Development of a novel data mining tool to find cis-elements in rice gene promoter regions
| Autor: | Kouji Satoh, Richard Bruskiewich, Michael Jonathan Mendoza, Aeni Hosaka, Ramil Mauleon, Koji Doi, Toshifumi Nagata, Kohji Suzuki, Shoshi Kikuchi |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2008 |
| Předmět: |
medicine.medical_specialty
Association rule learning DNA Plant Databases Factual Sequence analysis Plant Science Biology lcsh:Botany Molecular genetics Sequence Homology Nucleic Acid Gene expression medicine Coding region Genomic library Regulatory Elements Transcriptional Promoter Regions Genetic Gene Gene Library Oligonucleotide Array Sequence Analysis Genetics Base Sequence Computational Biology Promoter Oryza Sequence Analysis DNA lcsh:QK1-989 Software |
| Zdroj: | BMC Plant Biology BMC Plant Biology, Vol 8, Iss 1, p 20 (2008) |
| ISSN: | 1471-2229 |
| Popis: | 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 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 http://hpc.irri.cgiar.org/tool/nias/ces. 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. Conclusion 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. |
| Databáze: | OpenAIRE |
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