Plant & Animal Genomes XVIII Conference

January 9-13, 2010
Town & Country Convention Center
San Diego, CA

Data Mining At PLEXdb: The Plant And Plant Pathogen Expression Database For Functional And Comparative Genomics

Sudhansu Dash^1,2,6 , Hong Lu³ , Ethalinda K. Cannon^1,2 , Nick Lauter^4,5 , Roger P. Wise^4,5 , Julie A. Dickerson^1,2

¹  Virtual Reality App. Ctr., Iowa State University, 2624, Howe Hall, Ames, IA, 50011, U.S.A.

²  Dept. of Electrical and Computer Eng., Iowa State University, Ames,IA, 50011, U.S.A.

³  Dept. of Genetics, Dev. and Cell Bio., Iowa State University, Ames, IA, 50011, U.S.A.

⁴  Dept. of Plant Pathology, Iowa State University, Ames, IA, 50011, U.S.A.

⁵  USDA-ARS Corn Insect and Crop Genetics Research.

⁶  1023, Crop Genome Informatics Lab., Iowa State University.

PLEXdb is an interactive gene expression resource with annotation, visualization, and exploration tools. It is MIAME/Plant compliant and supports all Affymetrix microarray designs for plants and plant pathogens. To facilitate the use of PLEXdb at any stage of data analysis, experiments may be kept private, group shared with collaborators and reviewers, or released directly to the public. On request, PLEXdb also deposits data at NCBI GEO on behalf of the submitter. The Gene List Suite tool helps create, analyze and annotate gene lists. Lists can be created by treatment specific expression, fold change over another treatment, profile neighbors, GO category, etc. Such lists can be further analyzed using expression graphs, hierarchical or partitional clustering (K-means, K-medoids) with Silhouette Plots to help select optimal cluster numbers, translated to another platform, etc. or be compared with others using the Venn Diagram tool. This suite supports annotation (GO, KEGG, etc.) with up-to-date BLAST results from RefSeq, UniProt, TAIR, DFCI, and other sources. The Model Genome Interrogator (MGI) tool translates and maps probe sets onto model genomes while the Gene OscilloScope works as a data miner that scans experiments for fluctuation in the expression of a specific gene. PLEXdb uses standardized vocabularies such as the gene and plant ontologies and has recently added more than 80 experiments from NCBI GEO making a total of 215 experiments or data from over 6,000 hybridizations in 17 different organisms.