JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles.

Autor:	Rauluseviciute I; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway., Riudavets-Puig R; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway., Blanc-Mathieu R; Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, F-38054, Grenoble, France., Castro-Mondragon JA; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway., Ferenc K; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway., Kumar V; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway., Lemma RB; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway., Lucas J; Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, F-38054, Grenoble, France., Chèneby J; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway., Baranasic D; MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.; Division of Electronics, Ruđer Bošković Institute, Bijenička cesta, 10000 Zagreb, Croatia., Khan A; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA., Fornes O; 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., Gundersen S; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway., Johansen M; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway., Hovig E; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway.; Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway., Lenhard B; MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK., Sandelin A; Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark., Wasserman WW; 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., Parcy F; Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, F-38054, Grenoble, France., Mathelier A; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway.; Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2024 Jan 05; Vol. 52 (D1), pp. D174-D182.
DOI:	10.1093/nar/gkad1059
Abstrakt:	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. (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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