PATENT ABSTRACT
The present invention relates to a method for screening proteins related to and/or involved in plant cell cycle. It further relates to proteins isolated with the method and the use of those proteins and/or the genes encoding those proteins for modulating plant yield and plant growth.

PATENT DESCRIPTION
CROSS-REFERENCE TO RELATED APPLICATION(S) 
       [0001]    This is a national phase entry under 35 U.S.C. §371 of International Patent Application PCT/EP2009/066856, filed Dec. 10, 2009, published in English as International Patent Publication WO 2010/066849 A1 on Jun. 17, 2010, which claims the benefit under Article 8 of the Patent Cooperation Treaty to European Patent Application Serial No. 08171187.1, filed Dec. 10, 2008. 
     
    
     TECHNICAL FIELD 
       [0002]    The present invention relates to a novel method for screening proteins related to and/or involved in plant cell cycles. It further relates to proteins isolated with the method and the use of those proteins and/or the genes encoding those proteins for modulating plant yield and plant growth. 
       BACKGROUND 
       [0003]    Knowledge of the basic cell cycle machinery is a prerequisite to grasp how signaling pathways impinge on and regulate cell proliferation during plant growth and development in a changing environment. The fundamental underlying mechanisms of cell division are conserved among all eukaryotes, however, due to their sessile lifestyle, plants have evolved unique features. Plant genome sequence analysis revealed the existence of an unexpected high number of genes involved in cell proliferation (Capron et al., 2003; Vandepoele et al., 2002; Menges et al., 2005; Schultz et al., 2007), compared to other organisms. Microarray analysis showed that a lot of these follow a cell cycle-dependent expression profile (Menges et al., 2005), sustaining their role in cell cycle regulation. 
       SUMMARY OF THE INVENTION 
       [0004]    To elucidate which molecular machines are involved in plant cell division, we isolated cellular complexes by TAP from  Arabidopsis thaliana  cell suspension cultures (Van Leene et al., 2007; Van Leene et al., 2008) using “core” cell cycle proteins as baits. The dataset was corrected for non-specific interactions and divided in a “core” dataset of interactions that were biologically confirmed in at least two independent repeats, and a “non-core” dataset. Surprisingly, we found that the datasets, apart from known cell cycle proteins, were also comprising proteins of which the role in cell cycle never has been illustrated before. 
         [0005]    The robustness of both the core and non-core datasets is demonstrated through different computational analysis and through the biological interpretation of the network. The interactome serves as an excellent hypothesis-generating tool, and the power of it is reached in particular when integrated with other data. Combining our interactome data with cell cycle-related expression profiles, for example, gives insight in which CDK/cyclin complexes are active during cell division and when. The data prove that the high numbers of cell cycle regulators in plants are not the sole consequence of redundancy, but that different cell cycle regulators are combined in complexes providing functional diversity leading to increased complexity and flexibility of the plant cell cycle. 
         [0006]    Disclosed herein is a method to isolate novel cell cycle-related proteins, comprising (1) performing a tap analysis using a known cell cycle protein as bait, (2) correcting the results for non-specific interactions, and (3) reconfirming the corrected results. “Reconfirming the result,” as used here, can be done either by repeating the tap-tag experiment or by carrying out a reversed tap-tag, wherein the original prey is now used as bait. 
         [0007]    Also disclosed herein is the use of a cell cycle-related protein isolated with the method of the invention for the modulation of plant growth and/or yield. In a particular embodiment, the plant is a crop plant, preferably a monocot or a cereal, even more preferably it is a cereal selected from the group consisting of rice, maize, wheat, barley, millet, rye, sorghum and oats. 
         [0008]    The use, as indicated here, is the use of the protein and/or the use of a nucleic acid encoding this protein, or the complement thereof It includes, but is not limited to, genomic DNA, cDNA, messenger RNA (including the 5′ and 3′ untranslated regions) and RNAi; the use can result, as a non-limiting example, in overexpression or repression of the expression of the gene. Overexpression or repression of expression of a target gene can be obtained by transfer of a genetic construct, intended for the overexpression or the repression of expression into a plant. The transfer of foreign genes into the genome of a plant is called transformation. Transformation of plant species is a fairly routine technique known to the person skilled in the art. Advantageously, any of several transformation methods may be used to introduce the gene of interest into a suitable ancestor cell. The methods described for the transformation and regeneration of plants from plant tissues or plant cells may be utilized for transient or for stable transformation. Transformation methods include, but are not limited to, agrobacterium-mediated transformation, the use of liposomes, electroporation, chemicals that increase free DNA uptake, injection of the DNA directly into the plant, particle gun bombardment, transformation using viruses or pollen and microprojection. 
         [0009]    Preferably, the cell cycle-related proteins are selected from the group consisting of At1g56110, At3g17020, At3g21140, At5g25460, At5g60790, At4g38900, At3g49240, At5g24690, At1g06070, At4g34150, At1g20480, At5g20920, At3g15970, At5g13030, At1g01880, At5g07310, At2g46610, At1g10690, At3g04710, At3g24690, At4g16130, At2g05830, At1g29220, At1g55890, At1g60650, At1g70830, At2g43140, At1g77180, At5g18620, At5g02530, At5g14170, At1g52730, At2g33340, At1g03060, At3g62240, At4g38740, At5g61220, At3g53880, At3g56860, At1g01970, At1g19520, At1g14620, At2g03820, At3g01280, At3g56690, At5g41190, At5g03740, At1g42440, At2g28450, At1g09760, At1g10840, At3g11830, At5g54900, At1g31760, At1g61870, At3g11760, At1g05805, At1g29200, At4g13850, At4g38780, At1g71380, At3g13640, At5g25060, At1g43700, At2g46020, At3g55760 and At5g21160 or a variant thereof. “Variants,” as used here, are including, but not limited to, homologues, orthologues and paralogues of the cell cycle-related proteins. “Homologues” of a protein encompass peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified protein in question and having similar biological and functional activity as the unmodified protein from which they are derived. Orthologues and paralogues encompass evolutionary concepts used to describe the ancestral relationships of genes. Paralogues are genes within the same species that have originated through duplication of an ancestral gene; orthologues are genes from different organisms that have originated through speciation, and are also derived from a common ancestral gene. Preferably, the homologue, orthologue or paralogue has a sequence identity at a protein level of at least 50%, 51%, 52%, 53%, 54% or 55%, 56%, 57%, 58%, 59%, preferably 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, more preferably 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, even more preferably 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, and most preferably 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more as measured in a BLASTp (Altschul et al., 1997; Altschul et al., 2005). 
         [0010]    Preferably, the use is overexpression of the gene encoding the cell cycle-related protein, even more preferably it is overexpression of a cell cycle-related protein according to the invention, selected from the group consisting of At1g56110, At3g17020, At3g21140, At5g25460, At5g60790 (SEQ ID NOS:1-5), or a variant thereof. Preferably, overexpression results in an increase of plant growth and/or yield. Increase of plant growth and/or yield is measured by comparing the test plant, comprising a gene used according to the invention, with the parental, non-transformed plant, grown under the same conditions as control. Preferably, increase of growth is measured as an increase of biomass production. “Yield” refers to a situation where only a part of the plant, preferably an economically important part of the plant, such as the leaves, roots or seeds, is increased in biomass. The term “increase” as used here means at least a 5%, 6%, 7%, 8%, 9% or 10%, preferably at least 15% or 20%, more preferably 25%, 30%, 35% or 40% more yield and/or growth in comparison to control plants as defined herein. “Increase of plant growth,” as used here, is preferably measured as increase of any one or more of total plant biomass, leaf biomass, root biomass and seed biomass. In one preferred embodiment, the increase is an increase in total plant biomass. In a preferred embodiment, the plant is a crop plant, preferably a monocot or a cereal; even more preferably, it is a cereal selected from the group consisting of rice, maize, wheat, barley, millet, rye, sorghum and oats. 
         [0011]    Still another aspect of the invention is a novel cell cycle-related protein, isolated with the method according to the invention. 
     
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
         [0012]      FIG. 1 : Panel A: Enrichment analysis on the core and non-core datasets. Statistically significant enrichments are indicated with * (p-value&lt;0.05) or with ** (p-value&lt;0.01). An enrichment analysis was performed for genes showing cell cycle-regulated expression (Periodic), for genes containing an E2F or MSA consensus motif in their promoter and for proteins containing a CDK consensus phosphorylation site. Panel B: Percentage of the whole gene pool (genome-wide), a cell cycle collection of 518 genes, bait proteins (without reverse baits), and core and non-core preys (without the cell cycle collection) having at least two features. P-values are shown in red. Panel C: Distribution of the transcript PCC of the core (red curve) and non-core dataset (green curve), compared to the average distribution (black and grey curves) of 100 random networks containing an equal number of interactions and genes. 
           [0013]      FIG. 2 : Distribution of the number of cell cycle-related features among the whole gene pool (genome-wide), a collection of 518 cell cycle genes, and bait proteins (without reverse baits). 
           [0014]      FIG. 3 : Overview of the subnetworks. 
           [0015]      FIG. 4 : Fresh weight of control lines transformed with empty vector. About 100 plants were analyzed for each independent line (C1 and C2). 
           [0016]      FIG. 5 : Distribution of plants in function of their fresh weight. The graphs represent the frequency of a plant belonging to a certain category of weight. 
           [0017]      FIG. 6 : Distribution of plants in function of their fresh weight. The graphs represent the frequency of a plant belonging to a certain category of weight (% of plants versus fresh weight category, as in  FIG. 5 ). The lines analyzed are independent lines of the ones presented in  FIG. 5 . 
       
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     EXAMPLES 
     MATERIALS AND METHODS TO THE EXAMPLES 
     Cloning and TAP Purification 
       [0018]    Cloning of transgenes encoding tag fusions under control of the constitutive Cauliflower tobacco mosaic virus 35S promoter, transformation of  Arabidopsis  cell suspension cultures, protein extract preparation, TAP purification, protein precipitation and separation were done as previously described (Van Leene et al., 2007). The adapted protocol used for purification of protein complexes incorporating GS-tagged bait is described elsewhere (Van Leen et al., 2008). For identification by mass spectrometry, minor adjustments were implemented compared to previously described protocols (Van Leene et al., 2007), as described below. 
       Proteolysis and Peptide Isolation 
       [0019]    After destaining, gel slabs were washed for 1 hour in H 2 O, polypeptide disulfide bridges were reduced for 40 minutes in 25 mL of 6.66 mM DTT in 50 mM NH 4 HCO 3  and, sequentially, the thiol groups were alkylated for 30 minutes in 25 mL 55 mM IAM in 50 mM NH 4 HCO 3 . After washing the gel slabs three times with water, complete lanes from the protein gels were cut into slices, collected in microtiter plates and treated essentially as described before with minor modifications (Van Leene et al., 2007). Per microtiter plate well, dehydrated gel particles were rehydrated in 20 μL digest buffer containing 250 ng trypsin (MS Gold; Promega, Madison, Wis.), 50 mM NH 4 HCO 3  and 10% CH 3 CN (v/v) for 30 minutes at 4° C. After adding 10 μL of a buffer containing 50 mM NH 4 HCO 3  and 10% CH 3 CN (v/v), proteins were digested at 37° C. for 3 hours. The resulting peptides were concentrated and desalted with microcolumn solid phase tips (PerfectPure™ C18 tip, 200 nL bed volume; Eppendorf, Hamburg, Germany) and eluted directly onto a MALDI target plate (Opti-TOFTM384 Well Insert; Applied Biosystems, Foster City, Calif.) using 1.2 μL of 50% CH 3 CN:0.1% CF 3 COOH solution saturated with α-cyano-4-hydroxycinnamic acid and spiked with 20 fmole/μL Glu1 Fibrinopeptide B (Sigma Aldrich), 20 fmole/μL des-Pro2-Bradykinin (Sigma Aldrich), and 20 fmole/μL Adrenocorticotropic Hormone Fragment 18-39 human (Sigma Aldrich). 
       Acquisition of Mass Spectra 
       [0020]    A MALDI tandem MS instrument (4700 and 4800 Proteomics Analyzer; Applied Biosystems) was used to acquire peptide mass fingerprints and subsequent 1 kV CID fragmentation spectra of selected peptides. Peptide mass spectra and peptide sequence spectra were obtained using the settings essentially as previously presented (Van Leene et al., 2007). Each MALDI plate was calibrated according to the manufacturers&#39; specifications. All peptide mass fingerprinting (PMF) spectra were internally calibrated with three internal standards at m/z 963.516 (des-Pro2-Bradykinin), m/z 1570.677 (Glu1-Fibrinopeptide B), and m/z 2465,198 (Adrenocorticotropic Hormone Fragment 18-39) resulting in an average mass accuracy of 5 ppm±10 ppm for each analyzed peptide spot on the analyzed MALDI targets. Using the individual PMF spectra, up to sixteen peptides, exceeding a signal-to-noise ratio of 20 that passed through a mass exclusion filter, were submitted to fragmentation analysis. 
       MS-Based Protein Homology Identification 
       [0021]    PMF spectra and the peptide sequence spectra of each sample were processed using the accompanied software suite (GPS Explorer 3.6, Applied Biosystems) with parameter settings essentially as previously described (Van Leene et al, 2007). Data search files were generated and submitted for protein homology identification by using a local database search engine (Mascot 2.1, Matrix Science). An in-house non-redundant  Arabidopsis  protein database called SNAPS  Arabidopsis thaliana  version 0.4 (SNAPS=Simple Non-redundant Assembly of Protein Sequences, 77488 sequence entries, 30468560 residues; available at WorldWideWeb.ptools.ua.ac.be/snaps) was compiled from nine public databases. Protein homology identifications of the top hit (first rank) with a relative score exceeding 95% probability were retained. Additional positive identifications (second rank and more) were retained when the score exceeded the 98% probability threshold. Because identifications were done with different versions of the SNAPS database (Van Leen et al., 2007), and with the goal to obtain more uniformity between the identifications, all identifications from the core and the non-core dataset were resubmitted to Mascot and identified with the protein sequence repertoire from the latest TAIR database (TAIR8.0). Furthermore, an additional restriction was implemented to reduce the number of false positive identifications and, as so, identifications for which more than 50% of the corresponding peptides had a trypsin miss-cleavage, were discarded. 
       GO Enrichment Analysis 
       [0022]    Analysis of over- and under-representation of GO terms was done with the BiNGO tool (Maere et al., 2005) in Cytoscape (Shannon et al., 2003). The hypergeometric test was chosen at a significance value of 0.05 with the Benjamini and Hochberg False Discovery Rate Correction for multiple testing. The  Arabidopsis  gene annotation file used in the analysis was downloaded from the gene ontology website on the 4th of October 2008. 
       Cell Cycle Enrichment Analysis 
       [0023]    For the periodic gene enrichment analysis, a list of 1258 genes showing cell cycle-regulated and cell cycle-associated expression was compiled from two datasets (Menges et al., 2003; Jensen et al., 2006). Genome wide corresponds to all 23834 genes present on the Affymtetrix ATH1 microarray. Genes containing E2F or M-specific activator (MSA) motifs in their promoter sequence were in silico determined by combining transcript expression data and comparative genomics (Vandepoele et al, 2006). Here, genome wide corresponds to 19173 genes for which a unique probe set is available on the ATH1 microarray. Proteins containing the CDK consensus phosphorylation site [ST]PX[KR], a known hallmark of CDK substrates (De Veylder et al., 1997), were considered as potential CDK substrates. The presence of the consensus motif was screened with the patmatch tool available at TAIR and, hence, genome wide corresponds here to all 27235 proteins present in the TAIR8.0 release. For all enrichment analysis, p-values were calculated with the hypergeometric cumulative distribution function of the Matlab 7.5 software. Proteins that could not be assigned to a specific gene locus were discarded from all enrichment analysis. 
         [0000]    Overlap with Protein-Protein Databases 
         [0024]    To assess the novelty of the cell cycle interactome, we screened for the overlap of our datasets with the following databases containing protein-protein interactions: TAIR (Huala et al., 2001), InTact (Kerrien et al., 2007),  Arabidopsis  Reactome (Tsesmetzis et al., 2008), AtPID (Cui et al., 2008), Reactome (Vastrik et al., 2007) and The Bio-Array Resource (BAR) for  Arabidopsis  Functional Genomics (Geisler-Lee et al., 2007). 
       Co-Expression Analysis 
       [0025]    Transcript Pearson Correlation Coefficients (PCC), representing the degree of co-expression of gene pairs, were calculated based on an  Arabidopsis  ATH1 micro-array compendium of 518 experiments focused towards cell cycle or plant growth and development (Table 7). We compared the PCC distribution of both datasets with the PCC distribution of 100 randomized datasets with an equal number of randomly chosen proteins and interactions. 
       Constructs and Plant Transformation 
       [0026]    The overexpressing constructs were produced by using gateway cloning technology. The cDNA of the genes of interest (table, sheet OE produced and LOF requested) were amplified by PCR from reverse transcribed RNA extracted from tissues of  Arabidopsis thaliana  ecotype Columbia. The PCR reactions were performed using the Phusion High fidelity DNA polymerase (Finnzymes) according to the manufacturer&#39;s instructions. The PCR fragments, corresponding to complete cDNA of the genes of interest were introduced into pDONr 201 using the Gateway system (Invitrogen) by attBXattP recombination sites and subsequently recombined into the pK7WG2 expression vector by attL XattR sites recombination. The sequence was confirmed by sequencing. The constructs containing the genes of interest under the control of the CaMV 35S promoter were used to transform  Arabidopsis thaliana  by the flowerdip method (Clough and Bent, 1998). 
       Plant Material and Growth Condition 
       [0027]    Transgenic lines were identified by selection on MS medium (half-strength Murashige and Skoog medium (Duchefa, Haarlem, The Netherlands), Sucrose 1%) supplemented with 50 mg/l kanamycin and later transferred to soil for seed production. A second selection on MS plus kanamycine allowed the selection of lines containing one site of insertion of the transgene. Plants were grown under a 16-hour day and 8-hour night regime at 21° C. 
       Biomass Test 
       [0028]    For the biomass measurement, the vegetative part of a 20-day-old plant grown on MS medium was harvested and the fresh weight was measured by weighing about 60 plants of each line. 
       Example 1 
     Isolation of the TAP Complexes 
       [0029]    As baits, we used 73 “core” cell cycle regulatory proteins (Vandepoele et al., 2002; Menges et al., 2006; Perez et al., 2007), four mitotic checkpoint proteins (Menges et al., 2005), eight anaphase promoting complex (APC) subunits and six APC activators (Capron et al., 2003), one 26S proteasome subunit (Brukhin et al., 2005), ten proteins involved in DNA replication or repair (Schultz et al., 2007), and as proof of concept, six proteins for reverse TAP experiments (Table 1). Of the 108 TAP fusions, 102 were expressed successfully. In total, 303 purifications were performed with at least two independent purifications per bait. 
       Example 2 
     Identification of the Prey Proteins 
       [0030]    Purified proteins were identified via MALDI-TOFTOF. Non-specific proteins, determined by control purifications, were subtracted from the hit lists (Table 2), generating a non-redundant dataset of 857 interactions among 393 proteins. This dataset was divided in a “core” dataset of 371 interactions among 196 proteins, containing interactions that were biologically confirmed in at least two independent repeats or in the reciprocal experiment, and a “non-core” dataset with the remainder 486 interactions among 320 proteins. 
       Example 3 
     Enrichment Analysis 
       [0031]    To assess the quality of the interactome, we performed different enrichment analysis on the core and non-core preys. In both datasets, the GO term “cell cycle” was highly enriched (Table 3). Additional GO enrichments demonstrate that cell cycle is linked to a myriad of biological processes including growth and development, response to stress and hormone stimuli, energy production, chromatin remodeling and others. Next, we observed an enrichment in the core dataset for genes periodically expressed during cell cycle ( FIG. 1 , Panel A). Furthermore, both datasets were enriched for genes with E2F or M-specific activator (MSA) motifs in their promoter. The less pronounced enrichments for the non-core dataset indicate that it is more biased for interactions linking the core cell cycle machinery with other pathways. This is supported by the fact that the non-core dataset is more enriched for potential CDK substrates, as assessed by the presence of CDK phosphorylation sites. The fact that these interactions were often not confirmed is likely due to the transient nature of, e.g., CDK/substrate interactions. 
       Example 4 
     Isolation of Novel Cell Cycle Genes 
       [0032]    In a quest for new cell cycle-related proteins, we integrated different cell cycle-related features (Table 4). The distribution of the number of features per gene shows that a collection of known cell cycle genes (Table 5) is enriched for these features compared to the whole gene pool ( FIG. 2 ). A clear shift between the whole gene pool and the cell cycle collection was visible at two features, as it was the case for the original bait list, validating the choice of our baits. In search for new cell cycle proteins, we started from the core and non-core prey list and subtracted the collection of known cell cycle genes. The percentage meeting the criterion of having at least two features is shown ( FIG. 1 , Panel B), and all classes are significantly enriched compared to the whole gene pool. By filtering for genes containing at least two features, we generated a list of 123 potential new cell cycle genes from the core and non-core dataset (Table 6). 
         [0033]    The robustness of the data is further exemplified by the observation that 46% of the core and 8% of the non-core dataset interactions are between baits, as our baits are supposed to act in common pathways. Screening our data for overlap with existing protein-protein interaction databases learned that 66% of the core and 95% of the non-core dataset interactions are new. On the other hand, this implicates that one-third of the core dataset is validated by other means. Finally, interactions from both datasets tend to be more co-expressed compared to interactions from randomized datasets as assessed by calculation of the transcript Pearson Correlation Coefficient (PCC) ( FIG. 1 , Panel C). The integrated cell cycle interactome can be accessed through a Cytoscape webstart and is provided as a matrix pivot table that allows easy querying of the interactome. To demonstrate the biological importance of the interactome, a selection of subnetworks is discussed below, covering interactions from both the core and non-core dataset ( FIG. 3 ). 
       Example 5 
     Isolated Genes of the CDK Complexes 
       [0034]    Key players in cell cycle progression are cyclin-dependent kinase (CDK) complexes. CDKA;1, the Arabidopsis ortholog of yeast cdc2/cdc28, co-purified with all tested D-type cyclins and with A3-type cyclins, but not with the mitotic A1-, A2- or B-type cyclins. Combining our interactome data with expression data (Menges et al. 2005), we speculate that at cell cycle reentry and early in G1-phase, CDKA;1 binds CYCD3;3 and CYCD5;1. Further on in G1-phase and at the G1/S checkpoint, CDKA;1 binds a variety of D-type cyclins, such as CYCD4;1, CYCD4;2, CYCD3;1, CYCD6;1 and CYCD7;1. In addition, CDKA;1 interacts with S-phase specific A3-type cyclins. The other A- and B-type cyclins, of which most possess a peak of expression at the G2/M-boundary, bind the plant-specific mitotic B-type CDKs. B1-type cyclins associate exclusively with B2-type CDKs, while the remainder A- and B-type cyclins preferentially bind B1-type CDKs. Although transient interactions are more difficult to screen with TAP, our interactome contains different potential CDK substrates. As predicted (Geisler-Lee et al., 2007), CDKA;1 is present as a highly connected hub in the core network. It co-purified the unknown protein AT4G14310, which was further present in complexes with CKS1, CKS2, CYCA3;1, CyCA3;4 and KRP2 and the reverse purification confirmed interaction with CDKA;1 and CKS2 and revealed interaction with the plant-specific kinesin motor protein KCA2 involved in division plane determination. Next, CDKA;1 was pulled down with the 26S proteasome complex, purified through RPN1a, possibly reflecting cell cycle regulation of the 26S proteasome. CDKA;1 further interacted with three proteins from the UDP-xylose biosynthesis pathway, coupling cell cycle regulation with cell wall synthesis (Siefert, 2004). With three A-type cyclins, we picked up a DNA repair protein and with CYCB1;3, we found γ-tubulin and a spindle pole body component, two proteins involved in microtubule nucleation during, e.g., assembly of the preprophase band, a plant-specific structure required for polarity determination during cell cycle (Erhardt et al., 2002). Furthermore, some interesting chromatin-remodeling proteins were identified with different cyclins: CHR17, an E2F-up-regulated ISWI protein (Huanca-Mamani et al., 2005) interacted with CYCD3;2 and CYCD5;1. CHC1 associated with CYCA1;1, CYCD7;1, CYCB2;3 and CKS2, and BRAHMA, a SWI/SNF chromatin-remodeling ATPase implicated in the formation and/or maintenance of cotyledon boundary cells during embryogenesis (Kwon et al., 2006), was identified with CYCB1;3 and CYCB2;3. 
       Example 6 
     Isolation of Positive Regulators of the Cell Cycle 
       [0035]    For full activity, CDKs require, next to cyclin binding, phosphorylation of a threonine residue within the T-loop by CDK-activating kinases (CAK). The  Arabidopsis  genome encodes four CAKs, namely, three D-type CDKs, homologous to human CDK7, and one cyclin-independent CAK-activating kinase (CAKAK) CDKF;1. Here, we show that both CDKD;2 and CDKD;3 form a trimeric complex with CYCH;1 and the CAK assembly factor MAT1. Like in rice (Rohila et al., 2006), CDKD;2 is also part of the basal TFIIH complex involved in transcription and DNA repair, as three members co-purified (UVH6/XPD, AT1G55750 and AT4G17020). In this complex, CDKD;2 activates transcription through phosphorylation of the C-Terminal Domain (CTD) of RNA polymerase II. With UVH6 and MAT1 as baits, we confirmed interaction with CDKD;2 and purified two more proteins of the TFIIH complex. CDKD;2 further co-purified proteins involved in nucleotide biosynthesis, namely, three ribose-phosphate pyrophosphokinases. More upstream, the monomeric CAKAK CDKF;1 activates CDKD;2 in a cyclin-independent manner. On the other hand, CDKF;1 also binds CDKG;2. The G-type CDK class has two members in  Arabidopsis , and is homologous to the human cytokinesis-associated p58 galactosyltransferase protein. Here, we discovered CYCL1, a cyclin with a SR-like splicing domain (Forment et al., 2002), as the regulatory cyclin partner of both G-type CDKs, validating the clustering of CYCL1 with CDKG;2 in a tissue-specific gene expression analysis (Menges et al., 2005). Both core and non-core interacting proteins hint for a function of CDKG/CYCL complexes in regulation of transcription and splicing, so activation of CDKF;1 could lead to altered splicing events during cell proliferation. 
       Example 7 
     Isolation of Negative Regulators of the Cell Cycle 
       [0036]    Negative regulation of cell cycle progression is achieved by docking of small proteins to the CDK/cyclin complexes.  Arabidopsis  encodes seven proteins related to the mammalian Kip/Cip inhibitors, known as Kip-related proteins (KRPs). Here, we show that all KRPs, except KRP1, interact with both CDKA;1 and D-type cyclins. With three KRPs, CDKB1;2 and two APC activators, we found an ethylene responsive AP2 transcription factor (TF), and with KRP2 we picked up a bZIP TF also found with B-type cyclins and CDKB1;2. In plants, a second family of cell cycle inhibitor proteins exist that are up-regulated by abiotic and biotic stress, comprising SIAMESE (SIM) and SIAMESE-Related (SMR) proteins (Peres et al., 2007; Churchman et al., 2006). SIM is a nuclear protein promoting endoreduplication in trichomes by suppression of mitosis. It was proposed that it inhibits mitosis through inhibition of CDKA;1/CYCD complexes (Churchman et al., 2006). In our dataset, however, SIM co-purifies CDKB1;1 and not CDKA;1, so endoreduplication may be triggered directly by inhibiting mitotic CDKB/cyclin complexes. Next to SIM, also SMR1 and SMR2 associate with CDKB1;1, and the CDKB1;1 interactor CYCB2;4 binds AT2G28330, an additional member of the SMR family. In contrast, SMR3-5 bind CDKA;1 and D-type cyclins. Besides, with CDKA;1 and different D-type cyclins as bait, we picked up two new members of the SMR clan, AT5G40460 and AT1G10690, and reverse purifications confirmed these interactions. As AT5G40460 was almost 20-fold induced in plants overexpressing E2Fa and DPa (Vandepoele et al., 2005), it may inhibit CDKA;1/CYCD complexes during S-phase preventing re-initiation of DNA replication. SMR1 further co-purified bZIP69, a TF also found with KRP3 and KRP5. Importins often co-purified both with KRPs and SMRs, supporting the importance of the regulation of their subcellular localization for their activity. 
       Example 8 
     Isolation of Genes Involved in Nucleotide Synthesis, DNA Replication and DNA Repair 
       [0037]    At the G1/S boundary, CDKs activate the E2F/DP pathway by phosphorylation of the repressor RBR, inducing transcription of genes mainly involved in nucleotide synthesis, DNA replication and DNA repair. We demonstrate that E2Fa and E2Fb can associate both with DPa and DPb, and that all E2F and DP proteins co-purify RBR. Since CDKB1;1 interacted with DEL3, an atypical E2F protein lacking the trans-activation domain, we propose that DEL3 is regulated by CDKB1;1 activity, consistent with a second expression peak of DEL3 at G2/M (Menges et al., 2005). Interestingly, the mitotic CDKB1;1, and not CDKA;1, co-purified with RBR, providing further evidence that the E2F/DP/RBR network is not only active at G1/S but also at G2/M transitions, as was previously suggested in plants (Magyar et al., 2005) and mammalian cells (Ishida et al., 2001), or that mitotic CDK/cyclin complexes are active during S-phase as in yeast (Wuarin et al., 2002). We further identified some complexes involved in DNA replication, like the MCM complex, possessing helicase activity for unwinding of double-stranded DNA during DNA replication. This complex was isolated with MCM6 as bait, together with the recently published (Takahashi et al., 2008) and highly co-expressed E2F-target gene 1 (ETG1). The co-purified fraction of proliferating cell nuclear antigen 1 (PCNA1), a sliding clamp for DNA polymerase and thus a key actor in DNA replication, contained PCNA2, two DNA polymerase delta subunits (POLD1-2), of which one also interacted with CYCA2;3, an armadillo/beta-catenin repeat family of unknown function and a DNA binding protein. Furthermore, we prove the existence of the alternative Ctf18 replication factor C complex in plants, required for sister chromatid cohesion in yeast (Mayer et al., 2001) and a protein complex involved in stabilization of single-stranded DNA during replication, repair and transcription, including RPA2, two RPA3 proteins and a putative replication protein (Schultz et al., 2007). 
       Example 9 
     Analysis of Overexpression Lines 
       [0038]    Thirty-two genes were cloned into expression vectors using Gateway cloning to produce plants overexpressing the genes of interest under the control of the CaMV35S promoter (table, sheet OE produced and LOF requested). These constructs were used for  Arabidopsis thaliana  transformation using the flower dip method. Primo-transformants were selected for all the constructs and grown for seed production. The seeds from eleven constructs (At5g25460, At3g01280, At1g31760, At3g21140, At3g17020, At1g05805, At1g10690, At1g56110, At5g24690, At5g60790, At1g09760) were harvested and used to select lines having one site of insertion of the transgene. A biomass test has been carried out on these segregating populations containing one insertion site. In this population, it is expected to find ¼ of wt, 2/4 of hemizygous and ¼ of homozygous plants. When the overexpression of a transgene leads to the production of larger plants, a fraction (¼ or ¾) of the plants analyzed will show an increased biomass. This method allows a fast screening of genes of which the overexpression gives a positive effect on plant growth. Plants were then grown under in vitro condition and the rosette fresh weight of approximately 60 plants was measured 20 days after stratification (table, sheet OE data+average). The control plants used in this experiment correspond to segregating plants transformed with an empty vector (C1 and C2). As shown in  FIG. 4 , for these two independent control lines, the plant fresh weight varies from 8 mg to 28 mg with an average of 20 mg. Among the eleven overexpressing lines analyzed, we found that for five (At1g56110, At3g17020, At3g21140, At5g25460, At5g60790), this distribution of weight is shifted towards larger plants than in the controls ( FIG. 5 ). This shift in biomass range was found for three of these lines in two independent transformants ( FIG. 6 ). The presence of larger plants in this segregating population proves that these five genes are involved in the control of growth. 
         [0000]    
       
         
               
             
               
               
               
               
               
               
               
             
               
               
               
               
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 Overview of bait proteins used to elucidate the core cell cycle interactome of 
               
               
                 
                   Arabidopsis thaliana. 
                 
               
               
                 Topology = C- or N-terminal tag fusions. Tag refers to the applied tag 
               
               
                 being either the traditional TAP tag developed for  Saccharomyces cerevisiae  (15), 
               
               
                 or an optimized dual affinity tag (GS) (2). Expression was indicated as (+) if the 
               
               
                 TAP fusion protein could be detected by western blot analysis. The total number of 
               
               
                 purifications performed per bait is shown, with a minimum of two experiments. 
               
