On 2013 Oct 24, Jeff Kiefer commented:

This is a great tool for analyzing one's gene set enrichment analysis (GSEA) results (http://www.broadinstitute.org/gsea/index.jsp). The output of a GSEA analysis is a ranked list of gene sets. The end-user is often at a loss in summarizing and interpreting the output. This is due to the redundant nature of gene sets and often less than useful names of the gene sets. The enrichment map (http://baderlab.org/Software/EnrichmentMap/) is just the tool to resolve the redundancy and assist in interpreting the biological meaning of the GSEA table of gene sets. The tool is relatively easy to use and has decent use case examples and user manual. In addition, a 'methods' paper for the use of Enrichment Map is published here Merico D, 2011. The authors also have an additional tool, WordCloud Oesper L, 2011 that assists in summarizing groups of gene sets visualized using the Enrichment Map. This helps the user to assign textual descriptions and aids in summarizing the represented biology. The WordCloud tool can be found here: http://baderlab.org/Software/WordCloudPlugin. I highly recommend these tools for interpreting GSEA results.

On 2013 Oct 24, Jeff Kiefer commented:

This is a great tool for analyzing one's gene set enrichment analysis (GSEA) results (http://www.broadinstitute.org/gsea/index.jsp). The output of a GSEA analysis is a ranked list of gene sets. The end-user is often at a loss in summarizing and interpreting the output. This is due to the redundant nature of gene sets and often less than useful names of the gene sets. The enrichment map (http://baderlab.org/Software/EnrichmentMap/) is just the tool to resolve the redundancy and assist in interpreting the biological meaning of the GSEA table of gene sets. The tool is relatively easy to use and has decent use case examples and user manual. In addition, a 'methods' paper for the use of Enrichment Map is published here Merico D, 2011. The authors also have an additional tool, WordCloud Oesper L, 2011 that assists in summarizing groups of gene sets visualized using the Enrichment Map. This helps the user to assign textual descriptions and aids in summarizing the represented biology. The WordCloud tool can be found here: http://baderlab.org/Software/WordCloudPlugin. I highly recommend these tools for interpreting GSEA results.