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. 2021 Oct 15;18(sup1):157-171.
doi: 10.1080/15476286.2021.1940037. Epub 2021 Jun 21.

SUVA: splicing site usage variation analysis from RNA-seq data reveals highly conserved complex splicing biomarkers in liver cancer

Chao Cheng  1   2 , Lei Liu  3 , Yongli Bao  3 , Jingwen Yi  3 , Weili Quan  1 , Yaqiang Xue  1 , Luguo Sun  3 , Yi Zhang  1   2
Affiliations

SUVA: splicing site usage variation analysis from RNA-seq data reveals highly conserved complex splicing biomarkers in liver cancer

Chao Cheng et al. RNA Biol. .

Abstract

Most of the current alternative splicing (AS) analysis tools are powerless to analyse complex splicing. To address this, we developed SUVA (Splice sites Usage Variation Analysis) that decomposes complex splicing events into five types of splice junction pairs. By analysing real and simulated data, SUVA showed higher sensitivity and accuracy in detecting AS events than the compared methods. Notably, SUVA detected extensive complex AS events and screened out 69 highly conserved and dominant AS events associated with cancer. The cancer-associated complex AS events in FN1 and the co-regulated RNA-binding proteins were significantly correlated with patient survival.

Keywords: Alternative splicing; as; complex splicing; fn1; liver cancer; splicing biomarker; splicing site usage.

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Figures

Figure 1.
Figure 1.
Overview of SUVA
Figure 2.
Figure 2.
Complex splicing result in inaccuracy of definition and quantitative for ‘simple’ definition of AS
Figure 3.
Figure 3.
SUVA was tested under multiple confounding factors
Figure 4.
Figure 4.
SUVA was compared with other methods for AS analysis using cancer samples data and simulated data with or without repetition
Figure 5.
Figure 5.
SUVA detects a mass of regulated complex alternative AS events in liver cancer
Figure 6.
Figure 6.
Recurrent complex AS of FN1 signature predicts poor overall patient survival
See this image and copyright information in PMC

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References

    1. Black DL. Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology. Cell. 2000;103(3):367–370. - PubMed
    1. Blencowe BJ. Alternative splicing: new insights from global analyses. Cell. 2006;126(1):37–47. - PubMed
    1. Pan Q, Shai O, Lee LJ, et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008;40(12):1413–1415. - PubMed
    1. Sultan M, Schulz MH, Richard H, et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (New York, NY). 2008;321(5891):956–960. - PubMed
    1. Nilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature. 2010;463(7280):457–463. - PMC - PubMed

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Grants and funding

This study is supported by grant from ABLife Inc. (ABL2013-05027);Research Foundation of Jilin Provincial Science & Technology Committee [20200404124YY;20200201135JC;20190304026YY].