SpliceImpactR

SpliceImpactR systematically identifies alternative RNA isoform switches across the human transcriptome and predicts their impact on encoded protein function.

Key Features:

• Alternative RNA Processing Event Detection: Identifies isoform switches including alternative first and last exons, exon skipping, intron retention, hybrid exons, and splice site variation.
• Protein Similarity Analysis: Assesses changes in protein sequences resulting from differentially used alternative RNA processing events.
• Functional Protein Domain Analysis: Evaluates how alternative RNA processing events alter functional protein domains.
• Domain-Domain Interaction Analysis: Predicts changes to protein-protein interactions arising from alternative RNA processing events.
• Event Swap Identification: Identifies alternative RNA processing event swaps across conditions.
• Holistic Impact Analysis: Performs comprehensive analyses regarding the impact of different RNA processing events.

Scientific Applications:

• Tissue-Specific Protein Domain Regulation: Enables analysis of how alternative first exons drive tissue-specific protein domain changes across human tissues.
• Protein-Protein Interaction Disruption Prediction: Predicts disruption of protein-protein interactions caused by alternative last exons.
• Isoform Regulation Buffering Mechanism Discovery: Identifies cases where frameshifts introduced by alternative splicing are rescued by co-regulated alternative downstream exons.
• Gradual Splicing Variation Analysis: Characterizes tissue-specific gradual variation in alternative splicing rather than binary on/off behavior.

Methodology:

SpliceImpactR takes in processed data from the HIT Index and/or rMATS and identifies how differentially used alternative RNA processing events lead to changes in protein function through protein similarity, functional protein domain analysis, and domain-domain interaction changes.