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Nucleic Acids Research Advance Access published online on May 3, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm226
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Paper

g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments

Jüri Reimand1, Meelis Kull1,2,3, Hedi Peterson2,3, Jaanus Hansen1 and Jaak Vilo1,2,3,*

1Institute of Computer Science, University of Tartu, Liivi 2, 50409 Tartu, Estonia, 2Estonian Biocentre, Riia 23b, 51010 Tartu, Estonia and 3EGeen, Ülikooli 6a, 51003 Tartu, Estonia

*To whom correspondence should be addressed. Tel: +372 50 49 365; Fax: +372 737 5468; Email: Jaak.Vilo{at}ut.ee

Received January 31, 2007. Revised March 22, 2007. Accepted March 28, 2007.

g:Profiler (http://biit.cs.ut.ee/gprofiler/) is a public web server for characterising and manipulating gene lists resulting from mining high-throughput genomic data. g:Profiler has a simple, user-friendly web interface with powerful visualisation for capturing Gene Ontology (GO), pathway, or transcription factor binding site enrichments down to individual gene levels. Besides standard multiple testing corrections, a new improved method for estimating the true effect of multiple testing over complex structures like GO has been introduced. Interpreting ranked gene lists is supported from the same interface with very efficient algorithms. Such ordered lists may arise when studying the most significantly affected genes from high-throughput data or genes co-expressed with the query gene. Other important aspects of practical data analysis are supported by modules tightly integrated with g:Profiler. These are: g:Convert for converting between different database identifiers; g:Orth for finding orthologous genes from other species; and g:Sorter for searching a large body of public gene expression data for co-expression. g:Profiler supports 31 different species, and underlying data is updated regularly from sources like the Ensembl database. Bioinformatics communities wishing to integrate with g:Profiler can use alternative simple textual outputs.


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