Enrichment Map pipeline

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

 (7)
2017
PMCID: 5772172
PMID: 29262348
DOI: 10.1016/j.immuni.2017.11.024

[…] respective cell type compared to the overall mean was mapped onto the network and displayed in colors ranging from blue (negative fold-change) over white to red (positive fold-change) using the app enrichment map v2.0.1 in cytoscape v3.2.0. based on the fold-change patterns, the networks were divided into four main clusters, where each cluster represents one of the four cell types, […]

2016
PMCID: 5260904
PMID: 27882944
DOI: 10.1038/cddis.2016.377

[…] was performed with genome assembly grcm37/mm9. data were aligned and calculated for differential expression with the tuxedo suite.49, 50 network analysis of over-represented pathways in rna-seq by enrichment map. gene sets were organized in a network, where each set was a node and edges represented gene overlap between sets. automated network layout groups related gene sets into network […]

2016
PMCID: 5389688
PMID: 27903893
DOI: 10.1093/nar/gkw1162

[…] expression analysis was performed using deseq2 (24). differentially expressed genes from each comparison were tested for functionally enriched pathways and gene ontology terms using goseq (25) and enrichment map (26)., for qpcr rna was extracted using trizol (invitrogen) according to manufacturer's instruction, and quantified using nanodrop cdna synthesis using the oligo dt primers and data […]

2015
PMCID: 4303425
PMID: 25611800
DOI: 10.1371/journal.pgen.1004919

[…] evaluated for enrichment of disease genes using fisher’s exact test (fdr p<0.01) and disease genes with ptm-related substitutions as test set. these pathways and processes were visualized as an enrichment map [65] where shades of light and dark blue represent negative selection, shades of orange and red represent positive selection, node fillings indicate significant selection […]

2013
PMCID: 3808538
PMID: 24194939
DOI: 10.1371/journal.pone.0078480

[…] 9th and 10th go terms, which relate to the ensheathment of neurons and axons., the list of go terms from gm and wm were then fed into cytoscape and used to modify the total gene list, creating an enrichment map (figure 9). the enrichment map revealed several large and distinct clusters related to vesicles and membrane: ion-gated channels, transporters and receptors, neuron morphogenesis, […]

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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