             
          
           
               
                 Bait 
                 Locus 
                 Category 
                 Topology 
                 Tag 
                 Expressed 
                 Purifications 
               
               
                   
               
             
          
           
               
                 CDKA; 1 
                 AT3G48750 
                 core cell cycle 
                 C + N 
                 TAP 
                 + 
                 11 
               
               
                 CDKB1; 1 
                 AT3G54180 
                 core cell cycle 
                 C + N 
                 TAP 
                 + 
                 4 
               
               
                 CDKB1; 2 
                 AT2G38620 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CDKB2; 1 
                 AT1G76540 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 CDKB2; 2 
                 AT1G20930 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 4 
               
               
                 CDKC; 1 
                 AT5G10270 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CDKC; 2 
                 AT5G64960 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 4 
               
               
                 CDKD; 1 
                 AT1G73690 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CDKD; 2 
                 AT1G66750 
                 core cell cycle 
                 C + N 
                 TAP + GS 
                 + 
                 10 
               
               
                 CDKD; 3 
                 AT1G18040 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CDKE; 1 
                 AT5G63610 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 CDKF; 1 
                 AT4G28980 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 3 
               
               
                 CDKG; 1 
                 AT5G63370 
                 core cell cycle 
                 C 
                 GS 
                 + 
                 2 
               
               
                 CDKG; 2 
                 AT1G67580 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CKS1 
                 AT2G27960 
                 core cell cycle 
                 C 
                 TAP + GS 
                 + 
                 10 
               
               
                 CKS2 
                 AT2G27970 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CYCA1; 1 
                 AT1G44110 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CYCA1; 2 
                 AT1G77390 
                 core cell cycle 
                 C 
                 TAP 
                 − 
               
               
                 CYCA2; 1 
                 AT5G25380 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 CYCA2; 2 
                 AT5G11300 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 4 
               
               
                 CYCA2; 3 
                 AT1G15570 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 4 
               
               
                 CYCA2; 4 
                 AT1G80370 
                 core cell cycle 
                 C 
                 TAP 
                 − 
               
               
                 CYCA3; 1 
                 AT5G43080 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 4 
               
               
                 CYCA3; 2 
                 AT1G47210 
                 core cell cycle 
                 N 
                 TAP 
                 − 
               
               
                 CYCA3; 3 
                 AT1G47220 
                 core cell cycle 
                 N 
                 GS 
                 + 
                 2 
               
               
                 CYCA3; 4 
                 AT1G47230 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 4 
               
               
                 CYCB1; 1 
                 AT4G37490 
                 core cell cycle 
                 C 
                 TAP + GS 
                 + 
                 4 
               
               
                 CYCB1; 2 
                 AT5G06150 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 4 
               
               
                 CYCB1; 3 
                 AT3G11520 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CYCB1; 4 
                 AT2G26760 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CYCB2; 1 
                 AT2G17620 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 CYCB2; 2 
                 AT4G35620 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 5 
               
               
                 CYCB2; 3 
                 AT1G20610 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 4 
               
               
                 CYCB2; 4 
                 AT1G76310 
                 core cell cycle 
                 C 
                 GS 
                 + 
                 2 
               
               
                 CYCB2; 5 
                 AT1G20590 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CYCB3; 1 
                 AT1G16330 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 4 
               
               
                 CYCD1; 1 
                 AT1G70210 
                 core cell cycle 
                 C 
                 TAP 
                 − 
               
               
                 CYCD2; 1 
                 AT2G22490 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 6 
               
               
                 CYCD3; 1 
                 AT4G34160 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 CYCD3; 2 
                 AT5G67260 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 3 
               
               
                 CYCD3; 3 
                 AT3G50070 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 4 
               
               
                 CYCD4; 1 
                 AT5G65420 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CYCD4; 2 
                 AT5G10440 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CYCD5; 1 
                 AT4G37630 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CYCD6; 1 
                 AT4G03270 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CYCD7; 1 
                 AT5G02110 
                 core cell cycle 
                 C 
                 GS 
                 + 
                 2 
               
               
                 CYCH; 1 
                 AT5G27620 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 4 
               
               
                 CYCT1; 3 
                 AT1G27630 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 DEL1 
                 AT3G48160 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 DEL2 
                 AT5G14960 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 DEL3 
                 AT3G01330 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 DPa 
                 AT5G02470 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 DPb 
                 AT5G03415 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 E2Fa 
                 AT2G36010 
                 core cell cycle 
                 C 
                 TAP + GS 
                 + 
                 5 
               
               
                 E2Fb 
                 AT5G22220 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 E2Fc 
                 AT1G47870 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 5 
               
               
                 KRP1 
                 AT2G23430 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 KRP2 
                 AT3G50630 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 6 
               
               
                 KRP3 
                 AT5G48820 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 4 
               
               
                 KRP4 
                 AT2G32710 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 6 
               
               
                 KRP5 
                 AT3G24810 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 KRP6 
                 AT3G19150 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 4 
               
               
                 KRP7 
                 AT1G49620 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 RBR 
                 AT3G12280 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 WEE1 
                 AT1G02970 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 4 
               
               
                 Cdc25-like 
                 AT5G03455 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 MAT1 
                 AT4G30820 
                 core cell cycle 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 SIM 
                 AT5G04470 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 4 
               
               
                 SMR1 
                 AT3G10525 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 4 
               
               
                 SMR2 
                 AT1G08180 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 SMR3 
                 AT5G02420 
                 core cell cycle 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 SMR4 
                 AT5G02220 
                 core cell cycle 
                 C + N 
                 TAP 
                 + 
                 4 
               
               
                 SMR5 
                 AT1G07500 
                 core cell cycle 
                 N 
                 GS 
                 + 
                 2 
               
               
                 APC2 
                 AT2G04660 
                 APC core 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 APC4 
                 AT4G21530 
                 APC core 
                 C 
                 TAP 
                 − 
               
               
                 APC7 
                 AT2G39090 
                 APC core 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 APC8 
                 AT3G48150 
                 APC core 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 APC10 
                 AT2G18290 
                 APC core 
                 N 
                 TAP 
                 + 
                 4 
               
               
                 APC11 
                 AT3G05870 
                 APC core 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CDC16 
                 AT1G78770 
                 APC core 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CDC27B 
                 AT2G20000 
                 APC core 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CCS52A1 
                 AT4G22910 
                 APC activator 
                 N 
                 TAP 
                 + 
                 4 
               
               
                 CCS52A2 
                 AT4G11920 
                 APC activator 
                 N 
                 TAP 
                 + 
                 6 
               
               
                 CCS52B 
                 AT5G13840 
                 APC activator 
                 N 
                 TAP 
                 + 
                 4 
               
               
                 CDC20.1 
                 AT4G33270 
                 APC activator 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 CDC20.3 
                 AT5G27080 
                 APC activator 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 CDC20.6 
                 AT5G27945 
                 APC activator 
                 C 
                 TAP 
                 − 
               
               
                 RPN1a 
                 AT2G20580 
                 26S proteasome 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 CDC6 
                 AT2G29680 
                 DNA replication 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 CDC6b 
                 AT1G07270 
                 DNA replication 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 CTF8 
                 AT5G52220 
                 DNA replication 
                 N 
                 GS 
                 + 
                 2 
               
               
                 ETG1 
                 AT2G40550 
                 DNA replication 
                 C + N 
                 TAP 
                 + 
                 4 
               
               
                 MCM6 
                 AT5G44635 
                 DNA replication 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 MCM7 
                 AT4G02060 
                 DNA replication 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 ORC1a 
                 AT4G14700 
                 DNA replication 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 PCNA1 
                 AT1G07370 
                 DNA replication 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 RPA2 
                 AT2G24490 
                 DNA replication 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 UVH6 
                 AT1G03190 
                 DNA repair 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 BUB3 
                 AT1G69400 
                 mitotic checkpoint 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 BUB3-like 
                 AT3G19590 
                 mitotic checkpoint 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 BUBR1-like 
                 AT2G33560 
                 mitotic checkpoint 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 MAD2-like 
                 AT3G25980 
                 mitotic checkpoint 
                 N 
                 TAP 
                 + 
                 3 
               
               
                 DL3195C 
                 AT4G14310 
                 reverse 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 F27G20.14 
                 AT1G32310 
                 reverse 
                 C 
                 GS 
                 + 
                 2 
               
               
                 expressed 
                 AT5G40460 
                 reverse 
                 C 
                 TAP 
                 + 
                 2 
               
               
                 expressed 
                 AT1G10690 
                 reverse 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 UVI4 
                 AT2G42260 
                 reverse 
                 N 
                 TAP 
                 + 
                 2 
               
               
                 UVI4-like 
                 AT3G57860 
                 reverse 
                 N 
                 TAP 
                 + 
                 2 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 List of control identifications. 
               
               
                 Control identifications determined by mock TAP (7) or GS (3) 
               
               
                 purifications, and by purifications with extracts from cultures 
               
               
                 expressing TAP fusions of heterologous GFP (7), RFP (2) or 
               
               
                 β-glucuronidase (5), or GS fusions of heterologous GFP (8), 
               
               
                 or β-glucuronidase (4). Ribosomal proteins, actins and tubulins 
               
               
                 identified in these control experiments were not included. 
               
               
                 The number of control experiments is shown between brackets. 
               
             
          
           
               
                 Accession 
                   
               
               
                 number 
                 Protein name 
               
               
                   
               
               
                 AT1G01460 
                 phosphatidylinositol-4-phosphate 5-kinase family protein 
               
               
                 AT1G02400 
                 gibberellin 2-oxidase, putative/GA2-oxidase, putative 
               
               
                 AT1G02500 
                 S-adenosylmethionine synthetase 1 (SAM1) 
               
               
                 AT1G02930 
                 glutathione S-transferase, putative 
               
               
                 AT1G04190 
                 tetratricopeptide repeat (TPR)-containing protein 
               
               
                 AT1G04600 
                 myosin, putative 
               
               
                 AT1G04690 
                 potassium channel protein, putative 
               
               
                 AT1G05320 
                 myosin-related 
               
               
                 AT1G05450 
                 protease inhibitor/seed storage/lipid transfer protein 
               
               
                   
                 (LTP)-related 
               
               
                 AT1G05970 
                 expressed protein 
               
               
                 AT1G06220 
                 elongation factor Tu family protein 
               
               
                 AT1G06780 
                 glycosyl transferase family 8 protein 
               
               
                 AT1G07920 
                 elongation factor 1-alpha 
               
               
                 AT1G07930 
                 elongation factor 1-alpha 
               
               
                 AT1G08520 
                 magnesium-chelatase subunit chlD, chloroplast, putative 
               
               
                 AT1G09080 
                 luminal binding protein 3 (BiP-3) (BP3) 
               
               
                 AT1G09450 
                 haspin-related 
               
               
                 AT1G09780 
                 2,3-biphosphoglycerate-independent phosphoglycerate 
               
               
                   
                 mutase, putative 
               
               
                 AT1G09980 
                 expressed protein 
               
               
                 AT1G10270 
                 pentatricopeptide (PPR) repeat-containing protein 
               
               
                 AT1G10390 
                 nucleoporin family protein 
               
               
                 AT1G10590 
                 DNA-binding protein-related 
               
               
                 AT1G11480 
                 eukaryotic translation initiation factor-related 
               
               
                 AT1G12410 
                 ATP-dependent Clp protease proteolytic subunit (ClpP2) 
               
               
                 AT1G13020 
                 eukaryotic translation initiation factor, putative 
               
               
                 AT1G13440 
                 glyceraldehyde 3-phosphate dehydrogenase, cytosolic, 
               
               
                   
                 putative 
               
               
                 AT1G13610 
                 expressed protein 
               
               
                 AT1G13910 
                 F16A14.12 (leucine-rich repeat family protein) 
               
               
                 AT1G14315 
                 Putative F-box protein 
               
               
                 AT1G14850 
                 non-repetitive/WGA-negative nucleoporin family protein 
               
               
                 AT1G14980 
                 10 kDa chaperonin (CPN10) 
               
               
                 AT1G15730 
                 PRLI-interacting factor L, putative (Fragment) 
               
               
                 AT1G16030 
                 heat shock protein 70, putative 
               
               
                 AT1G16410 
                 cytochrome P450, putative 
               
               
                 AT1G16750 
                 expressed protein 
               
               
                 AT1G18370 
                 kinesin motor family protein (NACK1) 
               
               
                 AT1G19290 
                 pentatricopeptide (PPR) repeat-containing protein 
               
               
                 AT1G19920 
                 sulfate adenylyltransferase 2/ATP-sulfurylase 2 
               
               
                 AT1G21480 
                 exostosin family protein 
               
               
                 AT1G23410 
                 ubiquitin extension protein, putative/40S ribosomal protein 
               
               
                   
                 S27A 
               
               
                 AT1G24300 
                 GYF domain-containing protein 
               
               
                 AT1G24510 
                 T-complex protein 1 epsilon subunit, putative 
               
               
                 AT1G24938 
                 hypothetical protein 
               
               
                 AT1G26750 
                 expressed protein 
               
               
                 AT1G27430 
                 GYF domain-containing protein 
               
               
                 AT1G27970 
                 nuclear transport factor 2 (NTF2), putative 
               
               
                 AT1G29350 
                 kinase-related 
               
               
                 AT1G29370 
                 kinase-related 
               
               
                 AT1G31230 
                 bifunctional aspartate kinase/homoserine dehydrogenase 
               
               
                 AT1G31280 
                 PAZ domain-containing protein/piwi domain-containing 
               
               
                   
                 protein (Fragment) 
               
               
                 AT1G31770 
                 ABC transporter family protein 
               
               
                 AT1G34610 
                 Ulp1 protease family protein 
               
               
                 AT1G35380 
                 hypothetical protein 
               
               
                 AT1G36120 
                 putative reverse transcriptase 
               
               
                 AT1G36280 
                 adenylosuccinate lyase, putative/adenylosuccinase, putative 
               
               
                 AT1G36580 
                 2,4-dienoyl-CoA reductase-related 
               
               
                 AT1G37200 
                 gypsy-like retrotransposon family protein 
               
               
                 AT1G44900 
                 DNA replication licensing factor, putative, similar to DNA 
               
               
                   
                 replication licensing factor MCM2 
               
               
                 AT1G48400 
                 F-box family protein 
               
               
                 AT1G48630 
                 guanine nucleotide-binding family protein/activated protein 
               
               
                   
                 kinase 
               
               
                 AT1G49040 
                 stomatal cytokinesis defective/SCD1 protein (SCD1) 
               
               
                 AT1G51380 
                 eukaryotic translation initiation factor 4A, putative 
               
               
                 AT1G51710 
                 ubiquitin-specific protease 6, putative (UBP6) 
               
               
                 AT1G52450 
                 ubiquitin carboxyl-terminal hydrolase-related 
               
               
                 AT1G52740 
                 histone H2A, putative 
               
               
                 AT1G53240 
                 malate dehydrogenase [NAD], mitochondrial, putative 
               
               
                 AT1G53550 
                 F-box family protein 
               
               
                 AT1G54270 
                 eukaryotic translation initiation factor 4A-2 
               
               
                 AT1G55490 
                 RuBisCO subunit binding-protein beta subunit, chloroplast 
               
               
                 AT1G56070 
                 elongation factor 2, putative 
               
               
                 AT1G56070 
                 elongation factor 2, putative 
               
               
                 AT1G56410 
                 heat shock cognate 70 kDa protein, putative 
               
               
                 AT1G58265 
                 cytochrome P450-related 
               
               
                 AT1G59610 
                 dynamin-like protein, putative (ADL3) 
               
               
                 AT1G61210 
                 WD-40 repeat family protein/katanin p80 subunit, putative 
               
               
                 AT1G61300 
                 disease resistance protein (NBS-LRR class), putative 
               
               
                 AT1G61570 
                 mitochondrial import inner membrane translocase (TIM13) 
               
               
                 AT1G62020 
                 coatomer protein complex, subunit alpha, putative 
               
               
                 AT1G62610 
                 short-chain dehydrogenase/reductase (SDR) family protein 
               
               
                 AT1G62630 
                 disease resistance protein (CC-NBS-LRR class), putative 
               
               
                 AT1G64520 
                 26S proteasome regulatory subunit, putative (RPN12) 
               
               
                 AT1G64550 
                 ABC transporter family protein 
               
               
                 AT1G65130 
                 ubiquitin carboxyl-terminal hydrolase-related 
               
               
                 AT1G65290 
                 acyl carrier family protein/ACP family protein 
               
               
                 AT1G65540 
                 calcium-binding EF hand family protein 
               
               
                 AT1G65870 
                 disease resistance-responsive family protein 
               
               
                 AT1G66410 
                 calmodulin 
               
               
                 AT1G66510 
                 AAR2 protein family 
               
               
                 AT1G67090 
                 ribulose bisphosphate carboxylase small chain 1A 
               
               
                 AT1G68750 
                 phosphoenolpyruvate carboxylase family protein 
               
               
                 AT1G68910 
                 expressed protein similar to Myosin heavy chain, 
               
               
                   
                 nonmuscle type B 
               
               
                 AT1G70100 
                 expressed protein 
               
               
                 AT1G71220 
                 UDP-glucose:glycoprotein glucosyltransferase, putative 
               
               
                 AT1G71270 
                 Vps52/Sac2 family protein 
               
               
                 AT1G72000 
                 beta-fructofuranosidase, putative/invertase, putative/ 
               
               
                   
                 saccharase, putative 
               
               
                 AT1G72730 
                 eukaryotic translation initiation factor 4A, putative 
               
               
                 AT1G73720 
                 transducin family protein/WD-40 repeat family protein 
               
               
                 AT1G75010 
                 MORN (Membrane Occupation and Recognition Nexus) 
               
               
                   
                 repeat-containing protein 
               
               
                 AT1G76520 
                 auxin efflux carrier family protein 
               
               
                 AT1G76530 
                 auxin efflux carrier family protein 
               
               
                 AT1G77120 
                 alcohol dehydrogenase (ADH) 
               
               
                 AT1G78130 
                 transporter-related low similarity to spinster type III 
               
               
                 AT1G78390 
                 9-cis-epoxycarotenoid dioxygenase, putative 
               
               
                 AT1G78900 
                 vacuolar ATP synthase catalytic subunit A 
               
               
                 AT1G79280 
                 expressed protein 
               
               
                 AT1G79550 
                 phosphoglycerate kinase, putative 
               
               
                 AT1G79920 
                 heat shock protein 70, putative 
               
               
                 AT1G79930 
                 heat shock protein, putative 
               
               
                 AT1G80070 
                 splicing factor, putative 
               
               
                 AT1G80270 
                 DNA-binding protein, putative 
               
               
                 AT1G80670 
                 transducin family protein/WD-40 repeat family protein 
               
               
                 AT2G01210 
                 leucine-rich repeat transmembrane protein kinase, putative 
               
               
                 AT2G01350 
                 quinolinate phosphoribosyl transferase family protein 
               
               
                 AT2G02160 
                 zinc finger (CCCH-type) family protein 
               
               
                 AT2G03430 
                 ankyrin repeat family protein 
               
               
                 AT2G04030 
                 heat shock protein, putative 
               
               
                 AT2G05990 
                 enoyl-[acyl-carrier protein] reductase [NADH], chloroplast, 
               
               
                   
                 putative 
               
               
                 AT2G06850 
                 xyloglucan:xyloglucosyl transferase 
               
               
                 AT2G07620 
                 putative helicase 
               
               
                 AT2G07714 
                 transcription factor-related similar to male sterility 1 
               
               
                   
                 proteins 
               
               
                 AT2G13680 
                 callose synthase 5 (1,3-beta-glucan synthase) 
               
               
                 AT2G14120 
                 dynamin-like protein 2b 
               
               
                 AT2G14880 
                 SWIB complex BAF60b domain-containing protein 
               
               
                 AT2G16600 
                 peptidyl-prolyl cis-trans isomerase, cytosolic/cyclophilin 
               
               
                 AT2G17130 
                 isocitrate dehydrogenase subunit 2/NAD+ isocitrate 
               
               
                   
                 dehydrogenase subunit 2 
               
               
                 AT2G18700 
                 glycosyl transferase family 20 protein 
               
               
                 AT2G19070 
                 transferase family protein 
               
               
                 AT2G19210 
                 leucine-rich repeat protein kinase, putative 
               
               
                 AT2G20330 
                 transducin family protein/WD-40 repeat family protein 
               
               
                 AT2G20420 
                 succinyl-CoA ligase [GDP-forming] beta-chain, 
               
               
                   
                 mitochondrial, putative 
               
               
                 AT2G20580 
                 26S proteasome regulatory subunit S2 (RPN1) 
               
               
                 AT2G20805 
                 hypothetical protein 
               
               
                 AT2G21170 
                 triosephosphate isomerase, chloroplast, putative 
               
               
                 AT2G21390 
                 coatomer protein complex, subunit alpha, putative 
               
               
                 AT2G21410 
                 vacuolar proton ATPase, putative 
               
               
                 AT2G21920 
                 hypothetical protein (Fragment) 
               
               
                 AT2G22230 
                 beta-hydroxyacyl-ACP dehydratase, putative 
               
               
                 AT2G23930 
                 small nuclear ribonucleoprotein G, putative 
               
               
                 AT2G24420 
                 DNA repair ATPase-related contains 2 transmembrane 
               
               
                   
                 domains 
               
               
                 AT2G26570 
                 expressed protein 
               
               
                 AT2G26890 
                 DNAJ heat shock N-terminal domain-containing protein 
               
               
                 AT2G27030 
                 calmodulin 
               
               
                 AT2G27610 
                 pentatricopeptide (PPR) repeat-containing protein 
               
               
                 AT2G27870 
                 hypothetical protein 
               
               
                 AT2G28000 
                 RuBisCO subunit binding-protein alpha subunit, chloroplast 
               
               
                 AT2G28620 
                 kinesin motor protein-related 
               
               
                 AT2G29540 
                 DNA-directed RNA polymerase I(A) and III(C) 14 kDa 
               
               
                   
                 subunit (RPAC14) 
               
               
                 AT2G31680 
                 Ras-related GTP-binding protein, putative 
               
               
                 AT2G32240 
                 putative myosin heavy chain 
               
               
                 AT2G33210 
                 chaperonin, putative 
               
               
                 AT2G33730 
                 DEAD box RNA helicase, putative 
               
               
                 AT2G34170 
                 expressed protein 
               
               
                 AT2G35605 
                 SWIB complex BAF60b domain-containing protein 
               
               
                 AT2G36060 
                 ubiquitin-conjugating enzyme family protein 
               
               
                 AT2G36260 
                 iron-sulfur cluster assembly complex protein, putative 
               
               
                 AT2G36460 
                 fructose-bisphosphate aldolase, putative 
               
               
                 AT2G36810 
                 expressed protein 
               
               
                 AT2G37230 
                 pentatricopeptide (PPR) repeat-containing protein 
               
               
                 AT2G37420 
                 kinesin motor protein-related 
               
               
                 AT2G38560 
                 transcription factor S-II (TFIIS) domain-containing protein 
               
               
                 AT2G38810 
                 histone H2A, putative 
               
               
                 AT2G39730 
                 ribulose bisphosphate carboxylase/oxygenase activase 
               
               
                 AT2G39990 
                 eukaryotic translation initiation factor 3 subunit 5 
               
               
                 AT2G40070 
                 expressed protein 
               
               
                 AT2G40270 
                 protein kinase family protein 
               
               
                 AT2G41450 
                 GCN5-related N-acetyltransferase (GNAT) family protein 
               
               
                 AT2G41800 
                 expressed protein 
               
               
                 AT2G42230 
                 tubulin-specific chaperone C-related 
               
               
                 AT2G42450 
                 lipase class 3 family protein 
               
               
                 AT2G42520 
                 DEAD box RNA helicase, putative 
               
               
                 AT2G43160 
                 epsin N-terminal homology (ENTH) domain-containing 
               
               
                   
                 protein 
               
               
                 AT2G43750 
                 cysteine synthase, chloroplast/O-acetylserine (thiol)-lyase 
               
               
                 AT2G44060 
                 late embryogenesis abundant family protein/LEA family 
               
               
                   
                 protein 
               
               
                 AT2G45030 
                 mitochondrial elongation factor, putative 
               
               
                 AT2G45620 
                 nucleotidyltransferase family protein 
               
               
                 AT2G46520 
                 cellular apoptosis susceptibility protein, putative/importin- 
               
               
                   
                 alpha 
               
               
                 AT2G47110 
                 ubiquitin extension protein 6 (UBQ6)/40S ribosomal protein 
               
               
                   
                 S27A 
               
               
                 AT3G01040 
                 glycosyl transferase family 8 protein 
               
               
                 AT3G01720 
                 expressed protein 
               
               
                 AT3G01740 
                 expressed protein 
               
               
                 AT3G02200 
                 proteasome family protein 
               
               
                 AT3G02230 
                 reversibly glycosylated polypeptide-1 
               
               
                 AT3G02500 
                 unknown protein 
               
               
                 AT3G02530 
                 chaperonin, putative 
               
               
                 AT3G02650 
                 pentatricopeptide (PPR) repeat-containing protein 
               
               
                 AT3G03300 
                 DEAD/DEAH box helicase carpel factory-related 
               
               
                 AT3G03780 
                 AtMS2|AtMS2 (Arabidopsis thaliana methionine 
               
               
                   
                 synthase 2) 
               
               
                 AT3G03960 
                 chaperonin, putative 
               
               
                 AT3G04120 
                 glyceraldehyde-3-phosphate dehydrogenase, cytosolic 
               
               
                 AT3G05810 
                 expressed protein 
               
               
                 AT3G07160 
                 glycosyl transferase family 48 protein 
               
               
                 AT3G07630 
                 prephenate dehydratase family protein 
               
               
                 AT3G07810 
                 heterogeneous nuclear ribonucleoprotein, putative 
               
               
                 AT3G08030 
                 expressed protein 
               
               
                 AT3G08530 
                 clathrin heavy chain, putative 
               
               
                 AT3G08590 
                 2,3-biphosphoglycerate-independent phosphoglycerate 
               
               
                   
                 mutase, putative 
               
               
                 AT3G09170 
                 Ulp1 protease family protein 
               
               
                 AT3G09350 
                 armadillo/beta-catenin repeat family protein 
               
               
                 AT3G09440 
                 heat shock cognate 70 kDa protein 3 
               
               
                 AT3G10310 
                 kinesin motor protein-related 
               
               
                 AT3G10860 
                 ubiquinol-cytochrome C reductase complex ubiquinone- 
               
               
                   
                 binding protein 
               
               
                 AT3G11130 
                 clathrin heavy chain, putative 
               
               
                 AT3G11400 
                 eukaryotic translation initiation factor 3G 
               
               
                 AT3G11770 
                 expressed protein 
               
               
                 AT3G11950 
                 ATHST; prenyltransferase 
               
               
                 AT3G12580 
                 heat shock protein 70, putative 
               
               
                 AT3G12800 
                 short-chain dehydrogenase/reductase (SDR) family protein 
               
               
                 AT3G13160 
                 pentatricopeptide (PPR) repeat-containing protein 
               
               
                 AT3G13460 
                 expressed protein 
               
               
                 AT3G13470 
                 chaperonin, putative 
               
               
                 AT3G13920 
                 eukaryotic translation initiation factor 4A-1 
               
               
                 AT3G14990 
                 4-methyl-5(b-hydroxyethyl)-thiazole monophosphate 
               
               
                   
                 biosynthesis protein 
               
               
                 AT3G15020 
                 malate dehydrogenase [NAD], mitochondrial, putative 
               
               
                 AT3G16230 
                 expressed protein similar to ASC-1 complex subunit P50 
               
               
                 AT3G16270 
                 expressed protein 
               
               
                 AT3G16540 
                 DegP protease, putative 
               
               
                 AT3G16640 
                 translationally controlled tumor family protein 
               
               
                 AT3G17300 
                 expressed protein 
               
               
                 AT3G17360 
                 kinesin motor protein-related similar to KLP2 protein 
               
               
                 AT3G17390 
                 S-adenosylmethionine synthetase, putative 
               
               
                 AT3G18000 
                 phosphoethanolamine N-methyltransferase 1 
               
               
                 AT3G18190 
                 chaperonin, putative 
               
               
                 AT3G18530 
                 expressed protein 
               
               
                 AT3G19050 
                 kinesin motor protein-related 
               
               
                 AT3G20670 
                 histone H2A, putative 
               
               
                 AT3G20780 
                 topoisomerase 6 subunit B (TOP6B) 
               
               
                 AT3G21070 
                 ATP-NAD kinase family protein 
               
               
                 AT3G22330 
                 DEAD box RNA helicase, putative 
               
               
                 AT3G22890 
                 sulfate adenylyltransferase 1/ATP-sulfurylase 1 
               
               
                 AT3G23990 
                 chaperonin (CPN60) (HSP60) 
               
               
                 AT3G24890 
                 synaptobrevin-related 
               
               
                 AT3G26020 
                 serine/threonine protein phosphatase 2A (PP2A) regulatory 
               
               
                   
                 subunit B′, putative 
               
               
                 AT3G26380 
                 glycosyl hydrolase family protein 27 
               
               
                 AT3G27400 
                 pectate lyase family protein 
               
               
                 AT3G28925 
                 hypothetical protein 
               
               
                 AT3G42100 
                 AT hook motif-containing protein-related 
               
               
                 AT3G42270 
                 putative protein 
               
               
                 AT3G43300 
                 guanine nucleotide exchange family protein 
               
               
                 AT3G43810 
                 calmodulin 
               
               
                 AT3G45770 
                 oxidoreductase, zinc-binding dehydrogenase family protein 
               
               
                 AT3G46560 
                 mitochondrial import inner membrane translocase (TIM9) 
               
               
                 AT3G46990 
                 hypothetical protein 
               
               
                 AT3G47850 
                 expressed protein 
               
               
                 AT3G48250 
                 pentatricopeptide (PPR) repeat-containing protein 
               
               
                 AT3G48670 
                 XH/XS domain-containing protein/XS zinc finger domain- 
               
               
                   
                 containing protein 
               
               
                 AT3G48870 
                 ATP-dependent Clp protease ATP-binding subunit (ClpC) 
               
               
                 AT3G49640 
                 nitrogen regulation family protein 
               
               
                 AT3G50280 
                 transferase family protein 
               
               
                 AT3G50370 
                 expressed protein 
               
               
                 AT3G51150 
                 kinesin motor family protein 
               
               
                 AT3G51570 
                 disease resistance protein (TIR-NBS-LRR class), putative 
               
               
                 AT3G51950 
                 zinc finger (CCCH-type) family protein/RNA recognition 
               
               
                   
                 motif (RRM) 
               
               
                 AT3G52140 
                 tetratricopeptide repeat (TPR)-containing protein 
               
               
                 AT3G52930 
                 fructose-bisphosphate aldolase, putative 
               
               
                 AT3G54360 
                 expressed protein DNA-binding Mel-18 protein 
               
               
                 AT3G54610 
                 histone acetyltransferase (GCN5) 
               
               
                 AT3G54940 
                 cysteine proteinase, putative 
               
               
                 AT3G55000 
                 Tonneau 1a 
               
               
                 AT3G55005 
                 Tonneau 1b 
               
               
                 AT3G55290 
                 short-chain dehydrogenase/reductase (SDR) family protein 
               
               
                 AT3G55310 
                 short-chain dehydrogenase/reductase (SDR) family protein 
               
               
                 AT3G55460 
                 SC35-like splicing factor, 30 kD (SCL30) 
               
               
                 AT3G55770 
                 LIM domain-containing protein 
               
               
                 AT3G57290 
                 eukaryotic translation initiation factor 3E 
               
               
                 AT3G58510 
                 DEAD box RNA helicase, putative (RH11) 
               
               
                 AT3G58610 
                 ketol-acid reductoisomerase 
               
               
                 AT3G59760 
                 cysteine synthase, mitochondrial, putative 
               
               
                 AT3G62010 
                 expressed protein 
               
               
                 AT3G62250 
                 ubiquitin extension protein 5 (UBQ5)/40S ribosomal 
               
               
                   
                 protein S27A 
               
               
                 AT4G00020 
                 BRCA2 repeat-containing protein 
               
               
                 AT4G01290 
                 expressed protein 
               
               
                 AT4G01800 
                 preprotein translocase secA subunit, putative 
               
               
                 AT4G02930 
                 elongation factor Tu, putative 
               
               
                 AT4G03550 
                 glycosyl transferase family 48 protein 
               
               
                 AT4G11150 
                 vacuolar ATP synthase subunit E 
               
               
                 AT4G11420 
                 eukaryotic translation initiation factor 3 subunit 10 
               
               
                 AT4G12130 
                 glycine cleavage T family protein 
               
               
                 AT4G12770 
                 auxilin-related 
               
               
                 AT4G12780 
                 auxilin-like protein 
               
               
                 AT4G14060 
                 major latex protein-related 
               
               
                 AT4G14130 
                 xyloglucan:xyloglucosyl transferase, putative 
               
               
                 AT4G14140 
                 DNA (cytosine-5-)-methyltransferase (METII) 
               
               
                 AT4G14260 
                 hypothetical protein 
               
               
                 AT4G15640 
                 expressed protein 
               
               
                 AT4G15760 
                 monooxygenase, putative (MO1) 
               
               
                 AT4G17150 
                 unknown protein 
               
               
                 AT4G17440 
                 expressed protein 
               
               
                 AT4G17720 
                 RNA recognition motif (RRM)-containing protein 
               
               
                 AT4G18040 
                 eukaryotic translation initiation factor 4E 1 
               
               
                 AT4G18080 
                 hypothetical protein 
               
               
                 AT4G19530 
                 disease resistance protein (TIR-NBS-LRR class), putative 
               
               
                 AT4G20160 
                 expressed protein 
               
               
                 AT4G20360 
                 elongation factor Tu 
               
               
                 AT4G20980 
                 eukaryotic translation initiation factor 3 subunit 7, putative 
               
               
                 AT4G23670 
                 major latex protein-related 
               
               
                 AT4G23850 
                 long-chain-fatty-acid--CoA ligase/long-chain acyl-CoA 
               
               
                   
                 synthetase 
               
               
                 AT4G24100 
                 protein kinase family protein 
               
               
                 AT4G24280 
                 heat shock protein 70, putative 
               
               
                 AT4G24760 
                 expressed protein 
               
               
                 AT4G25580 
                 stress-responsive protein-related 
               
               
                 AT4G26900 
                 imidazole glycerol phosphate synthase hisHF, chloroplast 
               
               
                 AT4G27440 
                 protochlorophyllide reductase B, chloroplast 
               
               
                 AT4G28400 
                 protein phosphatase 2C, putative 
               
               
                 AT4G29800 
                 patatin-related low similarity to patatin precursor 
               
               
                 AT4G31805 
                 WRKY family transcription factor 
               
               
                 AT4G31820 
                 phototropic-responsive NPH3 family protein 
               
               
                 AT4G31990 
                 aspartate aminotransferase, chloroplast/transaminase A 
               
               
                   
                 (ASP5) (AAT1) 
               
               
                 AT4G32500 
                 potassium channel protein, putative 
               
               
                 AT4G32551 
                 WD-40 repeat family protein (LEUNIG) 
               
