Shared and distinct exonic parts in alternative paths of splicing bubbles

TL;DR

This paper introduces a unified framework for analyzing complex alternative splicing events with multiple competing transcript paths, using a novel graph-based approach to compare shared and distinct exonic parts across samples.

Contribution

It presents a new method for comparing multiple splicing paths using a splicing graph and bipartitioning, improving analysis of complex alternative splicing bubbles.

Findings

Analyzed more splicing bubbles than previous tools.

Provided a tractable and interpretable framework.

Enabled differential usage detection across samples.

Abstract

Alternative splicing creates complex bubbles in splicing graphs where more than two transcript paths compete, challenging methods designed for simple binary events. We present a unified framework that compares paths using distinct exonic parts observed directly from reads. We build a GrASE splicing graph (DAG) per gene, enumerate bubbles, and quantify shared and distinct exonic parts across three comparison structures. (i) all-pairwise contrasts (ii) a multinomial n-way comparison and (iii) valid bipartitions of paths. For (iii) we introduce lower-set bipartitioning, which respects subset relations among paths by enumerating downward-closed sets in a containment graph, yielding valid two-group splits with nonempty distinguishing parts. Our test statistic is the fraction of reads mapped to distinct parts relative to distinct + shared parts, enabling differential usage across samples. Applied to genome annotations, the approach examines more bubbles than prior tools while remaining tractable and interpretable.