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PMID: 29140473 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

Nucleic acids research ·Vol. 46 ·No. D1 ·2018-00-04 ·Pages D260-D266

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A

Abstract

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 taxonomic 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.

MeSH Terms
Animals Binding Sites/genetics Databases, Genetic Genomics Humans Internet Plants/genetics,metabolism Position-Specific Scoring Matrices Protein Binding/genetics Transcription Factors/metabolism User-Computer Interface Vertebrates/genetics,metabolism
Chemicals
Transcription Factors
Authors & Affiliations
19 authors, click to expand affiliations / ORCID
Khan Aziz
Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.
Fornes Oriol
Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 28th Ave W, Vancouver, BC V5Z 4H4, Canada.
Stigliani Arnaud
University of Grenoble Alpes, CNRS, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
Gheorghe Marius
Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.
Castro-Mondragon Jaime A
Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.
van der Lee Robin
Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 28th Ave W, Vancouver, BC V5Z 4H4, Canada.
Bessy Adrien
University of Grenoble Alpes, CNRS, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
Chèneby Jeanne
INSERM, UMR1090 TAGC, Marseille, F-13288, France. | Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France.
Kulkarni Shubhada R
Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium. | VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium. | Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Ghent, Belgium.
Tan Ge
Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK. | Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, UK.
Baranasic Damir
Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK. | Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, UK.
Arenillas David J
Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 28th Ave W, Vancouver, BC V5Z 4H4, Canada.
Sandelin Albin
The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, DK2200 Copenhagen N, Denmark.
Vandepoele Klaas
Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium. | VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium. | Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Ghent, Belgium.
Lenhard Boris
Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK. | Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, UK. | Sars International Centre for Marine Molecular Biology, University of Bergen, N-5008 Bergen, Norway.
Ballester Benoît
INSERM, UMR1090 TAGC, Marseille, F-13288, France. | Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France.
Wasserman Wyeth W
Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 28th Ave W, Vancouver, BC V5Z 4H4, Canada.
Parcy François
University of Grenoble Alpes, CNRS, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
Mathelier Anthony
Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway. | Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway.
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkx1126
Published
2018-00-04
Pages
D260-D266
Language
English
Region
England
NLM ID
0411011
PMCID
PMC5753243
Grants
Medical Research Council · MC_EX_MR/S300007/1 · United Kingdom
Medical Research Council · MC_UP_1102/1 · United Kingdom
Wellcome Trust · United Kingdom
Biotechnology and Biological Sciences Research Council · United Kingdom
Corrections
ErratumIn
PMID: 29161433
External Links
PubMed source DOI: 10.1093/nar/gkx1126 PMC Full Text View journal details
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