title: MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data.
abstract: The ChIP-chip and ChIP-seq techniques enable genome-wide mapping of in vivo protein-DNA interactions and chromatin states. The cross-platform and between-laboratory variation poses a challenge to the comparison and integration of results from different ChIP experiments. We describe a novel method, MM-ChIP, which integrates information from cross-platform and between-laboratory ChIP-chip or ChIP-seq datasets. It improves both the sensitivity and the specificity of detecting ChIP-enriched regions, and is a useful meta-analysis tool for driving discoveries from multiple data sources.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 44 Binney Street, Boston, MA 02115, USA.
authors.forename: Yiwen
authors.initials: Y
authors.lastname: Chen
authors.forename: Clifford A
authors.initials: CA
authors.lastname: Meyer
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Jun S
authors.initials: JS
authors.lastname: Liu
authors.forename: Xiaole Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D002843:Chromatin / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002874:Chromosome Mapping / Q000379:methods*; D004268:DNA-Binding Proteins / Q000032:analysis* / Q000235:genetics; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins