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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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No version available

Documentation


Publication for Enrichment Map

Enrichment Map citations

 (148)
library_books

Leukaemic alterations of IKZF1 prime stemness and malignancy programs in human lymphocytes

2018
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 […]

library_books

Mtf2 PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis

2018
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 […]

library_books

Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia

2018
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 […]

library_books

Combined use of protein biomarkers and network analysis unveils deregulated regulatory circuits in Duchenne muscular dystrophy

2018
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 […]

library_books

Meta and cross species analyses of insulin resistance based on gene expression datasets in human white adipose tissues

2018
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) […]

library_books

A Potential Prognostic Long Noncoding RNA Signature to Predict Recurrence among ER positive Breast Cancer Patients Treated with Tamoxifen

2018
PMCID: 5816619
PMID: 29453409
DOI: 10.1038/s41598-018-21581-w

[…] performing 1,000 permutations were considered to be significantly enriched, and selected recurrence or metastasis related enrichment results were visualized by cytoscape (version 2.8.2) and the enrichment map software., all p or adjusted p values reported were two-sided, which less than 0.05 were considered statistically significant. all of statistical tests were done with spss 23 (spss, […]


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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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