Fig. 4: Proteomic and transcriptomic stratification of WT and corresponding molecular and pathway features.

a The subgroups identified by spectral clustering and their clinical relevance. Heatmap depicting the RNA and protein expression patterns of the representative genes in the three subgroups, Subgroup 1 (S1), Subgroup 2 (S2) and Subgroup 3 (S3). b Bar chart of the proportions of blastemal, stromal and epithelial components in S1 (n = 24), S2 (n = 13), and S3 (n = 22). A one-sided Chi-squared test was performed to test the difference. c Box plot of the stromal scores (left) and immune scores (right) in S1 (n = 24), S2 (n = 13) and S3 (n = 22). Data are presented as means \(\pm\) SEM. Boxplots show median value, box indicates 75 and 25th quartile and whiskers extend to the farthest value (largest and smallest). A two-sided Wilcoxon rank sum test was performed to determine the difference between the subtypes. The false discovery rate adjustments were made for multiple comparisons. d Heatmap of alteration pathways in the proteomic subgroups at the RNA, protein and phospho-protein levels. e The mRNA and protein expression level of the signature genes of the alteration pathways highly expressed in S1 (left), S2 (middle), and S3 (right). f Classification of activated kinases in S1, S2 and S3. g Heatmap depicting the subgroup-specific phosphorylation sites and corresponding kinases. The labels on the right represent the phosphorylated sites. h Kaplan‒Meier plots of event-free survival (left) and overall survival (right) of WT subgroups in the TARGET cohort. The p-value was calculated by the log-rank test. i The proportions of tumors with stages I, II, III, IV, or V in subtypes S1, S2, and S3 in database GSE31403. A Chi-square test was performed to test the difference. Source data are provided as a Source Data file.