A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors

Hongkai Ji, Steven A. Vokes, Wing H. Wong

Research output: Contribution to journalArticlepeer-review

Abstract

Genome-wide location analysis (ChIP-chip, ChIP-PET) is a powerful technique to study mammalian transcriptional regulation. In order to obtain a basic understanding of the location data generated for mammalian transcription factors and potential issues in their analysis, we conducted a comparative study of eight independent ChIP experiments involving six different transcription factors in human and mouse. Our cross-study comparisons, to the best of our knowledge the first to analyze multiple datasets, revealed the importance of carefully chosen genomic controls in the de novo identification of key transcription factor binding motifs, raised issues about the interpretation of ubiquitously occurring sequence motifs, and demonstrated the clustering tendency of protein-binding regions for certain transcription factors.

Original languageEnglish (US)
Article numbere146
JournalNucleic acids research
Volume34
Issue number21
DOIs
StatePublished - Dec 2006
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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