Identifying a transcription factor's regulatory targets from its binding targets

Fred Lai, Julie S. Chang, Wei Sheng Wu

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

ChIP-chip data, which shows binding of transcription factors (TFs) to promoter regions in vivo, are widely used by biologists to identify the regulatory targets of TFs. However, the binding of a TF to a gene does not necessarily imply regulation. Thus, it is important to develop computational methods which can extract a TF's regulatory targets from its binding targets. We developed a method, called REgulatory Targets Extraction Algorithm (RETEA), which uses partial correlation analysis on gene expression data to extract a TF's regulatory targets from its binding targets inferred from ChIP-chip data. We applied RETEA to yeast cell cycle microarray data and identified the plausible regulatory targets of eleven known cell cycle TFs. We validated our predictions by checking the enrichments for cell cycle-regulated genes, common cellular processes and common molecular functions. Finally, we showed that RETEA performs better than three published methods (MA-Network, TRIA and Garten et al's method).

Original languageEnglish
Pages (from-to)125-133
Number of pages9
JournalGene Regulation and Systems Biology
Volume2010
Issue number4
DOIs
Publication statusPublished - 2010 Dec 1

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Computer Science Applications

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