GENCODE reference annotation for the human and mouse genomes

Adam Frankish(European Bioinformatics Institute), Mark Diekhans(University of California, Santa Cruz), Anne-Maud Ferreira(University of Lausanne), Rory Johnson(University of Bern), Irwin Jungreis(Broad Institute), Jane Loveland(European Bioinformatics Institute), Jonathan M. Mudge(European Bioinformatics Institute), Cristina Sisu(Yale University), James C. Wright(Institute of Cancer Research), Joel Armstrong(University of California, Santa Cruz), If Barnes(European Bioinformatics Institute), Andrew Berry(European Bioinformatics Institute), Alexandra Bignell(European Bioinformatics Institute), Sílvia Carbonell Sala(Barcelona Institute of Science and Technology), Jacqueline Chrast(University of Lausanne), Fiona Cunningham(European Bioinformatics Institute), Tomás Di Domenico(Spanish National Cancer Research Centre), Sarah Donaldson(European Bioinformatics Institute), Ian T. Fiddes(University of California, Santa Cruz), Carlos García Girón(European Bioinformatics Institute), José M. González(European Bioinformatics Institute), Tiago Grego(European Bioinformatics Institute), Matthew P. Hardy(European Bioinformatics Institute), Thibaut Hourlier(European Bioinformatics Institute), Toby Hunt(European Bioinformatics Institute), Osagie Izuogu(European Bioinformatics Institute), Julien Lagarde(Barcelona Institute of Science and Technology), Fergal J. Martin(European Bioinformatics Institute), Laura Martínez Gómez(Spanish National Cancer Research Centre), Shamika Mohanan(European Bioinformatics Institute), Paul Muir(Yale University), Fábio C. P. Navarro(Yale University), Anne Parker(European Bioinformatics Institute), Baikang Pei(Yale University), Fernando Campo del Pozo(Spanish National Cancer Research Centre), Magali Ruffier(European Bioinformatics Institute), Bianca M. Schmitt(European Bioinformatics Institute), Eloise Stapleton(European Bioinformatics Institute), Marie‐Marthe Suner(European Bioinformatics Institute), Irina Sycheva(European Bioinformatics Institute), Barbara Uszczyńska-Ratajczak(University of Warsaw), Jinrui Xu(Yale University), Andrew Yates(European Bioinformatics Institute), Daniel R. Zerbino(European Bioinformatics Institute), Yan Zhang(Yale University), Bronwen Aken(European Bioinformatics Institute), Jyoti S. Choudhary(Institute of Cancer Research), Mark Gerstein(Whitney Museum of American Art), Roderic Guigó(Universitat Pompeu Fabra), Tim Hubbard(Guy's Hospital), Manolis Kellis(Broad Institute), Benedict Paten(University of California, Santa Cruz), Alexandre Reymond(University of Lausanne), Michael L. Tress(Spanish National Cancer Research Centre), Paul Flicek(European Bioinformatics Institute)
Nucleic Acids Research
October 8, 2018
10.1093/nar/gky955
Cited by 3,486Open Access
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Abstract

The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.

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