BCC2020

➞ Abstract
We have developed a pipeline in the form of R-package that includes methods to find; most common alternative splicing (AS) events (cassette exons and introns, S. S. Tabrez, Nat. Commun., vol. 8, no. 1, p. 306), the number of isoform expressed in particular condition using AS events, construction of isoform structure using information of alternative splicing events and meta‐features, and survival analysis based of these AS events. Most commonly used survival methods for retrospective study of clinical data undermine the contributions of differential alternative splicing of genes. SURVIV, a statistical method, identifies and associates mRNA isoform variation with survival time in both censored and uncensored large- scale RNA-seq data. In FASE pipeline, we have designed a novel strategy to predict survival analysis and isoform structure using exons/intron level RNA expression counts combined to associated meta-features in a given splicing condition, i.e. flanking junction and skipping junction to the respective exons/introns. Using TCGA-BRCA cohorts, we have shown that contribution of post-transcriptional regulatory events needs to be considered for better interpretation of clinical outcome of cancer patients (Unpublished data).
In addition, the pipelines can also be used to find differentially expressed gene using limma framework and has incorporated several automatic wrappers that allows pre-processing of RNA-Seq data for 1) Mapping of raw reads to genome using TopHat2 and 2) Counting of mapped reads through Rsubread package.