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Methods Mol Biol. 2011;781:257-77. doi: 10.1007/978-1-61779-276-2_12.

Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map.

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  • 1Banting and Best Department of Medical Research, Centre for Cellular and Biomolecular Research (CCBR), Toronto, ON, Canada.

Abstract

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.

PMID:
21877285
[PubMed - indexed for MEDLINE]
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