Plant & Animal Genome IX Conference

Poster: Genome Software
P9b_02.html

GENEX: A FLEXIBLE DATA MANAGEMENT AND ANALYSIS SYSTEM FOR GENE EXPRESSION DATA

¹ National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505

² Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, 1750 Kraft Drive (0477), 10 Suite 1400, Blacksburg, VA 25061

³ University of New Mexico, Computer Science Department, Farris Engineering Center, Room 157, Albuquerque, NM 87131

With the advent of technology that allows researchers to simultaneously probe the gene expression patterns of all genes in an organism, comes the challenge of managing, querying and analyzing large volumes of data. GeneX (http://genex.ncgr.org) was created to aid researchers in maintaining expression data and the associated experimental details that define the context. This information is critical for extracting information from these enormous data sets. GeneX consists of a database (Postgres or Sybase), a curation tool for formatting and uploading data into GeneX as well as other compatible databases, an XML-based file format for data exchange, and several web-based analytical and visualization tools. The technologies and methodologies involved in gene expression profiling are still evolving. Consequently, GeneX system was designed to be flexible, extensible, and broadly applicable to existing and emerging technologies and experimental designs. The GeneX curation tool has been used to fully annotate and upload gene expression experiment sets into the GeneX database. These experiment sets include the Saccharomyces cerevisiae diauxic shift (DeRisi et al.), and the Escherichia coli K12 integration host factor (Arfin et al.) data in order to demonstrate the flexibility and richness of the GeneX data model.