Correlation between copy number variation genes and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1XD0ZP4
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1XD0ZP4
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 66 peak regions and 12 molecular subtypes across 934 patients, 581 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1p22.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 2(1q21.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • Amp Peak 3(1q44) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 4(3p26.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Amp Peak 5(3q26.32) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 6(4q13.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 7(5p15.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 8(6p23) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 9(6q21) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 10(8p11.23) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 11(8p11.21) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 12(8q24.21) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 13(10p15.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 14(10q22.3) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Amp Peak 15(11p13) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 16(11q13.3) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • Amp Peak 17(11q14.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Amp Peak 18(12p13.33) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 19(12q15) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Amp Peak 20(13q12.3) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 21(13q34) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 22(14q21.1) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • Amp Peak 23(15q26.3) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 24(17q12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Amp Peak 25(17q23.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 26(19p13.12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 27(19q12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 28(19q13.42) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • Amp Peak 29(20q13.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 1(1p36.13) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Del Peak 2(1p22.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 3(2q37.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 4(3p21.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 5(4p16.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 6(4q35.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 7(5q11.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 8(5q21.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 9(6p25.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 10(6q15) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 11(6q27) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Del Peak 12(7p22.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 13(7q36.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Del Peak 14(8p23.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 15(8p11.21) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 16(9p21.