An integrated Arabidopsis annotation database for Affymetrix Genechip (R) data analysis, and tools for regulatory motif searches

Genome-scale sequencing projects have provided the essential information re quired for the construction of entire genome chips or microarrays for RNA e xpression studies. The Arabidopsis and rice genomes have been sequenced and whole-genome oligonucleotide arrays are being manufactured. These should s oon become available to researchers. Expression studies using genomic-scale expression arrays are providing us with a vast quantity of information at a rapid pace. The rate-limiting step in this type of experiments is not the data generation step but rather the data analysis component of experiments . We report improvements that should facilitate the analysis of Affymetrix Genechip (R) expression data.