Fig. 3

TNBC-specific SE heterogeneity analysis identifies a consistently high-risk mesenchymal development subtype. (a–d) EMT scores and status across different TNBC NMF subtypes (a). Mean expression levels of EMT marker genes (b), EMT scores (c), and the distribution of different EMT statuses (d) across TNBC NMF subtypes. (e) GSEA of differentially expressed genes between mesenchymal and non-mesenchymal TNBC subtypes in METABRIC and TCGA cohorts. (f) Lehmann bulk RNA-seq subtype gene signatures in TNBC samples from METABRIC (left) and TCGA (mid). The correlation between Lehmann bulk RNA-seq subtype gene signatures and NMF subtype gene signatures (right). (g-h) Kaplan–Meier OS (g) and RFS (h) curves for patients assigned to different NMF subtypes in METABRIC. (i-j) River plot and bar plot showing an overview of dataset sources, lesion locations, SCSA functional subtypes, and different NMF subtypes of TNBC tumor cells. (k) Expression of EMT marker genes CDH1 and VIM across different NMF subtypes of TNBC tumor cells. (l) Pathway enrichment analysis of different NMF subtypes of TNBC tumor cells using AUCell. (m-n) Enrichment of Rho GTPase cycle pathway activity (m) and the expression of corresponding marker genes (n) across different NMF subtypes of TNBC tumor cells. Statistical analysis was performed using the Wilcoxon rank-sum test. * p < 0.05, ** p < 0.01, *** p < 0.001, ****p < 0.0001.