Integrative Analysis of ChIP-Chip and ChIP-Seq Dataset

UMMS Affiliation

Program in Gene Function and Expression

Publication Date


Document Type

Book Chapter


Genetics and Genomics | Molecular Biology


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.

DOI of Published Version



Methods Mol Biol. 2013;1067:105-24. doi: 10.1007/978-1-62703-607-8_8. Link to article on publisher's site

Journal/Book/Conference Title

Methods in molecular biology (Clifton, N.J.)

Related Resources

Link to Article in PubMed

PubMed ID