Figure 2

GSEA analysis on significantly regulated gene sets across microarray platforms. Profile of the Running ES Score & Positions of Gene Set Members on the Rank Ordered List using 6 h EGF treatment data according to each of the three microarray platforms. In each panel, the vertical black lines indicate the position of each of the genes of the tested gene set in the reference data set (ranked by average of the three respective EGF versus control log2ratios of replicate experiments). The green curve plots the ES (enrichment score), which is the running sum of the weighted enrichment score obtained from GSEA software. Within each queried gene set, the farther the position of a gene to the left (red) implies a higher correlation with EGF up-regulated genes in the reference platform, and the farther to the right (blue) implies a higher correlation with genes down-regulated upon EGF treatment in the reference platform. Studied gene sets correspond to lists of up- or down-regulated genes in each platform at 6 h of EGF treatment. Significantly enriched data sets are defined according to GSEA default settings (p < 0.001 and a false discovery rate (FDR) < 0.25). R.L.M = ranked list metric.