Additional file 6: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

Protein-coding genes associated with HER2 amplification. (A) List of 43 protein-coding genes with subtype-independent expression differences between HER2A and non-HER2A breast tumors, after accounting for PAM50 subtype and differences in chromosomal instability, in the TCGA and Metabric cohort. These genes fulfilled the following criteria in at least one cohort: adjusted p value <0.05, and fold change >2 (linear model). (B) List of 14 protein-coding genes with cancer-independent expression differences between HER2A and non-HER2A tumors in a panel of 2838 non-breast TCGA tumors, after accounting for cancer and chromosomal instability. These genes fulfilled the following criteria: adjusted p value <0.001, and fold change >2. (XLSX 24 kb)