Quantitative Biology

, Volume 1, Issue 1, pp 54–70 | Cite as

Computational methodology for ChIP-seq analysis

  • Hyunjin Shin
  • Tao Liu
  • Xikun Duan
  • Yong Zhang
  • X. Shirley Liu
Review

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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Copyright information

© Higher Education Press and Springer-Verlag GmbH 2013

Authors and Affiliations

  • Hyunjin Shin
    • 1
  • Tao Liu
    • 1
  • Xikun Duan
    • 2
  • Yong Zhang
    • 2
  • X. Shirley Liu
    • 1
  1. 1.Department of Biostatistics and Computational BiologyDana-Farber Cancer Institute/Harvard School of Public HealthBostonUSA
  2. 2.Department of Bioinformatics, School of Life Science and TechnologyTongji UniversityShanghaiChina

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