FunFEA: an R package for fungal functional enrichment analysis

Abstract

Abstract Background The functional annotation of fungal genomes is critical for understanding their biological processes and ecological roles. While existing tools support functional enrichment analysis from publicly available annotations of well-established model organisms, few are tailored to the specific needs of the fungal research community. Furthermore, many tools struggle with processing functional annotations of novel species, for which no publicly available functional annotations are yet available. Results FunFEA is an R package designed for functional enrichment analysis of fungal genomes. It supports COG/KOG (Clusters of Orthologous Genes), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations, and generates background frequency models from publicly available annotations for overrepresentation analysis, within a set of experimentally defined genes or proteins. Additionally, FunFEA can process eggNOG-mapper annotations, thus enabling functional enrichment analysis of novel genomes. The package offers a suite of tools for generation of background frequency models, functional enrichment analysis, as well as visualization of enriched functional categories. On release, the package includes precomputed models for 65 commonly used fungal strains in academic research and strains listed on the WHO fungal priority pathogens list. Conclusions FunFEA fills a critical need for a specialized tool in fungal genomics, providing valuable insights into fungal biology. Additionally, its ability to process eggNOG-mapper annotations makes it an essential resource for researchers, helping to drive further exploration of fungal functional diversity and pathways and derive biological insights from novel genomes.

Keywords

• Clusters of orthologous genes (COG/KOG)
• Gene ontology (GO)
• KEGG pathway
• Fungi
• Functional enrichment analysis