Fig. 1

The seven input levels for integrative clustering and association with clinical/molecular classifications. Original subtypes/clusters of each input level and corresponding PAM50 gene expression subtype, estrogen receptor (ER), progesterone receptor (PR) and epidermal growth factor receptor 2 (HER2) status, and TP53 and PIK3CA mutation status of the tumor samples. The tumor samples are sorted in the following order: molecular level, PAM50 gene expression subtype, ER, PR, HER2, TP53 and PIK3CA status. a PAM50 gene expression subtypes (n = 377). b Reverse-phase protein array (RPPA) subtypes (n = 173). c Complex arm aberration index (CAAI) subtypes (n = 349). 0 no CAAI events, 1 one CAAI event, 2 at least two CAAI events. d miRNA clusters (n = 423). e Metabolic clusters (n = 233). f Integrated clusters (IntClust; n = 291). g Pathway recognition algorithm using data integration on genomic models (PARADIGM) clusters (n = 312). Lum luminal, Pos positive, Neg negative, Mut mutant, Wt wild-type, NA not applicable