Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map

  • Daniele Merico
  • Ruth Isserlin
  • Gary D. BaderEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 781)


Gene-set enrichment analysis finds functionally coherent gene-sets, such as pathways, that are statistically overrepresented in a given gene list. Ideally, the number of resulting sets is smaller than the number of genes in the list, thus simplifying interpretation. However, the increasing number and redundancy of ­gene-sets used by many current enrichment analysis resources work against this ideal. “Enrichment Map” is a Cytoscape plug-in that helps overcome gene-set redundancy and aids in the interpretation of enrichment results. Gene-sets are organized in a network, where each set is a node and links represent gene overlap between sets. Automated network layout groups related gene-sets into ­network clusters, enabling the user to quickly identify the major enriched functional themes and more easily interpret enrichment results.

Key words

Gene-set enrichment Functional enrichment Microarray data analysis Gene ontology Pathways 


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Daniele Merico
    • 1
    • 2
  • Ruth Isserlin
    • 1
    • 2
  • Gary D. Bader
    • 1
    • 2
    Email author
  1. 1.Banting and Best Department of Medical ResearchCentre for Cellular and Biomolecular Research (CCBR)TorontoCanada
  2. 2.Department of Molecular GeneticsUniversity of TorontoTorontoCanada

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