gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler
Open accessAbstract
g:Profiler ( https://biit.cs.ut.ee/gprofiler ) is a widely used gene list functional profiling and namespace conversion toolset that has been contributing to reproducible biological data analysis already since 2007. Here we introduce the accompanying R package, gprofiler2 , developed to facilitate programmatic access to g:Profiler computations and databases via REST API. The gprofiler2 package provides an easy-to-use functionality that enables researchers to incorporate functional enrichment analysis into automated analysis pipelines written in R. The package also implements interactive visualisation methods to help to interpret the enrichment results and to illustrate them for publications. In addition, gprofiler2 gives access to the versatile gene/protein identifier conversion functionality in g:Profiler enabling to map between hundreds of different identifier types or orthologous species. The gprofiler2 package is freely available at the CRAN repository .
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A total of 455 transcripts were shared between the two datasets and pathway analysis revealed significant enrichment in transcripts of proteins of medium expression levels associated with the cerebellum and its white matter processes (HPA:0091042) (p-value = 0.004).
“A total of 455 transcripts were shared between the two datasets and pathway analysis revealed significant enrichment in transcripts of proteins of medium expression levels associated with the cerebellum and its white matter processes (HPA:0091042) using the Human Protein Atlas via the gost function of the gprofiler2 R package (p-value = 0.004, 58).”
From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [58]
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“…datasets and pathway analysis revealed significant enrichment in transcripts of proteins of medium expression levels associated with the cerebellum and its white matter processes (HPA:0091042) using the Human Protein Atlas via the gost function of the gprofiler2 R package (p-value = 0.004, 58 ).”
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- Authors
- Kolberg, L., Raudvere, U., Kuzmin, I., Vilo, J., & Peterson, H.
- Affiliations
- University of Tartu (EE)
- Corresponding author
- Peterson, Hedi
- Venue
- F1000Research
- Publisher
- F1000 Research Ltd
- Published
- 2020-11-17
- Volume
- 9
- Pages
- 709
- ISSN
- 2046-1402 (ISSN-L)
- PMC
- PMC7859841
- OpenAlex
- W3042896257
- Cited by
- 1,098
- References
- 5
- Citations by year
- 2026: 247 · 2025: 269 · 2024: 237 · 2023: 189 · 2022: 118 · 2021: 35 · 2020: 2
- FWCI
- 28.07
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- F1000Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Eesti Teadusagentuur (IUT34-4, PSG59)
- Seventh Framework Programme (ELIXIR2014-2020.4.01.16-0271)
- European Regional Development Fund (EXCITE)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- g:Profiler, R package, REST API, automated pipeline, interactive visualization, ortholog mapping, functional profiling
- MeSH terms
- Software, Computational Biology, Gene Expression Profiling
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