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Nat Protoc. 2013 Dec;8(12):2502-15. doi: 10.1038/nprot.2013.150. Epub 2013 Nov 21.

Target analysis by integration of transcriptome and ChIP-seq data with BETA.

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1
Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China.

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/.

PMID:
24263090
PMCID:
PMC4135175
DOI:
10.1038/nprot.2013.150
[Indexed for MEDLINE]
Free PMC Article
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