Data Supplement from Chromosomal Instability Selects Gene Copy-Number Variants Encoding Core Regulators of Proliferation in ER<sup>+</sup> Breast Cancer

Supplementary Table S1: Genes that impair cell viability (Z-Score < -2) in at least 3/5 cell lines (PC9 (lung), RCC4 (kidney), HCT116 (colon), MCF-10A (breast) and HT1080 (fibrosarcoma)) in RNAi screens and their Z-scores. These genes were regarded as proliferation genes. Supplementary Table S2: GO Term Enrichment for Proliferation Genes (RNAi Screens) found in Supplementary Table S1. Supplementary Table S3: Candidate core regulators prior to CONEXIC analysis. Supplementary Table S4: GO Term Enrichment of Top 30 Key Regulators. Supplementary Table S5: Top 50 GO Terms Enriched for Module Genes Belonging to Core Regulators from Table 1. P-Values were derived by Fishers Exact Test. The GO analysis for each core regulator module was done independently of the other core regulator modules. Supplementary Table S6: The amplified core regulators TPX2, AURKA, UBE2C, EXO1, MYBL2, TPT1, KIF14 and UBE2T are also members of at least one breast cancer prognostic signature.