Fig. 3: Validation of the biological characteristics of the 5 HER2-positive breast cancer subtypes using hallmark gene sets and single genes/gene signatures in NeoALTTO, and comparison with ALTTO original subtypes.

a Comparisons across HER2-positive breast cancer subtypes using hallmark gene sets computed performing gene set variation analysis in ALTTO (left half of the circles) and NeoALTTO (right half of the circles). b Comparisons across HER2-positive breast cancer subtypes using single genes (ERBB2, ESR1) and gene expression signatures in ALTTO (left half of the circles) and NeoALTTO (right half of the circles). Wilcoxon rank-sum test was used to compare each subtype against the others (i.e., one vs. rest). The effect size represents the direction of the association (red, positive if >1, blue, negative if <1), and was calculated by applying a linear regression model. FDRs were obtained by adjusting P values with Benjamini & Hochberg method. The dimension of the circle varies proportionally to the effect size (see figure legend). For visualization, effect sizes ≤0.25, ≥0.66 and ≤1, >1 and ≤1.5, and ≥4 have fixed size; FDRs >0.1 are shown with lighter colors. The left halves of the circle represent the effect size for the original subtypes derived from the integration of NMF, k-means clustering and AIMS intrinsic subtypes in ALTTO, while the right halves represent results for NeoALTTO. All P values are two-sided. All analyses are on N = 386 ALTTO samples and N = 254 NeoALTTO samples (IM, N = 42; P/Met, N = 41; Mes/S, N = 59; LUM, N = 52; ERBB2-D, N = 60). Source data are provided as a Source Data file. ER estrogen receptor, ERBB2-D ERBB2-dependent, FDR false discovery rate, IM immune-enriched, LUM luminal, Mes/S mesenchymal/stroma-enriched, NMF non-negative matrix factorization, P/Met proliferative/metabolic-enriched.