Enrichment Map Logo

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.

Plugin Download

Cytoscape 3

Cytoscape 3.2 and higher require Java 7.

If you are on Mac OSx Snow leopard (10.6.8) and want to use Cytoscape 3.2 check out these instructions for installing Java 7 and Cytoscape 3.2 on your system.

  1. Updated at 11/20/2014 - Release 2.0.1 : Compatible with cytoscape 3.1

Development Versions

  1. Updated at 08/04/2015 - Release 2.1.0 (Release Candidate 2) : Compatible with cytoscape 3.2

Cytoscape 2.8

  1. Updated at 07/06/2011 - Release 1.2 : Compatible with cytoscape 2.6,2.7,2.8

  2. Updated at 02/7/2011 - Release 1.1: Compatible with cytoscape 2.6,2.7,2.8

Development Versions

  1. Updated at 04/9/2014 - Release 1.3 - Release Candidate 6 : Compatible with cytoscape 2.6,2.7,2.8

    • Added bug fix with missing leading edge on reloaded sessions files for down regulated gene sets.
    • Added command tool support
    • Added EDB support
    • Added values to heat map
    • Added ability to load GSEA class files directly
    • fixed misc bugs
    • Enrichment Map Plugin (v1.3 RC6)
      Download the zipped file, move it to the Cytoscape plugin directory and unzip it.

    • Source code can be found on github: https://github.com/BaderLab/EnrichmentMapApp

Tutorials and Examples

data used for the tutorials: Estradiol-treated MCF7 cells, 12 and 24hrs (Gene Expression Omnibus: GSE11352)

User Guide

Link to User Guide (and FAQ)

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 2015-08-04 14:05:08 by RuthIsserlin)

website tracker
MoinMoin Appliance - Powered by TurnKey Linux