Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.
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DOI：
10.1093/nar/gkq041
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发表时间：
2010-06
影响因子：
14.9
通讯作者：
Yaspo ML
中科院分区：
文献类型：
--
作者：
Richard H;Schulz MH;Sultan M;Nürnberger A;Schrinner S;Balzereit D;Dagand E;Rasche A;Lehrach H;Vingron M;Haas SA;Yaspo ML
选择性剪接、前信使RNA分子的聚腺苷酸化和差异启动子使用可以产生各种转录异构体，其各自的表达水平在时间和空间上受到调节，从而贡献特定的生物学功能。然而，哺乳动物的替代转录物和它们的调节的剧目仍然知之甚少。第二代测序正在开辟前所未有的途径，以解决整个转录组的分析。在这里，我们开发的方法，允许预测和定量的替代异构体仅来自外显子表达水平的RNA-Seq数据。这些都是基于明确的统计模型，并能够预测替代异构体内或之间的条件使用任何已知的基因注释，以及已知的转录本结构的相对定量。将这些方法应用于人类RNA-Seq数据集，我们通过RT-PCR验证了预测的重要部分。数据进一步表明，这些预测与源自连接读数的信息相关性良好。与外显子阵列的直接比较表明RNA-Seq在预测跳跃外显子方面优于微阵列。总之，这里提出的一套方法全面解决了替代异构体分析的多个方面。该软件可以在http://cmb.molgen.mpg.de/2ndGenerationSequencing/Solas/上作为一个名为Solas的开源R包获得。
Alternative splicing, polyadenylation of pre-messenger RNA molecules and differential promoter usage can produce a variety of transcript isoforms whose respective expression levels are regulated in time and space, thus contributing specific biological functions. However, the repertoire of mammalian alternative transcripts and their regulation are still poorly understood. Second-generation sequencing is now opening unprecedented routes to address the analysis of entire transcriptomes. Here, we developed methods that allow the prediction and quantification of alternative isoforms derived solely from exon expression levels in RNA-Seq data. These are based on an explicit statistical model and enable the prediction of alternative isoforms within or between conditions using any known gene annotation, as well as the relative quantification of known transcript structures. Applying these methods to a human RNA-Seq dataset, we validated a significant fraction of the predictions by RT-PCR. Data further showed that these predictions correlated well with information originating from junction reads. A direct comparison with exon arrays indicated improved performances of RNA-Seq over microarrays in the prediction of skipped exons. Altogether, the set of methods presented here comprehensively addresses multiple aspects of alternative isoform analysis. The software is available as an open-source R-package called Solas at http://cmb.molgen.mpg.de/2ndGenerationSequencing/Solas/.
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影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
14.9
作者：
Haas, SA;Hild, M;Vingron, M
通讯作者：
Vingron, M
DOI：
10.1186/bcr2097
发表时间：
2008
期刊：
Breast cancer research : BCR
影响因子：
--
作者：
Cork DM;Lennard TW;Tyson-Capper AJ
通讯作者：
Tyson-Capper AJ
影响因子：
48
作者：
Cloonan, Nicole;Forrest, Alistair R. R.;Grimmond, Sean M.
通讯作者：
Grimmond, Sean M.
影响因子：
5.8
作者：
Beissbarth, Tim;Hyde, Lavinia;Speed, Terence P.
通讯作者：
Speed, Terence P.