title: Target analysis by integration of transcriptome and ChIP-seq data with BETA.
abstract: The combination of ChIP-seq and transcriptome analysis is a compelling approach to unravel the regulation of gene expression. Several recently published methods combine transcription factor (TF) binding and gene expression for target prediction, but few of them provide an efficient software package for the community. Binding and expression target analysis (BETA) is a software package that integrates ChIP-seq of TFs or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (i) to predict whether the factor has activating or repressive function; (ii) to infer the factor's target genes; and (iii) to identify the motif of the factor and its collaborators, which might modulate the factor's activating or repressive function. Here we describe the implementation and features of BETA to demonstrate its application to several data sets. BETA requires ~1 GB of RAM, and the procedure takes 20 min to complete. BETA is available open source at http://cistrome.org/BETA/.
authors.affiliation: Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China.
authors.forename: Su
authors.initials: S
authors.lastname: Wang
authors.forename: Hanfei
authors.initials: H
authors.lastname: Sun
authors.forename: Jian
authors.initials: J
authors.lastname: Ma
authors.forename: Chongzhi
authors.initials: C
authors.lastname: Zang
authors.forename: Chenfei
authors.initials: C
authors.lastname: Wang
authors.forename: Juan
authors.initials: J
authors.lastname: Wang
authors.forename: Qianzi
authors.initials: Q
authors.lastname: Tang
authors.forename: Clifford A
authors.initials: CA
authors.lastname: Meyer
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D012984:Software; D059467:Transcriptome