The gene expression pattern of ER, PR, HER2 and the global copy-number pattern of the breast tumor samples are given in Supplementary figure 1 and Supplementary figure 2. The numbers of over-expressed/underexpressed genes for each tumor groups as well as the overlapped genes of them are shown in Supplementary figure 3 and Supplementary figure 4. The copy-number pattern for the breast cancer cell lines is shown in Supplementary figure 5. The 2,426 genes with CNVs and the 4,843 differ-entially expressed genes (DEGs) for all groups of tumor samples are listed in Supplementary table 1 and Supplementary table 2. The 384 individual genes showed copy number change associated with alteration in their expression for all tumor sample groups are listed in Supplementary table 3. The cor-relation between all the cancer cell lines in CCLE and breast tumor sample groups using copy-number information or gene expression profiles are given in Supplementary table 4 and Supplementary table 5.