FunFEA: an R package for fungal functional enrichment analysis

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...

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Vydáno v:BMC bioinformatics Ročník 26; číslo 1; s. 138 - 12
Hlavní autoři: Charest, Julien, Loebenstein, Paul, Mach, Robert L., Mach-Aigner, Astrid R.
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 27.05.2025
BioMed Central Ltd
Springer Nature B.V
BMC
Témata:
Algorithms
Annotations
Applications software
Bioinformatics
Biological activity
Biomedical and Life Sciences
Clusters of orthologous genes (COG/KOG)
Computational Biology - methods
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Databases, Genetic
Enrichment
Enzymes
Flexibility
Functional enrichment analysis
Fungi
Fungi - genetics
Gene expression
Gene Ontology
Gene ontology (GO)
Gene set enrichment analysis
Genes
Genetic aspects
Genome, Fungal
Genomes
Genomics
Genomics - methods
KEGG pathway
Life Sciences
Metabolism
Metabolites
Microarrays
Microbiological research
Molecular Sequence Annotation - methods
Ontology
Pathogens
Proteins
Proteomics
R (Programming language)
Software
Statistical analysis
Strains (organisms)
Austria
Fungi
Functional enrichment analysis
Gene ontology (GO)
KEGG pathway
Clusters of orthologous genes (COG/KOG)
ISSN:1471-2105, 1471-2105
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Shrnutí: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.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-025-06164-7