RiCES: Rice Cis-Element Searcher

RiCES is a cis-element searching tool optimized for rice (Oryza sativa) genome, available as the RiCES webservice.
It takes as input a list of identifiers of transcription unit IDs of Oryza sativa, defined in Pseudomolecule corresponding to KOME full length cDNA clones, and returns a list of cis-element sites that appear to be shared across the listed gene loci. The motif searching program, MEME, is applied in the front step of the analysis.

The 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.
The tool is designed so that any biological researchers can use it easily at the publicly accessible Internet site http://hpc.irri.cgiar.org/tool/nias/ces. It was developed by Dr. Koji Doi, National Institute of Agrobiological Sciences (NIAS), with funding from the Generation Challenge Programme.

RiCES is a novel tool that searches for cis-element candidates in the upstream, downstream, or coding regions of differentially regulated 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. The gathered 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.

It is assumed that motifs overrepresented in the promoter region could play specific roles in the regulation of expression of these genes.
As a first step the RiCES program lists cis-element candidates by motif searching, based on the supposition that cis-elements, playing important roles in the regulation of a given set of genes, will be statistically overrepresented. Subsequently likelihood scores of the listed candidate motifs by association rule analysis are evaluated.

The accuracy and utility of the RiCES was evaluated with a dataset of auxin-inducible genes, which have well-studied cis-elements. RiCES was succesfull in identifying significant relationships between cis-element candidates and related sets of genes.

This tool was developed by Dr. Koji Doi, National Institute of Agrobiological Sciences (NIAS), with funding from the Generation Challenge Programme.

reference: Doi K, Hosaka A, Nagata T, Satoh K, Suzuki K, Mauleon R, Mendoza MJ, Bruskiewich R, Kikuchi S, 2008.
Development of a novel data mining tool to find cis-elements in rice gene promoter regions.BMC Plant Biology 8:20. (pdf)

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