               
                 AT4G33200 
                 myosin, putative 
               
               
                 AT4G34290 
                 SWIB complex BAF60b domain-containing protein 
               
               
                 AT4G34350 
                 LytB family protein 
               
               
                 AT4G35260 
                 isocitrate dehydrogenase subunit 1/NAD+ isocitrate 
               
               
                   
                 dehydrogenase subunit 1 
               
               
                 AT4G35650 
                 isocitrate dehydrogenase, putative/NAD+ isocitrate 
               
               
                   
                 dehydrogenase, putative 
               
               
                 AT4G35890 
                 La domain-containing protein 
               
               
                 AT4G35970 
                 L-ascorbate peroxidase, putative 
               
               
                 AT4G36960 
                 RNA recognition motif (RRM)-containing protein 
               
               
                 AT4G37420 
                 hypothetical protein 
               
               
                 AT4G37580 
                 N-acetyltransferase, putative/hookless1 (HLS1) 
               
               
                 AT4G37910 
                 heat shock protein 70, mitochondrial, putative 
               
               
                 AT4G38030 
                 hypothetical protein 
               
               
                 AT4G38070 
                 bHLH family protein 
               
               
                 AT4G39580 
                 kelch repeat-containing F-box family protein 
               
               
                 AT5G01010 
                 expressed protein 
               
               
                 AT5G02490 
                 heat shock cognate 70 kDa protein 2 
               
               
                 AT5G02500 
                 heat shock cognate 70 kDa protein 1 
               
               
                 AT5G02590 
                 chloroplast lumen common family protein 
               
               
                 AT5G03340 
                 cell division cycle protein 48, putative 
               
               
                 AT5G03650 
                 1,4-alpha-glucan branching enzyme 
               
               
                 AT5G03690 
                 fructose-bisphosphate aldolase, putative 
               
               
                 AT5G04590 
                 sulfite reductase/ferredoxin 
               
               
                 AT5G05370 
                 ubiquinol-cytochrome C reductase complex ubiquinone- 
               
               
                   
                 binding protein 
               
               
                 AT5G05640 
                 nucleoprotein-related 
               
               
                 AT5G05780 
                 26S proteasome non-ATPase regulatory subunit 7, putative 
               
               
                 AT5G06140 
                 phox (PX) domain-containing protein 
               
               
                 AT5G06400 
                 pentatricopeptide (PPR) repeat-containing protein 
               
               
                 AT5G06450 
                 expressed protein 
               
               
                 AT5G06850 
                 anthranilate phosphoribosyltransferase-like protein 
               
               
                 AT5G08415 
                 lipoic acid synthase family protein 
               
               
                 AT5G08670 
                 ATP synthase beta chain, mitochondrial 
               
               
                 AT5G08680 
                 ATP synthase beta chain, mitochondrial 
               
               
                 AT5G08690 
                 ATP synthase beta chain, mitochondrial 
               
               
                 AT5G09590 
                 heat shock protein 70 
               
               
                 AT5G09900 
                 26S proteasome regulatory subunit, putative (RPN5) 
               
               
                 AT5G10160 
                 beta-hydroxyacyl-ACP dehydratase, putative 
               
               
                 AT5G11110 
                 sucrose-phosphate synthase-like protein 
               
               
                 AT5G11340 
                 GCN5-related N-acetyltransferase (GNAT) family protein 
               
               
                 AT5G12010 
                 expressed protein 
               
               
                 AT5G12240 
                 expressed protein 
               
               
                 AT5G12310 
                 zinc finger (C3HC4-type RING finger) family protein 
               
               
                 AT5G13130 
                 hypothetical protein low similarity to microrchidia 
               
               
                 AT5G14040 
                 mitochondrial phosphate transporter 
               
               
                 AT5G15580 
                 expressed protein 
               
               
                 AT5G15610 
                 proteasome family protein 
               
               
                 AT5G15650 
                 reversibly glycosylated polypeptide-2 
               
               
                 AT5G15920 
                 structural maintenance of chromosomes (SMC) family 
               
               
                   
                 protein 
               
               
                 AT5G16070 
                 chaperonin, putative 
               
               
                 AT5G17680 
                 disease resistance protein (TIR-NBS-LRR class), putative 
               
               
                 AT5G17890 
                 LIM domain-containing protein/disease resistance protein- 
               
               
                   
                 related 
               
               
                 AT5G17920 
                 5-methyltetrahydropteroyltriglutamate--homocysteine 
               
               
                   
                 methyltransferase 
               
               
                 AT5G18110 
                 novel cap-binding protein (nCBP) 
               
               
                 AT5G18730 
                 hypothetical protein 
               
               
                 AT5G19310 
                 homeotic gene regulator, putative 
               
               
                 AT5G19550 
                 aspartate aminotransferase, cytoplasmic isozyme 
               
               
                   
                 1/transaminase A 
               
               
                 AT5G20010 
                 Ras-related GTP-binding nuclear protein 
               
               
                 AT5G20020 
                 Ras-related GTP-binding nuclear protein 
               
               
                 AT5G20360 
                 octicosapeptide/Phox/Bem1p (PB1) domain-containing 
               
               
                   
                 protein (Fragment) 
               
               
                 AT5G20720 
                 20 kDa chaperonin, chloroplast 
               
               
                 AT5G20890 
                 chaperonin, putative 
               
               
                 AT5G21274 
                 calmodulin 
               
               
                 AT5G22650 
                 expressed protein 
               
               
                 AT5G23540 
                 26S proteasome regulatory subunit, putative 
               
               
                 AT5G23890 
                 expressed protein 
               
               
                 AT5G23930 
                 mitochondrial transcription termination factor-related 
               
               
                 AT5G24710 
                 WD-40 repeat family protein 
               
               
                 AT5G25230 
                 elongation factor Tu family protein 
               
               
                 AT5G25940 
                 early nodulin-related 
               
               
                 AT5G26200 
                 mitochondrial substrate carrier family protein 
               
               
                 AT5G26710 
                 glutamate-tRNA ligase, putative 
               
               
                 AT5G26742 
                 DEAD box RNA helicase (RH3) 
               
               
                 AT5G26800 
                 expressed protein 
               
               
                 AT5G27390 
                 expressed protein 
               
               
                 AT5G27920 
                 F-box family protein 
               
               
                 AT5G28430 
                 hypothetical protein 
               
               
                 AT5G28540 
                 luminal binding protein 1 
               
               
                 AT5G28850 
                 calcium-binding EF hand family protein 
               
               
                 AT5G35360 
                 acetyl-CoA carboxylase, biotin carboxylase subunit (CAC2) 
               
               
                 AT5G35620 
                 eukaryotic translation initiation factor 4E 2 
               
               
                 AT5G36670 
                 putative protein 
               
               
                 AT5G37150 
                 tRNA-splicing endonuclease positive effector-related 
               
               
                 AT5G37470 
                 hypothetical protein 
               
               
                 AT5G37510 
                 NADH-ubiquinone dehydrogenase, mitochondrial, putative 
               
               
                 AT5G39320 
                 UDP-glucose 6-dehydrogenase, putative 
               
               
                 AT5G40060 
                 disease resistance protein (TIR-NBS-LRR class), putative 
               
               
                 AT5G40760 
                 glucose-6-phosphate 1-dehydrogenase/G6PD 
               
               
                 AT5G42020 
                 luminal binding protein 2 
               
               
                 AT5G42080 
                 GTP-binding protein/phragmoplastin, putative 
               
               
                 AT5G42950 
                 GYF domain-containing protein 
               
               
                 AT5G42980 
                 thioredoxin H-type 3 
               
               
                 AT5G43780 
                 sulfate adenylyltransferase 4/ATP-sulfurylase 4 
               
               
                 AT5G44320 
                 eukaryotic translation initiation factor 3 subunit 7, putative 
               
               
                 AT5G44510 
                 disease resistance protein (TIR-NBS-LRR class), putative 
               
               
                   
                 (TAO1) 
               
               
                 AT5G45060 
                 disease resistance protein (TIR-NBS-LRR class), putative 
               
               
                 AT5G45140 
                 DNA-directed RNA polymerase, putative 
               
               
                 AT5G47460 
                 pentatricopeptide (PPR) repeat-containing protein 
               
               
                 AT5G47890 
                 NADH-ubiquinone oxidoreductase B8 subunit, putative 
               
               
                 AT5G48620 
                 disease resistance protein (CC-NBS-LRR class), putative 
               
               
                   
                 (Fragment) 
               
               
                 AT5G49030 
                 tRNA synthetase class I (I, L, M and V) family protein 
               
               
                 AT5G49910 
                 heat shock protein 70 
               
               
                 AT5G50370 
                 adenylate kinase, putative 
               
               
                 AT5G50810 
                 mitochondrial import inner membrane translocase (TIM8) 
               
               
                 AT5G50920 
                 ATP-dependent Clp protease ATP-binding subunit (ClpC) 
               
               
                 AT5G51000 
                 F-box family protein 
               
               
                 AT5G51670 
                 expressed protein 
               
               
                 AT5G51795 
                 Kin17 DNA-binding protein-related (Fragment) 
               
               
                 AT5G52040 
                 arginine/serine-rich splicing factor RSP41 (RSP41) 
               
               
                 AT5G52400 
                 cytochrome P450 family protein 
               
               
                 AT5G53460 
                 glutamate synthase [NADH], chloroplast, putative 
               
               
                 AT5G54640 
                 histone H2A 
               
               
                 AT5G54670 
                 kinesin-like protein C (KATC) 
               
               
                 AT5G55190 
                 Ras-related GTP-binding nuclear protein 
               
               
                 AT5G56000 
                 heat shock protein 81 
               
               
                 AT5G56030 
                 heat shock protein 81 
               
               
                 AT5G56500 
                 chaperonin, putative 
               
               
                 AT5G57350 
                 ATPase 3, plasma membrane-type/proton pump 3 
               
               
                 AT5G58070 
                 lipocalin, putative similar to temperature stress-induced 
               
               
                   
                 lipocalin 
               
               
                 AT5G59220 
                 protein phosphatase 2C, putative 
               
               
                 AT5G59620 
                 putative protein 
               
               
                 AT5G59880 
                 actin-depolymerizing factor 3 (ADF3) 
               
               
                 AT5G60390 
                 elongation factor 1-alpha 
               
               
                 AT5G60720 
                 expressed protein 
               
               
                 AT5G60980 
                 nuclear transport factor 2 (NTF2) family protein 
               
               
                 AT5G61780 
                 tudor domain-containing protein/nuclease family protein 
               
               
                 AT5G63020 
                 disease resistance protein (CC-NBS-LRR class), putative 
               
               
                 AT5G63400 
                 adenylate kinase 
               
               
                 AT5G63800 
                 glycosyl hydrolase family 35 protein 
               
               
                 AT5G64760 
                 26S proteasome regulatory subunit, putative (RPN5) 
               
               
                 AT5G66470 
                 expressed protein 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
             
               
             
               
               
               
               
               
               
             
               
             
               
               
             
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 3 
               
               
                   
               
               
                 Overrepresentation of Biological Processes among the preys of the core (A) and 
               
               
                 non-core (B) dataset as determined with the Cytoscape plugin BiNGO. 
               
               
                   
               
             
             
               
                 A. Overrepresentation of Biological Processes among the preys of the core dataset. 
               
               
                   
               
             
          
           
               
                   
                 Search parameters: 
               
               
                   
                 File created with BiNGO (c) on 22-okt-2008 at 16:17:17 
               
               
                   
                 ontology: process 
               
               
                   
                 curator: GO 
               
               
                   
                 Selected ontology file: BiNGO.jar!/GO_Biological_Process 
               
               
                   
                 Selected annotation file: gene_association_2008okt04.tair 
               
               
                   
                 Overrepresentation 
               
               
                   
                 Selected statistical test: Hypergeometric test 
               
               
                   
                 Selected correction: Benjamini &amp; Hochberg False Discovery Rate (FDR) correction 
               
               
                   
                 Selected significance level: 0.05 
               
               
                   
                 Testing option: Test cluster versus whole annotation 
               
               
                   
                 Number of annotated genes in selection: 137 
               
               
                   
                 Number of annotated genes in network/whole annotation: 25557 
               
               
                   
                   
               
             
          
           
               
                 Results: 
               
             
          
           
               
                   
                   
                 corr 
                 # 
                   
                   
               
               
                 GO-ID 
                 p-value 
                 p-value 
                 selected 
                 # total 
                 Description 
               
               
                   
               
               
                 7049 
                 2.30E−34 
                 7.17E−32 
                 28 
                 164 
                 cell cycle 
               
               
                 51726 
                 1.11E−28 
                 1.74E−26 
                 21 
                 93 
                 regulation of cell cycle 
               
               
                 6260 
                 2.09E−18 
                 2.17E−16 
                 16 
                 116 
                 DNA replication 
               
               
                 6263 
                 4.33E−18 
                 3.38E−16 
                 13 
                 58 
                 DNA-dependent DNA replication 
               
               
                 74 
                 8.10E−15 
                 5.05E−13 
                 9 
                 26 
                 regulation of progression through cell cycle 
               
               
                 6259 
                 7.00E−14 
                 3.60E−12 
                 21 
                 463 
                 DNA metabolism 
               
               
                 43285 
                 8.43E−14 
                 3.60E−12 
                 18 
                 312 
                 biopolymer catabolism 
               
               
                 30163 
                 9.23E−14 
                 3.60E−12 
                 17 
                 268 
                 protein catabolism 
               
               
                 9057 
                 3.38E−13 
                 1.10E−11 
                 19 
                 390 
                 macromolecule catabolism 
               
               
                 6511 
                 4.22E−13 
                 1.10E−11 
                 16 
                 249 
                 ubiquitin-dependent protein catabolism 
               
               
                 43632 
                 4.22E−13 
                 1.10E−11 
                 16 
                 249 
                 modification-dependent macromolecule catabolism 
               
               
                 19941 
                 4.22E−13 
                 1.10E−11 
                 16 
                 249 
                 modification-dependent protein catabolism 
               
               
                 51603 
                 4.77E−13 
                 1.15E−11 
                 16 
                 251 
                 proteolysis during cellular protein catabolism 
               
               
                 44257 
                 6.86E−13 
                 1.53E−11 
                 16 
                 257 
                 cellular protein catabolism 
               
               
                 44265 
                 1.05E−12 
                 2.19E−11 
                 18 
                 362 
                 cellular macromolecule catabolism 
               
               
                 79 
                 4.38E−12 
                 8.55E−11 
                 6 
                 10 
                 regulation of cyclin-dependent protein kinase activity 
               
               
                 6270 
                 1.91E−11 
                 3.51E−10 
                 6 
                 12 
                 DNA replication initiation 
               
               
                 278 
                 3.69E−11 
                 6.40E−10 
                 8 
                 40 
                 mitotic cell cycle 
               
               
                 6469 
                 2.27E−10 
                 3.38E−09 
                 5 
                 8 
                 negative regulation of protein kinase activity 
               
               
                 45736 
                 2.27E−10 
                 3.38E−09 
                 5 
                 8 
                 negative regulation of cyclin-dependent protein kinase activity 
               
               
                 51348 
                 2.27E−10 
                 3.38E−09 
                 5 
                 8 
                 negative regulation of transferase activity 
               
               
                 8151 
                 2.45E−10 
                 3.47E−09 
                 97 
                 11293 
                 cellular physiological process 
               
               
                 9056 
                 3.36E−10 
                 4.55E−09 
                 19 
                 582 
                 catabolism 
               
               
                 45786 
                 5.09E−10 
                 6.62E−09 
                 5 
                 9 
                 negative regulation of progression through cell cycle 
               
               
                 42023 
                 5.44E−10 
                 6.79E−09 
                 6 
                 19 
                 DNA endoreduplication 
               
               
                 43086 
                 1.01E−09 
                 1.22E−08 
                 5 
                 10 
                 negative regulation of enzyme activity 
               
               
                 44248 
                 1.30E−09 
                 1.50E−08 
                 18 
                 560 
                 cellular catabolism 
               
               
                 43283 
                 1.38E−09 
                 1.54E−08 
                 48 
                 3695 
                 biopolymer metabolism 
               
               
                 45859 
                 1.99E−09 
                 2.04E−08 
                 6 
                 23 
                 regulation of protein kinase activity 
               
               
                 43549 
                 1.99E−09 
                 2.04E−08 
                 6 
                 23 
                 regulation of kinase activity 
               
               
                 9987 
                 2.03E−09 
                 2.04E−08 
                 98 
                 11858 
                 cellular process 
               
               
                 51338 
                 2.64E−09 
                 2.58E−08 
                 6 
                 24 
                 regulation of transferase activity 
               
               
                 50794 
                 6.88E−09 
                 6.51E−08 
                 33 
                 2040 
                 regulation of cellular process 
               
               
                 51325 
                 7.92E−09 
                 7.06E−08 
                 5 
                 14 
                 interphase 
               
               
                 51329 
                 7.92E−09 
                 7.06E−08 
                 5 
                 14 
                 interphase of mitotic cell cycle 
               
               
                 51244 
                 1.26E−08 
                 1.09E−07 
                 32 
                 1980 
                 regulation of cellular physiological process 
               
               
                 50791 
                 3.60E−08 
                 3.04E−07 
                 32 
                 2070 
                 regulation of physiological process 
               
               
                 7582 
                 1.33E−07 
                 1.09E−06 
                 100 
                 13066 
                 physiological process 
               
               
                 50789 
                 2.21E−07 
                 1.77E−06 
                 33 
                 2359 
                 regulation of biological process 
               
               
                 50790 
                 2.72E−07 
                 2.12E−06 
                 7 
                 81 
                 regulation of catalytic activity 
               
               
                 6139 
                 6.29E−07 
                 4.79E−06 
                 37 
                 2974 
                 nucleobase, nucleoside, nucleotide and nucleic acid 
               
               
                   
                   
                   
                   
                   
                 metabolism 
               
               
                 43170 
                 1.23E−06 
                 9.17E−06 
                 60 
                 6396 
                 macromolecule metabolism 
               
               
                 6508 
                 1.61E−06 
                 1.17E−05 
                 16 
                 718 
                 proteolysis 
               
               
                 51302 
                 1.24E−05 
                 8.77E−05 
                 3 
                 9 
                 regulation of cell division 
               
               
                 44238 
                 1.87E−05 
                 1.30E−04 
                 69 
                 8433 
                 primary metabolism 
               
               
                 51510 
                 2.85E−05 
                 1.93E−04 
                 2 
                 2 
                 regulation of unidimensional cell growth 
               
               
                 44237 
                 1.45E−04 
                 9.61E−04 
                 67 
                 8584 
                 cellular metabolism 
               
               
                 80 
                 1.70E−04 
                 1.06E−03 
                 2 
                 4 
                 G1 phase of mitotic cell cycle 
               
               
                 82 
                 1.70E−04 
                 1.06E−03 
                 2 
                 4 
                 G1/S transition of mitotic cell cycle 
               
               
                 51318 
                 1.70E−04 
                 1.06E−03 
                 2 
                 4 
                 G1 phase 
               
               
                 7346 
                 2.82E−04 
                 1.73E−03 
                 2 
                 5 
                 regulation of progression through mitotic cell cycle 
               
               
                 48856 
                 3.80E−04 
                 2.28E−03 
                 17 
                 1248 
                 anatomical structure development 
               
               
                 48519 
                 4.57E−04 
                 2.69E−03 
                 6 
                 182 
                 negative regulation of biological process 
               
               
                 9653 
                 5.58E−04 
                 3.22E−03 
                 10 
                 526 
                 morphogenesis 
               
               
                 51243 
                 6.65E−04 
                 3.72E−03 
                 5 
                 129 
                 negative regulation of cellular physiological process 
               
               
                 51301 
                 6.67E−04 
                 3.72E−03 
                 3 
                 32 
                 cell division 
               
               
                 48523 
                 6.89E−04 
                 3.77E−03 
                 5 
                 130 
                 negative regulation of cellular process 
               
               
                 1558 
                 7.82E−04 
                 4.21E−03 
                 2 
                 8 
                 regulation of cell growth 
               
               
                 43118 
                 1.02E−03 
                 5.42E−03 
                 5 
                 142 
                 negative regulation of physiological process 
               
               
                 6281 
                 1.09E−03 
                 5.67E−03 
                 5 
                 144 
                 DNA repair 
               
               
                 9793 
                 1.28E−03 
                 6.56E−03 
                 9 
                 487 
                 embryonic development (sensu Magnoliophyta) 
               
               
                 6974 
                 1.47E−03 
                 7.39E−03 
                 5 
                 154 
                 response to DNA damage stimulus 
               
               
                 9790 
                 2.01E−03 
                 9.94E−03 
                 9 
                 520 
                 embryonic development 
               
               
                 48316 
                 2.28E−03 
                 1.11E−02 
                 9 
                 530 
                 seed development 
               
               
                 48272 
                 2.32E−03 
                 1.11E−02 
                 3 
                 49 
                 trichome morphogenesis (sensu Magnoliophyta) 
               
               
                 48608 
                 2.37E−03 
                 1.12E−02 
                 9 
                 533 
                 reproductive structure development 
               
               
                 7148 
                 2.43E−03 
                 1.13E−02 
                 6 
                 252 
                 cell morphogenesis 
               
               
                 6457 
                 2.58E−03 
                 1.18E−02 
                 6 
                 255 
                 protein folding 
               
               
                 904 
                 2.60E−03 
                 1.18E−02 
                 3 
                 51 
                 cellular morphogenesis during differentiation 
               
               
                 7017 
                 2.66E−03 
                 1.19E−02 
                 4 
                 107 
                 microtubule-based process 
               
               
                 7275 
                 2.81E−03 
                 1.23E−02 
                 19 
                 1765 
                 development 
               
               
                 9965 
                 2.94E−03 
                 1.27E−02 
                 4 
                 110 
                 leaf morphogenesis 
               
               
                 7018 
                 3.23E−03 
                 1.37E−02 
                 3 
                 55 
                 microtubule-based movement 
               
               
                 9934 
                 3.26E−03 
                 1.37E−02 
                 2 
                 16 
                 regulation of meristem organization 
               
               
                 8152 
                 3.29E−03 
                 1.37E−02 
                 70 
                 10044 
                 metabolism 
               
               
                 19952 
                 3.72E−03 
                 1.53E−02 
                 11 
                 794 
                 reproduction 
               
               
                 48827 
                 3.90E−03 
                 1.58E−02 
                 5 
                 193 
                 phyllome development 
               
               
                 16043 
                 3.95E−03 
                 1.58E−02 
                 16 
                 1420 
                 cell organization and biogenesis 
               
               
                 9117 
                 4.64E−03 
                 1.83E−02 
                 4 
                 125 
                 nucleotide metabolism 
               
               
                 35315 
                 4.95E−03 
                 1.91E−02 
                 3 
                 64 
                 hair cell differentiation 
               
               
                 10026 
                 4.95E−03 
                 1.91E−02 
                 3 
                 64 
                 trichome differentiation (sensu Magnoliophyta) 
               
               
                 51446 
                 5.36E−03 
                 2.02E−02 
                 1 
                 1 
                 positive regulation of progression through meiotic cell cycle 
               
               
                 51445 
                 5.36E−03 
                 2.02E−02 
                 1 
                 1 
                 regulation of progression through meiotic cell cycle 
               
               
                 30154 
                 5.56E−03 
                 2.07E−02 
                 5 
                 210 
                 cell differentiation 
               
               
                 9887 
                 5.67E−03 
                 2.08E−02 
                 5 
                 211 
                 organ morphogenesis 
               
               
                 30705 
                 6.86E−03 
                 2.49E−02 
                 3 
                 72 
                 cytoskeleton-dependent intracellular transport 
               
               
                 48468 
                 8.86E−03 
                 3.18E−02 
                 3 
                 79 
                 cell development 
               
               
                 10016 
                 8.97E−03 
                 3.18E−02 
                 4 
                 151 
                 shoot morphogenesis 
               
               
                 7276 
                 9.80E−03 
                 3.44E−02 
                 4 
                 155 
                 gametogenesis 
               
               
                 7050 
                 1.07E−02 
                 3.51E−02 
                 1 
                 2 
                 cell cycle arrest 
               
               
                 42276 
                 1.07E−02 
                 3.51E−02 
                 1 
                 2 
                 error-prone postreplication DNA repair 
               
               
                 86 
                 1.07E−02 
                 3.51E−02 
                 1 
                 2 
                 G2/M transition of mitotic cell cycle 
               
               
                 45020 
                 1.07E−02 
                 3.51E−02 
                 1 
                 2 
                 error-prone DNA repair 
               
               
                 184 
                 1.07E−02 
                 3.51E−02 
                 1 
                 2 
                 mRNA catabolism, nonsense-mediated decay 
               
               
                 6358 
                 1.07E−02 
                 3.51E−02 
                 1 
                 2 
                 regulation of global transcription from RNA polymerase II 
               
               
                   
                   
                   
                   
                   
                 promoter 
               
               
                 46907 
                 1.10E−02 
                 3.58E−02 
                 7 
                 451 
                 intracellular transport 
               
               
                 9165 
                 1.15E−02 
                 3.70E−02 
                 3 
                 87 
                 nucleotide biosynthesis 
               
               
                 51649 
                 1.18E−02 
                 3.75E−02 
                 7 
                 457 
                 establishment of cellular localization 
               
               
                 51641 
                 1.27E−02 
                 3.93E−02 
                 7 
                 464 
                 cellular localization 
               
               
                 9744 
                 1.27E−02 
                 3.93E−02 
                 2 
                 32 
                 response to sucrose stimulus 
               
               
                 40008 
                 1.27E−02 
                 3.93E−02 
                 2 
                 32 
                 regulation of growth 
               
               
                 48366 
                 1.59E−02 
                 4.76E−02 
                 4 
                 179 
                 leaf development 
               
               
                 16288 
                 1.60E−02 
                 4.76E−02 
                 2 
                 36 
                 cytokinesis 
               
               
                 10071 
                 1.60E−02 
                 4.76E−02 
                 1 
                 3 
                 root meristem specification 
               
               
                 48367 
                 1.60E−02 
                 4.76E−02 
                 5 
                 273 
                 shoot development 
               
               
                   
               
             
          
           
               
                 B. Overrepresentation of Biological Processes among the preys of the non-core dataset. 
               
               
                   
               
             
          
           
               
                   
                 Search parameters: 
               
               
                   
                 File created with BiNGO (c) on 22-okt-2008 at 16:28:37 
               
               
                   
                 ontology: process 
               
               
                   
                 curator: GO 
               
               
                   
                 Selected ontology file: BiNGO.jar!/GO_Biological_Process 
               
               
                   
                 Selected annotation file: gene_association_2008okt04.tair 
               
               
                   
                 Overrepresentation 
               
               
                   
                 Selected statistical test: Hypergeometric test 
               
               
                   
                 Selected correction: Benjamini &amp; Hochberg False Discovery Rate (FDR) correction 
               
               
                   
                 Selected significance level: 0.05 
               
               
                   
                 Testing option: Test cluster versus whole annotation 
               
               
                   
                 Number of annotated genes in selection: 197 
               
               
                   
                 Number of annotated genes in network/whole annotation: 25538 
               
               
                   
                   
               
             
          
           
               
                 Results: 
               
             
          
           
               
                   
                   
                 corr 
                 # 
                   
                   
               
               
                 GO-ID 
                 p-value 
                 p-value 
                 selected 
                 # total 
                 Description 
               
               
                   
               
               
                 46686 
                 5.78E−13 
                 3.14E−10 
                 22 
                 396 
                 response to cadmium ion 
               
               
                 10038 
                 4.07E−12 
                 1.11E−09 
                 22 
                 437 
                 response to metal ion 
               
               
                 10035 
                 9.76E−12 
                 1.77E−09 
                 22 
                 457 
                 response to inorganic substance 
               
               
                 7049 
                 4.69E−11 
                 6.38E−09 
                 14 
                 166 
                 cell cycle 
               
               
                 51726 
                 2.75E−09 
                 2.99E−07 
                 10 
                 93 
                 regulation of cell cycle 
               
               
                 42221 
                 1.01E−08 
                 9.16E−07 
                 38 
                 1789 
                 response to chemical stimulus 
               
               
                 6259 
                 2.22E−08 
                 1.73E−06 
                 18 
                 462 
                 DNA metabolism 
               
               
                 8151 
                 8.57E−08 
                 5.83E−06 
                 124 
                 11291 
                 cellular physiological process 
               
               
                 50896 
                 1.42E−07 
                 8.56E−06 
                 56 
                 3617 
                 response to stimulus 
               
               
                 9987 
                 2.38E−07 
                 1.29E−05 
                 127 
                 11856 
                 cellular process 
               
               
                 42023 
                 2.76E−07 
                 1.36E−05 
                 5 
                 19 
                 DNA endoreduplication 
               
               
                 6263 
                 3.15E−07 
                 1.36E−05 
                 7 
                 58 
                 DNA-dependent DNA replication 
               
               
                 6260 
                 3.24E−07 
                 1.36E−05 
                 9 
                 117 
                 DNA replication 
               
               
                 6950 
                 8.79E−07 
                 3.42E−05 
                 28 
                 1300 
                 response to stress 
               
               
                 74 
                 1.50E−06 
                 5.43E−05 
                 5 
                 26 
                 regulation of progression through cell cycle 
               
               
                 7582 
                 2.21E−06 
                 7.53E−05 
                 133 
                 13063 
                 physiological process 
               
               
                 6970 
                 2.77E−06 
                 8.87E−05 
                 14 
                 397 
                 response to osmotic stress 
               
               
                 6139 
                 6.40E−06 
                 1.94E−04 
                 45 
                 2973 
                 nucleobase, nucleoside, nucleotide and nucleic acid 
               
               
                   
                   
                   
                   
                   
                 metabolism 
               
               
                 9056 
                 1.27E−05 
                 3.64E−04 
                 16 
                 582 
                 catabolism 
               
               
                 9628 
                 2.56E−05 
                 6.96E−04 
                 23 
                 1140 
                 response to abiotic stimulus 
               
               
                 9651 
                 3.21E−05 
                 7.96E−04 
                 12 
                 369 
                 response to salt stress 
               
               
                 44248 
                 3.22E−05 
                 7.96E−04 
                 15 
                 560 
                 cellular catabolism 
               
               
                 6454 
                 3.40E−05 
                 8.04E−04 
                 6 
                 79 
                 translational initiation 
               
               
                 79 
                 5.21E−05 
                 1.18E−03 
                 3 
                 10 
                 regulation of cyclin-dependent protein kinase activity 
               
               
                 9057 
                 5.47E−05 
                 1.19E−03 
                 12 
                 390 
                 macromolecule catabolism 
               
               
                 51510 
                 5.92E−05 
                 1.24E−03 
                 2 
                 2 
                 regulation of unidimensional cell growth 
               
               
                 44237 
                 8.90E−05 
                 1.79E−03 
                 92 
                 8580 
                 cellular metabolism 
               
               
                 15980 
                 1.10E−04 
                 2.15E−03 
                 7 
                 140 
                 energy derivation by oxidation of organic compounds 
               
               
                 44265 
                 1.25E−04 
                 2.35E−03 
                 11 
                 362 
                 cellular macromolecule catabolism 
               
               
                 45333 
                 1.33E−04 
                 2.41E−03 
                 4 
                 34 
                 cellular respiration 
               
               
                 43283 
                 1.51E−04 
                 2.66E−03 
                 48 
                 3692 
                 biopolymer metabolism 
               
               
                 9826 
                 1.63E−04 
                 2.77E−03 
                 7 
                 149 
                 unidimensional cell growth 
               
               
                 43044 
                 1.77E−04 
                 2.91E−03 
                 2 
                 3 
                 ATP-dependent chromatin remodeling 
               
               
                 7275 
                 2.23E−04 
                 3.56E−03 
                 28 
                 1765 
                 development 
               
               
                 278 
                 2.53E−04 
                 3.93E−03 
                 4 
                 40 
                 mitotic cell cycle 
               
               
                 9266 
                 3.13E−04 
                 4.74E−03 
                 10 
                 338 
                 response to temperature stimulus 
               
               
                 9719 
                 4.96E−04 
                 7.30E−03 
                 20 
                 1131 
                 response to endogenous stimulus 
               
               
                 6084 
                 5.43E−04 
                 7.77E−03 
                 3 
                 21 
                 acetyl-CoA metabolism 
               
               
                 6561 
                 5.83E−04 
                 8.05E−03 
                 2 
                 5 
                 proline biosynthesis 
               
               
                 9737 
                 5.92E−04 
                 8.05E−03 
                 8 
                 241 
                 response to abscisic acid stimulus 
               
               
                 40007 
                 6.59E−04 
                 8.74E−03 
                 8 
                 245 
                 growth 
               
               
                 45859 
                 7.14E−04 
                 9.04E−03 
                 3 
                 23 
                 regulation of protein kinase activity 
               
               
                 43549 
                 7.14E−04 
                 9.04E−03 
                 3 
                 23 
                 regulation of kinase activity 
               
               
                 43285 
                 7.46E−04 
                 9.23E−03 
                 9 
                 312 
                 biopolymer catabolism 
               
               
                 7148 
                 7.91E−04 
                 9.46E−03 
                 8 
                 252 
                 cell morphogenesis 
               
               
                 51338 
                 8.12E−04 
                 9.46E−03 
                 3 
                 24 
                 regulation of transferase activity 
               
               
                 6092 
                 8.18E−04 
                 9.46E−03 
                 5 
                 94 
                 main pathways of carbohydrate metabolism 
               
               
                 16049 
                 9.82E−04 
                 1.11E−02 
                 7 
                 201 
                 cell growth 
               
               
                 43170 
                 1.08E−03 
                 1.20E−02 
                 69 
                 6392 
                 macromolecule metabolism 
               
               
                 8361 
                 1.13E−03 
                 1.23E−02 
                 7 
                 206 
                 regulation of cell size 
               
               
                 30163 
                 1.17E−03 
                 1.24E−02 
                 8 
                 268 
                 protein catabolism 
               
               
                 50789 
                 1.18E−03 
                 1.24E−02 
                 32 
                 2359 
                 regulation of biological process 
               
               
                 50791 
                 1.26E−03 
                 1.30E−02 
                 29 
                 2070 
                 regulation of physiological process 
               
               
                 6091 
                 1.29E−03 
                 1.30E−02 
                 8 
                 272 
                 generation of precursor metabolites and energy 
               
