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Cited by 1,673Bioinformatics and Genomic NetworksGenomics and Phylogenetic StudiesBiomedical Text Mining and Ontologies

g:Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update)

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Kolberg, Liis, Raudvere, Uku, Kuzmin, Ivan, Adler, Priit, Vilo, Jaak, Peterson, Hedi·2023·Nucleic Acids Research
DOI 10.1093/nar/gkad347PMC PMC10320099
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Abstract

g:Profiler is a reliable and up-to-date functional enrichment analysis tool that supports various evidence types, identifier types and organisms. The toolset integrates many databases, including Gene Ontology, KEGG and TRANSFAC, to provide a comprehensive and in-depth analysis of gene lists. It also provides interactive and intuitive user interfaces and supports ordered queries and custom statistical backgrounds, among other settings. g:Profiler provides multiple programmatic interfaces to access its functionality. These can be easily integrated into custom workflows and external tools, making them valuable resources for researchers who want to develop their own solutions. g:Profiler has been available since 2007 and is used to analyse millions of queries. Research reproducibility and transparency are achieved by maintaining working versions of all past database releases since 2015. g:Profiler supports 849 species, including vertebrates, plants, fungi, insects and parasites, and can analyse any organism through user-uploaded custom annotation files. In this update article, we introduce a novel filtering method highlighting Gene Ontology driver terms, accompanied by new graph visualizations providing a broader context for significant Gene Ontology terms. As a leading enrichment analysis and gene list interoperability service, g:Profiler offers a valuable resource for genetics, biology and medical researchers. It is freely accessible at https://biit.cs.ut.ee/gprofiler.

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  • Functional enrichment analysis was done using the g:Profiler web interface, querying cluster markers against the GO biological process database with g:SCS multiple testing correction and a significance threshold of 0.05.

    “This was done using g:Profiler web interface, where the cluster markers were queried against GO biological process database, with g:SCS multiple testing correction method applying significance threshold of 0.05 (Kolberg et al, 2023).”

    From APOE from astrocytes restores Alzheimer’s Aβ-pathology and DAM-like responses in APOE deficient microglia (2024) · cites this paper as Kolberg et al, 2023

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Cited by

Sorted by citations

Authors
Kolberg, L., Raudvere, U., Kuzmin, I., Adler, P., Vilo, J., & Peterson, H.
Affiliations
  • University of Tartu (EE)
  • Software Technology and Applications Competence Center (EE)
Corresponding author
Peterson, Hedi
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2023-05-05
Volume
51
Issue
W1
Pages
W207-W212
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkad347
PMC
PMC10320099
OpenAlex
W4372332501
Cited by
1,673
References
3
Citations by year
2026: 663 · 2025: 656 · 2024: 340 · 2023: 12 · 2021: 2
FWCI
145.35
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • European Regional Development Fund (2014-2020.4.01.16-0271)
  • Estonian Research Council (TT11, PRG1844)
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
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
Keywords
g:Profiler, functional enrichment, Gene Ontology, KEGG, TRANSFAC, web services, network visualization, reproducibility
MeSH terms
Animals, Chromosome Mapping, Genes, Humans, Software, User-Computer Interface, Reproducibility of Results, Computational Biology, Internet, Databases, Genetic

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