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 17(9q21.11) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 18(10q23.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 19(10q26.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 20(11p15.5) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 21(11q13.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 22(11q23.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 23(11q25) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 24(12p13.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 25(12q24.21) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 26(13q14.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 27(14q24.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 28(15q13.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 29(16q24.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 30(17p12) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 31(17q21.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 32(18q23) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Del Peak 33(19p13.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 34(19q13.32) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 35(20p13) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 36(21q11.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 37(22q11.1) cnvs correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 66 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 581 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Chi-square test Fisher's exact test Chi-square test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
Amp Peak 1(1p22 3) 0 (0%) 721 4.05e-14
(2.46e-11) 		3.63e-12
(2.06e-09) 		3.44e-16
(2.24e-13) 		2.76e-17
(1.84e-14) 		0.000139
(0.0372) 		1.28e-07
(5.36e-05) 		7.32e-24
(5.34e-21) 		4.95e-21
(3.52e-18) 		1.36e-13
(8.16e-11) 		1.36e-15
(8.73e-13) 		1.2e-12
(6.99e-10) 		4e-10
(2.01e-07)
Amp Peak 5(3q26 32) 0 (0%) 640 5.51e-11
(2.92e-08) 		4.13e-11
(2.22e-08) 		1.51e-38
(1.16e-35) 		2.77e-16
(1.81e-13) 		7.16e-07
(0.000274) 		2.92e-06
(0.00102) 		1.94e-25
(1.43e-22) 		4.17e-22
(2.99e-19) 		1.63e-15
(1.04e-12) 		6.39e-24
(4.67e-21) 		1.3e-17
(8.71e-15) 		5.23e-10
(2.61e-07)
Amp Peak 8(6p23) 0 (0%) 684 1.79e-07
(7.39e-05) 		1.45e-07
(6.05e-05) 		3.57e-34
(2.72e-31) 		6.83e-18
(4.6e-15) 		9.24e-07
(0.000348) 		4.4e-05
(0.013) 		2.75e-19
(1.91e-16) 		2.14e-13
(1.27e-10) 		1.52e-18
(1.04e-15) 		2.51e-15
(1.59e-12) 		2.97e-13
(1.76e-10) 		1.89e-10
(9.72e-08)
Amp Peak 9(6q21) 0 (0%) 759 1.24e-13
(7.45e-11) 		5.33e-10
(2.66e-07) 		2.98e-39
(2.29e-36) 		2.48e-13
(1.47e-10) 		1.04e-08
(4.78e-06) 		4.64e-07
(0.000181) 		1.44e-23
(1.05e-20) 		4.6e-20
(3.24e-17) 		3.42e-19
(2.38e-16) 		4.33e-23
(3.14e-20) 		1.65e-17
(1.11e-14) 		3.51e-15
(2.21e-12)
Amp Peak 12(8q24 21) 0 (0%) 336 6.27e-16
(4.07e-13) 		1.89e-08
(8.5e-06) 		8.45e-49
(6.61e-46) 		3.89e-25
(2.87e-22) 		4.58e-08
(2.02e-05) 		9.36e-07
(0.000352) 		1.07e-26
(7.93e-24) 		5.28e-18
(3.58e-15) 		1.31e-21
(9.37e-19) 		2.37e-19
(1.65e-16) 		1.68e-19
(1.18e-16) 		8.96e-16
(5.81e-13)
Amp Peak 13(10p15 1) 0 (0%) 669 2.47e-21
(1.76e-18) 		5.89e-19
(4.07e-16) 		5.83e-38
(4.47e-35) 		8.61e-28
(6.4e-25) 		7e-11
(3.69e-08) 		2.33e-12
