FunNet protocols

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FunNet specifications

Information


Unique identifier OMICS_18786
Name FunNet
Interface Web user interface
Restrictions to use None
Input data One set of transcriptional profiles, or the simultaneous analysis of two sets of gene expression profiles.
Programming languages PHP
Computer skills Basic
Stability Stable
Source code URL http://www2.uaem.mx/r-mirror/src/contrib/FunNet_1.00-12.tar.gz
Maintained Yes

Maintainer


  • person_outline Edi Prifti <>

Additional information


http://www2.uaem.mx/r-mirror/web/packages/FunNet/index.html https://github.com/cran/FunNet Tuto: http://funnet.integromics.fr/index.php?menu=2

Information


Unique identifier OMICS_18786
Name FunNet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data One set of transcriptional profiles, or the simultaneous analysis of two sets of gene expression profiles.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.00-12
Stability Stable
Source code URL http://www2.uaem.mx/r-mirror/src/contrib/FunNet_1.00-12.tar.gz
Maintained Yes

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Maintainer


  • person_outline Edi Prifti <>

Additional information


http://www2.uaem.mx/r-mirror/web/packages/FunNet/index.html https://github.com/cran/FunNet Tuto: http://funnet.integromics.fr/index.php?menu=2

Publication for FunNet

FunNet in pipelines

 (6)
2017
PMCID: 5593459
PMID: 28765881
DOI: 10.3892/ijmm.2017.3086

[…] software, version 12.5). these putative target genes were subjected to gene ontology (go) biological process annotation and kyoto encyclopedia of genes and genomes (kegg) pathway analysis using funnet algorithm. the p-value was calculated with a unilateral fisher's exact test and corrected by false discovery rate (fdr). gos and pathways with p-value <0.05 and fdr <0.05 were considered […]

2016
PMCID: 4705764
PMID: 26742487
DOI: 10.1186/s40246-015-0059-6

[…] quadrant, as they show high betweenness but low degree values.v)functional enrichment analysis. overrepresented biological functions were searched in the differential transcriptomic datasets using funnet, a bioinformatics tool that performs functional profiling of gene expression data [].vi)analysis of subnetworks derived from central nodes. subnetworks were built with the aid of cytoscape [], […]

2016
PMCID: 4705764
PMID: 26742487
DOI: 10.1186/s40246-015-0059-6

[…] quadrant, as they show high betweenness but low degree values., functional enrichment analysis. overrepresented biological functions were searched in the differential transcriptomic datasets using funnet, a bioinformatics tool that performs functional profiling of gene expression data []., analysis of subnetworks derived from central nodes. subnetworks were built with the aid of cytoscape [], […]

2014
PMCID: 4240170
PMID: 25484892
DOI: 10.3389/fgene.2014.00411

[…] were set as cutoff values for significance., online software and databases were used for the functional classification of differentially expressed genes or differentially methylated cpg sites: funnet transcriptional networks analysis (www.funnet.info), david bioninformatics resources 6.7 (huang da et al., ,), and the genecards database (http://www.genecards.org) (safran et al., )., […]

2013
PMCID: 3617172
PMID: 23593176
DOI: 10.1371/journal.pone.0060213

[…] . the module-trait correlation and module identification studies were done in the wgcna r package . the functional analysis of transcriptional networks was analyzed by funnet and visualized in cytoscape software. the customized entrez keyword enrichment analysis and tabular heatmaps were done with the geneanswers r package . details of each analysis are described […]


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FunNet in publications

 (34)
PMCID: 5664104
PMID: 28972549
DOI: 10.3390/genes8100254

[…] were then presented in a venn diagram [], and the genes in the intersection of the three databases were chosen for go and kegg pathway analyses. go categories and the pathways were classified by funnet algorithm, and the corresponding results were evaluated with a unilateral fisher exact test. false discovery rate (fdr) analysis was calculated to correct the p value. enrich factor […]

PMCID: 5511834
PMID: 28769946
DOI: 10.3389/fpls.2017.01231

[…] metabolism based on the web gene ontology (go) (http://wego.genomics.org.cn/cgi-bin/wego/index.pl) and kyoto encyclopedia of genes and genomes (kegg) pathway enrichment analysis (http://www.funnet.ws/). topsis (the technique for order preference by similarity to ideal solution) also test and determine the salt concentration and processing time, to provide a base for other researchers. […]

PMCID: 5469215
PMID: 28659953
DOI: 10.3389/fpls.2017.01010

[…] power, which was set to six (). the outputted, co-expressed genes having strong interconnections were defined as hub genes. we then chose specific genes from the hub genes for further analyses with funnet and amigo 2. the co-expression network was constructed using cytoscape software ()., at least 10 plants were analyzed in each treatment. all the experiments were repeated at least three times. […]

PMCID: 5476288
PMID: 28591144
DOI: 10.1371/journal.ppat.1006347

[…] by errα inhibition. shctrl and sherrα-2 clones in the 293t cell line () were analyzed by microarray assay 12 h after vsv infection. first, we subjected genes that exhibited 1.5-fold changes to funnet analysis to determine the several top pathways regulated by errα upon viral infection. based on this analysis, the top eight most significant downregulated kegg pathways following errα […]

PMCID: 5282675
PMID: 28091410
DOI: 10.4103/0366-6999.197999

[…] (anova). gene ontology (go) database and kegg were applied to determine functions of these differentially expressed messenger rnas (mrnas).[] then, differentially expressed genes were researched by funnet and uniprot database (http://www.uniprot.org)., sybr green quantitative real-time reverse transcription-polymerase chain reaction (rt-pcr) was performed on the genes atp2a1, erp27, fkbp1b, […]


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FunNet institution(s)
INSERM, UMR-S 872, Les Cordeliers, Eq. 7 Nutriomique, Paris, France; Pierre et Marie Curie-Paris 6 University, Cordeliers Research Center, UMR-S 872, Paris, France; IRD, UR Géodes, Centre IRD de l’Ile de France, Bondy, France; Assistance Publique-Hôpitaux de Paris, Pitié Salpêtrière Hospital, Nutrition and Endocrinology department, Paris, France
FunNet funding source(s)
Supported by European Community 6th framework HEPADIP project; the ‘Association de Langue Française pour l’Etude du Diabète et des Maladies Métaboliques’ (ALFEDIAM).

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