Expedition

Expedition analyzes single-cell alternative splicing to detect and characterize isoform diversity and splicing modality dynamics across individual cells.

Key Features:

• Outrigger: A de novo splice graph transversal algorithm that detects alternative splicing events within individual cells by constructing a comprehensive map of possible exon combinations.
• Anchor: A Bayesian approach that assigns modalities to detected AS events, distinguishing unimodal and bimodal splicing patterns.
• Bonvoyage: Uses non-negative matrix factorization to visualize changes in modality across single cells.
• Bimodal exon characterization: Identifies bimodal exons that exhibit flanking conserved intronic sequences with distinct cis-regulatory motifs and that preserve the reading frame.
• Quantitative detection: Quantifies that up to 20% of AS exons exhibit bimodality during neuronal differentiation of pluripotent stem cells.
• Dynamic splicing analysis: Detects changes in splicing modality across cellular transitions to reveal cell-type-specific splicing dynamics.

Scientific Applications:

• Single-cell differentiation profiling: Applied to single pluripotent stem cells undergoing neuronal differentiation to reveal widespread bimodal splicing.
• Cell-type-specific splicing discovery: Reveals isoform-level variation that can distinguish cellular states beyond conventional gene expression analysis.
• Cis-regulatory motif analysis: Associates bimodal exons with conserved intronic motifs to investigate regulatory mechanisms of alternative splicing.

Methodology:

Computational methods include Outrigger's de novo splice graph transversal algorithm to map exon combinations, Anchor's Bayesian modality assignment for unimodal versus bimodal classification, and Bonvoyage's non-negative matrix factorization for visualization of modality changes.