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

ABSTRACT: 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.

SUBMITTER: Won KJ 

PROVIDER: S-EPMC2847719 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature

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

Won Kyoung-Jae KJ   Ren Bing B   Wang Wei W  

Genome biology 20100122 1

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-  ...[more]

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