TY - JOUR
T1 - Constructing human transcriptional regulatory subnets from crossgenome comparison and gene expression profile analysis
AU - Karmaker, Amitava
AU - Harris, Stephen E.
AU - Kwek, Stephen
PY - 2007/12/1
Y1 - 2007/12/1
N2 - With the completion of Human Genome Project (HGP), understanding the complex interaction between trans- and cis-regulatory elements comprehensively and identifying these potential functional elements are fundamental problems in functional genomics. Although many computational approaches have been developed for lower eukaryotes and prokaryotes, most of them often do not generalize to vertebrates. Here, we use a decay function to characterize transcriptional behavior, and analyze correlations on gene expression profiles of human and mouse to construct coregulated gene groups. Using these two closely related species, we perform comparative genome analysis and identify target genes and conserved functional cis-regulatory elements by motif overrepresentation. Moreover, we presented experimental evidences (ChIP-Chip) for E2F to assert our findings.
AB - With the completion of Human Genome Project (HGP), understanding the complex interaction between trans- and cis-regulatory elements comprehensively and identifying these potential functional elements are fundamental problems in functional genomics. Although many computational approaches have been developed for lower eukaryotes and prokaryotes, most of them often do not generalize to vertebrates. Here, we use a decay function to characterize transcriptional behavior, and analyze correlations on gene expression profiles of human and mouse to construct coregulated gene groups. Using these two closely related species, we perform comparative genome analysis and identify target genes and conserved functional cis-regulatory elements by motif overrepresentation. Moreover, we presented experimental evidences (ChIP-Chip) for E2F to assert our findings.
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U2 - 10.1089/omi.2007.0028
DO - 10.1089/omi.2007.0028
M3 - Article
C2 - 18092911
AN - SCOPUS:37349107832
SN - 1536-2310
VL - 11
SP - 397
EP - 412
JO - OMICS A Journal of Integrative Biology
JF - OMICS A Journal of Integrative Biology
IS - 4
ER -