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Nucleic Acids Res. 2018 Jan 4;46(D1):D260-D266. doi: 10.1093/nar/gkx1126.

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

Author information

1
Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.
2
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.
3
University of Grenoble Alpes, CNRS, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
4
INSERM, UMR1090 TAGC, Marseille, F-13288, France.
5
Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France.
6
Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium.
7
VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium.
8
Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Ghent, Belgium.
9
Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK.
10
Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, UK.
11
The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, DK2200 Copenhagen N, Denmark.
12
Sars International Centre for Marine Molecular Biology, University of Bergen, N-5008 Bergen, Norway.
13
Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway.

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.

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