Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

PLEXdb: Plant And Pathogen Expression Database And Tools For Comparative And Functional Genomics Analysis

Sudhansu Dash¹ , Ethalinda K Cannon¹ , Hong Lu³ , Dinanath Nadkarni¹ , Emmanuel Owusu¹ , Nick Lauter^2,4 , Roger P Wise^2,4 , Julie A Dickerson¹

¹  Electrical and Computer, Iowa State University, 2624, Howe Hall, Ames, IA, 50011, U.S.A.

²  Dept. of Plant Pathology, Iowa State University, Ames, IA, 50011, U.S.A.

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

⁴  USDA-ARS Corn Insect and Crop Genetics Research

PLEXdb is a plant expression database that supports all Affymetrix microarray designs for plants and plant pathogens. PLEXdb provides microarray annotation and visualizations of raw and normalized experiment data across treatments in the form of boxplots, heatmaps, dendrograms, expression graphs, scatterplots and quality control plots. Experiment data deposited in PLEXdb is hand-checked for MIAME/Plant compliance and completeness then processed by normalizing the raw data using RMA and MAS5.0, producing tables and graphics from the resulting data. To facilitate the use of PLEXdb at any stage of data analysis, experiments may be kept private, shared worldwide with collaborators and reviewers, or released directly to the public. A suite of analysis and visualization tools permits in-depth exploration including searching for homolgous genes on different microarray platforms and translating microarray probe sets onto model genomes. New features include: submission of experiment data to GEO on researchers' request; GO, EC, and KEGG annotation of probe sets; the Microarray Platform Translator; a gene variance tool which searches experiments by the amount of variation in the expression of a specific gene; and tools for creating, analyzing, and annotating gene lists. PLEXdb uses standardized vocabularies such as the gene and plant ontologies to improve searching and cross-experiment comparisons. PLEXdb also links to plant and pathogen databases such as PlantGDB, Gramene, GrainGenes, HarvEST, and UniProt.