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Genome-wide prediction of transcription factor binding sites using an integrated model

Kyoung-Jae Won1, Bing Ren2 and Wei Wang1*

Author Affiliations

1 University of California, San Diego, Department of Chemistry and Biochemistry, 9500 Gilman Drive, La Jolla CA 92093, USA

2 Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA

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Genome Biology 2010, 11:R7  doi:10.1186/gb-2010-11-1-r7

Published: 22 January 2010


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.