A note on an exon-based strategy to identify differentially expressed genes in RNA-seq experiments.
A note on an exon-based strategy to identify differentially expressed genes in RNA-seq experiments.
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DOI：
10.1371/journal.pone.0115964
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Elo LL
中科院分区：
文献类型：
--
作者：
Laiho A;Elo LL
RNA测序（RNA-seq）已迅速成为许多全基因组转录组学研究的首选方法。为了满足这项技术带来的高期望，需要强大的计算技术将测量转化为生物和生物医学的理解。已经开发了许多统计程序来识别不同样品组之间的差异表达基因。使用这些方法，通常在基因水平上汇总数据后进行统计检验。作为一种替代策略，开发的目的是改善结果，我们展示了一种方法，在该方法中，在外显子水平的统计测试进行之前，在基因水平上的结果的总结。使用公开的RNA-seq数据集作为案例研究，我们说明了这种基于外显子的策略如何提高广泛使用的差异表达软件包的性能相比，传统的基于基因的策略。特别是，我们展示了它如何能够稳健地检测仅依赖单个基因水平汇总计数时错过的中度但系统性的变化。
RNA-sequencing (RNA-seq) has rapidly become the method of choice in many genome-wide transcriptomic studies. To meet the high expectations posed by this technology, powerful computational techniques are needed to translate the measurements into biological and biomedical understanding. A number of statistical procedures have already been developed to identify differentially expressed genes between distinct sample groups. With these methods statistical testing is typically performed after the data has been summarized at the gene level. As an alternative strategy, developed with the aim to improve the results, we demonstrate a method in which statistical testing at the exon level is performed prior to the summary of the results at the gene level. Using publicly available RNA-seq datasets as case studies, we illustrate how this exon-based strategy can improve the performance of the widely used differential expression software packages as compared to the conventional gene-based strategy. In particular, we show how it enables robust detection of moderate but systematic changes that are missed when relying on single gene-level summary counts only.
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影响因子：
12.3
作者：
Laajala E;Aittokallio T;Lahesmaa R;Elo LL
通讯作者：
Elo LL
影响因子：
48
作者：
Pepke, Shirley;Wold, Barbara;Mortazavi, Ali
通讯作者：
Mortazavi, Ali
影响因子：
12.3
作者：
Rapaport F;Khanin R;Liang Y;Pirun M;Krek A;Zumbo P;Mason CE;Socci ND;Betel D
通讯作者：
Betel D
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
5.8
作者：
Roberts, Adam;Pimentel, Harold;Pachter, Lior
通讯作者：
Pachter, Lior