SCGB1D2 and cancer: These genes, though often co-amplified with HER2, are not more highly expressed in HER2A than non-HER2A tumors (Additional file 6A), and only one of these is a known cancer gene, ubiquitin ligase CCNB1IP1. Genes SCGB1D2 and SCGB2A2 that are differentially expressed by HER2A status (FC >4) are not significantly co-amplified with HER2.