Computational methodology for ChIP-seq analysis.
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.
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute/Harvard School of Public Health, Boston, MA 02115, USA.
Hyunjin
H
Shin
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute/Harvard School of Public Health, Boston, MA 02115, USA.
Tao
T
Liu
Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
Xikun
X
Duan
Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
Yong
Y
Zhang
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute/Harvard School of Public Health, Boston, MA 02115, USA.
X Shirley
XS
Liu