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PLoS One. 2010 Nov 15;5(11):e13984. doi: 10.1371/journal.pone.0013984.

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.

Author information

1
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.

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.

PRINCIPAL FINDINGS:

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/).

PMID:
21085593
PMCID:
PMC2981572
DOI:
10.1371/journal.pone.0013984
[Indexed for MEDLINE]
Free PMC Article

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