Differential transcript usage analysis incorporating quantification uncertainty via compositional measurement error regression modeling.

ABSTRACT: Differential transcript usage (DTU) occurs when the relative expression of multiple transcripts arising from the same gene changes between different conditions. Existing approaches to detect DTU often rely on computational procedures that can have speed and scalability issues as the number of samples increases. Here we propose a new method, CompDTU, that uses compositional regression to model the relative abundance proportions of each transcript that are of interest in DTU analyses. This procedure leverages fast matrix-based computations that make it ideally suited for DTU analysis with larger sample sizes. This method also allows for the testing of and adjustment for multiple categorical or continuous covariates. Additionally, many existing approaches for DTU ignore quantification uncerta

SUBMITTER: Young AM 

PROVIDER: S-EPMC11017126 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature