1. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
- Author
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François Parcy, Chih-Yu Chen, David J. Arenillas, Wyeth W. Wasserman, Casper Shyr, Boris Lenhard, Rebecca Worsley-Hunt, Grégoire Denay, Albin Sandelin, Oriol Fornes, Ge Tan, Jessica J. Y. Lee, Wenqiang Shi, Anthony Mathelier, Allen W. Zhang, Department of Medical Genetics, Faculty of Medicine-Child and Family Research Institute-Centre for Molecular Medicine and Therapeutics-University of British Columbia (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), Computational Regulatory Genomics, Imperial College London, Biotech Research and Innovation Centre (BRIC), University of Copenhagen = Københavns Universitet (UCPH), Genome Canada Large Scaled Applied Research Grant [174CDE], Canadian Institute of Health Research (CIHR) Operating Grant [MOP-119586], Child and Family Research Institute (CFRI), British Columbia Children’s Hospital Foundation, University of British Columbia (UBC), Genome Sci-ence And Technology program NSERC-CREATE scholarship, University of Zurich, China Scholarship Council, UBC Teaching and Learning Enhancement fund, NSERC Discovery Grant [RGPIN 355532-10], Funding for open access charge: Genome Canada Large Scaled Applied ResearchGrant [174CDE], ANR-11-BSV2-0005,CHARMFUL,Caractérisation de la fonction méristématique de LEAFY(2011), European Project: 242048,EC:FP7:HEALTH,FP7-HEALTH-2009-two-stage,ZF-HEALTH(2010), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (KU), Wellcome Trust, and Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
- Subjects
0301 basic medicine ,Transcription Factor ,Nematodes ,05 Environmental Sciences ,champignon ,Biology ,computer.software_genre ,Bioconductor ,Database ,03 medical and health sciences ,Protein sequencing ,Open Acces ,Databases, Genetic ,Genetics ,Database Issue ,Animals ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Regulatory Elements, Transcriptional ,Binding site ,Transcription factor ,nématode ,base de données ,08 Information And Computing Sciences ,Binding Sites ,Fungi ,insecta ,Structural classification ,DNA-binding domain ,06 Biological Sciences ,Plants ,Multiple species ,transcription factor ,database ,open acces ,vertebrate ,nematode ,plant ,fungi ,insect ,Protein Structure, Tertiary ,DNA-Binding Proteins ,Insects ,030104 developmental biology ,Vertebrates ,plante ,TF binding ,computer ,facteur de transcription ,Software ,Transcription Factors ,Developmental Biology - Abstract
International audience; JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release.
- Published
- 2016