ClueGO pipeline

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

 (9)
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 […]

2017
PMCID: 5290407
PMID: 28217095
DOI: 10.3389/fphar.2017.00023

[…] manually removed from the lists of interacting proteins prior to pathway enrichment analysis. ugt1a interacting partners were classified according to kegg pathways (update november 12, 2016) using cluego and cluepedia apps (v2.3.2) in cytoscape 3.4 (bindea et al., 2009, 2013). enrichment was determined based on a two-sided hypergeometric statistical test and a bonferroni step down correction […]

2017
PMCID: 5426002
PMID: 28494812
DOI: 10.1186/s12967-017-1201-0

[…] of genes obtained from deseq 2 was done by uploading all degs into humanmine [49]. network visualization and functional enrichment analysis was conducted through cytoscape software 3.3. and cluego 2.3.2 [50]. log2 of fold change of the expression value (after normalization) was imported into qiagen ingenuity pathways analysis (ipa) for an upstream transcriptional factor analysis as well […]

2017
PMCID: 5627882
PMID: 28949383
DOI: 10.3892/ijmm.2017.3146

[…] from pcos patients, and 3 normal granulosa cell samples. differentially expressed genes (degs) were screened between pcos and normal samples. pathway enrichment analysis was conducted for degs using cluego and cluepedia plugin of cytoscape. a reactome functional interaction (fi) network of the degs was built using reactomefiviz, and then network modules were extracted, followed by pathway […]

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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