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.

• 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 OScilloScopeSearch 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.26001.3.S1_at in experiment OS2 across hybridizations:

Repressed in salt stress condition.

VISUALIZATION: Expression of an individual gene

CONTROL SALT STRESS