Development of a novel data mining tool to find cis-elements in rice gene promoter regions
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 un...
| Autores principales: | , , , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2008
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/166362 |
| _version_ | 1855524513068875776 |
|---|---|
| author | Doi, Koji Hosaka, Aeni Nagata, Toshifumi Satoh, Kouji Suzuki, Kohji Mauleon, Ramil Mendoza, Michael J. Bruskiewich, Richard Kikuchi, Shoshi |
| author_browse | Bruskiewich, Richard Doi, Koji Hosaka, Aeni Kikuchi, Shoshi Mauleon, Ramil Mendoza, Michael J. Nagata, Toshifumi Satoh, Kouji Suzuki, Kohji |
| author_facet | Doi, Koji Hosaka, Aeni Nagata, Toshifumi Satoh, Kouji Suzuki, Kohji Mauleon, Ramil Mendoza, Michael J. Bruskiewich, Richard Kikuchi, Shoshi |
| author_sort | Doi, Koji |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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 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.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. |
| format | Journal Article |
| id | CGSpace166362 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2008 |
| publishDateRange | 2008 |
| publishDateSort | 2008 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1663622025-05-14T10:24:07Z Development of a novel data mining tool to find cis-elements in rice gene promoter regions Doi, Koji Hosaka, Aeni Nagata, Toshifumi Satoh, Kouji Suzuki, Kohji Mauleon, Ramil Mendoza, Michael J. Bruskiewich, Richard Kikuchi, Shoshi complementary dna dna binding motifs genes gene expression promoters 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 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.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. 2008-12 2024-12-19T12:56:10Z 2024-12-19T12:56:10Z Journal Article https://hdl.handle.net/10568/166362 en Springer Doi, Koji; Hosaka, Aeni; Nagata, Toshifumi; Satoh, Kouji; Suzuki, Kohji; Mauleon, Ramil; Mendoza, Michael J; Bruskiewich, Richard and Kikuchi, Shoshi. 2008. Development of a novel data mining tool to find cis-elements in rice gene promoter regions. BMC Plant Biol, Volume 8, no. 1 |
| spellingShingle | complementary dna dna binding motifs genes gene expression promoters Doi, Koji Hosaka, Aeni Nagata, Toshifumi Satoh, Kouji Suzuki, Kohji Mauleon, Ramil Mendoza, Michael J. Bruskiewich, Richard Kikuchi, Shoshi Development of a novel data mining tool to find cis-elements in rice gene promoter regions |
| title | Development of a novel data mining tool to find cis-elements in rice gene promoter regions |
| title_full | Development of a novel data mining tool to find cis-elements in rice gene promoter regions |
| title_fullStr | Development of a novel data mining tool to find cis-elements in rice gene promoter regions |
| title_full_unstemmed | Development of a novel data mining tool to find cis-elements in rice gene promoter regions |
| title_short | Development of a novel data mining tool to find cis-elements in rice gene promoter regions |
| title_sort | development of a novel data mining tool to find cis elements in rice gene promoter regions |
| topic | complementary dna dna binding motifs genes gene expression promoters |
| url | https://hdl.handle.net/10568/166362 |
| work_keys_str_mv | AT doikoji developmentofanoveldataminingtooltofindciselementsinricegenepromoterregions AT hosakaaeni developmentofanoveldataminingtooltofindciselementsinricegenepromoterregions AT nagatatoshifumi developmentofanoveldataminingtooltofindciselementsinricegenepromoterregions AT satohkouji developmentofanoveldataminingtooltofindciselementsinricegenepromoterregions AT suzukikohji developmentofanoveldataminingtooltofindciselementsinricegenepromoterregions AT mauleonramil developmentofanoveldataminingtooltofindciselementsinricegenepromoterregions AT mendozamichaelj developmentofanoveldataminingtooltofindciselementsinricegenepromoterregions AT bruskiewichrichard developmentofanoveldataminingtooltofindciselementsinricegenepromoterregions AT kikuchishoshi developmentofanoveldataminingtooltofindciselementsinricegenepromoterregions |