J. Reimand, T. Arak, P. Adler, L. Kolberg, S. Reisberg, H. Peterson, J. Vilo:
g:Profiler -- a web server for functional interpretation of gene lists (2016
update) Nucleic Acids Research 2016; doi: 10.1093/nar/gkw199 (PDF
Welcome to g:Profiler!
public web server for characterising and manipulating gene lists of
high-throughput genomics. g:Profiler has a simple user-friendly web
interface with powerful visualisation and is currently available for 80+
species, including mammals, plants, fungi, insects, etc from Ensembl and
Ensembl Genomes. g:Profiler is normally updated every two months in sync
with Ensembl. g:Profiler consists of the following tools:
- g:GOSt, the core of the
g:Profiler, performs statistical enrichment analysis to provide
interpretation to user-provided gene lists, ordered gene lists and
chromosomal regions. We study multiple sources of functional evidence,
including Gene Ontology terms, biological pathways, regulatory motifs
of transcription factors and microRNAs, human disease annotations and
- g:Cocoa is an enrichment
tool for collections of several gene lists. The compact output of
g:Cocoa allows a condensed and minimal view of functional enrichments
in dozens of gene lists, and provides means to rank and compare gene
lists through their functional annotations.
- g:Convert is a gene
identifier conversion tool. It uses information in Ensembl databases to
handle hundreds of types of IDs for genes, proteins, transcripts,
microarray probesets, etc, for many species, experimental platforms and
biological databases. g:Convert is flexible: it accepts a mixed list of
IDs and recognises their types automatically.
- g:Orth is a tool for
mapping homologous genes across related organisms. Given a selected
target organism, g:Orth retrieves the genes of the target that are
similar in sequence to the initial genes in input.
- g:SNPense is a tool for
mapping human single nucleotide polymorphisms (SNP) to gene names, chromosomal locations
and variant consequence terms from Sequence Ontology.
g:Profiler has a R package and other
for integration into your codebase.
g:Profiler is developed and maintained in Estonia
, at the University of
, Institute of Computer Science
Bioinformatics, Algorithmics and Data Mining
. The main development has been done over the years by Jüri Reimand, Tambet Arak, Ivan Kuzmin, Uku Raudvere.
The development team is lead by Prof. Jaak Vilo (principal investigator of BIIT).
Over the time, g:Profiler has received valuable contributions from BIIT members, notably
Priit Adler, Jaanus Hansen, Liis Kolberg, Raivo Kolde, Meelis Kull, Hedi Peterson and Sulev Reisberg.
The first version of g:Profiler was known as GOSt (Gene Ontology Statistics) and became available in early 2005.
g:Profiler tool is freely available through web application and various
programatic access points
g:Profiler is an ELIXIR
Publications and theses:
- Jüri Reimand, Tambet Arak, Priit Adler, Liis Kolberg, Sulev Reisberg, Hedi Peterson,
Jaak Vilo: g:Profiler -- a web server for functional interpretation of gene lists (2016
update) Nucleic Acids Research 2016; doi: 10.1093/nar/gkw199 [PDF].
- Jüri Reimand, Tambet Arak, Jaak Vilo: g:Profiler -- a web server for functional
interpretation of gene lists (2011 update) Nucleic Acids Research 2011; doi:
- Jüri Reimand, Meelis Kull, Hedi Peterson, Jaanus Hansen, Jaak Vilo: g:Profiler
— a web-based toolset for functional profiling of gene lists from large-scale
experiments. (2007) Nucleic Acids Research 35 Web Server issue [PDF].
- Jüri Reimand: Functional analysis of gene lists, networks and regulatory
systems. (2010) Doctor of Philosophy (PhD) thesis, University of Tartu, Estonia.
- Jüri Reimand: Gene Ontology mining tool GOSt.
(2006) Master of Science thesis, University of Tartu [PDF].
We acknowledge financial support from EU FP6 COBRED, ENFIN, ETF7437 MEM, EITSA, ERDF through EXCS and BioMedIT funding projects,
Estonian Research Council (IUT34-4); European Regional Development Fund for CoE of Estonian ICT research EXCITE projects;
Estonia’s Integration to the European Bioinformatics Infrastructure (ELIXIR); European Union through the Structural Fund
(Project No 2014-2020.4.01.16-0271, ELIXIR). JR thanks M.Curie Biostar, and U.Agur and A.Lind foundations for fellowships.
University of Tartu HPC centre has provided valuable computing resources.
Bioinformatics, Algorithmics, and Data Mining group BIIT
Institute of Computer Science
University of Tartu
Address: Liivi 2-314, Tartu 50409, Estonia
Please use our online contact
questions and software support.