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JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
Abstract JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 n...
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| Published in: | Nucleic acids research 2024-01, Vol.52 (D1), p.D174-D182 |
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| Main Authors: | , , , , , , , , , , , , , , , , , , , |
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| cited_by | cdi_FETCH-LOGICAL-c416t-831212086b31dcdd8659e248ac8d95debaa27167c6f469beaaf4ef30ccef7ef63 |
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| container_end_page | D182 |
| container_issue | D1 |
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| container_title | Nucleic acids research |
| container_volume | 52 |
| creator | Rauluseviciute, Ieva Riudavets-Puig, Rafael Blanc-Mathieu, Romain Castro-Mondragon, Jaime A Ferenc, Katalin Kumar, Vipin Lemma, Roza Berhanu Lucas, Jérémy Chèneby, Jeanne Baranasic, Damir Khan, Aziz Fornes, Oriol Gundersen, Sveinung Johansen, Morten Hovig, Eivind Lenhard, Boris Sandelin, Albin Wasserman, Wyeth W Parcy, François Mathelier, Anthony |
| description | Abstract
JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs’ structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.
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| doi_str_mv | 10.1093/nar/gkad1059 |
| format | article |
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JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs’ structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.
Graphical Abstract
Graphical Abstract</description><identifier>ISSN: 0305-1048</identifier><identifier>ISSN: 1362-4962</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkad1059</identifier><identifier>PMID: 37962376</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Animals ; Biochemistry, Molecular Biology ; Computer Science ; Databases, Genetic ; Databases, Genetic - standards ; Databases, Genetic - trends ; Genomics ; Humans ; Life Sciences ; Mice ; Plants ; Plants - genetics ; Protein Binding ; Quantitative Methods ; Transcription Factors ; Transcription Factors - genetics ; Transcription Factors - metabolism</subject><ispartof>Nucleic acids research, 2024-01, Vol.52 (D1), p.D174-D182</ispartof><rights>The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. 2024</rights><rights>The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><rights>info:eu-repo/semantics/openAccess</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c416t-831212086b31dcdd8659e248ac8d95debaa27167c6f469beaaf4ef30ccef7ef63</citedby><cites>FETCH-LOGICAL-c416t-831212086b31dcdd8659e248ac8d95debaa27167c6f469beaaf4ef30ccef7ef63</cites><orcidid>0000-0003-4069-357X ; 0000-0002-6459-6224 ; 0000-0002-5969-3054 ; 0000-0002-7109-7378 ; 0000-0002-2855-9952 ; 0000-0001-5127-5459 ; 0000-0002-3006-4297 ; 0000-0003-2191-500X ; 0000-0002-9485-6330 ; 0000-0002-9103-1077 ; 0000-0002-1114-1509 ; 0000-0001-5948-0932 ; 0000-0001-6098-6412 ; 0000-0003-1069-8011 ; 0000-0001-9253-8825 ; 0000-0002-2252-4732</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,1604,26567,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37962376$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-04500187$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Rauluseviciute, Ieva</creatorcontrib><creatorcontrib>Riudavets-Puig, Rafael</creatorcontrib><creatorcontrib>Blanc-Mathieu, Romain</creatorcontrib><creatorcontrib>Castro-Mondragon, Jaime A</creatorcontrib><creatorcontrib>Ferenc, Katalin</creatorcontrib><creatorcontrib>Kumar, Vipin</creatorcontrib><creatorcontrib>Lemma, Roza Berhanu</creatorcontrib><creatorcontrib>Lucas, Jérémy</creatorcontrib><creatorcontrib>Chèneby, Jeanne</creatorcontrib><creatorcontrib>Baranasic, Damir</creatorcontrib><creatorcontrib>Khan, Aziz</creatorcontrib><creatorcontrib>Fornes, Oriol</creatorcontrib><creatorcontrib>Gundersen, Sveinung</creatorcontrib><creatorcontrib>Johansen, Morten</creatorcontrib><creatorcontrib>Hovig, Eivind</creatorcontrib><creatorcontrib>Lenhard, Boris</creatorcontrib><creatorcontrib>Sandelin, Albin</creatorcontrib><creatorcontrib>Wasserman, Wyeth W</creatorcontrib><creatorcontrib>Parcy, François</creatorcontrib><creatorcontrib>Mathelier, Anthony</creatorcontrib><title>JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs’ structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.
Graphical Abstract
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JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs’ structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.
Graphical Abstract
Graphical Abstract</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>37962376</pmid><doi>10.1093/nar/gkad1059</doi><orcidid>https://orcid.org/0000-0003-4069-357X</orcidid><orcidid>https://orcid.org/0000-0002-6459-6224</orcidid><orcidid>https://orcid.org/0000-0002-5969-3054</orcidid><orcidid>https://orcid.org/0000-0002-7109-7378</orcidid><orcidid>https://orcid.org/0000-0002-2855-9952</orcidid><orcidid>https://orcid.org/0000-0001-5127-5459</orcidid><orcidid>https://orcid.org/0000-0002-3006-4297</orcidid><orcidid>https://orcid.org/0000-0003-2191-500X</orcidid><orcidid>https://orcid.org/0000-0002-9485-6330</orcidid><orcidid>https://orcid.org/0000-0002-9103-1077</orcidid><orcidid>https://orcid.org/0000-0002-1114-1509</orcidid><orcidid>https://orcid.org/0000-0001-5948-0932</orcidid><orcidid>https://orcid.org/0000-0001-6098-6412</orcidid><orcidid>https://orcid.org/0000-0003-1069-8011</orcidid><orcidid>https://orcid.org/0000-0001-9253-8825</orcidid><orcidid>https://orcid.org/0000-0002-2252-4732</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Oxford Journals Open Access Collection; NORA - Norwegian Open Research Archives; PubMed Central |
| subjects | Animals Biochemistry, Molecular Biology Computer Science Databases, Genetic Databases, Genetic - standards Databases, Genetic - trends Genomics Humans Life Sciences Mice Plants Plants - genetics Protein Binding Quantitative Methods Transcription Factors Transcription Factors - genetics Transcription Factors - metabolism |
| title | JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles |
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