CluePedia protocols

View CluePedia computational protocol

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CluePedia specifications

Information


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

Versioning


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Documentation


Maintainer


  • person_outline Bernhard Mlecnik <>

Publication for CluePedia

CluePedia in pipelines

 (25)
2018
PMCID: 5855710
PMID: 29415502
DOI: 10.3390/ijms19020488

[…] the false discovery rate. genes with an adjusted p-value < 0.05 (q-value < 0.05) and fold change > 2 in deseq analysis were assigned as differentially expressed genes (degs). , cluego and cluepedia were used to perform gene ontology (go) enrichment analysis [,]. in go enrichment analysis, only categories with a p-value < 0.05 were considered as enriched in the network., the kyoto […]

2018
PMCID: 5880952
PMID: 29636678
DOI: 10.3389/fnagi.2018.00086

[…] expression in aged mice compared with young adult mice. a go (ashburner et al., ) network analysis for each deg group was performed using cytoscape version 3.3.0 (bindea et al., ) with the cluego/cluepedia plugin (bindea et al., ) as described previously, with some modifications (shichino et al., ). significantly enriched go-biological process terms (gene ontology, ) (go levels: 4–7) […]

2018
PMCID: 5928633
PMID: 29532896
DOI: 10.3892/mmr.2018.8716

[…] terms with various levels of significance (p<0.1-<0.0005) were taken into consideration using the plug-in cluego (), which was followed by enrichment of the functional network with the plug-in cluepedia ()., 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 […]

2017
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., , ). enrichment was determined based on a two-sided hypergeometric statistical test and a bonferroni step down correction method. […]

2017
PMCID: 5377924
PMID: 28421049
DOI: 10.3389/fmicb.2017.00548

[…] pathway analysis was performed on the 349 downregulated genes at the three time points (). this pathway enrichment analysis based on kappa statistics and visualization was conducted through cluego/cluepedia plugin of the cytoscape software with default parameters (kappa score threshold = 0.4, over view term = smallest p-value, sharing group percentage = 50.0) (figure ) (). the downregulated […]


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CluePedia in publications

 (66)
PMCID: 5955949
PMID: 29769539
DOI: 10.1038/s41598-018-25743-8

[…] 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: 5899352
PMID: 29653539
DOI: 10.1186/s13046-018-0753-z

[…] the gene ontology and kegg pathway analysis of proteins down-regulated by ddhd1 silencing was performed using the online tool david (http://david.abcc.ncifcrf.gov/) [] 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 […]

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 […]

PMCID: 5902267
PMID: 29620629
DOI: 10.1097/MD.0000000000010152

[…] kyoto encyclopedia of genes and genomes pathway enrichment analysis based on the cluego plugin with p-value < .05 and kappa score = 0.4. the degs enriched in the pathways were displayed using cluepedia[] plugin in cytoscape., we downloaded the comprehensive interaction information of human proteins from the search tool for the retrieval of interacting genes database […]

PMCID: 5884799
PMID: 29618802
DOI: 10.1038/s41598-018-24032-8

[…] the disease treated (control) versus disease group (“treated” group)., functional analyses of the three groups were carried out. gene ontology (go) and pathway term clustering using cluego v2.4 and cluepedia version 1.5, and the cytoscape network analysis framework were performed. the default parameters were used with an overall statistical significance value set to p-value < 0.05., […]


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

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