GENCODE reference annotation for the human and mouse genomes

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ID: 290143
2018
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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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Authors Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew Berry, Alexandra Bignell, Sílvia Carbonell Sala, Jacqueline Chrast, Fiona Cunningham, Tomás Di Domenico, Sarah Donaldson, Ian T. Fiddes, Carlos García Girón, José M. González, Tiago Grego, Matthew P. Hardy, Thibaut Hourlier, Toby Hunt, Osagie Izuogu, Julien Lagarde, Fergal J. Martin, Laura Martínez Gómez, Shamika Mohanan, Paul Muir, Fábio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Campo del Pozo, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie‐Marthe Suner, Irina Sycheva, Barbara Uszczyńska-Ratajczak, Jinrui Xu, Andrew Yates, Daniel R. Zerbino, Yan Zhang, Bronwen Aken, Jyoti S. Choudhary, Mark Gerstein, Roderic Guigó, Tim Hubbard, Manolis Kellis, Benedict Paten, Alexandre Reymond, Michael L. Tress, Paul Flicek
Journal Nucleic Acids Research
Year 2018
DOI
10.1093/nar/gky955
URL
https://academic.oup.com/nar/article-pdf/47/D1/D766/27436288/gky955.pdf
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