title: Using CisGenome to analyze ChIP-chip and ChIP-seq data.
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.
authors.affiliation: The Johns Hopkins University, Baltimore, Maryland, USA.
authors.forename: Hongkai
authors.initials: H
authors.lastname: Ji
authors.forename: Hui
authors.initials: H
authors.lastname: Jiang
authors.forename: Wenxiu
authors.initials: W
authors.lastname: Ma
authors.forename: Wing Hung
authors.initials: WH
authors.lastname: Wong
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D016678:Genome; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software