Fig. 6: Consensus clustering analysis of the SBC cohort identified four proteomic subtypes. | Nature Communications

Fig. 6: Consensus clustering analysis of the SBC cohort identified four proteomic subtypes.

From: Proteogenomic characterization of skull-base chordoma

Fig. 6

A Heatmap illustrating the characterizations of four proteomic subtypes (Kruskal–Wallis test), annotated with clinical features (Fisher’s exact test), n = 187. Fisher’s exact test was used for categorical variables. B Pathways significantly enriched in the proteomic subtypes (FDR < 0.05). C, D Boxplots illustrating CIN score (C) and immune score (D) across proteomic subtypes (Wilcoxon rank-sum test used for comparisons between two subtypes, Anova test and Kruskal–Wallis test used for comparisons among four subtypes; P-I: n = 54; P-II: n = 38; P-III: n = 50; P-IV: n = 45). E Heatmap illustrating the overlap of immune clusters with proteomic subtypes. F, G Survival Kaplan–Meier curves showing (F) OS and (G) PFS of primary tumors within the four proteomic subtypes (log-rank test). P-I = 40, P-II = 19, P-III = 31, and P-IV = 31. H Heatmap of PROGENy pathway scores between P-II and P-III subtypes (Wilcoxon rank-sum test). The p-value is displayed in asterisks. I Boxplot showing lower TRAIL pathway score in P-II subtype compared with P-III subtype (Wilcoxon rank-sum test; P-II: n = 38, P-III: n = 50). J Boxplot showing lower IRF1 TF activity score in P-II subtype compared with P-III subtype (Wilcoxon rank-sum test; P-II: n = 38; P-III: n = 50). K Scatterplot showing the Spearman’s correlation (two-sided) of the IRF1 TF activity score versus TRAIL pathway score, n = 180. L Heatmap showing representative TRAIL pathway related genes significantly downregulated in P-II subtype compared with P-III subtype. M Plot showing qPCR result of IRF1 gene between the IRF1 KD cells and the control cells (n = 2 for each group, biological replicates). N Boxplot showing apoptosis pathway score between the IRF1 KD cells and the control cells (Paired t-test, two-sided; n = 3 for each group, biological replicates). For boxplot in (C, D, I, J, and N) the middle bar represents the median, and the box represents the interquartile range; bars extend to 1.5 × the interquartile range.

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