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

Nature Protocols volume 8, pages 2502–2515 (2013)Cite this article

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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/.

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Figure 1: BETA workflow.
Figure 2: BETA output of activating/repressive function prediction and motif analysis of AR.
Figure 3: Activating and repressive function prediction of Tet1 in mouse ES cells and ESR1 in MCF-7 cells.
Figure 4: Screenshots of summarized BETA-plus analysis of ESR1 motifs in html format.

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Gene Expression Omnibus

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Acknowledgements

This project was supported by the National Basic Research (973) Program of China (2010CB944904), the National Natural Science Foundation of China (31329003) and the US National Institutes of Health (HG4069 and U41 HG007000).

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Authors and Affiliations

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

    Su Wang, Hanfei Sun, Jian Ma, Chenfei Wang, Juan Wang, Qianzi Tang & Yong Zhang

  2. Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA

    Chongzhi Zang, Clifford A Meyer & X Shirley Liu

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Contributions

S.W., C.A.M., Q.T. and X.S.L. designed the method; S.W., H.S., J.M., C.W., C.Z., J.W. and X.S.L. implemented the algorithm; S.W. performed the data analysis; and S.W. and X.S.L. wrote the initial manuscript. All authors contributed to the discussion and writing of the final manuscript.

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Correspondence to Yong Zhang or X Shirley Liu.

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Wang, S., Sun, H., Ma, J. et al. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat Protoc 8, 2502–2515 (2013). https://doi.org/10.1038/nprot.2013.150

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