*This App is part of the [https://apps.cytoscape.org/apps/enrichmentmappipelinecollection EnrichmentMap Collection].*
The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network. It will operate on any generic enrichment results as well as specifically on Gene Set Enrichment Analysis (GSEA) results. Nodes represent gene-sets and edges represent mutual overlap; in this way, highly redundant gene-sets are grouped together as clusters, dramatically improving the capability to navigate and interpret enrichment results.
Gene-set enrichment is a data analysis technique taking as input:
* A (ranked) gene list, from a genomic experiment
* Gene-sets, grouping genes on the basis of a-priori knowledge (e.g. Gene Ontology) or experimental data (e.g. co-expression modules)
and generating as output the list of enriched gene-sets, i.e. best sets that summarizing the gene-list. It is common to refer to gene-set enrichment as functional enrichment because functional categories (e.g. Gene Ontology) are commonly used as gene-sets.
Links:
* [https://enrichmentmap.readthedocs.io User Guide]
* [https://enrichmentmap.readthedocs.io/en/latest/Automating.html Automation Guide]
* [https://github.com/BaderLab/EnrichmentMapApp Code Repository]
