Tumour phenotypes in relation to the identified genomic subgroups. (a) Expression of oestrogen-receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor (HER)-2 was available in all cases enabling classification of all tumours as luminal or non-luminal. The tumours were then further subdivided using the five biomarker scheme based on expression analysis of ER, PR, HER-2, epidermal growth factor receptor (EGFR) and cytokeratin (CK) 5/6. The left part of each rectangle represents the proportion of luminal phenotypes within each of the four subgroups, as indicated, whereas the right part represents the proportion of non-luminal tumours. Sub-categories of these phenotypes are represented there within as proportions of either luminal or non-luminal phenotypes, see bottom of the figure. (b) Projection of all tumours through principal component analysis (PCA) is shown with cluster outcomes, BRCA status and the assigned tumour phenotypes indicated. Colours indicate tumour phenotypes matching those given at the bottom left panel with the addition of high PR expression immunohistochemistry scores 2+ and ≥ 3+ indicated by dark and light orange character outlines, respectively. Cluster memberships and BRCA status are indicated as shown at the bottom of the figure. In terms of tumour phenotypes, it can be hypothesised that component three reflects differences in luminal vs. non-luminal phenotypes whereas component two separates two populations of luminal tumours, which relate to differential PR expression.