               
                 51244 
                 1.34E−03 
                 1.33E−02 
                 28 
                 1980 
                 regulation of cellular physiological process 
               
               
                 16043 
                 1.47E−03 
                 1.42E−02 
                 22 
                 1419 
                 cell organization and biogenesis 
               
               
                 6560 
                 1.61E−03 
                 1.42E−02 
                 2 
                 8 
                 proline metabolism 
               
               
                 6469 
                 1.61E−03 
                 1.42E−02 
                 2 
                 8 
                 negative regulation of protein kinase activity 
               
               
                 45736 
                 1.61E−03 
                 1.42E−02 
                 2 
                 8 
                 negative regulation of cyclin-dependent protein 
               
               
                   
                   
                   
                   
                   
                 kinase activity 
               
               
                 51348 
                 1.61E−03 
                 1.42E−02 
                 2 
                 8 
                 negative regulation of transferase activity 
               
               
                 1558 
                 1.61E−03 
                 1.42E−02 
                 2 
                 8 
                 regulation of cell growth 
               
               
                 48856 
                 1.64E−03 
                 1.42E−02 
                 20 
                 1248 
                 anatomical structure development 
               
               
                 9725 
                 1.65E−03 
                 1.42E−02 
                 14 
                 729 
                 response to hormone stimulus 
               
               
                 44238 
                 1.81E−03 
                 1.53E−02 
                 85 
                 8429 
                 primary metabolism 
               
               
                 8152 
                 1.82E−03 
                 1.53E−02 
                 98 
                 10040 
                 metabolism 
               
               
                 9409 
                 1.92E−03 
                 1.59E−02 
                 7 
                 226 
                 response to cold 
               
               
                 45786 
                 2.06E−03 
                 1.64E−02 
                 2 
                 9 
                 negative regulation of progression through cell cycle 
               
               
                 51302 
                 2.06E−03 
                 1.64E−02 
                 2 
                 9 
                 regulation of cell division 
               
               
                 50794 
                 2.08E−03 
                 1.64E−02 
                 28 
                 2040 
                 regulation of cellular process 
               
               
                 51170 
                 2.27E−03 
                 1.76E−02 
                 3 
                 34 
                 nuclear import 
               
               
                 9790 
                 2.47E−03 
                 1.89E−02 
                 11 
                 520 
                 embryonic development 
               
               
                 43086 
                 2.56E−03 
                 1.93E−02 
                 2 
                 10 
                 negative regulation of enzyme activity 
               
               
                 6395 
                 2.59E−03 
                 1.93E−02 
                 4 
                 74 
                 RNA splicing 
               
               
                 6099 
                 3.11E−03 
                 2.26E−02 
                 2 
                 11 
                 tricarboxylic acid cycle 
               
               
                 46356 
                 3.11E−03 
                 2.26E−02 
                 2 
                 11 
                 acetyl-CoA catabolism 
               
               
                 6511 
                 3.30E−03 
                 2.30E−02 
                 7 
                 249 
                 ubiquitin-dependent protein catabolism 
               
               
                 43632 
                 3.30E−03 
                 2.30E−02 
                 7 
                 249 
                 modification-dependent macromolecule catabolism 
               
               
                 19941 
                 3.30E−03 
                 2.30E−02 
                 7 
                 249 
                 modification-dependent protein catabolism 
               
               
                 51603 
                 3.45E−03 
                 2.37E−02 
                 7 
                 251 
                 proteolysis during cellular protein catabolism 
               
               
                 6270 
                 3.71E−03 
                 2.53E−02 
                 2 
                 12 
                 DNA replication initiation 
               
               
                 9064 
                 3.88E−03 
                 2.55E−02 
                 3 
                 41 
                 glutamine family amino acid metabolism 
               
               
                 9615 
                 3.88E−03 
                 2.55E−02 
                 3 
                 41 
                 response to virus 
               
               
                 44257 
                 3.92E−03 
                 2.55E−02 
                 7 
                 257 
                 cellular protein catabolism 
               
               
                 48827 
                 3.94E−03 
                 2.55E−02 
                 6 
                 193 
                 phyllome development 
               
               
                 51169 
                 4.16E−03 
                 2.66E−02 
                 3 
                 42 
                 nuclear transport 
               
               
                 16071 
                 4.40E−03 
                 2.78E−02 
                 5 
                 138 
                 mRNA metabolism 
               
               
                 9793 
                 4.72E−03 
                 2.95E−02 
                 10 
                 487 
                 embryonic development (sensu Magnoliophyta) 
               
               
                 9109 
                 5.07E−03 
                 3.13E−02 
                 2 
                 14 
                 coenzyme catabolism 
               
               
                 6800 
                 5.22E−03 
                 3.19E−02 
                 7 
                 271 
                 oxygen and reactive oxygen species metabolism 
               
               
                 398 
                 5.38E−03 
                 3.25E−02 
                 3 
                 46 
                 nuclear mRNA splicing, via spliceosome 
               
               
                 48367 
                 5.43E−03 
                 3.25E−02 
                 7 
                 273 
                 shoot development 
               
               
                 6096 
                 5.71E−03 
                 3.38E−02 
                 3 
                 47 
                 glycolysis 
               
               
                 9060 
                 5.82E−03 
                 3.40E−02 
                 2 
                 15 
                 aerobic respiration 
               
               
                 375 
                 6.06E−03 
                 3.47E−02 
                 3 
                 48 
                 RNA splicing, via transesterification reactions 
               
               
                 377 
                 6.06E−03 
                 3.47E−02 
                 3 
                 48 
                 RNA splicing, via transesterification reactions with 
               
               
                   
                   
                   
                   
                   
                 bulged adenosine as nucleophile 
               
               
                 9084 
                 7.46E−03 
                 4.23E−02 
                 2 
                 17 
                 glutamine family amino acid biosynthesis 
               
               
                 42891 
                 7.71E−03 
                 4.24E−02 
                 1 
                 1 
                 antibiotic transport 
               
               
                 7091 
                 7.71E−03 
                 4.24E−02 
                 1 
                 1 
                 mitotic metaphase/anaphase transition 
               
               
                 30071 
                 7.71E−03 
                 4.24E−02 
                 1 
                 1 
                 regulation of mitotic metaphase/anaphase transition 
               
               
                 48316 
                 8.36E−03 
                 4.55E−02 
                 10 
                 530 
                 seed development 
               
               
                 48608 
                 8.68E−03 
                 4.68E−02 
                 10 
                 533 
                 reproductive structure development 
               
               
                 19952 
                 8.92E−03 
                 4.76E−02 
                 13 
                 794 
                 reproduction 
               
               
                 6732 
                 9.45E−03 
                 4.99E−02 
                 5 
                 166 
                 coenzyme metabolism 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 4 
               
             
             
               
                   
               
               
                 Overview of cell cycle-related features used in the computational 
               
               
                 analysis to search for new cell cycle proteins. 
               
             
          
           
               
                 Cell cycle feature 
                 Category 
                 # of genes 
                 References 
               
               
                   
               
             
          
           
               
                 Periodicity 
                 Gene expression 
                 1258 
                 (5, 6) 
               
               
                 MSA-like 
                 Promotor motif 
                 2295 
                 (7) 
               
               
                 E2Fa-like 
                 Promotor motif 
                 1809 
                 (7) 
               
               
                 E2F10SPCNA 
                 Promotor motif 
                 2221 
                 (7) 
               
               
                 OS_motifslandIIa 
                 Promotor motif 
                 2310 
                 (7) 
               
               
                 UP1ATMSD 
                 Promotor motif 
                 3738 
                 (7) 
               
               
                 wrrmGCGn 
                 Promotor motif 
                 2179 
                 (7) 
               
               
                 CDK consensus site 
                 Phosphorylation motif 
                 6321 
                 (8) 
               
               
                 [IM]R-tail 
                 Protein sequence motif 
                 116 
                 (16, 17) 
               
               
                 PEST-sequence 
                 Destruction motif 
                 2719 
                 (18)  
               
               
                 D-box 
                 Destruction motif 
                 2369 
                 (19)  
               
               
                 KEN-box 
                 Destruction motif 
                 410 
                 (19)  
               
               
                 GxEN-box 
                 Destruction motif 
                 300 
                 (20)  
               
               
                 A-box 
                 Destruction motif 
                 1779 
                 (21)  
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
             
               
               
               
             
           
               
                 TABLE 5 
               
             
             
               
                   
               
               
                 collection of cell cycle genes. 
               
               
                 Collection of 518 genes annotated as cell cycle by gene ontology, including all genes 
               
               
                 described as core cell cycle genes or related to cell cycle (19, 22-24). The following GO terms 
               
               
                 were used to build the collection: cell cycle (GO: 0007049), cell division (GO: 0051301), cell 
               
               
                 proliferation (GO: 0008283), chromosome segregation (GO: 0007059), DNA replication 
               
               
                 (GO: 0006260), DNA replication and chromosome cycle (GO: 0000067). For every gene, the 
               
               
                 number of cell cycle-related features present is shown. This collection was subtracted from the 
               
               
                 prey lists to find novel cell cycle proteins. 
               
             
          
           
               
                 Accession 
                   
                   
               
               
                 number 
                 Name 
                 # features 
               
               
                   
               
             
          
           
               
                 AT2G31270 
                 CDT1a 
                 8 
               
               
                 AT5G13840 
                 CCS52B 
                 7 
               
               
                 AT3G16320 
                 cdc27a 
                 7 
               
               
                 AT1G07270 
                 cdc6b 
                 7 
               
               
                 AT3G59550 
                 cohesion family protein SYN3 (SYN3) 
                 7 
               
               
                 AT5G25380 
                 CYCA2; 1 
                 7 
               
               
                 AT3G11450 
                 DNAJ HEAT SHOCK N-TERMINAL DOMAIN-CONTAINING PROTEIN/ 
                 7 
               
               
                   
                 CELL DIVISION PROTEIN-RELATED 
               
               
                 AT1G65470 
                 chromatin assembly factor-1 (FASCIATA1) (FAS1), identical to FAS1 
                 6 
               
               
                   
                 ( Arabidopsis thaliana ) GI: 4887626 
               
               
                 AT1G77390 
                 CYCA1; 2 
                 6 
               
               
                 AT5G43080 
                 CYCA3; 1 
                 6 
               
               
                 AT3G11520 
                 CYCB1; 3 
                 6 
               
               
                 AT3G10690 
                 DNA gyrase subunit A family protein 
                 6 
               
               
                 AT4G25540 
                 DNA mismatch repair protein MSH3; AtMsh3 
                 6 
               
               
                 AT1G47870 
                 E2Fc 
                 6 
               
               
                 AT4G38600 
                 KAK (KAKTUS) 
                 6 
               
               
                 AT5G46280 
                 MCM3 
                 6 
               
               
                 AT5G07280 
                 receptor-like protein kinase-like protein; receptor-like protein kinase - 
                 6 
               
               
                   
                 lpomoea nil (Japanese morning glory), PIR: T18536 
               
               
                 AT5G61000 
                 Replication protein A1; Putative RNA helicase 
                 6 
               
               
                 AT5G42190 
                 ASK2 ( ARABIDOPSIS  SKP1-LIKE 2); UBIQUITIN-PROTEIN LIGASE 
                 5 
               
               
                 AT2G29680 
                 cdc6 
                 5 
               
               
                 AT1G18670 
                 CKL3 
                 5 
               
               
                 AT1G70210 
                 CYCD1; 1 
                 5 
               
               
                 AT4G37630 
                 CYCD5; 1 
                 5 
               
               
                 AT5G49160 
                 DNA (cytosine-5-)-methyltransferase (AtHIM), identical to SP: P34881 
                 5 
               
               
                   
                 DNA (cytosine-5)-methyltransferase AthI (EC 2.1.1.37) { Arabidopsis   
               
               
                   
                   thaliana } 
               
               
                 AT1G08130 
                 DNA ligase/polydeoxyribonucleotide synthase [AtP] identical to 
                 5 
               
               
                   
                 SP|Q42572 DNA ligase (EC 6.5.1.1) (Polydeoxyribonucleotide 
               
               
                   
                 synthase [AtP]) { Arabidopsis thaliana }; contains Pfam profiles: 
               
               
                   
                 PF01068 AtP dependent DNA ligase domain, PF04679 AtP dependent 
               
               
                   
                 DNA 
               
               
                 AT5G41880 
                 DNA polymerase alpha subunit IV (Primase)-like protein 
                 5 
               
               
                 AT3G13170 
                 DNA TOPOISOMERASE VIA (SPO11-1), IDENTICAL TO ATSPO11-1 
                 5 
               
               
                   
                 ( ARABIDOPSIS THALIANA ) GI: 13383478; CONTAINS PFAM 
               
               
                   
                 PROFILE PF04406: TYPE IIB DNA TOPOISOMERASE; IDENTICAL 
               
               
                   
                 TO CDNA PUTATIVE TOPOISOMERASE VIA (SPO11 GENE 1) 
               
               
                   
                 GI: 7270974|CHR3: 4231567-4234199 REVERSE|ALIASES: 
               
               
                   
                 MJG19.19 
               
               
                 AT5G67100 
                 DNA-directed DNA polymerase alpha catalytic subunit, putative, similar 
                 5 
               
               
                   
                 to SP: O48653 DNA polymerase alpha catalytic subunit (EC 2.7.7.7) 
               
               
                   
                 { Oryza sativa }; contains Pfam profiles: PF03175 DNA polymerase type 
               
               
                   
                 B, organellar and viral, PF00136 DNA polymerase fa 
               
               
                 AT5G02470 
                 DPa 
                 5 
               
               
                 AT5G22220 
                 E2Fb 
                 5 
               
               
                 AT3G43210 
                 kinesin motor family protein (NACK2) 
                 5 
               
               
                 AT1G18800 
                 NRP2 (NAP1-RELATED PROTEIN 2); DNA BINDING/CHROMATIN 
                 5 
               
               
                   
                 BINDING/HISTONE BINDING 
               
               
                 AT2G37560 
                 ORC2 
                 5 
               
               
                 AT1G26840 
                 ORC6 
                 5 
               
               
                 AT5G16270 
                 Rad21/Rec8-like family protein weak similarity to cohesion family 
                 5 
               
               
                   
                 protein SYN2 [ Arabidopsis thaliana ] gI: 12006360; contains Pfam 
               
               
                   
                 profiles PF04824: Conserved region of Rad21/Rec8 like protein, 
               
               
                   
                 PF04825: N terminus of Rad21/Rec8 like protein; supporting 
               
               
                 AT3G12280 
                 RBR 
                 5 
               
               
                 AT5G61210 
                 SNAP33 (SYNAPTOSOMAL-ASSOCIATED PROTEIN 33); T-SNARE 
                 5 
               
               
                 AT5G48600 
                 structural maintenance of chromosomes (SMC) family protein, similar 
                 5 
               
               
                   
                 to SP: P50532 Chromosome assembly protein XCAP-C { Xenopus   
               
               
                   
                   laevis }; contains Pfam profiles PF02483: SMC family C-terminal 
               
               
                   
                 domain, PF02463: RecF/RecN/SMC N terminal domain 
               
               
                 AT5G55220 
                 trigger factor type chaperone family protein, contains Pfam profiles 
                 5 
               
               
                   
                 PF05697: Bacterial trigger factor protein (TF), PF05698: Bacterial 
               
               
                   
                 trigger factor protein (TF) C-terminus, PF00254: peptidyl-prolyl 
               
               
                   
                 cis-trans isomerase, FKBP-type 
               
               
                 AT3G60740 
                 tubulin folding cofactor D 
                 5 
               
               
                 AT3G19770 
                 vacuolar sorting protein 9 domain-containing protein 
                 5 
               
               
                 AT5G05560 
                 APC1 
                 4 
               
               
                 AT1G06590 
                 APC5 
                 4 
               
               
                 AT3G28730 
                 ATHMG (HIGH MOBILITY GROUP, STRUCTURE-SPECIFIC 
                 4 
               
               
                   
                 RECOGNITION PROTEIN 1); TRANSCRIPTION FACTOR 
               
               
                 AT3G53230 
                 CDC48, putative 
                 4 
               
               
                 AT3G01610 
                 CDC48C|AAA-TYPE ATPASE FAMILY PROTEIN, CONTAINS PFAM 
                 4 
               
               
                   
                 DOMAIN, PF00004: ATPASE, AAA FAMILY (‘A’TPASES 
               
               
                   
                 ‘A’SSOCIATED WITH DIVERSE CELLULAR ‘A’CTIVITIES)| 
               
               
                   
                 CHR3: 231658-235196 FORWARD|ALIASES: EMB1354, EMBRYO 
               
               
                   
                 DEFECTIVE 1354, F4P135, F4P13_15 
               
               
                 AT1G18040 
                 CDKD; 3 
                 4 
               
               
                 AT5G03340 
                 CELL DIVISION CONTROL PROTEIN 48 HOMOLOG E; ATPASE 
                 4 
               
               
                 AT5G11300 
                 CYCA2; 2 
                 4 
               
               
                 AT1G15570 
                 CYCA2; 3 
                 4 
               
               
                 AT1G80370 
                 CYCA2; 4 
                 4 
               
               
                 AT2G26760 
                 CYCB1; 4 
                 4 
               
               
                 AT2G17620 
                 CYCB2; 1 
                 4 
               
               
                 AT4G35620 
                 CYCB2; 2 
                 4 
               
               
                 AT3G50070 
                 CYCD3; 3 
                 4 
               
               
                 AT3G05330 
                 cyclin family low similarity to microtubule-binding protein TANGLED1 
                 4 
               
               
                 AT5G05490 
                 DIF1/SYN1 
                 4 
               
               
                 AT1G69770 
                 DNA (cytosine-5)-methyltransferase CMt3; Chromomethylase 3; 
                 4 
               
               
                   
                 Protein CHROMOMETHYLASE3 
               
               
                 AT4G02460 
                 DNA mismatch repair protein 
                 4 
               
               
                 AT1G67320 
                 DNA primase, large subunit family, contains Pfam profile PF04104: 
                 4 
               
               
                   
                 Eukaryotic-type DNA primase, large subunit; similar to DNA primase 
               
               
                   
                 large subunit (EC 2.7.7.—) (DNA primase 58 kDa subunit) (p58) 
               
               
                   
                 (Swiss-Prot: P49643) ( Homo sapiens ) 
               
               
                 AT4G31210 
                 DNA topoisomerase family protein, similar to DNA Topoisomerase I 
                 4 
               
               
                   
                 (SP: Q9X3X7) { Zymomonas mobilis } 
               
               
                 AT5G63920 
                 DNA topoisomerase III 
                 4 
               
               
                 AT5G06110 
                 DNAJ heat shock N-terminal domain-containing protein/cell division 
                 4 
               
               
                   
                 protein-related, similar to GlsA ( Volvox carteri  f.  nagariensis ) 
               
               
                   
                 GI: 4633129; contains Pfam profiles PF00226 DnaJ domain, PF00249 
               
               
                   
                 Myb-like DNA-binding domain 
               
               
                 AT1G78650 
                 expressed protein, weak similarity to DNA polymerase delta subunit 3 
                 4 
               
               
                   
                 (DNA polymerase delta subunit p66) (Swiss-Prot: Q15054) ( Homo   
               
               
                   
                   sapiens ) 
               
               
                 AT2G13330 
                 F14O4.9 
                 4 
               
               
                 AT2G23430 
                 KRP1 
                 4 
               
               
                 AT2G20980 
                 MCM10 
                 4 
               
               
                 AT2G29570 
                 PCNA2 
                 4 
               
               
                 AT4G14150 
                 phragmoplast-associated kinesin-related protein (PAKRP1) 
                 4 
               
               
                 AT3G23670 
                 phragmoplast-associated kinesin-related protein, putative, similar to 
                 4 
               
               
                   
                 kinesin-like protein GB: CAB10194 from ( Arabidopsis thaliana ) 
               
               
                 AT5G58720 
                 PRLI-INTERACTING FACTOR, PUTATIVE 
                 4 
               
               
                 AT1G53710 
                 PROTEIN SERINE/THREONINE PHOSPHATASE 
                 4 
               
               
                 AT3G02920 
                 replication protein-related, similar to replication protein A 30 kDa ( Oryza   
                 4 
               
               
                   
                   sativa  (japonica cultivar-group)) GI: 13516746; contains InterPro entry 
               
               
                   
                 IPR004365: OB-fold nucleic acid binding domain 
               
               
                 AT4G22970 
                 similar to hypothetical protein [ Arabidopsis thaliana ] 
                 4 
               
               
                   
                 (TAIR: At5g28550.1); similar to BIMB_EMENI CELL 
               
               
                   
                 DIVISION-ASSOCIATED PROTEIN BIMB [ Aspergillus nidulans  FGSC 
               
               
                   
                 A4] (GB: EAA60576.1); similar to probable spindle pole body 
               
               
                   
                 component bimB -  Emericella nidula   
               
               
                 AT5G61460 
                 SMC-like protein 
                 4 
               
               
                 AT1G65660 
                 SMP1 (SWELLMAP 1); NUCLEIC ACID BINDING 
                 4 
               
               
                 AT5G62000 
                 transcriptional factor B3 family protein/auxin-responsive factor 
                 4 
               
               
                 AT5G16750 
                 transducin family protein/WD-40 repeat family protein contains 8 
                 4 
               
               
                   
                 WD-40 repeats (PF00400); similar to transducin homolog sazD -  Homo   
               
               
                   
                   sapiens , EMBL: U02609 
               
               
                 AT2G14400 
                 transposable element gene 
                 4 
               
               
                 AT2G42260 
                 UVI4 
                 4 
               
               
                 AT1G57820 
                 VARIANT IN METHYLATION 1 
                 4 
               
               
                 AT3G02820 
                 zinc knuckle (CCHC-type) family protein, contains Pfam domain, 
                 4 
               
               
                   
                 PF00098: Zinc knuckle 
               
               
                 AT5G22010 
                 AAA-TYPE ATPASE FAMILY PROTEIN/BRCT 
                 3 
               
               
                   
                 DOMAIN-CONTAINING PROTEIN 
               
               
                 AT2G14120 
                 ADL2b 
                 3 
               
               
                 AT5G57160 
                 ATLIG4 ( ARABIDOPSIS THALIANA  DNA LIGASE IV) 
                 3 
               
               
                 AT5G45720 
                 ATP BINDING/DNA-DIRECTED DNA POLYMERASE/ 
                 3 
               
               
                   
                 NUCLEOSIDE-TRIPHOSPHATASE/NUCLEOTIDE BINDING 
               
               
                 AT1G66730 
                 ATP DEPENDENT DNA LIGASE FAMILY PROTEIN 
                 3 
               
               
                 AT2G32590 
                 barren family protein, low similarity to SP: Q9Y7R3 Condensin complex 
                 3 
               
               
                   
                 subunit 2 (p105) { Schizosaccharomyces pombe }; contains Pfam profile 
               
               
                   
                 PF05786: Barren protein 
               
               
                 AT3G19590 
                 BUB3-like2 
                 3 
               
               
                 AT4G22910 
                 CCS52A1 
                 3 
               
               
                 AT4G11920 
                 CCS52A2 
                 3 
               
               
                 AT4G33270 
                 cdc20-1 
                 3 
               
               
                 AT3G25100 
                 CDC45 (Cell division cycle 45)-like protein; Putative cell division cycle 
                 3 
               
               
                   
                 protein 45 
               
               
                 AT3G09840 
                 CDC48 
                 3 
               
               
                 AT1G20930 
                 CDKB2; 2 
                 3 
               
               
                 AT1G73690 
                 CDKD; 1 
                 3 
               
               
                 AT4G28980 
                 CDKF; 1 
                 3 
               
               
                 AT2G32900 
                 centromere/kinetochore protein, putative (ZW10) 
                 3 
               
               
                 AT5G62410 
                 Chromosome assembly protein homolog 
                 3 
               
               
                 AT1G44110 
                 CYCA1; 1 
                 3 
               
               
                 AT1G47210 
                 CYCA3; 2 
                 3 
               
               
                 AT4G37490 
                 CYCB1; 1 
                 3 
               
               
                 AT1G76310 
                 CYCB2; 4 
                 3 
               
               
                 AT4G34160 
                 CYCD3; 1 
                 3 
               
               
                 AT4G34090 
                 CYL1 
                 3 
               
               
                 AT3G20550 
                 DDL (DAWDLE) 
                 3 
               
               
                 AT5G14960 
                 DEL2 
                 3 
               
               
                 AT4G09140 
                 DNA mismatch repair protein MLH1 
                 3 
               
               
                 AT3G18524 
                 DNA mismatch repair protein MSH2 (MSH2) identical to SP|O24617 
                 3 
               
               
                   
                 DNA mismatch repair protein MSH2 (AtMsh2) { Arabidopsis thaliana } 
               
               
                 AT4G02070 
                 DNA mismatch repair protein MSH6-1 (MSH6-1) (AGAA.3) 
                 3 
               
               
                 AT5G55300 
                 DNA topoisomerase I 
                 3 
               
               
                 AT3G17830 
                 DNAJ HEAT SHOCK FAMILY PROTEIN 
                 3 
               
               
                 AT1G80030 
                 DNAJ HEAT SHOCK PROTEIN, PUTATIVE 
                 3 
               
               
                 AT1G08840 
                 EMB2411|DNA REPLICATION HELICASE, PUTATIVE, SIMILAR TO 
                 3 
               
               
                   
                 HELICASE ( XENOPUS LAEVIS ) GI: 18845092: GB: AAL79550| 
               
               
                   
                 CHR1: 2829582-2838372 REVERSE|ALIASES: EMB2411, EMBRYO 
               
               
                   
                 DEFECTIVE 2411, F7G19.26 
               
               
                 AT4G37120 
                 expressed protein 
                 3 
               
               
                 AT5G58870 
                 FTSH9 (FTSH PROTEASE 9); ATP-DEPENDENT PEPTIDASE/ 
                 3 
               
               
                   
                 ATPASE/METALLOPEPTIDASE 
               
               
                 AT1G13980 
                 GN (GNOM) 
                 3 
               
               
                 AT5G24330 
                 Histone-lysine N-methyltransferase AtXR6; Protein SET DOMAIN 
                 3 
               
               
                   
                 GROUP 34; trithorax-related protein 6; tRX-related protein 6 
               
               
                 AT5G06830 
                 IDENTICAL TO CDK5RAP3-LIKE PROTEIN [ ARABIDOPSIS   
                 3 
               
               
                   
                   THALIANA ] (GB: Q9FG23); SIMILAR TO OS06G0320100 [ ORYZA   
               
               
                   
                   SATIVA  (JAPONICA CULTIVAR-GROUP)] (GB: NP_001057510.1); 
               
               
                   
                 SIMILAR TO CDK5 REGULATORY SUBUNIT ASSOCIATED 
               
               
                   
                 PROTEIN 3 [ MUS MUSCULUS ] (GB: NP_084524.1); CONTAINS 
               
               
                   
                 INTERPRO DOMAIN PROTEIN OF UNKNOWN FUNCTION DUF773; 
               
               
                   
                 (INTERPRO: IPR008491) 
               
               
                 AT1G49620 
                 KRP7 
                 3 
               
               
                 AT1G71830 
                 leucine-rich repeat family protein/protein kinase family protein, 
                 3 
               
               
                   
                 contains Pfam domains PF00560: Leucine Rich Repeat and PF00069: 
               
               
                   
                 Protein kinase domain 
               
               
                 AT1G80080 
                 leucine-rich repeat family protein, contains leucine rich-repeat domains 
                 3 
               
               
                   
                 Pfam: PF00560, INTERPRO: IPR001611; contains some similarity to 
               
               
                   
                 Hcr2-5D ( Lycopersicon esculentum ) gi: 3894393: gb: AAC78596 
               
               
                 AT3G25980 
                 MAD2-like 
                 3 
               
               
                 AT5G51600 
                 MAP65-3 
                 3 
               
               
                 AT1G44900 
                 MCM2 
                 3 
               
               
                 AT2G16440 
                 MCM4 
                 3 
               
               
                 AT2G07690 
                 MCM5 
                 3 
               
               
                 AT5G54260 
                 MRE11|DNA REPAIR AND MEIOSIS PROTEIN (MRE11), 
                 3 
               
               
                   
                 IDENTICAL TO DNA REPAIR AND MEIOSIS PROTEIN (MRE11) 
               
               
                   
                 GI: 5524769 FROM ( ARABIDOPSIS THALIANA )| 
               
               
                   
                 CHR5: 22049295-22055217 FORWARD|ALIASES: MDK4.8, MDK4_8 
               
               
                 AT5G58230 
                 MSI1 (MULTICOPY SUPRESSOR OF IRA1) 
                 3 
               
               
                 AT1G61000 
                 Nuf2 family protein contains Pfam PF03800: Nuf2 family 
                 3 
               
               
                   
                 domain/kinetochore protein NUF2 
               
               
                 AT5G16690 
                 ORC3 
                 3 
               
               
                 AT1G72150 
                 PATL1 (PATELLIN 1); TRANSPORTER 
                 3 
               
               
                 AT1G50840 
                 poll-like DNA polymerase, putative, similar to Poll-like DNA 
                 3 
               
               
                   
                 polymerase ( Oryza sativa ) GI: 19912795 contains Pfam profiles 
               
               
                   
                 PF01612: 3′-5′ exonuclease, PF00476: DNA polymerase I family A 
               
               
                 AT1G80190 
                 PSF1 (GINS complex DNA replication) 
                 3 
               
               
                 AT2G45280 
                 putative RAD51C-like DNA repair protein; supported by cDNA: 
                 3 
               
               
                   
                 gi_15425730_dbj_AB062456.1_AB062456 
               
               
                 AT2G31970 
                 RAD50|DNA REPAIR-RECOMBINATION PROTEIN (RAD50), 
                 3 
               
               
                   
                 IDENTICAL TO DNA REPAIR-RECOMBINATION PROTEIN 
               
               
                   
                 GI: 7110148 FROM ( ARABIDOPSIS THALIANA )| 
               
               
                   
                 CHR2: 13607589-13616146 FORWARD|ALIASES: ATRAD50, DNA 
               
               
                   
                 REPAIR RECOMBINATION PROTEIN, F22D22.28, F22D22_28 
               
               
                 AT5G08020 
                 Replication factor A-like protein 
                 3 
               
               
                 AT2G21790 
                 Ribonucleoside-diphosphate reductase large subunit; AtRNR1; 
                 3 
               
               
                   
                 Ribonucleoside-diphosphate reductase R1 subunit 
               
               
                 AT3G27060 
                 ribonucleoside-diphosphate reductase small chain, putative/ 
                 3 
               
               
                   
                 ribonucleotide reductase, putative, similar to ribonucleotide reductase 
               
               
                   
                 R2 ( Nicotiana tabacum ) GI: 1044912; contains Pfam profile PF00268: 
               
               
                   
                 Ribonucleotide reductase, small chain 
               
               
                 AT2G24490 
                 RPA2 
                 3 
               
               
                 AT4G18590 
                 RPA3 
                 3 
               
               
                 AT1G30690 
                 SEC14 cytosolic factor family protein/phosphoglyceride transfer family 
                 3 
               
               
                   
                 protein, contains Pfam PF00650: CRAL/TRIO domain; contains Pfam 
               
               
                   
                 PF03765: CRAL/TRIO, N-terminus; similar to cytosolic factor 
               
               
                   
                 (Phosphatidylinositol/phosphatidylcholine transfer prot 
               
               
                 AT1G74560 
                 similar to nucleosome assembly protein (NAP) family protein 
                 3 
               
               
                   
                 [ Arabidopsis thaliana ] (TAIR: At1g18800.1); similar to 
               
               
                   
                 nucleosome/chromatin assembly factor A [ Zea mays ] 
               
               
                   
                 (GB: AAK67146.1); contains InterPro domain Nucleosome assembly 
               
               
                   
                 protein (NAP) (InterPro: IPR00 
               
               
                 AT5G04320 
                 similar to unknown protein [ Arabidopsis thaliana ] (TAIR: AT3G10440.1); 
                 3 
               
               
                   
                 similar to hypothetical protein Osl_009118 [ Oryza sativa  (indica 
               
               
                   
                 cultivar-group)] (GB: EAY87885.1); contains InterPro domain 
               
               
                   
                 Shugoshin, C-terminal; (InterPro: IPR011515) 
               
               
                 AT5G49010 
                 SLD5 (DNA replication) 
                 3 
               
               
                 AT5G51330 
                 SWI1 (SWITCH1); PHOSPHOLIPASE C 
                 3 
               
               
                 AT4G02110 
                 TOPBP1 
                 3 
               
               
                 AT2G01550 
                 transposable element gene 
                 3 
               
               
                 AT2G15410 
                 transposable element gene 
                 3 
               
               
                 AT4G33790 
                 ACYL COA REDUCTASE, PUTATIVE 
                 2 
               
               
                 AT5G22420 
                 ACYL COA REDUCTASE, PUTATIVE 
                 2 
               
               
                 AT4G16420 
                 ADA2B (PROPORZ1); DNA BINDING/TRANSCRIPTION FACTOR 
                 2 
               
               
                 AT1G78580 
                 alpha, alpha-trehalose-phosphate synthase, UDP-forming, putative 
                 2 
               
               
                   
                 (Fragment) 
               
               
                 AT1G54960 
                 ANP2 ( ARABIDOPSIS  NPK1-RELATED PROTEIN KINASE 2); 
                 2 
               
               
                   
                 KINASE 
               
               
                 AT4G37750 
                 ANT 
                 2 
               
               
                 AT1G78770 
                 APC6 
                 2 
               
               
                 AT2G39090 
                 APC7 
                 2 
               
               
                 AT3G48150 
                 APC8 
                 2 
               
               
                 AT4G30080 
                 ARF16 (AUXIN RESPONSE FACTOR 16); MIRNA BINDING/ 
                 2 
               
               
                   
                 TRANSCRIPTION FACTOR 
               
               
                 AT1G50240 
                 armadillo/beta-catenin repeat family protein, contains Pfam profile: 
                 2 
               
               
                   
