IsoformSwitchAnalyzeR

IsoformSwitchAnalyzer identifies and analyzes isoform switches with predicted functional consequences from RNA-seq datasets to investigate alternative transcript usage and its effects on protein domains and nonsense-mediated decay (NMD) sensitivity.

Key Features:

• Identification of Isoform Switches: Detects changes in the usage of transcript isoforms from the same gene between different conditions (isoform switching).
• Functional Consequence Prediction: Predicts potential functional consequences of switches, including gains or losses of protein domains and alterations in NMD sensitivity.
• Data Compatibility: Supports direct import of transcript quantification outputs from Cufflinks/Cuffdiff, Kallisto, Salmon, and RSEM.
• Visualization: Provides methods for visualization of identified isoform switches.

Scientific Applications:

• Cancer Research: Systematically characterizes isoform switching across cancer using RNA-seq data from over 5,500 patients spanning 12 solid cancer types, finding that approximately 19% of multiple-transcript genes exhibited isoform switches with potential functional consequences.
• Biomarker Discovery: Identified isoform switches as candidate biomarkers, including 31 switches that were highly predictive of patient survival across different cancer types.

Methodology:

Employs computational methods for identification and visualization of isoform switches and accepts transcript quantification outputs from Cufflinks/Cuffdiff, Kallisto, Salmon, and RSEM.