The importance of identifying alternative splicing in vertebrate genome annotation.
The importance of identifying alternative splicing in vertebrate genome annotation.
复制标题
DOI：
10.1093/database/bas014
复制
发表时间：
2012
期刊：
影响因子：
--
通讯作者：
Harrow J
中科院分区：
文献类型：
--
作者：
Frankish A;Mudge JM;Thomas M;Harrow J
虽然选择性剪接（AS）可以潜在地扩展脊椎动物基因组的功能库，但相对较少的AS转录物已被实验表征。我们描述了脊椎动物基因组的详细手工注释，生成了一个公开可用的富含AS的基因集。为了实现这一目标，我们采用了一种高度敏感的方法来注释基因模型，该方法由正确定位的、标准拼接的转录证据支持，并结合了一种高度谨慎的方法来添加不支持的扩展到模型中，并对其功能潜力做出决定。我们利用在蛋白质编码位点或非编码位点注释的每个AS转录本的预测功能潜力和结构特性信息，将它们划分为11个亚类之一。我们描述了将新的测序和蛋白质组学技术整合到我们的注释管道中，用于识别和验证AS。结合所有的数据来源，产生了一个丰富的基因集，每个人类多外显子蛋白质编码基因平均包含6.3个AS转录本。所产生的数据集已被证明非常有用，为研究基因的功能潜力和变异可能对基因结构和功能的影响提供了背景。数据库地址：http://www.ensembl.org/index.html, http://vega.sanger.ac.uk/index.html
While alternative splicing (AS) can potentially expand the functional repertoire of vertebrate genomes, relatively few AS transcripts have been experimentally characterized. We describe our detailed manual annotation of vertebrate genomes, which is generating a publicly available geneset rich in AS. In order to achieve this we have adopted a highly sensitive approach to annotating gene models supported by correctly mapped, canonically spliced transcriptional evidence combined with a highly cautious approach to adding unsupported extensions to models and making decisions on their functional potential. We use information about the predicted functional potential and structural properties of every AS transcript annotated at a protein-coding or non-coding locus to place them into one of eleven subclasses. We describe the incorporation of new sequencing and proteomics technologies into our annotation pipelines, which are used to identify and validate AS. Combining all data sources has led to the production of a rich geneset containing an average of 6.3 AS transcripts for every human multi-exon protein-coding gene. The datasets produced have proved very useful in providing context to studies investigating the functional potential of genes and the effect of variation may have on gene structure and function. Database URL: http://www.ensembl.org/index.html, http://vega.sanger.ac.uk/index.html
登录
查看更多内容
DOI：
10.1126/science.1215040
发表时间：
2012-02-17
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
MacArthur DG;Balasubramanian S;Frankish A;Huang N;Morris J;Walter K;Jostins L;Habegger L;Pickrell JK;Montgomery SB;Albers CA;Zhang ZD;Conrad DF;Lunter G;Zheng H;Ayub Q;DePristo MA;Banks E;Hu M;Handsaker RE;Rosenfeld JA;Fromer M;Jin M;Mu XJ;Khurana E;Ye K;Kay M;Saunders GI;Suner MM;Hunt T;Barnes IH;Amid C;Carvalho-Silva DR;Bignell AH;Snow C;Yngvadottir B;Bumpstead S;Cooper DN;Xue Y;Romero IG;1000 Genomes Project Consortium;Wang J;Li Y;Gibbs RA;McCarroll SA;Dermitzakis ET;Pritchard JK;Barrett JC;Harrow J;Hurles ME;Gerstein MB;Tyler-Smith C
通讯作者：
Tyler-Smith C
影响因子：
4.5
作者：
Hansen KD;Lareau LF;Blanchette M;Green RE;Meng Q;Rehwinkel J;Gallusser FL;Izaurralde E;Rio DC;Dudoit S;Brenner SE
通讯作者：
Brenner SE
影响因子：
7
作者：
Curwen, V;Eyras, E;Clamp, M
通讯作者：
Clamp, M
影响因子：
4.5
作者：
Galante, PAF;Sakabe, NJ;De Souza, SJ
通讯作者：
De Souza, SJ
影响因子：
30.8
作者：
Mendell, JT;Sharifi, NA;Dietz, HC
通讯作者：
Dietz, HC