Fig. 5

Pathway analysis of differentially expressed genes between control and EMP3 KO cells. A, B Venn diagram showing the overlap of (A) downregulated genes (log2-FC ≤ -1, FDR P-value ≤ 0.05) and (B) inhibited master regulators (activation z-score ≤ -2, P-value ≤ 0.05) between DK-MG and U-118 EMP3 KOs. C, D KEGG pathways enriched based on the list of (C) commonly downregulated genes and (D) commonly inhibited MRs. E, F GSEA results showing upregulation of the gene sets KOBAYASHI_EGFR_SIGNALING_24HR_DN (E) and _UP (F) in U-118 control and EMP3 KO cells, respectively. Genes were sorted from left to right based on the difference of the log2 expression levels between control and EMP3 KO cells. Vertical black bars indicate the location of the genes contributing to the enrichment scores (ES). The ES, which indicate upregulation (ES > 0) or downregulation (ES < 0) of a certain gene, are plotted on the y-axis. NES: normalized enrichment score. G qPCR results validating the downregulation of selected genes in U-118 EMP3 KOs (unpaired one-tailed t-test; *P =  < 0.05; ** P =  < 0.01)