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www.plexdb.org Data Mining at PLEXdb : Plant and Plant Pathogen Gene Expression Database www.plexdb.org Sudhansu Dash1,2,3, Hong Lu5, Ethalinda KS Cannon3,5, Nick Lauter3,4, Volker Brendel5, Roger P Wise4, Julie A Dickerson1,2 1Virtual Reality Application Center; 2Dept. of Electrical & Computer Engg.; 3Crop Genome Informatics Lab; 4Dept. of Plant Pathology and Corn Insects and Crop Genetics Research, USDA-ARS; 5GDCB. Iowa State University. PLEXdb Features: • Supports all Affymetrix microarrays for plants and plant pathogens including annotation. • MIAME/Plant compliant data submission. • Experiment Visibility: private / collaborators and reviewers / public. • Uses standard ontologies. • Links to PlantGDB, Gramene, GrainGenes, UniProt, etc. • Option to submit data at NCBI GEO • Data from 217 microarray experiments, > 6000 chips • Experiments from 14 Affymetrix arrays. • Species: Arabidopsis, Barley, Citrus, Fusarium, Grape, Maize, Medicago, Poplar, Rice, Soybean, Sugarcane, Tomato, Wheat. DATA MINING: The Microarray Platform Translator tool Translates probe sets of one microarray chip to another in a different species. DATA MINING: Gene OScilloScope Search for experiments where expression of queried genes fluctuate (oscillate) the most. DATA MINING: Find co-expressed genes Co-expressed genes or profile neighbors can be downloaded and viewed as heatmap or expression graph GENELIST SUITE: Tools to Create GeneLists GO category Treatment specific expression Fold change GENELIST SUITE: Analyze GeneLists Partitional clustering based on K Means GENELIST SUITE: Annotate a GeneList TOOLS: Map Interesting Genes from Your Analysis on the rice/Arabidopsis Genome Model Genome Interrogator Get the gene model, promoter, 5’UTR sequences, etc. VISUALIZATION: Emphasis on data exploration VISUALIZATION: Expression of an individual gene Expression Graph of probe set OsAffx.26001.3.S1_at in experiment OS2 across hybridizations: Repressed in salt stress condition. CONTROL SALT STRESS