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/.

journal_name

Nat Protoc

journal_title

Nature protocols

authors

Wang S,Sun H,Ma J,Zang C,Wang C,Wang J,Tang Q,Meyer CA,Zhang Y,Liu XS

doi

10.1038/nprot.2013.150

subject

Has Abstract

pub_date

2013-12-01 00:00:00

pages

2502-15

issue

12

eissn

1754-2189

issn

1750-2799

pii

nprot.2013.150

journal_volume

8

pub_type

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