g:Profiler specifications

Unique identifier:
OMICS_02223
Restrictions to use:
None
Computer skills:
Basic
Maintained:
Yes
Interface:
Web user interface, Application programming interface
Input data:
A list of genes.
Stability:
Beta

Subtools

  • g:GOST
  • g:Cocoa
  • g:Convert
  • g:Sorter
  • g:Orth
  • g:SNPense
  • Animals
    • Bos taurus
    • Caenorhabditis elegans
    • Danio rerio
    • Drosophila melanogaster
    • Gallus gallus
    • Homo sapiens
    • Mus musculus
    • Rattus norvegicus
    • Xenopus tropicalis
  • Fungi
    • Saccharomyces cerevisiae
  • Plants
    • Arabidopsis thaliana

g:Profiler specifications

Unique identifier:
OMICS_02223
Restrictions to use:
None
Programming languages:
Python, R
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 3.0
Version:
0.6.1

Subtools

  • g:GOST
  • g:Cocoa
  • g:Convert
  • g:Sorter
  • g:Orth
  • g:SNPense
  • Animals
    • Bos taurus
    • Caenorhabditis elegans
    • Danio rerio
    • Drosophila melanogaster
    • Gallus gallus
    • Homo sapiens
    • Mus musculus
    • Rattus norvegicus
    • Xenopus tropicalis
  • Fungi
    • Saccharomyces cerevisiae
  • Plants
    • Arabidopsis thaliana

versioning

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No versioning.

g:Profiler distribution

download

g:Profiler support

Documentation

Maintainers

  • Jaak Vilo <>
  • Tambet Arak <>
This tool is not maintained anymore.

Additional information

https://pypi.python.org/pypi/gprofiler-official

forum

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Credits

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Publications

Institution(s)

Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Institute of Computer Science, University of Tartu, Tartu, Estonia

Funding source(s)

Estonian Research Council (IUT34-4), European Regional Development fund through the EXCS and BioMedIT projects, Estonia’s Integration to the European Bioinformatics Infrastructure (ELIXIR) and OICR Investigator Award.

User review

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1 user review

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xtYaoNYU

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Functional annotation enrichment analysis is a powerful first step to understanding an interesting list of genes or gene products.

When I do it, I want the tool to have at least these features:
1) Up-to-date GO annotation data, and support as many other databases as possible;
2) Recognizing multiple types of gene or protein identifier, and do the conversion in the background;
3) Comprehensive filter to reduce or organize the hierarchically inter-related terms to minimize redundancy;
4) Good visualization;
5) Fast.

Of about a dozen different tools I have tried, gProfiler is the only one I found satisfying all. Plus, it has an API in R, which is a life-saver.

One thing that could be improved is to include annotation term clustering according to their semantic or functional similarity (you can try DAVID for this).

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