leading_edge and core_enrichment columns in clusterProfiler GSEA output

[sanjanasood]

Hi,

I am using GSEA in clusterprofiler which returns gseaResult object. I am struggling a bit to interpret and understand the two columns in the output that have header leading_edge and core_enrichment. It will be helpful if you could help me understand what do these columns refer to and how to interpret them?

Thanks in advnace
Sanj

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[guidohooiveld]

Please check the GSEA documentation on the Broad website....

Leading edge genes: "As described in the Gene Set Enrichment Analysis PNAS paper, the leading-edge subset in a gene set are those genes that appear in the ranked list at or before the point at which the running sum reaches its maximum deviation from zero. The leading-edge subset can be interpreted as the core that accounts for the gene set’s enrichment signal." Source..

Core enrichment genes: "Genes that contribute to the leading-edge subset within the gene set. This is the subset of genes that contributes most to the enrichment result." Source.

The leading edge information is given as percentages (tags, list, signal), and these metrics are used to define the leading edge subset, which are thus the core enrichment genes.... See halfway this page (section "Detailed Enrichment Results"). I agree it is somewhat confusing....

Maybethis clusterProfiler page on visualization is also of interest.