Additional file 2: of The molecular landscape of premenopausal breast cancer

Abstract

Stratified analysis TCGA. Table S1 and Table S2: Gene expression-Agilent (ER-pos) (Table S1) and RNA-Seq (ER-pos) (Table S2). Output from R package “limma” for ER+ tumors. Table S3: Methylation (ER-pos). Table S4: Copy Number Variation (ER-pos). Table S5: RPPA (ER-pos). Table S6: Somatic Mutation (ER-pos) (MutSig). Table S7: Power Analysis for comparison of two mutation rates with fixed sample size (n1 = 102, n2 = 384), and alpha = 0.05. Table S8: Gene expression-Agilent (ER-neg). Output from R package “limma” for ER- tumors. No genes were significant when FDR was controlled at 5 %. Table S9: Gene expression-RNA-Seq(ER-neg). Output from R package “limma” for ER- tumors. No genes were significant when FDR was controlled at 5 %. For all tabs, genes highlighted in yellow are significant when FDR is controlled at 5 %. For methylation analysis, there was additional requirement for absolute difference between average beta-value of two groups to be > 0.1. (XLSX 25246 kb