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GENCODE: reference annotation for the human and mouse genomes in 2023.
Frankish, Adam; Carbonell-Sala, Sílvia; Diekhans, Mark; Jungreis, Irwin; Loveland, Jane E; Mudge, Jonathan M; Sisu, Cristina; Wright, James C; Arnan, Carme; Barnes, If; Banerjee, Abhimanyu; Bennett, Ruth; Berry, Andrew; Bignell, Alexandra; Boix, Carles; Calvet, Ferriol; Cerdán-Vélez, Daniel; Cunningham, Fiona; Davidson, Claire; Donaldson, Sarah; Dursun, Cagatay; Fatima, Reham; Giorgetti, Stefano; Giron, Carlos Garcia; Gonzalez, Jose Manuel; Hardy, Matthew; Harrison, Peter W; Hourlier, Thibaut; Hollis, Zoe; Hunt, Toby; James, Benjamin; Jiang, Yunzhe; Johnson, Rory; Kay, Mike; Lagarde, Julien; Martin, Fergal J; Gómez, Laura Martínez; Nair, Surag; Ni, Pengyu; Pozo, Fernando; Ramalingam, Vivek; Ruffier, Magali; Schmitt, Bianca M; Schreiber, Jacob M; Steed, Emily; Suner, Marie-Marthe; Sumathipala, Dulika; Sycheva, Irina; Uszczynska-Ratajczak, Barbara; Wass, Elizabeth.
Afiliação
  • Frankish A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • 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.
  • Diekhans M; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.
  • Jungreis I; MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA.
  • Loveland JE; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
  • Mudge JM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Sisu C; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Wright JC; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
  • Arnan C; Department of Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
  • Barnes I; Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
  • Banerjee A; Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
  • Bennett R; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Berry A; Department of Genetics, Stanford University, Palo Alto, CA, USA.
  • Bignell A; Department of Computer Science, Stanford University, Palo Alto, CA, USA.
  • Boix C; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Calvet F; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Cerdán-Vélez D; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Cunningham F; MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA.
  • Davidson C; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
  • Donaldson S; Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
  • Dursun C; Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.
  • Fatima R; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Giorgetti S; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Giron CG; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Gonzalez JM; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
  • Hardy M; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
  • Harrison PW; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Hourlier T; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Hollis Z; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Hunt T; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • James B; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Jiang Y; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Johnson R; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Kay M; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Lagarde J; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Martin FJ; MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA.
  • Gómez LM; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
  • Nair S; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
  • Ni P; Department of Medical Oncology, Bern University Hospital, Murtenstrasse 35, 3008 Bern, Switzerland.
  • Pozo F; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland.
  • Ramalingam V; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Ruffier M; Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
  • Schmitt BM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Schreiber JM; Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.
  • Steed E; Department of Genetics, Stanford University, Palo Alto, CA, USA.
  • Suner MM; Department of Computer Science, Stanford University, Palo Alto, CA, USA.
  • Sumathipala D; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
  • Sycheva I; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
  • Uszczynska-Ratajczak B; Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain.
  • Wass E; Department of Genetics, Stanford University, Palo Alto, CA, USA.
Nucleic Acids Res ; 51(D1): D942-D949, 2023 01 06.
Article em En | MEDLINE | ID: mdl-36420896
ABSTRACT
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.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genoma Humano / Biologia Computacional Limite: Animals / Humans Idioma: En Ano de publicação: 2023 Tipo de documento: Article
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genoma Humano / Biologia Computacional Limite: Animals / Humans Idioma: En Ano de publicação: 2023 Tipo de documento: Article