JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
2018
Khan, Aziz | Fornés, Oriol | Stigliani, Arnaud | Gheorghe, Marius | Castro-Mondragon, Jaime A. | Van der lee, Robin | Bessy, Adrien | Chèneby, Jeanne | Kulkarni, Shubhada R. | Tan, Ge | Baranasic, Damir | Arenillas, David J. | Sandelin, Albin | Vandepoele, Klaas | Lenhard, Boris | Ballester, Benoit | Wasserman, Wyeth W. | Parcy, François | Mathelier, Anthony | Centre for Molecular Medicine Norway (NCMM) ; Faculty of Medicine [Oslo] ; University of Oslo (UiO)-University of Oslo (UiO)-Rigshospitalet [Copenhagen, Denmark] ; Copenhagen University Hospital [Denmark] = Københavns Universitetshospital [Danmark] (KUH)-Copenhagen University Hospital [Denmark] = Københavns Universitetshospital [Danmark] (KUH) | Department of Medical Genetics ; Faculty of Medicine-Child and Family Research Institute-Centre for Molecular Medicine and Therapeutics-University of British Columbia [Canada] (UBC) | Physiologie cellulaire et végétale (LPCV) ; Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG) ; Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) | Theories and Approaches of Genomic Complexity (TAGC) ; Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM) | Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics ; Universiteit Gent = Ghent University = Université de Gand (UGENT) | Computational Regulatory Genomics ; Imperial College London | Imperial College London | Bioinformatics Centre ; Department of Biology [Copenhagen] ; Faculty of Science [Copenhagen] ; University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen] ; University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH) | Sars International Centre for Marine Molecular Biology ; University of Bergen (UiB) | Oslo University Hospital Radiumhospitalet | Genome Canada and Canadian Institutes of Health Research (On-Target Grants) [255ONT and BOP-149430] | Natural Sciences and Engineering Research Council of Canada (Discovery Grant) [RGPIN-2017–06824] | Independent Research Fund Denmark | Innovation Fund Denmark | Elixir Denmark | Wellcome Trust [106954] | Biotechnology and Biological Sciences Research Council [BB/N023358/1] | Medical Research Council UK [MC UP 1102/1] | Weston Brain Institute: [20R74681] | Research Foundation Flanders Grant [G001015N] | Lundbeck Foundation | ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010)
International audience
Show more [+] Less [-]English. JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six tax-onomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition , we have introduced 316 TFFMs (95 for vertebrates , 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally , this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package .
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Bibliographic information
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