GOATEA: gene set enrichment analysis in R with shiny interactive visualizations

High-throughput genomic and proteomic technologies are used to study biological systems by performing differential expression analysis across various experimental conditions. Geneset Ordinal Association Test (GOAT) is an analytic method recently introduced to statistically evaluate the differential expression of a defined set of genes or proteins. Despite the availability of numerous enrichment tools, many lack accessibility for users without programming expertise, provide limited continuation beyond listing top enriched terms, and offer little support for interactive visual exploration or hypothesis generation. Moreover, existing web-based platforms rarely support multi-contrast comparisons and generally omit gene-level or network-based context for pathway analysis.

To address these limitations, we present Geneset Ordinal Association Test Enrichment Analysis (GOATEA), an R/Shiny application that implements and extends the GOAT algorithm with interactive visualization, multi-contrast comparison, and integrated gene- and network-based context for bottom-up pathway analysis, enabling comprehensive enrichment analysis. GOATEA supports independent analysis of transcriptomic and proteomic data. To demonstrate its capability to integrate matched modalities, we applied it to the Colameo dataset containing paired mass spectrometry and RNA sequencing data. This proof-of-concept example highlights the tool's strength in enabling multi-omics analyses and simultaneous comparison of multiple contrasts. An interactive overlap analysis identified 458 shared genes for focused enrichment and network exploration. By integrating these results in a gene- and network-based context for bottom-up pathway analysis, GOATEA applies a stringent interaction confidence threshold to emphasize qualitative protein-protein interactions, highlighting topic-relevant associations for further hypothesis generation.

GOATEA streamlines enrichment analysis workflows by combining the GOAT algorithm with interactive visualizations in a user-friendly graphical interface. It facilitates exploratory analysis and hypothesis generation for researchers with or without programming expertise. GOATEA is available as an open-source tool, with full documentation, including usage vignettes ( https://mauritsunkel.github.io/goatea/ ).