AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation.
AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation.
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AltTrans：针对替代剪接和替代聚腺苷酸化的转录本模式变体。
DOI：
10.1186/1471-2105-7-169
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发表时间：
2006-03-23
影响因子：
3
通讯作者：
Thanaraj, TA
中科院分区：
文献类型：
--
作者：
Le Texier, V;Riethoven, JJ;Kumanduri, V;Gopalakrishnan, C;Lopez, F;Gautheret, D;Thanaraj, TA
调节转录物形成的三种主要机制涉及选择转录开始（TS），剪接和聚腺苷酸化的替代位点。当前，正在为每种变体中的每一个分别收集数据和注释。重要的是要对这些数据集进行集成视图，并得出一组替代成绩单以及合并注释的数据集。在过去的计算管道中，我们一直在开发基因组规模上的单个变体类型的增值数据。这些包括在剪接上的AltSplice和altpas的聚腺苷酸化。现在，我们扩展了这些管道并整合了所得数据集，以促进在形成转录本变体中剪接和聚腺苷酸化的贡献的综合视图。
AltSplice管道检查了基因转录比对，并描述了替代性剪接事件和剪接模式。该管道作为AltTrans扩展，以描绘每个内含子/外显子和“终止” Polya位点的同工型转录模式；符合转录图模式的EST/mRNA序列证实了潜在的剪接和聚腺苷酸化。 AltPAS管道检查基因转录比对，并描述所有潜在的polya位点，而与基础剪接模式无关。来自AltTrans和AltPA的合并位点合并。生成的数据库报告了有关替代剪接，替代聚腺苷酸化和所得替代成绩单模式的数据；针对各种生物学特征，将基础数据注释。针对人和鼠标生成的数据（称为集成的AltTrans数据）通过替代的转录本多样性网站提供。
报道的数据集呈现出替代的转录本模式，这些模式均可用于替代剪接和替代聚腺苷酸化。基于当前转录组数据的结果表明，替代剪接的贡献大于替代聚腺苷酸化的贡献。
The three major mechanisms that regulate transcript formation involve the selection of alternative sites for transcription start (TS), splicing, and polyadenylation. Currently there are efforts that collect data & annotation individually for each of these variants. It is important to take an integrated view of these data sets and to derive a data set of alternate transcripts along with consolidated annotation. We have been developing in the past computational pipelines that generate value-added data at genome-scale on individual variant types; these include AltSplice on splicing and AltPAS on polyadenylation. We now extend these pipelines and integrate the resultant data sets to facilitate an integrated view of the contributions from splicing and polyadenylation in the formation of transcript variants. The AltSplice pipeline examines gene-transcript alignments and delineates alternative splice events and splice patterns; this pipeline is extended as AltTrans to delineate isoform transcript patterns for each of which both introns/exons and 'terminating' polyA site are delineated; EST/mRNA sequences that qualify the transcript pattern confirm both the underlying splicing and polyadenylation. The AltPAS pipeline examines gene-transcript alignments and delineates all potential polyA sites irrespective of underlying splicing patterns. Resultant polyA sites from both AltTrans and AltPAS are merged. The generated database reports data on alternative splicing, alternative polyadenylation and the resultant alternate transcript patterns; the basal data is annotated for various biological features. The data (named as integrated AltTrans data) generated for both the organisms of human and mouse is made available through the Alternate Transcript Diversity web site at . The reported data set presents alternate transcript patterns that are annotated for both alternative splicing and alternative polyadenylation. Results based on current transcriptome data indicate that the contribution of alternative splicing is larger than that of alternative polyadenylation.
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影响因子：
9.8
作者：
Imanishi T;Itoh T;Suzuki Y;O'Donovan C;Fukuchi S;Koyanagi KO;Barrero RA;Tamura T;Yamaguchi-Kabata Y;Tanino M;Yura K;Miyazaki S;Ikeo K;Homma K;Kasprzyk A;Nishikawa T;Hirakawa M;Thierry-Mieg J;Thierry-Mieg D;Ashurst J;Jia L;Nakao M;Thomas MA;Mulder N;Karavidopoulou Y;Jin L;Kim S;Yasuda T;Lenhard B;Eveno E;Suzuki Y;Yamasaki C;Takeda J;Gough C;Hilton P;Fujii Y;Sakai H;Tanaka S;Amid C;Bellgard M;Bonaldo Mde F;Bono H;Bromberg SK;Brookes AJ;Bruford E;Carninci P;Chelala C;Couillault C;de Souza SJ;Debily MA;Devignes MD;Dubchak I;Endo T;Estreicher A;Eyras E;Fukami-Kobayashi K;Gopinath GR;Graudens E;Hahn Y;Han M;Han ZG;Hanada K;Hanaoka H;Harada E;Hashimoto K;Hinz U;Hirai M;Hishiki T;Hopkinson I;Imbeaud S;Inoko H;Kanapin A;Kaneko Y;Kasukawa T;Kelso J;Kersey P;Kikuno R;Kimura K;Korn B;Kuryshev V;Makalowska I;Makino T;Mano S;Mariage-Samson R;Mashima J;Matsuda H;Mewes HW;Minoshima S;Nagai K;Nagasaki H;Nagata N;Nigam R;Ogasawara O;Ohara O;Ohtsubo M;Okada N;Okido T;Oota S;Ota M;Ota T;Otsuki T;Piatier-Tonneau D;Poustka A;Ren SX;Saitou N;Sakai K;Sakamoto S;Sakate R;Schupp I;Servant F;Sherry S;Shiba R;Shimizu N;Shimoyama M;Simpson AJ;Soares B;Steward C;Suwa M;Suzuki M;Takahashi A;Tamiya G;Tanaka H;Taylor T;Terwilliger JD;Unneberg P;Veeramachaneni V;Watanabe S;Wilming L;Yasuda N;Yoo HS;Stodolsky M;Makalowski W;Go M;Nakai K;Takagi T;Kanehisa M;Sakaki Y;Quackenbush J;Okazaki Y;Hayashizaki Y;Hide W;Chakraborty R;Nishikawa K;Sugawara H;Tateno Y;Chen Z;Oishi M;Tonellato P;Apweiler R;Okubo K;Wagner L;Wiemann S;Strausberg RL;Isogai T;Auffray C;Nomura N;Gojobori T;Sugano S
通讯作者：
Sugano S
影响因子：
7
作者：
Ashburner, M;Ball, CA;Yoon, J
通讯作者：
Yoon, J
影响因子：
14.9
作者：
Leipzig, J;Pevzner, P;Heber, S
通讯作者：
Heber, S
影响因子：
7
作者：
Kan, ZY;Rouchka, EC;States, DJ
通讯作者：
States, DJ
影响因子：
7
作者：
Beaudoing, E;Gautheret, D
通讯作者：
Gautheret, D