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Abstract
BackgroundInformation 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.ResultsWe 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 scores of the listed candidate motifs by association rule analysis. This strategy depends on the idea that motifs overrepresented in the promoter region could play specific roles in the regulation of expression of these genes. The tool is designed so that any biological researchers can use it easily at the publicly accessible Internet site . We evaluated the accuracy and utility of the tool by using a dataset of auxin-inducible genes that have well-studied cis-elements. The test showed the effectiveness of the tool in identifying significant relationships between cis-element candidates and related sets of genes.ConclusionThe tool lists possible cis-element motifs corresponding to genes of interest, and it will contribute to the deeper understanding of gene regulatory mechanisms in plants.
Highlights
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 cisregulatory elements with key roles under the various conditions
With the completion of rice genome sequencing by the International Rice Genome Sequencing Project [1], the Beijing Genomics Institute (BGI) [2], and Syngenta [3], many rice functional genomic resources have become available, including whole genome sequences from ssp. japonica 'Nipponbare' and ssp. indica line 93-11; a set of rice full-length cDNA clones and their complete and par
BMC Plant Biology 2008, 8:20 http://www.biomedcentral.com/1471-2229/8/20 tial end sequences [4,5], microarray gene expression systems based on full-length cDNA sequences, ESTs (Expressed Sequence Tag), MPSS (Massively Parallel Signature Sequencing), SAGE (Serial Analysis of Gene Expression), and predicted genes in the genome sequences; and many kinds of insertion mutants with Tos17, Ac-Ds, and T-DNAs [6]
Summary
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. It evaluates the likelihood scores of the listed candidate motifs by association rule analysis. This strategy depends on the idea that motifs overrepresented in the promoter region could play specific roles in the regulation of expression of these genes. The test showed the effectiveness of the tool in identifying significant relationships between cis-element candidates and related sets of genes
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