GENCODE: the reference human genome annotation for The ENCODE Project.
GENCODE: the reference human genome annotation for The ENCODE Project.
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DOI：
10.1101/gr.135350.111
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发表时间：
2012-09
期刊：
影响因子：
7
通讯作者：
Hubbard TJ
中科院分区：
文献类型：
--
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
GENCODE联盟的目标是使用计算分析，手动注释和实验验证的组合来识别人类基因组中的所有基因特征。自该注释数据集首次公开发布以来，几乎没有新的蛋白质编码位点被添加，但注释的选择性剪接转录本的数量稳步增加。GENCODE 7版本包含20，687个蛋白质编码和9640个长非编码RNA基因座，并具有33，977个在UCSC基因和RefSeq中不存在的编码转录本。它也有最全面的注释长非编码RNA（lncRNA）基因座公开可用的主要转录形式组成的两个外显子。我们已经检查了转录本注释的完整性，发现35%的转录起始位点由CAGE簇支持，62%的蛋白质编码基因具有注释的polyA位点。超过三分之一的GENCODE蛋白质编码基因得到了来自提交给Peptide Atlas的质谱谱的肽命中的支持。来自Illumina Body Map 2.0 RNA-seq数据的新模型识别了3689个目前不在GENCODE中的新基因座，其中3127个由两个外显子模型组成，表明它们可能是未注释的长非编码基因座。GENCODE 7可从gencodegenes.org和通过Ensembl和UCSC基因组浏览器公开获得。
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 (lncRNA) 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.
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影响因子：
9.8
作者：
Church DM;Goodstadt L;Hillier LW;Zody MC;Goldstein S;She X;Bult CJ;Agarwala R;Cherry JL;DiCuccio M;Hlavina W;Kapustin Y;Meric P;Maglott D;Birtle Z;Marques AC;Graves T;Zhou S;Teague B;Potamousis K;Churas C;Place M;Herschleb J;Runnheim R;Forrest D;Amos-Landgraf J;Schwartz DC;Cheng Z;Lindblad-Toh K;Eichler EE;Ponting CP;Mouse Genome Sequencing Consortium
通讯作者：
Mouse Genome Sequencing Consortium
影响因子：
56.9
作者：
Bertone, P;Stolc, V;Snyder, M
通讯作者：
Snyder, M
影响因子：
10.5
作者：
Cabili, Moran N.;Trapnell, Cole;Rinn, John L.
通讯作者：
Rinn, John L.
影响因子：
4.4
作者：
Craig, R;Cortens, JP;Beavis, RC
通讯作者：
Beavis, RC
影响因子：
5.8
作者：
Craig, R;Beavis, RC
通讯作者：
Beavis, RC