<?xml version="1.0" encoding="utf-8"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:hal="http://hal.archives-ouvertes.fr/" xmlns:gml="http://www.opengis.net/gml/3.3/" xmlns:gmlce="http://www.opengis.net/gml/3.3/ce" version="1.1" xsi:schemaLocation="http://www.tei-c.org/ns/1.0 http://api.archives-ouvertes.fr/documents/aofr-sword.xsd">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title>HAL TEI export of hal-01821485</title>
      </titleStmt>
      <publicationStmt>
        <distributor>CCSD</distributor>
        <availability status="restricted">
          <licence target="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 - Universal</licence>
        </availability>
        <date when="2026-05-17T07:49:30+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Modeling transcription factor combinatorics in promoters and enhancers</title>
            <author role="aut">
              <persName>
                <forename type="first">Jimmy</forename>
                <surname>Vandel</surname>
              </persName>
              <idno type="halauthorid">823006-0</idno>
              <affiliation ref="#struct-388224"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Océane</forename>
                <surname>Cassan</surname>
              </persName>
              <email type="md5">ead8108282b45a582be0e3903f2e48d9</email>
              <email type="domain">cnrs.fr</email>
              <idno type="idhal" notation="numeric">791917</idno>
              <idno type="halauthorid" notation="string">1385976-791917</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-4595-2457</idno>
              <idno type="IDREF">https://www.idref.fr/269814299</idno>
              <affiliation ref="#struct-388224"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Sophie</forename>
                <surname>Lèbre</surname>
              </persName>
              <email type="md5">cb63ea2df4174c6b2437b1964b7a04d8</email>
              <email type="domain">umontpellier.fr</email>
              <idno type="idhal" notation="string">sophie-lebre</idno>
              <idno type="idhal" notation="numeric">176564</idno>
              <idno type="halauthorid" notation="string">32112-176564</idno>
              <idno type="ORCID">https://orcid.org/0000-0003-3444-2416</idno>
              <affiliation ref="#struct-424479"/>
              <affiliation ref="#struct-410122"/>
              <affiliation ref="#struct-42812"/>
              <affiliation ref="#struct-441569"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Charles-Henri</forename>
                <surname>Lecellier</surname>
              </persName>
              <email type="md5">6d61db88b894ee1f3a830eff195dc40b</email>
              <email type="domain">igmm.cnrs.fr</email>
              <idno type="idhal" notation="string">charles-henri-lecellier</idno>
              <idno type="idhal" notation="numeric">858643</idno>
              <idno type="halauthorid" notation="string">382339-858643</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-0229-5434</idno>
              <affiliation ref="#struct-712"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Laurent</forename>
                <surname>Brehelin</surname>
              </persName>
              <email type="md5">827a9b207531918060b05b33f4e1ad0e</email>
              <email type="domain">lirmm.fr</email>
              <idno type="idhal" notation="string">laurent-brehelin</idno>
              <idno type="idhal" notation="numeric">21572</idno>
              <idno type="halauthorid" notation="string">17654-21572</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-2582-2831</idno>
              <idno type="IDREF">https://www.idref.fr/068625626</idno>
              <affiliation ref="#struct-388224"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Sophie</forename>
                <surname>Lèbre</surname>
              </persName>
              <email type="md5">cb63ea2df4174c6b2437b1964b7a04d8</email>
              <email type="domain">umontpellier.fr</email>
            </editor>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2018-06-22 14:55:00</date>
              <date type="whenModified">2025-01-08 15:28:03</date>
              <date type="whenReleased">2018-07-02 16:33:03</date>
              <date type="whenProduced">2018-06-22</date>
              <date type="whenEndEmbargoed">2018-06-22</date>
              <ref type="file" target="https://hal.science/hal-01821485v1/document">
                <date notBefore="2018-06-22"/>
              </ref>
              <ref type="file" subtype="author" n="1" target="https://hal.science/hal-01821485v1/file/Modeling%20transcription%20factor%20combinatorics%20in%20promoters%20and%20enhancers.pdf" id="file-1821485-1848955">
                <date notBefore="2018-06-22"/>
              </ref>
              <ref type="externalLink" target="https://www.biorxiv.org/content/biorxiv/early/2018/03/02/197418.full.pdf"/>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="546882">
                <persName>
                  <forename>Sophie</forename>
                  <surname>Lèbre</surname>
                </persName>
                <email type="md5">cb63ea2df4174c6b2437b1964b7a04d8</email>
                <email type="domain">umontpellier.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-01821485</idno>
            <idno type="halUri">https://hal.science/hal-01821485</idno>
            <idno type="halBibtex">vandel:hal-01821485</idno>
            <idno type="halRefHtml">2018</idno>
            <idno type="halRef">2018</idno>
            <availability status="restricted">
