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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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  • person_outline Jérôme Galon

Publication for ClueGO

ClueGO citations

 (496)
library_books

Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

2018
Nat Commun
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 […]

library_books

Integrated analysis of hepatic mRNA and miRNA profiles identified molecular networks and potential biomarkers of NAFLD

2018
Sci Rep
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. […]

library_books

Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus

2018
BMC Genomics
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, […]

library_books

Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

2018
GigaScience
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 […]

library_books

Expression Profiling Analysis Reveals Key MicroRNA–mRNA Interactions in Early Retinal Degeneration in Retinitis Pigmentosa

2018
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, […]

library_books

The Correlation Between the Immune and Epithelial Mesenchymal Transition Signatures Suggests Potential Therapeutic Targets and Prognosis Prediction Approaches in Kidney Cancer

2018
Sci Rep
PMCID: 5919934
PMID: 29700419
DOI: 10.1038/s41598-018-25002-w

[…] genomics,., the functional annotation and pathway enrichment analyses for differentially expressed emt genes and interactive immune checkpoint targets were executed by online analysis tools and cluego in cytoscape (version 3.5.1). the kegg pathway with a p value < 0.05 and a fold enrichment >2.0, and go terms with a p value < 0.05 and an enrichment score >1.0 were considered […]


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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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