title: Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.
abstract: BACKGROUND
  Gene-set enrichment analysis is a useful technique to help functionally characterize large gene lists, such as the results of gene expression experiments. This technique finds functionally coherent gene-sets, such as pathways, that are statistically over-represented 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 software works against this ideal.
  
  
  RESULTS
  To overcome gene-set redundancy and help in the interpretation of large gene lists, we developed "Enrichment Map", a network-based visualization method for gene-set enrichment results. Gene-sets are organized in a network, where each set is a node and edges 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 the enrichment results.
  
  
  CONCLUSIONS
  Enrichment Map is a significant advance in the interpretation of enrichment analysis. Any research project that generates a list of genes can take advantage of this visualization framework. Enrichment Map is implemented as a freely available and user friendly plug-in for the Cytoscape network visualization software (http://baderlab.org/Software/EnrichmentMap/).
authors.affiliation: Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Daniele
authors.initials: D
authors.lastname: Merico
authors.forename: Ruth
authors.initials: R
authors.lastname: Isserlin
authors.forename: Oliver
authors.initials: O
authors.lastname: Stueker
authors.forename: Andrew
authors.initials: A
authors.lastname: Emili
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics; D016000:Cluster Analysis; D003110:Colonic Neoplasms / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004967:Estrogens / Q000494:pharmacology; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D053263:Gene Regulatory Networks; D006801:Humans; D020407:Internet; D015203:Reproducibility of Results; D012984:Software
chemical_list: D004967:Estrogens