The Promoter Signatures in Rice LEA Genes Can Be Used to Build a Co-expressing LEA Gene Network

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• 作者：Stuart Meier (1)
  Chris Gehring (2)
  Cameron Ross MacPherson (1)
  Mandeep Kaur (1)
  Monique Maqungo (1)
  Sheela Reuben (3)
  Samson Muyanga (1)
  Ming-Der Shih (4)
  Fu-Jin Wei (4)
  Samart Wanchana (5)
  Ramil Mauleon (5)
  Aleksandar Radovanovic (1)
  Richard Bruskiewich (5)
  Tsuyoshi Tanaka (6)
  Bijayalaxmi Mohanty (1)
  Takeshi Itoh (6)
  Rod Wing (7)
  Takashi Gojobori (8)
  Takuji Sasaki (6)
  Sanjay Swarup (3)
  Yue-ie Hsing (4)
  Vladimir B. Bajic (1)
  
• 关键词：Transcription regulation ; Co ; expression ; Co ; regulation
• 刊名：Rice
• 出版年：2008
• 出版时间：December 2008
• 年：2008
• 卷：1
• 期：2
• 页码：177-187
• 全文大小：284KB
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• 作者单位：Stuart Meier (1)
  Chris Gehring (2)
  Cameron Ross MacPherson (1)
  Mandeep Kaur (1)
  Monique Maqungo (1)
  Sheela Reuben (3)
  Samson Muyanga (1)
  Ming-Der Shih (4)
  Fu-Jin Wei (4)
  Samart Wanchana (5)
  Ramil Mauleon (5)
  Aleksandar Radovanovic (1)
  Richard Bruskiewich (5)
  Tsuyoshi Tanaka (6)
  Bijayalaxmi Mohanty (1)
  Takeshi Itoh (6)
  Rod Wing (7)
  Takashi Gojobori (8)
  Takuji Sasaki (6)
  Sanjay Swarup (3)
  Yue-ie Hsing (4)
  Vladimir B. Bajic (1)
  
  1. South African National Bioinformatics Institute (SANBI), University of the Western Cape, Cape Town, South Africa
  2. Department of Biotechnology, University of the Western Cape, Cape Town, South Africa
  3. Department of Biological Sciences, National University of Singapore, Singapore, Singapore
  4. Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
  5. International Rice Research Institute (IRRI), Metro Manila, Philippines
  6. National Institute of Agrobiological Sciences, Tsukuba, Japan
  7. Department of Plant Sciences, University of Arizona, Tucson, USA
  8. National Institute of Genetics, Shizuoka, Japan
  

文摘

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.