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

Koji Doi1, Aeni Hosaka1, Toshifumi Nagata1, Kouji Satoh1, Kohji Suzuki2, Ramil Mauleon3, Michael J Mendoza3, Richard Bruskiewich3 and Shoshi Kikuchi1*

Author Affiliations

1 National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan

2 Hitachi Software Engineering Japan Co., Ltd., 6-81 Onoe-cho, Naka-ku, Yokohama 231-0015, Japan

3 International Rice Research Institute, DAPO 7777, Metro Manila, Philippines

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BMC Plant Biology 2008, 8:20  doi:10.1186/1471-2229-8-20

Published: 27 February 2008



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.


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 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 webcite. 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.


The 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.