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Curr Protoc Bioinformatics. 2011 Mar;Chapter 2:Unit2.13. doi: 10.1002/0471250953.bi0213s33.

Using CisGenome to analyze ChIP-chip and ChIP-seq data.

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1
The Johns Hopkins University, Baltimore, Maryland, USA.

Abstract

Chromatin immunoprecipitation (ChIP) coupled with genome tiling array hybridization (ChIP-chip) and ChIP followed by massively parallel sequencing (ChIP-seq) are high-throughput approaches to profiling genome-wide protein-DNA interactions. Both technologies are increasingly used to study transcription-factor binding sites and chromatin modifications. CisGenome is an integrated software system for analyzing ChIP-chip and ChIP-seq data. This unit describes basic functions of CisGenome and how to use them to find genomic regions with protein-DNA interactions, visualize binding signals, associate binding regions with nearby genes, search for novel transcription-factor binding motifs, and map existing DNA sequence motifs to user-supplied genomic regions to define their exact locations.

PMID:
21400695
PMCID:
PMC3072298
DOI:
10.1002/0471250953.bi0213s33
[Indexed for MEDLINE]
Free PMC Article
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