                 PF00514 armadillo/beta-catenin-like repeat 
               
               
                 AT1G67370 
                 ASY1 (ASYNAPTIC 1); DNA BINDING 
                 2 
               
               
                 AT3G12400 
                 ATELC/ELC; ubiquitin binding 
                 2 
               
               
                 AT3G52115 
                 ATGR1 (GAMMA RESPONSE 1) 
                 2 
               
               
                 AT5G55230 
                 ATMAP65-1 (MICROTUBULE-ASSOCIATED PROTEINS 65-1); 
                 2 
               
               
                   
                 MICROTUBULE BINDING 
               
               
                 AT3G27730 
                 ATP-dependent DNA helicase, putative 
                 2 
               
               
                 AT5G40820 
                 ATR 
                 2 
               
               
                 AT5G16850 
                 ATTERT (TELOMERASE REVERSE TRANSCRIPTASE); 
                 2 
               
               
                   
                 TELOMERIC TEMPLATE RNA REVERSE TRANSCRIPTASE 
               
               
                 AT4G00020 
                 BRCA2A (BREAST CANCER 2 LIKE 2A, EMBRYO SAC 
                 2 
               
               
                   
                 DEVELOPMENT ARREST 20, MATERNAL EFFECT EMBRYO 
               
               
                   
                 ARREST 43) 
               
               
                 AT5G01630 
                 BRCA2B_ATBRCA2(V)_BRCA2(V)_BRCA2B (breast cancer 2 like 
                 2 
               
               
                   
                 2B) 
               
               
                 AT2G13680 
                 CALS5 (CALLOSE SYNTHASE 5); 1,3-BETA-GLUCAN SYNTHASE 
                 2 
               
               
                 AT2G20000 
                 cdc27b 
                 2 
               
               
                 AT2G03670 
                 CDC48B; ATPASE 
                 2 
               
               
                 AT1G76540 
                 CDKB2; 1 
                 2 
               
               
                 AT5G64960 
                 CDKC; 2 
                 2 
               
               
                 AT5G63370 
                 CDKG; 1 
                 2 
               
               
                 AT3G02450 
                 CELL DIVISION PROTEIN FTSH, PUTATIVE 
                 2 
               
               
                 AT5G55280 
                 cell division protein FtsZ, chloroplast, putative 
                 2 
               
               
                 AT5G37630 
                 chromosome condensation family protein, contains pfam profile: 
                 2 
               
               
                   
                 PF04154 chromosome condensation protein 3, C-terminal region 
               
               
                 AT1G09600 
                 CKL11 
                 2 
               
               
                 AT4G22940 
                 CKL4 
                 2 
               
               
                 AT5G44290 
                 CKL5 
                 2 
               
               
                 AT1G03740 
                 CKL6 
                 2 
               
               
                 AT1G54610 
                 CKL9 
                 2 
               
               
                 AT2G27970 
                 CKS2 
                 2 
               
               
                 AT5G40840 
                 cohesion family protein SYN2 (SYN2) 
                 2 
               
               
                 AT4G02570 
                 cullin family protein NCBI Chain C, Crystal Structure Of the 
                 2 
               
               
                   
                 Ddb1-Cul4a-Rbx1-Sv5v Complex 
               
               
                 AT1G26830 
                 cullin3a 
                 2 
               
               
                 AT5G06150 
                 CYCB1; 2 
                 2 
               
               
                 AT1G34460 
                 CYCB1; 5 
                 2 
               
               
                 AT5G48640 
                 CYCC1; 1 
                 2 
               
               
                 AT2G26430 
                 CYCL1 
                 2 
               
               
                 AT4G19560 
                 CYCT1; 2 
                 2 
               
               
                 AT5G45190 
                 CYCT1; 5 
                 2 
               
               
                 AT3G01330 
                 DEL3 
                 2 
               
               
                 AT4G35520 
                 DNA mismatch repair family protein 
                 2 
               
               
                 AT1G65070 
                 DNA MISMATCH REPAIR MUTS FAMILY PROTEIN 
                 2 
               
               
                 AT1G67630 
                 DNA polymerase alpha subunit B family, contains Pfam profile: 
                 2 
               
               
                   
                 PF04058 DNA polymerase alpha subunit B 
               
               
                 AT1G09815 
                 DNA polymerase delta subunit 4 family, contains similarity to 
                 2 
               
               
                   
                 Swiss-Prot: Q9HCU8 DNA polymerase delta subunit 4 (DNA 
               
               
                   
                 polymerase delta subunit p12) ( Homo sapiens ) 
               
               
                 AT5G64420 
                 DNA polymerase V family, contains Pfam domain PF04931: DNA 
                 2 
               
               
                   
                 polymerase V 
               
               
                 AT1G14460 
                 DNA polymerase-related, weak similarity to DNA polymerase III 
                 2 
               
               
                   
                 holoenzyme tau subunit ( Thermus thermophilus ) GI: 2583049 
               
               
                 AT5G55310 
                 DNA topoisomerase I, putative 
                 2 
               
               
                 AT5G44610 
                 DREPP PLASMA MEMBRANE POLYPEPTIDE-RELATED 
                 2 
               
               
                 AT2G36010 
                 E2Fa 
                 2 
               
               
                 AT3G11220 
                 ELP4 
                 2 
               
               
                 AT4G32700 
                 Encodes a homolog of  Drosophila  MUS308 and mammalian DNA 
                 2 
               
               
                   
                 polymerase, which prevent spontaneous or DNA damage-induced 
               
               
                   
                 production of DNA double strand breaks. 
               
               
                 AT5G64630 
                 Encodes the second largest subunit of the chromatin assembly 
                 2 
               
               
                   
                 factor-1. Involved in organization of the shoot and root apical 
               
               
                   
                 meristems. 
               
               
                 AT4G24790 
                 expressed protein; expression supported by MPSS 
                 2 
               
               
                 AT3G24495 
                 Expressed protein; GC donor splice site at exon 11; supported by 
                 2 
               
               
                   
                 cDNA: gi_6224916_gb_AF193018.1_AF193018 
               
               
                 AT4G23940 
                 FTSH PROTEASE, PUTATIVE 
                 2 
               
               
                 AT5G01230 
                 FtsJ-like methyltransferase family protein, contains Pfam profile: 
                 2 
               
               
                   
                 PF01728 FtsJ-like methyltransferase 
               
               
                 AT1G48270 
                 GCR1 (G-PROTEIN-COUPLED RECEPTOR 1) 
                 2 
               
               
                 AT1G10270 
                 GRP23 (GLUTAMINE-RICH PROTEIN23); BINDING 
                 2 
               
               
                 AT2G26890 
                 GRV2 (KATAMARI2); binding/heat shock protein binding 
                 2 
               
               
                 AT4G32880 
                 homeobox-leucine zipper transcription factor (HB-8), identical to 
                 2 
               
               
                   
                 HD-zip transcription factor (athb-8) (GI: 7270235) ( Arabidopsis thaliana ) 
               
               
                 AT5G46920 
                 intron maturase, type II family protein 
                 2 
               
               
                 AT5G54670 
                 kinesin-like protein C (KATC) 
                 2 
               
               
                 AT3G19150 
                 KRP6 
                 2 
               
               
                 AT5G44635 
                 MCM6 
                 2 
               
               
                 AT4G02060 
                 MCM7 
                 2 
               
               
                 AT3G09660 
                 MCM8 
                 2 
               
               
                 AT2G14050 
                 MCM9 
                 2 
               
               
                 AT1G77320 
                 MEI1 (MEIOSIS DEFECTIVE 1); TRANSCRIPTION COACTIVATOR 
                 2 
               
               
                 AT3G22880 
                 meiotic recombination protein, putative 
                 2 
               
               
                 AT5G50110 
                 METHYLTRANSFERASE-RELATED 
                 2 
               
               
                 AT5G24020 
                 MIND (ACCUMULATION AND REPLICATION OF CHLOROPLAST 
                 2 
               
               
                   
                 11) 
               
               
                 AT3G24320 
                 mismatch binding protein, putative; similar to mismatch binding protein 
                 2 
               
               
                   
                 Mus3 GB: AAF35250 from ( Zea mays ) 
               
               
                 AT5G49880 
                 MITOTIC CHECKPOINT FAMILY PROTEIN 
                 2 
               
               
                 AT2G35630 
                 MOR1|MICROTUBULE ORGANIZATION 1 PROTEIN (MOR1), 
                 2 
               
               
                   
                 IDENTICAL TO MICROTUBULE ORGANIZATION 1 PROTEIN 
               
               
                   
                 GI: 14317953 FROM ( ARABIDOPSIS THALIANA )| 
               
               
                   
                 CHR2: 14973757-14987661 FORWARD|ALIASES: GEM1, 
               
               
                   
                 MICROTUBULE ORGANIZATION 1, T20F21.17, T20F21_17 
               
               
                 AT4G17380 
                 MSH4, similar to DNA mismatch repair protein MSH2 
                 2 
               
               
                 AT1G63680 
                 Mur ligase family protein, contains Pfam profile: PF01225 Mur ligase 
                 2 
               
               
                   
                 family, catalytic domain 
               
               
                 AT5G11510 
                 MYB 3R4 
                 2 
               
               
                 AT3G02680 
                 NBS1 (NIJMEGEN BREAKAGE SYNDROME 1) 
                 2 
               
               
                 AT3G57060 
                 non-SMC condensin subunit, XCAP-D2/Cnd1 family protein, similar to 
                 2 
               
               
                   
                 13S condensin XCAP-D2 subunit ( Xenopus laevis ) GI: 3764087; 
               
               
                   
                 contains Pfam profile PF04594: Non-SMC condensin subunit, 
               
               
                   
                 XCAP-D2/Cnd1 
               
               
                 AT4G14700 
                 ORC1A 
                 2 
               
               
                 AT4G29910 
                 ORC5 
                 2 
               
               
                 AT4G30825 
                 pentatricopeptide (PPR) repeat-containing protein, contains Pfam 
                 2 
               
               
                   
                 profile PF01535: PPR repeat 
               
               
                 AT5G14520 
                 pescadillo-related 
                 2 
               
               
                 AT2G13840 
                 PHP DOMAIN-CONTAINING PROTEIN 
                 2 
               
               
                 AT3G63120 
                 PLP1; 1 
                 2 
               
               
                 AT1G50230 
                 protein kinase family protein, contains protein kinase domain, 
                 2 
               
               
                   
                 Pfam: PF00069 
               
               
                 AT3G63130 
                 RAN GTPase activating protein 1 (RanGAP1), contains Pfam 
                 2 
               
               
                   
                 PF00560: Leucine Rich Repeat domains; identical to RAN GTPase 
               
               
                   
                 activating protein 1 (GI: 6708466)( Arabidopsis thaliana ) 
               
               
                 AT1G16590 
                 REV7 (REVERSIONLESS 7); DNA BINDING 
                 2 
               
               
                 AT5G27740 
                 RFC3 
                 2 
               
               
                 AT1G21690 
                 RFC4 
                 2 
               
               
                 AT1G77470 
                 RFC5 
                 2 
               
               
                 AT1G48380 
                 RHL1 (ROOT HAIRLESS 1) 
                 2 
               
               
                 AT4G33495 
                 RPD1 (ROOT PRIMORDIUM DEFECTIVE 1) 
                 2 
               
               
                 AT5G35770 
                 SAP (STERILE APETALA); TRANSCRIPTION FACTOR 
                 2 
               
               
                 AT1G72160 
                 SEC14 CYTOSOLIC FACTOR FAMILY PROTEIN/ 
                 2 
               
               
                   
                 PHOSPHOGLYCERIDE TRANSFER FAMILY PROTEIN 
               
               
                 AT4G09160 
                 SEC14 CYTOSOLIC FACTOR FAMILY PROTEIN/ 
                 2 
               
               
                   
                 PHOSPHOGLYCERIDE TRANSFER FAMILY PROTEIN 
               
               
                 AT3G51670 
                 SEC14 cytosolic factor family protein/phosphoglyceride transfer family 
                 2 
               
               
                   
                 protein, similar to polyphosphoinositide binding protein Ssh2p 
               
               
                   
                 (GI: 2739046) { Glycine max };; contains Pfam PF00650: CRAL/TRIO 
               
               
                   
                 domain; contains Pfam PF03765: CRAL/TRIO, N-terminus 
               
               
                 AT5G03730 
                 SERINE/THREONINE-PROTEIN KINASE CTR1 
                 2 
               
               
                 AT4G14180 
                 SIMILAR TO OS04G0347800 [ ORYZA SATIVA  (JAPONICA 
                 2 
               
               
                   
                 CULTIVAR-GROUP)] (GB: NP_001052517.1); SIMILAR TO 
               
               
                   
                 OSIGBA0130K07.4 [ ORYZA SATIVA (INDICA CULTIVAR-GROUP)]   
               
               
                   
                 (GB: CAH66368.1); SIMILAR TO OSJNBA0020I02.9 [ ORYZA SATIVA   
               
               
                   
                 (JAPONICA CULTIVAR-GROUP)] (GB: CAE02100.2); CONTAINS 
               
               
                   
                 DOMAIN ARM REPEAT (SSF48371) 
               
               
                 AT1G08260 
                 SIMILAR TO POL2A. DNA POLYMERASE EPSILON CATALYTIC 
                 2 
               
               
                   
                 SUBUNIT. ESSENTIAL FOR  ARABIDOPSIS  GROWTH. NULL 
               
               
                   
                 HOMOZYGOTES ARE EMBRYO LETHAL. PARTIAL LOSS OF 
               
               
                   
                 FUNCTION ALLELES SHOW EMBRYO PATTERNING DEFECTS 
               
               
                   
                 SUCH AS ROOT POLE DISPLACEMENT. DELAYED 
               
               
                   
                 PROGRESSION THROUGH CELL CYCLE RESULTS IN EMBRYOS 
               
               
                   
                 WITH SMALLER NUMBERS OF LARGER CELLS. 
               
               
                 AT2G27170 
                 similar to SMC2-like condensin, putative (SMC2) (TITAN3) 
                 2 
               
               
                 AT5G24630 
                 SIMILAR TO UNKNOWN PROTEIN [ ARABIDOPSIS THALIANA ] 
                 2 
               
               
                   
                 (TAIR: AT2G22795.1); SIMILAR TO UNKNOWN PROTEIN [ ORYZA   
               
               
                   
                   SATIVA  (JAPONICA CULTIVAR-GROUP)] (GB: BAD13052.1); 
               
               
                   
                 SIMILAR TO OS02G0147700 [ ORYZA SATIVA  (JAPONICA 
               
               
                   
                 CULTIVAR-GROUP)] (GB: NP_001045886.1) 
               
               
                 AT3G10440 
                 SIMILAR TO UNKNOWN PROTEIN [ ARABIDOPSIS THALIANA ] 
                 2 
               
               
                   
                 (TAIR: AT5G04320 
               
               
                 AT3G17590 
                 SNF5 homolog BSH (bsh) mRNA, complete cds 
                 2 
               
               
                 AT1G49040 
                 stomatal cytokinesis defective/SCD1 protein (SCD1) 
                 2 
               
               
                 AT5G15920 
                 structural maintenance of chromosomes (SMC) family protein (MSS2), 
                 2 
               
               
                   
                 similar to SMC-related protein MSS2 ( Arabidopsis thaliana ) 
               
               
                   
                 GI: 9965743 
               
               
                 AT1G04110 
                 subtilase family protein, contains similarity to subtilisin-like protease 
                 2 
               
               
                   
                 gI: 3687307 
               
               
                 AT3G04740 
                 SWP (STRUWWELPETER) 
                 2 
               
               
                 AT1G08560 
                 syntaxin-related protein KNOLLE 
                 2 
               
               
                 AT3G62980 
                 TIR1 (TRANSPORT INHIBITOR RESPONSE 1); ubiquitin-protein 
                 2 
               
               
                   
                 ligase 
               
               
                 AT1G30660 
                 toprim domain-containing protein 
                 2 
               
               
                 AT1G30680 
                 TOPRIM DOMAIN-CONTAINING PROTEIN 
                 2 
               
               
                 AT4G10710 
                 transcriptional regulator-related 
                 2 
               
               
                 AT3G44540 
                 TRANSDUCIN FAMILY PROTEIN/WD-40 REPEAT FAMILY 
                 2 
               
               
                   
                 PROTEIN, CONTAINS 6 (4 SIGNIFICANT) WD-40 REPEATS 
               
               
                   
                 (PF0400 
               
               
                 AT2G15380 
                 transposable element gene 
                 2 
               
               
                 AT2G15540 
                 transposable element gene 
                 2 
               
               
                 AT2G18820 
                 transposable element gene 
                 2 
               
               
                 AT2G28980 
                 transposable element gene 
                 2 
               
               
                 AT4G04000 
                 transposable element gene 
                 2 
               
               
                 AT3G54670 
                 TTN8|SIMILAR TO STRUCTURAL MAINTENANCE OF 
                 2 
               
               
                   
                 CHROMOSOMES (SMC) FAMILY PROTEIN [ ARABIDOPSIS   
               
               
                   
                   THALIANA ] (TAIR: AT5G48600.1 
               
               
                 AT3G20060 
                 UBC19 (UBIQUITIN-CONJUGATING ENZYME 19); UBIQUITIN- 
                 2 
               
               
                   
                 PROTEIN LIGASE 
               
               
                 AT1G50490 
                 UBC20 
                 2 
               
               
                 AT1G02970 
                 WEE1 
                 2 
               
               
                 AT5G08290 
                 YLS8 (yellow-leaf-specific gene 8); catalytic 
                 2 
               
               
                 AT4G02980 
                 ABP1 (ENDOPLASMIC RETICULUM AUXIN BINDING PROTEIN 1) 
                 1 
               
               
                 AT5G22500 
                 ACYL COA REDUCTASE, PUTATIVE/MALE-STERILITY PROTEIN, 
                 1 
               
               
                   
                 PUTATIVE 
               
               
                 AT1G14830 
                 ADL1C/ADL5 (DYNAMIN-LIKE PROTEIN 5); GTP binding/GTPase 
                 1 
               
               
                 AT4G33650 
                 ADL2a 
                 1 
               
               
                 AT5G61960 
                 AML1 ( ARABIDOPSIS  MEI2-LIKE PROTEIN 1); RNA binding 
                 1 
               
               
                 AT4G01540 
                 ANAC068/NTM1 (NAC WITH TRANSMEMBRANE MOTIF1); 
                 1 
               
               
                   
                 TRANSCRIPTION FACTOR/TRANSCRIPTIONAL ACTIVATOR 
               
               
                 AT2G18290 
                 APC10 
                 1 
               
               
                 AT2G04660 
                 APC2 
                 1 
               
               
                 AT4G21530 
                 APC4 
                 1 
               
               
                 AT3G54710 
                 ATCDT1B/CDT1/CDT1B ( ARABIDOPSIS  HOMOLOG OF YEAST 
                 1 
               
               
                   
                 CDT1 B); CYCLIN-DEPENDENT PROTEIN KINASE 
               
               
                 AT2G20190 
                 ATCLASP/CLASP; binding 
               
               
                 AT4G18820 
                 ATP BINDING/DNA-DIRECTED DNA POLYMERASE/ 
                 1 
               
               
                   
                 NUCLEOSIDE-TRIPHOSPHATASE/NUCLEOTIDE BINDING 
               
               
                 AT4G21800 
                 ATP-binding family protein 
                 1 
               
               
                 AT3G49780 
                 ATPSK3|PHYTOSULFOKINES 3 (PSK3), IDENTICAL TO 
                 1 
               
               
                   
                 PHYTOSULFOKINES 3 (PSK3) SP: Q9M2Y0 FROM ( ARABIDOPSIS   
               
               
                   
                   THALIANA )|CHR3: 18476664-18477361 FORWARD|ALIASES: 
               
               
                   
                 PHYTOSULFOKINE 3 PRECURSOR, T16K530 
               
               
                 AT1G58470 
                 ATRBP1 ( ARABIDOPSIS THALIANA  RNA-BINDING PROTEIN 1); 
                 1 
               
               
                   
                 RNA binding 
               
               
                 AT4G00100 
                 ATRPS13A (RIBOSOMAL PROTEIN S13A); structural constituent of 
                 1 
               
               
                   
                 ribosome 
               
               
                 AT3G20780 
                 ATTOP6B (BRASSINOSTEROID INSENSITIVE 3, ROOT HAIRLESS 
                 1 
               
               
                   
                 3) 
               
               
                 AT2G28350 
                 auxin-responsive factor (ARF10) 
                 1 
               
               
                 AT1G69400 
                 BUB3-like1 
                 1 
               
               
                 AT5G27080 
                 cdc20-3 
                 1 
               
               
                 AT5G03455 
                 cdc25 
                 1 
               
               
                 AT2G38620 
                 CDKB1; 2 
                 1 
               
               
                 AT5G10270 
                 CDKC; 1 
                 1 
               
               
                 AT1G66750 
                 CDKD; 2 
                 1 
               
               
                 AT5G63610 
                 CDKE; 1 
                 1 
               
               
                 AT1G67580 
                 CDKG; 2 
                 1 
               
               
                 AT2G46520 
                 CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN, PUTATIVE/ 
                 1 
               
               
                   
                 IMPORTIN-ALPHA RE-EXPORTER, PUTATIVE 
               
               
                 AT2G25170 
                 chromatin remodeling factor CHD3 (PICKLE) 
                 1 
               
               
                 AT2G26280 
                 CID7; ATP BINDING/DAMAGED DNA BINDING 
                 1 
               
               
                 AT5G39420 
                 CKL1 
                 1 
               
               
                 AT1G57700 
                 CKL10 
                 1 
               
               
                 AT1G71530 
                 CKL12 
                 1 
               
               
                 AT4G10010 
                 CKL13 
                 1 
               
               
                 AT1G33770 
                 CKL14 
                 1 
               
               
                 AT1G74330 
                 CKL2 
                 1 
               
               
                 AT5G50860 
                 CKL7 
                 1 
               
               
                 AT2G27960 
                 CKS1 
                 1 
               
               
                 AT1G02980 
                 cullin family protein, similar to cullin 1 ( Homo sapiens ) GI: 3139077; 
                 1 
               
               
                   
                 contains Pfam profile PF00888: Cullin family 
               
               
                 AT1G69670 
                 cullin3b 
                 1 
               
               
                 AT5G46210 
                 cullin4 
                 1 
               
               
                 AT1G47220 
                 CYCA3; 3 
                 1 
               
               
                 AT1G47230 
                 CYCA3; 4 
                 1 
               
               
                 AT1G20590 
                 CYCB2; 5 
                 1 
               
               
                 AT1G16330 
                 CYCB3; 1 
                 1 
               
               
                 AT2G22490 
                 CYCD2; 1 
                 1 
               
               
                 AT5G67260 
                 CYCD3; 2 
                 1 
               
               
                 AT5G65420 
                 CYCD4; 1 
                 1 
               
               
                 AT4G03270 
                 CYCD6; 1 
                 1 
               
               
                 AT5G27620 
                 CYCH; 1 
                 1 
               
               
                 AT3G21870 
                 CYCLIN FAMILY PROTEIN, SIMILAR TO CYCLIN 2 
                 1 
               
               
                   
                 ( TRYPANOSOMA BRUCEI ) GI: 7339572, CYCLIN 6 ( TRYPANOSOMA   
               
               
                   
                   CRUZI ) GI: 12005317; CONTAINS PFAM PROFILE PF00134: 
               
               
                   
                 CYCLIN, N-TERMINAL DOMAIN|CHR3: 7703878-7704836 
               
               
                   
                 REVERSE|ALIASES: MEK6.1 
               
               
                 AT5G50375 
                 cyclopropyl isomerase (CPI1) 
                 1 
               
               
                 AT2G45080 
                 CYCP3; 1 (CYCLIN P3; 1); CYCLIN-DEPENDENT PROTEIN KINASE 
                 1 
               
               
                 AT3G60550 
                 CYCP3; 2 
                 1 
               
               
                 AT5G61650 
                 CYCP4; 2|CYCLIN FAMILY PROTEIN, SIMILAR TO CYCLIN 2 
                 1 
               
               
                   
                 ( TRYPANOSOMA BRUCEI ) GI: 7339572, CYCLIN 6 ( TRYPANOSOMA   
               
               
                   
                   CRUZI ) GI: 12005317; CONTAINS PFAM PROFILE PF00134: 
               
               
                   
                 CYCLIN, N-TERMINAL DOMAIN|CHR5: 24795491-24796245 
               
               
                   
                 FORWARD|ALIASES: CYCP4, K11J9.17, K11J9_17 
               
               
                 AT1G35440 
                 CYCT1; 1 
                 1 
               
               
                 AT1G27630 
                 CYCT1; 3 
                 1 
               
               
                 AT4G19600 
                 CYCT1; 4 
                 1 
               
               
                 AT1G01040 
                 DEAD/DEAH box helicase carpel factory/CAF 
                 1 
               
               
                 AT3G48160 
                 DEL1 
                 1 
               
               
                 AT5G54090 
                 DNA mismatch repair MutS family protein 
                 1 
               
               
                 AT2G42120 
                 DNA polymerase delta small subunit 
                 1 
               
               
                 AT1G10520 
                 DNA polymerase lambda (POLL) 
                 1 
               
               
                 AT2G32000 
                 DNA TOPOISOMERASE FAMILY PROTEIN 
                 1 
               
               
                 AT5G63960 
                 DNA-directed DNA polymerase delta catalytic subunit, putative 
                 1 
               
               
                   
                 (POLD1) 
               
               
                 AT2G27120 
                 DNA-directed DNA polymerase epsilon catalytic subunit, putative, 
                 1 
               
               
                   
                 similar to SP|Q07864 DNA polymerase epsilon, catalytic subunit A (EC 
               
               
                   
                 2.7.7.7) (DNA polymerase II subunit A) { Homo sapiens }; contains Pfam 
               
               
                   
                 profiles: PF03175 DNA polymerase type B, organellar 
               
               
                 AT2G22360 
                 DNAJ heat shock family protein 
                 1 
               
               
                 AT3G60190 
                 dynamin-like protein E 
                 1 
               
               
                 AT5G13680 
                 ELO2 
                 1 
               
               
                 AT1G12360 
                 ENCODES A SEC1 PROTEIN AND EXPRESSED THROUGHOUT 
                 1 
               
               
                   
                 THE PLANT. PHYSICALLY INTERACTS WITH SYNTAXIN1 AND IS 
               
               
                   
                 REQUIRED FOR CYTOKINESIS. 
               
               
                 AT3G23580 
                 ENCODES ONE OF THE 3 RIBONUCLEOTIDE REDUCTASE (RNR) 
                 1 
               
               
                   
                 SMALL SUBUNIT GENES (RNR2A). FUNCTIONALLY REDUNDANT 
               
               
                   
                 WITH THE RIBONUCLEOTIDE REDUCTASE TSO2. MRNA WAS 
               
               
                   
                 SHOWN TO SPECIFICALLY ACCUMULATE DURING THE S-PHASE 
               
               
                   
                 OF THE CELL CYCLE IN SYNCHRONIZED TOBACCO BY2 CELLS. 
               
               
                   
                 CRITICAL FOR CELL CYCLE PROGRESSION. DNA DAMAGE 
               
               
                   
                 REPAIR AND PLANT DEVELOPMENT. 
               
               
                 AT1G50250 
                 FTSH1 (FTSH PROTEASE 1); ATP-DEPENDENT PEPTIDASE/ 
                 1 
               
               
                   
                 ATPASE/METALLOPEPTIDASE 
               
               
                 AT5G53170 
                 FTSH11 (FTSH PROTEASE 11); ATP-DEPENDENT PEPTIDASE/ 
                 1 
               
               
                   
                 ATPASE/METALLOPEPTIDASE 
               
               
                 AT2G36250 
                 FTSZ2-1 (FTSZ HOMOLOG 2-1); STRUCTURAL MOLECULE 
                 1 
               
               
                 AT3G52750 
                 FTSZ2-2 (FtsZ2-2); structural molecule 
                 1 
               
               
                 AT2G22475 
                 GRAM DOMAIN-CONTAINING PROTEIN/ABA-RESPONSIVE 
                 1 
               
               
                   
                 PROTEIN-RELATED 
               
               
                 ATMG01250 
                 HYPOTHETICAL PROTEIN 
                 1 
               
               
                 AT5G08550 
                 ILP1 (INCREASED LEVEL OF POLYPLOIDY1-1D); TRANSLATION 
                 1 
               
               
                   
                 REPRESSOR 
               
               
                 AT1G30010 
                 INTRON MATURASE, TYPE II FAMILY PROTEIN 
                 1 
               
               
                 AT4G21270 
                 kinesin-like protein A (KATA) 
                 1 
               
               
                 AT5G35520 
                 kinetochore protein-related 
                 1 
               
               
                 AT3G50630 
                 KRP2 
                 1 
               
               
                 AT5G48820 
                 KRP3 
                 1 
               
               
                 AT2G32710 
                 KRP4 
                 1 
               
               
                 AT3G24810 
                 KRP5 
                 1 
               
               
                 AT2G26330 
                 leucine-rich repeat protein kinase, putative (ERECtA), identical to 
                 1 
               
               
                   
                 uncharacterized receptor protein kinase ERECtA ( Arabidopsis thaliana ) 
               
               
                   
                 gi: 1389566: dbj: BAA11869; contains Pfam domains PF00560: Leucine 
               
               
                   
                 Rich Repeat and PF00069: Protein kinase domain 
               
               
                 AT3G56700 
                 MALE STERILITY PROTEIN, PUTATIVE 
                 1 
               
               
                 AT4G30820 
                 MAT1 
                 1 
               
               
                 AT1G66170 
                 MMD1 (MALE MEIOCYTE DEATH 1); DNA BINDING 
                 1 
               
               
                 AT4G20900 
                 MS5 (MALE-STERILE 5) 
                 1 
               
               
                 AT1G79150 
                 NOC3_DNA replication initiation 
                 1 
               
               
                 AT2G01840 
                 non-LTR retrotransposon family (LINE), has a 9.6e−34 P-value blast 
                 1 
               
               
                   
                 match to GB: NP_038607 L1 repeat, Tf subfamily, member 9 
               
               
                   
                 (LINE-element) ( Mus musculus ) 
               
               
                 AT2G35190 
                 NPSN11 (NOVEL PLANT SNARE 11); protein transporter 
                 1 
               
               
                 AT1G77620 
                 NUCLEOSIDE-TRIPHOSPHATASE/NUCLEOTIDE BINDING 
                 1 
               
               
                 AT4G12620 
                 ORC1 
                 1 
               
               
                 AT3G44550 
                 OXIDOREDUCTASE, ACTING ON THE CH-CH GROUP OF DONORS 
                 1 
               
               
                 AT3G44560 
                 OXIDOREDUCTASE, ACTING ON THE CH-CH GROUP OF DONORS 
                 1 
               
               
                 AT5G10480 
                 PAS2 (PASTICCINO 2) 
                 1 
               
               
                 AT1G07370 
                 PCNA1 
                 1 
               
               
                 AT1G71440 
                 PFI_TFC E_PFI (PFIFFERLING) 
                 1 
               
               
                 AT2G18040 
                 PIN1 
                 1 
               
               
                 AT5G22130 
                 PNT1 (PEANUT 1); MANNOSYLTRANSFERASE/TRANSFERASE, 
                 1 
               
               
                   
                 TRANSFERRING GLYCOSYL GROUPS 
               
               
                 AT3G20540 
                 POLGAMMA1 (POLYMERASE GAMMA 1); DNA BINDING/ 
                 1 
               
               
                   
                 DNA-DIRECTED DNA POLYMERASE 
               
               
                 AT4G14713 
                 PPD1 (PEAPOD 1) 
                 1 
               
               
                 AT1G49180 
                 protein kinase family protein 
                 1 
               
               
                 AT3G12530 
                 PSF2 (GINS complex DNA replication) 
                 1 
               
               
                 AT2G17910 
                 putative non-LTR retroelement reverse transcriptase 
                 1 
               
               
                 AT4G36390 
                 radical SAM domain-containing protein/TRAM domain-containing 
                 1 
               
               
                   
                 protein 
               
               
                 AT1G63160 
                 replication factor, putative; similar to GI: 4972952 from ( Mus musculus ) 
                 1 
               
               
                   
                 (Mamm. Genome (2000) In press) 
               
               
                 AT5G45400 
                 replication protein, putative, similar to replication protein A 70 kDa 
                 1 
               
               
                   
                 ( Oryza sativa  (japonica cultivar-group)) GI: 13536993; contains InterPro 
               
               
                   
                 entry IPR004365: OB-fold nucleic acid binding domain, PF04057: 
               
               
                   
                 Replication factor-A protein 1, N-terminal domain 
               
               
                 AT4G19130 
                 replication protein-related, similar to replication protein A 70 kDa ( Oryza   
                 1 
               
               
                   
                   sativa ) GI: 13536993; contains Pfam profile PF00098: Zinc knuckle 
               
               
                 AT4G20520 
                 RNA binding/RNA-directed DNA polymerase 
                 1 
               
               
                 AT2G20580 
                 RPN1 
                 1 
               
               
                 AT3G54220 
                 SCR (SCARECROW); TRANSCRIPTION FACTOR 
                 1 
               
               
                 AT1G14750 
                 SDS 
                 1 
               
               
                 AT1G22530 
                 SEC14 cytosolic factor family protein 
                 1 
               
               
                 AT1G34210 
                 SERK2 (SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 2); 
                 1 
               
               
                   
                 KINASE 
               
               
                 AT5G52800 
                 SIMILAR TO PREDICTED: HYPOTHETICAL PROTEIN [ RATTUS   
                 1 
               
               
                   
                 NORVE (GB: XP_001060721.1); SIMILAR TO OS07G0467900 
               
               
                   
                 [ ORYZA SATIVA  (JAPONICA CULTIVAR-GR 
               
               
                 AT5G58650 
                 SIMILAR TO UNKNOWN PROTEIN [ ARABIDOPSIS THALIANA ] 
                 1 
               
               
                   
                 (TAIR: AT3G47295.1) 
               
               
                 AT1G75950 
                 SKP1 ( ARABIDOPSIS  SKP1 HOMOLOGUE); ubiquitin-protein ligase 
                 1 
               
