g38500 
                 Protein of unknown function (DUF616) 
               
               
                 At5g53130 
                 ATCNGC1, CNGC1, cyclic nucleotide gated channel 1 
               
               
                 At1g03090 
                 MCCA, methylcrotonyl-CoA carboxylase alpha chain, mitochondrial/3-methylcrotonyl-CoA 
               
               
                   
                 carboxylase 1 (MCCA) 
               
               
                 At1g44100 
                 AAP5, amino acid permease 5 
               
               
                 At3g61850 
                 DAG1, Dof-type zinc finger DNA-binding family protein 
               
               
                 At1g18270 
                 ketose-bisphosphate aldolase class-II family protein 
               
               
                 At1g26730 
                 EXS (ERD1/XPR1/SYG1) family protein 
               
               
                 At5g46710 
                 PLATZ transcription factor family protein 
               
               
                 At3g48850 
                 PHT3; 2, phosphate transporter 3; 2 
               
               
                 At2g02700 
                 Cysteine/Histidine-rich C1 domain family protein 
               
               
                   
               
            
           
         
       
     
     The Class III transient bZIP1 primary targets comprise “first responders” in rapid N-signaling. In line with its role as a master regulator in a N-response gene network, all three classes of bZIP1 primary targets uncovered in this cell-based study are significantly enriched with N-responsive genes observed in whole plants (Krouk et al., 2010, Genome Biology 11(12):R123; Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939-4944; Wang et al., 2003, Plant Physiol. 132(2):556-567; Wang et al., 2004, Plant physiology 136(1):2512-2522) ( FIG. 29C ; overlap with the “union” of N-responsive genes in planta). Unexpectedly, the “transient” Class III bZIP1 targets—regulated by, but not stably bound to bZIP1—are uniquely relevant to rapid and dynamic N-signaling in planta ( FIG. 29C ). This conclusion is based on the following evidence: First, the Class IIIA transient bZIP1 targets have the largest and most significant overlap (p-val&lt;0.001;  FIG. 29C ) with the 147 genes induced by N-signals in this cell-based TARGET study (Table 12). Second, only Class III transient bZIP1 targets have a significant enrichment in genes involved in N-related biological processes (enrichment of GO terms p-val&lt;0.01) including amino acid metabolism ( FIG. 29A ;  FIG. 32 ; Table 21), a role also supported by in planta studies of bZIP1 (Dietrich et al., 2011, The Plant Cell 23:381-395). Third, the Class III transient genes comprise the bulk of the bZIP1 targets in the N-assimilation pathway ( FIG. 33  &amp; Table 22), including the “early N-responders”, such as the high-affinity nitrate transporter, NRT2.1, induced rapidly (&lt;12 minutes) and transiently following N-signal perturbation in planta (Krouk et al., 2010, Genome Biology 11(12):R123). Fourth, the Class III transient targets exclusively comprise all of the genes regulated by a N-treatment×bZIP1 interaction (28 genes) ( FIG. 29C ;  FIG. 28 ). These include well-known early mediators of N-signaling induced at 6-12 min after N-provision (Krouk et al., 2010, Genome Biology 11(12):R123), including the NIN-like transcription factor 3 (NLP3; At4g38340) (Konishi et al., 2013, Nature Communications 4: 1617), and the LBD39 transcription factor (At4g37540) (Rubin et al., 2009, The Plant Cell 21(11):3567-3584). NLP3 belongs to the NIN-like transcription factor family which plays an essential role in nitrate signaling (Konishi et al., 2013, Nature Communications 4: 1617). In this study, NLP3 is a transient bZIP1 target whose up-regulation by bZIP1 is dependent on the N-signal ( FIG. 28 ; Table 17). LBD39, which has been reported to fine-tune the magnitude of the N-response in planta (Rubin et al., 2009, The Plant Cell 21(11):3567-3584), is a transient bZIP1 target that is only induced by bZIP1 in the presence of the N-signal in this cell-based study ( FIG. 28 ; Table 17). This N-signal×bZIP1 interaction could be a post-translational modification of bZIP1, reminiscent of its post-translational modification in response to other abiotic signals (e.g. sugar and stress signals) (Dietrich et al., 2011, The Plant Cell 23:381-395). The N-signal x bZIP1 interaction could also involve translational/transcriptional effects of the N-signal on its interacting TF partners, as depicted in  FIG. 24B . 
     
       
         
           
               
             
               
                 TABLE 21 
               
             
            
               
                   
               
               
                 Significantly over-represented GO terms (FDR adjusted p-val &lt; 0.01) identified for 
               
               
                 genes in each of the five subclasses of bZIP1 targets. (Nitrogen related biological processes are 
               
               
                 in bold) 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                 Observed 
                 Expected 
                   
                   
               
               
                   
                 GO ID 
                 Term 
                 Frequency 
                 Frequency 
                 p-value 
                 Genes 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                 ClassI 
                 GO: 0006950 
                 response to 
                 86 out of 
                 2104 out of 
                 1.69E−10 
                 AT5G49480|AT1G17870|AT1G80850|AT4G23190| 
               
               
                   
                   
                 stress 
                 275 genes, 
                 15002 
                   
                 AT5G06320|AT3G09440|AT4G17615| 
               
               
                   
                   
                   
                 31.3% 
                 genes, 14% 
                   
                 AT2G40000|AT5G47230|AT3G17390| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G55450|AT3G50980|AT1G27760|AT5G15090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G42560|AT3G52930|AT3G23250| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G09080|AT2G26690|AT3G06510| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G02020|AT1G74310|AT2G30250|AT1G19020| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G05100|AT2G05710|AT1G68760| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G44260|AT1G32920|AT3G52450| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G41430|AT3G22370|AT1G01060|AT5G14740| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G78080|AT3G13790|AT3G10920| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G15500|AT2G24570|AT5G59820| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G19180|AT3G19580|AT1G22070|AT2G43130| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G05680|AT1G45145|AT2G40140| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G32120|AT2G03760|AT1G42990| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G63790|AT4G39090|AT5G45110|AT5G64905| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G49530|AT1G01720|AT1G76180| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G39580|AT1G59870|AT3G51920| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G06290|AT5G61890|AT1G62300|AT3G55440| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G01370|AT2G46830|AT2G17840| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G73080|AT5G58070|AT4G39640| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G10985|AT1G20440|AT1G10170|AT4G37010| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G33950|AT5G62530|AT2G35930| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G29395|AT1G33590|AT3G50970| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G37500|AT1G20450|AT4G20830|AT1G32640| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G39080|AT1G71697 
               
               
                   
                 GO: 0009628 
                 response to 
                 66 out of 
                 1360 out of 
                 1.69E−10 
                 AT5G49480|AT1G17870|AT2G43130|AT1G05680| 
               
               
                   
                   
                 abiotic 
                 275 genes, 
                 15002 
                   
                 AT3G09440|AT2G40140|AT4G27280| 
               
               
                   
                   
                 stimulus 
                 24% 
                 genes, 9.1% 
                   
                 AT4G17615|AT2G32120|AT2G03760| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G47230|AT3G17390|AT1G56590|AT1G55450| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G50980|AT1G27760|AT4G39090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G49530|AT1G76180|AT3G51920| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G05600|AT5G06290|AT3G55440|AT4G01370| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G46830|AT3G52930|AT1G61890| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G37370|AT2G17840|AT5G58070| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G23250|AT1G09080|AT3G06510|AT5G02020| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G74310|AT1G20440|AT2G30250| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G47000|AT4G05100|AT1G10170| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G33950|AT1G78290|AT5G62530|AT2G05710| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G35930|AT1G29395|AT1G33590| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G50970|AT4G37270|AT3G52450| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G37500|AT3G62410|AT2G41430|AT1G20450| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G22370|AT1G80010|AT1G01060| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G32640|AT1G78080|AT3G13790| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G39080|AT3G10920|AT3G15500|AT5G59820| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G01500|AT3G19580 
               
               
                   
                 GO: 0042221 
                 response to 
                 79 out of 
                 1892 out of 
                 5.36E−10 
                 AT1G22070|AT1G17870|AT4G23190|AT1G68765| 
               
               
                   
                   
                 chemical 
                 275 genes, 
                 15002 
                   
                 AT1G05680|AT3G15210|AT1G45145| 
               
               
                   
                   
                 stimulus 
                 28.7% 
                 genes, 
                   
                 AT3G16857|AT3G09440|AT2G40140| 
               
               
                   
                   
                   
                   
                 12.6% 
                   
                 AT1G43910|AT4G17615|AT3G53480|AT2G32120| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G40000|AT2G03760|AT1G15080| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G47230|AT3G08590|AT1G42990| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G50980|AT5G63790|AT4G39090|AT3G49530| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G34160|AT1G76180|AT1G59870| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G51920|AT3G04730|AT1G62300| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G08950|AT3G55440|AT4G01370|AT2G46830| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G11670|AT3G52930|AT2G17840| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G27420|AT1G73080|AT4G39640| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G23250|AT2G26690|AT1G74310|AT1G20440| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G02240|AT2G25490|AT1G19020| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G47000|AT4G05100|AT1G10170| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G59450|AT3G46620|AT4G33950|AT3G13920| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G37260|AT2G05710|AT2G35930| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G29395|AT3G50970|AT4G37270| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G52450|AT5G37500|AT3G62410|AT2G41430| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G20450|AT4G20830|AT1G01060| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G32640|AT1G78080|AT3G10920| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G15500|AT3G52800|AT2G24570|AT4G05320| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G04880|AT5G59820|AT1G19180| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G19580|AT2G23320 
               
               
                   
                 GO: 0050896 
                 response to 
                 121 out of 
                 3689 out of 
                 6.14E−10 
                 AT5G49480|AT1G17870|AT1G80850|AT4G23190| 
               
               
                   
                   
                 stimulus 
                 275 genes, 
                 15002 
                   
                 AT3G15210|AT5G06320|AT3G09440| 
               
               
                   
                   
                   
                 44% 
                 genes, 
                   
                 AT4G27280|AT4G17615|AT2G40000| 
               
               
                   
                   
                   
                   
                 24.6% 
                   
                 AT1G15080|AT5G47230|AT3G17390|AT1G55450| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G50980|AT1G27760|AT5G15090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G04730|AT4G08950|AT1G42560| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G52930|AT5G27420|AT3G23250|AT1G09080| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G26690|AT3G06510|AT5G02020| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G74310|AT2G30250|AT1G19020| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G47000|AT4G05100|AT5G59450|AT3G46620| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G78290|AT2G05710|AT1G68760| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G44260|AT1G32920|AT3G52450| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G41430|AT3G22370|AT1G01060|AT5G14740| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G78080|AT3G13790|AT3G10920| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G15500|AT4G36010|AT2G24570| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G04880|AT5G59820|AT5G01500|AT1G19180| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G19580|AT2G23320|AT1G22070| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G43130|AT1G05680|AT1G68765| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G45145|AT3G16857|AT2G40140|AT1G43910| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G53480|AT2G32120|AT2G03760| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G56590|AT3G08590|AT1G42990| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G63790|AT4G39090|AT5G45110|AT5G64905| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G49530|AT1G01720|AT4G34160| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G76180|AT5G39580|AT1G59870| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G51920|AT5G05600|AT5G06290|AT5G61890| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G62300|AT3G55440|AT4G01370| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G46830|AT5G11670|AT1G61890| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G37370|AT2G17840|AT1G73080|AT5G58070| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G39640|AT3G10985|AT1G20440| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G02240|AT2G25490|AT1G10170| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G37010|AT4G33950|AT3G13920|AT5G62530| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G37260|AT2G35930|AT1G29395| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G33590|AT3G50970|AT4G37270| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G37500|AT3G62410|AT1G20450|AT4G20830| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G80010|AT1G32640|AT4G39080| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G71697|AT3G52800|AT4G05320| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G29690 
               
               
                   
                 GO: 0010033 
                 response to 
                 57 out of 
                 1148 out of 
                 1.64E−09 
                 AT1G22070|AT1G68765|AT1G05680|AT3G15210| 
               
               
                   
                   
                 organic 
                 275 genes, 
                 15002 
                   
                 AT3G16857|AT2G40140|AT1G43910| 
               
               
                   
                   
                 substance 
                 20.7% 
                 genes, 7.7% 
                   
                 AT4G17615|AT3G53480|AT2G40000| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G03760|AT1G15080|AT5G47230|AT1G42990| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G49530|AT4G34160|AT1G76180| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G59870|AT3G51920|AT3G04730| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G62300|AT4G08950|AT4G01370|AT2G46830| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G27420|AT1G73080|AT3G23250| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G26690|AT1G20440|AT5G02240| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G25490|AT2G47000|AT4G05100|AT5G59450| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G46620|AT4G33950|AT4G37260| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G05710|AT2G35930|AT1G29395| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G50970|AT3G52450|AT5G37500|AT3G62410| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G20450|AT1G01060|AT1G32640| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G78080|AT3G15500|AT3G52800| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G24570|AT4G05320|AT2G04880|AT5G59820| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G19180|AT3G19580|AT2G23320 
               
               
                   
                 GO: 0010200 
                 response to 
                 19 out of 
                 127 out of 
                 2.22E−09 
                 AT5G27420|AT1G32640|AT3G49530|AT2G40140| 
               
               
                   
                   
                 chitin 
                 275 genes, 
                 15002 
                   
                 AT4G37260|AT1G42990|AT3G19580| 
               
               
                   
                   
                   
                 6.9% 
                 genes, 0.8% 
                   
                 AT5G59450|AT3G15210|AT3G46620| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G59820|AT5G47230|AT3G23250|AT2G35930| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G52800|AT2G23320|AT1G62300| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G24570|AT3G52450 
               
               
                   
                 GO: 0009743 
                 response to 
                 21 out of 
                 203 out of 
                 8.31E−08 
                 AT5G27420|AT3G49530|AT4G34160|AT5G59450| 
               
               
                   
                   
                 carbohydrate 
                 275 genes, 
                 15002 
                   
                 AT3G15210|AT3G46620|AT5G59820| 
               
               
                   
                   
                 stimulus 
                 7.6% 
                 genes, 1.4% 
                   
                 AT5G47230|AT3G23250|AT1G62300| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G52450|AT1G32640|AT2G40140|AT4G37260| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G42990|AT3G19580|AT2G35930| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G52800|AT3G62410|AT2G23320| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G24570 
               
               
                   
                 GO: 0006970 
                 response to 
                 29 out of 
                 425 out of 
                 3.21E−07 
                 AT5G49480|AT4G05100|AT1G10170|AT1G05680| 
               
               
                   
                   
                 osmotic 
                 275 genes, 
                 15002 
                   
                 AT3G51920|AT1G01060|AT4G33950| 
               
               
                   
                   
                 stress 
                 10.5% 
                 genes, 2.8% 
                   
                 AT5G62530|AT1G78080|AT4G39080| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G55440|AT3G10920|AT4G01370|AT2G46830| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G05710|AT4G17615|AT3G52930| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G17840|AT5G58070|AT2G03760| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G59820|AT3G23250|AT1G55450|AT5G02020| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G20440|AT3G19580|AT1G27760| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G30250|AT4G39090 
               
               
                   
                 GO: 0009651 
                 response to 
                 28 out of 
                 397 out of 
                 3.21E−07 
                 AT5G49480|AT4G05100|AT1G10170|AT1G05680| 
               
               
                   
                   
                 salt stress 
                 275 genes, 
                 15002 
                   
                 AT3G51920|AT1G01060|AT4G33950| 
               
               
                   
                   
                   
                 10.2% 
                 genes, 2.6% 
                   
                 AT5G62530|AT1G78080|AT4G39080| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G55440|AT3G10920|AT4G01370|AT2G46830| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G05710|AT4G17615|AT3G52930| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G17840|AT5G58070|AT2G03760| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G59820|AT3G23250|AT1G55450|AT5G02020| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G19580|AT1G27760|AT2G30250| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G39090 
               
               
                   
                 GO: 0009415 
                 response to 
                 20 out of 
                 211 out of 
                 5.96E−07 
                 AT1G76180|AT1G05680|AT3G51920|AT3G50970| 
               
               
                   
                   
                 water 
                 275 genes, 
                 15002 
                   
                 AT4G33950|AT3G52450|AT1G32640| 
               
               
                   
                   
                   
                 7.3% 
                 genes, 1.4% 
                   
                 AT1G78080|AT5G37500|AT1G20440| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G19580|AT3G15500|AT3G50980|AT2G35930| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G29395|AT4G39090|AT4G17615| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G41430|AT1G20450|AT2G17840 
               
               
                   
                 GO: 0009414 
                 response to 
                 19 out of 
                 202 out of 
                 1.46E−06 
                 AT1G76180|AT1G05680|AT3G51920|AT3G50970| 
               
               
                   
                   
                 water 
                 275 genes, 
                 15002 
                   
                 AT4G33950|AT3G52450|AT1G32640| 
               
               
                   
