Figure 4.

Molecular Phenotypic Abnormalities and Tumor Individuality Are Linked to Features of Poor Prognosis

(A) Phenotypic abnormality, individuality, and richness shown schematically using hypothetical phenotypes (shape) and tumors (color).

(B) Phenotypic abnormality scores of all epithelial clusters.

(C) Phenotypic abnormality scores of tumors and the median score of juxta-tumoral samples.

(D and E) Stacked histograms of (D) frequencies of cells per epithelial cluster group per tumor ordered by increasing phenotypic abnormality and (E) the average frequencies for juxta-tumoral tissue.

(F–H) Tumor phenotypic abnormality scores by (F) grade, (G) ER status, and (H) subtype.

(I) Phenotypic abnormality scores versus the percentage of Ki-67⁺ and CA9⁺ cells for tumors.

(J) Individuality scores for juxta-tumoral (JT) and tumor (T) tissue.

(K) Individuality scores versus phenotypic abnormality scores for tumors.

(L) Individuality scores for ER⁺ and ER⁻ tumors.

(M) Individuality scores versus the percentage of ERα⁺ cells for ER⁺ tumors.

(N) Heatmap of presence and proportion of the 45 epithelial clusters for all samples.

(O) Richness scores for mammoplasty (M), juxta-tumoral (JT), and tumor (T) samples.

(P) Individuality scores versus richness scores for tumors.

(Q) Cluster frequency map for ten tumors that had not regressed despite neoadjuvant chemotherapy.

Wilcoxon rank-sum test was used for statistical analysis. ^∗p < 0.05, ^∗∗p < 0.01, ^∗∗∗p < 0.001. See also Figure S4.