               
                 AT3G47460 
                 SMC2-like condensin, putative/chromosome assembly protein 
                 1 
               
               
                   
                 homolog; CHROMOSOME ASSEMBLY PROTEIN XCAP-E -  Xenopus   
               
               
                   
                   laevis , SWISSPROT: XCPE_XENLA 
               
               
                 AT2G02480 
                 STI (STICHEL); ATP BINDING/DNA-DIRECTED DNA 
                 1 
               
               
                   
                 POLYMERASE 
               
               
                 AT5G07660 
                 structural maintenance of chromosomes (SMC) family protein 
                 1 
               
               
                 AT3G51770 
                 tetratricopeptide repeat (TPR)-containing protein 
                 1 
               
               
                 AT5G23070 
                 thymidine kinase, putative, similar to thymidine kinase ( Oryza sativa ) 
                 1 
               
               
                   
                 SWISS-PROT: O81263 
               
               
                 AT3G01780 
                 TPLATE 
                 1 
               
               
                 AT4G07600 
                 transposable element gene 
                 1 
               
               
                 AT4G09710 
                 transposable element gene 
                 1 
               
               
                 AT4G14470 
                 transposable element gene 
                 1 
               
               
                 AT4G04230 
                 transposable element gene 
                 1 
               
               
                 AT3G18730 
                 TSK (TONSOKU) 
                 1 
               
               
                 AT1G22275 
                 unknown protein 
                 1 
               
               
                 AT5G42270 
                 VAR1 (VARIEGATED 1); ATP-DEPENDENT PEPTIDASE/ATPASE/ 
                 1 
               
               
                   
                 METALLOPEPTIDASE 
               
               
                 AT2G33880 
                 WOX9 (STIMPY); transcription factor 
                 1 
               
               
                 AT1G24490 
                 ALB4 (ALBINA 4) 
                 0 
               
               
                 AT5G28640 
                 AN3 
                 0 
               
               
                 AT3G05870 
                 APC11 
                 0 
               
               
                 AT2G37630 
                 AS1/ATMYB91/ATPHAN/MYB91 (ASYMMETRIC LEAVES 1, MYB 
                 0 
               
               
                   
                 DOMAIN PROTEIN 91); DNA binding/protein homodimerization/ 
               
               
                   
                 transcription factor 
               
               
                 AT3G21850 
                 ASK9 ( ARABIDOPSIS  SKP1-LIKE 9); ubiquitin-protein ligase 
                 0 
               
               
                 AT4G32200 
                 ASY2; DNA binding 
                 0 
               
               
                 AT3G33520 
                 ATARP6; structural constituent of cytoskeleton 
                 0 
               
               
                 AT3G48190 
                 ataxia-telangiectasia mutated protein AtATM 
                 0 
               
               
                 AT5G05620 
                 ATGCP2/TUBG2 (GAMMA-TUBULIN); structural molecule 
                 0 
               
               
                 AT3G20475 
                 ATP binding/damaged DNA binding 
                 0 
               
               
                 AT1G49250 
                 ATP dependent DNA ligase family protein 
                 0 
               
               
                 AT1G13590 
                 ATPSK1 (PHYTOSULFOKINE 1 PRECURSOR); growth factor 
                 0 
               
               
                 AT2G22860 
                 ATPSK2_ATPSK2 (PHYTOSULFOKINE 2 PRECURSOR); growth 
                 0 
               
               
                   
                 factor 
               
               
                 AT5G65870 
                 ATPSK5 (PHYTOSULFOKINE 5 PRECURSOR); growth factor 
                 0 
               
               
                 AT4G37720 
                 ATPSK6 (PHYTOSULFOKINE 6 PRECURSOR); growth factor 
                 0 
               
               
                 AT1G14410 
                 ATWHY1/PTAC1 (A. THALIANA WHIRLY 1); DNA binding/telomeric 
                 0 
               
               
                   
                 DNA binding 
               
               
                 AT5G09790 
                 ATXR5 (SETDOMAIN GROUP 15); DNA binding 
                 0 
               
               
                 AT3G24730 
                 catalytic 
                 0 
               
               
                 AT3G48750 
                 CDKA; 1 
                 0 
               
               
                 AT3G54180 
                 CDKB1; 1 
                 0 
               
               
                 AT5G66130 
                 cell cycle checkpoint protein-related, weak similarity to cell cycle 
                 0 
               
               
                   
                 checkpoint protein RAD17 ( Homo sapiens ) GI: 4102916 
               
               
                 Q94G54 
                 Cell division control protein 6 
                 0 
               
               
                 Q9C8M6 
                 Cell division control protein, putative; 15914-18846 
                 0 
               
               
                 Q9LFB3 
                 Cell division-like protein 
                 0 
               
               
                 AT1G53050 
                 CKL15 
                 0 
               
               
                 AT3G05050 
                 CKL8 
                 0 
               
               
                 AT3G15170 
                 CUC1 (CUP-SHAPED COTYLEDON1); transcription factor 
                 0 
               
               
                 AT1G20610 
                 CYCB2; 3 
                 0 
               
               
                 AT5G48630 
                 CYCC1; 2 
                 0 
               
               
                 AT5G10440 
                 CYCD4; 2 
                 0 
               
               
                 AT5G02110 
                 CYCD7; 1 
                 0 
               
               
                 AT2G01905 
                 CYCJ18 
                 0 
               
               
                 Q38818 
                 Cyclin 2 
                 0 
               
               
                 AT2G44740 
                 CYCLIN FAMILY PROTEIN, SIMILAR TO CYCLIN 2 
                 0 
               
               
                   
                 ( TRYPANOSOMA BRUCEI ) GI: 7339572, CYCLIN 6 ( TRYPANOSOMA   
               
               
                   
                   CRUZI ) GI: 12005317; CONTAINS PFAM PROFILE PF00134: 
               
               
                   
                 CYCLIN, N-TERMINAL DOMAIN|CHR2: 18449064-18450471 
               
               
                   
                 REVERSE|ALIASES: F16B22.23 
               
               
                 AT5G07450 
                 CYCLIN FAMILY PROTEIN, SIMILAR TO CYCLIN 2 
                 0 
               
               
                   
                 ( TRYPANOSOMA BRUCEI ) GI: 7339572, CYCLIN 6 ( TRYPANOSOMA   
               
               
                   
                   CRUZI ) GI: 12005317; CONTAINS PFAM PROFILE PF00134: 
               
               
                   
                 CYCLIN, N-TERMINAL DOMAIN|CHR5: 2358353-2359309 
               
               
                   
                 REVERSE|ALIASES: T2I1.160, T2I1_160 
               
               
                 AT1G22840 
                 cytochrome c, putative 
                 0 
               
               
                 AT4G26701 
                 DNA binding/DNA topoisomerase type I 
                 0 
               
               
                 AT3G15960 
                 DNA mismatch repair MutS family protein 
                 0 
               
               
                 AT5G22110 
                 DNA POLYMERASE EPSILON SUBUNIT B FAMILY, CONTAINS 
                 0 
               
               
                   
                 PFAM PROFILE: PF04042 DNA POLYMERASE EPSILON SUBUNIT 
               
               
                   
                 B|CHR5: 7330828-7334181 REVERSE|ALIASES: NONE 
               
               
                 AT5G64520 
                 DNA repair protein-related 
                 0 
               
               
                 AT1G63990 
                 DNA topoisomerase VIA, putative (SPO11-2) 
                 0 
               
               
                 AT4G39960 
                 DNAJ heat shock family protein 
                 0 
               
               
                 AT5G62450 
                 DOMINO1 
                 0 
               
               
                 AT5G03415 
                 DPb 
                 0 
               
               
                 AT5G50320 
                 ELO3 
                 0 
               
               
                 Q9FMR4 
                 Emb|CAB92117.1 
                 0 
               
               
                 AT1G24590 
                 ENCODES A MEMBER OF THE ERF (ETHYLENE RESPONSE 
                 0 
               
               
                   
                 FACTOR) SUBFAMILY B-1 OF ERF/AP2 TRANSCRIPTION FACTOR 
               
               
                   
                 FAMILY. THE PROTEIN CONTAINS ONE AP2 DOMAIN. THERE ARE 
               
               
                   
                 15 MEMBERS IN THIS SUBFAMILY INCLUDING ATERF-3. ATERF-4. 
               
               
                   
                 ATERF-7. AND LEAFY PETIOLE. THIS GENE FUNCTIONS IN THE 
               
               
                   
                 REGENERATION OF SHOOTS IN TISSUE CULTURE. PROBABLY 
               
               
                   
                 THROUGH TRANSCRIPTIONAL REGULATION OF CUC1. MAY 
               
               
                   
                 ALSO BE INVOLVED IN ACTIVATION OF THE CELL CYCLE VIA 
               
               
                   
                 CYCD1; 1. 
               
               
                 AT5G26680 
                 ENDONUCLEASE, PUTATIVE, SIMILAR TO SWISS-PROT: P39748 
                 0 
               
               
                   
                 FLAP ENDONUCLEASE-1 (MATURATION FACTOR 1) (MF1) ( HOMO   
               
               
                   
                   SAPIENS )|CHR5: 9311885-9315478 REVERSE|ALIASES: NONE 
               
               
                 AT1G22260 
                 expressed protein 
                 0 
               
               
                 Q9M874 
                 F16B3.31 protein 
                 0 
               
               
                 Q9FX75 
                 F19K19.10 protein 
                 0 
               
               
                 Q9FYF5 
                 F1N21.20 
                 0 
               
               
                 O81303 
                 F6N15.14 protein (Putative BRCA2 homolog) 
                 0 
               
               
                 AT2G14650 
                 F9D12.11 protein (contains similarity to reverse transcriptases) 
                 0 
               
               
                 AT3G24140 
                 FMA (FAMA); DNA binding/transcription activator/transcription factor 
                 0 
               
               
                 AT2G22942 
                 growth factor 
                 0 
               
               
                 AT5G42080 
                 GTP-binding protein/phragmoplastin, putative 
                 0 
               
               
                 AT1G47840 
                 hexokinase, putative 
                 0 
               
               
                 AT5G03410 
                 histidyl-tRNA synthetase - like protein 
                 0 
               
               
                 AT2G44950 
                 HUB1 
                 0 
               
               
                 AT2G44960 
                 HUB1 
                 0 
               
               
                 AT3G52630 
                 hypothetical protein 
                 0 
               
               
                 AT1G74350 
                 intron maturase, type II family protein 
                 0 
               
               
                 AT5G03150 
                 JKD (JACKDAW); nucleic acid binding/protein binding/protein 
                 0 
               
               
                   
                 homodimerization/transcription factor/zinc ion binding 
               
               
                 Q2V0Z5 
                 Kinetochore protein 
                 0 
               
               
                 AT2G30410 
                 KIS (KIESEL); unfolded protein binding 
                 0 
               
               
                 ATMG00520 
                 MATR 
                 0 
               
               
                 AT5G22260 
                 MS1 (MALE STERILITY 1); DNA binding 
                 0 
               
               
                 AT3G11980 
                 MS2 (MALE STERILITY 2) 
                 0 
               
               
                 AT2G01120 
                 ORC4 
                 0 
               
               
                 AT4G27650 
                 PEL1 (PELOTA); translation release factor 
                 0 
               
               
                 AT2G01500 
                 PFS2 (PRETTY FEW SEEDS 2); transcription factor 
                 0 
               
               
                 AT3G44735 
                 PSK1 (PHYTOSULFOKINE 3 PRECURSOR); growth factor 
                 0 
               
               
                 Q9M8S3 
                 Putative CCHC-type zinc finger protein 
                 0 
               
               
                 AT4G39920 
                 putative protein 
                 0 
               
               
                 AT5G22370 
                 putative protein; similar to unknown protein (emb|CAB92117.1) 
                 0 
               
               
                 AT2G07660 
                 putative retroelement pol polyprotein 
                 0 
               
               
                 O80896 
                 Putative uncharacterized protein At2g32590 
                 0 
               
               
                 Q9M013 
                 Putative uncharacterized protein F7A7_150 
                 0 
               
               
                 O82745 
                 Putative uncharacterized protein F7H19.150 (Putative uncharacterized 
                 0 
               
               
                   
                 protein AT4g22970) 
               
               
                 Q9C953 
                 Putative uncharacterized protein T7P1.14 
                 0 
               
               
                 AT4G20050 
                 QRT3 (QUARTET 3) 
                 0 
               
               
                 AT2G06510 
                 replication protein, putative similar to replication protein A 70 kDa 
                 0 
               
               
                 AT4G29090 
                 reverse transcriptase, putative/RNA-dependent DNA polymerase, 
                 0 
               
               
                   
                 putative 
               
               
                 AT2G25100 
                 ribonuclease HII family protein 
                 0 
               
               
                 AT5G40942 
                 RNR2B 
                 0 
               
               
                 AT2G36985 
                 ROT4 (ROTUNDIFOLIA4) 
                 0 
               
               
                 AT4G18730 
                 RPL16B (ribosomal protein L16B); structural constituent of ribosome 
                 0 
               
               
                 AT1G17235 
                 RTFL11 (ROTUNDIFOLIA LIKE 11) 
                 0 
               
               
                 AT4G37650 
                 SHR (SHORT ROOT); transcription factor 
                 0 
               
               
                 AT5G04470 
                 SIM 
                 0 
               
               
                 AT3G55490 
                 similar to TTN10 (TITAN 10) 
                 0 
               
               
                 AT5G62440 
                 similar to unnamed protein product [ Vitis vinifera ] (GB: CAO64547.1) 
                 0 
               
               
                 Q9FGA0 
                 Similarity to glucose inhibited division protein B 
                 0 
               
               
                 AT1G20330 
                 SMT2 (STEROL METHYLTRANSFERASE 2) 
                 0 
               
               
                 AT4G27330 
                 SPL (SPOROCYTELESS) 
                 0 
               
               
                 AT1G02065 
                 SPL8 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8); DNA 
                 0 
               
               
                   
                 binding 
               
               
                 AT3G07800 
                 thymidine kinase, putative, similar to thymidine kinase ( Oryza sativa ) 
                 0 
               
               
                   
                 SWISS-PROT: O81263 
               
               
                 AT2G05610 
                 transposable element gene 
                 0 
               
               
                 AT4G08830 
                 transposable element gene 
                 0 
               
               
                 AT4G10580 
                 transposable element gene 
                 0 
               
               
                 Q9FLP1 
                 Trigger factor-like protein 
                 0 
               
               
                 AT1G19080 
                 TTN10 (TITAN 10) 
                 0 
               
               
                 AT3G61650 
                 TUBG1 (GAMMA-TUBULIN); STRUCTURAL MOLECULE 
                 0 
               
               
                 AT1G05560 
                 UGT1 (UDP-glucosyl transferase 75B1); UDP-glycosyltransferase/ 
                 0 
               
               
                   
                 transferase, transferring glycosyl groups 
               
               
                 AT1G47200 
                 WPP2 (WPP domain protein 2) 
                 0 
               
               
                 AT5G57450 
                 XRCC3|DNA REPAIR FAMILY PROTEIN, CONTAINS SIMILARITY 
                 0 
               
               
                   
                 TO SWISS-PROT: O43542 DNA-REPAIR PROTEIN XRCC3 (X-RAY 
               
               
                   
                 REPAIR CROSS-COMPLEMENTING PROTEIN 3) ( HOMO SAPIENS )| 
               
               
                   
                 CHR5: 23290319-23292202 REVERSE|ALIASES: ATXRCC3, 
               
               
                   
                 MUA2.3, MUA2_3 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
             
               
             
               
               
               
             
               
             
               
               
               
             
           
               
                 TABLE 6 
               
             
             
               
                   
               
               
                 New candidate cell cycle proteins. 
               
             
          
           
               
                 Locus 
                 Description 
                 # of motifs 
               
               
                   
               
             
          
           
               
                 Overview of 40 putative new cell cycle proteins identified in the core dataset containing 
               
               
                 at least two of the cell cycle-related features listed in Table S4. The number of identified 
               
               
                 features per protein is shown. 
               
             
          
           
               
                 AT2G44580 
                 DCC1 
                 6 
               
               
                 AT3G57860 
                 UVI4-like 
                 5 
               
               
                 AT4G38900 
                 bZIP protein 
                 5 
               
               
                 AT1G32310 
                 F27G20.14 
                 5 
               
               
                 AT4G17020 
                 transcription factor-related 
                 4 
               
               
                 AT5G09900 
                 EMB2107, RPN5A, MSA 
                 4 
               
               
                 AT5G40460 
                 expressed 
                 4 
               
               
                 AT3G49240 
                 EMB1796 
                 4 
               
               
                 AT2G17350 
                 similar to hypothetical protein [ Vitis vinifera ] (GB: CAN62847.1) 
                 4 
               
               
                 AT5G24690 
                 similar to RER1 (RETICULATA-RELATED 1) [ Arabidopsis thaliana ] 
                 4 
               
               
                   
                 (TAIR: AT5G22790.1) 
               
               
                 AT4G25550 
                 M7J2_80 
                 4 
               
               
                 AT3G15180 
                 proteasome-related 
                 3 
               
               
                 AT2G36130 
                 peptidyl-prolyl cis-trans isomerase, putative/cyclophilin, putative/rotamase 
                 3 
               
               
                 AT3G16060 
                 kinesin motor family protein 
                 3 
               
               
                 AT3G10180 
                 kinesin motor protein-related 
                 3 
               
               
                 AT5G65460 
                 KCA2 
                 3 
               
               
                 AT5G05780 
                 RPN8A, AE3, ATHMOV34 
                 3 
               
               
                 AT1G06070 
                 bZIP transcription factor, putative (bZIP69) 
                 3 
               
               
                 AT1G71380 
                 ATGH9B3, ATCEL3 
                 3 
               
               
                 AT3G05530 
                 ATS6A.2, RPT5A 
                 2 
               
               
                 AT1G01880 
                 DNA repair protein, putative 
                 2 
               
               
                 AT4G34150 
                 C2 domain-containing protein 
                 2 
               
               
                 AT5G13030 
                 similar to hypothetical protein Osl_021963 [ Oryza sativa ] (GB: EAZ00731.1) 
                 2 
               
               
                 AT4G14310 
                 DL3195C 
                 2 
               
               
                 AT5G26360 
                 chaperonin, putative 
                 2 
               
               
                 AT5G49510 
                 VHL binding protein, putative/prefoldin, putative 
                 2 
               
               
                 AT3G20050 
                 ATTCP-1 
                 2 
               
               
                 AT1G29150 
                 RPN6, ATS9 
                 2 
               
               
                 AT3G15970 
                 Ran-binding protein 1 domain-containing protein/RanBP1 domain-containing 
                 2 
               
               
                   
                 protein 
               
               
                 AT4G28230 
                 similar to unnamed protein product [ Vitis vinifera ] (GB: CAO41238.1) 
                 2 
               
               
                 AT5G23540 
                 26S proteasome regulatory subunit, putative 
                 2 
               
               
                 AT5G41190 
                 similar to hypothetical protein [ Vitis vinifera ] (GB: CAN66411.1) 
                 2 
               
               
                 AT2G03820 
                 nonsense-mediated mRNA decay NMD3 family protein 
                 2 
               
               
                 AT1G20480 
                 4-coumarate--CoA ligase family protein/4-coumaroyl-CoA synthase family 
                 2 
               
               
                   
                 protein 
               
               
                 AT1G09270 
                 importin alpha-1 subunit, putative (IMPA4) 
                 2 
               
               
                 AT1G23190 
                 phosphoglucomutase, cytoplasmic, putative/glucose phosphomutase, putative 
                 2 
               
               
                 AT2G06990 
                 HEN2 
                 2 
               
               
                 AT5G58290 
                 RPT3 
                 2 
               
               
                 AT5G20920 
                 EMB1401, EIF2 BETA 
                 2 
               
               
                 AT1G20200 
                 EMB2719 
                 2 
               
             
          
           
               
                 Overview of 82 putative new cell cycle proteins identified in the non-core dataset 
               
               
                 containing at least two of the cell cycle-related features listed in Table S4. The number of 
               
               
                 identified features per protein is shown. 
               
             
          
           
               
                 AT5G18620 
                 CHR17 
                 6 
               
               
                 AT4G38780 
                 splicing factor, putative 
                 5 
               
               
                 AT1G01970 
                 pentatricopeptide (PPR) repeat-containing protein 
                 5 
               
               
                 AT4G38900 
                 bZIP protein 
                 5 
               
               
                 AT4G17020 
                 transcription factor-related 
                 4 
               
               
                 AT2G46020 
                 ATBRM, CHR2, BRM 
                 4 
               
               
                 AT5G10800 
                 RNA recognition motif (RRM)-containing protein 
                 4 
               
               
                 AT5G40460 
                 expressed 
                 4 
               
               
                 AT1G36160 
                 AT-ACC1, EMB22, GK, PAS3, ACC1 
                 4 
               
               
                 AT1G77180 
                 chromatin protein family 
                 4 
               
               
                 AT1G16520 
                 similar to unknown protein [ Arabidopsis thaliana ] (TAIR: AT1G56080.1) 
                 4 
               
               
                 AT3G49240 
                 EMB1796 
                 4 
               
               
                 AT4G24680 
                 similar to unnamed protein product [ Vitis vinifera ] (GB: CAO64289.1) 
                 4 
               
               
                 AT2G25730 
                 binding/heme binding 
                 4 
               
               
                 AT5G38480 
                 RCI1, GRF3 
                 4 
               
               
                 AT4G25550 
                 M7J2_80 
                 4 
               
               
                 AT3G05190 
                 aminotransferase class IV family protein 
                 4 
               
               
                 AT4G35740 
                 RecQI3 
                 4 
               
               
                 AT3G62240 
                 zinc finger (C2H2 type) family protein 
                 3 
               
               
                 AT3G45970 
                 EXPL1, ATEXPL1, ATHEXP BETA 2.1, ATEXLA1 
                 3 
               
               
                 AT3G56690 
                 CIP111 
                 3 
               
               
                 AT3G56860 
                 UBA2A 
                 3 
               
               
                 AT3G01280 
                 porin, putative 
                 3 
               
               
                 AT3G20390 
                 endoribonuclease L-PSP family protein 
                 3 
               
               
                 AT5G03740 
                 HDT3, HD2C 
                 3 
               
               
                 AT5G25210 
                 similar to unknown protein [ Arabidopsis thaliana ] (TAIR: AT4G32030.1) 
                 3 
               
               
                 AT1G48920 
                 ATNUC-L1, PARL1 
                 3 
               
               
                 AT5G58150 
                 leucine-rich repeat transmembrane protein kinase, putative 
                 3 
               
               
                 AT1G17340 
                 phosphoinositide phosphatase family protein 
                 3 
               
               
                 AT1G23860 
                 RSZP21, SRZ21, SRZ-21 
                 3 
               
               
                 AT2G16950 
                 protein transporter 
                 3 
               
               
                 AT1G06070 
                 bZIP transcription factor, putative (bZIP69) 
                 3 
               
               
                 AT1G71380 
                 ATGH9B3, ATCEL3 
                 3 
               
               
                 AT2G44350 
                 CSY4, ATCS 
                 3 
               
               
                 AT1G30860 
                 protein binding/zinc ion binding 
                 3 
               
               
                 AT3G47930 
                 ATGLDH 
                 3 
               
               
                 AT1G03060 
                 WD-40 repeat family protein/beige-related 
                 3 
               
               
                 AT4G21860 
                 MSRB2 
                 3 
               
               
                 AT2G30470 
                 HSI2 
                 2 
               
               
                 AT1G80720 
                 mitochondrial glycoprotein family protein/MAM33 family protein 
                 2 
               
               
                 AT1G09760 
                 U2A′ 
                 2 
               
               
                 AT1G52360 
                 coatomer protein complex, subunit beta 2 (beta prime), putative 
                 2 
               
               
                 AT1G22300 
                 GF14 EPSILON, GRF10 
                 2 
               
               
                 AT3G13640 
                 ATRLI1 
                 2 
               
               
                 AT5G12140 
                 ATCYS1 
                 2 
               
               
                 AT1G66340 
                 EIN1, ETR, ETR1 
                 2 
               
               
                 AT1G42440 
                 similar to unknown protein [ Arabidopsis thaliana ] (TAIR: AT1G06720.1) 
                 2 
               
               
                 AT4G09320 
                 NDPK1 
                 2 
               
               
                 AT5G54900 
                 ATRBP45A 
                 2 
               
               
                 AT1G09100 
                 RPT5B 
                 2 
               
               
                 AT1G52730 
                 transducin family protein/WD-40 repeat family protein 
                 2 
               
               
                 AT3G49430 
                 SRP34A 
                 2 
               
               
                 AT3G53880 
                 aldo/keto reductase family protein 
                 2 
               
               
                 AT4G16630 
                 DEAD/DEAH box helicase, putative (RH28) 
                 2 
               
               
                 AT2G03820 
                 nonsense-mediated mRNA decay NMD3 family protein 
                 2 
               
               
                 AT1G23190 
                 phosphoglucomutase, cytoplasmic, putative/glucose phosphomutase, 
                 2 
               
               
                   
                 putative 
               
               
                 AT3G01540 
                 ATDRH1, DRH1 
                 2 
               
               
                 AT5G20920 
                 EMB1401, EIF2 BETA 
                 2 
               
               
                 AT4G14310 
                 DL3195C 
                 2 
               
               
                 AT1G09430 
                 ACLA-3 
                 2 
               
               
                 AT2G33340 
                 transducin family protein/WD-40 repeat family protein 
                 2 
               
               
                 AT1G01880 
                 DNA repair protein, putative 
                 2 
               
               
                 AT5G62350 
                 invertase/pectin methylesterase inhibitor family protein/DC 1.2 homolog 
                 2 
               
               
                   
                 (FL5-2I22) 
               
               
                 AT4G34150 
                 C2 domain-containing protein 
                 2 
               
               
                 AT5G46780 
                 VQ motif-containing protein 
                 2 
               
               
                 AT5G26360 
                 chaperonin, putative 
                 2 
               
               
                 AT4G38440 
                 similar to hypothetical protein [ Vitis vinifera ] (GB: CAN83259.1) 
                 2 
               
               
                 AT3G29800 
                 AAA-type ATPase family 
                 2 
               
               
                 AT5G58290 
                 RPT3 
                 2 
               
               
                 AT3G20050 
                 ATTCP-1 
                 2 
               
               
                 AT1G19520 
                 NFD5 
                 2 
               
               
                 AT4G26870 
                 aspartyl-tRNA synthetase, putative/aspartate--tRNA ligase, putative 
                 2 
               
               
                 AT1G56080 
                 similar to unknown protein [ Arabidopsis thaliana ] (TAIR: AT1G16520.1) 
                 2 
               
               
                 AT5G12380 
                 annexin, putative 
                 2 
               
               
                 AT4G28230 
                 similar to unnamed protein product [ Vitis vinifera ] (GB: CAO41238.1) 
                 2 
               
               
                 AT2G06210 
                 VIP6, ELF8 
                 2 
               
               
                 ATCG00480 
                 ATPB 
                 2 
               
               
                 AT5G02530 
                 RNA and export factor-binding protein, putative 
                 2 
               
               
                 AT1G31760 
                 SWIB complex BAF60b domain-containing protein 
                 2 
               
               
                 AT5G06680 
                 ATSPC98, SPC98 
                 2 
               
               
                 AT2G16570 
                 ATASE1, ATASE 
                 2 
               
               
                 AT1G62390 
                 octicosapeptide/Phox/Bem1p (PB1) domain-containing protein/ 
                 2 
               
               
                   
                 tetratricopeptide repeat (TPR)-containing protein 
               
               
                 AT1G43800 
                 acyl-(acyl-carrier-protein) desaturase, putative/stearoyl-ACP desaturase, 
                 2 
               
               
                   
                 putative 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
             
           
               
                 TABLE 7 
               
             
             
               
                   
               
               
                 Overview of microarray experiments used to calculate the transcript PCCs. 
               
               
                 List of experiments used to build an  Arabidopsis  ATH1 micro-array compendium of 518 
               
               
                 experiments focused on cell cycle or plant growth and development used to calculate the 
               
               
                 transcript Pearson correlation coefficients. 
               
             
          
           
               
                 Description 
                 Reference 
               
               
                   
               
               
                 co-2; 3 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/co-3-1.CEL 
               
               
                 Col-0; 3 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/Col-3-1.CEL 
               
               
                 ft-2; 3 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/ft-3-1.CEL 
               
               
                 Ler; 3 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/Ler-3-1.CEL 
               
               
                 lfy-12; 3 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/lfy-3-1.CEL 
               
               
                 co-2; 5 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/co-5-1.CEL 
               
               
                 Col-0; 5 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/Col-5-1.CEL 
               
               
                 ft-2; 5 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/ft-5-1.CEL 
               
               
                 Ler; 5 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/Ler-5-1.CEL 
               
               
                 lfy-12; 5 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/lfy-5-1.CEL 
               
               
                 co-2; 7 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/co-7-1.CEL 
               
               
                 Col-0; 7 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/Col-7-1.CEL 
               
               
                 ft-2; 7 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/ft-7-1.CEL 
               
               
                 Ler; 7 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/Ler-7-1.CEL 
               
               
                 lfy-12; 7 days long day condition; apical region; 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                 rosette stage 
                 CEL/lfy-7-1.CEL 
               
               
                 co-2; no treatment; apical region; rosette stage 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                   
                 CEL/co-0-1.CEL 
               
               
                 Col-0; no treatment; apical region; rosette stage 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                   
                 CEL/Col-0-1.CEL 
               
               
                 ft-2; no treatment; apical region; rosette stage 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                   
                 CEL/ft-0-1.CEL 
               
               
                 Ler; no treatment; apical region; rosette stage 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                   
                 CEL/Ler-0-1.CEL 
               
               
                 lfy-12; no treatment; apical region; rosette stage 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_mutants_and_other_ecotypes/ 
               
               
                   
                 CEL/lfy-0-1.CEL 
               
               
                 Wt roots; 7 days; continuous light; soil 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ 
               
               
                   
                 CEL/ATGE_3_A. 
               
               
                   
                 CEL 
               
               
                 Wt roots; 17 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ 
               
               
                   
                 CEL/ATGE_9_A. 
               
               
                   
                 CEL 
               
               
                 Wt root; 15 days long day (16/8) 1x MS agar, 1% 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ 
               
               
                 sucrose 
                 CEL/ATGE_93_A. 
               
               
                   
                 CEL 
               
               
                 Wt root; 8 days continuous light 1x MS agar 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ 
               
               
                   
                 CEL/ATGE_94_A. 
               
               
                   
                 CEL 
               
               
                 Wt root; 8 days continuous light 1x MS agar, 1% sucrose 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ 
               
               
                   
                 CEL/ATGE_95_A. 
               
               
                   
                 CEL 
               
               
                 Wt root; 21 days continuous light 1x MS agar 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ 
               
               
                   
                 CEL/ATGE_98_A. 
               
               
                   
                 CEL 
               
               
                 Wt root; 21 days continuous light 1x MS agar, 1% 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_roots/ 
               
               
                 sucrose 
                 CEL/ATGE_99_A. 
               
