Work

Using CisGenome to Analyze ChIP‐chip and ChIP‐seq Data

Year: 2011

Type: article

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.

Source: Current Protocols in Bioinformatics

DOI: 10.1002/0471250953.bi0213s33

Authors: Hongkai Ji, Hui Jiang, Wenxiu Ma, Wing Hung Wong

Institutions: Johns Hopkins University, Stanford University

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Institutes of Health, National Human Genome Research Institute

Awards: Statistical Analysis of Exon Arrays, Overcoming bias and unwanted variability in next generation sequencing