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Cited by 1,935Genomics and Chromatin DynamicsGenomics and Phylogenetic StudiesBioinformatics and Genomic Networks

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

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Castro-Mondragon, Jaime A, Riudavets-Puig, Rafael, Rauluseviciute, Ieva, Berhanu Lemma, Roza, Turchi, Laura, Blanc-Mathieu, Romain, Lucas, Jeremy, Boddie, Paul +15 more·2022·Nucleic Acids Research
DOI 10.1093/nar/gkab1113PMC PMC8728201
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Abstract

JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.

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  • R2[R4], R1R2R3[R4] and R1R2HS1[R4] donors were screened with Sasquatch and JASPAR to ensure no novel accessibility sites or motifs were predicted at the newly created junctions.

    “R2[R4], R1R2R3[R4] and R1R2HS1[R4] donors were screened with Sasquatch 43and JASPAR42,43 to ensure no novel accessibility sites or motifs were predicted at the newly created junctions,43,44 prior to synthesis and transfection.”

    From Super-enhancers include classical enhancers and facilitators to fully activate gene expression (2023) · cites this paper as [42]

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Authors
Castro-Mondragon, J. A., Riudavets-Puig, R., Rauluseviciute, I., Berhanu Lemma, R., Turchi, L., Blanc-Mathieu, R., Lucas, J., Boddie, P., Khan, A., Manosalva Pérez, N., Fornes, O., Leung, T. Y., Aguirre, A., Hammal, F., Schmelter, D., Baranasic, D., Ballester, B., Sandelin, A., Lenhard, B., Vandepoele, K., Wasserman, W. W., Parcy, F., & Mathelier, A.
Affiliations
  • University of Oslo (NO)
  • Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
  • Centre National de la Recherche Scientifique (FR)
  • Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
  • Stanford Medicine (US)
  • Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
  • Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
  • University of British Columbia (CA)
  • Inserm (FR)
  • University of California, Santa Cruz (US)
  • MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
  • Aix Marseille Univ, INSERM, TAGC, Marseille, France
  • University of Copenhagen (DK)
  • Hammersmith Hospital (GB)
  • Ghent University (BE)
  • Oslo University Hospital (NO)
Corresponding author
  • Sandelin, Albin
  • Lenhard, Boris
  • Wasserman, Wyeth W
  • Parcy, François
  • Mathelier, Anthony
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2021-11-30
Volume
50
Issue
D1
Pages
D165-D173
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkab1113
PMC
PMC8728201
OpenAlex
W3215596355
Cited by
1,935
References
8
Citations by year
2026: 223 · 2025: 345 · 2024: 597 · 2023: 517 · 2022: 244 · 2021: 3 · 2020: 1 · 2019: 1 · 2013: 1 · 2012: 1
FWCI
115.14
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Ghent University Academic Bibliography (Ghent University) (publishedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by-nc)
  • Ghent University Academic Bibliography (Ghent University) (submittedVersion, cc-by-nc)
  • HAL (submittedVersion, cc-by-nc)
  • NORA - Norwegian Open Research Archives (submittedVersion, other-oa)
  • NORA - Norwegian Open Research Archives (submittedVersion, cc-by-nc)
Funders
  • Norwegian Research Council (187615, 288404)
  • Helse Sør-Øst
  • University of Oslo
  • Norwegian Cancer Society (197884)
  • GRAL program (ANR-10-LABX-49-01)
  • CBH-EUR-GS (ANR-17-EURE-0003)
  • CNRS Prime80
  • NHGRI (5U41HG002371-20)
  • Ghent University (BOF24Y2019001901)
  • Provence-Alpes-Côte d’Azur Regional Council
  • Institut National de la Santé et de la Recherche Médicale
  • Novo Nordisk Foundation (NNF20OC0059951, NNF19OC0058262)
  • Danish Cancer Foundation (R204-A12359)
  • Danish Independent Research Fund (6110-00207B, 7014-00120B)
  • Carlsberg Foundation
  • ERC
  • Canadian Institutes of Health Research (PJT-162120)
  • Natural Sciences and Engineering Research Council of Canada (RGPIN-2017-06824)
  • BC Children's Hospital Foundation and Research Institute
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
JASPAR, transcription factor binding sites, DNA-binding domain, transcription factor families, plant transcription factors, tunicates, insects, REST API, Bioconductor
MeSH terms
Animals, Binding Sites, Humans, Plants, Protein Binding, Software, Transcription Factors, Vertebrates, Genome, Computational Biology, Genomics, Databases, Genetic, Mice

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