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

Using CisGenome to analyze ChIP-chip and ChIP-seq data. Curr Protoc Bioinformatics. 2011 Mar;Chapter 2:Unit2.13 Authors: Ji H, Jiang H, Ma W, Wong WH 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 [PubMed - indexed for MEDLINE]
Source: Current Protocols in Bioinformatics - Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research