ClueGO protocols

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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

 (116)
2018
PMCID: 5753478
PMID: 29298683
DOI: 10.1186/s12864-017-4386-y

[…] changes > 1.5 and a benjamini-hochberg corrected p value < 0.05 (default parameter used in the cuffdiff algorithm) were considered to be differentially expressed., we used the cytoscape plugin cluego [] (together with the go annotation (goa embl-ebi) (http://www.ebi.ac.uk/goa) released on 11/17/2016. the background set for go was all genes with annotated go entries for the goa annotation […]

2018
PMCID: 5753908
PMID: 29291611
DOI: 10.5056/jnm17021

[…] u test, and the student’s t test. the selected 1564 features were then mapped to genes, and the list of 858 unique genes were subjected to ontology/pathway analysis and visualized by using the “cluego” and “reactomefi” packages in cytoscape, from which enriched terms with p-value < 0.05 were identified., dnase-treated total rna (1 μg) was reverse-transcribed via an iscript cdna synthesis […]

2018
PMCID: 5755453
PMID: 29301495
DOI: 10.1186/s12865-017-0238-4

[…] parameters remained at their default settings., in each module, a transcript was considered as an intra-modular hub node if its connectivity was equal or more than 90% of the most connected node., cluego [], a widely used cytoscape plugin, was used to identify potential biological interpretation of functional modules in the network. the latest updates of gene ontology annotation database (goa) […]

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 []., functional annotations and pathway analyses of degs were carried out using the cluego plug-in of cytoscape []. 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: 5797083
PMID: 29396540
DOI: 10.1038/s41598-018-20661-1

[…] clustering method. log2fold-change values were used. after clustering, genes related with euclidean distance less than 2.5 were determined as a gene cluster., pathway enrichment analysis was done by cluego plug-in version 2.2.4 of cytoscape version 3.3.0. degs were used as an input (up and down-regulated degs were analyzed separately). go biological function and kegg database were used […]


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ClueGO in publications

 (463)
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] which expression was negatively or positively correlated to the basal-classical component, were regarded as classical or basal tfs, respectively. cytoscape was used for network visualization and the cluego app was applied to target genes for clustered enriched pathway network representation., cells (3e5) were plated in six-well plates and 24 h later transfected with a pool of 4 met sirnas […]

PMCID: 5955949
PMID: 29769539
DOI: 10.1038/s41598-018-25743-8

[…] significant modules were identified with the plug-in mcode of cytoscape with a cutoff mcode score of >5. the enriched pathway interaction networks were constructed using the cytoscape plug-ins cluego and cluepedia. negatively correlated, differentially expressed mirna-mrna pairs were selected for screening, and the regulatory networks were constructed and visualized by cytoscape software. […]

PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] of proteins from uniprot, pfam-database of protein families and kegg-database of metabolic pathways. go analysis of protein sequences were conducted by blast2go []. go enrichment was performed by cluego with p value < 0.05 []., to construct the phylogenomic tree of c. pseudoreteaudii and 13 other ascomycota isolates, including botrytis cinerea, colletotrichum gloeosporioides, eutypa lata, […]

PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] an equal number of psgs with an fdr <0.05 for the branch-site model. for massively enriched go terms with similar functions, categorizer [] was used to classify the genes into basic categories. cluego [] with the hypergeometric test and a bonferroni adjustment were performed to enrich the kegg pathways []., geneious (version 8.1.5) [] was utilized with the default settings to assemble […]

PMCID: 5939684
DOI: 10.1167/iovs.18-24091

[…] genes whose transcript levels were inversely expressed relative to the relevant de mirnas (inversely expressed genes) underwent analysis of gene ontology. for this purpose, we used cytoscape's cluego app (version 2.2.3) and analysis of biological pathways based on the database for annotation, visualization and integrated discovery (david, available in the public domain, […]


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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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