title: An integrated software system for analyzing ChIP-chip and ChIP-seq data.
abstract: We present CisGenome, a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data. CisGenome is designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis. In addition to implementing previously published ChIP-microarray (ChIP-chip) analysis methods, the software contains statistical methods designed specifically for ChlP sequencing (ChIP-seq) data obtained by coupling ChIP with massively parallel sequencing. The modular design of CisGenome enables it to support interactive analyses through a graphic user interface as well as customized batch-mode computation for advanced data mining. A built-in browser allows visualization of array images, signals, gene structure, conservation, and DNA sequence and motif information. We demonstrate the use of these tools by a comparative analysis of ChIP-chip and ChIP-seq data for the transcription factor NRSF/REST, a study of ChIP-seq analysis with or without a negative control sample, and an analysis of a new motif in Nanog- and Sox2-binding regions.
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, 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: David S
authors.initials: DS
authors.lastname: Johnson
authors.forename: Richard M
authors.initials: RM
authors.lastname: Myers
authors.forename: Wing H
authors.initials: WH
authors.lastname: Wong
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D016678:Genome; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012097:Repressor Proteins / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000235:genetics; D014584:User-Computer Interface; D000099229:RE1-Silencing Transcription Factor
chemical_list: D012097:Repressor Proteins; D014157:Transcription Factors; D000099229:RE1-Silencing Transcription Factor