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ClueGO specifications


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
Maintained Yes




No version available


  • person_outline Jérôme Galon

Publication for ClueGO

ClueGO citations


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

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

[…] e most 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. S […]


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

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

[…] ets 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 []. […]


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

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

[…] ining 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 []. […]


Shape Shifted Red Blood Cells: A Novel Red Blood Cell Stage?

PMCID: 5946108
PMID: 29671811
DOI: 10.3390/cells7040031
call_split See protocol

[…] ClueGO [], CluePedia [] and Cytoscape [] plugins were used to performed Gene Ontology (GO) and pathway annotation networks of the expressed genes and proteins pathway enrichment analysis. The GO Biolo […]


Nuclear receptor NR2F6 inhibition potentiates responses to PD L1/PD 1 cancer immune checkpoint blockade

Nat Commun
PMCID: 5906604
PMID: 29670099
DOI: 10.1038/s41467-018-04004-2
call_split See protocol

[…] testing based on false discovery rate (FDR) using the Benjamini−Hochberg approach. Analysis and visualization of Gene Ontology terms associated with differentially expressed genes was performed using ClueGO. Both groups of genes (up and downregulated, p-value <0.05) were used as dual input for GO analysis. The biological terms are grouped together based on their shared genes where the similarity b […]


An Integrated Proteomics and Bioinformatics Approach Reveals the Anti inflammatory Mechanism of Carnosic Acid

Front Pharmacol
PMCID: 5911474
PMID: 29713284
DOI: 10.3389/fphar.2018.00370

[…] ry Relationships database (PANTHER). The signaling pathway enrichment analysis was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG), REACTOME pathway, and Wiki pathway database from ClueGO program, a plug-in Cytoscape software (v.3.5.1). […]


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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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