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Number of citations per year for the bioinformatics software tool CluePedia

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CluePedia specifications


Unique identifier OMICS_04143
Name CluePedia
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes


No version available



  • person_outline Bernhard Mlecnik

Publication for CluePedia

CluePedia 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

[…] ificant 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. Sub-networks […]


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 Biological Proce […]


The phospholipase DDHD1 as a new target in colorectal cancer therapy

PMCID: 5899352
PMID: 29653539
DOI: 10.1186/s13046-018-0753-z

[…] sformed.The Gene Ontology and KEGG pathway analysis of proteins down-regulated by DDHD1 silencing was performed using the online tool DAVID ( [] and the ClueGO v2.3.3 + CluePedia v1.3.3, a Cytoscape v3.4.0 plug-in was used to visualize GO terms and pathways in functionally organized networks reflecting the relations between the biological terms based on the similarit […]


In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling

PMCID: 5924544
PMID: 29642539
DOI: 10.3390/genes9040202

[…] In order to evaluate functionally grouped Gene Ontology (GO) and pathway annotation networks of expressed genes and proteins, pathway enrichment analysis was performed using the ClueGO [] and CluePedia [] Cytoscape [] plugins. The GO Immune System Process functional pathway database was used. p value ≤ 0.05 and Kappa score of 0.4 served as threshold values. Protein-protein interaction (PPI […]


Microarray profiling of miRNA and mRNA expression in Rag2 knockout and wild type mouse spleens

Sci Data
PMCID: 5759371
PMID: 29313843
DOI: 10.1038/sdata.2017.199

[…] ps array data. These databases include but are not limited to, DAVID, PANTHER, Gene Set Expression Analysis (GSEA), STRING, and Cytoscape. In addition, different analysis tools such as Bingo, ClueGO, CluePedia, cyTransFinder, GeneMania, MetDisease, MetScape, ReactomeFIPlugin as well as commercially available software such as QIAGEN's Ingenuity Pathway Analysis (IPA), could all be of use in analysi […]


Global transcriptome analysis of the maize (Zea mays L.) inbred line 08LF during leaf senescence initiated by pollination prevention

PLoS One
PMCID: 5626513
PMID: 28973044
DOI: 10.1371/journal.pone.0185838

[…] sult files were identified as DEGs.Functional analysis was performed using Gene Ontology ( and WEGO ( The Cytoscape (v3.0.2) plugin ClueGO + Cluepedia v2.1.3 [,] was employed for gene function enrichment analysis [] of the identified DEGs in the FNP plants, specific up- and down-regulated genes in FNP plants. GO term fusion and restriction […]

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CluePedia institution(s)
INSERM, Laboratory of Integrative Cancer Immunology, Paris, France

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