1. SUVA: splicing site usage variation analysis from RNA-seq data reveals highly conserved complex splicing biomarkers in liver cancer.
- Author
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Cheng C, Liu L, Bao Y, Yi J, Quan W, Xue Y, Sun L, and Zhang Y
- Subjects
- Biomarkers, Tumor genetics, Computational Biology methods, Humans, Liver Neoplasms genetics, Liver Neoplasms metabolism, Prognosis, RNA-Binding Proteins genetics, Sequence Analysis, RNA, Survival Rate, Alternative Splicing, Biomarkers, Tumor metabolism, Gene Expression Regulation, Neoplastic, Liver Neoplasms pathology, RNA-Binding Proteins metabolism, RNA-Seq methods, Software
- 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.
- Published
- 2021
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