g:Profiler pipeline

g:Profiler specifications

Information


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

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Mammals
    • Bos taurus
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus
    • Xenopus tropicalis

Subtools


  • g:Cocoa
  • g:Convert
  • g:GOST
  • g:Orth
  • g:SNPense
  • g:Sorter

Documentation


Maintainers


  • person_outline Jaak Vilo <>
  • person_outline Tambet Arak <>

Additional information


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

Information


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

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Mammals
    • Bos taurus
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus
    • Xenopus tropicalis

Subtools


  • g:Cocoa
  • g:Convert
  • g:GOST
  • g:Orth
  • g:SNPense
  • g:Sorter

Download


Versioning


Add your version

Documentation


Maintainers


This tool is not maintained anymore.

Additional information


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

Publications for g:Profiler

g:Profiler IN pipelines

 (8)
2017
PMCID: 5415337
PMID: 28508063
DOI: 10.1126/sciadv.1602505

[…] analyzed using mtt solution provided with the kit according to the manufacturer’s protocol. the data from six independent experiments were expressed as means ± sd., go analysis was peformed using g:profiler. subsets of genes that were enriched in go function were queried against the physical protein interaction databases corum and biogrid (biological general repository for interaction […]

2016
PMCID: 5049392
PMID: 27543604
DOI: 10.1093/jxb/erw307

[…] hy5 and hyh ‘guide’ genes were retained from the three data sets and merged into a final aggregate network. enrichment of gene ontology (go) categories within co-expressed genes was determined using g:profiler (http://biit.cs.ut.ee/gprofiler/) at a significance threshold of fdr <0.05., grapevine promoter sequences (1kb upstream of the transcription start sites, tss) were downloaded […]

2015
PMCID: 4303425
PMID: 25611800
DOI: 10.1371/journal.pgen.1004919

[…] corresponds to robust z-score z≥2 of tissues per gene. ubiquitous proteins were removed from tissue-specific categories., protein lists corresponding to pathways and processes were retrieved from g:profiler [55]. we selected biological processes from gene ontology [61], pathways from reactome [62] and kegg [63], and protein complexes from the corum database [64], restricting the analysis […]

2015
PMCID: 4314081
PMID: 25642713
DOI: 10.1371/journal.pone.0116839

[…] the complete expression microarray dataset was been deposited in the gene expression omnibus (geo) database repository, accession number gse62849. gene ontology (go) analysis was performed using g:profiler (http://biit.cs.ut.ee/gprofiler/). uncharacterized genes were not included in the analysis., western blot analyses were performed using standard methods. the following primary antibodies […]

2015
PMCID: 4514711
PMID: 26207738
DOI: 10.1371/journal.pone.0133607

[…] with a p-value ≤ 0.05. the data set containing the affymetrix probe identifiers, selected as differentially expressed in transduced hmnpcs, and the corresponding fold changes, were uploaded into g:profiler (updated version 23/7/2013). ggost gene group functional profiling was set with the following parameters: i) significant only, ii) hierarchical sorting, and iii) as specified […]

g:Profiler 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
g:Profiler 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.

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