The alternative splicing gallery (ASG): bridging the gap between genome and transcriptome
The alternative splicing gallery (ASG): bridging the gap between genome and transcriptome
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DOI：
10.1093/nar/gkh731
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Heber, S
中科院分区：
文献类型：
--
作者：
Leipzig, J;Pevzner, P;Heber, S
替代剪接基本上增加了转录组的多样性，并且对疾病的生理学，发育和起源具有重要意义。从传统上讲，以逐案的方式研究替代剪接，但是如果基因显示出大量不同的剪接变体，这将变得繁琐且容易出错。我们使用不同的方法，并将从基因得出的所有转录本集成到单个剪接图中。每个转录物对应于图中的路径，并通过分叉显示替代剪接。该表示形式保留了不同剪接变体之间的关系，并使我们能够系统地研究所有可能的推定成绩单。我们使用来自各种主要来源（Ensembl，RefSeq，stack，Tigr和Unigene）的转录本信息构建了一个用于人基因的剪接图的数据库。 Web接口允许用户显示剪接图，交互式组装成绩单并访问其序列以及相邻的基因组区域。我们还为每个基因提供了详尽的预先计算的推定转录本总数超过120万个序列的目录。我们发现，与65％的研究基因相似，显示了替代剪接的证据，在5％的病例中，单个基因可能会产生100多种转录本。
Alternative splicing essentially increases the diversity of the transcriptome and has important implications for physiology, development and the genesis of diseases. Conventionally, alternative splicing is investigated in a case-by-case fashion, but this becomes cumbersome and error prone if genes show a huge abundance of different splice variants. We use a different approach and integrate all transcripts derived from a gene into a single splicing graph. Each transcript corresponds to a path in the graph, and alternative splicing is displayed by bifurcations. This representation preserves the relationships between different splicing variants and allows us to investigate systematically all possible putative transcripts. We built a database of splicing graphs for human genes, using transcript information from various major sources (Ensembl, RefSeq, STACK, TIGR and UniGene). A Web interface allows users to display the splicing graphs, to interactively assemble transcripts and to access their sequences as well as neighboring genomic regions. We also provide for each gene an exhaustive pre-computed catalog of putative transcripts-in total more than 1.2 million sequences. We found that similar to65% of the investigated genes show evidence for alternative splicing, and in 5% of the cases, a single gene might produce over 100 transcripts.