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Enrichment Map Plugin Download Page

Brief Description

Enrichment Map is a Cytoscape plugin for functional enrichment visualization. Enrichment results have to be generated outside Enrichment Map, using any of the available methods. Gene-sets, such as pathways and Gene Ontology terms, are organized into a network (i.e. the "enrichment map"). In this way, mutually overlapping gene-sets cluster together, making interpretation easier. Enrichment Map also enables the comparison of two different enrichment results in the same map.

Follow this link for more details and an analysis example.


For easier figure creation download our template legends that contains all the visual properties used in a standard enrichment map. Download and customize legend to fit your network


Cytoscape can be downloaded from: http://cytoscape.org/

EnrichmentMap is available on the Cytoscape App Store: http://apps.cytoscape.org/apps/enrichmentmap

Alternatively download the EnrichmentMap Pipeline Collection. This will install EnrichmentMap as well as a suite of other apps that work well with EnrichmentMap, including AutoAnnotate, WordCloud and clusterMaker2: http://apps.cytoscape.org/apps/enrichmentmappipelinecollection

Tutorials and Examples

Tuturials and protocols for EnrichmentMap 3.0 are here: https://baderlab.github.io/Cytoscape_workflows/EnrichmentMapPipeline/

Tutorials for the older 2.2 version of EnrichmentMap are here: http://enrichmentmap.readthedocs.io/en/docs-2.2/Tutorials.html

User Guide

The EnrichmentMap User Guide has been moved to: http://enrichmentmap.readthedocs.io

User Guide for older 2.2 version of EnrichmentMap (including tutorials) is here: http://enrichmentmap.readthedocs.io/en/docs-2.2/

Gene-sets for Enrichment Analysis


Cite EM

Examples of Use

Papers Citing Enrichment Map

Report a Bug or a Problem

  1. please make sure you don't have formatting issues (have a look at the User Guide (and FAQ))

    • if you are still not sure how to handle formats,
    • or you don't know what's the best suitable analysis for you,
    • please send an email to: daniele[AT]merico[DOT]gmail.com
  2. please check what's your
    • plugin version and build (from the Cytoscape menu / Plugins / Enrichment Map / About)
    • Cytoscape version (from the Cytoscape menu / Cytoscape)
    • Operating System (e.g. Windows Vista)

    and send your bug report to ruth[DOT]isserlin[AT]utoronto.ca
    report the bug to the Enrichment map issue tracker:

    1. go to https://github.com/BaderLab/EnrichmentMapApp

    2. click on "Issues"
    3. click on "New Issue"
    4. write a short description of the issue
    5. attached session file (.cys) file or example input files if applicable
    6. Make sure to enter plugin version and build, cytoscape version and operating system.
    7. click on "Submit new issue"
  3. For Feature requests please send to enrichmentmap-dev@googlegroups.com

Software/EnrichmentMap (last edited 2018-04-19 18:08:18 by MikeKucera)

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