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 Protocjournal_title
Nature protocolsauthors
Wang S,Sun H,Ma J,Zang C,Wang C,Wang J,Tang Q,Meyer CA,Zhang Y,Liu XSdoi
10.1038/nprot.2013.150subject
Has Abstractpub_date
2013-12-01 00:00:00pages
2502-15issue
12eissn
1754-2189issn
1750-2799pii
nprot.2013.150journal_volume
8pub_type
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