Fig. 3

Proteomic analysis of H460 and MCF7 cell lines grown in 2D and 3D culture conditions. A Heatmap of 3DEPs in 3D vs 2D conditions of both cell lines. Common DEPs in all 3D vs 2D conditions are labeled with (*). Color intensity is proportional to the magnitude of changes. Relative expression levels are shown in red (upregulation) and blue (downregulation). B KEGG pathway analysis of DEPs in all 3D vs 2D conditions of both cell lines. The dot size denotes the number of DEPs, while colors correspond to the adjusted p-value range. C Dot plots showing ALDOC, ENO2, and NOL3 protein levels of H460 and MCF7 cell lines in 3D vs 2D conditions. D The distribution of gene-wise mRNA-protein correlations computed as Spearman’s Rho (x-axis). A histogram of 20 bins is shown with height of each bar proportional to the number of genes in each bin. The median correlation is depicted by a red vertical line