Enhancing Interpretation of Functional Enrichment Analysis Results with Advanced Network Visualizations

Functional enrichment analysis is a cornerstone of bioinformatics data analysis, enabling researchers to put high-throughput transcriptomics or proteomics data into biological context by identifying relevant pathways, processes, and mechanisms. The clusterProfiler R package is widely used for its robust statistical methods and versatile visualization options, including bar plots, dot plots, and enrichment maps. Whereas enrichment maps reveal relationships between terms through shared gene content, their static R implementations provide limited interactive exploration and customization for complex networks with hundreds of enriched terms and also provide limited built-in support for displaying node-level properties such as pathway coverage or expression directionality. We present a complete workflow for enrichment analysis and network visualization. The protocols cover performing over-representation analysis and gene set enrichment analysis using clusterProfiler, calculating term similarity between enriched terms, and exporting networks to Cytoscape using our cyemapplot function. The approach demonstrates three complementary visualization styles: basic networks reveal functional modules and term relationships, pie chart networks quantify pathway coverage to prioritize complete versus partial perturbations, and differentially expressed gene networks integrate expression directionality and regulatory heterogeneity within biological processes. By revealing shared gene content, expression patterns, and network topology, this approach helps researchers move beyond independent term lists to extract richer mechanistic insights from high-throughput datasets. The support protocols cover established clusterProfiler and enrichplot functionality required to generate enrichment results, whereas the Basic Protocol describes the main methodological contribution of this work, the cyemapplot function and its three visualization styles. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Advanced network visualization using Cytoscape Support Protocol 1: Installing required software and packages Support Protocol 2: Preparing gene expression data Support Protocol 3: Performing enrichment analysis and calculating term similarity.