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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network
Rice, Volume 1, No. 2, Year 2008
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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 coexpressing 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 inmaturing rice embryos,making thismethodology a promising tool for biological systems analyses. © The Author(s) 2008.
Authors & Co-Authors
Meier, Stuart K.
South Africa, Bellville
University of the Western Cape
Gehring, Chris A.
South Africa, Bellville
University of the Western Cape
MacPherson, Cameron Ross
South Africa, Bellville
University of the Western Cape
Kaur, Mandeep
South Africa, Bellville
University of the Western Cape
Maqungo, Monique
South Africa, Bellville
University of the Western Cape
Reuben, Sheela
Singapore, Singapore City
National University of Singapore
Muyanga, Samson
South Africa, Bellville
University of the Western Cape
Shih, Ming Der
Taiwan, Taipei
Academia Sinica, Institute of Plant and Microbial Biology
Wei, Fu Jin
Taiwan, Taipei
Academia Sinica, Institute of Plant and Microbial Biology
Wanchana, Samart
Philippines, Makati
International Rice Research Institute
Mauleon, Ramil
Philippines, Makati
International Rice Research Institute
Radovanovic, Aleksandar
South Africa, Bellville
University of the Western Cape
Bruskiewich, Richard
Philippines, Makati
International Rice Research Institute
Tanaka, Tsuyoshi
Japan, Tsukuba
Institute of Agrobiological Sciences, Naro
Mohanty, Bijayalaxmi
South Africa, Bellville
University of the Western Cape
Itoh, Takeshi
Japan, Tsukuba
Institute of Agrobiological Sciences, Naro
Wing, Rod A.
United States, Tucson
The University of Arizona
Gojobori, Takashi
Japan, Mishima
National Institute of Genetics Mishima
Sasaki, Takuji
Japan, Tsukuba
Institute of Agrobiological Sciences, Naro
Swarup, Sanjay
Singapore, Singapore City
National University of Singapore
Hsing, Yue ie
Taiwan, Taipei
Academia Sinica, Institute of Plant and Microbial Biology
Bajic, Vladimir B.
South Africa, Bellville
University of the Western Cape
Statistics
Citations: 22
Authors: 22
Affiliations: 7
Identifiers
Doi:
10.1007/s12284-008-9017-4
ISSN:
19398425
e-ISSN:
19398433
Research Areas
Genetics And Genomics