               
                   
                 CEL 
               
               
                 Wt seedling, green parts 21 days continuous light 1x MS 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ 
               
               
                 agar 
                 CEL/ATGE_100_A.CEL 
               
               
                 Wt seedling, green parts 21 days continuous light 1x MS 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ 
               
               
                 agar, 1% sucrose 
                 CEL/ATGE_101_A.CEL 
               
               
                 Wt developmental drift, entire rosette after transition 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/CEL/ 
               
               
                 to flowering, but before bolting 21 days continuous 
                 ATGE_22_A.CEL 
               
               
                 light soil 
               
               
                 Wt as above 22 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ 
               
               
                   
                 CEL/ATGE_23_A.CEL 
               
               
                 Wt as above 23 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ 
               
               
                   
                 CEL/ATGE_24_A.CEL 
               
               
                 Wt seedling, green parts; 7 days; continuous light; soil 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ 
               
               
                   
                 CEL/ATGE_7_A2.CEL 
               
               
                 Wt seedling, green parts 8 days continuous light 1x MS 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ 
               
               
                 agar 
                 CEL/ATGE_96_A.CEL 
               
               
                 Wt seedling, green parts 8 days continuous light 1x MS 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_seedlings_and_whole_plants/ 
               
               
                 agar, 1% sucrose 
                 CEL/ATGE_97_A.CEL 
               
               
                 Wt siliques, w/ seeds stage 3; mid globular to early 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ 
               
               
                 heart embryos 8 wk long day (16/8) soil 
                 CEL/ATGE_76_B.CEL 
               
               
                 Wt siliques, w/ seeds stage 4; early to late heart embryos 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ 
               
               
                 8 wk long day (16/8) soil 
                 CEL/ATGE_77_D.CEL 
               
               
                 Wt siliques, w/ seeds stage 5; late heart to mid torpedo 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ 
               
               
                 embryos 8 wk long day (16/8) soil 
                 CEL/ATGE_78_D.CEL 
               
               
                 Wt seeds, stage 6, w/o siliques; mid to late torpedo 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ 
               
               
                 embryos 8 wk long day (16/8) soil 
                 CEL/ATGE_79_A.CEL 
               
               
                 Wt seeds, stage 7, w/o siliques; late torpedo to early 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ 
               
               
                 walking-stick embryos 8 wk long day (16/8) soil 
                 CEL/ATGE_81_A.CEL 
               
               
                 Wt seeds, stage 8, w/o siliques; walking-stick to early 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ 
               
               
                 curled cotyledons 
                 CEL/ATGE_82_A.CEL 
               
               
                 Wt seeds, stage 9, w/o siliques; curled cotyledons to 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ 
               
               
                 early green cotyledons embryos; 8 wk long day 
                 CEL/ATGE_83_A.CEL 
               
               
                 (16/8) soil 
               
               
                 Wt seeds, stage 10, w/o siliques; green cotyledons 
                 AtGenExpress; /share/nasc/AtGenExpress_dev_series_siliques_and_seeds/ 
               
               
                 embryos 8 wk long day (16/8) soil 
                 CEL/ATGE_84_A.CEL 
               
               
                 Wt flowers stage 9, 21+ days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                   
                 CEL/ATGE_31_A2.CEL 
               
               
                 Wt flowers stage 10/11, 21+ days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                   
                 CEL/ATGE_32_A2.CEL 
               
               
                 Wt flowers stage 12, 21+ days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                   
                 CEL/ATGE_33_A.CEL 
               
               
                 Wt flowers stage 12, sepals 21+ days continuous light 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 soil 
                 CEL/ATGE_34_A.CEL 
               
               
                 Wt flowers stage 12, petals 21+ days continuous light 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 soil 
                 CEL/ATGE_35_A.CEL 
               
               
                 Wt flowers stage 12, stamens 21+ days continuous light 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 soil 
                 CEL/ATGE_36_A.CEL 
               
               
                 Wt flowers stage 12, carpels 21+ days continuous light 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 soil 
                 CEL/ATGE_37_A.CEL 
               
               
                 Wt flowers stage 15, 21+ days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                   
                 CEL/ATGE_39_A.CEL 
               
               
                 Wt flowers stage 15, pedicels 21+ days continuous 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 light soil 
                 CEL/ATGE_40_A.CEL 
               
               
                 Wt flowers stage 15, sepals 21+ days continuous light 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 soil 
                 CEL/ATGE_41_A.CEL 
               
               
                 Wt flowers stage 15, petals 21+ days continuous light 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 soil 
                 CEL/ATGE_42_B.CEL 
               
               
                 Wt flowers stage 15, stamen 21+ days continuous light 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 soil 
                 CEL/ATGE_43_A.CEL 
               
               
                 Wt flowers stage 15, carpels 21+ days continuous light 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 soil 
                 CEL/ATGE_45_A.CEL 
               
               
                 Wt mature pollen 6 wk continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                   
                 CEL/ATGE_73_A.CEL 
               
               
                 Wt flower 28 days long day (16/8) soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                   
                 CEL/ATGE_92_A.CEL 
               
               
                 clv3-7 flower stage 12; multi-carpel gynoeceum; enlarged 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 meristem; increased organ number; 21+ days continuous 
                 CEL/ATGE_53_A.CEL 
               
               
                 light soil 
               
               
                 lfy-12 flower stage 12; shoot characteristics; most organs 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 leaf-like 21+ days continuous light soil 
                 CEL/ATGE_54_A.CEL 
               
               
                 ap1-15 flower stage 12; sepals replaced by leaf-like 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 organs, petals mostly lacking, 2° flowers; 21+ days 
                 CEL/ATGE_55_A.CEL 
               
               
                 continuous light soil 
               
               
                 ap2-6 flower stage 12; no sepals or petals 21+ days 
                 AtGen Express; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 continuous light soil 
                 CEL/ATGE_56_A.CEL 
               
               
                 ap3-6 flower stage 12; no petals or stamens 21+ days 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 continuous light soil 
                 CEL/ATGE_57_A.CEL 
               
               
                 ag-12 flower stage 12; no stamens or carpels 21+ days 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 continuous light soil 
                 CEL/ATGE_58_A.CEL 
               
               
                 ufo-1 flower stage 12; filamentous organs in whorls two 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_flowers_and_pollen/ 
               
               
                 and three 21+ days continuous light soil 
                 CEL/ATGE_59_A.CEL 
               
               
                 Wt cotyledons; 7 days; continuous light; soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_1_A.CEL 
               
               
                 Wt rosette leaf #4, 1 cm long 10 days continuous light 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                 soil 
                 CEL/ATGE_10_A.CEL 
               
               
                 gl1-T rosette leaf #4, 1 cm long 10 days continuous 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                 light soil 
                 CEL/ATGE_11_A.CEL 
               
               
                 Wt rosette leaf #2, 17 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_12_A.CEL 
               
               
                 Wt rosette leaf #4, 17 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_13_A.CEL 
               
               
                 Wt rosette leaf #6, 17 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_14_A.CEL 
               
               
                 Wt rosette leaf #8, 17 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_15_A.CEL 
               
               
                 Wt rosette leaf #10, 17 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_16_A.CEL 
               
               
                 Wt rosette leaf #12, 17 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_17_A.CEL 
               
               
                 gl1-T rosette leaf #12, 17 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_18_A.CEL 
               
               
                 Wt leaf 7, petiole 17 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_19_A.CEL 
               
               
                 Wt leaf 7, proximal half 17 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_20_A.CEL 
               
               
                 Wt leaf 7, distal half 17 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_21_A.CEL 
               
               
                 Wt senescing leaves 35 days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_25_A.CEL 
               
               
                 Wt cauline leaves 21+ days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_26_A.CEL 
               
               
                 Wt leaves 1 + 2; 7 days; continuous light; soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_5_A.CEL 
               
               
                 Wt vegetative rosette 7 days short day (10/14) soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_87_A.CEL 
               
               
                 Wt vegetative rosette 14 days short day (10/14) soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_89_A.CEL 
               
               
                 Wt vegetative rosette 21 days short day (10/14) soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_90_A.CEL 
               
               
                 Wt leaf 15 days long day (16/8) 1x MS agar, 1% sucrose 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_leaves/ 
               
               
                   
                 CEL/ATGE_91_A.CEL 
               
               
                 Wt hypocotyl; 7 days; continuous light; soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                   
                 CEL/ATGE_2_A.CEL 
               
               
                 Wt stem, 2nd internode 21+ days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                   
                 CEL/ATGE_27_A.CEL 
               
               
                 Wt 1st node 21+ days continuous light soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                   
                 CEL/ATGE_28_A2.CEL 
               
               
                 Wt shoot apex, inflorescence (after bolting) 21 days 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                 continuous light soil 
                 CEL/ATGE_29_A2.CEL 
               
               
                 Wt shoot apex, vegetative + young leaves; 7 days; 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                 continuous light; soil 
                 CEL/ATGE_4_A.CEL 
               
               
                 Wt shoot apex, vegetative; 7 days; continuous light; soil 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                   
                 CEL/ATGE_6_A.CEL 
               
               
                 Wt shoot apex, transition (before bolting) 14 days 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                 continuous light soil 
                 CEL/ATGE_8_A.CEL 
               
               
                 clv3-7 shoot apex, inflorescence (after bolting) 21+ days 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                 continuous light soil 
                 CEL/ATGE_46_A.CEL 
               
               
                 lfy-12 shoot apex, inflorescence (after bolting) 21+ days 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                 continuous light soil 
                 CEL/ATGE_47_A.CEL 
               
               
                 ap1-15 shoot apex, inflorescence (after bolting) 21+ days 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                 continuous light soil 
                 CEL/ATGE_48_A.CEL 
               
               
                 ap2-6 shoot apex, inflorescence (after bolting) 21+ days 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                 continuous light soil 
                 CEL/ATGE_49_A.CEL 
               
               
                 ap3-6 shoot apex, inflorescence (after bolting) 21+ days 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                 continuous light soil 
                 CEL/ATGE_50_A.CEL 
               
               
                 ag-12 shoot apex, inflorescence (after bolting) 21+ days 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                 continuous light soil 
                 CEL/ATGE_51_A.CEL 
               
               
                 ufo-1 shoot apex, inflorescence (after bolting) 21+ days 
                 AtGenExpress; /share/nasc/AtGenExpress_Developmental_series_shoots_and_stems/ 
               
               
                 continuous light soil 
                 CEL/ATGE_52_A.CEL 
               
               
                 Root Quiescent Center; AGL42; quiescent center, 
                 Birnbaum_arexdb; 
               
               
                 non-specific pattern when roots grow old/long; 
               
               
                 QC only and at very early stages 
               
               
                 Root Phloem; APL; developing pSE and mSE and CC 
                 Birnbaum_arexdb; 
               
               
                 between the two: loss of GFP in mature pSE is 
               
               
                 accompanied by strong GFP in neighboring CC; 
               
               
                 GFP reappears in immature mSE; 
               
               
                 Root Cortex; C1 (or 315.1.1) (AT1G09750 promoter); 
                 Birnbaum_arexdb; 
               
               
                 cortex; from elongation to at least immature root hair dif. 
               
               
                 Root Epidermis; GL2; atrichoblasts; from QC and up 
                 Birnbaum_arexdb; 
               
               
                 Root Ground tissue; J0571; ground: endo + cortex + qc; 
                 Birnbaum_arexdb; 
               
               
                 from tip all the way up 
               
               
                 Lateral Root Cap; J3411; lateral root cap plus epidermis; 
                 Birnbaum_arexdb; 
               
               
                 from tip to exactly where? at least the differentiation 
               
               
                 zone; GFP is about 5X weaker in dif. zone 
               
               
                 Root Columella; PET111; columnella - tier 2,3,4; 
                 Birnbaum_arexdb; 
               
               
                 Root Xylem; S18 (477.1.3) (AT5G12870 promoter); 
                 Birnbaum_arexdb; 
               
               
                 maturing xylem cells; starts from mid-elongation 
               
               
                 and stops half way; GFP switches from pSE to mSE 
               
               
                 Root Endodermis; SCR; Marks the QC and the 
                 Birnbaum_arexdb; 
               
               
                 endodermis at least past the mature hair zone; from QC 
               
               
                 all the way up? At least past mature hair zone 
               
               
                 Tissue microdissection; Stage I; all radial tissues; 
                 Birnbaum_arexdb; 
               
               
                 where the root tip reaches its full diameter (about 
               
               
                 0.15 mm from the root tip) 
               
               
                 Tissue microdissection; Stage II; all radial tissues; 
                 Birnbaum_arexdb; 
               
               
                 where cells transition from being optically dense to 
               
               
                 a more transparent appearance as they begin 
               
               
                 longitudinal expansion 
               
               
                 Tissue microdissection; Stage III; all radial tissues; 
                 Birnbaum_arexdb; 
               
               
                 where root hairs are fully elongated (about 0.45 to 2 mm 
               
               
                 from the root tip) 
               
               
                 Root Stele; WOL; stele; from QC and starts to fade from 
                 Birnbaum_arexdb; 
               
               
                 elongation zone 
               
               
                 Campb-Col0-Suc 
                 Malcolm_Campbell_1; /share/nasc/Malcolm_Campbell_1/ 
               
               
                   
                 CEL/MC001_ATH1_A1- 
               
               
                   
                 Campb-317.CEL 
               
               
                 Campb-Col0-noSuc 
                 Malcolm_Campbell_1; /share/nasc/Malcolm_Campbell_1/ 
               
               
                   
                 CEL/MC001_ATH1_A4- 
               
               
                   
                 Campb-320.CEL 
               
               
                 Campb-MYB61-Suc 
                 Malcolm_Campbell_1; /share/nasc/Malcolm_Campbell_1/ 
               
               
                   
                 CEL/MC001_ATH1_A7- 
               
               
                   
                 Campb-323.CEL 
               
               
                 Campb-MYB61-noSuc 
                 Malcolm_Campbell_1; /share/nasc/Malcolm_Campbell_1/ 
               
               
                   
                 CEL/MC001_ATH1_A10- 
               
               
                   
                 Campb-326.CEL 
               
               
                 Campb-MYB61oe-Suc 
                 Malcolm_Campbell_1; /share/nasc/Malcolm_Campbell_1/ 
               
               
                   
                 CEL/MC001_ATH1_A13- 
               
               
                   
                 Campb-329(new).CEL 
               
               
                 Campb-MYB61oe-noSuc 
                 Malcolm_Campbell_1; /share/nasc/Malcolm_Campbell_1/ 
               
               
                   
                 CEL/MC001_ATH1_A16- 
               
               
                   
                 Campb-332.CEL 
               
               
                 col; hypocotyl 
                 Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ 
               
               
                   
                 CEL/MC002_ATH1_A10.1- 
               
               
                   
                 dubos-wth.CEL 
               
               
                 max4; hypocotyl 
                 Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ 
               
               
                   
                 CEL/MC002_ATH1_A11.1- 
               
               
                   
                 dubos-mxh.CEL 
               
               
                 axr1; hypocotyl 
                 Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ 
               
               
                   
                 CEL/MC002_ATH1_A12.1- 
               
               
                   
                 dubos-arh.CEL 
               
               
                 col; xylem 
                 Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ 
               
               
                   
                 CEL/MC002_ATH1_A1.1- 
               
               
                   
                 dubos-wtx.CEL 
               
               
                 col; cork 
                 Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ 
               
               
                   
                 CEL/MC002_ATH1_A2.1- 
               
               
                   
                 dubos-wtc.CEL 
               
               
                 myb61 ko; xylem 
                 Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ 
               
               
                   
                 CEL/MC002_ATH1_A3.1- 
               
               
                   
                 dubos-6kx.CEL 
               
               
                 myb61 ko; cork 
                 Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ 
               
               
                   
                 CEL/MC002_ATH1_A4.1- 
               
               
                   
                 dubos-6kc.CEL 
               
               
                 myb50 ko; xylem 
                 Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ 
               
               
                   
                 CEL/MC002_ATH1_A5.1- 
               
               
                   
                 dubos-5kx.CEL 
               
               
                 myb50; cork 
                 Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ 
               
               
                   
                 CEL/MC002_ATH1_A6.1- 
               
               
                   
                 dubos-5kc.CEL 
               
               
                 ler; hypocotyl 
                 Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ 
               
               
                   
                 CEL/MC002_ATH1_A7.1- 
               
               
                   
                 dubos-wLh.CEL 
               
               
                 abi1; hypocotyl (ler background) 
                 Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ 
               
               
                   
                 CEL/MC002_ATH1_A8.1- 
               
               
                   
                 dubos-aih.CEL 
               
               
                 aba1; hypocotyl (ler background) 
                 Malcolm_Campbell_2; /share/nasc/Malcolm_Campbell_2/ 
               
               
                   
                 CEL/MC002_ATH1_A9.1- 
               
               
                   
                 dubos-aah.CEL 
               
               
                 seedling; Col0; 10 nM BL for 1 h 
                 AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ 
               
               
                   
                 CEL/RIKENGODA16A.cel 
               
               
                 seedling; Col0; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ 
               
               
                   
                 CEL/RIKENGODA17AC.cel 
               
               
                 seedling; Col0; mock treatment for 30 min 
                 AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ 
               
               
                   
                 CEL/RIKENGODA1AC.cel 
               
               
                 seedling; Col0; 10 nM BL for 3 h 
                 AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ 
               
               
                   
                 CEL/RIKENGODA24A.cel 
               
               
                 seedling; de-etiolated; mock treatment for 30 min 
                 AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ 
               
               
                   
                 CEL/RIKENGODA31A.cel 
               
               
                 seedling; de-etiolated; 10 nM BL for 30 min 
                 AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ 
               
               
                   
                 CEL/RIKENGODA32A.cel 
               
               
                 seedling; de-etiolated; mock treatment for 1 h 
                 AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ 
               
               
                   
                 CEL/RIKENGODA33A.cel 
               
               
                 seedling; de-etiolated; 10 nM BL for 1 h 
                 AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ 
               
               
                   
                 CEL/RIKENGODA34A.cel 
               
               
                 seedling; de-etiolated; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ 
               
               
                   
                 CEL/RIKENGODA35A.cel 
               
               
                 seedling; de-etiolated; 10 nM BL for 3 h 
                 AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ 
               
               
                   
                 CEL/RIKENGODA36A.cel 
               
               
                 seedling; Col0; 10 nM BL for 30 min 
                 AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ 
               
               
                   
                 CEL/RIKENGODA8A.cel 
               
               
                 seedling; Col0; mock treatment for 1 h 
                 AtGenExpress; /share/nasc/AtGen_Brassinolide_timecource_wt_det2_seedlings/ 
               
               
                   
                 CEL/RIKENGODA9AC.cel 
               
               
                 complete plant; 10 uM brassinazole 91 (Brz91) 
                 AtGenExpress; /share/nasc/AtGen_effect_brassinosteroid_inhibitors_seeds/ 
               
               
                 (brassinosteroid biosynthesis inhibitor) for 12 h 
                 CEL/RIKENGODA10A4.cel 
               
               
                 complete plant; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGen_effect_brassinosteroid_inhibitors_seeds/ 
               
               
                   
                 CEL/RIKENGODA1A4.cel 
               
               
                 complete plant; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGen_effect_brassinosteroid_inhibitors_seeds/ 
               
               
                   
                 CEL/RIKENGODA28A4.cel 
               
               
                 complete plant; mock treatment for 12 h 
                 AtGenExpress; /share/nasc/AtGen_effect_brassinosteroid_inhibitors_seeds/ 
               
               
                   
                 CEL/RIKENGODA2A4.cel 
               
               
                 complete plant; 3 uM brassinazole 220 (Brz220) 
                 AtGenExpress; /share/nasc/AtGen_effect_brassinosteroid_inhibitors_seeds/ 
               
               
                 (brassinosteroid biosynthesis inhibitor) for 3 h 
                 CEL/RIKENGODA30A4.cel 
               
               
                 complete plant; 10 uM brassinazole 220 (Brz220) 
                 AtGenExpress; /share/nasc/AtGen_effect_brassinosteroid_inhibitors_seeds/ 
               
               
                 (brassinosteroid biosynthesis inhibitor) for 3 h 
                 CEL/RIKENGODA7A4.cel 
               
               
                 complete plant; 10 uM paclobutrazol (GA biosynthesis 
                 AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ 
               
               
                 inhibitor) for 3 h 
                 CEL/ 
               
               
                   
                 RIKENGODA11A2.cel 
               
               
                 complete plant; 10 uM paclobutrazol (GA biosynthesis 
                 AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ 
               
               
                 inhibitor) for 12 h 
                 CEL/ 
               
               
                   
                 RIKENGODA12A2.cel 
               
               
                 complete plant; 10 uM prohexadione (GA biosynthesis 
                 AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ 
               
               
                 inhibitor) for 3 h 
                 CEL/ 
               
               
                   
                 RIKENGODA13A2.cel 
               
               
                 complete plant; 10 uM prohexadione (GA biosynthesis 
                 AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ 
               
               
                 inhibitor) for 12 h 
                 CEL/ 
               
               
                   
                 RIKENGODA14A2.cel 
               
               
                 complete plant; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ 
               
               
                   
                 CEL/ 
               
               
                   
                 RIKENGODA1A2.cel 
               
               
                 complete plant; mock treatment for 12 h 
                 AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ 
               
               
                   
                 CEL/ 
               
               
                   
                 RIKENGODA2A2.cel 
               
               
                 complete plant; 10 uM propiconazole (GA biosynthesis 
                 AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ 
               
               
                 inhibitor) for 3 h 
                 CEL/ 
               
               
                   
                 RIKENGODA3A2.cel 
               
               
                 complete plant; 10 uM propiconazole (GA biosynthesis 
                 AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ 
               
               
                 inhibitor) for 12 h 
                 CEL/ 
               
               
                   
                 RIKENGODA4A2.cel 
               
               
                 complete plant; 10 uM uniconazole (GA biosynthesis 
                 AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ 
               
               
                 inhibitor) for 3 h 
                 CEL/ 
               
               
                   
                 RIKENGODA5A2.cel 
               
               
                 complete plant; 10 uM uniconazole (GA biosynthesis 
                 AtGenExpress; /share/nasc/AtGen_effect_GA_inhibitors_on_seeds/ 
               
               
                 inhibitor) for 12 h 
                 CEL/ 
               
               
                   
                 RIKENGODA6A2.cel 
               
               
                 complete plant; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGen_Effect_of_proteasome_inhibitor_MG13_on_seedlings/ 
               
               
                   
                 CEL/RIKENGODA1A9. 
               
               
                   
                 cel 
               
               
                 complete plant; 10 uM MG132 
                 AtGenExpress; /share/nasc/AtGen_Effect_of_proteasome_inhibitor_MG13_on_seedlings/ 
               
               
                 (carbobenzoxyl-leucinyl-leucinyl-leucinal) for 3 h 
                 CEL/RIKENGODA22A9. 
               
               
                   
                 cel 
               
               
                 seed; no treatment 
                 AtGenExpress; /share/nasc/AtGen_exp_profiling_early_germinating_seeds/ 
               
               
                   
                 CEL/RIKENPRESTON0A.cel 
               
               
                 seed; imbibed in water (1 hour) 
                 AtGenExpress; /share/nasc/AtGen_exp_profiling_early_germinating_seeds/ 
               
               
                   
                 CEL/RIKENPRESTON1A.cel 
               
               
                 seed; imbibed in water (3 hours) 
                 AtGenExpress; /share/nasc/AtGen_exp_profiling_early_germinating_seeds/ 
               
               
                   
                 CEL/RIKENPRESTON2A.cel 
               
               
                 seedling; 10 uM ABA for 1 h 
                 AtGenExpress; /share/nasc/AtGenExpress_ABA_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA13A. 
               
               
                   
                 cel 
               
               
                 seedling; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_ABA_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA17A. 
               
               
                   
                 cel 
               
               
                 seedling; mock treatment for 30 min 
                 AtGenExpress; /share/nasc/AtGenExpress_ABA_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA1A.cel 
               
               
                 seedling; 10 uM ABA for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_ABA_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA21A. 
               
               
                   
                 cel 
               
               
                 seedling; 10 uM ABA for 30 min 
                 AtGenExpress; /share/nasc/AtGenExpress_ABA_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA5A.cel 
               
               
                 seedling; mock treatment for 1 h 
                 AtGenExpress; /share/nasc/AtGenExpress_ABA_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA9A.cel 
               
               
                 seedling; 10 uM ACC for 1 h 
                 AtGenExpress; /share/nasc/AtGenExpress_ACC_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA15A. 
               
               
                   
                 cel 
               
               
                 seedling; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_ACC_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA17AA. 
               
               
                   
                 cel 
               
               
                 seedling; mock treatment for 30 min 
                 AtGenExpress; /share/nasc/AtGenExpress_ACC_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA1AA. 
               
               
                   
                 cel 
               
               
                 seedling; 10 uM ACC for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_ACC_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA23A. 
               
               
                   
                 cel 
               
               
                 seedling; 10 uM ACC for 30 min 
                 AtGenExpress; /share/nasc/AtGenExpress_ACC_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA7A.cel 
               
               
                 seedling; mock treatment for 1 h 
                 AtGenExpress; /share/nasc/AtGenExpress_ACC_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA9AA. 
               
               
                   
                 cel 
               
               
                 complete plant; 10 uM 2,4,6-T (2,4,6- 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_auxin_inhibitors_on_seedlings/ 
               
               
                 trihydroxybenzamide) for 3 h 
                 CEL/RIKENGODA23A3. 
               
               
                   
                 cel 
               
               
                 complete plant; 10 uM NPA (naphthylphthalamic 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_auxin_inhibitors_on_seedlings/ 
               
               
                 acid) (inhibitor of auxin transport) for 3 h 
                 CEL/RIKENGODA26A3. 
               
               
                   
                 cel 
               
               
                 complete plant; 10 uM PCIB (p-chlorophenoxyisobutyric 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_auxin_inhibitors_on_seedlings/ 
               
               
                 acid) (auxin inhibitor) for 3 h 
                 CEL/RIKENGODA24A3. 
               
               
                   
                 cel 
               
               
                 complete plant; 10 uM TIBA (2,3,5-triiodobenzoic acid) 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_auxin_inhibitors_on_seedlings/ 
               
               
                 (inhibitor of auxin transport) for 3 h 
                 CEL/RIKENGODA25A3. 
               
               
                   
                 cel 
               
               
                 complete plant; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_auxin_inhibitors_on_seedlings/ 
               
               
                   
                 CEL/RIKENGODA1A3.cel 
               
               
                 whole plant; 100 nM castasterone for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA12A6. 
               
               
                   
                 cel 
               
               
                 whole plant; 10 nM brassinolide for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA13A6. 
               
               
                   
                 cel 
               
               
                 whole plant; 10 uM campestanol for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA2A6.cel 
               
               
                 whole plant; 1 uM 3-dehydro-6-deoxoteasterone for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA7A6.cel 
               
               
                 whole plant; 1 uM 3-dehydroteasterone for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA8A6.cel 
               
               
                 whole plant; 1 uM 6-deoxocastasterone for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA11A6. 
               
               
                   
                 cel 
               
               
                 whole plant; 1 uM 6-deoxocathasterone for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA3A6.cel 
               
               
                 whole plant; 1 uM 6-deoxoteasterone for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA5A6.cel 
               
               
                 whole plant; 1 uM 6-deoxotyphasterol for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA9A6.cel 
               
               
                 whole plant; 1 uM cathasterone for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA4A6.cel 
               
               
                 whole plant; 1 uM teasterone for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA6A6.cel 
               
               
                 whole plant; 1 uM typhasterol for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA10A6. 
               
               
                   
                 cel 
               
               
                 whole plant; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_brassinosteroids_in_seedlings/ 
               
               
                   
                 CEL/RIKENGODA1A6.cel 
               
               
                 complete plant; 10 uM AgNO3 (ethylene inhibitor) 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ethylene_inhibitors_on_seedlings/ 
               
               
                 for 3 h 
                 CEL/RIKENGODA19A7. 
               
               
                   
                 cel 
               
               
                 complete plant; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ethylene_inhibitors_on_seedlings/ 
               
               
                   
                 CEL/RIKENGODA1A7. 
               
               
                   
                 cel 
               
               
                 complete plant; 10 uM AVG (aminoethoxyvinylglycine) 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ethylene_inhibitors_on_seedlings/ 
               
               
                 (ethylene inhibitor) for 3 h 
                 CEL/RIKENGODA20A7. 
               
               
                   
                 cel 
               
               
                 seedling; 1 uM IAA for 1 h 
                 AtGenExpress; /share/nasc/AtGenExpress_IAA_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA10A.cel 
               
               
                 seedling; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_IAA_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA17AD. 
               
               
                   
                 cel 
               
               
                 seedling; 1 uM IAA for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_IAA_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA18A.cel 
               
               
                 seedling; mock treatment for 30 min 
                 AtGenExpress; /share/nasc/AtGenExpress_IAA_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA1AD.cel 
               
               
                 seedling; 1 uM IAA for 30 min 
                 AtGenExpress; /share/nasc/AtGenExpress_IAA_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA2A.cel 
               
               
                 seedling; mock treatment for 1 h 
                 AtGenExpress; /share/nasc/AtGenExpress_IAA_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA9AD.cel 
               
               
                 seedling; 10 uM MJ for 1 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Methyl_Jasmonate_time_course_in_wildtype/ 
               
               
                   
                 CEL/RIKENGODA14A. 
               
               
                   
                 cel 
               
               
                 seedling; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Methyl_Jasmonate_time_course_in_wildtype/ 
               
               
                   
                 CEL/RIKENGODA17AF. 
               
               
                   
                 cel 
               
               
                 seedling; mock treatment for 30 min 
                 AtGenExpress; /share/nasc/AtGenExpress_Methyl_Jasmonate_time_course_in_wildtype/ 
               
               
                   
                 CEL/RIKENGODA1AF. 
               
               
                   
                 cel 
               
               
                 seedling; 10 uM MJ for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Methyl_Jasmonate_time_course_in_wildtype/ 
               
               
                   
                 CEL/RIKENGODA22A. 
               
               
                   
                 cel 
               
               
                 seedling; 10 uM MJ for 30 min 
                 AtGenExpress; /share/nasc/AtGenExpress_Methyl_Jasmonate_time_course_in_wildtype/ 
               
               
                   
                 CEL/RIKENGODA6A. 
               
               
                   
                 cel 
               
               
                 seedling; mock treatment for 1 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Methyl_Jasmonate_time_course_in_wildtype/ 
               
               
                   
                 CEL/RIKENGODA9AF. 
               
               
                   
                 cel 
               
               
                 seedling; 1 uM zeatin for 1 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Zeatin_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA11A. 
               
               
                   
                 cel 
               
               
                 seedling; 1 uM zeatin for 30 min 
                 AtGenExpress; /share/nasc/AtGenExpress_Zeatin_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA3A. 
               
               
                   
                 cel 
               
               
                 seedling; 1 uM zeatin for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Zeatin_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA19A. 
               
               
                   
                 cel 
               
               
                 seedling; mock treatment for 1 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Zeatin_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA9AG. 
               
               
                   
                 cel 
               
               
                 seedling; mock treatment for 30 min 
                 AtGenExpress; /share/nasc/AtGenExpress_Zeatin_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA1AG. 
               
               
                   
                 cel 
               
               
                 seedling; mock treatment for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Zeatin_time_course_in_wildtype_seedlings/ 
               
               
                   
                 CEL/RIKENGODA17AG. 
               
               
                   
                 cel 
               
               
                 seeds; water treatment for 3 hours 
                 AtGenExpress; /share/nasc/AtGenExpress_Basic_hormone_treatment_of_seeds/ 
               
               
                   
                 CEL/RIKENLI1A.cel 
               
               
                 seeds; water treatment for 6 hours 
                 AtGenExpress; /share/nasc/AtGenExpress_Basic_hormone_treatment_of_seeds/ 
               
               
                   
                 CEL/RIKENLI2A.cel 
               
               
                 seeds; water treatment for 9 hours 
                 AtGenExpress; /share/nasc/AtGenExpress_Basic_hormone_treatment_of_seeds/ 
               
               
                   
                 CEL/RIKENLI3A.cel 
               
               
                 seeds; 5 uM gibberellin treatment for 3 hours 
                 AtGenExpress; /share/nasc/AtGenExpress_Basic_hormone_treatment_of_seeds/ 
               
               
                   
                 CEL/RIKENLI4A.cel 
               
               
                 seeds; 5 uM gibberellin treatment for 6 hours 
                 AtGenExpress; /share/nasc/AtGenExpress_Basic_hormone_treatment_of_seeds/ 
               
               
                   
                 CEL/RIKENLI5A.cel 
               
               
                 seeds; 5 uM gibberellin treatment for 9 hours 
                 AtGenExpress; /share/nasc/AtGenExpress_Basic_hormone_treatment_of_seeds/ 
               
               
                   
                 CEL/RIKENLI6A.cel 
               
               
                 Col0; complete plant; No treatment 
                 AtGenExpress; /share/nasc/AtGenExpress_Cytokinin_treatment_of_seedlings/ 
               
               
                   
                 CEL/NO10.cel 
               
               
                 Col0; complete plant; 20 uM t-zeatin for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Cytokinin_treatment_of_seedlings/ 
               
               
                   
                 CEL/NO192.cel 
               
               
                 ARR22-ox; complete plant; No treatment 
                 AtGenExpress; /share/nasc/AtGenExpress_Cytokinin_treatment_of_seedlings/ 
               
               
                   
                 CEL/NO28.cel 
               
               
                 ARR22-ox; complete plant; 20 uM t-zeatin for 3 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Cytokinin_treatment_of_seedlings/ 
               
               
                   
                 CEL/NO31.cel 
               
               
                 seed; 24 h imbibed in 3 uM ABA 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ABA_during_seed_imbibition/ 
               
               
                   
                 CEL/RIKENNAKABAYASHI3A. 
               
               
                   
                 cel 
               
               
                 seed; 24 h imbibed in 30 uM ABA 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ABA_during_seed_imbibition/ 
               
               
                   
                 CEL/RIKENNAKABAYASHI4A. 
               
               
                   
                 cel 
               
               
                 seed; 24 h imbibed in water 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ABA_during_seed_imbibition/ 
               
               
                   
                 CEL/RIKENNAKABAYASHI2A. 
               
               
                   
                 cel 
               
               
                 seed; no treatment 
                 AtGenExpress; /share/nasc/AtGenExpress_Effect_of_ABA_during_seed_imbibition/ 
               
               
                   
                 CEL/RIKENNAKABAYASHI1A. 
               