                   
                 deprivation 
                 6.9% 
                 genes, 1.3% 
                   
                 AT1G78080|AT5G37500|AT1G20440| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G19580|AT3G15500|AT2G35930|AT1G29395| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G39090|AT4G17615|AT2G41430| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G20450|AT2G17840 
               
               
                   
                 GO: 0009737 
                 response to 
                 24 out of 
                 340 out of 
                 3.21E−06 
                 AT4G05100|AT1G76180|AT1G05680|AT3G15210| 
               
               
                   
                   
                 abscisic 
                 275 genes, 
                 15002 
                   
                 AT1G59870|AT3G51920|AT1G01060| 
               
               
                   
                   
                 acid 
                 8.7% 
                 genes, 2.3% 
                   
                 AT4G33950|AT1G32640|AT4G37260| 
               
               
                   
                   
                 stimulus 
                   
                   
                   
                 AT4G01370|AT2G46830|AT1G43910|AT2G05710| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G29395|AT4G17615|AT5G27420| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G15080|AT3G50970|AT5G37500| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G20440|AT3G19580|AT1G20450|AT5G02240 
               
               
                   
                 GO: 0009266 
                 response to 
                 25 out of 
                 399 out of 
                 1.33E−05 
                 AT3G49530|AT3G22370|AT1G17870|AT2G43130| 
               
               
                   
                   
                 temperature 
                 275 genes, 
                 15002 
                   
                 AT1G76180|AT5G06290|AT3G09440| 
               
               
                   
                   
                 stimulus 
                 9.1% 
                 genes, 2.7% 
                   
                 AT2G40140|AT4G01370|AT1G29395| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G17615|AT2G17840|AT2G32120|AT5G58070| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G59820|AT5G47230|AT3G50970| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G09080|AT3G17390|AT3G06510| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G37500|AT1G74310|AT1G20440|AT2G30250| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G20450 
               
               
                   
                 GO: 0009409 
                 response to 
                 19 out of 
                 269 out of 
                 7.22E−05 
                 AT3G49530|AT3G22370|AT1G76180|AT5G06290| 
               
               
                   
                   
                 cold 
                 275 genes, 
                 15002 
                   
                 AT2G40140|AT4G01370|AT1G29395| 
               
               
                   
                   
                   
                 6.9% 
                 genes, 1.8% 
                   
                 AT4G17615|AT2G17840|AT5G58070| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G47230|AT5G59820|AT3G50970|AT3G17390| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G06510|AT5G37500|AT1G20440| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G30250|AT1G20450 
               
               
                   
                 GO: 0009719 
                 response to 
                 39 out of 
                 920 out of 
                 8.19E−05 
                 AT2G47000|AT4G05100|AT1G68765|AT1G05680| 
               
               
                   
                   
                 endogenous 
                 275 genes, 
                 15002 
                   
                 AT3G15210|AT4G33950|AT3G16857| 
               
               
                   
                   
                 stimulus 
                 14.2% 
                 genes, 6.1% 
                   
                 AT4G37260|AT1G43910|AT2G05710| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G29395|AT4G17615|AT3G53480|AT1G15080| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G47230|AT3G50970|AT5G37500| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G20450|AT4G34160|AT1G76180| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G59870|AT3G51920|AT3G04730|AT1G01060| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G08950|AT1G32640|AT1G78080| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G15500|AT4G01370|AT2G46830| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G27420|AT1G73080|AT3G23250|AT2G26690| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G19180|AT1G20440|AT3G19580| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G02240|AT2G25490 
               
               
                   
                 GO: 0042742 
                 defense 
                 15 out of 
                 201 out of 
                 0.000464 
                 AT1G22070|AT2G40000|AT5G15090|AT1G10170| 
               
               
                   
                   
                 response to 
                 275 genes, 
                 15002 
                   
                 AT4G23190|AT5G06320|AT1G59870| 
               
               
                   
                   
                 bacterium 
                 5.5% 
                 genes, 1.3% 
                   
                 AT5G06290|AT4G33950|AT5G14740| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G19180|AT3G10920|AT4G39090|AT2G24570| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G45110 
               
               
                   
                 GO: 0009725 
                 response to 
                 35 out of 
                 849 out of 
                 0.000474 
                 AT2G47000|AT4G05100|AT1G68765|AT1G05680| 
               
               
                   
                   
                 hormone 
                 275 genes, 
                 15002 
                   
                 AT3G15210|AT4G33950|AT3G16857| 
               
               
                   
                   
                 stimulus 
                 12.7% 
                 genes, 5.7% 
                   
                 AT4G37260|AT1G43910|AT2G05710| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G29395|AT4G17615|AT3G53480|AT1G15080| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G47230|AT3G50970|AT5G37500| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G20450|AT4G34160|AT1G76180| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G59870|AT3G51920|AT3G04730|AT1G01060| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G08950|AT1G32640|AT1G78080| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G01370|AT2G46830|AT5G27420| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G23250|AT1G20440|AT3G19580|AT5G02240| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G25490 
               
               
                   
                 GO: 0009607 
                 response to 
                 28 out of 
                 610 out of 
                 0.000597 
                 AT1G22070|AT1G10170|AT4G23190|AT5G06320| 
               
               
                   
                   
                 biotic 
                 275 genes, 
                 15002 
                   
                 AT4G33950|AT1G45145|AT2G40140| 
               
               
                   
                   
                 stimulus 
                 10.2% 
                 genes, 4.1% 
                   
                 AT3G44260|AT2G40000|AT3G50970| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G42990|AT4G39090|AT2G41430|AT5G45110| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G49530|AT5G15090|AT5G39580| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G59870|AT5G06290|AT5G61890| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G14740|AT3G10920|AT4G36010|AT4G01370| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G24570|AT3G10985|AT1G19180| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G20440 
               
               
                   
                 GO: 0009753 
                 response to 
                 13 out of 
                 158 out of 
                 0.000597 
                 AT1G73080|AT4G05100|AT3G15210|AT1G01060| 
               
               
                   
                   
                 jasmonic 
                 275 genes, 
                 15002 
                   
                 AT3G23250|AT2G26690|AT1G32640| 
               
               
                   
                   
                 acid 
                 4.7% 
                 genes, 1.1% 
                   
                 AT1G19180|AT5G37500|AT4G37260| 
               
               
                   
                   
                 stimulus 
                   
                   
                   
                 AT3G15500|AT4G01370|AT2G46830 
               
               
                   
                 GO: 0051707 
                 response to 
                 26 out of 
                 558 out of 
                 0.000872 
                 AT1G22070|AT1G10170|AT4G23190|AT5G06320| 
               
               
                   
                   
                 other 
                 275 genes, 
                 15002 
                   
                 AT4G33950|AT1G45145|AT2G40140| 
               
               
                   
                   
                 organism 
                 9.5% 
                 genes, 3.7% 
                   
                 AT2G40000|AT3G50970|AT4G39090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G41430|AT5G45110|AT3G49530|AT5G15090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G39580|AT1G59870|AT5G06290| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G61890|AT5G14740|AT3G10920| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G36010|AT4G01370|AT2G24570|AT3G10985| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G19180|AT1G20440 
               
               
                   
                 GO: 0070887 
                 cellular 
                 20 out of 
                 374 out of 
                 0.00127 
                 AT1G22070|AT1G05680|AT3G15210|AT1G59870| 
               
               
                   
                   
                 response to 
                 275 genes, 
                 15002 
                   
                 AT4G33950|AT1G62300|AT1G32640| 
               
               
                   
                   
                 chemical 
                 7.3% 
                 genes, 2.5% 
                   
                 AT3G16857|AT1G78080|AT3G10920| 
               
               
                   
                   
                 stimulus 
                   
                   
                   
                 AT3G15500|AT4G01370|AT1G29395|AT4G17615| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G53480|AT2G04880|AT1G15080| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G47230|AT1G19180|AT1G42990 
               
               
                   
                 GO: 0009617 
                 response to 
                 16 out of 
                 256 out of 
                 0.00134 
                 AT1G22070|AT2G40000|AT5G15090|AT1G10170| 
               
               
                   
                   
                 bacterium 
                 275 genes, 
                 15002 
                   
                 AT4G23190|AT5G06320|AT1G59870| 
               
               
                   
                   
                   
                 5.8% 
                 genes, 1.7% 
                   
                 AT5G06290|AT4G33950|AT5G14740| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G19180|AT3G10920|AT4G39090|AT2G24570| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G41430|AT5G45110 
               
               
                   
                 GO: 0051704 
                 multi- 
                 26 out of 
                 589 out of 
                 0.00182 
                 AT1G22070|AT1G10170|AT4G23190|AT5G06320| 
               
               
                   
                   
                 organism 
                 275 genes, 
                 15002 
                   
                 AT4G33950|AT1G45145|AT2G40140| 
               
               
                   
                   
                 process 
                 9.5% 
                 genes, 3.9% 
                   
                 AT2G40000|AT3G50970|AT4G39090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G41430|AT5G45110|AT3G49530|AT5G15090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G39580|AT1G59870|AT5G06290| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G61890|AT5G14740|AT3G10920| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G36010|AT4G01370|AT2G24570|AT3G10985| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G19180|AT1G20440 
               
               
                   
                 GO: 0006952 
                 defense 
                 30 out of 
                 747 out of 
                 0.00242 
                 AT1G22070|AT1G10170|AT4G23190|AT5G06320| 
               
               
                   
                   
                 response 
                 275 genes, 
                 15002 
                   
                 AT4G33950|AT1G45145|AT2G40140| 
               
               
                   
                   
                   
                 10.9% 
                 genes, 5% 
                   
                 AT2G35930|AT1G33590|AT2G40000| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G03760|AT3G50970|AT3G52450|AT4G39090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G45110|AT5G64905|AT3G49530| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G15090|AT5G39580|AT1G59870| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G06290|AT5G61890|AT5G14740|AT3G10920| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G01370|AT1G42560|AT2G24570| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G73080|AT1G19180|AT1G20440 
               
               
                   
                 GO: 0009631 
                 cold 
                 5 out of 275 
                 21 out of 
                 0.00297 
                 AT5G59820|AT1G20440|AT1G20450|AT1G29395| 
               
               
                   
                   
                 acclimation 
                 genes, 1.8% 
                 15002 
                   
                 AT3G50970 
               
               
                   
                   
                   
                   
                 genes, 0.1% 
               
               
                   
                 GO: 0009642 
                 response to 
                 8 out of 275 
                 78 out of 
                 0.0051 
                 AT2G32120|AT1G17870|AT1G74310|AT1G10170| 
               
               
                   
                   
                 light 
                 genes, 2.9% 
                 15002 
                   
                 AT5G59820|AT4G37270|AT2G41430| 
               
               
                   
                   
                 intensity 
                   
                 genes, 0.5% 
                   
                 AT2G17840 
               
               
                   
                 GO: 0072511 
                 divalent 
                 6 out of 275 
                 40 out of 
                 0.00516 
                 AT3G13320|AT4G37270|AT3G63380|AT1G59870| 
               
               
                   
                   
                 inorganic 
                 genes, 2.2% 
                 15002 
                   
                 AT2G04040|AT1G27770 
               
               
                   
                   
                 cation 
                   
                 genes, 0.3% 
               
               
                   
                   
                 transport 
               
               
                   
                 GO: 0080167 
                 response to 
                 10 out of 
                 127 out of 
                 0.00564 
                 AT3G13790|AT3G09440|AT1G05680|AT5G05600| 
               
               
                   
                   
                 karrikin 
                 275 genes, 
                 15002 
                   
                 AT4G27280|AT1G33590|AT3G52930| 
               
               
                   
                   
                   
                 3.6% 
                 genes, 0.8% 
                   
                 AT1G61890|AT4G37370|AT1G78290 
               
               
                   
                 GO: 0071310 
                 cellular 
                 17 out of 
                 337 out of 
                 0.00701 
                 AT1G22070|AT1G05680|AT3G15210|AT1G59870| 
               
               
                   
                   
                 response to 
                 275 genes, 
                 15002 
                   
                 AT4G33950|AT1G32640|AT3G16857| 
               
               
                   
                   
                 organic 
                 6.2% 
                 genes, 2.2% 
                   
                 AT1G78080|AT3G15500|AT4G01370| 
               
               
                   
                   
                 substance 
                   
                   
                   
                 AT4G17615|AT3G53480|AT2G04880|AT1G15080| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G47230|AT1G19180|AT1G42990 
               
               
                   
                 GO: 0009723 
                 response to 
                 10 out of 
                 134 out of 
                 0.00789 
                 AT4G05100|AT1G68765|AT3G15210|AT5G47230| 
               
               
                   
                   
                 ethylene 
                 275 genes, 
                 15002 
                   
                 AT1G01060|AT3G23250|AT1G78080| 
               
               
                   
                   
                 stimulus 
                 3.6% 
                 genes, 0.9% 
                   
                 AT4G37260|AT2G46830|AT2G25490 
               
               
                 ClassI 
                 None 
               
               
                 ClassIIB 
                 GO: 0006950 
                 response to 
                 18 out of 49 
                 1943 out of 
                 0.03 
                 AT2G35980|AT1G80820|AT2G46140|AT3G24550| 
               
               
                   
                   
                 stress 
                 genes, 
                 12802 
                   
                 AT4G12720|AT4G39260|AT3G06490| 
               
               
                   
                   
                   
                 36.7% 
                 genes, 
                   
                 AT1G73010|AT4G37910|AT2G39660| 
               
               
                   
                   
                   
                   
                 15.2% 
                   
                 AT5G37770|AT4G34150|AT4G02380|AT1G14550| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G26030|AT2G38470|AT5G47910| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G14540 
               
               
                   
                 GO: 0006979 
                 response to 
                 6 out of 49 
                 271 out of 
                 0.03 
                 AT1G14550|AT5G26030|AT4G12720|AT4G02380| 
               
               
                   
                   
                 oxidative 
                 genes, 
                 12802 
                   
                 AT1G14540|AT5G37770 
               
               
                   
                   
                 stress 
                 12.2% 
                 genes, 2.1% 
               
               
                   
                 GO: 0009266 
                 response to 
                 8 out of 49 
                 388 out of 
                 0.03 
                 AT4G34150|AT4G37910|AT5G47910|AT2G38470| 
               
               
                   
                   
                 temperature 
                 genes, 
                 12802 
                   
                 AT1G80820|AT4G02380|AT5G37770| 
               
               
                   
                   
                 stimulus 
                 16.3% 
                 genes, 3% 
                   
                 AT4G39260 
               
               
                   
                 GO: 0009409 
                 response to 
                 6 out of 49 
                 264 out of 
                 0.03 
                 AT4G34150|AT2G38470|AT1G80820|AT4G02380| 
               
               
                   
                   
                 cold 
                 genes, 
                 12802 
                   
                 AT5G37770|AT4G39260 
               
               
                   
                   
                   
                 12.2% 
                 genes, 2.1% 
               
               
                   
                 GO: 0009620 
                 response to 
                 5 out of 49 
                 159 out of 
                 0.03 
                 AT2G38470|AT3G06490|AT2G39660|AT5G47910| 
               
               
                   
                   
                 fungus 
                 genes, 
                 12802 
                   
                 AT3G24550 
               
               
                   
                   
                   
                 10.2% 
                 genes, 1.2% 
               
               
                   
                 GO: 0010411 
                 xyloglucan 
                 2 out of 49 
                 6 out of 
                 0.03 
                 AT4G30280|AT4G30290 
               
               
                   
                   
                 metabolic 
                 genes, 4.1% 
                 12802 
               
               
                   
                   
                 process 
                   
                 genes, 0% 
               
               
                   
                 GO: 0042221 
                 response to 
                 16 out of 49 
                 1763 out of 
                 0.03 
                 AT4G37910|AT2G46140|AT5G37770|AT3G02880| 
               
               
                   
                   
                 chemical 
                 genes, 
                 12802 
                   
                 AT5G01540|AT4G12720|AT2G17660| 
               
               
                   
                   
                 stimulus 
                 32.7% 
                 genes, 
                   
                 AT4G02380|AT4G39260|AT1G14550| 
               
               
                   
                   
                   
                   
                 13.8% 
                   
                 AT5G26030|AT2G38470|AT3G06490|AT4G18880| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G11360|AT1G14540 
               
               
                   
                 GO: 0006334 
                 nucleosome 
                 3 out of 49 
                 58 out of 
                 0.05 
                 AT4G40030|AT1G06760|AT4G40040 
               
               
                   
                   
                 assembly 
                 genes, 6.1% 
                 12802 
               
               
                   
                   
                   
                   
                 genes, 0.5% 
               
               
                   
                 GO: 0034728 
                 nucleosome 
                 3 out of 49 
                 58 out of 
                 0.05 
                 AT4G40030|AT1G06760|AT4G40040 
               
               
                   
