title: ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.
abstract: A cell's epigenome arises from interactions among regulatory factors-transcription factors and histone modifications-co-localized at particular genomic regions. We developed a novel statistical method, ChromNet, to infer a network of these interactions, the chromatin network, by inferring conditional-dependence relationships among a large number of ChIP-seq data sets. We applied ChromNet to all available 1451 ChIP-seq data sets from the ENCODE Project, and showed that ChromNet revealed previously known physical interactions better than alternative approaches. We experimentally validated one of the previously unreported interactions, MYC-HCFC1. An interactive visualization tool is available at http://chromnet.cs.washington.edu.
authors.affiliation: Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
authors.forename: Scott M
authors.initials: SM
authors.lastname: Lundberg
authors.affiliation: Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.|Princess Margaret Cancer Centre, Toronto, ON, Canada.
authors.forename: William B
authors.initials: WB
authors.lastname: Tu
authors.affiliation: Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.|Princess Margaret Cancer Centre, Toronto, ON, Canada.
authors.forename: Brian
authors.initials: B
authors.lastname: Raught
authors.affiliation: Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.|Princess Margaret Cancer Centre, Toronto, ON, Canada.
authors.forename: Linda Z
authors.initials: LZ
authors.lastname: Penn
authors.affiliation: Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.|Princess Margaret Cancer Centre, Toronto, ON, Canada.|Department of Computer Science, University of Toronto, Toronto, ON, Canada.
authors.forename: Michael M
authors.initials: MM
authors.lastname: Hoffman
authors.affiliation: Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA. suinlee@uw.edu.|Department of Genome Sciences, University of Washington, Seattle, WA, USA. suinlee@uw.edu.
authors.forename: Su-In
authors.initials: SI
authors.lastname: Lee
mesh_terms: D002843:Chromatin / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D053263:Gene Regulatory Networks; D006657:Histones / Q000378:metabolism; D006801:Humans; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D006657:Histones; D014157:Transcription Factors