CluePedia protocols

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
Requirements Cytoscape
Maintained Yes


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  • person_outline Bernhard Mlecnik <>

Publication for CluePedia

CluePedia IN pipelines

PMCID: 5915011
PMID: 29455584
DOI: 10.1080/15548627.2017.1419118

[…] size of 100; bejamini-yekutieli p-value correction; and rank and metric scatter plot generation. pathway enrichment analysis on differentially expressed genes was performed using cluego (v2.1.7) and cluepedia (v1.1.7) plug-ins in cytoscape (v3.1.0) with the kegg pathway database (10.04.2016 download) [63-65]. the pathways with a benjamin-hochberg corrected p-value <0.005 are shown. […]

PMCID: 5928633
PMID: 29532896
DOI: 10.3892/mmr.2018.8716

[…] with various levels of significance (p<0.1-<0.0005) were taken into consideration using the plug-in cluego (14), which was followed by enrichment of the functional network with the plug-in cluepedia (15)., results of rt-qpcr for each gene are presented as the fold-change over the expression in the sample not treated with fluconazole, which was set as 1. the difference in triplicate cq […]

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

[…] 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 method. […]

PMCID: 5345195
PMID: 28283027
DOI: 10.1186/s40478-017-0421-0

[…] with the funrich tool [81], exploiting the extracellular vesicles database [52]. next, we performed gene ontology and pathway analysis using a web based tool, enrichr [56], as well as cluego and cluepedia [14] implemented in cytoscape and supplemented with enrichment analysis in wgcna. complementary to these analyses, our functional interpretation of gene modules exploited several biological […]

PMCID: 5465539
PMID: 28595568
DOI: 10.1186/s12864-017-3824-1

[…] an adjusted p-value <0.05 (q value <0.05) in deseq analysis were assigned as differentially expressed genes (degs)., gene ontology (go) annotation of the genes was performed using cluego and cluepedia [20, 21]. in go enrichment analysis, only categories with a low p-value (p < 0.05) were considered as enriched in the network as determined by two-sided hypergeometric statistical tests […]

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

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