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. 2016 Jul 8;44(W1):W83-9.
doi: 10.1093/nar/gkw199. Epub 2016 Apr 20.

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

Jüri Reimand  1 , Tambet Arak  2 , Priit Adler  2 , Liis Kolberg  2 , Sulev Reisberg  2 , Hedi Peterson  2 , Jaak Vilo  3
Affiliations

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

Jüri Reimand et al. Nucleic Acids Res. .

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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Figures

Figure 1.
Figure 1.
We predicted regulatory motifs from the TRANSFAC database for nine species shown on the x-axis. We used 6 kb promoter regions (±3 kb) upstream the transcription start sites for vertebrates, 2 kb promoters for fly and worm and 1000 bp promoters for yeast. TFBS matches per promoter are given with boxplots on the y-axis where the mean number of sites per promoter per TF is depicted with a black diamond.
Figure 2.
Figure 2.
Total number of annotations terms per eight most common organisms in g:GOSt. Each colour represents different functional resource and the largest one (GO) is depicted with orange. Supplementary Figure S1 shows a similar overview of all 213 organisms.
Figure 3.
Figure 3.
BioJS output from the MEM tool depicting processes and functions related to embryonic stem cells.
Figure 4.
Figure 4.
Since 2011 the underlying human datasets in g:Profiler have been steadily growing. The majority of the functional resources have grown as depicted over the 13 latest g:Profiler versions. The number of mapped human genes has also grown by 20% from 26 000 to 31 000. As an exception, the Reactome dataset has decreased as we filtered out gene sets corresponding to reactions starting from g:Profiler version R1353.
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