(1.34e-09) 		1.69e-35
(1.29e-32) 		7.03e-29
(5.25e-26) 		6.23e-28
(4.65e-25) 		1.2e-30
(9.05e-28) 		8.49e-20
(5.96e-17) 		3.54e-17
(2.36e-14)
Amp Peak 18(12p13 33) 0 (0%) 691 6.85e-12
(3.81e-09) 		9.63e-12
(5.32e-09) 		1.54e-30
(1.16e-27) 		1.37e-16
(9.03e-14) 		2.7e-08
(1.21e-05) 		2.37e-07
(9.61e-05) 		9.08e-24
(6.61e-21) 		4e-19
(2.78e-16) 		9.18e-22
(6.55e-19) 		5.5e-18
(3.72e-15) 		9.01e-18
(6.06e-15) 		2.85e-12
(1.63e-09)
Amp Peak 21(13q34) 0 (0%) 773 1.45e-09
(6.96e-07) 		2.67e-09
(1.26e-06) 		6.6e-19
(4.55e-16) 		3.17e-14
(1.93e-11) 		8.21e-06
(0.00269) 		5.1e-08
(2.24e-05) 		5.14e-19
(3.56e-16) 		3.26e-18
(2.23e-15) 		1.41e-13
(8.46e-11) 		5.59e-20
(3.93e-17) 		1.47e-12
(8.49e-10) 		3.49e-10
(1.77e-07)
Amp Peak 27(19q12) 0 (0%) 696 4.35e-12
(2.45e-09) 		9.44e-11
(4.97e-08) 		8.25e-25
(6.04e-22) 		3.98e-12
(2.25e-09) 		6.19e-07
(0.000238) 		9.68e-07
(0.000363) 		2e-21
(1.43e-18) 		5.4e-17
(3.58e-14) 		6.49e-13
(3.81e-10) 		2.82e-18
(1.93e-15) 		9.58e-11
(5.03e-08) 		6.3e-10
(3.13e-07)
Del Peak 3(2q37 3) 0 (0%) 663 1.51e-06
(0.000552) 		3.28e-09
(1.53e-06) 		1.25e-20
(8.83e-18) 		1.75e-09
(8.27e-07) 		1.03e-08
(4.74e-06) 		1.11e-07
(4.69e-05) 		2.43e-10
(1.25e-07) 		3.39e-10
(1.73e-07) 		4.66e-11
(2.49e-08) 		2.63e-07
(0.000106) 		9.84e-10
(4.79e-07) 		1.45e-05
(0.00454)
Del Peak 4(3p21 31) 0 (0%) 643 2.91e-11
(1.57e-08) 		4.45e-08
(1.97e-05) 		4.55e-36
(3.48e-33) 		1.2e-13
(7.26e-11) 		2.03e-08
(9.11e-06) 		6.18e-06
(0.00206) 		1.72e-19
(1.2e-16) 		6.03e-12
(3.36e-09) 		3.86e-18
(2.63e-15) 		1.17e-12
(6.82e-10) 		1.82e-13
(1.09e-10) 		9.3e-10
(4.55e-07)
Del Peak 5(4p16 3) 0 (0%) 648 2.7e-11
(1.47e-08) 		2.23e-11
(1.22e-08) 		1.07e-29
(8.02e-27) 		8.23e-14
(4.98e-11) 		4.6e-07
(0.000181) 		1.62e-06
(0.000588) 		2.51e-22
(1.8e-19) 		4.85e-20
(3.41e-17) 		9.97e-15
(6.14e-12) 		4.7e-18
(3.2e-15) 		4.76e-15
(2.98e-12) 		1.8e-10
(9.27e-08)
Del Peak 6(4q35 2) 0 (0%) 643 1.17e-06
(0.000432) 		1.24e-06
(0.000457) 		1.36e-38
(1.05e-35) 		7.49e-15
(4.66e-12) 		1.51e-08
(6.85e-06) 		1.78e-06
(0.000637) 		6.54e-21
(4.64e-18) 		2.35e-15
(1.5e-12) 		2.84e-13
(1.68e-10) 		6.73e-18
(4.55e-15) 		1.82e-13
(1.09e-10) 		1.64e-11
(9.05e-09)
Del Peak 7(5q11 2) 0 (0%) 693 2.5e-27
(1.85e-24) 		6.92e-25
(5.08e-22) 		5.53e-66
(4.37e-63) 		7.27e-43
(5.67e-40) 		3.33e-16
(2.17e-13) 		7.43e-19
(5.11e-16) 		2.21e-51
(1.74e-48) 		1.53e-48
(1.2e-45) 		8.36e-40
(6.47e-37) 		5.41e-49
(4.24e-46) 		7.61e-40
(5.89e-37) 		1.03e-33
(7.8e-31)
Del Peak 8(5q21 3) 0 (0%) 704 3.82e-29
(2.86e-26) 		2.12e-26
(1.57e-23) 		1.01e-74
(8e-72) 		5.17e-55
(4.08e-52) 		2.6e-15
(1.65e-12) 		8.97e-16
(5.81e-13) 		3.05e-60
(2.41e-57) 		3.25e-53
(2.56e-50) 		1.28e-39
(9.89e-37) 		1.67e-54
(1.32e-51) 		5.34e-42
(4.15e-39) 		1.27e-39
(9.78e-37)
Del Peak 18(10q23 31) 0 (0%) 664 2.45e-05
(0.00756) 		5.63e-05
(0.0164) 		2.26e-22
(1.63e-19) 		3.88e-12
(2.19e-09) 		1.9e-07
(7.83e-05) 		7.37e-05
(0.021) 		5.35e-15
(3.35e-12) 		1.02e-10
(5.33e-08) 		5.47e-09
(2.54e-06) 		3.97e-09
(1.84e-06) 		3.18e-08
(1.42e-05) 		7.54e-10
(3.72e-07)
Del Peak 19(10q26 3) 0 (0%) 661 1.01e-08
(4.63e-06) 		2.75e-07
(0.00011) 		5.72e-24
(4.18e-21) 		3.41e-12
(1.94e-09) 		3.06e-08
(1.37e-05) 		8.25e-07
(0.000314) 		1.9e-19
(1.33e-16) 		3.02e-15
