Fig. 3: The application of FDGC subtyping algorithm in multiple independent cohorts, and the association of MSI/MSS characteristics with clinical outcomes.

a Sankey diagram indicating the comparison of FDGC subtype and BPRC subtype or EOGC subtype. b Sankey diagram and barplot indicating the comparison of FDGC subtype and ACRG subtype. Survival analysis of ACRG cohort classified by FDGC subtyping (two-sided log rank test). c Heatmap of CNV GI (copy number variation genomic instability index), MSI-H assay status, mutations, and MSI/MSS-sig (microsatellite instability/microsatellite stability gene expression signatures assessment) of ACRG cohort classified by FDGC subtyping (upper). Heatmap of MSI/MSS-sig of FDGC subtype (bottom). P-values are calculated by two-sided Fisher’s exact test (categorical variables) and two-way ANOVA test (continuous variables). d The association of MSI/MSS-sig level with OS in ACRG and FDGC cohorts (two-sided log rank test). e Heatmap illustrating significantly differential expressed proteins in MSI/MSS-sig high and low group (two-sided Wilcoxon rank-sum test). f Heatmap illustrating down-regulated proteins in G-IV compared with other subtypes (Kruskal-Wallis test). g Heatmap illustrating the dominant cell type compositions of G-II, G-III, and G-IV (two-sided Student’s t test). h Boxplot showing the xCell score of Macrophages M1 and monocytes among four proteomic subtypes (two-sided Student’s t test). n (G-I) = 28, n (G-II) = 56, n (G-III) = 75, n (G-IV) = 20 biologically independent samples examined. Boxplots show median (central line), upper and lower quartiles (box limits), 1.5× interquartile range (whiskers). i Correlation between MSI/MSS-sig with Macrophages M1 and monocytes (two-sided Pearson’s correlation test). j The association of Macrophages M1 and monocytes with OS in FDGC and ACRG cohorts (two-sided Gehan-Breslow-Wilcoxon or two-sided log rank test). k The abundance of Macrophages M1 markers in MSI/MSS-sig high and low groups (two-sided Wilcoxon rank-sum test). l Correlation between IL18 abundance with MSI/MSS-sig (two-sided Pearson’s correlation test), and survival analysis of IL18 expression with OS (two-sided log rank test). m Diagram illustrating the potential association between MSS/MSI characteristics with drug response. *P < 0.05 is considered statistically significant. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. Source data are provided as a Source Data file.