Data Mining at PLEXdb : Plant and Plant Pathogen Gene Expression Database

Sudhansu Dash 1,2,3, Hong Lu 5, Ethalinda KS Cannon 3,5, Nick Lauter 3,4, Volker Brendel 5, Roger P Wise 4, Julie A Dickerson 1,2 1 Virtual Reality Application Center; 2 Dept. of Electrical & Computer Engg.; 3 Crop Genome Informatics Lab; 4 Dept. of Plant Pathology and Corn Insects and Crop Genetics Research, USDA-ARS; 5 GDCB. Iowa State University.

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. PLEXdb Features:

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.

Co-expressed genes or profile neighbors can be downloaded and viewed as heatmap or expression graph DATA MINING: Find co-expressed genes

GENELIST SUITE: Tools to Create GeneLists Fold change Treatment specific expression GO category

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

Expression Graph of probe set OsAffx S1_at in experiment OS2 across hybridizations: Repressed in salt stress condition. VISUALIZATION: Expression of an individual gene CONTROLSALT STRESS