72 A Practical Guide to Cancer Systems Biology
IV.Data interpretation using EnrichmentMap
Interpret GSEA results (Fig. 9).
Figure 9. Interpret GSEA results. To perform EnrichmentMap of GSEA results, set the
parameters as follows: 1. Select “GSEA” as analysis type; 2. Select the assigned GMT file
used to perform GSEA; 3. Select the expression TXT file; 4 and 5. Select the enrichment
results from GSEA output folder for each class; 6. Select the ranking file from GSEA
output folder; 7. Select the phenotype CLS file as Classes; 8. Define the phenotype label;
- Click “Build” to perform EnrichmentMap.
Launch Cytoscape program, install EnrichmentMap App from App>
App Manager, and apply EnrichmentMap by click App>EnrichmentMap>
Create Enrichment Map.