Journal
NUCLEIC ACIDS RESEARCH
Volume 50, Issue D1, Pages D165-D173Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkab1113
Keywords
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Categories
Funding
- Norwegian Research Council [187615, 288404]
- Helse Sor-Ost
- University of Oslo through the Centre for Molecular Medicine Norway (NCMM)
- Norwegian Cancer Society [197884]
- GRAL program [ANR-10-LABX-49-01, ANR-17-EURE-0003]
- CNRS Prime80
- NHGRI [5U41HG002371-20]
- BOF grant from Ghent University [BOF24Y2019001901]
- Provence-Alpes-Cote d'Azur Regional Council (Region SUD)
- Institut National de la Sante et de la Recherche Medicale (INSERM)
- Novo Nordisk Foundation [NNF20OC0059951, NNF19OC0058262]
- Danish Cancer Foundation [R204A12359]
- Danish Independent Research Fund [6110-00207B, 7014-00120B]
- Carlsberg Foundation
- ERC the European Union's Horizon 2020 research and innovation programme (MSCA ITN pHioniC)
- Canadian Institutes of Health Research [PJT-162120]
- Natural Sciences and EngineeringResearch Council of Canada (NSERC) [RGPIN-2017-06824]
- BC Children's Hospital Foundation and Research Institute
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JASPAR is an open-access database containing manually curated, non-redundant transcription factor binding profiles across six taxonomic groups. The latest release introduces new profiles for plants, vertebrates, urochordates, and insects, as well as new tools for TFBS enrichment analysis and data access. The database can be accessed through various platforms, including the JASPAR website, RESTful API, R/Bioconductor data package, and a new Python package pyJASPAR.
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.
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