Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

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

Ethalinda KS Cannon , Matthew J Moscou , Hong Lu , Shiquan Wu , Jianqiang Xin , Rico A Caldo , Dan Nettleton , Roger P Wise , Volker Brendel , Julie A Dickerson

  Iowa State University, Ames, IA 50011

PLEXdb (www.plexdb.org) is a comprehensive plant and plant pathogen
microarray database. PLEXdb includes an expanded microarray database,
including all currently-available Affymetrix microarrays for plants and
plant pathogens, with continued work toward supporting long oligo arrays.
PLEXdb includes a new database schema which meets the criteria set out by
MIAME/Plant, more generalized tools and an improved experiment submission
process. PLEXdb also provides integration with standard ontologies such as
the gene, plant, and growth stage ontologies to improve searching and
cross-experiment comparisons.
PLEXdb enables researchers to make experiment data available to the
public, or to share data only within a research group. The analysis tools
are based on the concept of gene lists which can be created from analyses
of gene expression, physiology (all genes in a particular pathway),
function (all genes encoding a particular type of enzyme), chromosomal
context (all genes in a particular region) or other criteria. Links to
plant and pathogen databases such as PlantGDB, Gramene, GrainGenes, MIPS
Fusarium graminearum Genome Database, and UniProt provide detailed
sequence data and annotation information. Tools such as the Microarray
Platform Translator and the Rice Genome Mapper allow users to search for
homologous genes on different microarray platforms and to translate
microarray probes onto the rice genome.
PLEXdb is funded by USDA-NRI grant no. 2002-35300-12619 and NSF DBI 0543441.