The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network
Coordinated transcriptional modulation of large gene sets depends on the combinatorial use of cis-regulatory motifs in promoters. We postulate that promoter content similarities are diagnostic for co-expressing genes that function coherently during specific cellular responses. To find the co-express...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2008
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/166246 |
| _version_ | 1855542972592947200 |
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| author | Meier, Stuart Gehring, Chris MacPherson, Cameron Ross Kaur, Mandeep Maqungo, Monique Reuben, Sheela Muyanga, Samson Shih, Ming-Der Wei, Fu-Jin Wanchana, Samart Mauleon, Ramil Radovanovic, Aleksandar Bruskiewich, Richard Tanaka, Tsuyoshi Mohanty, Bijayalaxmi Itoh, Takeshi Wing, Rod Gojobori, Takashi Sasaki, Takuji Swarup, Sanjay Hsing, Yue-ie Bajic, Vladimir B. |
| author_browse | Bajic, Vladimir B. Bruskiewich, Richard Gehring, Chris Gojobori, Takashi Hsing, Yue-ie Itoh, Takeshi Kaur, Mandeep MacPherson, Cameron Ross Maqungo, Monique Mauleon, Ramil Meier, Stuart Mohanty, Bijayalaxmi Muyanga, Samson Radovanovic, Aleksandar Reuben, Sheela Sasaki, Takuji Shih, Ming-Der Swarup, Sanjay Tanaka, Tsuyoshi Wanchana, Samart Wei, Fu-Jin Wing, Rod |
| author_facet | Meier, Stuart Gehring, Chris MacPherson, Cameron Ross Kaur, Mandeep Maqungo, Monique Reuben, Sheela Muyanga, Samson Shih, Ming-Der Wei, Fu-Jin Wanchana, Samart Mauleon, Ramil Radovanovic, Aleksandar Bruskiewich, Richard Tanaka, Tsuyoshi Mohanty, Bijayalaxmi Itoh, Takeshi Wing, Rod Gojobori, Takashi Sasaki, Takuji Swarup, Sanjay Hsing, Yue-ie Bajic, Vladimir B. |
| author_sort | Meier, Stuart |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Coordinated transcriptional modulation of large gene sets depends on the combinatorial use of cis-regulatory motifs in promoters. We postulate that promoter content similarities are diagnostic for co-expressing genes that function coherently during specific cellular responses. To find the co-expressing genes we propose an ab initio method that identifies motif families in promoters of target gene groups, map these families to the promoters of all genes in the genome, and determine the best matches of each of the target group gene promoters with all other promoters. When the method was tested in rice starting from a group of co-expressing Late Embryogenesis Abundant (LEA) genes, we obtained a promoter similarity-based network that contained candidate genes that could plausibly complement the function of LEA genes. Importantly, 73.36% of 244 genes predicted by our method were experimentally confirmed to co-express with the LEA genes in maturing rice embryos, making this methodology a promising tool for biological systems analyses. |
| format | Journal Article |
| id | CGSpace166246 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2008 |
| publishDateRange | 2008 |
| publishDateSort | 2008 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1662462024-12-19T14:13:49Z The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network Meier, Stuart Gehring, Chris MacPherson, Cameron Ross Kaur, Mandeep Maqungo, Monique Reuben, Sheela Muyanga, Samson Shih, Ming-Der Wei, Fu-Jin Wanchana, Samart Mauleon, Ramil Radovanovic, Aleksandar Bruskiewich, Richard Tanaka, Tsuyoshi Mohanty, Bijayalaxmi Itoh, Takeshi Wing, Rod Gojobori, Takashi Sasaki, Takuji Swarup, Sanjay Hsing, Yue-ie Bajic, Vladimir B. genes gene expression genetic regulation transcription promoters Coordinated transcriptional modulation of large gene sets depends on the combinatorial use of cis-regulatory motifs in promoters. We postulate that promoter content similarities are diagnostic for co-expressing genes that function coherently during specific cellular responses. To find the co-expressing genes we propose an ab initio method that identifies motif families in promoters of target gene groups, map these families to the promoters of all genes in the genome, and determine the best matches of each of the target group gene promoters with all other promoters. When the method was tested in rice starting from a group of co-expressing Late Embryogenesis Abundant (LEA) genes, we obtained a promoter similarity-based network that contained candidate genes that could plausibly complement the function of LEA genes. Importantly, 73.36% of 244 genes predicted by our method were experimentally confirmed to co-express with the LEA genes in maturing rice embryos, making this methodology a promising tool for biological systems analyses. 2008-12 2024-12-19T12:56:02Z 2024-12-19T12:56:02Z Journal Article https://hdl.handle.net/10568/166246 en Open Access Springer Meier, Stuart; Gehring, Chris; MacPherson, Cameron Ross; Kaur, Mandeep; Maqungo, Monique; Reuben, Sheela; Muyanga, Samson; Shih, Ming-Der; Wei, Fu-Jin; Wanchana, Samart; Mauleon, Ramil; Radovanovic, Aleksandar; Bruskiewich, Richard; Tanaka, Tsuyoshi; Mohanty, Bijayalaxmi; Itoh, Takeshi; Wing, Rod; Gojobori, Takashi; Sasaki, Takuji; Swarup, Sanjay; Hsing, Yue-ie and Bajic, Vladimir B. 2008. The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network. Rice, Volume 1 no. 2 p. 177-187 |
| spellingShingle | genes gene expression genetic regulation transcription promoters Meier, Stuart Gehring, Chris MacPherson, Cameron Ross Kaur, Mandeep Maqungo, Monique Reuben, Sheela Muyanga, Samson Shih, Ming-Der Wei, Fu-Jin Wanchana, Samart Mauleon, Ramil Radovanovic, Aleksandar Bruskiewich, Richard Tanaka, Tsuyoshi Mohanty, Bijayalaxmi Itoh, Takeshi Wing, Rod Gojobori, Takashi Sasaki, Takuji Swarup, Sanjay Hsing, Yue-ie Bajic, Vladimir B. The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network |
| title | The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network |
| title_full | The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network |
| title_fullStr | The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network |
| title_full_unstemmed | The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network |
| title_short | The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network |
| title_sort | promoter signatures in rice lea genes can be used to build a co expressing lea gene network |
| topic | genes gene expression genetic regulation transcription promoters |
| url | https://hdl.handle.net/10568/166246 |
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