              <licence target="https://about.hal.science/hal-authorisation-v1/">HAL Authorization<ref corresp="#file-1821485-1848955"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="UNIV-MONTP3">Université de Montpellier Paul-Valéry</idno>
            <idno type="stamp" n="I3M_UMR5149">Institut de Mathématiques et de Modélisation de Montpellier</idno>
            <idno type="stamp" n="IGMM">Institut de génétique moléculaire de Montpellier</idno>
            <idno type="stamp" n="INSMI">CNRS-INSMI - INstitut des Sciences Mathématiques et de leurs Interactions</idno>
            <idno type="stamp" n="MAB" corresp="LIRMM">Méthodes et Algorithmes pour la Bioinformatique</idno>
            <idno type="stamp" n="LIRMM">Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier</idno>
            <idno type="stamp" n="IMAG-MONTPELLIER">Institut Montpelliérain Alexander Grothendieck</idno>
            <idno type="stamp" n="MIPS">Mathématiques, Informatique, Physique et Systèmes</idno>
            <idno type="stamp" n="BS">Biologie-Santé</idno>
            <idno type="stamp" n="UNIV-MONTPELLIER">Université de Montpellier</idno>
            <idno type="stamp" n="UPVM-TI" corresp="UNIV-MONTP3">Publications UPVM texte intégral</idno>
            <idno type="stamp" n="UM-2015-2021" corresp="UNIV-MONTPELLIER">Université de Montpellier (2015-2021)</idno>
            <idno type="stamp" n="AMIS">AMIS</idno>
          </seriesStmt>
          <notesStmt/>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">Modeling transcription factor combinatorics in promoters and enhancers</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Jimmy</forename>
                    <surname>Vandel</surname>
                  </persName>
                  <idno type="halauthorid">823006-0</idno>
                  <affiliation ref="#struct-388224"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Océane</forename>
                    <surname>Cassan</surname>
                  </persName>
                  <email type="md5">ead8108282b45a582be0e3903f2e48d9</email>
                  <email type="domain">cnrs.fr</email>
                  <idno type="idhal" notation="numeric">791917</idno>
                  <idno type="halauthorid" notation="string">1385976-791917</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-4595-2457</idno>
                  <idno type="IDREF">https://www.idref.fr/269814299</idno>
                  <affiliation ref="#struct-388224"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Sophie</forename>
                    <surname>Lèbre</surname>
                  </persName>
                  <email type="md5">cb63ea2df4174c6b2437b1964b7a04d8</email>
                  <email type="domain">umontpellier.fr</email>
                  <idno type="idhal" notation="string">sophie-lebre</idno>
                  <idno type="idhal" notation="numeric">176564</idno>
                  <idno type="halauthorid" notation="string">32112-176564</idno>
                  <idno type="ORCID">https://orcid.org/0000-0003-3444-2416</idno>
                  <affiliation ref="#struct-424479"/>
                  <affiliation ref="#struct-410122"/>
                  <affiliation ref="#struct-42812"/>
                  <affiliation ref="#struct-441569"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Charles-Henri</forename>
                    <surname>Lecellier</surname>
                  </persName>
                  <email type="md5">6d61db88b894ee1f3a830eff195dc40b</email>
                  <email type="domain">igmm.cnrs.fr</email>
                  <idno type="idhal" notation="string">charles-henri-lecellier</idno>
                  <idno type="idhal" notation="numeric">858643</idno>
                  <idno type="halauthorid" notation="string">382339-858643</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-0229-5434</idno>
                  <affiliation ref="#struct-712"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Laurent</forename>
                    <surname>Brehelin</surname>
                  </persName>
                  <email type="md5">827a9b207531918060b05b33f4e1ad0e</email>
                  <email type="domain">lirmm.fr</email>
                  <idno type="idhal" notation="string">laurent-brehelin</idno>
                  <idno type="idhal" notation="numeric">21572</idno>
                  <idno type="halauthorid" notation="string">17654-21572</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-2582-2831</idno>
                  <idno type="IDREF">https://www.idref.fr/068625626</idno>
                  <affiliation ref="#struct-388224"/>
                </author>
              </analytic>
              <monogr>
                <imprint/>
              </monogr>
              <idno type="doi">10.1101/197418</idno>
              <relatedItem target="https://hal.science/hal-02070201v1" type="IsDescribedBy" subtype="http://purl.org/coar/resource_type/c_6501"/>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <classCode scheme="halDomain" n="stat.ap">Statistics [stat]/Applications [stat.AP]</classCode>
              <classCode scheme="halDomain" n="sdv.bbm.gtp">Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]</classCode>
              <classCode scheme="halTypology" n="UNDEFINED">Preprints, Working Papers, ...</classCode>
              <classCode scheme="halOldTypology" n="UNDEFINED">Preprints, Working Papers, ...</classCode>
