Fig. 1: Unique molecular characteristics of malignant phyllodes tumours (MPTs).

a Prevalence of somatic mutations, measured by the number of somatic mutations per Mb of covered target sequence, in MPT compared to that in invasive ductal carcinoma (IDC) (MPT, n = 8; IDC, n = 18; Mann–Whitney test). b Comparison of the prevalence of signatures between MPT and IDC identified by SigMA (MPT, n = 8; IDC, n = 18; Fisher’s exact test). “Sig3 hc” means signature 3 with high confidence, and “Sig3 lc” means signature 3 with low confidence. c Somatic mutations and copy number alterations in cancer-related genes and specific regions in the nine MPT. Genes associated with clinical action are denoted in bold font, based on TARGET v3 from the Broad Institute. Genes marked with “copy amp” indicate genes with a copy number ≥5. d PCA plot showing unique gene expression profiles of MPT compared to normal breast and IDC tissues. e KEGG pathways enriched with upregulated genes in MPT compared to normal breast tissues (top) or IDC tissues (bottom). f Cytoscape network analysis showing significantly altered pathways in MPT compared to normal breast tissues (left) or IDC tissues (right). The colour-filing nodes reflect statistical significance of the term (pathway). Node size refers to the number of genes associated with the term among the differentially expressed genes. Terms with high significance were clearly labelled. **p < 0.01, ****p < 0.0001.