Development of a novel data mining tool to find cis-elements in rice gene promoter regions.

ABSTRACT:

Background

Information on more than 35 000 full-length Oryza sativa cDNAs, together with associated microarray gene expression data collected under various treatment conditions, has made it feasible to identify motifs that are conserved in gene promoters and may act as cis-regulatory elements with key roles under the various conditions.

Results

We have developed a novel tool that searches for cis-element candidates in the upstream, downstream, or coding regions of differentially regulated genes. The tool first lists cis-element candidates by motif searching based on the supposition that if there are cis-elements playing important roles in the regulation of a given set of genes, they will be statistically overrepresented and will be conserved. Then it evaluates the likelihood

SUBMITTER: Doi K 

PROVIDER: S-EPMC2270273 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature