Target analysis by integration of transcriptome and ChIP-seq data with BETA
Open accessAbstract
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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The combination of RNA-seq and transcription factor (TF) ChIP-seq data can be used to remove false positives in ChIP-seq analysis and to suggest the activating or repressive effect of a TF on its target genes.
“The combination of RNA-seq and transcription factor (TF) chromatin immunoprecipitation sequencing (ChIP-seq) data can be used to remove false positives in ChIP-seq analysis and to suggest the activating or repressive effect of a TF on its target genes.”
From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [146]
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Self-citation
- Authors
- Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., Tang, Q., Meyer, C. A., Zhang, Y., & Liu, X. S.
- Affiliations
- Tongji University (CN)
- Harvard University (US)
- Corresponding author
- Zhang, Yong
- Liu, X Shirley
- ORCID
- Venue
- Nature Protocols
- Published
- 2013-11-21
- Volume
- 8
- Issue
- 12
- Pages
- 2502-2515
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- PMC
- PMC4135175
- OpenAlex
- W2000672459
- Cited by
- 544
- References
- 42
- Citations by year
- 2026: 38 · 2025: 47 · 2024: 52 · 2023: 64 · 2022: 71 · 2021: 53 · 2020: 59 · 2019: 43 · 2018: 43 · 2017: 28 · 2016: 29 · 2015: 14 · 2014: 2
- FWCI
- 6.71
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Protocols (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Human Genome Research Institute (U41HG007000, HG4069, R01HG004069)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- transcription factor target genes, ChIP-seq, transcriptome, differential gene expression, gene expression regulation, transcription factor binding motifs, chromatin regulators, motif discovery, open source software
- MeSH terms
- Software, Gene Expression Profiling, Chromatin Immunoprecipitation, Transcriptome
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