TY - GEN
T1 - A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks
AU - Gao, Zhen
AU - Zhao, Ruizhe
AU - Ruan, Jianhua
PY - 2012/12/1
Y1 - 2012/12/1
N2 - Deciphering cis-regulatory networks has become an attractive yet challenging task. This paper presents a simple model for cis-regulatory network discovery which aims to avoid most of the common problems of previous approaches. Using promoter sequences and gene co-expression profiles as input, rather than clustering the genes by the co-expression data, it includes neighborhood co-expression information for each individual gene from the co-expression data, thereby overcoming the disadvantages of current clustering based models which miss specific information for individual genes. Applications on Saccharomyces cerevisiae have shown a good prediction accuracy, which outperforms a phylogenetic footprinting approach. In addition, the top dozens of discovered gene-motif regulatory clusters are evidently functionally coregulated.
AB - Deciphering cis-regulatory networks has become an attractive yet challenging task. This paper presents a simple model for cis-regulatory network discovery which aims to avoid most of the common problems of previous approaches. Using promoter sequences and gene co-expression profiles as input, rather than clustering the genes by the co-expression data, it includes neighborhood co-expression information for each individual gene from the co-expression data, thereby overcoming the disadvantages of current clustering based models which miss specific information for individual genes. Applications on Saccharomyces cerevisiae have shown a good prediction accuracy, which outperforms a phylogenetic footprinting approach. In addition, the top dozens of discovered gene-motif regulatory clusters are evidently functionally coregulated.
KW - Cis-regulatory element discovery
KW - Gene co-expression networks
KW - Promoter sequences
UR - http://www.scopus.com/inward/record.url?scp=84871640207&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84871640207&partnerID=8YFLogxK
U2 - 10.1145/2401603.2401620
DO - 10.1145/2401603.2401620
M3 - Conference contribution
AN - SCOPUS:84871640207
SN - 9781450314923
T3 - Proceeding of the 2012 ACM Research in Applied Computation Symposium, RACS 2012
SP - 74
EP - 75
BT - Proceeding of the 2012 ACM Research in Applied Computation Symposium, RACS 2012
T2 - 2012 ACM Research in Applied Computation Symposium, RACS 2012
Y2 - 23 October 2012 through 26 October 2012
ER -