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

TY - JOUR

T1 - Genome-wide prediction of transcription factor binding sites using an integrated model

AU - Won, Kyoung-Jae

AU - Ren, Bing

AU - Wang, Wei

PY - 2010/1/22

Y1 - 2010/1/22

N2 - 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 a 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 (RNAi knockdown) experiments.

AB - 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 a 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 (RNAi knockdown) experiments.

KW - Amino Acid Motifs

KW - Animals

KW - Binding Sites

KW - Chromatin/metabolism

KW - Chromatin Immunoprecipitation

KW - Computational Biology/methods

KW - Embryonic Stem Cells/cytology

KW - Enhancer Elements, Genetic

KW - Genome

KW - Mice

KW - Models, Genetic

KW - Promoter Regions, Genetic

KW - RNA Interference

KW - ROC Curve

KW - Transcription Factors/genetics

U2 - 10.1186/gb-2010-11-1-r7

DO - 10.1186/gb-2010-11-1-r7

M3 - Journal article

C2 - 20096096

SN - 1474-7596

VL - 11

SP - R7

JO - Genome Biology (Online Edition)

JF - Genome Biology (Online Edition)

IS - 1

ER -