Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases

Abstract

Alternative splicing (AS) is an important aspect of gene regulation. Nevertheless, its role in molecular processes and pathobiology is far from understood. A roadblock is that tools for the functional analysis of AS-set events are lacking. To mitigate this, we developed NEASE, a tool integrating pathways with protein-protein and domain-domain interactions to functionally characterize AS events. We show in four application cases how NEASE can identify pathways contributing to tissue identity and cell type development, and how it highlights splicing-related biomarkers. With a unique view on AS, NEASE generates unique and meaningful biological insights complementary to classical pathways analysis.

ASTK: a machine learning-based integrative software for alternative splicing analysis

“…In fact, not all AS events have functional relevance, therefore, identifying the meaningful changes in the protein structure and protein-protein interactions caused by spliced exons will provide important biological insights into individual AS events or isoform switches. We took advantage of NEASE [21], a bioinformatics tool integrating pathways with structural annotations of protein-protein interactions for human genes, to functionally characterize AS events in the human transcriptomes. Using RNAseq data of human embryonic stem cells at seven early neural differentiation time points (0-72 h) [34], we demonstrated that NEASE can reveal the functional impact of spliced exons, which are complementary to the gene-level enrichment analysis.…”

“…Even though various computational tools have been developed to quantify transcript isoforms and identify splicing events [20][21][22][23][24], functional characterization of AS events has proven to be challenging. Gene-level enrichment analyses such as GO, KEGG, and GSEA generally focus on differential AS genes.…”

“…Hence, we use simplifyEnrichment R package [26] to simplify enrichment results generated by clusterProfiler. Exon-level enrichment analysis is performed by the NEASE method, which allows us to specifically identify the structural impacts of spliced exons and how the protein-protein interactions remodeled in human [21]. Furthermore, alternative exons often encode intrinsically disordered regions, which are enriched with functional peptide modules, named short linear motifs (SLiMs) [27, 28].…”

Systematic analysis of alternative splicing in time course data using Spycone

“…With temporal patterns of the clusters, Spycone dissects context-specific processes in terms of AS. In order to gain functional knowledge of the clusters, Spycone offers GSEApy [18] and NEASE [19] for gene set enrichment analysis. The former conducts classical enrichment analysis for multiple ontologies and pathway databases [20].…”

“…Gene set enrichment method is performed using Fisher's exact test. NEASE [19] is an enrichment method for co-regulated alternative exons. We used NEASE with KEGG and Reactome pathways.…”