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

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          Abstract

          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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          NCBI GEO: archive for functional genomics data sets—update

          The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.
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            UniProt: the universal protein knowledgebase in 2021

            (2020)
            Abstract The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.
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              Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

              R. Edgar (2002)
              The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. GEO is not intended to replace in house gene expression databases that benefit from coherent data sets, and which are constructed to facilitate a particular analytic method, but rather complement these by acting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.
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                Author and article information

                Contributors
                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                07 January 2022
                30 November 2021
                30 November 2021
                : 50
                : D1
                : D165-D173
                Affiliations
                Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , 0318 Oslo, Norway
                Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , 0318 Oslo, Norway
                Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , 0318 Oslo, Norway
                Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , 0318 Oslo, Norway
                Laboratoire Physiologie Cellulaire et Végétale , Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
                Laboratoire Physiologie Cellulaire et Végétale , Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
                Laboratoire Physiologie Cellulaire et Végétale , Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
                Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , 0318 Oslo, Norway
                Stanford Cancer Institute, Stanford University School of Medicine , Stanford, CA94305, USA
                Department of Plant Biotechnology and Bioinformatics, Ghent University , Technologiepark 71, 9052 Ghent, Belgium
                VIB Center for Plant Systems Biology , Technologiepark 71, 9052 Ghent, Belgium
                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
                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
                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
                Aix Marseille Univ , INSERM, TAGC, Marseille, France
                UCSC Genome Browser, University of California Santa Cruz , Santa Cruz, CA95060, USA
                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
                Aix Marseille Univ , INSERM, TAGC, Marseille, France
                The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen , Ole Maaloes Vej 5, DK2200 Copenhagen N, Denmark
                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
                Department of Plant Biotechnology and Bioinformatics, Ghent University , Technologiepark 71, 9052 Ghent, Belgium
                VIB Center for Plant Systems Biology , Technologiepark 71, 9052 Ghent, Belgium
                Bioinformatics Institute Ghent, Ghent University , Technologiepark 71, 9052 Ghent, Belgium
                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
                Laboratoire Physiologie Cellulaire et Végétale , Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
                Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , 0318 Oslo, Norway
                Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital , Oslo, Norway
                Author notes
                To whom correspondence should be addressed. Email: anthony.mathelier@ 123456ncmm.uio.no
                Correspondence may also be addressed to François Parcy. Email: francois.parcy@ 123456cea.fr
                Correspondence may also be addressed to Wyeth W. Wasserman. Email: wyeth@ 123456cmmt.ubc.ca
                Correspondence may also be addressed to Boris Lenhard. Email: b.lenhard@ 123456imperial.ac.uk
                Correspondence may also be addressed to Albin Sandelin. Email: albin@ 123456binf.ku.dk

                The authors wish it to be known that, in their opinion, the first three authors should be regarded as Joint First Authors.

                Author information
                https://orcid.org/0000-0003-4069-357X
                https://orcid.org/0000-0002-2855-9952
                https://orcid.org/0000-0001-9253-8825
                https://orcid.org/0000-0003-1069-8011
                https://orcid.org/0000-0002-2791-5505
                https://orcid.org/0000-0002-9485-6330
                https://orcid.org/0000-0002-2252-4732
                https://orcid.org/0000-0002-6459-6224
                https://orcid.org/0000-0002-1559-7802
                https://orcid.org/0000-0002-5969-3054
                https://orcid.org/0000-0002-1714-4268
                https://orcid.org/0000-0002-3390-8301
                https://orcid.org/0000-0002-7612-4953
                https://orcid.org/0000-0002-0834-7135
                https://orcid.org/0000-0002-7109-7378
                https://orcid.org/0000-0002-1114-1509
                https://orcid.org/0000-0003-4790-2725
                https://orcid.org/0000-0001-6098-6412
                https://orcid.org/0000-0003-2191-500X
                https://orcid.org/0000-0001-5127-5459
                Article
                gkab1113
                10.1093/nar/gkab1113
                8728201
                34850907
                3c493312-807a-4573-aa0a-dc7b207a321c
                © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                : 22 October 2021
                : 20 October 2021
                : 15 September 2021
                Page count
                Pages: 9
                Funding
                Funded by: Norwegian Research Council, DOI 10.13039/501100005416;
                Award ID: 187615
                Award ID: 288404
                Funded by: Helse Sør-Øst;
                Funded by: University of Oslo, DOI 10.13039/501100005366;
                Funded by: Norwegian Cancer Society, DOI 10.13039/100008730;
                Award ID: 197884
                Funded by: GRAL program;
                Award ID: ANR-10-LABX-49-01
                Funded by: CBH-EUR-GS;
                Award ID: ANR-17-EURE-0003
                Funded by: CNRS Prime80;
                Funded by: NHGRI, DOI 10.13039/100000051;
                Award ID: 5U41HG002371-20
                Funded by: Ghent University, DOI 10.13039/501100004385;
                Award ID: BOF24Y2019001901
                Funded by: Provence-Alpes-Côte d’Azur Regional Council;
                Funded by: Institut National de la Santé et de la Recherche Médicale, DOI 10.13039/501100001677;
                Funded by: Novo Nordisk Foundation, DOI 10.13039/501100009708;
                Award ID: NNF20OC0059951
                Award ID: NNF19OC0058262
                Funded by: Danish Cancer Foundation;
                Award ID: R204-A12359
                Funded by: Danish Independent Research Fund;
                Award ID: 6110-00207B
                Award ID: 7014-00120B
                Funded by: Carlsberg Foundation, DOI 10.13039/501100002808;
                Funded by: ERC, DOI 10.13039/501100000781;
                Funded by: Canadian Institutes of Health Research, DOI 10.13039/501100000024;
                Award ID: PJT-162120
                Funded by: Natural Sciences and Engineering Research Council of Canada, DOI 10.13039/501100000038;
                Award ID: RGPIN-2017-06824
                Funded by: BC Children's Hospital Foundation and Research Institute;
                Categories
                AcademicSubjects/SCI00010
                Database Issue

                Genetics
                Genetics

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