                   
                 organization 
                 genes, 6.1% 
                 12802 
               
               
                   
                   
                   
                   
                 genes, 0.5% 
               
               
                   
                 GO: 0050896 
                 response to 
                 23 out of 49 
                 3396 out of 
                 0.05 
                 AT2G35980|AT1G80820|AT2G46140|AT3G02880| 
               
               
                   
                   
                 stimulus 
                 genes, 
                 12802 
                   
                 AT3G24550|AT5G01540|AT4G12720| 
               
               
                   
                   
                   
                 46.9% 
                 genes, 
                   
                 AT4G39260|AT3G06490|AT1G73010| 
               
               
                   
                   
                   
                   
                 26.5% 
                   
                 AT4G11360|AT4G37910|AT2G39660|AT5G37770| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G34150|AT2G17660|AT4G02380| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G14550|AT5G26030|AT2G38470| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G18880|AT5G47910|AT1G14540 
               
               
                   
                 GO: 0065004 
                 protein- 
                 3 out of 49 
                 60 out of 
                 0.05 
                 AT4G40030|AT1G06760|AT4G40040 
               
               
                   
                   
                 DNA 
                 genes, 6.1% 
                 12802 
               
               
                   
                   
                 complex 
                   
                 genes, 0.5% 
               
               
                   
                   
                 assembly 
               
               
                   
                 GO: 0071824 
                 protein- 
                 3 out of 49 
                 60 out of 
                 0.05 
                 AT4G40030|AT1G06760|AT4G40040 
               
               
                   
                   
                 DNA 
                 genes, 6.1% 
                 12802 
               
               
                   
                   
                 complex 
                   
                 genes, 0.5% 
               
               
                   
                   
                 subunit 
               
               
                   
                   
                 organization 
               
               
                 ClassIIIA 
                 GO: 0009081 
                 
                   branched 
                 
                 6 out of 269 
                 27 out of 
                 0.01 
                 AT1G18270|AT1G10070|AT5G43430|AT1G10060| 
               
               
                   
                   
                 
                   chain 
                 
                 genes, 2.2% 
                 12802 
                   
                 AT1G03090|AT2G43400 
               
               
                   
                   
                 
                   family 
                 
                   
                 genes, 0.2% 
               
               
                   
                   
                 
                   amino 
                 
               
               
                   
                   
                 
                   acid 
                 
               
               
                   
                   
                 
                   metabolic 
                 
               
               
                   
                   
                 
                   process 
                 
               
               
                   
                 GO: 0009310 
                 
                   amine 
                 
                 7 out of 269 
                 40 out of 
                 0.01 
                 AT4G33150|AT2G43400|AT1G08630|AT5G43430| 
               
               
                   
                   
                 
                   catabolic 
                 
                 genes, 2.6% 
                 12802 
                   
                 AT1G03090|AT1G65840|AT5G54080 
               
               
                   
                   
                 
                   process 
                 
                   
                 genes, 0.3% 
               
               
                   
                 GO: 0016054 
                 organic 
                 9 out of 269 
                 79 out of 
                 0.01 
                 AT2G43400|AT2G33150|AT5G43430|AT4G33150| 
               
               
                   
                   
                 acid 
                 genes, 3.3% 
                 12802 
                   
                 AT3G51840|AT1G08630|AT5G65110| 
               
               
                   
                   
                 catabolic 
                   
                 genes, 0.6% 
                   
                 AT1G03090|AT5G54080 
               
               
                   
                   
                 process 
               
               
                   
                 GO: 0042221 
                 response to 
                 62 out of 
                 1763 out of 
                 0.01 
                 AT1G08720|AT1G08920|AT5G66400|AT2G40170| 
               
               
                   
                   
                 chemical 
                 269 genes, 
                 12802 
                   
                 AT2G22080|AT4G13430|AT4G37790| 
               
               
                   
                   
                 stimulus 
                 23% 
                 genes, 
                   
                 AT2G34600|AT1G54100|AT5G37260| 
               
               
                   
                   
                   
                   
                 13.8% 
                   
                 AT3G51860|AT5G61590|AT5G47390|AT5G16970| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G38750|AT4G37220|AT5G16960| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G04410|AT1G49670|AT3G11410| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G32320|AT5G67450|AT1G08090|AT5G54500| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G50200|AT1G08830|AT3G56240| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G55020|AT4G33420|AT1G20340| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G27260|AT5G59220|AT1G28130|AT2G19810| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G05200|AT2G46270|AT5G03720| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G23230|AT1G73260|AT1G08930| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G39040|AT5G44380|AT1G18330|AT5G13740| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G30170|AT4G35770|AT1G16150| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G15050|AT2G14170|AT1G80460| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G10450|AT4G39070|AT3G14050|AT4G21440| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G02860|AT5G18170|AT1G68850| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G34350|AT2G01570|AT3G60690| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G05340|AT1G17190 
               
               
                   
                 GO: 0046395 
                 carboxylic 
                 9 out of 269 
                 79 out of 
                 0.01 
                 AT2G43400|AT2G33150|AT5G43430|AT4G33150| 
               
               
                   
                   
                 acid 
                 genes, 3.3% 
                 12802 
                   
                 AT3G51840|AT1G08630|AT5G65110| 
               
               
                   
                   
                 catabolic 
                   
                 genes, 0.6% 
                   
                 AT1G03090|AT5G54080 
               
               
                   
                   
                 process 
               
               
                   
                 GO: 0006552 
                 leucine 
                 3 out of 269 
                 4 out of 
                 0.03 
                 AT2G43400|AT5G43430|AT1G03090 
               
               
                   
                   
                 catabolic 
                 genes, 1.1% 
                 12802 
               
               
                   
                   
                 process 
                   
                 genes, 0% 
               
               
                   
                 GO: 0006979 
                 response to 
                 16 out of 
                 271 out of 
                 0.03 
                 AT2G19810|AT2G22080|AT1G73260|AT1G08830| 
               
               
                   
                   
                 oxidative 
                 269 genes, 
                 12802 
                   
                 AT3G56240|AT5G16970|AT1G68850| 
               
               
                   
                   
                 stress 
                 5.9% 
                 genes, 2.1% 
                   
                 AT4G33420|AT5G44380|AT4G30170| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G16960|AT4G35770|AT5G05340|AT2G14170| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G49670|AT4G32320 
               
               
                   
                 GO: 0009063 
                 
                   cellular 
                 
                 6 out of 269 
                 38 out of 
                 0.03 
                 AT4G33150|AT2G43400|AT1G08630|AT5G43430| 
               
               
                   
                   
                 
                   amino 
                 
                 genes, 2.2% 
                 12802 
                   
                 AT1G03090|AT5G54080 
               
               
                   
                   
                 
                   acid 
                 
                   
                 genes, 0.3% 
               
               
                   
                   
                 
                   catabolic 
                 
               
               
                   
                   
                 
                   process 
                 
               
               
                   
                 GO: 0009083 
                 
                   branched 
                 
                 3 out of 269 
                 5 out of 
                 0.03 
                 AT2G43400|AT5G43430|AT1G03090 
               
               
                   
                   
                 
                   chain 
                 
                 genes, 1.1% 
                 12802 
               
               
                   
                   
                 
                   family 
                 
                   
                 genes, 0% 
               
               
                   
                   
                 
                   amino 
                 
               
               
                   
                   
                 
                   acid 
                 
               
               
                   
                   
                 
                   catabolic 
                 
               
               
                   
                   
                 
                   process 
                 
               
               
                   
                 GO: 0050896 
                 response to 
                 97 out of 
                 3396 out of 
                 0.03 
                 AT1G08920|AT2G43400|AT2G33150|AT2G40170| 
               
               
                   
                   
                 stimulus 
                 269 genes, 
                 12802 
                   
                 AT2G22080|AT4G13430|AT4G37790| 
               
               
                   
                   
                   
                 36.1% 
                 genes, 
                   
                 AT1G54100|AT1G02670|AT5G61590| 
               
               
                   
                   
                   
                   
                 26.5% 
                   
                 AT5G47390|AT3G54960|AT2G38750|AT4G37220| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G16960|AT1G04410|AT1G49670| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G11410|AT4G32320|AT1G08090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G54500|AT1G08830|AT1G25275|AT3G15950| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G33420|AT4G27260|AT5G59220| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G28130|AT5G24470|AT2G46270| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G03720|AT3G23230|AT1G06520|AT5G67320| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G73260|AT5G39040|AT4G30170| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G35770|AT1G16150|AT1G31480| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G80460|AT5G24530|AT1G75800|AT2G39980| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G39070|AT3G14050|AT1G60940| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G06980|AT1G02860|AT3G47640| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G68850|AT2G26280|AT5G13750|AT3G45060| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G17190|AT5G67440|AT5G27350| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G08720|AT5G66400|AT5G47740| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G52250|AT4G24220|AT2G34600|AT5G37260| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G51860|AT5G16970|AT3G61060| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G27690|AT5G67450|AT5G47240| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G50200|AT4G01120|AT5G61510|AT3G56240| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G55020|AT1G20340|AT5G04770| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G19810|AT3G05200|AT1G08930| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G44380|AT1G18330|AT5G13740|AT1G15050| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G14170|AT1G13080|AT5G10450| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G20250|AT2G32660|AT4G21440| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G75230|AT5G18170|AT4G34350|AT2G01570| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G60690|AT5G05340|AT5G61600 
               
               
                 ClassIIIB 
                 GO: 0006952 
                 defense 
                 36 out of 
                 683 out of 
                 1.43E−05 
                 AT2G38870|AT3G52430|AT3G25070|AT4G11850| 
               
               
                   
                   
                 response 
                 234 genes, 
                 12802 
                   
                 AT4G23440|AT1G11000|AT1G57630| 
               
               
                   
                   
                   
                 15.4% 
                 genes, 5.3% 
                   
                 AT1G18570|AT5G41550|AT5G58120| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G34930|AT3G05360|AT3G11840|AT1G11310| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G11820|AT2G26380|AT1G74710| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G61560|AT2G26560|AT1G15890| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G48090|AT5G04720|AT2G16870|AT4G39030| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G44070|AT1G56510|AT5G22690| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G11170|AT3G52400|AT3G28740| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G19190|AT1G17750|AT1G05800|AT3G13650| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G66090|AT4G33300 
               
               
                   
                 GO: 0050896 
                 response to 
                 100 out of 
                 3396 out of 
                 3.02E−05 
                 AT4G23440|AT3G52360|AT4G17230|AT4G16780| 
               
               
                   
                   
                 stimulus 
                 234 genes, 
                 12802 
                   
                 AT5G24620|AT4G17260|AT4G34180| 
               
               
                   
                   
                   
                 42.7% 
                 genes, 
                   
                 AT3G11840|AT5G62390|AT1G61560| 
               
               
                   
                   
                   
                   
                 26.5% 
                   
                 AT1G18890|AT4G02200|AT4G30080|AT5G44070| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G61850|AT1G11210|AT1G09940| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G01150|AT5G51190|AT1G13340| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G44720|AT2G17040|AT1G55920|AT1G20510| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G61900|AT4G33300|AT3G45640| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G38870|AT3G25070|AT1G57630| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G07520|AT2G34930|AT3G17020|AT3G50480| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G62680|AT1G80530|AT5G61210| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G44610|AT5G66070|AT2G26560| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G07390|AT2G40180|AT1G56510|AT5G63770| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G11170|AT2G41380|AT5G25190| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G65020|AT3G13650|AT2G06050| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G52430|AT1G11000|AT5G06720|AT5G66880| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G59900|AT5G48540|AT1G18570| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G04160|AT3G05360|AT1G72060| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G11310|AT1G15890|AT3G48090|AT5G04720| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G26120|AT4G39030|AT1G52560| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G05710|AT5G24540|AT5G22690| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G52400|AT1G05055|AT3G28740|AT2G19190| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G52200|AT1G17750|AT1G74430| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G05800|AT1G66090|AT3G17700| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G30040|AT4G14630|AT4G11850|AT5G09980| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G41550|AT5G58120|AT3G28580| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G19220|AT3G11820|AT2G26380| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G74710|AT2G16870|AT2G16500|AT1G57560| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G70940|AT1G02400|AT5G54170| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G46590|AT3G09270|AT5G49620 
               
               
                   
                 GO: 0031348 
                 negative 
                 7 out of 234 
                 18 out of 
                 4.84E−05 
                 AT3G25070|AT1G11310|AT3G52400|AT3G11820| 
               
               
                   
                   
                 regulation 
                 genes, 3% 
                 12802 
                   
                 AT4G39030|AT1G74710|AT3G52430 
               
               
                   
                   
                 of defense 
                   
                 genes, 0.1% 
               
               
                   
                   
                 response 
               
               
                   
                 GO: 0051707 
                 response to 
                 27 out of 
                 533 out of 
                 0.000515 
                 AT3G45640|AT2G06050|AT2G38870|AT3G52430| 
               
               
                   
                   
                 other 
                 234 genes, 
                 12802 
                   
                 AT3G25070|AT4G11850|AT5G24620| 
               
               
                   
                   
                 organism 
                 11.5% 
                 genes, 4.2% 
                   
                 AT1G18570|AT2G34930|AT3G50480| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G61210|AT1G11310|AT3G11820|AT1G74710| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G61560|AT2G26560|AT3G48090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G39030|AT5G44070|AT1G56510| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G24540|AT3G52400|AT3G28740|AT2G19190| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G17750|AT1G05800|AT3G17700 
               
               
                   
                 GO: 0002376 
                 immune 
                 18 out of 
                 277 out of 
                 0.000657 
                 AT3G48090|AT3G52430|AT2G16870|AT3G25070| 
               
               
                   
                   
                 system 
                 234 genes, 
                 12802 
                   
                 AT4G11850|AT4G23440|AT1G57630| 
               
               
                   
                   
                 process 
                 7.7% 
                 genes, 2.2% 
                   
                 AT1G56510|AT5G41550|AT5G58120| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G22690|AT3G05360|AT3G11840|AT1G11310| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G74710|AT1G66090|AT1G61560| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G26560 
               
               
                   
                 GO: 0006950 
                 response to 
                 62 out of 
                 1943 out of 
                 0.000657 
                 AT4G23440|AT4G17260|AT4G34180|AT3G11840| 
               
               
                   
                   
                 stress 
                 234 genes, 
                 12802 
                   
                 AT5G62390|AT1G61560|AT4G02200| 
               
               
                   
                   
                   
                 26.5% 
                 genes, 
                   
                 AT5G44070|AT1G11210|AT1G09940| 
               
               
                   
                   
                   
                   
                 15.2% 
                   
                 AT1G13340|AT1G55920|AT1G20510|AT4G33300| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G45640|AT2G38870|AT3G25070| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G57630|AT2G34930|AT3G17020| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G44610|AT2G26560|AT1G56510|AT5G63770| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G11170|AT5G65020|AT3G13650| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G06050|AT3G52430|AT1G11000| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G66880|AT5G06720|AT1G18570|AT3G05360| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G72060|AT1G11310|AT1G15890| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G48090|AT5G04720|AT4G39030| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G52560|AT5G22690|AT3G52400|AT1G05055| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G28740|AT2G19190|AT1G52200| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G17750|AT1G05800|AT1G66090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G14630|AT4G11850|AT5G41550|AT5G58120| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G11820|AT2G26380|AT1G74710| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G16870|AT2G16500|AT5G54170| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G46590|AT5G49620 
               
               
                   
                 GO: 0009607 
                 response to 
                 28 out of 
                 582 out of 
                 0.000657 
                 AT3G45640|AT2G06050|AT2G38870|AT3G52430| 
               
               
                   
                   
                 biotic 
                 234 genes, 
                 12802 
                   
                 AT3G25070|AT4G11850|AT5G24620| 
               
               
                   
                   
                 stimulus 
                 12% 
                 genes, 4.5% 
                   
                 AT1G18570|AT2G34930|AT3G50480| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G61210|AT5G62390|AT1G11310|AT3G11820| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G74710|AT1G61560|AT2G26560| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G48090|AT4G39030|AT5G44070| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G56510|AT5G24540|AT3G52400|AT3G28740| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G19190|AT1G17750|AT1G05800| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G17700 
               
               
                   
                 GO: 0051704 
                 multi- 
                 27 out of 
                 562 out of 
                 0.000657 
                 AT3G45640|AT2G06050|AT2G38870|AT3G52430| 
               
               
                   
                   
                 organism 
                 234 genes, 
                 12802 
                   
                 AT3G25070|AT4G11850|AT5G24620| 
               
               
                   
                   
                 process 
                 11.5% 
                 genes, 4.4% 
                   
                 AT1G18570|AT2G34930|AT3G50480| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G61210|AT1G11310|AT3G11820|AT1G74710| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G61560|AT2G26560|AT3G48090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G39030|AT5G44070|AT1G56510| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G24540|AT3G52400|AT3G28740|AT2G19190| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G17750|AT1G05800|AT3G17700 
               