(1.91e-12) 		7.81e-12
(4.33e-09) 		3.48e-15
(2.2e-12) 		4.91e-11
(2.61e-08) 		2.02e-12
(1.16e-09)
Del Peak 20(11p15 5) 0 (0%) 666 3.55e-07
(0.00014) 		2.1e-07
(8.58e-05) 		1.32e-36
(1.01e-33) 		1.47e-12
(8.49e-10) 		1.27e-09
(6.14e-07) 		1.65e-06
(0.000596) 		3.49e-18
(2.38e-15) 		4.86e-16
(3.16e-13) 		3.87e-15
(2.44e-12) 		1.42e-16
(9.3e-14) 		2.71e-14
(1.65e-11) 		8.09e-10
(3.98e-07)
Del Peak 25(12q24 21) 0 (0%) 754 3.42e-11
(1.84e-08) 		2.7e-10
(1.38e-07) 		2.64e-15
(1.67e-12) 		2.94e-14
(1.8e-11) 		0.000209
(0.0527) 		1.05e-06
(0.000392) 		4.05e-15
(2.54e-12) 		1.99e-14
(1.22e-11) 		1.17e-08
(5.33e-06) 		3.27e-13
(1.93e-10) 		1.19e-07
(4.97e-05) 		6.37e-07
(0.000244)
Del Peak 27(14q24 3) 0 (0%) 633 2.41e-13
(1.43e-10) 		8.08e-09
(3.73e-06) 		3.07e-40
(2.38e-37) 		6.06e-15
(3.78e-12) 		5.29e-07
(0.000205) 		5.53e-06
(0.00187) 		6.41e-29
(4.8e-26) 		1.14e-16
(7.5e-14) 		5.44e-18
(3.69e-15) 		1.52e-16
(9.95e-14) 		8.08e-15
(5.01e-12) 		3.29e-12
(1.87e-09)
Del Peak 28(15q13 1) 0 (0%) 613 4.93e-07
(0.000192) 		1.62e-07
(6.73e-05) 		5.79e-34
(4.4e-31) 		2.35e-12
(1.35e-09) 		0.000193
(0.0493) 		2.32e-05
(0.00717) 		3.32e-18
(2.27e-15) 		2.26e-15
(1.44e-12) 		6.32e-19
(4.36e-16) 		1.96e-18
(1.35e-15) 		2.64e-17
(1.76e-14) 		5.17e-12
(2.9e-09)
Del Peak 29(16q24 3) 0 (0%) 334 9.32e-17
(6.15e-14) 		2.67e-14
(1.64e-11) 		6.75e-15
(4.2e-12) 		1.14e-11
(6.29e-09) 		1.14e-09
(5.55e-07) 		3.45e-11
(1.86e-08) 		1.01e-30
(7.65e-28) 		6.89e-23
(4.98e-20) 		9.22e-15
(5.7e-12) 		8.49e-22
(6.07e-19) 		1.37e-13
(8.22e-11) 		1.13e-15
(7.26e-13)
Del Peak 31(17q21 31) 0 (0%) 612 1.97e-15
(1.26e-12) 		2.29e-07
(9.33e-05) 		1.05e-23
(7.66e-21) 		3.7e-13
(2.18e-10) 		1.86e-11
(1.02e-08) 		3.12e-11
(1.69e-08) 		1.29e-32
(9.74e-30) 		1.89e-17
(1.27e-14) 		1.14e-12
(6.66e-10) 		1.76e-11
(9.66e-09) 		8.43e-10
(4.14e-07) 		7.84e-06
(0.00257)
Del Peak 33(19p13 3) 0 (0%) 623 3.9e-11
(2.1e-08) 		1.45e-08
(6.59e-06) 		6.28e-47
(4.9e-44) 		6.89e-18
(4.64e-15) 		3.03e-06
(0.00106) 		3.39e-05
(0.0102) 		6.91e-25
(5.08e-22) 		5.57e-11
(2.95e-08) 		9.67e-16
(6.25e-13) 		6.54e-17
(4.33e-14) 		7.5e-12
(4.17e-09) 		1e-10
(5.23e-08)
Del Peak 34(19q13 32) 0 (0%) 750 8.89e-07
(0.000337) 		1.37e-05
(0.00432) 		7.77e-21
(5.5e-18) 		1.08e-10
(5.61e-08) 		0.000783
(0.171) 		4.95e-05
(0.0146) 		1.34e-12
(7.78e-10) 		2.73e-09
(1.28e-06) 		3.6e-10
(1.82e-07) 		5.78e-12
(3.23e-09) 		3.28e-12
(1.87e-09) 		1.96e-08
(8.8e-06)
Amp Peak 26(19p13 12) 0 (0%) 737 6.52e-06
(0.00216) 		5.01e-05
(0.0147) 		3.88e-15
(2.44e-12) 		3.53e-07
(0.00014) 		0.000125
(0.0339) 		0.00163
(0.336) 		2.42e-11
(1.31e-08) 		5.79e-08
(2.53e-05) 		7.66e-08
(3.3e-05) 		4.77e-11
(2.54e-08) 		8.41e-08
(3.6e-05) 		3.17e-06
(0.0011)
Amp Peak 29(20q13 2) 0 (0%) 459 1.81e-10
(9.33e-08) 		3.67e-05
(0.011) 		4.27e-52
(3.36e-49) 		3e-22
(2.16e-19) 		0.000604
(0.138) 		0.0154
(1.00) 		1.91e-20
(1.35e-17) 		2.59e-07
(0.000104) 		7.41e-10
(3.67e-07) 		1.16e-06
(0.000432) 		6.83e-08
(2.96e-05) 		1.06e-05
(0.00339)
Amp Peak 23(15q26 3) 0 (0%) 764 2.4e-07
(9.7e-05) 		0.00169
(0.346) 		5.72e-17
(3.79e-14) 		6.68e-05
(0.0193) 		0.000153
(0.0403) 		0.0384
(1.00) 		1.72e-09
(8.15e-07) 		1.61e-06
(0.000585) 		5.92e-08
(2.58e-05) 		7.56e-09
(3.5e-06) 		0.000152
(0.0402) 		0.000257
