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

Identifieur interne : 000012 ( France/Analysis ); précédent : 000011; suivant : 000013

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

Auteurs : Oriol Fornés [Canada] ; Jaime Castro-Mondragon [Norvège] ; Aziz Khan [Norvège] ; Robin Van Der Lee [Canada] ; Xi Zhang [Canada] ; Phillip Richmond [Canada] ; Bhavi Modi [Canada] ; Solenne Correard [Canada] ; Marius Gheorghe [Norvège] ; Damir Baranaši [Royaume-Uni] ; Walter Santana-Garcia [France] ; Ge Tan [Suisse] ; Jeanne Chèneby [France] ; Benoit Ballester [France] ; François Parcy [France] ; Albin Sandelin [Danemark] ; Boris Lenhard [Royaume-Uni] ; Wyeth Wasserman [Canada] ; Anthony Mathelier [Norvège]

Source :

RBID : Hal:hal-02365013

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.


Url:
DOI: 10.1093/nar/gkz1001


Affiliations:

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Hal:hal-02365013

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<addrLine>Direction de Recherche FondamentaleFundamental Research DivisionCEA Saclay91191 Gif-sur-Yvette</addrLine>
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<orgName type="university">Université Grenoble-Alpes</orgName>
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<idno type="DOI">10.1093/nar/gkz1001</idno>
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<title level="j">Nucleic Acids Research</title>
<idno type="ISSN">0305-1048</idno>
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<date type="datePub">2020</date>
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<div type="abstract" xml:lang="en">
<p>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.</p>
</div>
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<li>Canada</li>
<li>Danemark</li>
<li>France</li>
<li>Norvège</li>
<li>Royaume-Uni</li>
<li>Suisse</li>
</country>
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<li>Provence-Alpes-Côte d'Azur</li>
<li>Rhône-Alpes</li>
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<li>Marseille</li>
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<name sortKey="Ballester, Benoit" sort="Ballester, Benoit" uniqKey="Ballester B" first="Benoit" last="Ballester">Benoit Ballester</name>
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<name sortKey="Sandelin, Albin" sort="Sandelin, Albin" uniqKey="Sandelin A" first="Albin" last="Sandelin">Albin Sandelin</name>
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