JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
Identifieur interne : 000072 ( France/Analysis ); précédent : 000071; suivant : 000073JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
Auteurs : Aziz Khan [Norvège] ; Oriol Fornés [Canada] ; Arnaud Stigliani [France] ; Marius Gheorghe [Norvège] ; Jaime A. Castro-Mondragon [Norvège] ; Robin Van Der Lee [Canada] ; Adrien Bessy [France] ; Jeanne Chèneby [France] ; Shubhada R. Kulkarni [Belgique] ; Ge Tan [Royaume-Uni] ; Damir Baranasic [Royaume-Uni] ; David J. Arenillas [Canada] ; Albin Sandelin [Danemark] ; Klaas Vandepoele [Belgique] ; Boris Lenhard [Royaume-Uni] ; Benoit Ballester [France] ; Wyeth Wasserman [Canada] ; François Parcy [France] ; Anthony Mathelier [Norvège]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2018-01.
Descripteurs français
- Wicri :
- topic : Base de données.
English descriptors
- mix :
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 tax-onomic 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 .
Url:
DOI: 10.1093/nar/gkx1126
Affiliations:
- Belgique, Canada, Danemark, France, Norvège, Royaume-Uni
- Auvergne-Rhône-Alpes, Provence-Alpes-Côte d'Azur, Rhône-Alpes
- Grenoble, Marseille
- Université Grenoble-Alpes, Université d'Aix-Marseille
Links toward previous steps (curation, corpus...)
- to stream Hal, to step Corpus: 000096
- to stream Hal, to step Curation: 000096
- to stream Hal, to step Checkpoint: 000043
- to stream Main, to step Merge: 000C02
- to stream Main, to step Curation: 000C00
- to stream Main, to step Exploration: 000C00
- to stream France, to step Extraction: 000072
Links to Exploration step
Hal:hal-01646126Le document en format XML
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first="Aziz" last="Khan">Aziz Khan</name><affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-530985" status="VALID"> <orgName>Centre for Molecular Medicine Norway</orgName> <orgName type="acronym">NCMM</orgName> <desc> <address> <addrLine>Nordic EMBL Partnership, 0318 Oslo</addrLine> <country key="NO"></country> </address> <ref type="url">https://www.med.uio.no/ncmm/english/</ref> </desc> <listRelation> <relation active="#struct-105240" type="direct"></relation> <relation active="#struct-50791" type="indirect"></relation> <relation active="#struct-308687" type="direct"></relation> </listRelation> <tutelles><tutelle active="#struct-105240" type="direct"><org type="regrouplaboratory" xml:id="struct-105240" status="VALID"> <orgName>Faculty of Medicine [Oslo]</orgName> <desc> <address> <addrLine>PO BOX 1078 Blindern, 0316 Oslo</addrLine> <country key="NO"></country> </address> <ref type="url">https://www.med.uio.no/english/</ref> </desc> <listRelation> <relation 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type="direct"></relation> </listRelation> </org></tutelle><tutelle active="#struct-300016" type="indirect"><org type="institution" xml:id="struct-300016" status="VALID"> <orgName>Commissariat à l'énergie atomique et aux énergies alternatives</orgName> <orgName type="acronym">CEA</orgName> <desc> <address> <addrLine>Centre de SaclayCentre de GrenobleCentre de Cadaracheetc</addrLine> <country key="FR"></country> </address> <ref type="url">http://www.cea.fr/</ref> </desc> </org></tutelle></tutelles></hal:affiliation><country>France</country><placeName><settlement type="city">Grenoble</settlement><region type="region" nuts="2">Auvergne-Rhône-Alpes</region><region type="old region" nuts="2">Rhône-Alpes</region></placeName><orgName type="university">Université Grenoble-Alpes</orgName></affiliation></author><author><name sortKey="Mathelier, Anthony" sort="Mathelier, Anthony" uniqKey="Mathelier A" first="Anthony" last="Mathelier">Anthony Mathelier</name><affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-530985" status="VALID"> <orgName>Centre for Molecular Medicine Norway</orgName> <orgName type="acronym">NCMM</orgName> <desc> <address> <addrLine>Nordic EMBL Partnership, 0318 Oslo</addrLine> <country key="NO"></country> </address> <ref type="url">https://www.med.uio.no/ncmm/english/</ref> </desc> <listRelation> <relation active="#struct-105240" type="direct"></relation> <relation active="#struct-50791" type="indirect"></relation> <relation active="#struct-308687" type="direct"></relation> </listRelation> <tutelles><tutelle active="#struct-105240" type="direct"><org type="regrouplaboratory" xml:id="struct-105240" status="VALID"> <orgName>Faculty of Medicine [Oslo]</orgName> <desc> <address> <addrLine>PO BOX 1078 Blindern, 0316 Oslo</addrLine> <country key="NO"></country> </address> <ref type="url">https://www.med.uio.no/english/</ref> </desc> <listRelation> <relation active="#struct-50791" type="direct"></relation> </listRelation> </org></tutelle><tutelle active="#struct-50791" type="indirect"><org