The identification of switch-like alternative splicing exons among multiple samples with RNA-Seq data

Zhiyi Qin and Xuegong Zhang

PLOS ONE, 2017, vol. 12, issue 5, 1-12

Abstract: Alternative splicing is an ubiquitous phenomenon in most human genes and has important functions. The switch-like exon is the type of exon that has a high level of usage in some tissues, but has a low level of usage in the other tissues. They usually undergo strong tissue-specific regulations. There is still a lack a systematic method to identify switch-like exons from multiple RNA-seq samples. We proposed a novel method called iterative Tertile Absolute Deviation around the mode (iTAD) to profile the distribution of exon relative usages among multiple samples and to identify switch-like exons and other types of exons using a robust statistic estimator. We validated the method with simulation data, and applied it on RNA-seq data of 16 human body tissues and detected 3,100 switch-like exons. We found that switch-like exons tend to be more associated with Alu elements in their flanking intron regions than other types of exons.

Date: 2017
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0178320

DOI: 10.1371/journal.pone.0178320

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