Constructing human transcriptional regulatory subnets from crossgenome comparison and gene expression profile analysis

Amitava Karmaker, Stephen E. Harris, Stephen Kwek

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Pages (from-to)397-412
Number of pages16
JournalOMICS A Journal of Integrative Biology
Volume11
Issue number4
DOIs
StatePublished - Dec 1 2007

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Genetics

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