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. 2019 Jul 2;47(W1):W191-W198.
doi: 10.1093/nar/gkz369.

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

Uku Raudvere  1 , Liis Kolberg  1 , Ivan Kuzmin  1 , Tambet Arak  1 , Priit Adler  1   2 , Hedi Peterson  1   2 , Jaak Vilo  1   2   3
Affiliations

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

Uku Raudvere et al. Nucleic Acids Res. .

Abstract

Biological data analysis often deals with lists of genes arising from various studies. The g:Profiler toolset is widely used for finding biological categories enriched in gene lists, conversions between gene identifiers and mappings to their orthologs. The mission of g:Profiler is to provide a reliable service based on up-to-date high quality data in a convenient manner across many evidence types, identifier spaces and organisms. g:Profiler relies on Ensembl as a primary data source and follows their quarterly release cycle while updating the other data sources simultaneously. The current update provides a better user experience due to a modern responsive web interface, standardised API and libraries. The results are delivered through an interactive and configurable web design. Results can be downloaded as publication ready visualisations or delimited text files. In the current update we have extended the support to 467 species and strains, including vertebrates, plants, fungi, insects and parasites. By supporting user uploaded custom GMT files, g:Profiler is now capable of analysing data from any organism. All past releases are maintained for reproducibility and transparency. The 2019 update introduces an extensive technical rewrite making the services faster and more flexible. g:Profiler is freely available at https://biit.cs.ut.ee/gprofiler.

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Figures

Figure 1.
Figure 1.
The growth of available species/strains in g:Profiler since 2012. Each column represents an archive version, the current version is highlighted in blue. The isolated peak in 1185_e69_eg16 refers to a version where we incorporated bacterial species to g:Profiler but due to differences in the underlying database structure we dropped them again from further releases.
Figure 2.
Figure 2.
Example of g:GOSt multiquery Manhattan plot. (A) Name of the query. (B) X-axis shows the functional terms grouped and colour-coded by data source. (C, D) The position of terms in the plots is fixed and terms from the same (GO) branch are close to each other. (E) P-values in the table outputs are color-coded from yellow (insignificant) to blue (highly significant). (F) Data sources that were not included in the analysis are shown in grey. (G) Hovering over the term circle shows a tooltip with the most relevant information. (H) In case of a multiquery, the same term is also highlighted on other plots. (I) The P-values from other queries are indicated in red next to the y-axis for easier comparison. (J) A click allows to pin the circles to the plot together with a numeric ID and creates a more detailed result table below the image.
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