(0.0635)
Del Peak 12(7p22 3) 0 (0%) 813 0.00104
(0.221) 		7.95e-05
(0.0224) 		8.24e-17
(5.44e-14) 		6.11e-07
(0.000236) 		0.0214
(1.00) 		0.00553
(1.00) 		8.51e-08
(3.63e-05) 		1.02e-09
(4.94e-07) 		3.96e-11
(2.12e-08) 		1.38e-10
(7.14e-08) 		3.87e-07
(0.000152) 		0.000239
(0.0596)
Del Peak 14(8p23 2) 0 (0%) 445 1.61e-09
(7.68e-07) 		9.89e-06
(0.00318) 		1.09e-32
(8.27e-30) 		2.68e-10
(1.37e-07) 		0.00955
(1.00) 		0.0341
(1.00) 		1.28e-16
(8.43e-14) 		2.97e-09
(1.39e-06) 		5.68e-06
(0.00191) 		4.79e-12
(2.69e-09) 		1.49e-09
(7.12e-07) 		4.84e-07
(0.000189)
Del Peak 16(9p21 3) 0 (0%) 619 2e-06
(0.00071) 		4.31e-05
(0.0128) 		4.89e-30
(3.67e-27) 		9.03e-15
(5.59e-12) 		0.00341
(0.662) 		0.444
(1.00) 		9.52e-15
(5.87e-12) 		2.58e-07
(0.000104) 		4.02e-06
(0.00138) 		4.15e-12
(2.34e-09) 		1.12e-07
(4.7e-05) 		1.91e-07
(7.83e-05)
Del Peak 17(9q21 11) 0 (0%) 681 0.0061
(1.00) 		2.17e-05
(0.00674) 		5.55e-18
(3.75e-15) 		1.43e-09
(6.86e-07) 		1.04e-05
(0.00334) 		0.00653
(1.00) 		8.82e-09
(4.07e-06) 		9.99e-07
(0.000374) 		1.41e-08
(6.41e-06) 		9.33e-13
(5.46e-10) 		1.14e-06
(0.000425) 		1.56e-09
(7.45e-07)
Del Peak 26(13q14 2) 0 (0%) 509 6.7e-05
(0.0193) 		2.5e-05
(0.00768) 		4.2e-27
(3.11e-24) 		7.87e-08
(3.39e-05) 		0.538
(1.00) 		0.111
(1.00) 		4.8e-10
(2.4e-07) 		7.41e-10
(3.67e-07) 		3.86e-10
(1.95e-07) 		1.12e-07
(4.7e-05) 		2.05e-07
(8.41e-05) 		0.000164
(0.0427)
Del Peak 35(20p13) 0 (0%) 796 4.49e-06
(0.00153) 		6.53e-05
(0.019) 		1.45e-15
(9.28e-13) 		4.16e-08
(1.84e-05) 		0.00154
(0.318) 		0.0119
(1.00) 		4.16e-13
(2.45e-10) 		1.32e-10
(6.88e-08) 		2.69e-12
(1.54e-09) 		1.91e-13
(1.14e-10) 		2.67e-09
(1.26e-06) 		1.26e-09
(6.08e-07)
Amp Peak 6(4q13 3) 0 (0%) 788 3.63e-05
(0.0109) 		6.73e-05
(0.0193) 		5.19e-14
(3.15e-11) 		7.16e-06
(0.00235) 		0.0471
(1.00) 		0.524
(1.00) 		5.44e-10
(2.7e-07) 		1.2e-05
(0.00383) 		0.00138
(0.288) 		1.11e-07
(4.69e-05) 		3.43e-05
(0.0103) 		0.000127
(0.0342)
Amp Peak 19(12q15) 0 (0%) 695 3.35e-07
(0.000133) 		5.01e-06
(0.0017) 		2.45e-30
(1.85e-27) 		1.27e-14
(7.77e-12) 		0.188
(1.00) 		0.0652
(1.00) 		3.95e-10
(1.99e-07) 		4.68e-06
(0.00159) 		9.16e-08
(3.89e-05) 		0.000644
(0.145) 		3.18e-05
(0.00966) 		0.0338
(1.00)
Del Peak 1(1p36 13) 0 (0%) 545 7.82e-05
(0.0222) 		0.00012
(0.0328) 		3.3e-31
(2.5e-28) 		1.19e-10
(6.16e-08) 		0.00726
(1.00) 		0.0805
(1.00) 		4.32e-11
(2.31e-08) 		8.61e-07
(0.000327) 		2.37e-07
(9.61e-05) 		0.00056
(0.129) 		8.07e-05
(0.0226) 		0.0191
(1.00)
Amp Peak 4(3p26 1) 0 (0%) 741 0.00647
(1.00) 		0.00103
(0.22) 		1.21e-14
(7.42e-12) 		1.61e-07
(6.7e-05) 		0.00573
(1.00) 		0.00869
(1.00) 		3.19e-08
(1.42e-05) 		5.4e-07
(0.000209) 		5.97e-06
(0.00199) 		1.18e-08
(5.38e-06) 		2.1e-07
(8.58e-05) 		0.00804
(1.00)
Amp Peak 7(5p15 33) 0 (0%) 595 0.012
(1.00) 		0.00281
(0.553) 		3.36e-22
(2.42e-19) 		4.17e-06
(0.00143) 		0.082
(1.00) 		0.581
(1.00) 		3.62e-06
(0.00125) 		4.6e-07
(0.000181) 		2.07e-05
(0.00643) 		2.79e-05
(0.00852) 		2.11e-06
(0.000748) 		0.000378
(0.0901)
Amp Peak 15(11p13) 0 (0%) 740 0.207
(1.00) 		0.127
(1.00) 		8.69e-11
(4.58e-08) 		0.000117
(0.0321) 		0.105
(1.00) 		0.229
(1.00) 		3.47e-06
(0.0012) 		0.000422
(0.0995) 		1.33e-06
(0.000489) 		1.91e-08
(8.6e-06) 		0.000103
(0.0285) 		0.00103
