Show simple item record

dc.contributor.authorNg, Felicia SLen
dc.contributor.authorRuau, Daviden
dc.contributor.authorWernisch, Lorenzen
dc.contributor.authorGottgens, Bertholden
dc.date.accessioned2016-11-18T12:30:12Z
dc.date.available2016-11-18T12:30:12Z
dc.date.issued2016-10-25en
dc.identifier.issn1467-5463
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/261213
dc.description.abstractIntegrated analysis of multiple genome-wide transcription factor (TF)-binding profiles will be vital to advance our understanding of the global impact of TF binding. However, existing methods for measuring similarity in large numbers of chromatin immunoprecipitation assays with sequencing (ChIP-seq), such as correlation, mutual information or enrichment analysis, are limited in their ability to display functionally relevant TF relationships. In this study, we propose the use of graphical models to determine conditional independence between TFs and showed that network visualization provides a promising alternative to distinguish ‘direct’ versus ‘indirect’ TF interactions. We applied four algorithms to measure ‘direct’ dependence to a compendium of 367 mouse haematopoietic TF ChIP-seq samples and obtained a consensus network known as a ‘TF association network’ where edges in the network corresponded to likely causal pairwise relationships between TFs. The ‘TF association network’ illustrates the role of TFs in developmental pathways, is reminiscent of combinatorial TF regulation, corresponds to known protein–protein interactions and indicates substantial TF-binding reorganization in leukemic cell types. With the rapid increase in TF ChIP-Seq data sets, the approach presented here will be a powerful tool to study transcriptional programmes across a wide range of biological systems.
dc.description.sponsorshipBloodwise, the Biotechnology and Biological Sciences Research Council, the Leukaemia and Lymphoma Society, Cancer Research UK, the National Institute for Health Research Cambridge Biomedical Research Centre, and the Wellcome Trust and MRC Cambridge Institute for Medical Research and Wellcome Trust—Medical Research Council Cambridge Stem Cell Institute; Yousef Jameel scholarship awarded by the Cambridge Commonwealth, European and International Trust (to F.S.L.N.).
dc.languageEnglishen
dc.language.isoenen
dc.publisherOxford University Press
dc.rightsAttribution 4.0 International*
dc.rightsAttribution 4.0 Internationalen
dc.rightsAttribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectChIP-seqen
dc.subjectnetworken
dc.subjecttranscriptional regulationen
dc.subjecthaematopoiesisen
dc.titleA graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profilesen
dc.typeArticle
dc.description.versionThis is the final version of the article. It first appeared from Oxford University Press via https://doi.org/10.1093/bib/bbw102en
prism.publicationDate2016en
prism.publicationNameBriefings in Bioinformaticsen
dc.identifier.doi10.17863/CAM.6384
dcterms.dateAccepted2016-09-21en
rioxxterms.versionofrecord10.1093/bib/bbw102en
rioxxterms.versionVoRen
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/en
rioxxterms.licenseref.startdate2016-10-25en
dc.contributor.orcidGottgens, Berthold [0000-0001-6302-5705]
dc.identifier.eissn1477-4054
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idLeukaemia & Lymphoma Research (12029)
pubs.funder-project-idBBSRC (BB/I00050X/1)
pubs.funder-project-idCancer Research UK (12765)
pubs.funder-project-idWellcome Trust (097922/Z/11/Z)
pubs.funder-project-idMRC (MC_PC_12009)
cam.orpheus.successThu Jan 30 12:56:59 GMT 2020 - The item has an open VoR version.*
rioxxterms.freetoread.startdate2100-01-01


Files in this item

Thumbnail
Thumbnail
Thumbnail

This item appears in the following Collection(s)

Show simple item record

Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International