a A volcano plot represents differentially expressed genes between anti-MDK antibody- and IgG-treated NCI131, N783 and NCI827 cells. The x-axis represents the log2-fold change values, and the y-axis represents the log q-values. The red or blue dots indicate genes significantly (q < 0.05) upregulated (log2-fold change ≥ 0.5) or downregulated (log2-fold change ≤ −0.5) upon anti-MDK treatment (12 h), respectively. b The bar charts depict the top ranked pathway analyzed from the functional classification based on the GO biological process using gene expression data from (a). The red (top) and blue (bottom) bars represent upregulated and downregulated pathways, respectively, upon anti-MDK treatment compared to IgG treatment. c The heatmap shows single-sample gene set enrichment (ssGSEA) enrichment scores analyzed using mRNA expression data from IgG- or anti-MDK-treated (12 h) NCI131, N783 and NCI827 cells, classified according to cellular process. d The normalized ssGSEA enrichment scores of three different cells upon treatment with IgG (gray bar) or the anti-MDK antibody (red bar) for the indicated pathways are shown as box plots. e A correlation plot of the normalized protein levels in NCI827 cells treated with IgG or anti-MDK (12 h), obtained from a protein array, is shown. The red and blue dots represent proteins upregulated and downregulated, respectively, upon treatment with anti-MDK compared to IgG control. f A radar plot of the fold enrichment of the indicated pathways in accordance with their functional classifications (GOBP on DAVID) using protein expression data from (e) is shown. The fold change in enrichment increases by five on the radar plot. The pink and green areas represent upregulated and downregulated pathways, respectively, upon treatment with the anti-MDK antibody compared to control IgG.