Fig. 7

Determining the importance of key regulatory (KR) gene subnetworks in comprehensive genes under multiple regulatory controls (CGMC) network using gene set enrichment analysis. The figure shows enrichment plots from the top four KR subnetworks that are significantly enriched in the CGMC network. The significance was determined from nominal P-values (≤0.05) and false discovery rate (≤ 0.25) obtained from gene set enrichment analysis (GSEA). Each enrichment plot shows the following: Top: running enrichment score (ES) of the gene set (KR subnetwork) as a running-sum statistic working down the ranked list of CGMC network genes. The peak of the plot is the ES for the gene set (shown with red line). Middle: black vertical bars show the position of genes in the KR subnetwork in the ranked list of CGMC genes. The leading edge is the subset of genes that contribute most towards the ES and are the most differentially expressed genes in the CGMC network. Bottom: a colored bar showing positive (red) and negative (blue) correlation to phenotype and a plot showing the ranked list of CGMC genes based on the t-test that measures the gene’s correlation with the phenotype. Normalized enrichment score (NES) and nominal P-value (NOM) obtained from the GSEA analysis are shown on top of each plot