Integrative analysis of ChIP-chip and ChIP-seq dataset

Methods in Molecular Biology
Lihua J Zhu

Abstract

Epigenetic regulation and interactions between transcription factors and regulatory genomic regions play crucial roles in controlling transcriptional regulatory networks that drive development, environmental responses, and disease. Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) and ChIP followed by genomic tiling microarray hybridization (ChIP-chip) are the two of the most widely used technologies for genome-wide identification of DNA protein interactions and histone modification in vivo. Many algorithms and tools have been developed and evaluated that allow identification of transcription factor binding sites from ChIP-seq or ChIP-chip datasets. However, binding site identification is only the first step; the ultimate goal is to discover the regulatory network of the transcription factor (TF). Here, we present a common workflow for downstream analysis of ChIP-chip and ChIP-seq with an emphasis on annotating binding sites and integration with gene expression data to identify direct and indirect targets of the TF. These tools will help with the overall goal of unraveling transcriptional regulatory networks using datasets publicly available in GEO.

Citations

Mar 3, 2018·Applied Microbiology and Biotechnology·Nan XuLiming Liu
Mar 27, 2018·Yeast·David SegorbeGregor D Gilfillan
Jan 1, 2019·Nucleic Acids Research·Katelyn E ConnellyEmily C Dykhuizen
Jun 16, 2019·Genome Research·Anastassiia VertiiPaul D Kaufman
Oct 20, 2015·Nature Methods·Mehmet Fatih BolukbasiScot A Wolfe
Jan 10, 2020·The Journal of Experimental Biology·Alice E Harada, Ronald S Burton
Apr 16, 2020·Circulation Research·Ozanna Burnicka-TurekIvan P Moskowitz
Mar 29, 2020·Chromosoma·Aizhan BizhanovaPaul D Kaufman
Oct 17, 2019·Life Science Alliance·Antonio VitobelloRémi Terranova
Nov 13, 2020·Blood Cancer Discovery·Juliette RoelsPieter Van Vlierberghe
Feb 24, 2021·ELife·Feng WangIngolf Bach
Dec 5, 2019·Cell Reports·Huapeng LiJunhao Mao

Related Concepts

Plasma Protein Binding Capacity
Computer Programs and Programming
Transcription Factor
Cdna Microarrays
Genomics
Chromatin Immunoprecipitation
Gene Modules
High-Throughput Nucleotide Sequencing
Environment
Gene Expression

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