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plexdb

www.plexdb.org. Data Mining at PLEXdb : Pl ant and Plant Pathogen Gene Ex pression D ata b ase. www.plexdb.org. 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

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plexdb

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  1. www.plexdb.org Data Mining at PLEXdb: Plant and Plant Pathogen Gene Expression Database

  2. 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.

  3. 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.

  4. DATA MINING: The Microarray Platform Translator tool Translates probe sets of one microarray chip to another in a different species.

  5. DATA MINING: Gene OScilloScope Search for experiments where expression of queried genes fluctuate (oscillate) the most.

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

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

  8. GENELIST SUITE: Analyze GeneLists Partitional clustering based on K Means

  9. GENELIST SUITE: Annotate a GeneList

  10. TOOLS: Map Interesting Genes from Your Analysis on the rice/Arabidopsis Genome Model Genome Interrogator Get the gene model, promoter, 5’UTR sequences, etc.

  11. VISUALIZATION: Emphasis on data exploration

  12. 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

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