GENCODE: The reference human genome annotation for The ENCODE Project

被引：3367

作者：

Harrow, Jennifer ^{[1
]}

Frankish, Adam ^{[1
]}

Gonzalez, Jose M. ^{[1
]}

Tapanari, Electra ^{[1
]}

Diekhans, Mark ^{[2
]}

Kokocinski, Felix ^{[1
]}

Aken, Bronwen L. ^{[1
]}

Barrell, Daniel ^{[1
]}

Zadissa, Amonida ^{[1
]}

Searle, Stephen ^{[1
]}

Barnes, If ^{[1
]}

Bignell, Alexandra ^{[1
]}

Boychenko, Veronika ^{[1
]}

Hunt, Toby ^{[1
]}

Kay, Mike ^{[1
]}

Mukherjee, Gaurab ^{[1
]}

Rajan, Jeena ^{[1
]}

Despacio-Reyes, Gloria ^{[1
]}

Saunders, Gary ^{[1
]}

Steward, Charles ^{[1
]}

Harte, Rachel ^{[2
]}

Lin, Michael ^{[3
]}

Howald, Cedric ^{[4
]}

Tanzer, Andrea ^{[5
,6
]}

Derrien, Thomas ^{[4
]}

Chrast, Jacqueline ^{[4
]}

Walters, Nathalie ^{[4
]}

Balasubramanian, Suganthi ^{[7
]}

Pei, Baikang ^{[7
]}

Tress, Michael ^{[8
]}

Manuel Rodriguez, Jose ^{[8
]}

Ezkurdia, Iakes ^{[8
]}

van Baren, Jeltje ^{[9
]}

Brent, Michael ^{[9
]}

Haussler, David ^{[2
]}

Kellis, Manolis ^{[3
]}

Valencia, Alfonso ^{[8
]}

Reymond, Alexandre ^{[4
]}

Gerstein, Mark ^{[7
]}

Guigo, Roderic ^{[5
,6
]}

Hubbard, Tim J. ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[2] Univ Calif Santa Cruz, Santa Cruz, CA 95064 USA

[3] MIT, Cambridge, MA 02139 USA

[4] Univ Lausanne, Ctr Integrat Genom, CH-1015 Lausanne, Switzerland

[5] Ctr Genom Regulat CRG, Barcelona 08003, Catalonia, Spain

[6] UPF, Barcelona 08003, Catalonia, Spain

[7] Yale Univ, New Haven, CT 06520 USA

[8] Spanish Natl Canc Res Ctr CNIO, E-28029 Madrid, Spain

[9] Ctr Genome Sci & Syst Biol, St Louis, MO 63130 USA

来源：

GENOME RESEARCH | 2012年 / 22卷 / 09期

基金：

美国国家卫生研究院; 美国国家科学基金会; 英国惠康基金;

关键词：

GENE-EXPRESSION; NONCODING RNAS; IDENTIFICATION; SEQUENCES; REVEALS; PSEUDOGENE; PREDICTION; TOPOLOGY; TRANSCRIPTION; COMPLEXITY;

D O I：

10.1101/gr.135350.111

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (IncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.

引用

页码：1760 / 1774

页数：15

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