Bioconductor and the Affymetrix Power Tools. For ex- periments using multi-species GeneChips (Soybean, Medicago), custom probe deﬁnition ﬁles are used for the RMA normalization step to enable masking out expres- sion elements from species that are not relevant to the experiment. With improvement in sequencing and sequence assembly technology, there have been signiﬁcant revisions of the gene model versions available in many species. As a consequence, the current probe conﬁguration of a signiﬁ- cant number of probe sets is not congruent with the updated versions of the corresponding gene models. To address this issue, PLEXdb has begun, on a pilot basis, remapping probes as assemblies evolve. For example, the Nimblegen Maize platform is being mapped to the gene models from the maize RefGen V2 build in collaboration with MaizeGDB. Data has been re-normalized based on the new conﬁguration where the gene models serve as the revised probe sets. The new data set has been released as a clone of the original data set which corresponds to the V1 build (10). This approach will make it easier to integrate microarray data with RNAseq/NGS expression data that relies on alignment to the most recent gene models avail- able in a species. PLEXdb analysis tools PLEXdb provides a number of tools for submitting, viewing and analyzing experiments, and for creating, and analyzing gene lists. In addition, extensive tutorials have been written on the tools in the database that de- scribes how the tools work with detailed examples. MODEL GENOME INTERROGATOR The Model Genome Interrogator (MGI), Version 3 provides structural genomic support for integrated and comparative exploration of gene expression data (2). Based on user input of single or batch queries of micro- array probe set identiﬁers from most of the microarray platforms supported by PLEXdb, MGI uses the sequenced genomes, the annotate protein-coding genes, cDNA and locus coordinate data of either rice or Arabidopsis to identify putative orthologs for the source gene that correspond to the probesets. For each putative ortholog identiﬁed, MGI allows researchers to view anno- tations, visually evaluate gene models and extract sequence data from promoters, exons, introns and UTRs (Figure 2). On the input page, users must enter a list of gene iden- tiﬁers or probe set names, specify the expression platform from which they originate, choose the model genome to interrogate and select desired output options. Links to sample data that show format are available on the input page. These are helpful for exploring MGI utilities without requiring prior data analysis. The output consists of a map of where potential orthologs physically map in the model genome and their identities and annotations. Query probesets that cannot be mapped onto the chosen model genome are listed as ‘Missed Genes’. The GeneSeqer and BLAST results Nucleic Acids Research, 2012, Vol. 40, Database issue D1197 describe the quality of the match and its evidence. The other four columns in the table provide annotations of the query probesets and their matching model gene loci, including direct links to Gramene (13) for rice or TAIR for Arabidopsis (14). More than one row of data is used to summarize the results if more than one locus qualiﬁes as a match. It is common for a query to match multiple annotated protein-coding genes or full length cDNAs associated with a single locus. The tools allow single or batch extraction of promoter, 50-UTR, 1st exon, 1st intron and 30-UTR se- quences. The researcher may select the source of evidence to be the annotated protein-coding gene only, or also include full-length cDNA evidence provided by PlantGDB (8). The 16 microarray platforms mapped onto the rice and Arabidopsis genomes by the PLEXdb implementation of MGI display three levels of connectivity and ﬁdelity that are directly related to phylogenetic distance. GENE OSCILLOSCOPE The Gene OscilloScope is a data-mining tool that searches for microarray experiments in PLEXdb where the expres- sion of a queried gene ﬂuctuates (oscillates) the most. Given an expression element, it displays the extent of ﬂuc- tuation of the treatment means in each of the experiments visible to the user at PLEXdb for the corresponding microarray platform. Expression of most genes does not change signiﬁcantly from one treatment to another in any given experiment except those responding to the treatment and are of bio- logical interest. The extent of ﬂuctuation of the expression of a gene in any experiment is measured by the coefﬁcient of variation (CV) of the treatment means for this gene. CV is a measure of the deviation from the mean and is ex- pressed as a percentage from the mean. CV is unaffected by high or low values of the treatment means. As a result, this indicator is not biased towards genes with more tran- script abundance. CV tends to underestimate the extent of ﬂuctuation in an experiment with more treatments. For this reason, the Gene OscilloScope tool displays the number of treatments in the table to aid users in making their decision. The Fluctuation Filter also scans for genes based on their ﬂuctuation in expression measured by the same metric, CV. Given a data set, it searches for all the genes in the data set that have a speciﬁed range of CV, e.g. <1% or >25%, etc. It can ﬁnd genes that show high or low responses to the treatments in a set of experiments. It can ﬁnd genes that are suitable for steady-state controls in a variety of studies that are less likely to ﬂuctuate under diverse experimental conditions. GENE LIST SUITE The gene-list-processing wizard guides users through PLEXdb functions for creating, analyzing, annotating and managing gene lists. Users can upload their own lists or create them from the output of PLEXdb tools,