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g:Profiler—a web server for functional interpretation of gene lists (2016 update)

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Reimand, Jüri, Arak, Tambet, Adler, Priit, Kolberg, Liis, Reisberg, Sulev, Peterson, Hedi, Vilo, Jaak·2016·Nucleic Acids Research
DOI 10.1093/nar/gkw199PMC PMC4987867
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Abstract

Functional enrichment analysis is a key step in interpreting gene lists discovered in diverse high-throughput experiments. g:Profiler studies flat and ranked gene lists and finds statistically significant Gene Ontology terms, pathways and other gene function related terms. Translation of hundreds of gene identifiers is another core feature of g:Profiler. Since its first publication in 2007, our web server has become a popular tool of choice among basic and translational researchers. Timeliness is a major advantage of g:Profiler as genome and pathway information is synchronized with the Ensembl database in quarterly updates. g:Profiler supports 213 species including mammals and other vertebrates, plants, insects and fungi. The 2016 update of g:Profiler introduces several novel features. We have added further functional datasets to interpret gene lists, including transcription factor binding site predictions, Mendelian disease annotations, information about protein expression and complexes and gene mappings of human genetic polymorphisms. Besides the interactive web interface, g:Profiler can be accessed in computational pipelines using our R package, Python interface and BioJS component. g:Profiler is freely available at http://biit.cs.ut.ee/gprofiler/.

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  • Significantly SV genes in breast cancer were enriched for collagens, which distinguish tissue substructure (Reactome "Collagen formation", P = 3.38 * 10-14).

    “Significantly SV genes were enriched for collagens, which distinguish tissue substructure13 (Reactome “Collagen formation”, P = 3.38 * 10-14, gProfiler14, Supp. Table 1).”

    From SpatialDE: identification of spatially variable genes (2018) · cites this paper as [14]

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Cited by

Sorted by citations

Authors
Reimand, J., Arak, T., Adler, P., Kolberg, L., Reisberg, S., Peterson, H., & Vilo, J.
Affiliations
  • Ontario Institute for Cancer Research (CA)
  • University of Tartu (EE)
Corresponding author
Vilo, Jaak
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2016-04-20
Volume
44
Issue
W1
Pages
W83-W89
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkw199
PMC
PMC4987867
OpenAlex
W2918086501
Cited by
1,229
References
2
Citations by year
2026: 38 · 2025: 57 · 2024: 108 · 2023: 88 · 2022: 109 · 2021: 160 · 2020: 167 · 2019: 209 · 2018: 156 · 2017: 111 · 2016: 18 · 2015: 6 · 2014: 1 · 2013: 1
FWCI
70.48
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HighWire Press Open Archive (submittedVersion)
Funders
  • Eesti Teadusagentuur (IUT34-4)
  • European Regional Development Fund
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
g:Profiler, functional enrichment, gene list, Gene Ontology, biological pathways, web server, transcription factor binding sites, protein complexes, genetic polymorphism, R package
MeSH terms
Animals, Binding Sites, Computer Graphics, Fungi, Gene Expression Regulation, Humans, Insecta, Plants, Protein Binding, Transcription Factors, User-Computer Interface, Vertebrates, Internet, Gene Expression Profiling, Molecular Sequence Annotation, Gene Ontology

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