JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

Autor: Aziz Khan, Damir Baranasic, Benoit Ballester, Ieva Rauluseviciute, Fayrouz Hammal, Klaas Vandepoele, Paul Boddie, Anthony Mathelier, Daniel Schmelter, Rafael Riudavets-Puig, Wyeth W. Wasserman, Jérémy Lucas, François Parcy, Oriol Fornes, Boris Lenhard, Laura Turchi, Romain Blanc-Mathieu, Jaime A. Castro-Mondragon, Albin Sandelin, Nicolás Manosalva Pérez, Roza Berhanu Lemma, Tiffany Y. Leung, Alejandro Aguirre
Přispěvatelé: Centre for Molecular Medicine Norway (NCMM), Faculty of Medicine [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Rigshospitalet [Copenhagen], Copenhagen University Hospital-Copenhagen University Hospital, Régulateurs du développement de la fleur (Flo_RE ), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Stanford Cancer Institute - Stanford University School of Medicine, Department of Plant Biotechnology and Bioinformatics, Ghent University, VIBUGent Center for Plant Systems Biology, BC Children's Hospital Research Institute [Vancouver, BC, Canada] (BCCHR), University of British Columbia (UBC), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), UCSC Genome Browser, University of California Santa Cruz, MRC London Institute of Medical Sciences (LMC), Institute of Clinical Sciences, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, NorwegianResearch Council [187615] and [288404], South-Eastern Norway Regional Health Authority (Helse Sør-Øst), Canadian Institutes of Health Research [PJT-162120], Natural Sciences andEngineeringResearch Council of Canada (NSERC) Discovery Grant [RGPIN-2017-06824], Norwegian Cancer Society [197884], NHGRI (National Human Genome Research Institute) [5U41HG002371-20], BOFgrant from Ghent University [BOF24Y2019001901], Novo Nordisk Foundation [NNF20OC0059951, NNF19OC0058262], Danish Cancer Foundation [R204A12359], Danish Independent Research Fund [611000207B, 7014-00120B], Carlsberg Foundation, ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), European Project: MSCA-ITN 2018,pHioniC, Universiteit Gent = Ghent University (UGENT), Imperial College London, University of Copenhagen = Københavns Universitet (UCPH), University of Oslo (UiO), Martin-Laffon, Jacqueline, CBH-EUR-GS - - CBH-EUR-GS2017 - ANR-17-EURE-0003 - EURE - VALID, Grenoble Alliance for Integrated Structural Cell Biology - - GRAL2010 - ANR-10-LABX-0049 - LABX - VALID, pH and Ion Transport in Pancreatic Cancer - pHioniC - MSCA-ITN 2018 - INCOMING
Jazyk: angličtina
Rok vydání: 2021
Předmět:
Zdroj: Nucleic Acids Research
Nucleic Acids Research, Oxford University Press, 2021, ⟨10.1093/nar/gkab1113⟩
NUCLEIC ACIDS RESEARCH
Nucleic Acids Research, 2022, 50 (D1), pp.D165-D173. ⟨10.1093/nar/gkab1113⟩
Castro-Mondragon, J A, Riudavets-Puig, R, Rauluseviciute, I, Lemma, R B, Turchi, L, Blanc-Mathieu, R, Lucas, J, Boddie, P, Khan, A, Perez, N M, Fornes, O, Leung, T Y, Aguirre, A, Hammal, F, Schmelter, D, Baranasic, D, Ballester, B, Sandelin, A, Lenhard, B, Vandepoele, K, Wasserman, W W, Parcy, F & Mathelier, A 2022, ' JASPAR 2022 : the 9th release of the open-access database of transcription factor binding profiles ', Nucleic acids symposium series, vol. 50, no. D1, pp. D165-D173 . https://doi.org/10.1093/nar/gkab1113
ISSN: 0305-1048
1362-4962
DOI: 10.1093/nar/gkab1113⟩
Popis: JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.
Databáze: OpenAIRE
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