               
                   
                 GO: 0080134 
                 regulation 
                 10 out of 
                 86 out of 
                 0.000674 
                 AT3G45640|AT1G11310|AT3G11820|AT2G31880| 
               
               
                   
                   
                 of 
                 234 genes, 
                 12802 
                   
                 AT3G52430|AT3G25070|AT3G52400| 
               
               
                   
                   
                 response to 
                 4.3% 
                 genes, 0.7% 
                   
                 AT4G39030|AT1G74710|AT3G05360 
               
               
                   
                   
                 stress 
               
               
                   
                 GO: 0031347 
                 regulation 
                 9 out of 234 
                 72 out of 
                 0.00102 
                 AT1G11310|AT3G11820|AT2G31880|AT3G52430| 
               
               
                   
                   
                 of defense 
                 genes, 3.8% 
                 12802 
                   
                 AT3G25070|AT3G52400|AT4G39030| 
               
               
                   
                   
                 response 
                   
                 genes, 0.6% 
                   
                 AT1G74710|AT3G05360 
               
               
                   
                 GO: 0045087 
                 innate 
                 16 out of 
                 241 out of 
                 0.00106 
                 AT3G48090|AT3G52430|AT2G16870|AT3G25070| 
               
               
                   
                   
                 immune 
                 234 genes, 
                 12802 
                   
                 AT4G11850|AT4G23440|AT1G57630| 
               
               
                   
                   
                 response 
                 6.8% 
                 genes, 1.9% 
                   
                 AT1G56510|AT5G41550|AT5G58120| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G22690|AT1G11310|AT1G74710|AT1G66090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G61560|AT2G26560 
               
               
                   
                 GO: 0006955 
                 immune 
                 16 out of 
                 245 out of 
                 0.00118 
                 AT3G48090|AT3G52430|AT2G16870|AT3G25070| 
               
               
                   
                   
                 response 
                 234 genes, 
                 12802 
                   
                 AT4G11850|AT4G23440|AT1G57630| 
               
               
                   
                   
                   
                 6.8% 
                 genes, 1.9% 
                   
                 AT1G56510|AT5G41550|AT5G58120| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G22690|AT1G11310|AT1G74710|AT1G66090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G61560|AT2G26560 
               
               
                   
                 GO: 0008219 
                 cell death 
                 15 out of 
                 221 out of 
                 0.00121 
                 AT5G22690|AT3G48090|AT5G04720|AT2G16870| 
               
               
                   
                   
                   
                 234 genes, 
                 12802 
                   
                 AT3G25070|AT4G23440|AT1G11000| 
               
               
                   
                   
                   
                 6.4% 
                 genes, 1.7% 
                   
                 AT1G11310|AT1G66090|AT5G41550| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G61560|AT5G58120|AT4G33300|AT2G26560| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G15890 
               
               
                   
                 GO: 0016265 
                 death 
                 15 out of 
                 221 out of 
                 0.00121 
                 AT5G22690|AT3G48090|AT5G04720|AT2G16870| 
               
               
                   
                   
                   
                 234 genes, 
                 12802 
                   
                 AT3G25070|AT4G23440|AT1G11000| 
               
               
                   
                   
                   
                 6.4% 
                 genes, 1.7% 
                   
                 AT1G11310|AT1G66090|AT5G41550| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G61560|AT5G58120|AT4G33300|AT2G26560| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G15890 
               
               
                   
                 GO: 0016310 
                 phosphorylation 
                 33 out of 
                 872 out of 
                 0.00364 
                 AT3G45640|AT5G40540|AT3G25070|AT1G55610| 
               
               
                   
                   
                   
                 234 genes, 
                 12802 
                   
                 AT5G41680|AT2G17220|AT1G51940| 
               
               
                   
                   
                   
                 14.1% 
                 genes, 6.8% 
                   
                 AT4G09570|AT2G31880|AT4G28350| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G19130|AT5G38210|AT1G70130|AT3G55950| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G37840|AT3G16030|AT1G51620| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G70530|AT1G53430|AT1G61370| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G08760|AT2G11520|AT1G18890|AT4G21390| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G07620|AT1G53440|AT1G28390| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G65600|AT1G04440|AT2G39110| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G17750|AT1G53050|AT4G39940 
               
               
                   
                 GO: 0048583 
                 regulation 
                 12 out of 
                 170 out of 
                 0.00495 
                 AT3G45640|AT3G52430|AT3G25070|AT3G52400| 
               
               
                   
                   
                 of 
                 234 genes, 
                 12802 
                   
                 AT4G39030|AT3G05360|AT5G66880| 
               
               
                   
                   
                 response to 
                 5.1% 
                 genes, 1.3% 
                   
                 AT4G09570|AT1G11310|AT3G11820| 
               
               
                   
                   
                 stimulus 
                   
                   
                   
                 AT2G31880|AT1G74710 
               
               
                   
                 GO: 0006468 
                 protein 
                 32 out of 
                 856 out of 
                 0.00519 
                 AT3G45640|AT5G40540|AT3G25070|AT1G55610| 
               
               
                   
                   
                 phosphorylation 
                 234 genes, 
                 12802 
                   
                 AT5G41680|AT2G17220|AT1G51940| 
               
               
                   
                   
                   
                 13.7% 
                 genes, 6.7% 
                   
                 AT4G09570|AT2G31880|AT4G28350| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G19130|AT5G38210|AT1G70130|AT3G55950| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G37840|AT3G16030|AT1G51620| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G70530|AT1G53430|AT1G61370| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G08760|AT2G11520|AT1G18890|AT4G21390| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G07620|AT1G53440|AT1G28390| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G65600|AT1G04440|AT2G39110| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G17750|AT1G53050 
               
               
                   
                 GO: 0006793 
                 phosphorus 
                 34 out of 
                 948 out of 
                 0.00605 
                 AT3G45640|AT5G40540|AT3G25070|AT1G55610| 
               
               
                   
                   
                 metabolic 
                 234 genes, 
                 12802 
                   
                 AT5G41680|AT2G17220|AT1G51940| 
               
               
                   
                   
                 process 
                 14.5% 
                 genes, 7.4% 
                   
                 AT4G09570|AT2G31880|AT4G28350| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G19130|AT5G38210|AT1G70130|AT3G55950| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G37840|AT3G16030|AT1G51620| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G70530|AT1G53430|AT1G61370| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G08760|AT2G11520|AT1G18890|AT4G21390| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G07620|AT1G53440|AT1G28390| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G65600|AT1G04440|AT3G02800| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G39110|AT1G17750|AT1G53050|AT4G39940 
               
               
                   
                 GO: 0006796 
                 phosphate 
                 34 out of 
                 947 out of 
                 0.00605 
                 AT3G45640|AT5G40540|AT3G25070|AT1G55610| 
               
               
                   
                   
                 metabolic 
                 234 genes, 
                 12802 
                   
                 AT5G41680|AT2G17220|AT1G51940| 
               
               
                   
                   
                 process 
                 14.5% 
                 genes, 7.4% 
                   
                 AT4G09570|AT2G31880|AT4G28350| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G19130|AT5G38210|AT1G70130|AT3G55950| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G37840|AT3G16030|AT1G51620| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G70530|AT1G53430|AT1G61370| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G08760|AT2G11520|AT1G18890|AT4G21390| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G07620|AT1G53440|AT1G28390| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G65600|AT1G04440|AT3G02800| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G39110|AT1G17750|AT1G53050|AT4G39940 
               
               
                   
                 GO: 0012501 
                 programmed 
                 12 out of 
                 185 out of 
                 0.00793 
                 AT5G22690|AT3G48090|AT5G04720|AT2G16870| 
               
               
                   
                   
                 cell 
                 234 genes, 
                 12802 
                   
                 AT3G25070|AT4G23440|AT1G66090| 
               
               
                   
                   
                 death 
                 5.1% 
                 genes, 1.4% 
                   
                 AT5G41550|AT5G58120|AT4G33300| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G26560|AT1G15890 
               
               
                   
                 GO: 0048585 
                 negative 
                 7 out of 234 
                 62 out of 
                 0.00793 
                 AT1G11310|AT3G11820|AT3G52430|AT3G25070| 
               
               
                   
                   
                 regulation 
                 genes, 3% 
                 12802 
                   
                 AT3G52400|AT4G39030|AT1G74710 
               
               
                   
                   
                 of 
                   
                 genes, 0.5% 
               
               
                   
                   
                 response to 
               
               
                   
                   
                 stimulus 
               
               
                   
                 GO: 0010033 
                 response to 
                 36 out of 
                 1059 out of 
                 0.00907 
                 AT3G52430|AT4G17230|AT5G66880|AT3G59900| 
               
               
                   
                   
                 organic 
                 234 genes, 
                 12802 
                   
                 AT4G16780|AT1G18570|AT2G04160| 
               
               
                   
                   
                 substance 
                 15.4% 
                 genes, 8.3% 
                   
                 AT4G17260|AT3G11840|AT5G62390| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G48090|AT4G26120|AT1G18890|AT4G30080| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G05710|AT5G51190|AT3G52400| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G17040|AT1G17750|AT1G74430| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G61900|AT3G45640|AT3G25070|AT1G07520| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G09980|AT3G28580|AT1G19220| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G61210|AT5G44610|AT3G11820| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G66070|AT3G07390|AT1G57560| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G40180|AT5G25190|AT5G49620 
               
               
                   
                 GO: 0042221 
                 response to 
                 52 out of 
                 1763 out of 
                 0.01 
                 AT2G06050|AT3G52430|AT4G17230|AT5G06720| 
               
               
                   
                   
                 chemical 
                 234 genes, 
                 12802 
                   
                 AT5G66880|AT3G59900|AT4G16780| 
               
               
                   
                   
                 stimulus 
                 22.2% 
                 genes, 
                   
                 AT1G18570|AT2G04160|AT4G17260| 
               
               
                   
                   
                   
                   
                 13.8% 
                   
                 AT1G72060|AT3G11840|AT5G62390|AT3G48090| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G26120|AT1G18890|AT4G02200| 
               
               
                   
                   
                   
                   
                   
                   
                 AT4G30080|AT5G44070|AT1G52560| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G11210|AT1G05710|AT1G09940|AT5G51190| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G52400|AT1G13340|AT1G52200| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G17040|AT1G17750|AT1G74430| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G61900|AT3G45640|AT3G25070|AT1G07520| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G09980|AT3G28580|AT1G19220| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G61210|AT5G44610|AT3G11820| 
               
               
                   
                   
                   
                   
                   
                   
                 AT5G66070|AT2G26560|AT3G07390|AT2G16500| 
               
               
                   
                   
                   
                   
                   
                   
                 AT1G57560|AT2G40180|AT4G11170| 
               
               
                   
                   
                   
                   
                   
                   
                 AT2G41380|AT5G25190|AT5G65020| 
               
               
                   
                   
                   
                   
                   
                   
                 AT3G09270|AT5G49620 
               
               
                   
                 GO: 0009814 
                 defense 
                 8 out of 234 
                 94 out of 
                 0.01 
                 AT3G48090|AT1G56510|AT1G11310|AT3G52430| 
               
               
                   
                   
                 response, 
                 genes, 3.4% 
                 12802 
                   
                 AT3G25070|AT4G11850|AT1G74710| 
               
               
                   
                   
                 incompatible 
                   
                 genes, 0.7% 
                   
                 AT1G61560 
               
               
                   
                   
                 interaction 
               
               
                   
                 GO: 0080135 
                 regulation 
                 4 out of 234 
                 17 out of 
                 0.01 
                 AT3G45640|AT3G25070|AT3G52400|AT3G11820 
               
               
                   
                   
                 of cellular 
                 genes, 1.7% 
                 12802 
               
               
                   
                   
                 response to 
                   
                 genes, 0.1% 
               
               
                   
                   
                 stress 
               
               
                   
                 GO: 0050832 
                 defense 
                 9 out of 234 
                 124 out of 
                 0.02 
                 AT2G34930|AT2G38870|AT3G52400|AT1G56510| 
               
               
                   
                   
                 response to 
                 genes, 3.8% 
                 12802 
                   
                 AT1G11310|AT3G11820|AT1G05800| 
               
               
                   
                   
                 fungus 
                   
                 genes, 1% 
                   
                 AT1G74710|AT1G61560 
               
               
                   
                 GO: 0010363 
                 regulation 
                 3 out of 234 
                 8 out of 
                 0.02 
                 AT3G25070|AT3G52400|AT3G11820 
               
               
                   
                   
                 of plant- 
                 genes, 1.3% 
                 12802 
               
               
                   
                   
                 type 
                   
                 genes, 0.1% 
               
               
                   
                   
                 hypersensitive 
               
               
                   
                   
                 response 
               
               
                   
                 GO: 0009620 
                 response to 
                 10 out of 
                 159 out of 
                 0.02 
                 AT2G06050|AT2G34930|AT2G38870|AT3G52400| 
               
               
                   
                   
                 fungus 
                 234 genes, 
                 12802 
                   
                 AT1G56510|AT1G11310|AT3G11820| 
               
               
                   
                   
                   
                 4.3% 
                 genes, 1.2% 
                   
                 AT1G05800|AT1G74710|AT1G61560 
               
               
                   
                 GO: 0006915 
                 apoptosis 
                 9 out of 234 
                 134 out of 
                 0.03 
                 AT5G22690|AT5G04720|AT2G16870|AT4G23440| 
               
               
                   
                   
                   
                 genes, 3.8% 
                 12802 
                   
                 AT1G66090|AT5G41550|AT5G58120| 
               
               
                   
                   
                   
                   
                 genes, 1% 
                   
                 AT4G33300|AT1G15890 
               
               
                   
                 GO: 0009863 
                 salicylic 
                 4 out of 234 
                 26 out of 
                 0.04 
                 AT3G52400|AT3G11820|AT3G48090|AT3G52430 
               
               
                   
                   
                 acid 
                 genes, 1.7% 
                 12802 
               
               
                   
                   
                 mediated 
                   
                 genes, 0.2% 
               
               
                   
                   
                 signaling 
               
               
                   
                   
                 pathway 
               
               
                   
                 GO: 0010200 
                 response to 
                 8 out of 234 
                 116 out of 
                 0.04 
                 AT3G45640|AT2G17040|AT3G11840|AT1G07520| 
               
               
                   
                   
                 chitin 
                 genes, 3.4% 
                 12802 
                   
                 AT5G51190|AT4G26120|AT5G66070| 
               
               
                   
                   
                   
                   
                 genes, 0.9% 
                   
                 AT4G17230 
               
               
                   
                 GO: 0051245 
                 negative 
                 2 out of 234 
                 2 out of 
                 0.04 
                 AT3G11820|AT3G52400 
               
               
                   
                   
                 regulation 
                 genes, 0.9% 
                 12802 
               
               
                   
                   
                 of cellular 
                   
                 genes, 0% 
               
               
                   
                   
                 defense 
               
               
                   
                   
                 response 
               
               
                   
                 GO: 0071446 
                 cellular 
                 4 out of 234 
                 26 out of 
                 0.04 
                 AT3G52400|AT3G11820|AT3G48090|AT3G52430 
               
               
                   
                   
                 response to 
                 genes, 1.7% 
                 12802 
               
               
                   
                   
                 salicylic 
                   
                 genes, 0.2% 
               
               
                   
                   
                 acid 
               
               
                   
                   
                 stimulus 
               
               
                   
                 GO: 0031408 
                 oxylipin 
                 4 out of 234 
                 27 out of 
                 0.05 
                 AT2G06050|AT1G05800|AT2G26560|AT1G20510 
               
               
                   
                   
                 biosynthetic 
                 genes, 1.7% 
                 12802 
               
               
                   
                   
                 process 
                   
                 genes, 0.2% 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 22 
               
             
            
               
                   
               
               
                 bZIP1 primary targets in the N-assimilation pathway.  
               
