IsoformSwitchAnalyzeR

IsoformSwitchAnalyzeR is a software tool to comprehensively characterize the differential usage of gene transcripts (isoform switching) with predicted functional consequences, particularly in the context of cancers. The tool employs methods for identifying and visualizing isoform switches, focusing on RNA-seq data from over 5,500 cancer patients across 12 solid cancer types. Approximately 19% of genes with multiple transcripts exhibit isoform switching, often leading to the loss of DNA sequence encoding protein domains. Notably, pan-cancer switches display a higher frequency of such events. The tool identifies isoform switches that serve as potent biomarkers, with 31 switches demonstrating high predictive value for patient survival across diverse cancer types.