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

Open access
Khan, Aziz, Fornes, Oriol, Stigliani, Arnaud, Gheorghe, Marius, Castro-Mondragon, Jaime A, van der Lee, Robin, Bessy, Adrien, Chèneby, Jeanne, Kulkarni, Shubhada R, Tan, Ge, Baranasic, Damir, Arenillas, David J, Sandelin, Albin, Vandepoele, Klaas, Lenhard, Boris, Ballester, Benoît, Wasserman, Wyeth W, Parcy, François, Mathelier, Anthony·2018·Nucleic Acids Research
DOI 10.1093/nar/gkx1126
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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) 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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Metadata

Authors
Khan, A., Fornes, O., Stigliani, A., Gheorghe, M., Castro-Mondragon, J. A., van der Lee, R., Bessy, A., Chèneby, J., Kulkarni, S. R., Tan, G., Baranasic, D., Arenillas, D. J., Sandelin, A., Vandepoele, K., Lenhard, B., Ballester, B., Wasserman, W. W., Parcy, F., & Mathelier, A.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2017-11-13
Volume
46
Issue
D1
Pages
D260-D266
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkx1126
OpenAlex
W2770178180
Cited by
1,471
References
2
FWCI
74.15
Type
journal article
Language
en
Open access
gold
Licence
creativecommons.org/licenses/by-nc/4.0/ (vor)

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CoChat. (2026). Citation check: JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. https://app.cochat.ai/papers/10.1093/nar/gkx1126
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Khan, A., Fornes, O., Stigliani, A., Gheorghe, M., Castro-Mondragon, J. A., van der Lee, R., Bessy, A., Chèneby, J., Kulkarni, S. R., Tan, G., Baranasic, D., Arenillas, D. J., Sandelin, A., Vandepoele, K., Lenhard, B., Ballester, B., Wasserman, W. W., Parcy, F., & Mathelier, A. (2018). JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx1126

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