            
           
           
               
               
               
               
            
               
                   
                 Gene 
                 Pathway role 
                 bZIP1 target class 
               
               
                   
                   
               
               
                   
                 At2g26690 
                 Nitrate Transporter  
                 Class I 
               
               
                   
                 At5g07440 
                 GDH  
                 Class IIA 
               
               
                   
                 At1g08090 
                 Nitrate Transporter  
                 ClassIIIA 
               
               
                   
                 At3g45060 
                 Nitrate Transporter  
                 ClassIIIA 
               
               
                   
                 At5g18170 
                 GDH  
                 ClassIIIA 
               
               
                   
                 At3g16150 
                 Asparaginase  
                 ClassIIIA 
               
               
                   
                 At5g11520 
                 ASP  
                 ClassIIIA 
               
               
                   
                 At5g50200 
                 Nitrate Transporter  
                 ClassIIIA 
               
               
                   
                   
               
            
           
         
       
     
     Lastly, Class III transient target genes are uniquely enriched in genes that respond early and transiently to the N-signal in planta ( FIG. 29C ). While all three classes of bZIP1 target genes have significant intersections with N-regulated genes in planta (p-val&lt;0.001) (Krouk et al., 2010, Genome Biology 11(12):R123; Gutierrez et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105:4939-4944; Wang et al., 2003, Plant Physiol. 132(2):556-567; Wang et al., 2004, Plant physiology 136(1):2512-2522) ( FIG. 29C , “Union” of N-response genes in planta), only Class IIIA transient targets have a significant overlap with genes induced transiently or early in response to a N-signal (within 3-6 minutes) (p-val&lt;0.001), based on fine-scale kinetic studies of N-treatments performed in planta (Krouk et al., 2010, Genome Biology 11(12):R123) ( FIG. 29C ; Table 23). These transient bZIP1 targets include known early N-responders, such as the transcription factors LBD38 (At3g49940) and LBD39 (At4g37540), which respond to N-signals in as early as 3-6 min (Krouk et al., 2010, Genome Biology 11(12):R123), and are involved in regulating N-uptake and assimilation genes in planta (Rubin et al., 2009, The Plant Cell 21(11):3567-3584). Additionally, Class IIIA transient targets are uniquely enriched in rapid N-responders ( FIG. 29C ; Table 23), identified as genes induced within 20 min after a supply of 250 uM nitrate to roots (Wang et al., 2003, Plant Physiol. 132(2):556-567), including the nitrate transporters, NRT3.1 and NRT2.1. This result further supports the notion that the Class IIIA transient bZIP1 targets are specifically relevant to a rapid N-signaling response in planta. 
     
       
         
           
               
             
               
                 TABLE 23 
               
               
                   
               
               
                 Class IIIA bZIP1 primary targets that transiently and rapidly up-regulated by N. 
               
               
                   
               
             
            
               
                 A. The 15 genes that are (1) ClassIIIA, i.e. no binding but activated and (2) transiently upregulated by N (Krouk 
               
               
                 et al., 2010). 
               
            
           
           
               
               
            
               
                 At1g08090 
                 ACH1, ATNRT2.1, ATNRT2:1, LIN1, NRT2, NRT2.1, NRT2:1, NRT2; 1AT, nitrate transporter 2:1 
               
               
                 At5g57655 
                 xylose isomerase family protein 
               
               
                 At3g14050 
                 AT-RSH2, ATRSH2, RSH2, RELA/SPOT homolog 2 
               
               
                 At3g28510 
                 P-loop containing nucleoside triphosphate hydrolases superfamily protein 
               
               
                 At1g15380 
                 Lactoylglutathione lyase/glyoxalase I family protein 
               
               
                 At5g56870 
                 BGAL4, beta-galactosidase 4 
               
               
                 At1g73260 
                 ATKTI1, KTI1, kunitz trypsin inhibitor 1 
               
               
                 At2g43400 
                 ETFQO, electron-transfer flavoprotein: ubiquinone oxidoreductase 
               
               
                 At1g80460 
                 GLI1, NHO1, Actin-like ATPase superfamily protein 
               
               
                 At1g22400 
                 ATUGT85A1, UGT85A1, UDP-Glycosyltransferase superfamily protein 
               
               
                 At4g38490 
                 unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae-12; Bacteria- 
               
               
                   
                 1396; Metazoa-17338; Fungi-3422; Plants-5037; Viruses-0; Other Eukaryotes-2996 (source:  
               
               
                   
                 NCBI BLink). 
               
               
                 At5g65110 
                 ACX2, ATACX2, acyl-CoA oxidase 2 
               
               
                 At5g04310 
                 Pectin lyase-like superfamily protein 
               
               
                 At3g16150 
                 N-terminal nucleophile aminohydrolases (Ntn hydrolases) superfamily protein 
               
               
                 At4g13430 
                 ATLEUC1, IIL1 isopropyl malate isomerase large subunit 1 
               
            
           
           
               
            
               
                 B. The 9 genes that are (1) ClassIIIA, i.e. no binding but activated and (2) rapidly (3-6 min) upregulated by N  
               
               
                 (Krouk et al., 2010). 
               
            
           
           
               
               
            
               
                 At3g49940 
                 LBD38, LOB domain-containing protein 38 
               
               
                 At5g10210 
                 CONTAINS InterPro DOMAIN/s: C2 calcium-dependent membrane targeting 
               
               
                   
                 (InterPro: IPR000008); BEST  Arabidopsis   thaliana  protein match is: unknown protein 
               
               
                   
                 (TAIR: AT5G65030.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae-0; Bacteria-0;  
               
               
                   
                 Metazoa-736; Fungi-347; Plants-385; Viruses-0; Other Eukaryotes-339 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At2g43400 
                 ETFQO, electron-transfer flavoprotein: ubiquinone oxidoreductase 
               
               
                 At1g22400 
                 ATUGT85A1, UGT85A1, UDP-Glycosyltransferase superfamily protein 
               
               
                 At4g38490 
                 unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae-12; Bacteria- 
               
               
                   
                 1396; Metazoa-17338; Fungi-3422; Plants-5037; Viruses-0; Other Eukaryotes-2996 (source:  
               
               
                   
                 NCBI BLink). 
               
               
                 At4g37540 
                 LBD39, LOB domain-containing protein 39 
               
               
                 At5g65110 
                 ACX2, ATACX2, acyl-CoA oxidase 2 
               
               
                 At5g04310 
                 Pectin lyase-like superfamily protein 
               
               
                 At4g39780 
                 Integrase-type DNA-binding superfamily protein 
               
            
           
           
               
            
               
                 C. The 37 genes that are (1) ClassIIIA, i.e. no binding but activated and (2) early responder (20 min) upregulated  
               
               
                 by N (Wang et al. 2003) 
               
            
           
           
               
               
            
               
                 At5g28610 
                 BEST  Arabidopsis   thaliana  protein match is: glycine-rich protein (TAIR: AT5G28630.1); Has 1536 
               
               
                   
                 Blast hits to 1202 proteins in 136 species: Archae-0; Bacteria-8; Metazoa-888; Fungi-120; 
               
               
                   
                 Plants-71; Viruses-39; Other Eukaryotes-410 (source: NCBI BLink). 
               
               
                 At5g50200 
                 ATNRT3.1, NRT3.1, WR3, nitrate transmembrane transporters 
               
               
                 At3g11410 
                 AHG3, ATPP2CA, PP2CA, protein phosphatase 2CA 
               
               
                 At5g46590 
                 anac096, NAC096, NAC domain containing protein 96 
               
               
                 At3g49940 
                 LBD38, LOB domain-containing protein 38 
               
               
                 At1g14340 
                 RNA-binding (RRM/RBD/RNP motifs) family protein 
               
               
                 At3g60690 
                 SAUR-like auxin-responsive protein family 
               
               
                 At1g71980 
                 Protease-associated (PA) RING/U-box zinc finger family protein 
               
               
                 At5g37260 
                 CIR1, RVE2, Homeodomain-like superfamily protein 
               
               
                 At1g23870 
                 ATTPS9, TPS9, TPS9, trehalose-phosphatase/synthase 9 
               
               
                 At4g18340 
                 Glycosyl hydrolase superfamily protein 
               
               
                 At4g03510 
                 ATRMA1, RMA1, RING membrane-anchor 1 
               
               
                 At1g08090 
                 ACH1, ATNRT2.1, ATNRT2:1, LIN1, NRT2, NRT2.1, NRT2:1, NRT2; 1AT, nitrate transporter 2:1 
               
               
                 At3g53150 
                 UGT73D1, UDP-glucosyl transferase 73D1 
               
               
                 At5g13750 
                 ZIFL1, zinc induced facilitator-like 1 
               
               
                 At5g67440 
                 NPY3, Phototropic-responsive NPH3 family protein 
               
               
                 At4g36670 
                 Major facilitator superfamily protein 
               
               
                 At5g20885 
                 RING/U-box superfamily protein 
               
               
                 At4g32950 
                 Protein phosphatase 2C family protein 
               
               
                 At4g32960 
                 unknown protein; BEST  Arabidopsis   thaliana  protein match is: unknown protein 
               
               
                   
                 (TAIR: AT4G32970.1); Has 106 Blast hits to 106 proteins in 39 species: Archae-0; Bacteria-0;  
               
               
                   
                 Metazoa-62; Fungi-0; Plants-37; Viruses-0; Other Eukaryotes-7 (source: NCBI BLink). 
               
               
                 At5g13110 
                 G6PD2, glucose-6-phosphate dehydrogenase 2 
               
               
                 At1g61740 
                 Sulfite exporter TauE/SafE family protein 
               
               
                 At4g29950 
                 Ypt/Rab-GAP domain of gyp1p superfamily protein 
               
               
                 At5g47740 
                 Adenine nucleotide alpha hydrolases-like superfamily protein 
               
               
                 At2g46270 
                 GBF3, G-box binding factor 3 
               
               
                 At5g10210 
                 CONTAINS InterPro DOMAIN/s: C2 calcium-dependent membrane targeting 
               
               
                   
                 (InterPro: IPR000008); BEST  Arabidopsis   thaliana  protein match is: unknown protein 
               
               
                   
                 (TAIR: AT5G65030.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae-0; Bacteria-0;  
               
               
                   
                 Metazoa-736; Fung-347; Plants-385; Viruses-0; Other Eukaryotes-339 (source: NCBI 
               
               
                   
                 BLink). 
               
               
                 At5g47560 
                 ATSDAT, ATTDT, TDT, tonoplast dicalboxylate transporter 
               
               
                 At3g16150 
                 N-terminal nucleophile aminohydrolases (Ntn hydrolases) superfamily protein 
               
               
                 At4g38340 
                 NLP3; Plant regulator RWP-RK family protein 
               
               
                 At4g39780 
                 Integrase-type DNA-binding superfamily protein 
               
               
                 At3g15650 
                 alpha/beta-Hydrolases superfamily protein 
               
               
                 At3g24520 
                 AT-HSFC1, HSFC1, heat shock transcription factor C1 
               
               
                 At4g38470 
                 ACT-like protein tyrosine kinase family protein 
               
               
                 At1g15380 
                 Lactoylglutathione lyase/glyoxalase I family protein 
               
               
                 At4g37540 
                 LBD39, LOB domain-containing protein 39 
               
               
                 At1g61660 
                 basic helix-loop-helix (bHLH) DNA-binding superfamily protein 
               
               
                 At3g05200 
                 ATL6, RING/U-box superfamily protein 
               
               
                   
               
            
           
         
       
     
     A transient mode of bZIP1 action invokes a “hit-and-run” model for N-signaling. The significant enrichment of N-relevant genes in Class III targets, links the transient mode-of-action of bZIP1 with early and transient aspects of N-nutrient signaling ( FIG. 29C  &amp; D). This transient mode-of-action could allow a small number of bZIP1 molecules to initiate and catalyze a large response to an N-signal in the GRN within minutes, without having to wait for a significant buildup of the bZIP1 protein. Two unique properties of Class III “transient” targets support this hypothesis. First, pioneer TFs have been shown to facilitate and/or initiate gene expression (Ni et al., 2009, Gene Dev 23(11):1351-1363; Magnani et al., 2011, Trends Genet 27(11):465-474). Accordingly, bZIP1 binding to the promoter of Class III transient targets should be detected at very early time-points after DEX-induced nuclear localization of the GR-bZIP1 fusion protein (e.g. within minutes). Second, cis-motif analysis of target genes of a pioneer TF in  Drosophila  highlighted the specific enrichment of other TF binding motifs in close proximity to the pioneer TF motif (Satij a et al., 2012, Genome Res 22(4):656-665), suggesting either active recruitment or passive enabling of binding by additional TF partners. By this model, the promoters of Class III transient bZIP1 targets should show specific enrichment for binding sites of other TFs in addition to bZIP1. Indeed, we find bZIP1 shares both of these properties, as detailed below. 
     To experimentally determine if any of the Class III transient targets are bound by bZIP1 at very early time-points, ChIP-Seq analysis was performed on four additional time-points after the DEX-induced nuclear import of bZIP1. 41 genes were revealed from Class III transient targets that have detectable bZIP1 binding at one or more of the earlier time-points (1, 5, 30, 60 min) ( FIG. 29D ; Table 20), but are not bound by bZIP1 at the 5 hour time point of our original study ( FIG. 29A ). Crucially, these 41 transiently bound bZIP1 targets are significantly enriched in GO-terms related to the N-signal (e.g. amino acid metabolism, p&lt;0.05). The validated bZIP1 binding site (hybrid “ACGT” motif) (Baena-Gonzalez et al., 2007, Nature 448:938; Kang et al., 2010, Molecular Plant 3:361-373; Dietrich et al., 2011, The Plant Cell 23:381-395) is enriched in the promoters of these 41 genes (E=2.7e−3), as well as in the remaining Class III transient targets (E=1e−26). These transiently bound bZIP1 targets include NLP3, a key early regulator of nitrate signaling in plants (Konishi et al., 2013, Nature Communications 4: 1617). In this study, NLP3 is bound by bZIP1 at very early time-points (1 and 5 min), but not at the later points (30 and 60 min) following TF perturbation ( FIG. 29D ). Similarly, the promoter of an early response gene encoding the high-affinity nitrate transporter NRT2.1 (Krouk et al., 2010, Genome Biology 11(12):R123, is bound by bZIP1 as early as 1 and 5 min after the DEX-induced nuclear import of bZIP1, but binding is weakened at 30 min and disappears at 60 min ( FIG. 29D ). In summary, this time-course analysis provides physical evidence that some Class III targets are indeed transiently bound to bZIP1, only at very early time-points after bZIP1 nuclear import (1-5 min). We note that such transient TF-binding is difficult to capture, unless multiple early time-points are designed for ChIP-seq study. However, the cell-based TARGET system can identify primary targets based on the outcome of TF-binding (e.g. TF-induced gene regulation), even if TF binding is highly transient (e.g. within seconds), or is never bound stably enough to be detected at any time-point. 
     Finally, the hypothesis that bZIP1 acts as a “pioneer/catalyst” TF in N-signal propagation through a GRN, is further supported by cis-motif analysis. Specifically, the promoters of Class III “transient” bZIP1 target genes contained the largest number and most significant enrichment of cis-regulatory motifs, in addition to bZIP1-binding sites ( FIG. 30 ). In particular, the Class IIIA transient activated genes contain the most significant enrichment of the known bZIP1 binding site (E=1.3e−52), and are specifically enriched in co-inherited cis-elements that belong to the bZIP, MYB, and GATA families (Yilmaz et al., 2011, Nucleic Acids Research 39:D1118-1122) ( FIG. 30 ). These results support the hypothesis that bZIP1 is a pioneer TF that interacts and/or recruits other TFs, including other bZIPs and/or MYB/GATA binding factors, to temporally co-regulate target genes in response to a N-signal ( FIG. 34 ). Indeed, bZIP1 has been reported to interact with other TFs in vitro (Ehlert et al., 2006, Plant J 46(5):890-900). (Table 24) and in vivo (Ehlert et al., 2006, Plant J 46(5):890-900; (Baena-Gonzalez et al., 2007, Nature 448:938; Kang et al., 2010, Molecular Plant 3:361-373). This list of bZIP1 interactors includes bZIP25, a gene in the Class III transient bZIP1 primary targets. In support of a collaborative relationship between bZIP1 and the GATA family TFs in mediating the N-response, one GATA TF was reported to be nitrate-inducible and involved in regulating energy metabolism, thus serving as a functional analog to bZIP1 (Bi et al., 2005, Plant Journal 44(4):680-692). Taken together, the transient binding of bZIP1 and enrichment of co-inherited binding sites for additional TFs specifically in Class III transient bZIP1 targets, supports a role for bZIP1 as a TF “pioneer/catalyst” (Satij a et al., 2012, Genome Res 22(4):656-665) and a model for “hit-and-run” transcription (Schaffner, 1988, Nature 336:427-428), as depicted in  FIG. 34  and discussed below. 
     
