GENCODE 2021-Reference-Cited by-同舟云学术

GENCODE 2021

Published:2020-12-03 Issue:D1 Volume:49 Page:D916-D923
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Frankish Adam¹^ORCID,Diekhans Mark²^ORCID,Jungreis Irwin³⁴^ORCID,Lagarde Julien⁵,Loveland Jane E¹^ORCID,Mudge Jonathan M¹,Sisu Cristina⁶⁷,Wright James C⁸,Armstrong Joel²,Barnes If¹,Berry Andrew¹,Bignell Alexandra¹,Boix Carles³⁴⁹,Carbonell Sala Silvia⁵,Cunningham Fiona¹^ORCID,Di Domenico Tomás¹⁰,Donaldson Sarah¹,Fiddes Ian T²,García Girón Carlos¹^ORCID,Gonzalez Jose Manuel¹,Grego Tiago¹,Hardy Matthew¹,Hourlier Thibaut¹^ORCID,Howe Kevin L¹^ORCID,Hunt Toby¹,Izuogu Osagie G¹,Johnson Rory¹¹¹²^ORCID,Martin Fergal J¹^ORCID,Martínez Laura¹⁰,Mohanan Shamika¹,Muir Paul¹³¹⁴,Navarro Fabio C P⁶,Parker Anne¹,Pei Baikang⁶,Pozo Fernando¹⁰,Riera Ferriol Calvet¹,Ruffier Magali¹^ORCID,Schmitt Bianca M¹,Stapleton Eloise¹,Suner Marie-Marthe¹^ORCID,Sycheva Irina¹,Uszczynska-Ratajczak Barbara¹⁵,Wolf Maxim Y¹⁶,Xu Jinuri⁶,Yang Yucheng T⁶¹⁷,Yates Andrew¹^ORCID,Zerbino Daniel¹^ORCID,Zhang Yan⁶¹⁸^ORCID,Choudhary Jyoti S⁸,Gerstein Mark⁶¹⁷¹⁹,Guigó Roderic⁵²⁰,Hubbard Tim J P²¹,Kellis Manolis³⁴,Paten Benedict²,Tress Michael L¹⁰^ORCID,Flicek Paul¹^ORCID

Affiliation:

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

2. UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA

3. MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139, USA

4. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA

5. Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain

6. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA

7. Department of Bioscience, Brunel University London, Uxbridge UB8 3PH, UK

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

9. Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA

10. Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain

11. Department of Medical Oncology, Inselspital, University Hospital, University of Bern, Bern, Switzerland

12. Department of Biomedical Research (DBMR), University of Bern, Bern, Switzerland

13. Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA

14. Systems Biology Institute, Yale University, West Haven, CT 06516, USA

15. Centre of New Technologies, University of Warsaw, Warsaw, Poland

16. Department of Biomedical Informatics at Harvard Medical School, 10 Shattuck Street, Suite 514, Boston, MA 02115, USA

17. Program in Computational Biology & Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA

18. Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA

19. Department of Computer Science, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA

20. Universitat Pompeu Fabra (UPF), Barcelona, E-08003 Catalonia, Spain

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

Abstract

Abstract The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.

Funder

National Institutes of Health

Wellcome Trust

European Molecular Biology Laboratory

Swiss National Science Foundation

University of Bern

Publisher

Oxford University Press (OUP)

Subject

Genetics

Link

http://academic.oup.com/nar/article-pdf/49/D1/D916/35363795/gkaa1087.pdf