By the company they keep: interaction networks define the binding ability of transcription factors

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• dc.contributor.author Cirillo, Davideca
• dc.contributor.author Botta Orfila, Teresaca
• dc.contributor.author Tartaglia, Gian Gaetanoca
• dc.date.accessioned 2015-11-17T15:32:41Z
• dc.date.available 2015-11-17T15:32:41Z
• dc.date.issued 2015
• dc.description.abstract Access to genome-wide data provides the opportunity to address questions concerning the ability of transcription factors (TFs) to assemble in distinct macromolecular complexes. Here, we introduce the PAnDA (Protein And DNA Associations) approach to characterize DNA associations with human TFs using expression profiles, protein-protein interactions and recognition motifs. Our method predicts TF binding events with >0.80 accuracy revealing cell-specific regulatory patterns that can be exploited for future investigations. Even when the precise DNA-binding motifs of a specific TF are not available, the information derived from protein-protein networks is sufficient to perform high-confidence predictions (area under the ROC curve of 0.89). PAnDA is freely available at http://service.tartaglialab.com/new_submission/panda.en
• dc.description.sponsorship The research leading to these results has received funding from the European Research Council under the European/nUnion’s Seventh Framework Programme (FP7/2007-2013)/ ERC grant agreementRIBOMYLOME 309545; the Fundació La Marató de TV3 (20142731); and the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’ (SEV-2012-0208). Funding for Open Access charge: European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement RIBOMYLOME 309545 and Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’ (SEV-2012-0208).en
• dc.format.mimetype application/pdfca
• dc.identifier.citation Cirillo D, Botta-Orfila T, Tartaglia GG. By the company they keep: interaction networks define the binding ability of transcription factors. Nucleic Acids Res. 2015;43(19):e125. DOI: 10.1093/nar/gkv607en
• dc.identifier.doi http://dx.doi.org/10.1093/nar/gkv607
• dc.identifier.issn 0305-1048
• dc.identifier.uri http://hdl.handle.net/10230/25119
• dc.language.iso engca
• dc.publisher Oxford University Pressca
• dc.relation.ispartof Nucleic acids research. 2015;43(19):e125
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/309545
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/SEV2012-0208
• dc.rights © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.en
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/ca
• dc.subject.other ADN
• dc.subject.other Proteïnes
• dc.title By the company they keep: interaction networks define the binding ability of transcription factorsen
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca