g:Profiler protocols

View g:Profiler computational protocol

g:Profiler statistics

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Associated diseases

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g:Profiler specifications

Information


Unique identifier OMICS_02223
Name g:Profiler
Alternative name gprofiler
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
Alternative name gprofiler
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

 (33)
2018
PMCID: 5868854
PMID: 29538374
DOI: 10.1371/journal.pntd.0006343

[…] tissue of hev-day 5 (n = 2) where one sample from each group was removed from the analysis due to poor data quality. significantly regulated genes were subjected to functional classification using g:profiler [] for gene ontology and kegg pathways, and enrichr [] for protein-protein interaction (ppi) hubs of transcription factors., the sequencing data was deposited at the ncbi’s sequence read […]

2017
PMCID: 5305215
PMID: 28117667
DOI: 10.7554/eLife.21184.035

[…] examples) and n(i) denotes the number of negative examples in the top i%; while p denotes the total number of previously reported cargoes., go (rrid:scr_002811) analyses were performed using g:profiler (rrid:scr_006809; r1488-1536_e83_eg30) (). the search parameters were the following: organism, homo sapiens; significance threshold, g:scs; statistical domain size, all known genes; go […]

2017
PMCID: 5309719
PMID: 28169291
DOI: 10.1038/ncomms14400

[…] performed using taqman probes to phlda1 and myc. gapdh was used as an endogenous control., go analyses were performed on genes associated with recurrent gained and lost vels (g10+ and l14+) using g:profiler and the enrichment map plug-in to cytoscape. p value and fdr cutoffs used were both <0.05., tf motif enrichment analysis was performed with the findmotifsgenome tool in the homer […]

2017
PMCID: 5363043
PMID: 28330499
DOI: 10.1186/s13073-017-0417-1

[…] connected component of each network and performed spin-glass community detection as implemented in the igraph r package [] to obtain the functional modules. we annotated functional modules using g:profiler [] using all genes in a module as a query. all networks in this work were visualized using gephi []. the network layout was determined by community membership, the strength of connections […]

2017
PMCID: 5374559
PMID: 28361683
DOI: 10.1186/s12859-017-1462-x

[…] identified by frsvm and stsvm are general gene sets rather than functional gene groups by gsva, pathifier and aep; that’s why we first functionally label them with the top enriched terms by g:profiler []., the enrichment ratio boxplots are shown in fig. . it seems cns has the best performance on every dataset; frsvm has varied performance than other conventional approaches showing […]


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g:Profiler in publications

 (224)
PMCID: 5955978
PMID: 29769521
DOI: 10.1038/s41467-018-04148-1

[…] to identify cells and tissues in which the hr response to exercise and to recovery loci were highly expressed. subsequently, for the best candidate genes per locus (supplementary table ), we used g:profiler that performs functional profiling of gene lists using various kinds of biological evidence (including go, hpo annotation). enrichments with fdr < 0.05 were deemed significant., […]

PMCID: 5948854
PMID: 29753320
DOI: 10.1186/s12933-018-0713-0

[…] was applied in each group compared to unexposed wt. mammalian phenotype ontology enrichment analysis of mgi (http://www.informatics.jax.org) was used. enrichment analysis was performed using g:gost gene group functional profiling; g:profiler (http://biit.cs.ut.ee/gprofiler/). manual literature search and harmonizome database [] were used to identify direct hif-1 targets and predicted […]

PMCID: 5902304
PMID: 29449426
DOI: 10.1183/13993003.01068-2017

[…] novel asthma genes linked to important processes/pathways implicated in asthma pathophysiology including inflammatory, metabolic and proliferative pathways in asmcs from sa., pathway analysis using g:profiler [] indicated that the genes associated with dmps in healthy subjects versus nsa at baseline were involved in the regulation of cell proliferation and apoptosis (hippo signalling pathway) […]

PMCID: 5885317
PMID: 29618373
DOI: 10.1186/s13071-018-2817-5

[…] did not identify known or putative insecticide resistance genes in these regions. to test for enrichment of these 137 genes in gene functional category, we performed a gene ontology analysis using g:profiler []. this is important because it is possible that the contribution of mutations involving several genes in the same biological pathway result in an overall adaptive phenotype (e.g. […]

PMCID: 5940169
PMID: 29599177
DOI: 10.1534/g3.118.200201

[…] id of the human ortholog in the uniprotkb/swiss-prot database (www.uniprot.org/, the , last accessed march 08th, 2017). gene ids were used to test for enrichment in gene ontology (go) terms with g:profiler (http://biit.cs.ut.ee/gprofiler/) () using default parameters and the human genome as background. the significance threshold for enrichment was set at 0.05 (corrected p-value for multiple […]


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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.

g:Profiler review

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Anonymous user #499

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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).