Figure 3

Comparison of GSEA based methods on breast cancer datasets. a. The Pearson correlation between datasets was calculated based on the Normalized Enrichment Score (NES) of each KEGG PATHWAY gene set generated by the original GSEA or with the integration of gene appearance frequency (AF), random frequency (RF), inverse weight (IW). Error bars show the standard error of the mean. b. Ranked list of KEGG Pathways was generated for each method and each dataset separately. The number of overlapping KEGG Pathways was calculated between datasets for each method for increasing length of ranked list. Only pathways with FDR < = 0.05 are considered.