A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data

Desmond S. Lun, Ashley Sherrid, Brian Weiner, David R. Sherman, James E. Galagan

Research output: Contribution to journalArticlepeer-review

52 Scopus citations

Abstract

We present CSDeconv, a computational method that determines locations of transcription factor binding from ChIP-seq data. CSDeconv differs from prior methods in that it uses a blind deconvolution approach that allows closely-spaced binding sites to be called accurately. We apply CSDeconv to novel ChIP-seq data for DosR binding in Mycobacterium tuberculosis and to existing data for GABP in humans and show that it can discriminate binding sites separated by as few as 40 bp.

Original languageEnglish (US)
Article numberR142
JournalGenome biology
Volume10
Issue number12
DOIs
StatePublished - Dec 22 2009
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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