Quantitative visualization of alternative exon expression from RNA-seq data
Quantitative visualization of alternative exon expression from RNA-seq data
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DOI：
10.1093/bioinformatics/btv034
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发表时间：
2015-07-15
期刊：
影响因子：
5.8
通讯作者：
Burge, Christopher B.
中科院分区：
文献类型：
--
作者：
Katz, Yarden;Wang, Eric T.;Burge, Christopher B.
动机：RNA测序（RNA-Seq）数据分析显示，绝大多数人类基因表达多种mRNA亚型，通过选择性前mRNA剪接和其他机制产生，并且大多数选择性亚型在人类组织之间的表达不同。随着RNA-Seq数据集规模的增长，在多个样本中可视化异构体表达仍然具有挑战性。结果：为了帮助解决这个问题，我们提出了Sashimi图，对齐的RNA-Seq读数的定量可视化，可以在样本或实验条件下定量比较外显子的使用。生鱼片图可以使用Broad Integrated Genome Viewer或独立的命令行程序制作。
Motivation: Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples.Results: To help address this problem, we present Sashimi plots, a quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer or with a stand-alone command line program.