       
         
           
               
             
               
                 TABLE 24 
               
               
                   
               
               
                 bZIP1 protein-protein interaction partners. 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                 At5g37780 
                 ACAM-1, CAM1, TCH1, calmodulin 1 
               
               
                 At1g66410 
                 ACAM-4, CAM4, calmodulin 4 
               
               
                 At5g21274 
                 ACAM-6, CAM6, calmodulin 6 
               
               
                 At2g41100 
                 ATCAL4, TCH3, Calcium-binding EF hand family protein 
               
               
                 At3g51920 
                 ATCML9, CAM9, CML9, calmodulin 9 
               
               
                 At2g41090 
                 Calcium-binding EF-hand family protein 
               
               
                 At3g43810 
                 CAM7, calmodulin 7 
               
               
                 At4g14640 
                 CAM8, calmodulin 8 
               
               
                 At5g41910 
                 MED10A, Mediator complex, subunit Med10 
               
               
                 At4g34590 
                 ATB2, AtbZIP11, BZIP11, GBF6, G-box binding factor 6 
               
               
                 At5g49450 
                 AtbZIP1, bZIP1, basic leucine-zipper 1 
               
               
                 At4g02640 
                 ATBZIP10, BZO2H1, bZIP transcription factor family  
               
               
                   
                 protein 
               
               
                 At2g18160 
                 ATBZIP2, bZIP2, GBF5, basic leucine-zipper 2 
               
               
                 At3g54620 
                 ATBZIP25, BZIP25, BZO2H4, basic leucine zipper 25 
               
               
                 At1g59530 
                 ATBZIP4, bZIP4, basic leucine-zipper 4 
               
               
                 At3g30530 
                 ATBZIP42, bZIP42, basic leucine-zipper 42 
               
               
                 At1g75390 
                 AtbZIP44, bZIP44, basic leucine-zipper 44 
               
               
                 At3g62420 
                 ATBZIP53, BZIP53, basic region/leucine zipper motif 53 
               
               
                 At1g13600 
                 AtbZIP58, bZIP58, basic leucine-zipper 58 
               
               
                 At5g28770 
                 AtbZIP63, BZO2H3, bZIP transcription factor family  
               
               
                   
                 protein 
               
               
                 At5g24800 
                 ATBZIP9, BZIP9, BZO2H2, basic leucine zipper 9 
               
               
                   
               
            
           
         
       
     
     10.4. Discussion 
     The discovery of a large and typically overlooked class of transient primary targets of the master TF bZIP1, disclosed herein, introduces a novel perspective in the general field of dynamic GRNs. Dynamic TF-target binding studies across eukaryotes have captured many transient TF-targets (Ni et al., 2009,  Gene Dev  23(11):1351-1363; Chang et al., 2013,  Elife  2:e00675). However, even those fine-scale time-series ChIP studies likely miss highly temporal connections, as they require biochemically detectable TF binding in at least one time-point to identify primary TF targets. Key to the discovery of the transient targets of bZIP1 involved in rapid N-signaling, disclosed herein, is the ability to identify primary targets based on TF-induced changes in mRNA that can occur even in the absence of detectable TF binding. The cell-based system also enabled the detection of rapid and transient binding within 1 minute of TF nuclear import, owing to rapid fixation of protein-DNA complexes in plant cells lacking a cell wall. Importantly, the in planta relevance of the cell-based TARGET studies disclosed herein ( FIG. 29A ), confirms and complements data from bZIP1 T-DNA mutants and transgenic plants (Kang et al., 2010, Molecular Plant 3:361-373) ( FIG. 29B ), which are unable to distinguish primary from secondary targets, or capture transient TF-target interactions. Therefore, the transient interactions between bZIP1 and its targets uncovered in the cell-based TARGET system disclosed herein help to refine an understanding of the in planta mechanism of bZIP1. 
     The discovery of these transient TF targets, disclosed herein, adds a new perspective to the field of dynamic GRNs. Recent time-series studies in yeast by Lickwar et. al. reported transitive TF-target binding described as a “tread-milling” mechanism, in which a TF exhibits weak and transitive binding to some of its targets, resulting in a lower level of gene activation (Lickwar et al., 2012, Nature 484(7393):251-255). The transient bZIP1 targets detected in this study do not fit this “tread-milling” model, since there is no significant difference between the expression fold-change distributions of for Class III “transient” targets, versus Class II “stable” targets. Instead, the transient TF-target interactions uncovered herein are conceptualized to a classic, but largely forgotten, “hit-and-run” model of transcription proposed in the 1980&#39;s (Schaffner, 1988, Nature 336:427-428) ( FIG. 34 ). This “hit-and-run” model posits that a TF can act as a trigger to organize a stable transcriptional complex, after which transcription by RNA polymerase II can continue without the TF being bound to the DNA (Schaffner, 1988, Nature 336:427-428). 
     In support of this “hit-and-run” transcription model, Class III “transient” targets include genes that are rapidly and transiently bound by bZIP1 at very early time-points (1-5 min) after TF nuclear import, and whose level of expression is maintained at a higher level, despite being no longer bound by bZIP1 at later time-points. Continued regulation of the bZIP1 targets (after bZIP1 is no longer bound) might be mediated by other TF partners recruited by the “trigger/pioneer” TF ( FIG. 34 ). This model is supported by the enrichment of cis-motifs co-inherited with the known bZIP1 binding motif (Baena-Gonzalez et al., 2007, Nature 448:938; Kang et al., 2010, Molecular Plant 3:361-373; Dietrich et al., 2011, The Plant Cell 23:381-395) in the Class III transient targets ( FIG. 30 ). This finding also supports other explanatory models for “continuous” TF networks (Biggin M D, 2011, Dev Cell 21(4):611-626; Walhout A J M, 2011, Genome Biol 12(4); Lickwar et al., 2012, Nature 484(7393):251-255), which converge on the idea that TF-binding data alone is insufficient to fully characterize regulatory networks, and that other factors (including chromatin and other TFs) may influence the action of a master TF. In this transient mode-of-action, bZIP1 can activate genes in response to a N-signal (“the hit”), while the transient nature of the TF-target association (“the run”), enables bZIP1 to act as a TF “catalyst” to rapidly induce a large set of genes needed for the N-response. In support of this “catalytic” TF model, the global targets of bZIP1 N-signaling are broad, covering 32% of the directly regulated targets of NLP7 related to the N-signal, a well-studied master regulator of the N-response (Marchive et al., 2013, Nature Communications 4). Importantly, the Class III transient bZIP1 targets play a unique role in mediating a rapid, early, and biologically relevant response to the N-signal in planta. This “hit-and-run” model, supported by our results for bZIP1, could represent a general mechanism for the deployment of an acute response to nutrient sensing, as well as other signals. 
     Importantly, these results have significance beyond bZIP1, N-signaling, and indeed transcend plants. Across eukaryotes, TFs are found to bind only to a small percentage of their regulated targets, as shown in plants (Monke et al., 2012, Nucleic Acids Research 40:82401; Arenhart et al., 2014, Molecular plant 7(4):709-721; Bolduc et al., 2012, Gene Dev 26(15):1685-1690), yeast (Hughes et al., 2013, Genetics 195(1):9-36) and animals (Gorski et al., 2011, Nucleic Acids Research 39:9536; Bianco et al., 2014, Cancer research 74(7):2015-2025). The large number of TF-regulated but unbound genes, including the false negatives of ChIP-seq (Chen et al., 2012, Nat Methods 9(6):609), must be dismissed as putative secondary targets in approaches that can only identify primary targets based on TF-DNA binding. Instead, it is shown herein that these typically dismissed targets, which can be identified as primary TF targets by a functional read-out in this cell-based TARGET approach (e.g. TF-induced regulation), are crucial for rapid and dynamic signal propagation, thus uncovering the “dark matter” of signal transduction that has been missed. More broadly, the approach described herein is applicable across eukaryotes, and can also be adapted to studying cell-specific GRNs, by using GFP-marked cell lines in the assay (Birnbaum K, et al., 2003, Science 302(5652):1956-1960). Moreover, this approach can identify primary targets even in cases where TF binding can never be physically detected. The transient targets thus uncovered, will reveal the elusive temporal interactions that mediate rapid and dynamic responses of GRNs to external signals. 
     11. EXAMPLE 6 
     As described herein, using the cell-based TARGET system, a novel class of transient TF targets that are directly regulated by the bZIP1 TF, but not detectably bound by it were identified. This class of transient targets (Class III) suggests a “hit-and-run” mode-of-action for bZIP1, where bZIP1 “hits” its target, initiates transcription, then dissociates (“run”), leaving the transcription going on even without bZIP1 binding to the promoter. 
     To test the hypothesis that transcription of a gene initiated by “the Hit” continues after “the Run,” an affinity-tagged UTP was used to label and capture newly synthesized mRNA. By adding this label at a time-point when the TF is not detectably bound, it can be determined whether a gene is still actively transcribed. Briefly, biosynthetic tagging of newly synthesized RNA performed using 4-thiouracil and uracil phosphoribosyltransferase (referred to as “4sU tagging” hereinafter) (Sidaway-Lee et al., 2014, Genome Biology 15 (3): R45; Zeiner et al., 2008, Methods in Molecular Biology 419: 135-46), was adapted for the cell based TARGET system in plants (Bargmann et al., 2013, Molecular Plant 6(3):978). Technically, 4sU is fed to plant protoplasts and incorporated into newly synthesized RNA. After that, total RNA is extracted from the protoplasts, and the newly synthesized RNA that is tagged with 4sU is isolated from the total RNA through biotinylation and Streptavidin magnetic beads. Next, the RNA is purified and used for transcriptomics profiling. The 4sU tagged RNA represents only the newly transcribed genes. 
     4sU tagged RNA can be detected as early as in 20 min after feeding 4sU to isolated protoplasts ( FIG. 35 ). Using this technique, it was shown here that Class III “transient” genes have incorporated UTP label. These transient bZIP1 target genes that are activated (Class IIIA: 121 genes) or repressed (Class IIIB 42 genes). These genes are actively transcribed by bZIP1, even when bZIP1 is not bound to these targets ( FIG. 29B ; Table 25). These bZIP1 transient targets include the NIN-like protein 3 (NLP3; At4g38340), bound by bZIP1 at 1-5 min after the nuclear import of bZIP1 ( FIG. 35C ), but no longer bound by bZIP1 at 20 min, 1 hr, or 5 hr after the nuclear import of bZIP1 ( FIG. 35C ). These 4sU RNA tagging results show that NLP3 is actively transcribed at a higher rate in the cells that express bZIP1, even when bZIP1 does not bind to the NLP3 promoter (i.e. 5 hr after the nuclear import of bZIP1) ( FIG. 35 ). The control in  FIG. 35D  is empty vector. This provides evidence for the “hit-and-run” model, which posit that bZIP1 can “hit” the target genes, and dissociate (“run”), while the induced transcription of target genes by bZIP1 can carry on even after the dissociation of bZIP1. 
     
       
         
           
               
             
               
                 TABLE 25 
               
               
                   
               
               
                 Transient targets that are actively transcribed due to bZIP1 as validated by 4sU tagging. 
               
               
                   
               
             
            
               
                 A. bZIP1 Class IIIA transient targets that are transcribed higher (FC &gt; 2) in the bZIP1 over-expressed cells  
               
               
                 compared to empty vector controls 5 hr after the bZIP1 nuclear import  
               
            
           
           
               
               
            
               
                 Gene ID 
                 Tair 10 annotation 
               
               
                   
               
               
                 At5g06980 
                 unknown protein; BEST  Arabidopsis   thaliana  protein match is: unknown protein  
               
               
                   
                 (TAIR: AT3G12320.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae-12;  
               
               
                   
                 Bacteria-1396; Metazoa-17338; Fungi-3422; Plants-5037; Viruses-0; Other Eukaryotes-2996  
               
               
                   
                 (source: NCBI BLink).  
               
               
                 At4g30170 
                 Peroxidase family protein  
               
               
                 At3g27690 
                 LHCB2, LHCB2.3, LHCB2.4, photosystem II light harvesting complex gene 2.3  
               
               
                 At3g14780 
                 CONTAINS InterPro DOMAIN/s: Transposase, Ptta/En/Spm, plant (InterPro: IPR004252); BEST  
               
               
                   
                   Arabidopsis   thaliana  protein match is: glucan synthase-like 4 (TAIR: AT3G14570.2); Has 315  
               
               
                   
                 Blast hits to 313 proteins in 50 species: Archae-2; Bacteria-16; Metazoa-11; Fungi-7; Plants-181;  
               
               
                   
                 Viruses-2; Other Eukaryotes-96 (source: NCBI BLink).  
               
               
                 At1g30820 
                 CTP synthase family protein  
               
               
                 At2g30600 
                 BTB/POZ domain-containing protein  
               
               
                 At2g19320 
                 unknown protein; Has 9 Blast hits to 9 proteins in 4 species: Archae-0; Bacteria-0; Metazoa-0;  
               
               
                   
                 Fungi-0; Plants-9; Viruses-0; Other Eukaryotes-0 (source: NCBI BLink).  
               
               
                 At1g04410 
                 Lactate/malate dehydrogenase family protein  
               
               
                 At5g65110 
                 ACX2, ATACX2, acyl-CoA oxidase 2  
               
               
                 At4g18340 
                 Glycosyl hydrolase superfamily protein  
               
               
                 At4g03510 
                 ATRMA1, RMA1, RING membrane-anchor 1  
               
               
                 At2g19800 
                 MIOX2, myo-inositol oxygenase 2  
               
               
                 At3g51730 
                 saposin B domain-containing protein  
               
               
                 At1g56700 
                 Peptidase C15, pyroglutamyl peptidase I-like  
               
               
                 At2g33150 
                 KAT2, PED1, PKT3, peroxisomal 3-ketoacyl-CoA thiolase 3  
               
               
                 At1g67810 
                 SUFE2, sulfur E2  
               
               
                 At5g67440 
                 NPY3, Phototropic-responsive NPH3 family protein  
               
               
                 At5g16110 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN:  
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast; EXPRESSED IN: 24 plant structures;  
               
               
                   
                 EXPRESSED DURING: 15 growth stages; BEST  Arabidopsis   thaliana  protein match is: unknown  
               
               
                   
                 protein (TAIR: AT3G02555.1); Has 133 Blast hits to 133 proteins in 18 species: Archae-0;  
               
               
                   
                 Bacteria-0; Metazoa-0; Fungi-0; Plants-133; Viruses-0; Other Eukaryotes-0 (source: NCBI  
               
               
                   
                 BLink).  
               
               
                 At1g75220 
                 Major facilitator superfamily protein  
               
               
                 At1g30900 
                 BP80-3; 3, VSR3; 3, VSR6, VACUOLAR SORTING RECEPTOR 6  
               
               
                 At1g66890 
                 FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown;  
               
               
                   
                 LOCATED IN: chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13  
               
               
                   
                 growth stages; BEST  Arabidopsis   thaliana  protein match is: 50S ribosomal protein-related  
               
               
                   
                 (TAIR: AT5G16200.1); Has 36 Blast hits to 36 proteins in 7 species: Archae-0; Bacteria-0;  
               
               
                   
                 Metazoa-0; Fungi-0; Plants-36; Viruses-0; Other Eukaryotes-0 (source: NCBI BLink).  
               
               
                 At3g49060 
                 U-box domain-containing protein kinase family protein  
               
               
                 At3g16800 
                 Protein phosphatase 2C family protein  
               
               
                 At1g61740 
                 Sulfite exporter TauE/SafE family protein  
               
               
                 At5g13740 
                 ZIF1, zinc induced facilitator 1  
               
               
                 At5g43430 
                 ETFBETA, electron transfer flavoprotein beta  
               
               
                 At4g21440 
                 ATM4, ATMYB102, MYB102, MYB102, MYB-like 102  
               
               
                 At1g55020 
                 ATLOX1, LOX1, lipoxygenase 1  
               
               
                 At5g19090 
                 Heavy metal transport/detoxification superfamily protein  
               
               
                 At1g64010 
                 Serine protease inhibitor (SERPIN) family protein  
               
               
                 At5g10210 
                 CONTAINS InterPro DOMAIN/s: C2 calcium-dependent membrane targeting  
               
               
                   
                 (InterPro:IPR000008); BEST  Arabidopsis   thaliana  protein match is: unknown protein  
               
               
                   
                 (TAIR: AT5G65030.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae-0; Bacteria-0;  
               
               
                   
                 Metazoa-736; Fungi-347; Plants-385; Viruses-0; Other Eukaryotes-339 (source: NCBI  
               
               
                   
                 BLink).  
               