              <classCode scheme="halTreeTypology" n="UNDEFINED">Preprints, Working Papers, ...</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>We propose a new approach (TFcoop) that takes into account cooperation between transcription factors (TFs) for predicting TF binding sites. For a given a TF, TFcoop bases its prediction upon the binding affinity of the target TF as well as any other TF identified as cooperating with this TF. The set of cooperating TFs and the model parameters are learned from ChIP-seq data of the target TF. We used TFcoop to investigate the TF combinations involved in the binding of 106 different TFs on 41 different cell types and in four different regulatory regions: promoters of mRNAs, lncRNAs and pri-miRNAs, and enhancers. Our experiments show that the approach is accurate and outperforms simple PWM methods. Moreover, analysis of the learned models sheds light on important properties of TF combinations. First, for a given TF and region, we show that TF combinations governing the binding of the target TF are similar for the different cell-types. Second, for a given TF, we observe that TF combinations are different between promoters and enhancers, but similar for promoters of distinct gene classes (mRNAs, lncRNAs and miRNAs). Analysis of the TFs cooperating with the different targets show over-representation of pioneer TFs and a clear preference for TFs with binding motif composition similar to that of the target. Lastly, our models accurately distinguish promoters into classes associated with specific biological processes.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="researchteam" xml:id="struct-388224" status="OLD">
          <orgName>Méthodes et Algorithmes pour la Bioinformatique</orgName>
          <orgName type="acronym">MAB</orgName>
          <date type="end">2021-12-31</date>
          <desc>
            <address>
              <addrLine>LIRMM, 161 rue Ada, 34000 Montpellier</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.lirmm.fr/equipes/MAB/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-181" type="direct"/>
            <relation name="UMR5506" active="#struct-410122" type="indirect"/>
            <relation name="UMR5506" active="#struct-441569" type="indirect"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-424479" status="OLD">
          <idno type="ISNI">0000000404890602</idno>
          <idno type="RNSR">200311827X</idno>
          <idno type="ROR">https://ror.org/044kxby82</idno>
          <orgName>Institut Montpelliérain Alexander Grothendieck</orgName>
          <orgName type="acronym">IMAG</orgName>
          <date type="start">2015-01-01</date>
          <date type="end">2021-12-31</date>
          <desc>
            <address>
              <addrLine>UMR CNRS 5149 - Université Montpellier 2, Case courrier 051, 34095 Montpellier cedex 5 - France</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://imag.umontpellier.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-410122" type="direct"/>
            <relation name="UMR5149" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-410122" status="OLD">
          <idno type="ISNI">0000000120970141</idno>
          <idno type="ROR">https://ror.org/051escj72</idno>
          <orgName>Université de Montpellier</orgName>
          <orgName type="acronym">UM</orgName>
          <date type="end">2021-12-31</date>
          <desc>
            <address>
              <addrLine>163 rue Auguste Broussonnet - 34090 Montpellier</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.umontpellier.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-42812" status="OLD">
          <idno type="IdRef">026404702</idno>
          <idno type="ISNI">000000012196152X</idno>
          <idno type="ROR">https://ror.org/00qhdy563</idno>
          <orgName>Université Paul-Valéry - Montpellier 3</orgName>
          <orgName type="acronym">UPVM</orgName>
          <date type="start">1970-11-18</date>
          <date type="end">2024-12-31</date>
          <desc>
            <address>
              <addrLine>Université Paul Valéry Montpellier 3Route de Mende 34199 Montpellier Cedex 5</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-montp3.fr/</ref>
          </desc>
        </org>
        <org type="regroupinstitution" xml:id="struct-441569" status="VALID">
          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <idno type="ROR">https://ror.org/02feahw73</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cnrs.fr/</ref>
          </desc>
        </org>
        <org type="laboratory" xml:id="struct-712" status="OLD">
          <idno type="ISNI">0000000405990285</idno>
          <idno type="RNSR">199111979P</idno>
          <idno type="ROR">https://ror.org/02785qs39</idno>
          <orgName>Institut de Génétique Moléculaire de Montpellier</orgName>
          <orgName type="acronym">IGMM</orgName>
          <date type="start">1993-01-01</date>
          <date type="end">2021-12-31</date>
          <desc>
            <address>
              <addrLine>1919 Route de Mende - 34293 Montpellier Cedex 5</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.igmm.cnrs.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-410122" type="direct"/>
            <relation name="UMR5535 / UMR9942" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-181" status="OLD">
          <idno type="IdRef">139590827</idno>
          <idno type="ISNI">0000000405990488</idno>
          <idno type="RNSR">199111950H</idno>
          <idno type="ROR">https://ror.org/013yean28</idno>
          <orgName>Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier</orgName>
          <orgName type="acronym">LIRMM</orgName>
          <date type="start">1995-01-01</date>
          <date type="end">2021-12-31</date>
          <desc>
            <address>
              <addrLine>161 rue Ada - 34095 Montpellier</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.lirmm.fr</ref>
          </desc>
          <listRelation>
            <relation name="UMR5506" active="#struct-410122" type="direct"/>
            <relation name="UMR5506" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>