GENCODE reference annotation for the human and mouse genomes

被引：2040

作者：

Frankish, Adam ^{[1
]}

Diekhans, Mark ^{[2
]}

Ferreira, Anne-Maud ^{[3
]}

Johnson, Rory ^{[4
,5
]}

Jungreis, Irwin ^{[6
,7
]}

Loveland, Jane ^{[1
]}

Mudge, Jonathan M. ^{[1
]}

Sisu, Cristina ^{[8
,9
]}

Wright, James ^{[10
]}

Armstrong, Joel ^{[2
]}

Barnes, If ^{[1
]}

Berry, Andrew ^{[1
]}

Bignell, Alexandra ^{[1
]}

Sala, Silvia Carbonell ^{[11
]}

Chrast, Jacqueline ^{[3
]}

Cunningham, Fiona ^{[1
]}

Di Domenico, Tomas ^{[12
]}

Donaldson, Sarah ^{[1
]}

Fiddes, Ian T. ^{[2
]}

Giron, Carlos Garcia ^{[1
]}

Gonzalez, Jose Manuel ^{[1
]}

Grego, Tiago ^{[1
]}

Hardy, Matthew ^{[1
]}

Hourlier, Thibaut ^{[1
]}

Hunt, Toby ^{[1
]}

Izuogu, Osagie G. ^{[1
]}

Lagarde, Julien ^{[11
]}

Martin, Fergal J. ^{[1
]}

Martinez, Laura ^{[12
]}

Mohanan, Shamika ^{[1
]}

Muir, Paul ^{[13
,14
]}

Navarro, Fabio C. P. ^{[8
]}

Parker, Anne ^{[1
]}

Pei, Baikang ^{[8
]}

Pozo, Fernando ^{[12
]}

Ruffier, Magali ^{[1
]}

Schmitt, Bianca M. ^{[1
]}

Stapleton, Eloise ^{[1
]}

Suner, Marie-Marthe ^{[1
]}

Sycheva, Irina ^{[1
]}

Uszczynska-Ratajczak, Barbara ^{[15
]}

Xu, Jinuri ^{[8
]}

Yates, Andrew ^{[1
]}

Zerbino, Daniel ^{[1
]}

Zhang, Yan ^{[8
,16
]}

Aken, Bronwen ^{[1
]}

Choudhary, Jyoti S. ^{[10
]}

Gerstein, Mark ^{[8
,17
,18
]}

Guigo, Roderic ^{[11
,19
]}

Hubbard, Tim J. P. ^{[20
]}

机构：

[1] European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England

[2] Univ Calif Santa Cruz, UC Santa Cruz Genom Inst, Santa Cruz, CA 95064 USA

[3] Univ Lausanne, CTr Integrat Genom, CH-1015 Lausanne, Switzerland

[4] Univ Bern, Univ Hosp, Inselspital, Dept Med Oncol, Bern, Switzerland

[5] Univ Bern, Dept Biomed Res DBMR, Bern, Switzerland

[6] MIT, Comp Sci & Artificial Intelligence Lab, 32 Vasser St, Cambridge, MA 02139 USA

[7] Broad Inst MIT & Harvard, 415 Main St, Cambridge, MA 02142 USA

[8] Yale Univ, Dept Mol Biophys & Biochem, POB 6666, New Haven, CT 06520 USA

[9] Brunel Univ London, Dept Biosci, Uxbridge UB8 3PH, Middx, England

[10] Inst Canc Res, Div Canc Biol, Funct Prote, 123 Old Brompton Rd, London SW7 3RP, England

[11] Barcelona Inst Sci & Technol, CRG, Dr Aiguader 88, E-08003 Barcelona, Spain

[12] Spanish Natl Canc Res Ctr CNIO, Bioinformat Unit, Madrid, Spain

[13] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA

[14] Yale Univ, Syst Biol Inst, West Haven, CT 06516 USA

[15] Univ Warsaw, Ctr New Technol, Warsaw, Poland

[16] Ohio State Univ, Coll Med, Dept Biomed Informat, Columbus, OH 43210 USA

[17] Yale Univ, Program Computat Biol & Bioinformat, Bass 432,266 Whitney Ave, New Haven, CT 06520 USA

[18] Yale Univ, Dept Comp Sci, Bass 432,266 Whitney Ave, New Haven, CT 06520 USA

[19] UPF, E-08003 Barcelona, Catalonia, Spain

[20] Guys Hosp, Kings Coll London, Dept Med & Mol Genet, London SE1 9RT, England

来源：

NUCLEIC ACIDS RESEARCH | 2019年 / 47卷 / D1期

基金：

英国惠康基金; 英国生物技术与生命科学研究理事会; 美国国家卫生研究院; 瑞士国家科学基金会;

关键词：

LONG NONCODING RNAS; DNA ELEMENTS; PROTEIN; GENES; IDENTIFICATION; ENCYCLOPEDIA; PRINCIPAL; DATABASE; PROGRAM; CATALOG;

D O I：

10.1093/nar/gky955

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

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.

引用

页码：D766 / D773

页数：8

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