FunFEA

FunFEA performs fungal functional enrichment analysis using COG/KOG, GO, and KEGG annotations, with support for generating background frequency models from publicly available annotations for overrepresentation analysis.

Key Features:

• Annotation Support: FunFEA supports COG/KOG (Clusters of Orthologous Genes), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations for functional enrichment analysis.
• Background Frequency Model Generation: FunFEA generates background frequency models from publicly available annotations for overrepresentation analysis within experimentally defined gene or protein sets.
• Novel Genome Processing: FunFEA processes eggNOG-mapper annotations to enable functional enrichment analysis of novel fungal genomes lacking publicly available functional annotations.
• Precomputed Models: FunFEA includes precomputed background frequency models for 65 commonly used fungal strains in academic research and strains listed on the WHO fungal priority pathogens list.
• Visualization: FunFEA provides tools for visualization of enriched functional categories.

Scientific Applications:

• Novel Fungal Species Analysis: FunFEA enables functional enrichment analysis of novel fungal species for which no publicly available functional annotations exist.
• Model Organism Analysis: FunFEA supports functional enrichment analysis of well-established fungal model organisms using standard COG/KOG, GO, and KEGG annotations.
• Pathogen Research: FunFEA facilitates functional analysis of strains on the WHO fungal priority pathogens list through included precomputed models.
• Biological Insight Generation: FunFEA helps derive biological insights from fungal genomes by identifying enriched functional categories and pathways.

Methodology:

FunFEA performs overrepresentation analysis using background frequency models generated from publicly available annotations, applied to experimentally defined gene or protein sets; the package processes eggNOG-mapper annotations to enable analysis of novel genomes.