TY - JOUR
T1 - The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network
AU - Meier, Stuart
AU - Gehring, Chris
AU - MacPherson, Cameron Ross
AU - Kaur, Mandeep
AU - Maqungo, Monique
AU - Reuben, Sheela
AU - Muyanga, Samson
AU - Shih, Ming Der
AU - Wei, Fu Jin
AU - Wanchana, Samart
AU - Mauleon, Ramil
AU - Radovanovic, Aleksandar
AU - Bruskiewich, Richard
AU - Tanaka, Tsuyoshi
AU - Mohanty, Bijayalaxmi
AU - Itoh, Takeshi
AU - Wing, Rod
AU - Gojobori, Takashi
AU - Sasaki, Takuji
AU - Swarup, Sanjay
AU - Hsing, Yue ie
AU - Bajic, Vladimir B.
N1 - Funding Information:
Acknowledgments SM received postdoctoral fellowship from NBN; CG received support from NRF; CRM received support from SSABMI program; MK received postdoctoral fellowship from the Claude Leon Foundation; MM received support from NBN and NRF FA2006040900002; YIH received support from NSC; VBB received partial support from the DST/NRF Research Chair grant, NBN, and NRF grants FA2007051400013, ICD2006071000003, and FA2006040900002.
PY - 2008/12
Y1 - 2008/12
N2 - 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.
AB - 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.
KW - Co-expression
KW - Co-regulation
KW - Transcription regulation
UR - http://www.scopus.com/inward/record.url?scp=84863011438&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84863011438&partnerID=8YFLogxK
U2 - 10.1007/s12284-008-9017-4
DO - 10.1007/s12284-008-9017-4
M3 - Article
AN - SCOPUS:84863011438
SN - 1939-8425
VL - 1
SP - 177
EP - 187
JO - Rice
JF - Rice
IS - 2
ER -