Fig. 1

Multi-omics landscape of UC samples. A The workflow of the experiment. B The number of samples for proteomics, phosphoproteomics, WES, and RNA-seq analysis. C The genomic profiles. Top to bottom: synonymous and non-synonymous somatic mutation rates; somatic mutations for significantly mutated genes (SMGs); and potential SMG. Mutation types and their frequencies are depicted by a bar plot in the right panel. D Gene mutation frequency in our cohort compared with other cohorts. E Correlation plot of the mutation frequencies observed in Fudan cohort compared to TCGA cohort and Beijing cohort. F Comparison of TMB in the tumors of our cohort and the Beijing cohort. G Mutational spectrum of the four mutational signatures extracted by Sigminer analysis. Corresponding COSMIC signatures are labeled in parentheses. H Comparison of TMB in the tumors with different mutational signatures. I Kaplan–Meier curves (Gehan–Breslow–Wilcoxon test) for overall survival based on different mutational signatures. J Left panel: mRNA–protein correlation in MNUs. Blue: pathways in which positively correlated genes were involved; green: pathways in which negatively correlated genes were involved. Right panel: mRNA–protein correlation in tumors. Red: pathways in which positively correlated genes were involved; orange: pathways in which negatively correlated genes were involved