Enrichment Map protocols

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Enrichment Map specifications

Information


Unique identifier OMICS_04137
Name Enrichment Map
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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Publication for Enrichment Map

Enrichment Map in pipelines

 (20)
2017
PMCID: 5309719
PMID: 28169291
DOI: 10.1038/ncomms14400

[…] taqman probes to phlda1 and myc. gapdh was used as an endogenous control., go analyses were performed on genes associated with recurrent gained and lost vels (g10+ and l14+) using g:profiler and the enrichment map plug-in to cytoscape. p value and fdr cutoffs used were both <0.05., tf motif enrichment analysis was performed with the findmotifsgenome tool in the homer command line software […]

2017
PMCID: 5428368
PMID: 28154416
DOI: 10.1038/s41598-017-00050-w

[…] pathway with a bonferroni p value of <0.05 were considered as a potential function of prognostic lncrnas. the significantly enriched go terms with a similar function were visualized using the enrichment map plugin in cytoscape., , electronic supplementary material , supplementary information accompanies this paper at doi:10.1038/s41598-017-00050-w , publisher's note: springer nature […]

2017
PMCID: 5429632
PMID: 28389671
DOI: 10.1038/s41598-017-00763-y

[…] and integrated discovery (version 6.7, david, https://david.ncifcrf.gov/) tool. significant go biological process terms with similar function were visualized as interaction networks using the enrichment map plugin in cytoscape, ., lasso penalized regression, time-dependent roc curve analysis and heat map analyses were conducted on penalized, survivalroc and gplots packages, respectively, […]

2017
PMCID: 5494615
PMID: 28693226
DOI: 10.3892/ol.2017.6183

[…] understanding of the function of genes in modules at the molecular level, functional annotation was performed using david and the functional enrichment network was visualized using the plug-in enrichment map in cytoscape (version 3.4.0; http://cytoscape.org/) ()., the university of california santa cruz database (http://genome.ucsc.edu/) () was used to obtain information […]

2017
PMCID: 5671410
PMID: 29096247
DOI: 10.1016/j.tranon.2017.09.005

[…] (version 6.8) , . clusters with enrichment score higher than 3.0 and functional annotations with p value lower than .001 were considered to be statistically significant. finally, cytoscape with the enrichment map plugin was used to visualize the significant enrichment results ., the microarray datasets downloaded from geo database were analyzed by r software (version 3.3.1) and bioconductor. […]


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Enrichment Map in publications

 (140)
PMCID: 5943605
PMID: 29743561
DOI: 10.1038/s41419-018-0600-3

[…] heat maps were generated using pheatmap_1.0.8 package., network analysis and visualisation were conducted in cytoscape_3.5.1 desktop software in combination with enrichmentmap_3.0.0 plugin. an enrichment map network of gsea results was generated using the gene sets with an enrichment p-value of <0.05 and fdr of <0.1, and an association coefficient threshold of ≤0.5. a node represents […]

PMCID: 5928144
PMID: 29736258
DOI: 10.1038/s41421-018-0022-5

[…] (geo; gse72288). data were analyzed using the david (the database for annotation, visualization and integrated discovery) bioinformatics tool for functional annotation, and cytoscape with the enrichment map plugin for visualization,. rna-seq targets were validated by qpcr after rna was converted to complementary dna (cdna) using superscript ii (lifetech)., for chip-seq, sorted cells […]

PMCID: 5929421
PMID: 29731978
DOI: 10.18632/oncotarget.24808

[…] function, goterm_bp_fat. this was performed against a background of all human genes and medium classification stringency (default). for visualization of the enrichment analysis the application enrichment map [] was used for the program cytoscape []. enriched sub-networks were identified using pathway studio’s expression regulatory sub-network enrichment, elsevier’s pathway studio […]

PMCID: 5846794
PMID: 29529088
DOI: 10.1371/journal.pone.0194225

[…] analysis. the significance of the overlap was calculated using one-sided fisher's exact test. the degree of overlap among the pathways identified by nasfinder was visualized using the cytoscape app enrichment map v2.1.0 [], run using cytoscape 3.4.0. enrichment map was run using default parameters and overlap coefficient as a measure of similarity., the network-based proximity analysis […]

PMCID: 5829071
PMID: 29487289
DOI: 10.1038/s41598-017-18082-7

[…] gene set enrichment analysis (gsea),. gene ontology (go) gene sets in the molecular signatures database (msigdb) were applied to gsea. the results of go enrichment analysis were visualized using an enrichment map with default settings. hallmark and kyoto encyclopedia of genes and genomes (kegg) pathway gene sets in msigdb were also used. for cross-species analysis, the up- (842 genes) […]


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Enrichment Map institution(s)
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada

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