Fig. 2

Higher protein translation in DN glomeruli compared to controls. a The t-SNE analyses of transcriptomic (top) and proteomic (bottom). Red nodes represented DN patients and blue nodes represented controls. b The volcano plot of transcriptomic (top) and proteomic (bottom). The differentially expressed genes (2-fold, FDR ≤ 0.01) were highlighted with red (upregulated) and blue (downregulated). c Two-dimensional annotation of biological process (BP) enrichment analysis of differential proteins and mRNAs. The signed -log10 (P-value) values of the BP enrichment at the protein and mRNA level are indicated in the x and y axes, respectively. Red nodes represented the BPs enriched by upregulated mRNAs and proteins, whereas blue nodes represented the BPs enriched by downregulated mRNAs and proteins. d Venn diagram showed the number of matched mRNA-protein pairs (top) as well as the overlap of significantly differentially expressed (DE) mRNA and protein (bottom). e Protein-per-mRNA FC ratio analysis illustrated the fold-change discordance between mRNA and the corresponding protein. The value of FC ratio was log10 transformed. The FC ratio value for 2961 matched genes (left) and 1809 unchanged genes (middle) were log-normally distributed; The FC ratio analysis for 1152 differentially expressed genes identified two populations of extreme values (right). f The violin plot showed the difference in protein-per-mRNA FC ratio between the differentially expressed genes and the non-differentially expressed genes. P-value was calculated by Mann-Whitney U test. g–h The mRNA (left) and protein (right) scatterplots for CYBR1 (g) and PDLIM1 (h) between DN and control samples-h The mRNA (left) and protein (right) scatterplots for CYBR1 (g) and PDLIM1 (h) between DN and control samples