Fig. 2: Impacts of somatic copy number variations in AMPAC Fudan cohort.

a Functional effect of CNVs on mRNA and proteins. Top panels, the correlations of CNV to mRNA and protein abundance. Positive and negative correlations are indicated in red and green, respectively. Genes were ordered by chromosomal location on the x and y axes. Diagonal lines indicate cis effects of CNV on mRNA or proteins. Bottom panels, the numbers of mRNAs or proteins that were significantly associated with a specific CNV. Gray bars indicate correlations specific to mRNA or proteins, and black bars indicate correlations with both mRNA and proteins. b Venn diagrams depicting the cascading effects of CNVs and the overlap between cis events via the transcriptome, proteome, and phosphoproteome analyses (Spearman’s correlation, p < 0.05). c The pathways enriched by 1114 significant cis effect genes overlapped with the transcriptome and proteome. d Venn diagram showing the CAGs with significant CNV cis effects via multi-omics data analyses (Spearman’s correlation, p < 0.05). e Locations of the CAGs with cascading copy number cis regulation of their cognate mRNA, protein, and phosphoprotein levels. f The protein–protein interaction network constructed by the 6 CAGs. g Cis and trans effects of significant cis effect genes from focal adhesion, cell cycle, and fatty acid metabolism pathways. h Top panel, heatmap of the GSVA score of focal adhesion, cell cycle, and fatty acid metabolism pathways in the different pathology subtypes. Bottom panel, boxplot of the GSVA score of focal adhesion, cell cycle, and fatty acid metabolism pathways in the different pathology subtypes (one-way ANOVA test).