Open AccessComputational methodology for ChIP‐seq analysis
Author(s) -
Shin Hyunjin,
Liu Tao,
Duan Xikun,
Zhang Yong,
Liu X. Shirley
Publication year - 2013
Publication title -
quantitative biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.707
H-Index - 15
eISSN - 2095-4697
pISSN - 2095-4689
DOI - 10.1007/s40484-013-0006-2
Subject(s) - chromatin immunoprecipitation , computational biology , epigenetics , histone , computer science , profiling (computer programming) , biology , workflow , genome , gene , gene expression , genetics , promoter , database , operating system
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.