               
                 At1g75800 
                 Pathogenesis-related thaumatin superfamily protein  
               
               
                 At5g07080 
                 HXXXD-type acyl-transferase family protein  
               
               
                 At1g61810 
                 BGLU45, beta-glucosidase 45  
               
               
                 At1g67880 
                 beta-1,4-N-acetylglucosaminyltransferase family protein  
               
               
                 At5g03720 
                 AT-HSFA3, HSFA3, heat shock transcription factor A3  
               
               
                 At2g38820 
                 Protein of unknown function (DUF506)  
               
               
                 At1g65840 
                 ATPAO4, PAO4, polyamine oxidase 4  
               
               
                 At1g08630 
                 THA1, threonine aldolase 1  
               
               
                 At5g61600 
                 ERF104, ethylene response factor 104  
               
               
                 At1g76240 
                   Arabidopsis  protein of unknown function (DUF241)  
               
               
                 At1g28130 
                 GH3.17, Auxin-responsive GH3 family protein  
               
               
                 At3g55150 
                 ATEXO70H1, EXO70H1, exocyst subunit exo70 family protein H1  
               
               
                 At3g16150 
                 N-terminal nucleophile aminohydrolases (Ntn hydrolases) superfamily protein  
               
               
                 At4g38340 
                 Plant regulator RWP-RK family protein  
               
               
                 At3g46690 
                 UDP-Glycosyltransferase superfamily protein  
               
               
                 At2g19350 
                 Eukaryotic protein of unknown function (DUF872)  
               
               
                 At1g10070 
                 ATBCAT-2, BCAT-2, branched-chain amino acid transaminase 2  
               
               
                 At3g43430 
                 RING/U-box superfamily protein  
               
               
                 At3g14770 
                 Nodulin MtN3 family protein  
               
               
                 At1g76990 
                 ACR3, ACT domain repeat 3  
               
               
                 At1g52240 
                 ATROPGEF11, PIRF1, ROPGEF11, RHO guanyl-nucleotide exchange factor 11  
               
               
                 At1g69570 
                 Dof-type zinc finger DNA-binding family protein  
               
               
                 At1g13080 
                 CYP71B2, cytochrome P450, family 71, subfamily B, polypeptide 2  
               
               
                 At1g15060 
                 Uncharacterised conserved protein UCP031088, alpha/beta hydrolase  
               
               
                 At2g14170 
                 ALDH6B2, aldehyde dehydrogenase 6B2  
               
               
                 At5g18650 
                 CHY-type/CTCHY-type/RING-type Zinc finger protein  
               
               
                 At3g20410 
                 CPK9, calmodulin-domain protein kinase 9  
               
               
                 At3g01270 
                 Pectate lyase family protein  
               
               
                 At2g10640 
                 transposable element gene  
               
               
                 At4g35780 
                 ACT-like protein tyrosine kinase family protein  
               
               
                 At3g06850 
                 BCE2, DIN3, LTA1, 2-oxoacid dehydrogenases acyltransferase family protein  
               
               
                 At5g49650 
                 XK-2, XK2, xylulose kinase-2  
               
               
                 At4g15620 
                 Uncharacterised protein family (UPF0497)  
               
               
                 At1g20340 
                 DRT112, PETE2, Cupredoxin superfamily protein  
               
               
                 At1g55510 
                 BCDH BETA1, branched-chain alpha-keto acid decarboxylase E1 beta subunit  
               
               
                 At2g39570 
                 ACT domain-containing protein  
               
               
                 At4g10840 
                 Tetratricopeptide repeat (TPR)-like superfamily protein  
               
               
                 At1g06520 
                 ATGPAT1, GPAT1, glycerol-3-phosphate acyltransferase 1  
               
               
                 At2g41190 
                 Transmembrane amino acid transporter family protein  
               
               
                 At2g43060 
                 IBH1, ILI1 binding bHLH 1  
               
               
                 At4g35770 
                 ATSEN1, DIN1, SEN1, SEN1, Rhodanese/Cell cycle control phosphatase superfamily protein  
               
               
                 At3g60690 
                 SAUR-like auxin-responsive protein family  
               
               
                 At3g14760 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN:  
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 6 plant  
               
               
                   
                 structures; EXPRESSED DURING: LP.04 four leaves visible, LP.02 two leaves visible; Has 63  
               
               
                   
                 Blast hits to 63 proteins in 13 species: Archae-0; Bacteria-0; Metazoa-0; Fungi-0; Plants-63;  
               
               
                   
                 Viruses-0; Other Eukaryotes-0 (source: NCBI BLink).  
               
               
                 At1g32460 
                 unknown protein; Has 19 Blast hits to 19 proteins in 8 species: Archae-0; Bacteria-0; Metazoa-0;  
               
               
                   
                 Fungi-0; Plants-19; Viruses-0; Other Eukaryotes-0 (source: NCBI BLink).  
               
               
                 At2g35230 
                 IKU1 IKU1, VQ motif-containing protein  
               
               
                 At1g09460 
                 Carbohydrate-binding X8 domain superfamily protein  
               
               
                 At3g57420 
                 Protein of unknown function (DUF288)  
               
               
                 At1g15050 
                 IAA34, indole-3-acetic acid inducible 34  
               
               
                 At3g61260 
                 Remorin family protein  
               
               
                 At5g57655 
                 xylose isomerase family protein  
               
               
                 At3g54960 
                 ATPDI1, ATPDIL1-3, PDI1, PDIL1-3, PDI-like 1-3  
               
               
                 At3g54620 
                 ATBZIP25, BZIP25, BZO2H4, basic leucine zipper 25  
               
               
                 At5g41610 
                 ATCHX18, CHX18, cation/H+ exchanger 18  
               
               
                 At4g33150 
                 LKR, LKR/SDH, SDH, lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional  
               
               
                   
                 enzyme  
               
               
                 At1g03870 
                 FLA9, FASCICLIN-like arabinoogalactan 9  
               
               
                 At4g32870 
                 Polyketide cyclase/dehydrase and lipid transport superfamily protein  
               
               
                 At5g01590 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN:  
               
               
                   
                 biological_process unknown; LOCATED IN: chloroplast, chloroplast envelope; EXPRESSED IN:  
               
               
                   
                 22 plant structures; EXPRESSED DURING: 13 growth stages; Has 60 Blast hits to 59 proteins in  
               
               
                   
                 31 species: Archae-0; Bacteria-20; Metazoa-1; Fungi-2; Plants-33; Viruses-0; Other  
               
               
                   
                 Eukaryotes-4 (source: NCBI BLink).  
               
               
                 At4g32950 
                 Protein phosphatase 2C family protein  
               
               
                 At4g19810 
                 Glycosyl hydrolase family protein with chitinase insertion domain  
               
               
                 At2g38400 
                 AGT3, alanine: glyoxylate aminotransferase 3  
               
               
                 At3g13965 
                 pseudogene, hypothetical protein  
               
               
                 At5g28050 
                 Cytidine/deoxycytidylate deaminase family protein  
               
               
                 At2g39980 
                 HXXXD-type acyl-transferase family protein  
               
               
                 At5g66030 
                 ATGRIP, GRIP, Golgi-localized GRIP domain-containing protein  
               
               
                 At1g06560 
                 NOL1/NOP2/sun family protein  
               
               
                 At5g20250 
                 DIN10, Raffinose synthase family protein  
               
               
                 At1g03100 
                 Pentatricopeptide repeat (PPR) superfamily protein  
               
               
                 At1g67480 
                 Galactose oxidase/kelch repeat superfamily protein  
               
               
                 At5g08350 
                 GRAM domain-containing protein/ABA-responsive protein-related  
               
               
                 At3g23230 
                 Integrase-type DNA-binding superfamily protein  
               
               
                 At5g18850 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN:  
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 23 plant  
               
               
                   
                 structures; EXPRESSED DURING: 13 growth stages; Has 1807 Blast hits to 1807 proteins in 277  
               
               
                   
                 species: Archae-0; Bacteria-0; Metazoa-736; Fungi-347; Plants-385; Viruses-0; Other  
               
               
                   
                 Eukaryotes-339 (source: NCBI BLink).  
               
               
                 At4g28040 
                 nodulin MtN21/EamA-like transporter family protein  
               
               
                 At5g04040 
                 SDP1, Patatin-like phospholipase family protein  
               
               
                 At3g30396 
                 transposable element gene  
               
               
                 At1g66550 
                 ATWRKY67, WRKY67, WRKY DNA-binding protein 67  
               
               
                 At1g79700 
                 Integrase-type DNA-binding superfamily protein  
               
               
                 At5g49360 
                 ATBXL1, BXL1, beta-xylosidase 1  
               
               
                 At4g38470 
                 ACT-like protein tyrosine kinase family protein  
               
               
                 At1g15380 
                 Lactoylglutathione lyase/glyoxalase I family protein  
               
               
                 At1g60940 
                 SNRK2-10, SNRK2.10, SRK2B, SNF 1-related protein kinase 2.10  
               
               
                 At1g48840 
                 Plant protein of unknown function (DUF639)  
               
               
                 At1g03090 
                 MCCA, methylcrotonyl-CoA carboxylase alpha chain, mitochondrial/3-methylcrotonyl-CoA  
               
               
                   
                 carboxylase 1 (MCCA)  
               
               
                 At3g19390 
                 Granulin repeat cysteine protease family protein  
               
               
                 At1g32200 
                 ACT1, ATS1, phospholipid/glycerol acyltransferase family protein  
               
               
                 At3g45300 
                 ATIVD, IVD, IVDH, isovaleryl-CoA-dehydrogenase  
               
               
                 At3g22920 
                 Cyclophilin-like peptidyl-prolyl cis-trans isomerase family protein  
               
               
                 At1g17190 
                 ATGSTU26, GSTU26, glutathione S-transferase tau 26  
               
               
                 At1g18270 
                 ketose-bisphosphate aldolase class-II family protein  
               
               
                 At4g39730 
                 Lipase/lipooxygenase, PLAT/LH2 family protein  
               
               
                 At4g14500 
                 Polyketide cyclase/dehydrase and lipid transport superfamily protein 
               
               
                   
               
            
           
           
               
            
               
                 B. bZIP1 Class IIIB transient targets that are transcribed lower (FC &lt; −2) in the bZIP1 over-expressed cells  
               
               
                 compared to empty vector controls 5 hr after the bZIP1 nuclear import  
               
            
           
           
               
               
            
               
                 Gene ID 
                 TAIR10 annotation 
               
               
                   
               
               
                 At5g13870 
                 EXGT-A4, XTH5, xyloglucan endotransglucosylase/hydrolase 5  
               
               
                 At2g17040 
                 anac036, NAC036, NAC domain containing protein 36  
               
               
                 At3g50480 
                 HR4, homolog of RPW8 4  
               
               
                 At5g60350 
                 unknown protein; Has 110 Blast hits to 97 proteins in 36 species: Archae-0; Bacteria-10;  
               
               
                   
                 Metazoa-39; Fungi-2; Plants-5; Viruses-0; Other Eukaryotes-54 (source: NCBI BLink).  
               
               
                 At2g11520 
                 CRCK3, calmodulin-binding receptor-like cytoplasmic kinase 3  
               
               
                 At4g39840 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN:  
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 23 plant  
               
               
                   
                 structures; EXPRESSED DURING: 13 growth stages; Has 20719 Blast hits to 6096 proteins in 607  
               
               
                   
                 species: Archae-22; Bacteria-3243; Metazoa-4364; Fungi-2270; Plants-237; Viruses-128;  
               
               
                   
                 Other Eukaryotes-10455 (source: NCBI BLink).  
               
               
                 At4g37400 
                 CYP81F3, cytochrome P450, family 81, subfamily F, polypeptide 3  
               
               
                 At5g56760 
                 ATSERAT1; 1, SAT-52, SAT5, SERAT1; 1, serine acetyltransferase 1; 1  
               
               
                 At5g24540 
                 BGLU31, beta glucosidase 31  
               
               
                 At3g05490 
                 RALFL22, ralf-like 22  
               
               
                 At3g18250 
                 Putative membrane lipoprotein  
               
               
                 At2g26480 
                 UGT76D1, UDP-glucosyl transferase 76D1  
               
               
                 At1g11000 
                 ATMLO4, MLO4, Seven transmembrane MLO family protein  
               
               
                 At5g43520 
                 Cysteine/Histidine-rich C1 domain family protein  
               
               
                 At4g28350 
                 Concanavalin A-like lectin protein kinase family protein  
               
               
                 At3g59900 
                 ARGOS, auxin-regulated gene involved in organ size  
               
               
                 At4g30080 
                 ARF16, auxin response factor 16  
               
               
                 At5g44610 
                 MAP18, PCAP2, microtubule-associated protein 18  
               
               
                 At1g24150 
                 ATFH4, FH4, formin homologue 4  
               
               
                 At5g41680 
                 Protein kinase superfamily protein  
               
               
                 At3g47380 
                 Plant invertase/pectin methylesterase inhibitor superfamily protein  
               
               
                 At5g24430 
                 Calcium-dependent protein kinase (CDPK) family protein  
               
               
                 At4g16780 
                 ATHB-2, ATHB2, HAT4, HB-2, homeobox protein 2  
               
               
                 At4g33960 
                 unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN:  
               
               
                   
                 biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 20 plant  
               
               
                   
                 structures; EXPRESSED DURING: 10 growth stages; BEST  Arabidopsis   thaliana  protein match is:  
               
               
                   
                 unknown protein (TAIR: AT2G15830.1); Has 32 Blast hits to 32 proteins in 4 species: Archae-0;  
               
               
                   
                 Bacteria-0; Metazoa-0; Fungi-0; Plants-32; Viruses-0; Other Eukaryotes-0 (source: NCBI  
               
               
                   
                 BLink).  
               
               
                 At4g34320 
                 Protein of unknown function (DUF677)  
               
               
                 At5g65600 
                 Concanavalin A-like lectin protein kinase family protein  
               
               
                 At3g28740 
                 CYP81D1, Cytochrome P450 superfamily protein  
               
               
                 At2g39700 
                 ATEXP4, ATEXPA4, ATHEXP ALPHA 1.6, EXPA4, expansin A4  
               
               
                 At3g20900 
                 unknown protein; Has 2 Blast hits to 2 proteins in 1 species: Archae-0; Bacteria-0; Metazoa-0;  
               
               
                   
                 Fungi-0; Plants-2; Viruses-0; Other Eukaryotes-0 (source: NCBI BLink).  
               
               
                 At3g54980 
                 Pentatricopeptide repeat (PPR) superfamily protein  
               
               
                 At1g53440 
                 Leucine-rich repeat transmembrane protein kinase  
               
               
                 At1g35200 
                 60S ribosomal protein L4/L1 (RPL4B), pseudogene, similar to 60S ribosomal protein L4 (fragment)  
               
               
                   
                 GB: P49691 from ( Arabidopsis   thaliana ); blastp match of 50% identity and 6.3e−17 P-value to  
               
               
                   
                 SP|Q9XF97|RL4_PRUAR 60S ribosomal protein L4 (L1). (Apricot) { Prunus   armeniaca } 
               
               
                 At2g43000 
                 anac042, NAC042, NA domain containing protein 42  
               
               
                 At4g15120 
                 VQ motif-containing protein  
               
               
                 At3g48090 
                 ATEDS1, EDS1, alpha/beta-Hydrolases superfamily protein  
               
               
                 At1g44100 
                 AAP5, amino acid permease 5  
               
               
                 At1g70530 
                 CRK3, cysteine-rich RLK (RECEPTOR-like protein kinase) 3  
               
               
                 At1g68150 
                 ATWRKY9, WRKY9, WRKY DNA-binding protein 9  
               
               
                 At3g02790 
                 zinc finger (C2H2 type) family protein  
               
               
                 At1g53980 
                 Ubiquitin-like superfamily protein  
               
               
                 At2g19190 
                 FRK1, FLG22-induced receptor-like kinase 1  
               
               
                 At3g29670 
                 HXXXD-type acyl-transferase family protein 
               
               
                   
               
            
           
         
       
     
