Fig. 3: Difference in the molecular background between HER2-low and HER2-0 breast cancers with different HR statuses.

a–c Bar plots comparing the distribution of PAM50 subtypes between HER2-low and HER2-0 breast cancers in the entire cohort (a), HR-positive subgroup (b) and HR-negative subgroup (c). P values were computed using the two-sided Fisher’s exact test. d, e Dot plots showing differentially expressed genes (DEGs) between HER2-low and HER2-0 tumors in the HR-positive (d) and HR-negative (e) subgroups. P values were computed using the two-sided Wald’s test and were adjusted for multiple testing using the false discovery rate method. Genes with abs(log₂(fold change))>1 and adjusted P value <0.05 were considered DEGs (colored blue or red). Lipid metabolism-related genes are represented by triangles, and others are represented by circles. f, g Boxplots showing REACTOME gene set activity scores changing with HER2 IHC scores in the HR-positive (f) and HR-negative (g) subgroups. The number (N) of increasing or decreasing gene sets is indicated. The centerline represents the median, the box limits represent the upper and lower quartiles, the whiskers represent the 1.5× interquartile range, and the points represent individual samples. h Heatmap showing the protein levels of lipid metabolism-related genes across HER2 IHC scores in the HR-positive and HR-negative subgroups. Proteins marked with * represent those that increase significantly with HER2 IHC scores. i Heatmap showing the abundance of lipids across HER2 IHC scores in the HR-positive and HR-negative subgroups. Lipids marked with * represent lipids that increase significantly with HER2 IHC scores. LumA luminal A, LumB luminal B, HER2 (in PAM50 section) HER2-enriched, basal basal-like, normal normal-like, ISH in situ hybridization. Source data are provided as a Source Data file.