GENCODE: reference annotation for the human and mouse genomes in 2023.

Humans Animals Mice Molecular Sequence Annotation Computational Biology / methods Genome, Human / genetics Transcriptome / genetics Gene Expression Profiling Databases, Genetic

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
06 01 2023
Historique:
accepted: 07 11 2022
revised: 15 10 2022
received: 22 09 2022
pubmed: 25 11 2022
medline: 12 1 2023
entrez: 24 11 2022
Statut: ppublish

Résumé

GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.

Identifiants

DOI: 10.1093/nar/gkac1071 PMID: 36420896 PMC: PMC9825462
pubmed: 36420896
pii: 6845433
doi: 10.1093/nar/gkac1071
pmc: PMC9825462
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

D942-D949

Subventions

Organisme : NHGRI NIH HHS
ID : R01 HG004037
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG007234
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom

Informations de copyright

© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Adam Frankish (A)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
ORCID: 0000-0002-4333-628X

Sílvia Carbonell-Sala (S)

Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.

Mark Diekhans (M)

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.
ORCID: 0000-0002-0430-0989

Irwin Jungreis (I)

MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA.
Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
ORCID: 0000-0002-3197-5367

Jane E Loveland (JE)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
ORCID: 0000-0002-7669-2934

Jonathan M Mudge (JM)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Cristina Sisu (C)

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Department of Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.

James C Wright (JC)

Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.

Carme Arnan (C)

Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
ORCID: 0000-0002-7431-2088

If Barnes (I)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Abhimanyu Banerjee (A)

Department of Genetics, Stanford University, Palo Alto, CA, USA.
Department of Computer Science, Stanford University, Palo Alto, CA, USA.

Ruth Bennett (R)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Andrew Berry (A)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Alexandra Bignell (A)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Carles Boix (C)

MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA.
Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.

Ferriol Calvet (F)

Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.

Daniel Cerdán-Vélez (D)

Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.

Fiona Cunningham (F)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
ORCID: 0000-0002-7445-2419

Claire Davidson (C)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Sarah Donaldson (S)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Cagatay Dursun (C)

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

Reham Fatima (R)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Stefano Giorgetti (S)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Carlos Garcıa Giron (CG)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
ORCID: 0000-0002-0935-7271

Jose Manuel Gonzalez (JM)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Matthew Hardy (M)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Peter W Harrison (PW)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
ORCID: 0000-0002-4007-2899

Thibaut Hourlier (T)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
ORCID: 0000-0003-4894-7773

Zoe Hollis (Z)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Toby Hunt (T)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Benjamin James (B)

MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA.
Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.

Yunzhe Jiang (Y)

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

Rory Johnson (R)

Department of Medical Oncology, Bern University Hospital, Murtenstrasse 35, 3008 Bern, Switzerland.
School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland.
ORCID: 0000-0003-4607-2782

Mike Kay (M)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Julien Lagarde (J)

Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.

Fergal J Martin (FJ)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
ORCID: 0000-0002-1672-050X

Laura Martínez Gómez (LM)

Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.

Surag Nair (S)

Department of Genetics, Stanford University, Palo Alto, CA, USA.
Department of Computer Science, Stanford University, Palo Alto, CA, USA.
ORCID: 0000-0002-6216-2457

Pengyu Ni (P)

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

Fernando Pozo (F)

Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.

Vivek Ramalingam (V)

Department of Genetics, Stanford University, Palo Alto, CA, USA.
Department of Computer Science, Stanford University, Palo Alto, CA, USA.

Magali Ruffier (M)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
ORCID: 0000-0002-8386-1580

Bianca M Schmitt (BM)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Jacob M Schreiber (JM)

Department of Genetics, Stanford University, Palo Alto, CA, USA.
Department of Computer Science, Stanford University, Palo Alto, CA, USA.

Emily Steed (E)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Marie-Marthe Suner (MM)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
ORCID: 0000-0002-0380-7171

Dulika Sumathipala (D)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Irina Sycheva (I)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Barbara Uszczynska-Ratajczak (B)

Computational Biology of Noncoding RNA, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.

Elizabeth Wass (E)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Yucheng T Yang (YT)

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China.

Andrew Yates (A)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
ORCID: 0000-0002-8886-4772

Zahoor Zafrulla (Z)

Department of Genetics, Stanford University, Palo Alto, CA, USA.
Department of Computer Science, Stanford University, Palo Alto, CA, USA.

Jyoti S Choudhary (JS)

Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.

Mark Gerstein (M)

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

Roderic Guigo (R)

Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, E-08003 Catalonia, Spain.

Tim J P Hubbard (TJP)

Department of Medical and Molecular Genetics, King's College London, Guys Hospital, Great Maze Pond, London SE1 9RT, UK.

Manolis Kellis (M)

MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA.
Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.

Anshul Kundaje (A)

Department of Genetics, Stanford University, Palo Alto, CA, USA.
Department of Computer Science, Stanford University, Palo Alto, CA, USA.
ORCID: 0000-0003-3084-2287

Benedict Paten (B)

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.
ORCID: 0000-0001-8863-3539

Michael L Tress (ML)

Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.
ORCID: 0000-0001-9046-6370

Paul Flicek (P)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
ORCID: 0000-0002-3897-7955

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › GENCODE: reference annotation for the human...
questionsmedicales.fr › Eucaryotes › Animaux › GENCODE: reference annotation for the human...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Rodentia › Muridae › Murinae › Souris › GENCODE: reference annotation for the human...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › GENCODE: reference annotation for the human...
questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › GENCODE: reference annotation for the human...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome humain › GENCODE: reference annotation for the human...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Transcriptome › GENCODE: reference annotation for the human...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de profil d'expression de gènes › GENCODE: reference annotation for the human...
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