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ClueGO computational protocol

ClueGO specifications

Information


Unique identifier OMICS_04142
Name ClueGO
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2.5.0
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Maintainer


  • person_outline Jérôme Galon <>

Publication for ClueGO

ClueGO IN pipelines

 (32)
2018
PMCID: 5774689
PMID: 29351308
DOI: 10.1371/journal.pone.0190933

[…] was utilized to assess the uncertainty in the hierarchical clustering analysis on 10,000 bootstrap replicates [22]., functional annotations and pathway analyses of degs were carried out using the cluego plug-in of cytoscape [23]. gene ontology (go) annotates genes to biological/cellular/molecular terms in a hierarchically structured manner, whereas the kyoto encyclopedia of genes and genomes […]

2018
PMCID: 5813909
PMID: 29447168
DOI: 10.1371/journal.pone.0190019

[…] >1., whole-genome gene ontology (go) term annotation was performed using blast2go [32] with a blastp e-value hit filter of 1×10−5, an annotation cutoff value of 55 and a go weight of 5. using cluego [33], observed go biological process were subjected to the right-sided hypergeometric enrichment test at medium network specificity selection and p-value correction was performed using […]

2018
PMCID: 5887416
PMID: 29394407
DOI: 10.1093/nar/gky049

[…] gene, the number of mapped reads was counted and deseq2 was used to analyze the differential expression (28) gene ontology (go) analyses were performed using default parameters and stringency in ‘cluego’: a cytoscape plug-in.(29) the significant ‘go biological processes’ were shown with p ≤ 0.05., tcf7l2 and h3k27ac chips in murine adult cardiac ventricular tissue were performed by 20 min […]

2018
PMCID: 5910864
PMID: 29610341
DOI: 10.1073/pnas.1722333115

[…] method (41). the corrected p value for multiple testing using the false discovery rate approach was used to determine the significance of de genes. for go analysis, the de genes were submitted to cluego (42), a cytoscape plug-in. all expressed genes were used as background, and the biological process and kyoto enclopedia of genes and genomes pathway tables were used to identify enriched go […]

2018
PMCID: 5915011
PMID: 29455584
DOI: 10.1080/15548627.2017.1419118

[…] were selected: step size of 100; bejamini-yekutieli p-value correction; and rank and metric scatter plot generation. pathway enrichment analysis on differentially expressed genes was performed using cluego (v2.1.7) and cluepedia (v1.1.7) plug-ins in cytoscape (v3.1.0) with the kegg pathway database (10.04.2016 download) [63-65]. the pathways with a benjamin-hochberg corrected p-value <0.005 […]

ClueGO institution(s)
INSERM, AVENIR Team, Integrative Cancer Immunology, Paris, France
ClueGO funding source(s)
Supported by INSERM, Ville de Paris, INCa, the Austrian Ministry for Science and Research, Project GEN-AU, BINII, and the European 7FP Grant Agreement 202230 (GENINCA).

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