TY - GEN
T1 - Exploring transcriptional modules through integrative gene clustering guided by transcription factor binding information
AU - Gong, Ting
AU - Xuan, Jianhua
AU - Riggins, Rebecca B.
AU - Wang, Yue
AU - Hoffman, Eric P.
AU - Clarke, Robert
PY - 2008
Y1 - 2008
N2 - Cluster analysis aims to infer regulatory modules or biological functions by grouping the genes with similar patterns. However, clustering results often fail to show strong biological relevance to underlying transcriptional modules. In this paper, we present a computational approach, namely integrative gene clustering guided by motif information, to identify condition-specific transcriptional modules. Specifically, the proposed approach is designed to discover the co-regulated genes from co-expressed genes by integrating ChIP-on-chip binding site (or motif) information and gene expression data. A statistical significance analysis procedure is performed to associate a set of significant motifs with each co-expressed gene cluster. An information-theoretic technique based on the entropy of the motif information is further developed to select an optimal balance point between expression patterns and motif patterns. The experimental results from simulated Saccharomyces cerevisiae data demonstrated that our approach can successfully uncover specific biological processes that are evidently regulated by one or more transcription factors.
AB - Cluster analysis aims to infer regulatory modules or biological functions by grouping the genes with similar patterns. However, clustering results often fail to show strong biological relevance to underlying transcriptional modules. In this paper, we present a computational approach, namely integrative gene clustering guided by motif information, to identify condition-specific transcriptional modules. Specifically, the proposed approach is designed to discover the co-regulated genes from co-expressed genes by integrating ChIP-on-chip binding site (or motif) information and gene expression data. A statistical significance analysis procedure is performed to associate a set of significant motifs with each co-expressed gene cluster. An information-theoretic technique based on the entropy of the motif information is further developed to select an optimal balance point between expression patterns and motif patterns. The experimental results from simulated Saccharomyces cerevisiae data demonstrated that our approach can successfully uncover specific biological processes that are evidently regulated by one or more transcription factors.
KW - Binding motifs
KW - Gene clustering
KW - Gene regulatory networks
KW - Microarray data analysis
KW - Transcription modules
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M3 - Conference contribution
AN - SCOPUS:62649122975
SN - 1601320558
SN - 9781601320551
T3 - Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008
SP - 191
EP - 197
BT - Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008
T2 - 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008
Y2 - 14 July 2008 through 17 July 2008
ER -