TMEM43 and breast cancer: To investigate the effect of CNA-driven enhancers on expression of target genes in the four breast cancer subtypes, we firstly identified subtype-specific differentially expressed genes (DEGs) and differentially expressed lncRNAs (DELs), with a threshold of FDR < 0.05 and logFC > 1 in the Basal-like, Her2, LumA, LumB subtypes, respectively (Figures 2A, B).