Fig 2: Redundancy of protein features and their relationships with basal and luminal subtypes. (A) Supervised clustering of immunohistochemistry (IHC) expression values recapitulates the expected patterns, defining tumor-cell phenotypes based on IHC subtypes. (B) Spearman correlation coefficients for the IHC expression levels of 24 proteins in all samples (n=193). Dot sizes correspond to correlation strengths. (C) Principal components analysis incorporating IHC expression data for urothelial-like (Uro), genomically unstable (GU), and basal (BaSq) subtypes. Abbreviations: Mes-L, mesenchymal-like; NE, neuroendocrine; CCNB1, cyclin B1; CCND1, cyclin D1; CDH1, cadherin 1; CDH3, cadherin 3; CDKN2A (p16), cyclin-dependent kinase inhibitor 2A; CGHA, chromogranin A; E2F3, E2F transcription factor 3; EPCAM, epithelial cell adhesion molecule; FGFR3, fibroblast growth factor receptor 3; FOXA1, forkhead box A1; GATA3, GATA-binding protein 3; KRT5, keratin 5; KRT14, keratin 14; KRT20, keratin 20; NCAM1, neural cell adhesion molecule 1; PPARG, peroxisome proliferator-activated receptor gamma; RB1, retinoblastoma protein; RXRA, retinoid X receptor alpha; SYP, synaptophysin; TP63, tumor protein 63; TUBB2B, tubulin beta 2B class IIb; UPK3, uroplakin 3; VIM, vimentin; ZEB2, zinc finger E-box binding homeobox 2.