dc.date.accessioned | 2019-12-09T20:21:03Z | |
dc.date.available | 2019-12-09T20:21:03Z | |
dc.date.created | 2019-01-21T10:53:15Z | |
dc.date.issued | 2018 | |
dc.identifier.citation | Gheorghe, Marius Sandve, Geir Kjetil Khan, Aziz Cheneby, Jeanne Ballester, Benoit Mathelier, Anthony . A map of direct TF–DNA interactions in the human genome. Nucleic Acids Research. 2018 | |
dc.identifier.uri | http://hdl.handle.net/10852/71478 | |
dc.description.abstract | Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most popular assay to identify genomic regions, called ChIP-seq peaks, that are bound in vivo by transcription factors (TFs). These regions are derived from direct TF–DNA interactions, indirect binding of the TF to the DNA (through a co-binding partner), nonspecific binding to the DNA, and noise/bias/artifacts. Delineating the bona fide direct TF–DNA interactions within the ChIP-seq peaks remains challenging. We developed a dedicated software, ChIP-eat, that combines computational TF binding models and ChIP-seq peaks to automatically predict direct TF–DNA interactions. Our work culminated with predicted interactions covering >2% of the human genome, obtained by uniformly processing 1983 ChIP-seq peak data sets from the ReMap database for 232 unique TFs. The predictions were a posteriori assessed using protein binding microarray and ChIP-exo data, and were predominantly found in high quality ChIP-seq peaks. The set of predicted direct TF–DNA interactions suggested that high-occupancy target regions are likely not derived from direct binding of the TFs to the DNA. Our predictions derived co-binding TFs supported by protein-protein interaction data and defined cis-regulatory modules enriched for disease- and trait-associated SNPs. We provide this collection of direct TF–DNA interactions and cis-regulatory modules through the UniBind web-interface (http://unibind.uio.no). | en_US |
dc.language | EN | |
dc.publisher | Oxford University Press | |
dc.relation.ispartof | Gheorghe, Marius (2020) Integrative approaches to study TF-DNA interactions. Doctoral thesis http://hdl.handle.net/10852/75931 | |
dc.relation.uri | http://hdl.handle.net/10852/75931 | |
dc.rights | Attribution-NonCommercial 4.0 International | |
dc.rights.uri | https://creativecommons.org/licenses/by-nc/4.0/ | |
dc.title | A map of direct TF–DNA interactions in the human genome | en_US |
dc.type | Journal article | en_US |
dc.creator.author | Gheorghe, Marius | |
dc.creator.author | Sandve, Geir Kjetil | |
dc.creator.author | Khan, Aziz | |
dc.creator.author | Cheneby, Jeanne | |
dc.creator.author | Ballester, Benoit | |
dc.creator.author | Mathelier, Anthony | |
cristin.unitcode | 185,57,12,0 | |
cristin.unitname | Anthony Mathelier Group - Computational Biology & Gene Regulation | |
cristin.ispublished | true | |
cristin.fulltext | original | |
cristin.qualitycode | 2 | |
dc.identifier.cristin | 1662020 | |
dc.identifier.bibliographiccitation | info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Nucleic Acids Research&rft.volume=&rft.spage=&rft.date=2018 | |
dc.identifier.jtitle | Nucleic Acids Research | |
dc.identifier.pagecount | 13 | |
dc.identifier.doi | https://doi.org/10.1093/nar/gky1210 | |
dc.identifier.urn | URN:NBN:no-74545 | |
dc.type.document | Tidsskriftartikkel | en_US |
dc.type.peerreviewed | Peer reviewed | |
dc.source.issn | 0305-1048 | |
dc.identifier.fulltext | Fulltext https://www.duo.uio.no/bitstream/handle/10852/71478/1/Gheorghe%2Bet%2Bal.%2B-%2BA%2Bmap%2Bof%2Bdirect%2BTF%25E2%2580%2593DNA%2Binteractions%2Bin%2Bthe%2Bhuman%2Bg.pdf | |
dc.type.version | PublishedVersion | |
dc.relation.project | NFR/187615 | |