The intrinsic breast cancer subtypes, and their defining gene sets, could be clearly identified including basal-like, luminal and HER2-Enriched expression signatures (Fig. 2b-d); however, now these gene clusters were often populated with multiple isoforms from the same gene that were typically co-clustered together, such as multiple isoforms of ESR1 and SCUBE2 in the luminal cluster (Fig. 2c), and multiple isoforms of HER2/ERBB2 in the HER2 amplicon cluster (Fig. 2d). This evidence concerns the gene SCUBE2 and breast cancer.