(0.22)
Amp Peak 25(17q23 1) 0 (0%) 550 6.72e-16
(4.36e-13) 		0.00033
(0.0798) 		1.8e-38
(1.38e-35) 		5.4e-11
(2.87e-08) 		0.191
(1.00) 		0.334
(1.00) 		1.28e-24
(9.4e-22) 		0.0035
(0.666) 		3.1e-07
(0.000124) 		3.57e-06
(0.00123) 		0.0161
(1.00) 		0.000384
(0.091)
Del Peak 32(18q23) 0 (0%) 632 0.000183
(0.0471) 		0.0629
(1.00) 		7.49e-15
(4.66e-12) 		9.79e-08
(4.15e-05) 		0.00413
(0.772) 		0.581
(1.00) 		4.31e-10
(2.16e-07) 		0.000188
(0.0483) 		0.000375
(0.0896) 		0.000143
(0.038) 		0.000171
(0.0445) 		0.0579
(1.00)
Amp Peak 2(1q21 3) 0 (0%) 263 1.25e-06
(0.000459) 		0.000537
(0.124) 		2.02e-11
(1.1e-08) 		3.07e-05
(0.00937) 		0.0586
(1.00) 		0.00703
(1.00) 		2.35e-09
(1.11e-06) 		0.000103
(0.0285) 		0.00102
(0.218) 		0.00262
(0.518) 		0.013
(1.00) 		0.00956
(1.00)
Amp Peak 14(10q22 3) 0 (0%) 799 9.27e-06
(0.00299) 		0.143
(1.00) 		1.7e-09
(8.07e-07) 		0.000151
(0.0401) 		0.0025
(0.498) 		0.0211
(1.00) 		1.46e-12
(8.45e-10) 		0.00347
(0.666) 		3.75e-05
(0.0112) 		0.000675
(0.151) 		0.00061
(0.138) 		0.103
(1.00)
Amp Peak 17(11q14 1) 0 (0%) 695 0.007
(1.00) 		0.0697
(1.00) 		1.22e-19
(8.52e-17) 		6.78e-06
(0.00224) 		0.148
(1.00) 		0.199
(1.00) 		1.18e-05
(0.00376) 		6.74e-05
(0.0193) 		8.98e-07
(0.000339) 		1.39e-05
(0.00436) 		8.91e-05
(0.0248) 		0.00612
(1.00)
Del Peak 10(6q15) 0 (0%) 628 2.42e-06
(0.000853) 		0.00128
(0.269) 		6.35e-28
(4.73e-25) 		8.08e-08
(3.47e-05) 		0.456
(1.00) 		0.0875
(1.00) 		1.35e-10
(7.02e-08) 		0.000293
(0.0713) 		0.0136
(1.00) 		5.04e-05
(0.0148) 		0.00284
(0.556) 		0.000153
(0.0403)
Del Peak 15(8p11 21) 0 (0%) 757 0.000194
(0.0495) 		0.00476
(0.87) 		1.73e-12
(9.96e-10) 		0.034
(1.00) 		0.0465
(1.00) 		0.0191
(1.00) 		8.59e-13
(5.03e-10) 		0.000438
(0.102) 		0.00401
(0.753) 		6.26e-06
(0.00208) 		1.89e-06
(0.000675) 		0.000275
(0.0678)
Del Peak 22(11q23 2) 0 (0%) 473 6.71e-08
(2.91e-05) 		0.00965
(1.00) 		7.27e-43
(5.67e-40) 		2.05e-13
(1.22e-10) 		0.975
(1.00) 		0.475
(1.00) 		2.17e-17
(1.45e-14) 		0.000521
(0.121) 		0.0196
(1.00) 		0.000137
(0.0368) 		0.0227
(1.00) 		0.00029
(0.071)
Del Peak 30(17p12) 0 (0%) 374 1.95e-11
(1.06e-08) 		0.168
(1.00) 		1.24e-23
(9.03e-21) 		8.79e-08
(3.74e-05) 		8.07e-05
(0.0226) 		0.00775
(1.00) 		1.07e-15
(6.89e-13) 		0.0811
(1.00) 		0.000255
(0.0633) 		0.000127
(0.0342) 		0.00573
(1.00) 		0.299
(1.00)
Amp Peak 22(14q21 1) 0 (0%) 748 7.91e-05
(0.0224) 		0.00208
(0.423) 		3.55e-09
(1.65e-06) 		5.89e-05
(0.0172) 		0.0823
(1.00) 		0.0385
(1.00) 		9.88e-11
(5.18e-08) 		1.68e-05
(0.00524) 		1.94e-06
(0.00069) 		0.0693
(1.00) 		0.0291
(1.00) 		0.532
(1.00)
Amp Peak 24(17q12) 0 (0%) 634 1.1e-15
(7.08e-13) 		1.34e-05
(0.00422) 		1.26e-35
(9.61e-33) 		2.43e-09
(1.15e-06) 		0.049
(1.00) 		0.00821
(1.00) 		1.11e-26
(8.22e-24) 		3.36e-05
(0.0102) 		0.0148
(1.00) 		0.0196
(1.00) 		0.0781
(1.00) 		0.00874
(1.00)
Del Peak 13(7q36 1) 0 (0%) 756 0.00992
(1.00) 		0.022
(1.00) 		1.23e-11
(6.8e-09) 		0.0577
(1.00) 		0.551
(1.00) 		0.0562
(1.00) 		0.00018
(0.0465) 		0.000721
(0.159) 		5.26e-08
(2.31e-05) 		1.6e-06
(0.000583) 		0.00012
(0.0328) 		0.00215
(0.434)
Amp Peak 3(1q44) 0 (0%) 264 1.22e-05
(0.00388) 		0.102
(1.00) 		8.74e-10
(4.28e-07) 		0.000361
(0.0867) 		0.864
(1.00) 		0.324
(1.00) 		6.43e-08