type="institution" xml:id="struct-50791" status="VALID"> <orgName>University of Oslo</orgName> <orgName type="acronym">UiO</orgName> <desc> <address> <addrLine>P.O 1072 Blindern 0316 Oslo</addrLine> <country key="NO"></country> </address> <ref type="url">http://www.uio.no/english/</ref> </desc> </org></tutelle><tutelle active="#struct-308687" type="direct"><org type="institution" xml:id="struct-308687" status="VALID"> <orgName>Rigshospitalet [Copenhagen]</orgName> <desc> <address> <addrLine>Blegdamsvej 92100 Copenhagen</addrLine> <country key="DK"></country> </address> <ref type="url">https://www.rigshospitalet.dk/english/</ref> </desc> </org></tutelle></tutelles></hal:affiliation><country>Norvège</country></affiliation></author></analytic><idno type="DOI">10.1093/nar/gkx1126</idno><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><imprint><date type="datePub">2018-01</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>Database</term><term>Fungi</term><term>Insects</term><term>Nematodes</term><term>Open Access</term><term>Plants</term><term>Transcription factor</term><term>Vertebrates</term></keywords><keywords scheme="Wicri" type="topic" xml:lang="fr"><term>Base de données</term></keywords></textClass></profileDesc></teiHeader><front><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) and TF flexible models (TFFMs) for TFs across multiple species in six tax-onomic 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 .</p> </div></front></TEI><affiliations><list><country><li>Belgique</li><li>Canada</li><li>Danemark</li><li>France</li><li>Norvège</li><li>Royaume-Uni</li></country><region><li>Auvergne-Rhône-Alpes</li><li>Provence-Alpes-Côte d'Azur</li><li>Rhône-Alpes</li></region><settlement><li>Grenoble</li><li>Marseille</li></settlement><orgName><li>Université Grenoble-Alpes</li><li>Université d'Aix-Marseille</li></orgName></list><tree><country name="Norvège"><noRegion><name sortKey="Khan, Aziz" sort="Khan, Aziz" uniqKey="Khan A" first="Aziz" last="Khan">Aziz Khan</name></noRegion><name sortKey="Castro Mondragon, Jaime A" sort="Castro Mondragon, Jaime A" uniqKey="Castro Mondragon J" first="Jaime A." last="Castro-Mondragon">Jaime A. Castro-Mondragon</name><name sortKey="Gheorghe, Marius" sort="Gheorghe, Marius" uniqKey="Gheorghe M" first="Marius" last="Gheorghe">Marius Gheorghe</name><name sortKey="Mathelier, Anthony" sort="Mathelier, Anthony" uniqKey="Mathelier A" first="Anthony" last="Mathelier">Anthony Mathelier</name></country><country name="Canada"><noRegion><name sortKey="Fornes, Oriol" sort="Fornes, Oriol" uniqKey="Fornes O" first="Oriol" last="Fornés">Oriol Fornés</name></noRegion><name sortKey="Arenillas, David J" sort="Arenillas, David J" uniqKey="Arenillas D" first="David J." last="Arenillas">David J. Arenillas</name><name sortKey="Van Der Lee, Robin" sort="Van Der Lee, Robin" uniqKey="Van Der Lee R" first="Robin" last="Van Der Lee">Robin Van Der Lee</name><name sortKey="Wasserman, Wyeth" sort="Wasserman, Wyeth" uniqKey="Wasserman W" first="Wyeth" last="Wasserman">Wyeth Wasserman</name></country><country name="France"><region name="Auvergne-Rhône-Alpes"><name sortKey="Stigliani, Arnaud" sort="Stigliani, Arnaud" uniqKey="Stigliani A" first="Arnaud" last="Stigliani">Arnaud Stigliani</name></region><name sortKey="Ballester, Benoit" sort="Ballester, Benoit" uniqKey="Ballester B" first="Benoit" last="Ballester">Benoit Ballester</name><name sortKey="Bessy, Adrien" sort="Bessy, Adrien" uniqKey="Bessy A" first="Adrien" last="Bessy">Adrien Bessy</name><name sortKey="Cheneby, Jeanne" sort="Cheneby, Jeanne" uniqKey="Cheneby J" first="Jeanne" last="Chèneby">Jeanne Chèneby</name><name sortKey="Parcy, Francois" sort="Parcy, Francois" uniqKey="Parcy F" first="François" last="Parcy">François Parcy</name></country><country name="Belgique"><noRegion><name sortKey="Kulkarni, Shubhada R" sort="Kulkarni, Shubhada R" uniqKey="Kulkarni S" first="Shubhada R." last="Kulkarni">Shubhada R. Kulkarni</name></noRegion><name sortKey="Vandepoele, Klaas" sort="Vandepoele, Klaas" uniqKey="Vandepoele K" first="Klaas" last="Vandepoele">Klaas Vandepoele</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Tan, Ge" sort="Tan, Ge" uniqKey="Tan G" first="Ge" last="Tan">Ge Tan</name></noRegion><name sortKey="Baranasic, Damir" sort="Baranasic, Damir" uniqKey="Baranasic D" first="Damir" last="Baranasic">Damir Baranasic</name><name sortKey="Lenhard, Boris" sort="Lenhard, Boris" uniqKey="Lenhard B" first="Boris" last="Lenhard">Boris Lenhard</name></country><country name="Danemark"><noRegion><name sortKey="Sandelin, Albin" sort="Sandelin, Albin" uniqKey="Sandelin A" first="Albin" last="Sandelin">Albin Sandelin</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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