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


: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


Nat Protoc


Nature protocols


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




Has Abstract


2013-12-01 00:00:00














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    更新日期:2007-01-01 00:00:00

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    authors: Graf M,Lihter M,Thakur M,Georgiou V,Topolancik J,Ilic BR,Liu K,Feng J,Astier Y,Radenovic A

    更新日期:2019-04-01 00:00:00

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    pub_type: 杂志文章


    authors: Villanueva J,Philip J,DeNoyer L,Tempst P

    更新日期:2007-01-01 00:00:00

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    pub_type: 杂志文章


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    更新日期:2018-12-01 00:00:00

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    更新日期:2020-12-01 00:00:00

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    pub_type: 杂志文章


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    更新日期:2008-01-01 00:00:00

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    pub_type: 杂志文章


    authors: Lin Z,Chiang NY,Chai N,Seshasayee D,Lee WP,Balazs M,Nakamura G,Swem LR

    更新日期:2014-07-01 00:00:00

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    pub_type: 杂志文章


    authors: O'Connor DT,Mahata SK,Mahata M,Jiang Q,Hook VY,Taupenot L

    更新日期:2007-01-01 00:00:00

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    journal_title:Nature protocols

    pub_type: 杂志文章


    authors: Fenech M

    更新日期:2007-01-01 00:00:00

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    journal_title:Nature protocols

    pub_type: 杂志文章


    authors: Bindels DS,Postma M,Haarbosch L,van Weeren L,Gadella TWJ Jr

    更新日期:2020-02-01 00:00:00

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    更新日期:2013-10-01 00:00:00

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    pub_type: 杂志文章


    authors: Ribelin TP,Aubé J

    更新日期:2008-01-01 00:00:00

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    abstract::This protocol is an extension to: Nat. Protoc. 6, 870-895 (2014); doi:10.1038/nprot.2011.328; published online 02 June 2011Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early- and late-replicating regions differ in terms of mutation rates, transcr...

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    authors: Marchal C,Sasaki T,Vera D,Wilson K,Sima J,Rivera-Mulia JC,Trevilla-García C,Nogues C,Nafie E,Gilbert DM

    更新日期:2018-05-01 00:00:00

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    更新日期:2014-01-01 00:00:00

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    pub_type: 杂志文章


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    更新日期:2011-06-01 00:00:00