Affordable Access

deepdyve-link
Publisher Website

JASPAR 2020: update of the open-access database of transcription factor binding profiles

Authors
  • Fornes, Oriol1
  • Castro-Mondragon, Jaime A2
  • Khan, Aziz2
  • van der Lee, Robin1
  • Zhang, Xi1
  • Richmond, Phillip A1
  • Modi, Bhavi P1
  • Correard, Solenne1
  • Gheorghe, Marius2
  • Baranašić, Damir3, 4
  • Santana-Garcia, Walter5
  • Tan, Ge6
  • Chèneby, Jeanne7
  • Ballester, Benoit7
  • Parcy, François8
  • Sandelin, Albin9
  • Lenhard, Boris3, 4, 10
  • Wasserman, Wyeth W1
  • Mathelier, Anthony2, 11
  • 1 Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Canada , (Canada)
  • 2 Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Norway , (Norway)
  • 3 Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, UK , (United Kingdom)
  • 4 Computational Regulatory Genomics, MRC London Institute of Medical Sciences, UK , (United Kingdom)
  • 5 Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, France , (France)
  • 6 Functional Genomics Centre Zurich, ETH Zurich, Switzerland , (Switzerland)
  • 7 Aix Marseille Univ, INSERM, TAGC, France , (France)
  • 8 CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG-LPCV, France , (France)
  • 9 The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, Denmark , (Denmark)
  • 10 Sars International Centre for Marine Molecular Biology, University of Bergen, Norway , (Norway)
  • 11 Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway , (Norway)
Type
Published Article
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Publication Date
Nov 08, 2019
Volume
48
Issue
D1
Identifiers
DOI: 10.1093/nar/gkz1001
PMID: 31701148
PMCID: PMC7145627
Source
PubMed Central
License
Unknown

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) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). These new profiles represent an 18% expansion compared to the previous release. JASPAR 2020 comes with a novel collection of unvalidated TF-binding profiles for which our curators did not find orthogonal supporting evidence in the literature. This collection has a dedicated web form to engage the community in the curation of unvalidated TF-binding profiles. Moreover, we created a Q&A forum to ease the communication between the user community and JASPAR curators. Finally, we updated the genomic tracks, inference tool, and TF-binding profile similarity clusters. All the data is available through the JASPAR website, its associated RESTful API, and through the JASPAR2020 R/Bioconductor package.

Report this publication

Statistics

Seen <100 times