(2.8e-05) 		0.474
(1.00) 		0.711
(1.00) 		0.0277
(1.00) 		0.318
(1.00) 		0.000603
(0.138)
Amp Peak 10(8p11 23) 0 (0%) 578 1.27e-06
(0.000466) 		0.00415
(0.773) 		4.33e-25
(3.19e-22) 		3.45e-10
(1.75e-07) 		0.0399
(1.00) 		0.00473
(0.869) 		8.28e-12
(4.59e-09) 		1.82e-08
(8.24e-06) 		0.0447
(1.00) 		0.0332
(1.00) 		0.665
(1.00) 		0.11
(1.00)
Amp Peak 16(11q13 3) 0 (0%) 582 0.000715
(0.159) 		0.0117
(1.00) 		2.12e-42
(1.65e-39) 		3.21e-10
(1.64e-07) 		0.966
(1.00) 		0.146
(1.00) 		4.75e-10
(2.38e-07) 		0.00512
(0.932) 		0.000292
(0.0712) 		0.0396
(1.00) 		0.0274
(1.00) 		0.0688
(1.00)
Amp Peak 20(13q12 3) 0 (0%) 805 0.0686
(1.00) 		0.0395
(1.00) 		2.34e-06
(0.000826) 		0.0146
(1.00) 		0.0155
(1.00) 		0.142
(1.00) 		5.88e-06
(0.00197) 		0.000614
(0.139) 		0.000196
(0.0498) 		0.00043
(0.101) 		0.00242
(0.484) 		0.0383
(1.00)
Amp Peak 28(19q13 42) 0 (0%) 694 0.000812
(0.176) 		0.0102
(1.00) 		9.78e-16
(6.31e-13) 		1.65e-06
(0.000596) 		0.00233
(0.468) 		0.0549
(1.00) 		1.65e-06
(0.000596) 		0.0513
(1.00) 		4.27e-06
(0.00146) 		0.00441
(0.816) 		0.224
(1.00) 		0.354
(1.00)
Del Peak 2(1p22 1) 0 (0%) 624 0.00343
(0.662) 		0.000233
(0.0581) 		4.81e-22
(3.44e-19) 		0.000103
(0.0285) 		0.0231
(1.00) 		0.049
(1.00) 		1.6e-07
(6.64e-05) 		5.52e-06
(0.00187) 		0.0125
(1.00) 		0.0329
(1.00) 		0.322
(1.00) 		0.827
(1.00)
Amp Peak 11(8p11 21) 0 (0%) 570 0.0516
(1.00) 		0.067
(1.00) 		1.22e-22
(8.84e-20) 		2.79e-06
(0.000978) 		0.791
(1.00) 		0.633
(1.00) 		7.54e-08
(3.26e-05) 		5.07e-08
(2.23e-05) 		0.0361
(1.00) 		0.0215
(1.00) 		0.0507
(1.00) 		0.00676
(1.00)
Del Peak 23(11q25) 0 (0%) 501 0.00072
(0.159) 		0.634
(1.00) 		1.59e-40
(1.23e-37) 		9.8e-10
(4.78e-07) 		0.126
(1.00) 		0.707
(1.00) 		4.69e-12
(2.63e-09) 		0.164
(1.00) 		0.093
(1.00) 		0.0331
(1.00) 		0.501
(1.00) 		0.0975
(1.00)
Del Peak 24(12p13 1) 0 (0%) 774 0.0315
(1.00) 		0.0843
(1.00) 		0.00099
(0.214) 		0.0202
(1.00) 		0.222
(1.00) 		0.042
(1.00) 		0.000717
(0.159) 		0.00141
(0.293) 		8.03e-05
(0.0226) 		8.68e-06
(0.00282) 		0.0114
(1.00) 		0.00656
(1.00)
Del Peak 36(21q11 2) 0 (0%) 749 0.000341
(0.0821) 		0.0505
(1.00) 		9.95e-13
(5.81e-10) 		0.000524
(0.122) 		0.225
(1.00) 		0.502
(1.00) 		9.01e-06
(0.00292) 		0.0328
(1.00) 		0.0142
(1.00) 		0.0194
(1.00) 		0.0833
(1.00) 		0.448
(1.00)
Del Peak 9(6p25 3) 0 (0%) 758 0.347
(1.00) 		0.449
(1.00) 		2.64e-07
(0.000106) 		8.62e-06
(0.00281) 		0.439
(1.00) 		0.597
(1.00) 		0.000205
(0.0519) 		0.00347
(0.666) 		0.299
(1.00) 		0.0417
(1.00) 		0.00305
(0.594) 		0.099
(1.00)
Del Peak 21(11q13 1) 0 (0%) 737 0.00395
(0.746) 		0.0958
(1.00) 		5.93e-19
(4.09e-16) 		6.11e-07
(0.000236) 		0.331
(1.00) 		0.393
(1.00) 		1.22e-09
(5.92e-07) 		0.00121
(0.254) 		0.596
(1.00) 		0.0297
(1.00) 		0.105
(1.00) 		0.103
(1.00)
Del Peak 11(6q27) 0 (0%) 614 0.0354
(1.00) 		0.368
(1.00) 		3.77e-14
(2.29e-11) 		0.00166
(0.34) 		0.0678
(1.00) 		0.675
(1.00) 		0.000224
(0.0563) 		0.628
(1.00) 		0.432
(1.00) 		0.132
(1.00) 		0.0781
(1.00) 		0.969
(1.00)
Del Peak 37(22q11 1) 0 (0%) 539 0.333
(1.00) 		0.314
(1.00) 		0.016
(1.00) 		0.000679
(0.151) 		0.226
(1.00) 		0.14
(1.00) 		0.194
(1.00) 		0.0149
(1.00) 		0.0891
(1.00) 		0.546
(1.00) 		0.0234
(1.00) 		0.402
(1.00)
'Amp Peak 1(1p22.3)' versus 'MRNA_CNMF'

