Kristoffer Vitting-Seerup1, Albin Sandelin1. 1. The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, 2200 Copenhagen N, Denmark.
Abstract
SUMMARY: Alternative splicing is an important mechanism involved in health and disease. Recent work highlights the importance of investigating genome-wide changes in splicing patterns and the subsequent functional consequences. Current computational methods only support such analysis on a gene-by-gene basis. Therefore, we extended IsoformSwitchAnalyzeR R library to enable analysis of genome-wide changes in specific types of alternative splicing and predicted functional consequences of the resulting isoform switches. As a case study, we analyzed RNA-seq data from The Cancer Genome Atlas and found systematic changes in alternative splicing and the consequences of the associated isoform switches. AVAILABILITY AND IMPLEMENTATION: Windows, Linux and Mac OS: http://bioconductor.org/packages/IsoformSwitchAnalyzeR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Alternative splicing is an important mechanism involved in health and disease. Recent work highlights the importance of investigating genome-wide changes in splicing patterns and the subsequent functional consequences. Current computational methods only support such analysis on a gene-by-gene basis. Therefore, we extended IsoformSwitchAnalyzeR R library to enable analysis of genome-wide changes in specific types of alternative splicing and predicted functional consequences of the resulting isoform switches. As a case study, we analyzed RNA-seq data from The Cancer Genome Atlas and found systematic changes in alternative splicing and the consequences of the associated isoform switches. AVAILABILITY AND IMPLEMENTATION: Windows, Linux and Mac OS: http://bioconductor.org/packages/IsoformSwitchAnalyzeR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Volker Boehm; Sabrina Kueckelmann; Jennifer V Gerbracht; Sebastian Kallabis; Thiago Britto-Borges; Janine Altmüller; Marcus Krüger; Christoph Dieterich; Niels H Gehring Journal: Nat Commun Date: 2021-06-25 Impact factor: 14.919