               
                   
                 cel 
               
               
                 Controlstress-Shoots-0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0011.CEL 
               
               
                 Controlstress-Roots-0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0021.CEL 
               
               
                 Controlstress-Shoots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0111.CEL 
               
               
                 Controlstress-Roots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0121.CEL 
               
               
                 Controlstress-Shoots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0211.CEL 
               
               
                 Controlstress-Roots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0221.CEL 
               
               
                 Controlstress-Shoots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0311.CEL 
               
               
                 Controlstress-Roots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0321.CEL 
               
               
                 Controlstress-Shoots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0411.CEL 
               
               
                 Controlstress-Roots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0421.CEL 
               
               
                 Controlstress-Shoots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0511.CEL 
               
               
                 Controlstress-Roots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0521.CEL 
               
               
                 Controlstress-Shoots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0611.CEL 
               
               
                 Controlstress-Roots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0621.CEL 
               
               
                 Controlstress-Shoots-0.25 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0711.CEL 
               
               
                 Controlstress-Roots-0.25 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0721.CEL 
               
               
                 Controlstress-Shoots-4.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0811.CEL 
               
               
                 Controlstress-Roots-4.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Control_plants/ 
               
               
                   
                 CEL/0821.CEL 
               
               
                 Coldstress(4?C)-Shoots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ 
               
               
                   
                 CEL/1111.CEL 
               
               
                 Coldstress(4?C)-Roots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ 
               
               
                   
                 CEL/1121.CEL 
               
               
                 Coldstress(4?C)-Shoots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ 
               
               
                   
                 CEL/1211.CEL 
               
               
                 Coldstress(4?C)-Roots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ 
               
               
                   
                 CEL/1221.CEL 
               
               
                 Coldstress(4?C)-Shoots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ 
               
               
                   
                 CEL/1311.CEL 
               
               
                 Coldstress(4?C)-Roots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ 
               
               
                   
                 CEL/1321.CEL 
               
               
                 Coldstress(4?C)-Shoots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ 
               
               
                   
                 CEL/1411.CEL 
               
               
                 Coldstress(4?C)-Roots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ 
               
               
                   
                 CEL/1421.CEL 
               
               
                 Coldstress(4?C)-Shoots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ 
               
               
                   
                 CEL/1511.CEL 
               
               
                 Coldstress(4?C)-Roots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ 
               
               
                   
                 CEL/1521.CEL 
               
               
                 Coldstress(4?C)-Shoots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ 
               
               
                   
                 CEL/1611.CEL 
               
               
                 Coldstress(4?C)-Roots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Cold_stress/ 
               
               
                   
                 CEL/1621.CEL 
               
               
                 Osmoticstress-Shoots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ 
               
               
                   
                 CEL/2111.CEL 
               
               
                 Osmoticstress-Roots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ 
               
               
                   
                 CEL/2121.CEL 
               
               
                 Osmoticstress-Shoots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ 
               
               
                   
                 CEL/2211.CEL 
               
               
                 Osmoticstress-Roots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ 
               
               
                   
                 CEL/2221.CEL 
               
               
                 Osmoticstress-Shoots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ 
               
               
                   
                 CEL/2311.CEL 
               
               
                 Osmoticstress-Roots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ 
               
               
                   
                 CEL/2321.CEL 
               
               
                 Osmoticstress-Shoots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ 
               
               
                   
                 CEL/2411.CEL 
               
               
                 Osmoticstress-Roots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ 
               
               
                   
                 CEL/2421.CEL 
               
               
                 Osmoticstress-Shoots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ 
               
               
                   
                 CEL/2511.CEL 
               
               
                 Osmoticstress-Roots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ 
               
               
                   
                 CEL/2521.CEL 
               
               
                 Osmoticstress-Shoots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ 
               
               
                   
                 CEL/2611.CEL 
               
               
                 Osmoticstress-Roots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Osmotic_stress/ 
               
               
                   
                 CEL/2621.CEL 
               
               
                 Saltstress-Shoots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ 
               
               
                   
                 CEL/3111.CEL 
               
               
                 Saltstress-Roots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ 
               
               
                   
                 CEL/3121.CEL 
               
               
                 Saltstress-Shoots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ 
               
               
                   
                 CEL/3211.CEL 
               
               
                 Saltstress-Roots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ 
               
               
                   
                 CEL/3221.CEL 
               
               
                 Saltstress-Shoots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ 
               
               
                   
                 CEL/3311.CEL 
               
               
                 Saltstress-Roots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ 
               
               
                   
                 CEL/3321.CEL 
               
               
                 Saltstress-Shoots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ 
               
               
                   
                 CEL/3411.CEL 
               
               
                 Saltstress-Roots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ 
               
               
                   
                 CEL/3421.CEL 
               
               
                 Saltstress-Shoots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ 
               
               
                   
                 CEL/3511.CEL 
               
               
                 Saltstress-Roots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ 
               
               
                   
                 CEL/3521.CEL 
               
               
                 Saltstress-Shoots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ 
               
               
                   
                 CEL/3611.CEL 
               
               
                 Saltstress-Roots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Salt_stress/ 
               
               
                   
                 CEL/3621.CEL 
               
               
                 Droughtstress-Shoots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4111.CEL 
               
               
                 Droughtstress-Roots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4121.CEL 
               
               
                 Droughtstress-Shoots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4211.CEL 
               
               
                 Droughtstress-Roots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4221.CEL 
               
               
                 Droughtstress-Shoots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4311.CEL 
               
               
                 Droughtstress-Roots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4321.CEL 
               
               
                 Droughtstress-Shoots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4411.CEL 
               
               
                 Droughtstress-Roots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4421.CEL 
               
               
                 Droughtstress-Shoots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4511.CEL 
               
               
                 Droughtstress-Roots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4521.CEL 
               
               
                 Droughtstress-Shoots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4611.CEL 
               
               
                 Droughtstress-Roots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4621.CEL 
               
               
                 Droughtstress-Shoots-0.25 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4711.CEL 
               
               
                 Droughtstress-Roots-0.25 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Drought_stress/ 
               
               
                   
                 CEL/4721.CEL 
               
               
                 Genotoxicstress-Shoots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ 
               
               
                   
                 CEL/5111.CEL 
               
               
                 Genotoxicstress-Roots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ 
               
               
                   
                 CEL/5121.CEL 
               
               
                 Genotoxicstress-Shoots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ 
               
               
                   
                 CEL/5211.CEL 
               
               
                 Genotoxicstress-Roots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ 
               
               
                   
                 CEL/5221.CEL 
               
               
                 Genotoxicstress-Shoots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ 
               
               
                   
                 CEL/5311.CEL 
               
               
                 Genotoxicstress-Roots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ 
               
               
                   
                 CEL/5321.CEL 
               
               
                 Genotoxicstress-Shoots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ 
               
               
                   
                 CEL/5411.CEL 
               
               
                 Genotoxicstress-Roots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ 
               
               
                   
                 CEL/5421.CEL 
               
               
                 Genotoxicstress-Shoots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ 
               
               
                   
                 CEL/5511.CEL 
               
               
                 Genotoxicstress-Roots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ 
               
               
                   
                 CEL/5521.CEL 
               
               
                 Genotoxicstress-Shoots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ 
               
               
                   
                 CEL/5611.CEL 
               
               
                 Genotoxicstress-Roots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Genotoxic_stress/ 
               
               
                   
                 CEL/5621.CEL 
               
               
                 Oxidativestress-Shoots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ 
               
               
                   
                 CEL/6111.CEL 
               
               
                 Oxidativestress-Roots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ 
               
               
                   
                 CEL/6122.CEL 
               
               
                 Oxidativestress-Shoots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ 
               
               
                   
                 CEL/6211.CEL 
               
               
                 Oxidativestress-Roots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ 
               
               
                   
                 CEL/6223.CEL 
               
               
                 Oxidativestress-Shoots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ 
               
               
                   
                 CEL/6311.CEL 
               
               
                 Oxidativestress-Roots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ 
               
               
                   
                 CEL/6322.CEL 
               
               
                 Oxidativestress-Shoots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ 
               
               
                   
                 CEL/6411.CEL 
               
               
                 Oxidativestress-Roots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ 
               
               
                   
                 CEL/6421.CEL 
               
               
                 Oxidativestress-Shoots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ 
               
               
                   
                 CEL/6511.CEL 
               
               
                 Oxidativestress-Roots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ 
               
               
                   
                 CEL/6523.CEL 
               
               
                 Oxidativestress-Shoots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ 
               
               
                   
                 CEL/6611.CEL 
               
               
                 Oxidativestress-Roots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Oxidative_stress/ 
               
               
                   
                 CEL/6621.CEL 
               
               
                 UV-Bstress-Shoots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7111.CEL 
               
               
                 UV-Bstress-Roots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7121.CEL 
               
               
                 UV-Bstress-Shoots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7211.CEL 
               
               
                 UV-Bstress-Roots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7221.CEL 
               
               
                 UV-Bstress-Shoots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7311.CEL 
               
               
                 UV-Bstress-Roots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7321.CEL 
               
               
                 UV-Bstress-Shoots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7411.CEL 
               
               
                 UV-Bstress-Roots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7421.CEL 
               
               
                 UV-Bstress-Shoots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7511.CEL 
               
               
                 UV-Bstress-Roots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7521.CEL 
               
               
                 UV-Bstress-Shoots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7611.CEL 
               
               
                 UV-Bstress-Roots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7621.CEL 
               
               
                 UV-Bstress-Shoots-0.25 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7711.CEL 
               
               
                 UV-Bstress-Roots-0.25 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_UV- 
               
               
                   
                 B_stress/CEL/7721.CEL 
               
               
                 Woundingstress-Shoots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8111.CEL 
               
               
                 Woundingstress-Roots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8124.CEL 
               
               
                 Woundingstress-Shoots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8211.CEL 
               
               
                 Woundingstress-Roots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8224.CEL 
               
               
                 Woundingstress-Shoots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8313.CEL 
               
               
                 Woundingstress-Roots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8324.CEL 
               
               
                 Woundingstress-Shoots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8411.CEL 
               
               
                 Woundingstress-Roots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8423.CEL 
               
               
                 Woundingstress-Shoots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8511.CEL 
               
               
                 Woundingstress-Roots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8524.CEL 
               
               
                 Woundingstress-Shoots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8611.CEL 
               
               
                 Woundingstress-Roots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8621.CEL 
               
               
                 Woundingstress-Shoots-0.25 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8712.CEL 
               
               
                 Woundingstress-Roots-0.25 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Wounding_stress/ 
               
               
                   
                 CEL/8723.CEL 
               
               
                 Heatstress-Shoots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9111.CEL 
               
               
                 Heatstress-Roots-0.5 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9121.CEL 
               
               
                 Heatstress-Shoots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9211.CEL 
               
               
                 Heatstress-Roots-1.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9221.CEL 
               
               
                 Heatstress-Shoots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9311.CEL 
               
               
                 Heatstress-Roots-3.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9321.CEL 
               
               
                 Heatstress (3 h) + 3 h recovery-Shoots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9411.CEL 
               
               
                 Heatstress (3 h) + 3 h recovery-Roots-6.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9421.CEL 
               
               
                 Heatstress (3 h) + 9 h recovery-Shoots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9511.CEL 
               
               
                 Heatstress (3 h) + 9 h recovery-Roots-12.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9521.CEL 
               
               
                 Heatstress (3 h) + 21 h recovery-Shoots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9611.CEL 
               
               
                 Heatstress (3 h) + 21 h recovery-Roots-24.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9621.CEL 
               
               
                 Heatstress-Shoots-0.25 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9711.CEL 
               
               
                 Heatstress-Roots-0.25 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9721.CEL 
               
               
                 Heatstress (3 h) + 1 h recovery-Shoots-4.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9811.CEL 
               
               
                 Heatstress (3 h) + 1 h recovery-Roots-4.0 h 
                 AtGenExpress; /share/nasc/AtGenExpress_Stress_Treatments_Heat_stress/ 
               
               
                   
                 CEL/9821.CEL 
               
               
                 lateral root initiation study in xylem pole pericycle cells; 
                 in-house experiment 
               
               
                 ivsme_Col-0_NPA 
               
               
                 lateral root initiation study in xylem pole pericycle cells; 
                 in-house experiment 
               
               
                 ivsme_Col-0_2hNAA 
               
               
                 lateral root initiation study in xylem pole pericycle cells; 
                 in-house experiment 
               
               
                 ivsme_Col-0_6hNAA 
               
               
                 overexpression of two prohibitins in seedlings; 
                 in-house experiment 
               
               
                 olake_AtPHB3_overexp 
               
               
                 overexpression of two prohibitins in seedlings; 
                 in-house experiment 
               
               
                 olake_AtPHB4_overexp 
               
               
                 overexpression of two prohibitins in seedlings; 
                 in-house experiment 
               
               
                 olake_overexp_control 
               
               
                 comparison of 3 mutants (2 prohibitin, 1 auxin 
                 in-house experiment 
               
               
                 glucosyltransferase) to wild-type in seedlings; 
               
               
                 olake_knockout_AtPHB3 
               
               
                 comparison of 3 mutants (2 prohibitin, 1 auxin 
                 in-house experiment 
               
               
                 glucosyltransferase) to wild-type in seedlings; 
               
               
                 olake_knockout_AtPHB4 
               
               
                 comparison of 3 mutants (2 prohibitin, 1 auxin 
                 in-house experiment 
               
               
                 glucosyltransferase) to wild-type in seedlings; 
               
               
                 olake_control 
               
               
                 comparison of 3 mutants (2 prohibitin, 1 auxin 
                 in-house experiment 
               
               
                 glucosyltransferase) to wild-type in seedlings; 
               
               
                 olake_overexpression_UGTx 
               
               
                 WT landsberg erecta shoot apex seedlings compared to 
                 in-house experiment 
               
               
                 narrow leaf mutants elongata 2, 3, 4, angusta 4, 
               
               
                 drl1-2; defle_Ler 
               
               
                 WT landsberg erecta shoot apex seedlings compared to 
                 in-house experiment 
               
               
                 narrow leaf mutants elongata 2, 3, 4, angusta 4, 
               
               
                 drl1-2; defle_elo2 
               
               
                 WT landsberg erecta shoot apex seedlings compared to 
                 in-house experiment 
               
               
                 narrow leaf mutants elongata 2, 3, 4, angusta 4, 
               
               
                 drl1-2; defle_drl1-2 
               
               
                 WT landsberg erecta shoot apex seedlings compared to 
                 in-house experiment 
               
               
                 narrow leaf mutants elongata 2, 3, 4, angusta 4, 
               
               
                 drl1-2; defle_ang4 
               
               
                 WT landsberg erecta shoot apex seedlings compared to 
                 in-house experiment 
               
               
                 narrow leaf mutants elongata 2, 3, 4, angusta 4, 
               
               
                 drl1-2; defle_elo3 
               
               
                 WT shoot apex seedlings compared to narrow leaf 
                 in-house experiment 
               
               
                 mutants ELP3 (2) and SWP1 (1); defle_Ws 
               
               
                 WT shoot apex seedlings compared to narrow leaf 
                 in-house experiment 
               
               
                 mutants ELP3 (2) and SWP1 (1); defle_N3983 
               
               
                 WT shoot apex seedlings compared to narrow leaf 
                 in-house experiment 
               
               
                 mutants ELP3 (2) and SWP1 (1); defle_219E08 
               
               
                 WT shoot apex seedlings compared to narrow leaf 
                 in-house experiment 
               
               
                 mutants ELP3 (2) and SWP1 (1); defle_Swp1 
               
               
                 WT landsberg erecta leaves 6 compared to broad 
                 in-house experiment 
               
               
                 leaf mutant rotunda 2; defle_ron2 
               
               
                 WT landsberg erecta leaves 6 compared to broad 
                 in-house experiment 
               
               
                 leaf mutant rotunda 2; defle_Ler 
               
               
                 WT landsberg erecta compared to broad leaf mutant 
                 in-house experiment 
               
               
                 rotunda 1; defle_Ler 
               
               
                 WT landsberg erecta compared to broad leaf mutant 
                 in-house experiment 
               
               
                 rotunda 1; defle_ron1 
               
               
                 WT leaves profiling at different stages of development 
                 in-house experiment 
               
               
                 (9, 15, 22 days); gebee_15 
               
               
                 WT leaves profiling at different stages of development 
                 in-house experiment 
               
               
                 (9, 15, 22 days); gebee_22 
               
               
                 WT leaves profiling at different stages of development 
                 in-house experiment 
               
               
                 (9, 15, 22 days); gebee_9 
               
               
                 Methyl jasmonate profiling at different time points; 
                 in-house experiment 
               
               
                 lapau_ATL-MeJA-0.5 
               
               
                 Methyl jasmonate profiling at different time points; 
                 in-house experiment 
               
               
                 lapau_ATL-MeJA-2 
               
               
                 Methyl jasmonate profiling at different time points; 
                 in-house experiment 
               
               
                 lapau_ATL-MeJA-6 
               
               
                 Methyl jasmonate profiling at different time points; 
                 in-house experiment 
               
               
                 lapau_ATL-DMSO-0.5 
               
               
                 Methyl jasmonate profiling at different time points; 
                 in-house experiment 
               
               
                 lapau_ATL-DMSO-2 
               
               
                 Methyl jasmonate profiling at different time points; 
                 in-house experiment 
               
               
                 lapau_ATL-DMSO-6 
               
               
                 Methyl jasmonate profiling at different time points; 
                 in-house experiment 
               
               
                 lapau_ATL-MeJA-CHX-6 
               
               
                 DEL1 knockouts versus control (columbia) in seedlings; 
                 in-house experiment 
               
               
                 livey_Wild-type_seedling_8d 
               
               
                 DEL1 knockouts versus control (columbia) in seedlings; 
                 in-house experiment 
               
               
                 livey_DEL1_KO_seedling_8d 
               
               
                 E2F overexpression versus control (columbia WT) in 
                 in-house experiment 
               
               
                 seedlings; livey_Wild-type_seedling_8d 
               
               
                 E2F overexpression versus control (columbia WT) in 
                 in-house experiment 
               
               
                 seedlings; livey_E2Fa-DPa_OE_seedling_8d 
               
               
                 DEL1 overexpression versus control (columbia WT) in 
                 in-house experiment 
               
               
                 leaf; livey_Wild-type_leaf_15d 
               
               
                 DEL1 overexpression versus control (columbia WT) in 
                 in-house experiment 
               
               
                 leaf; livey_DEL1_OE_leaf_15d 
               
               
                 endocycle exp. In leaf - control; 
                 in-house experiment 
               
               
                 livey_Wild-type_leaf_15d 
               
               
                 endocycle exp. In leaf - DEL1 knockout; 
                 in-house experiment 
               
               
                 livey_DEL1_KO_leaf_15d 
               
               
                 endocycle exp. In leaf - CCS52A1 knockout; 
                 in-house experiment 
               
               
                 livey_CCS52A1_KO_leaf_15d 
               
               
                 endocycle exp. In leaf - CCS52B knockout; 
                 in-house experiment 
               
               
                 livey_CCS52B_KO_leaf_15d 
               
               
                 endocycle exp. In leaf—CCKB1 DN; livey_CDKB1; 
                 in-house experiment 
               
               
                 1.DN_#9_15d 
               
               
                 endocycle exp. In leaf - KRP2 overexpression; 
                 in-house experiment 
               
               
                 livey_KRP2_OE_#7_15d 
               
               
                 endocycle exp. In leaf - DEL1 overexpression; 
                 in-house experiment 
               
               
                 livey_DEL1_OE_#2_15d 
               
               
                 WEE1 exp. - genotype columbia; livey_ROOT_TIP + 
                 in-house experiment 
               
               
                 0 h 
               
               
                 WEE1 exp. - genotype columbia; livey_ROOT_TIP + 
                 in-house experiment 
               
               
                 0 h_HU 
               
               
                 WEE1 exp. - genotype columbia; livey_ROOT_TIP + 
                 in-house experiment 
               
               
                 5 h 
               
               
                 WEE1 exp. - genotype columbia; livey_ROOT_TIP + 
                 in-house experiment 
               
               
                 5 h_HU 
               
               
                 WEE1 exp. - genotype columbia; livey_ROOT_TIP + 
                 in-house experiment 
               
               
                 1 day 
               
               
                 WEE1 exp. - genotype columbia; livey_ROOT_TIP + 
                 in-house experiment 
               
               
                 1 day_HU 
               
               
                 WEE1 exp. - genotype WEE1; livey_ROOT_TIP + 0 h 
                 in-house experiment 
               
               
                 WEE1 exp. - genotype WEE1; livey_ROOT_TIP + 
                 in-house experiment 
               
               
                 0 h_HU 
               
               
                 WEE1 exp. - genotype WEE1; livey_ROOT_TIP + 5 h 
                 in-house experiment 
               
               
                 WEE1 exp. - genotype WEE1; livey_ROOT_TIP + 
                 in-house experiment 
               
               
                 5 h_HU 
               
               
                 WEE1 exp. - genotype WEE1; livey_ROOT_TIP + 
                 in-house experiment 
               
               
                 1 day 
               
               
                 WEE1 exp. - genotype WEE1; livey_ROOT_TIP + 
                 in-house experiment 
               
               
                 1 day_HU 
               
               
                 lateral root initiation study WT versus mutant solitary 
                 in-house experiment 
               
               
                 root 1 (slr1) WT 0 h 
               
               
                 lateral root initiation study WT versus mutant solitary 
                 in-house experiment 
               
               
                 root 1 (slr1) WT 2 h 
               
               
                 lateral root initiation study WT versus mutant solitary 
                 in-house experiment 
               
               
                 root 1 (slr1) WT 6 h 
               
               
                 lateral root initiation study WT versus mutant solitary 
                 in-house experiment 
               
               
                 root 1 (slr1) slr1 0 h 
               
               
                 lateral root initiation study WT versus mutant solitary 
                 in-house experiment 
               
               
                 root 1 (slr1) slr1 2 h 
               
               
                 lateral root initiation study WT versus mutant solitary 
                 in-house experiment 
               
               
                 root 1 (slr1) slr1 6 h 
               
               
                 vascular tissue formation - callus formed from leaves - 
                 DB001_ATH1_A3-Brown-cal.CEL 
               
               
                 5 days after treatment; 0.2 mgl-1 auxin(2,4-D NA 
               
               
                 IAA) 1.0 mgl-1 BA 
               
               
                 vascular tissue formation - callus formed from leaves - 
                 DB001_ATH1_A4-Brown-cal.CEL 
               
               
                 9 days after treatment; 0.2 mgl-1 auxin(2,4-D NA 
               
               
                 IAA) 1.0 mgl-1 BA 
               
               
                 Arrested development mutant analysis - leaves - add 3 
                 BP001_ATH1_A1-Pickett-ADD3-1.CEL 
               
               
                 Arrested development mutant analysis - leaves - control 
                 BP001_ATH1_A3-Pickett-a1.CEL 
               
               
                   Agrobacterium  induced tumor vs control; Tumour tissue 
                 RD001_ATH1_A1-deeke-tum.CEL 
               
               
                 induced at the base of an inflorescence stalk with 
               
               
                 
                   Agrobacterium tumefaciens 
                 
               
               
                   Agrobacterium  induced tumor vs control; Inflorescence 
                 RD001_ATH1_A2-deeke-Inf.CEL 
               
               
                 stalk injured at the base with a injection needle (control) 
               
               
                 Polycomb binding protein knockout vs WT; WT 
                 KC001_ATH1_A1-Cain-WT1.CEL 
               
               
                 Polycomb binding protein knockout vs WT; CDB1 
                 KC001_ATH1_A3-Cain-CDBI.CEL 
               
               
                 knockout 
               
               
                 axillary bud dormancy_naphthalene-1-acetic acid 
                 E-MEXP-148 
               
               
                 wild-type 
               
               
                 axillary bud dormancy_max4-1 mutant 
                 E-MEXP-148 
               
               
                 axillary bud dormancy_wild type 
                 E-MEXP-148 
               
               
                 MPK4 on ethylene regulation 
                 E-MEXP-174 
               
               
                 (leaf)_wild_type_Landsberg erecta 
               
               
                 MPK4 on ethylene regulation 
                 E-MEXP-174 
               
               
                 (leaf)_ctr1 mutant_Columbia 
               
               
                 MPK4 on ethylene regulation (leaf)_mpk4 
                 E-MEXP-174 
               
               
                 mutant_Landsberg erecta 
               
               
                 MPK4 on ethylene regulation (leaf)_ctr1 mpk4 double 
                 E-MEXP-174 
               
               
                 mutant_Landsberg/Columbia 
               
               
                 systemic responses of MAPK to pathogens 
                 E-MEXP-173 
               
               
                 (leaf)_35S:mks1_eco_Landsberg 
               
               
                 systemic responses of MAPK to pathogens (leaf)_mpk4 
                 E-MEXP-173 
               
               
                 mutant_eco_Landsberg 
               
               
                 systemic responses of MAPK to pathogens (leaf)_wild 
                 E-MEXP-173 
               
               
                 type_eco_Landsberg 
               
               
                 secondary cell wall 
                 E-MEXP-265 
               
               
                 formation_hypocotyl_eco_Landsberg 
               
               
                 secondary cell wall formation_leaf_eco_Landsberg 
                 E-MEXP-265 
               
               
                 secondary cell wall formation_stem 
                 E-MEXP-265 
               
               
                 base_eco_Landsberg 
               
               
                 secondary cell wall formation_stem lower 
                 E-MEXP-265 
               
               
                 middle_eco_Landsberg 
               
               
                 secondary cell wall formation_stem tip_eco_Landsberg 
                 E-MEXP-265 
               
               
                 secondary cell wall formation_stem upper 
                 E-MEXP-265 
               
               
                 middle_eco_Landsberg 
               
               
                 comparison of mutants lacking CAF-1 
                 E-MEXP-694 
               
               
                 subunits_fas2-1_eco_Landsberg erecta 
               
               
                 comparison of mutants lacking CAF-1 
                 E-MEXP-694 
               
               
                 subunits_msi1-as_eco_Columbia 
               
               
                 comparison of mutants lacking CAF-1 
                 E-MEXP-694 
               
               
                 subunits_wild_type_eco_Columbia 
               
               
                 comparison of mutants lacking CAF-1 
                 E-MEXP-694 
               
               
                 subunits_wild_type_eco_Enkheim 
               
               
                 comparison of mutants lacking CAF-1 
                 E-MEXP-694 
               
               
                 subunits_wild_type_eco_Landsberg erecta 
               
               
                 AP2/ERF TF (bolita) (leaf)_bolita mutant 
                 E-MEXP-809 
               
               
                 AP2/ERF TF (bolita) (leaf)_wild_type 
                 E-MEXP-809 
               
               
                 tissue comparison_stem_greenhouse 
                 Somerville: Tissue Type Arrays of 
               
               
                   
                 Columbia-0_genome 
               
               
                 tissue comparison_leaf_greenhouse 
                 Somerville: Tissue Type Arrays of 
               
               
                   
                 Columbia-0_genome 
               
               
                 tissue comparison_flower_growth chamber 
                 Somerville: Tissue Type Arrays of 
               
               
                   
                 Columbia-0_genome 
               
               
                 tissue comparison_flower_greenhouse 
                 Somerville: Tissue Type Arrays of 
               
               
                   
                 Columbia-0_genome 
               
               
                 tissue comparison_stem_growth chamber 
                 Somerville: Tissue Type Arrays of 
               
               
                   
                 Columbia-0_genome 
               
               
                 flower_wild-type Columbia_0 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_wild-type Columbia_3 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_wild-type Columbia_7 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_wild-type Landsberg_0 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_wild-type Landsberg_3 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_wild-type Landsberg_5 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_wild-type Landsberg_7 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_mutant constans (co-2)_0 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_mutant constans (co-2)_3 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_mutant constans (co-2)_5 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_mutant constans (co-2)_7 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_mutant ft (ft-2)_0 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_mutant ft (ft-2)_3 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_mutant ft (ft-2)_5 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_mutant ft (ft-2)_7 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_mutant lfy-12 Columbia_0 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_mutant lfy-12 Columbia_3 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_mutant lfy-12 Columbia_5 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 flower_mutant lfy-12 Columbia_7 days 
                 Weigel: Floral transition and early 
               
               
                   
                 flower development 
               
               
                 laser-capture micro-dissected_embryo cotyledon (apical) 
                 /share/nasc/Casson_laser-capture_micro- 
               
               
                   
                 dissected_embryonic_tissues/ 
               
               
                   
                 CEL/KL001_ATH1_A1-Linds-cot.CEL 
               
               
                 laser-capture micro-dissected_embryo root (basal) 
                 /share/nasc/Casson_laser-capture_micro- 
               
               
                   
                 dissected_embryonic_tissues/ 
               
               
                   
                 CEL/KL001_ATH1_A1-Linds-roo.CEL 
               
               
                 laser-capture micro-dissected_globular embryo, 
                 /share/nasc/Casson_laser-capture_micro- 
               
               
                 apical tissue 
                 dissected_embryonic_tissues/ 
               
               
                   
                 CEL/SC001_ATH1_A1.1-casso-gla. 
               
               
                   
                 CEL 
               
               
                 laser-capture micro-dissected_globular embryo, 
                 /share/nasc/Casson_laser-capture_micro- 
               
               
                 basal tissue 
                 dissected_embryonic_tissues/ 
               
               
                   
                 CEL/SC001_ATH1_A2.1-casso-glb. 
               
               
                   
                 CEL 
               
               
                 laser-capture micro-dissected_heart stage embryo, 
                 /share/nasc/Casson_laser-capture_micro- 
               
               
                 cotyledon pole (apical) 
                 dissected_embryonic_tissues/ 
               
               
                   
                 CEL/SC001_ATH1_A3-1-casso-hec. 
               
               
                   
                 CEL 
               
               
                 laser-capture micro-dissected_heart stage embryo, 
                 /share/nasc/Casson_laser-capture_micro- 
               
               
                 root pole (basal) 
                 dissected_embryonic_tissues/ 
               
               
                   
                 CEL/SC001_ATH1_A4-1-casso-her. 
               
               
                   
                 CEL 
               
               
                 water-Col0-1 hr 
                 /share/nasc/De_Grauwe/CEL/DV001_ATH1_A2- 
               
               
                   
                 degra-Cc1.CEL 
               
               
                 water-etr1 (ethylene-insensitive mutant)-1 hr 
                 /share/nasc/De_Grauwe/CEL/DV001_ATH1_A7- 
               
               
                   
                 degra-Ec1.CEL 
               
               
                 GA4-Col0-1 hr 
                 /share/nasc/De_Grauwe/CEL/DV001_ATH1_A4- 
               
               
                   
                 degra-Cg1.CEL 
               
               
                 GA4-etr1 (ethylene-insensitive mutant)-1 hr 
                 /share/nasc/De_Grauwe/CEL/DV001_ATH1_A9- 
               
               
                   
                 degra-Eg1.CEL 
               
               
                 ms1ttg-young 
                 /share/nasc/Gema_Vizcay_Barrena/ 
               
               
                   
                 CEL/ZW001_ATH1_A1-Wilson-mla. 
               
               
                   
                 CEL 
               
               
                 ms1ttg-old 
                 /share/nasc/Gema_Vizcay_Barrena/ 
               
               
                   
                 CEL/ZW002_ATH1_A2_Wilson_Rep2. 
               
               
                   
                 CEL 
               
               
                 Ler-young 
                 /share/nasc/Gema_Vizcay_Barrena/ 
               
               
                   
                 CEL/ZW002_ATH1_A3_Wilson_Rep2. 
               
               
                   
                 CEL 
               
               
                 Ler-old 
                 /share/nasc/Gema_Vizcay_Barrena/ 
               
               
                   
                 CEL/ZW001_ATH1_A4-Wilson-Ler. 
               
               
                   
                 CEL 
               
               
                 Lerttg-young 
                 /share/nasc/Gema_Vizcay_Barrena/ 
               
               
                   
                 CEL/ZW003_ATH1_C1-GVB_rep1. 
               
               
                   
                 CEL 
               
               
                 Lerttg-old 
                 /share/nasc/Gema_Vizcay_Barrena/ 
               
               
                   
                 CEL/ZW003_ATH1_C2-GVB_rep1. 
               
               
                   
                 CEL 
               
               
                 Programmed Cell Death Control 
                 /share/nasc/Jodi_Swidzinski/CEL/JS001_ATH1_Control(3)new. 
               
               
                   
                 CEL 
               
               
                 Programmed Cell Death Heat 
                 /share/nasc/Jodi_Swidzinski/CEL/JS001_ATH1- 
               
               
                   
                 Heat(4).CEL 
               
               
                 Programmed Cell Death Senescence 
                 /share/nasc/Jodi_Swidzinski/CEL/JS001_ATH1_Sen(3)new. 
               
               
                   
                 CEL 
               
               
                 Wheeler-a05_SLD_SPH1 RNAi at stage 1.05, leaf 
                 /share/nasc/Mike_Wheeler/CEL/MW001_ATH1_A1- 
               
               
                   
                 Wheel-a05.CEL 
               
               
                 Wheeler-a14_SLD_SPH1 RNAi at stage 1.14, leaf 
                 /share/nasc/Mike_Wheeler/CEL/MW001_ATH1_A1- 
               
               
                   
                 Wheel-a14.CEL 
               
               
                 Wheeler-w05_SLD_wild type at stage 1.05, leaf 
                 /share/nasc/Mike_Wheeler/CEL/MW001_ATH1_A1- 
               
               
                   
                 Wheel-w05.CEL 
               
               
                 Wheeler-w14_SLD_wild type at stage 1.14, leaf 
                 /share/nasc/Mike_Wheeler/CEL/MW001_ATH1_A1- 
               
               
                   
                 Wheel-w14.CEL 
               
               
                 Ulm_1-1_4 days-345 nm 
                 /share/nasc/Ulm_UV-B_response_of_Arabidopsis/ 
               
               
                   
                 CEL/Ulm_1-1_4days-345nm_Rep1_ATH1. 
               
               
                   
                 CEL 
               
               
                 Ulm_1-4_4 days-305 nm 
                 /share/nasc/Ulm_UV-B_response_of_Arabidopsis/ 
               
               
                   
                 CEL/Ulm_1-4_4days-305m,_Rep1_ATH1. 
               
               
                   
                 CEL 
               
               
                 Ulm_1-9_4 days-345 nm, 1 hr-305 nm 
                 /share/nasc/Ulm_UV-B_response_of_Arabidopsis/ 
               
               
                   
                 CEL/Ulm_1-9_4days-345nm, 1hr- 
               
               
                   
                 305nm_Rep3_ATH1.CEL 
               
               
                 Ulm_1-10_4 days-345 nm, 6 hr-305 nm 
                 /share/nasc/Ulm_UV-B_response_of_Arabidopsis/ 
               
               
                   
                 CEL/Ulm_1-10_4days- 
               
               
                   
                 345nm,6hr-305nm_Rep1_ATH1.CEL 
               
               
                 microgametogenesisPollen_bicellular pollen 
                 /share/nasc/David_Honys/CEL/DH001_ATH1_A2- 
               
               
                   
                 BCP1.CEL 
               
               
                 microgametogenesisPollen_tricellular pollen 
                 /share/nasc/David_Honys/CEL/DH001_ATH1_A3- 
               
               
                   
                 TCP1.CEL 
               
               
                 microgametogenesisPollen_uninucleate microspores 
                 /share/nasc/David_Honys/CEL/DH001_ATH1_A1- 
               
               
                   
                 UNM1.CEL 
               
               
                 Pourtau_1-1_lowN_leaf senescence 
                 /share/nasc/Pourtau_sugar_acc_during_early_leaf_senescence/ 
               
               
                   
                 CEL/Pourtau_1- 
               
               
                   
                 1_lowN_Rep1_ATH1.CEL 
               
               
                 Pourtau_1-4_lowN-glu_leaf senescence_effect 
                 /share/nasc/Pourtau_sugar_acc_during_early_leaf_senescence/ 
               
               
                 of glucose 
                 CEL/Pourtau_1- 
               
               
                   
                 4_lowN-glu_Rep1_ATH1.CEL 
               
               
                 Pourtau_1-7_highN-glu_leaf senescence_effect 
                 /share/nasc/Pourtau_sugar_acc_during_early_leaf_senescence/ 
               
               
                 of nitrogen 
                 CEL/Pourtau_1- 
               
               
                   
                 7_highN-glu_Rep1_ATH1.CEL 
               
               
                 ozone-fumigated seedlings 
                 /share/nasc/Short_Functional_Genomics_of_Ozone_Stress_in_Arabidopsis/ 
               
               
                   
                 CEL/ES001_ATH1_A1-mcain-ozo. 
               
               
                   
                 CEL 
               
               
                 air-fumigated seedlings 
                 /share/nasc/Short_Functional_Genomics_of_Ozone_Stress_in_Arabidopsis/ 
               
               
                   
                 CEL/ES001_ATH1_A2-mcain-con. 
               
               
                   
                 CEL 
               
               
                   
               
             
          
         
       
     
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