Genome-wide Prediction of Transcription Factor Binding Sites Using an Integrated Model

Genome Biol. 2010 Jan 22;11(1):R7. doi: 10.1186/gb-2010-11-1-r7.


We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Motifs
  • Animals
  • Binding Sites
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation
  • Computational Biology / methods
  • Embryonic Stem Cells / cytology
  • Enhancer Elements, Genetic
  • Genome*
  • Mice
  • Models, Genetic
  • Promoter Regions, Genetic
  • RNA Interference
  • ROC Curve
  • Transcription Factors / genetics*


  • Chromatin
  • Transcription Factors