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Comprehensive Gene Expression Insights for Plants and Pathogens at PLEXdb

PLEXdb is a robust platform for plant and plant pathogen gene expression data, supporting all Affymetrix microarrays. It features MIAME/Plant compliant data submission, experiment visibility controls, and links to major databases like PlantGDB and UniProt. With over 217 microarray experiments and data from more than 6000 chips, PLEXdb allows efficient data mining through tools like the Microarray Platform Translator and Gene OScilloScope Search. Users can create and analyze gene lists, visualize expression patterns, and explore co-expression relationships across various plant species.

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Comprehensive Gene Expression Insights for Plants and Pathogens at 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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