ASpediaFI

ASpediaFI, the Alternative Splicing Encyclopedia: Functional Interaction, is a novel application designed to systematically identify differential alternative splicing (DAS) events and co-regulated genes and pathways. Traditional DAS gene test methods focus on statistical tests to extract DAS events, but more is needed to capture the relevant biological processes sufficiently. ASpediaFI addresses this limitation by establishing a heterogeneous interaction network that includes genes and their feature nodes (AS events and pathways) connected by co-expression or pathway gene set knowledge.
ASpediaFI utilizes the random walk with restart algorithm to explore the interaction network and assess the proximity from a query gene set. Based on this analysis, the tool then extracts significant AS events, genes, and pathways. Performance evaluations using simulated RNA sequencing datasets, considering various conditions of sequencing depth and sample size, demonstrate ASpediaFI's strong performance compared to other methods. Additionally, analysis of three public datasets of cancer patients or cell lines illustrates ASpediaFI's ability to detect biologically relevant candidates.