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. 2023 Jul 5;51(W1):W207-W212.
doi: 10.1093/nar/gkad347.

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

Liis Kolberg  1 , Uku Raudvere  1 , Ivan Kuzmin  1 , Priit Adler  1 , Jaak Vilo  1   2 , Hedi Peterson  1
Affiliations

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

Liis Kolberg et al. Nucleic Acids Res. .

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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Figures

Graphical Abstract
Graphical Abstract
g:Profiler is a versatile web service offering functional profiling, gene ID conversion, and orthology search capabilities. Compatible with all identifier types recognized by Ensembl, it produces detailed tables and generates interactive Manhattan plots and GO context graphs to capture essence of the results. Integration of external data is facilitated by the GMT Helper application.
Figure 1.
Figure 1.
The highlighted driver terms in a broader GO context. The driver terms have a yellow background, other significantly enriched terms have coloured frames corresponding to the enrichment P-values, and non-significantly enriched terms providing the broader context and connection to the root term have grey borders. There can be more than one driver term per component. The graph original layout was slightly modified to fit the page.
See this image and copyright information in PMC

References

    1. Cunningham F., Allen J.E., Allen J., Alvarez-Jarreta J., Amode M.R., Armean I.M., Austine-Orimoloye O., Azov A.G., Barnes I., Bennett R.et al. .. Ensembl 2022. Nucleic Acids Res. 2022; 50:D988–D995. - PMC - PubMed
    1. Gillespie M., Jassal B., Stephan R., Milacic M., Rothfels K., Senff-Ribeiro A., Griss J., Sevilla C., Matthews L., Gong C.et al. .. The Reactome Pathway Knowledgebase 2022. Nucleic Acids Res. 2022; 50:D687–D692. - PMC - PubMed
    1. Tsitsiridis G., Steinkamp R., Giurgiu M., Brauner B., Fobo G., Frishman G., Montrone C., Ruepp A.. CORUM: the comprehensive resource of mammalian protein complexes—2022. Nucleic Acids Res. 2023; 51:D539–D545. - PMC - PubMed
    1. Köhler S., Gargano M., Matentzoglu N., Carmody L.C., Lewis-Smith D., Vasilevsky N.A., Danis D., Balagura G., Baynam G., Brower A.M.et al. .. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 2021; 49:D1207–D1217. - PMC - PubMed
    1. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T.et al. .. Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000; 25:25–29. - PMC - PubMed

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