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Cited by 1,763Genomics and Chromatin DynamicsGenomics and Phylogenetic StudiesBioinformatics and Genomic Networks

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

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Fornes, Oriol, Castro-Mondragon, Jaime A, Khan, Aziz, van der Lee, Robin, Zhang, Xi, Richmond, Phillip A, Modi, Bhavi P, Correard, Solenne +11 more·2019·Nucleic Acids Research
DOI 10.1093/nar/gkz1001PMC PMC7145627
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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.

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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 [43]

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Authors
Fornes, O., Castro-Mondragon, J. A., Khan, A., van der Lee, R., Zhang, X., Richmond, P. A., Modi, B. P., Correard, S., Gheorghe, M., Baranašić, D., Santana-Garcia, W., Tan, G., Chèneby, J., Ballester, B., Parcy, F., Sandelin, A., Lenhard, B., Wasserman, W. W., & Mathelier, A.
Affiliations
  • 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 Oslo (NO)
  • University of British Columbia (CA)
  • Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK
  • Centre National de la Recherche Scientifique (FR)
  • ETH Zurich (CH)
  • Inserm (FR)
  • Aix Marseille Univ, INSERM, TAGC, Marseille, France
  • University of Copenhagen (DK)
  • MRC London Institute of Medical Sciences (GB)
  • Oslo University Hospital (NO)
Corresponding author
  • Sandelin, Albin
  • Lenhard, Boris
  • Wasserman, Wyeth W
  • Mathelier, Anthony
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2019-11-08
Volume
48
Issue
D1
Pages
D87-D92
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkz1001
PMC
PMC7145627
OpenAlex
W2988716798
Cited by
1,763
References
7
Citations by year
2026: 57 · 2025: 153 · 2024: 225 · 2023: 280 · 2022: 420 · 2021: 461 · 2020: 160 · 2019: 6
FWCI
87.90
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by-nc)
  • HAL (submittedVersion, cc-by)
  • NORA - Norwegian Open Research Archives (submittedVersion, cc-by-nc)
  • Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by-nc)
  • ETH Zürich Research Collection
Funders
  • Norwegian Research Council (187615, 288404)
  • Helse Sør-Øst
  • University of Oslo
  • Norwegian Cancer Society (197884)
  • Canadian Institutes of Health Research (BOP-149430, PJT-162120)
  • Genome Canada
  • Genome British Columbia (255ONT, 275SIL, SIP007)
  • Michael Smith Foundation for Health Research (17746)
  • Natural Sciences and Engineering Research Council of Canada (RGPIN-2017-06824)
  • Weston Brain Institute (20R74681)
  • BC Children's Hospital Foundation and Research Institute
  • Netherlands Organization for Scientific Research (452172015)
  • French National Agency for Research (ANR-16-CE92-0023-01, ANR-10-LABX-49-01)
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, database curation, community curation, vertebrates, plants, nematodes, insects, fungi, REST API, Bioconductor package
MeSH terms
Animals, Binding Sites, Protein Binding, Software, Transcription Factors, User-Computer Interface, Computational Biology, Genomics, Databases, Genetic, Web Browser

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