Fig. 3: Proteogenomic analysis of ITH.

A–D Pair-wise correlations between genomic and proteomic ranked cosine similarities across regions within each tumor in four ER+ breast cancer patients. For each patient, the solid line indicates the best-fit linear regression, with the regression equation, Pearson’s r, and p-value shown. The grey shaded area represents the 95% confidence interval of the fit. Pathway enrichment analysis was performed using a two-sided Mann-Whitney test in most constant (E) and most variable (F) proteins, defined by the 10% lowest and highest median absolute deviation (MAD) scores, respectively. Circle size reflects the number of proteins per enriched pathway, and color scale indicates FDR q-values. Pathway names marked with an asterisk (*) were edited for visualization. The complete enrichment results are provided in Supplementary Data 5.