Fig. 2: Proteogenomic analysis of CIN + SBC on mRNA, protein, and phosphoprotein expressions levels.

A Enrichment analysis of differential expressed proteins (FDR < 0.05) between CIN+ and CIN- SBCs. B Scatterplot showing the Spearman’s correlation coefficient and p-value of the MGPS score versus CIN score (two-sided, 95% CI for the regression band), n = 163. C The proliferation curve of the CIN+ cells and the control cells (n = 3, mean ± SEM, biological replicates). D The flow cytometry analysis showing cell cycle progression of the CIN+ cells compared with the control cells. E ssGSEA scores of known CIN cause pathways between CIN+ (n = 86) and CIN- (n = 77) SBC samples (Student’s t-test, two-sided). The middle bar represents the median, and the box represents the interquartile range; bars extend to 1.5 × the interquartile range. F The heatmap of CIN score and protein abundance of DNA replication stress (RS) markers, n = 163. The Spearman’s correlation p-values between the CIN score and the protein/pathway, and the Student’s t-test p-values (two-sided) between CIN+ and CIN- samples were displaying in asterisks. The significance is defined as: n.s., not significant; *p < 0.05; **p < 0.01; ***p < 0.001. G Scatterplot showing the Spearman’s correlation (two-sided) between the ssGSEA scores of the DNA RS pathway and hallmark pathways. H Scatterplot showing the Spearman’s correlation coefficients (two-sided) of the CIN score versus mRNA expression levels (x axis) and transcription factor (TF) activities (y axis) of E2Fs. I Scatterplot showing the Spearman’s correlation coefficients (two-sided) between the E2F3 TF activity and kinase activities, n = 157. J Heatmap of the multi-omics features related to regulation of cell cycle in CIN + SBC. K Apoptosis pathway expression score are negatively correlated with CIN score in SBC. Spearman’s correlation and p-value are shown (two-sided, 95% CI), n = 163. L The flow cytometry analysis showing decreased apoptosis in the CIN+ cells compared with the control cells. Annexin V-positive cells (early apoptotic cells, Q4) and Annexin V and PI double-positive cells (late apoptotic cells, Q2) are shown.