     12. EXAMPLE 7 
     Transient TF-targets detected in cells help to decipher dynamic N-regulatory networks operating in planta. The transient TF-targets detected specifically in the TARGET cell-based system make a unique contribution to understanding how signal transduction occurs in planta. First, as the TARGET cell-based system detects only primary TF targets, this data enables the identification of direct TF-targets in the in planta TF perturbation data, which on its own cannot distinguish primary vs. secondary targets. Second, the network inference studies described herein for the proof-of-principle example bZIP1 predict that the transient bZIP1 targets (detected only in cells) are TF2&#39;s predicted to regulate secondary bZIP1 targets (detected only in planta) ( FIG. 36 ). In  FIG. 37  an approach called “Network Walking” is described to construct networks that link transient TF1→TF2 data from the TARGET cell-based system, with TF1 perturbation data in planta. The Network Walking approach uses N-response data from time-series, and Network Inference approaches including one called State-Space modeling, a form of Directed Factor Graph that was previously validated (Krouk et al., 2010, Genome Biology 11:R123; Krouk et al., 2013, Genome Biology 14(6):123). The TF2→target predictions can then be experimentally validated in the cell-based TARGET system, as described herein. 
     Transient TF1→T2 targets detected in TARGET cell-based system are predicted to regulate secondary targets of TF1 identified in planta. The hypothesis that “transient” targets of bZIP1 detected in the cell-based TARGET system mediate N-regulation of downstream bZIP1 targets in planta was developed by the preliminary implementation of the “Network Walking” pipeline outlined in  FIG. 37 . 
     In Step 1, to identify genes potentially involved in bZIP1-mediated N-signaling in planta, bZIP1 targets identified using the cell-based TARGET system (primary targets), described herein, were combined with bZIP1 targets identified by TF perturbation in planta (primary and secondary targets) (Kang et al., 2010, Molecular Plant 3:361), and then this union of bZIP1 targets was intersected with the list of N-regulated genes from a time-course study of N-treatments performed in planta. 
     In Step 2, TF→target connections were inferred between the bZIP1 targets identified in the cell-based TARGET system with those identified by TF perturbation in planta, using the N-treatment time-series data and the network inference approach that was previously and validated in silico and experimentally (Directed Factor Graphs) (Krouk et al., 2010, Genome Biology 11:R123) (Step 2,  FIG. 37 ). 
     The resulting network (shown in  FIG. 36 ): The 22 TF&#39;s (depicted as triangles on the inner ring) which were identified in the cell-based TARGET system, are predicted to serve as intermediate TF2&#39;s linking bZIP1 and its downstream targets (gene Z) identified in planta (Kang et al., 2010, Molecular Plant 3:361). 
     Remarkably, 18/22 of these TF2&#39;s are Class III transient targets of bZIP1 detected only in the TARGET cell-based system, described herein (Inner ring of  FIG. 37 ). As validation of their predicted role in N-signaling in planta, these transient TF2 targets of bZIP1 include TFs known to involved in N-signaling in plants (e.g. NLP3 (Konishi et al., 2013, Nature Communications 4: 1617), LBD38,39 (Rubin et al., 2009, The Plant Cell 21(11):3567-3584)). Moreover, the in planta targets of these TF2 include 7/9 N-regulated genes involved in primary assimilation of nitrate (Wang et al., 2003, Plant Physiol. 132(2):556-567). These are deemed to be secondary targets of bZIP1, as collectively they are not enriched in any of the known bZIP1 binding sites (Baena-Gonzalez et al., 2007, Nature 448:938; Kang et al., 2010, Molecular Plant 3:361; Dietrich et al., 2011, The Plant Cell 23:381-395). These lists of genes are show in Table 26. 
     This result supports the hypothesis that transient bZIP1 targets detected only in the TARGET cell-based system described herein, are intermediate effectors of secondary bZIP1 targets detected only in planta (Kang et al., 2010, Molecular Plant 3:361). This combined experimental and computational approach is called “Network Walking”, because it enables a “walk” from pioneer TF1→transient target (TF2)→effector target in planta (e.g. N-assimilation gene), as described below. 
     The general “Network Walking” Pipeline ( FIG. 37 ): 
     Step 1A: Experimental: Perturb pioneer TF1 and identify symmetric difference between cell-based targets identified in TARGET (TF 2.1-j ), and in planta targets defined by TF perturbation in planta (Z 1-j ), as well as overlap. 
     Step 1B: Computational: Infer edges in network. This will infer edges between potential “transient” targets detected in the cell-based TARGET system (TF 2.1-j ) and in planta targets (Z 1-j ) of TF1 using time-series data and network inference approaches DFG (Krouk et al., 2010, Genome Biology 11:R123), Genie3 or Inferrelator (Krouk et al., 2013, Genome Biology 14(6): 123). 
     Step 2A: Experimental: Perturb TF2 in cell-based TARGET system to validate primary TF2→gene Z edges and also identify new transient targets of TF2 (e.g. TF 3.1-j ). 
     Step 2B: Computational: Rerun network inference (e.g. DFG) using time-series data from N-treated plants, this time using a directed matrix that starts with priors defined experimentally by TF2 target data (Step 3). 
     Outcome: This combined computational/experimental pipeline will result in a validated “Network Walk” from pioneer TF1→transient TF2.1 (identified in TARGET)→target gene Z&#39;s in planta. Another outcome will be new transient TF2→TF 3i-j&#39;s  which may drive a new round of TF perturbation e.g. Step 3A, in a true systems biology cycle. Each iterative cycle of TF perturbation and network modeling, will build a new set of edges in the network out from the original TF1. The networks generated in Aim 2A will test the general hypothesis that transient targets detected only in the rapid and temporal cell based system, reveal “hidden steps” that mediate downstream responses in planta—but cannot be detected in planta. Thus, rather than merely using the in planta data to confirm TF-targets identified in the TARGET cell-based system, these network connections show that the transient targets identified in the cell-based TARGET system add to and refine our understanding of how dynamic networks operate in vivo, but whose specific connections elude detection in planta. 
     
       
         
           
               
             
               
                 TABLE 26 
               
               
                   
               
               
                 Genes in bZIP1 network 
               
               
                   
               
             
            
               
                 &gt;bZIP1_innerRing (Transient targets of bZIP1 only identified in the TARGET cell-based system) 
               
            
           
           
               
               
               
            
               
                 At4g37180 
                 Homeodomain-like superfamily protein 
                   
               
               
                 At4g17230 
                 SCL13, SCARECROW-like 13 
                   
               
               
                 At5g46590 
                 anac096, NAC096, NAC domain containing protein 96 
                   
               
               
                 At3g49940 
                 LBD38, LOB domain-containing protein 38  
                 This transcription factor has been 
               
               
                   
                   
                 associated with N-signaling in 
               
               
                   
                   
                 plants (Rubin et al., 2009, The 
               
               
                   
                   
                 Plant Cell 21(11): 3567-3584). 
               
               
                 At2g17040 
                 anac036, NAC036, NAC domain containing protein 36 
                   
               
               
                 At5g57660 
                 ATCOL5, COLS, CONSTANS-like 5 
                   
               
               
                 At5g37260 
                 CIR1, RVE2, Homeodomain-like superfamily protein 
                   
               
               
                 At5g47390 
                 myb-like transcription factor family protein 
                   
               
               
                 At1g75540 
                 STH2, salt tolerance homolog2 
                   
               
               
                 At1g35560 
                 TCP family transcription factor 
                   
               
               
                 At4g39780 
                 Integrase-type DNA-binding superfamily protein 
                   
               
               
                 At4g38340 
                 Plant regulator RWP-RK family protein (NLP3)  
                 This transcription factor NLP3 has 
               
               
                   
                   
                 been associated with N-signaling 
               
               
                   
                   
                 in plants (Konishi et al., 2013,  
               
               
                   
                   
                 Nature Communications 4: 1617). 
               
               
                 At1g19700 
                 BEL10, BLH10, BELl-like homeodomain 10 
                   
               
               
                 At2g28200 
                 C2H2-type zinc finger family protein 
                   
               
               
                 At1g29860 
                 ATWRKY71, WRKY71, WRKY DNA-binding protein 71 
                   
               
               
                 At1g07520 
                 GRAS family transcription factor 
                   
               
               
                 At4g37540 
                 LBD39, LOB domain-containing protein 39  
                 This transcription factor has been 
               
               
                   
                   
                 associated with N-signaling in 
               
               
                   
                   
                 plants (Rubin et al., 2009, The 
               
               
                   
                   
                 Plant Cell 21(11): 3567-3584). 
               
               
                 At3g61850 
                 DAG1, Dof-type zinc finger DNA-binding family protein 
                   
               
            
           
           
               
            
               
                 &gt;bZIP1_outerRing (bZIP1 targets only identified in planta (secondary targets) (Kang et al., 2010, Molecular  
               
               
                 Plant 3:361) 
               
            
           
           
               
               
               
            
               
                 At5g66360 
                 Ribosomal RNA adenine dimethylase family protein 
                   
               
               
                 At4g31920 
                 ARR10, RR10, response regulator 10 
                   
               
               
                 At3g18560 
                 unknown protein; BEST  Arabidopsis   thaliana  protein  
                   
               
               
                   
                 match is: unknown protein (TAIR: AT1G49000.1); Has 95  
                   
               
               
                   
                 Blast hits to 95 proteins in 13 species: Archae-0;  
                   
               
               
                   
                 Bacteria-0; Metazoa-0; Fungi-0; Plants-95; Viruses-0;  
                   
               
               
                   
                 Other Eukaryotes-0 (source: NCBI BLink). 
                   
               
               
                 At4g36010 
                 Pathogenesis-related thaumatin superfamily protein 
                   
               
               
                 At5g62720 
                 Integral membrane HPP family protein 
                   
               
               
                 At1g80440 
                 Galactose oxidase/kelch repeat superfamily protein 
                   
               
               
                 At4g09620 
                 Mitochondrial transcription termination factor family  
                   
               
               
                   
                 protein 
                   
               
               
                 At5g04950 
                 ATNAS1, NAS1, nicotianamine synthase 1 
                   
               
               
                 At4g36540 
                 BEE2, BR enhanced expression 2 
                   
               
               
                 At1g78050 
                 PGM, phosphoglycerate/bisphosphoglycerate mutase 
                   
               
               
                 At1g63940 
                 MDAR6, monodehydroascorbate reductase 6 
                   
               
               
                 At2g26980 
                 CIPK3, SnRK3.17, CBL-interacting protein kinase 3 
                   
               
               
                 At4g27410 
                 ANAC072, RD26, NAC (No Apical Meristem) domain  
                   
               
               
                   
                 transcriptional regulator superfamily protein 
                   
               
               
                 At1g04770 
                 Tetratricopeptide repeat (TPR)-like superfamily protein 
                   
               
               
                 At1g32920 
                 unknow protein; FUNCTIONS IN: molecular_function  
                   
               
               
                   
                 unknown; INVOLVED IN: response to wounding;  
                   
               
               
                   
                 LOCATED IN: endomembrane system; EXPRESSED IN:  
                   
               
               
                   
                 23 plant structures; EXPRESSED DURING: 13 growth  
                   
               
               
                   
                 stages; BEST  Arabidopsis   thaliana  protein match is:  
                   
               
               
                   
                 unknown protein (TAIR: AT1G32928.1); Has 42 Blast  
                   
               
               
                   
                 hits to 42 proteins in 8 species: Archae-0; Bacteria-0;  
                   
               
               
                   
                 Metazoa-0; Fungi-0; Plants-42; Viruses-0; Other 
                   
               
               
                   
                 Eukaryotes-0 (source: NCBI BLink). 
                   
               
               
                 At4g02380 
                 AtLEA5, SAG21, senescence-associated gene 21 
                   
               
               
                 At1g72050 
                 TFIIIA, transcription factor IIIA 
                   
               
               
                 At1g15550 
                 ATGA3OX1, GA3OX1, GA4, gibberellin 3-oxidase 1 
                   
               
               
                 At4g01410 
                 Late embryogenesis abundant (LEA) hydroxyproline-rich  
                   
               
               
                   
                 glycoprotein family 
                   
               
               
                 At5g54170 
                 Polyketide cyclase/dehydrase and lipid transport  
                   
               
               
                   
                 superfamily protein 
                   
               
               
                 At1g75280 
                 NmrA-like negative transcriptional regulator family  
                   
               
               
                   
                 protein 
                   
               
               
                 At1g77760 
                 GNR1, NIA1, NR1, nitrate reductase 1  
                 N-regulated gene involved in  
               
               
                   
                   
                 N-reduction/assimilation (Wang  
               
               
                   
                   
                 et al., 2003, Plant Physiol.  
               
               
                   
                   
                 132(2): 556-567). 
               
               
                 At3g48360 
                 ATBT2, BT2, BTB and TAZ domain protein 2 
                   
               
               
                 At4g13510 
                 AMT1; 1, ATAMT1, ATAMT1; 1, ammonium  
                 N-regulated gene involved in  
               
               
                   
                 transporter 1; 1 
                 N-reduction/assimilation (Wang  
               
               
                   
                   
                 et al., 2003, Plant Physiol.  
               
               
                   
                   
                 132(2): 556-567). 
               
               
                 At5g52050 
                 MATE efflux family protein 
                   
               
               
                 At5g40850 
                 UPM1, urophorphyrin methylase 1  
                 N-regulated gene involved in  
               
               
                   
                   
                 N-reduction/assimilation (Wang  
               
               
                   
                   
                 et al., 2003, Plant Physiol.  
               
               
                   
                   
                 132(2): 556-567). 
               
               
                 At5g06570 
                 alpha/beta-Hydrolases superfamily protein 
                   
               
               
                 At4g30930 
                 NFD1, Ribosomal protein L21 
                   
               
               
                 At2g22540 
                 AGL22, SVP, K-box region and MADS-box transcription  
                   
               
               
                   
                 factor family protein 
                   
               
               
                 At4g15690 
                 Thioredoxin superfamily protein 
                   
               
               
                 At2g15620 
                 ATHNIR, NIR, NIR1, nitrite reductase 1  
                 N-regulated gene involved in  
               
               
                   
                   
                 N-reduction/assimilation (Wang  
               
               
                   
                   
                 et al., 2003, Plant Physiol.  
               
               
                   
                   
                 132(2): 556-567). 
               
               
                 At1g30510 
                 ATRFNR2, RFNR2, root FNR 2  
                 N-regulated gene involved in  
               
               
                   
                   
                 N-reduction/assimilation (Wang  
               
               
                   
                   
                 et al., 2003, Plant Physiol.  
               
               
                   
                   
                 132(2): 556-567). 
               
               
                 At1g66760 
                 MATIE efflux family protein 
                   
               
               
                 At4g05390 
                 ATRFNR1, RFNR1, root FNR 1  
                 N-regulated gene involved in  
               
               
                   
                   
                 N-reduction/assimilation (Wang  
               
               
                   
                   
                 et al., 2003, Plant Physiol.  
               
               
                   
                   
                 132(2): 556-567). 
               
               
                 At1g17170 
                 ATGSTU24, GST, GSTU24, glutathione S-transferase  
                   
               
               
                   
                 TAU 24 
                   
               
               
                 At1g67910 
                 unknown protein; FUNCTIONS IN: molecular_function  
                   
               
               
                   
                 unknown; INVOLVED IN: biological_process unknown;  
                   
               
               
                   
                 LOCATED IN: chloroplast; EXPRESSED IN: 21 plant  
                   
               
               
                   
                 structures; EXPRESSED DURING: 12 growth stages;  
                   
               
               
                   
                 BEST  Arabidopsis   thaliana  protein match is:  
                   
               
               
                   
                 unknown protein (TAIR: AT1G24577.1); Has 167 Blast  
                   
               
               
                   
                 hits to 167 proteins in 19 species: Archae-0; Bacteria-0;  
                   
               
               
                   
                 Metazoa-0; Fungi-0; Plants-167; Viruses-0; Other 
                   
               
               
                   
                 Eukaryotes-0 (source: NCBI BLink). 
                   
               
               
                 At1g71030 
                 ATMYBL2, MYBL2, MYB-like 2 
                   
               
               
                 At1g16170 
                 unknown protein; FUNCTIONS IN: molecular_function  
                   
               
               
                   
                 unknown; INVOLVED IN: biological_process unknown;  
                   
               
               
                   
                 LOCATED IN: cellular_component unknown;  
                   
               
               
                   
                 EXPRESSED IN: 24 plant structures; EXPRESSED  
                   
               
               
                   
                 DURING: 15 growth stages; BEST  Arabidopsis   thaliana   
                   
               
               
                   
                 protein match is: unknown protein (TAIR: AT1G79660.1);  
                   
               
               
                   
                 Has 55 Blast hits to 55 proteins in 13 species: Archae-0;  
                   
               
               
                   
                 Bacteria-0; Metazoa-0; Fungi-0; Plants-55; Viruses-0;  
                   
               
               
                   
                 Other Eukaryotes-0 (source: NCBI BLink). 
                   
               
               
                 At5g41670 
                 6-phosphogluconate dehydrogenase family protein 
                   
               
               
                 At1g22500 
                 RING/U-box superfamily protein 
                   
               
               
                 At2g45050 
                 GATA2, GATA transcription factor 2 
                   
               
               
                 At5g65010 
                 ASN2, asparagine synthetase 2  
                 N-regulated gene involved in  
               
               
                   
                   
                 N-reduction/assimilation (Wang  
               
               
                   
                   
                 et al., 2003, Plant Physiol.  
               
               
                   
                   
                 132(2): 556-567). 
               
               
                 At1g24280 
                 G6PD3, glucose-6-phosphate dehydrogenase 3  
                 N-regulated gene involved in  
               
               
                   
                   
                 N-reduction/assimilation (Wang  
               
               
                   
                   
                 et al., 2003, Plant Physiol.  
               
               
                   
                   
                 132(2): 556-567). 
               
               
                 At2g22500 
                 ATPUMP5, DIC1, UCP5, uncoupling protein 5 
                   
               
               
                 At3g16560 
                 Protein phosphatase 2C family protein 
                   
               
               
                 At1g73600 
                 S-adenosyl-L-methionine-dependent methyltransferases  
                   
               
               
                   
                 superfamily protein 
                   
               
               
                 At4g15700 
                 Thioredoxin superfamily protein 
               
               
                   
               
            
           
         
       
     
     13. EQUIVALENTS 
     Although the invention is described in detail with reference to specific embodiments thereof, it will be understood that variations which are functionally equivalent are within the scope of this invention. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and accompanying drawings. Such modifications are intended to fall within the scope of the appended claims. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims. 
     All publications, patents and patent applications mentioned in this specification are herein incorporated by reference into the specification to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference in their entireties.