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Shin H, Liu T, Duan X, et al. Computational methodology for ChIP-seq analysis. Quant Biol. 2013;1(1):54-70doi: 10.1007/s40484-013-0006-2.
Shin, H., Liu, T., Duan, X., Zhang, Y., & Liu, X. S. (2013). Computational methodology for ChIP-seq analysis. Quantitative biology (Beijing, China), 1(1), 54-70. https://doi.org/10.1007/s40484-013-0006-2
Shin, Hyunjin, et al. "Computational methodology for ChIP-seq analysis." Quantitative biology (Beijing, China) vol. 1,1 (2013): 54-70. doi: https://doi.org/10.1007/s40484-013-0006-2
Shin H, Liu T, Duan X, Zhang Y, Liu XS. Computational methodology for ChIP-seq analysis. Quant Biol. 2013 Mar 01;1(1):54-70. doi: 10.1007/s40484-013-0006-2. PMID: 25741452; PMCID: PMC4346130.
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Quant Biol. 2013 Mar 01;1(1):54-70. doi: 10.1007/s40484-013-0006-2.

Computational methodology for ChIP-seq analysis.

Quantitative biology (Beijing, China)

Hyunjin Shin, Tao Liu, Xikun Duan, Yong Zhang, X Shirley Liu

Affiliations

  1. Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute/Harvard School of Public Health, Boston, MA 02115, USA.
  2. Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.

PMID: 25741452 PMCID: PMC4346130 DOI: 10.1007/s40484-013-0006-2

Abstract

Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is a powerful technology to identify the genome-wide locations of DNA binding proteins such as transcription factors or modified histones. As more and more experimental laboratories are adopting ChIP-seq to unravel the transcriptional and epigenetic regulatory mechanisms, computational analyses of ChIP-seq also become increasingly comprehensive and sophisticated. In this article, we review current computational methodology for ChIP-seq analysis, recommend useful algorithms and workflows, and introduce quality control measures at different analytical steps. We also discuss how ChIP-seq could be integrated with other types of genomic assays, such as gene expression profiling and genome-wide association studies, to provide a more comprehensive view of gene regulatory mechanisms in important physiological and pathological processes.

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