Integrative Analysis of ChIP-Chip and ChIP-Seq Dataset
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.
Key wordsChIP-chip ChIP-seq Gene expression Regulatory network Microarray GO enrichment analysis Pathway analysis Integrated analysis Transcription factor Motif discovery
I would like to thank Dr. Michael Brodsky at Program in Gene Function and Expression in University of Massachusetts Medical School for his critical review of the manuscript and his excellent suggestions.
- 21.Ji H, Jiang H, Ma W, Wong WH (2011) Using CisGenome to analyze ChIP-chip and ChIP-seq data. Curr Protoc Bioinformatics Chapter 2:Unit2 13Google Scholar
- 38.Ihaka R, Gentlemen R (1996) R: a language for data analysis and graphics. J Comput Graph Stat 5:299–314Google Scholar