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

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  • Zhiyi Qin
  • Xuegong Zhang

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.

Suggested Citation

  • Zhiyi Qin & Xuegong Zhang, 2017. "The identification of switch-like alternative splicing exons among multiple samples with RNA-Seq data," PLOS ONE, Public Library of Science, vol. 12(5), pages 1-12, May.
    • Handle: RePEc:plo:pone00:0178320
    DOI: 10.1371/journal.pone.0178320
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    1. Eric T. Wang & Rickard Sandberg & Shujun Luo & Irina Khrebtukova & Lu Zhang & Christine Mayr & Stephen F. Kingsmore & Gary P. Schroth & Christopher B. Burge, 2008. "Alternative isoform regulation in human tissue transcriptomes," Nature, Nature, vol. 456(7221), pages 470-476, November.
    2. Timothy W. Nilsen & Brenton R. Graveley, 2010. "Expansion of the eukaryotic proteome by alternative splicing," Nature, Nature, vol. 463(7280), pages 457-463, January.
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