P value = 4.05e-14 (Chi-square test), Q value = 2.5e-11

Table S1.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 1(1P22.3) CNV 4 2 14 52 24 16 2 2
AMP PEAK 1(1P22.3) WILD-TYPE 17 34 105 44 85 56 18 38

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 1(1p22.3)' versus 'MRNA_CHIERARCHICAL'

P value = 3.63e-12 (Fisher's exact test), Q value = 2.1e-09

Table S2.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 1(1P22.3) CNV 10 57 49
AMP PEAK 1(1P22.3) WILD-TYPE 112 68 217

Figure S2.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 1(1p22.3)' versus 'CN_CNMF'

P value = 3.44e-16 (Chi-square test), Q value = 2.2e-13

Table S3.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 1(1P22.3) CNV 46 29 26 96 16
AMP PEAK 1(1P22.3) WILD-TYPE 310 183 45 145 38

Figure S3.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 1(1p22.3)' versus 'METHLYATION_CNMF'

P value = 2.76e-17 (Chi-square test), Q value = 1.8e-14

Table S4.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 1(1P22.3) CNV 58 22 24 13 2 17
AMP PEAK 1(1P22.3) WILD-TYPE 47 129 75 105 36 79

Figure S4.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 1(1p22.3)' versus 'RPPA_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.037

Table S5.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 1(1P22.3) CNV 52 28 16
AMP PEAK 1(1P22.3) WILD-TYPE 95 105 101

Figure S5.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 1(1p22.3)' versus 'RPPA_CHIERARCHICAL'

P value = 1.28e-07 (Fisher's exact test), Q value = 5.4e-05

Table S6.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 1(1P22.3) CNV 32 12 52
AMP PEAK 1(1P22.3) WILD-TYPE 129 98 74

Figure S6.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 1(1p22.3)' versus 'MRNASEQ_CNMF'

P value = 7.32e-24 (Chi-square test), Q value = 5.3e-21

Table S7.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 1(1P22.3) CNV 86 8 44 36 27 4 1
AMP PEAK 1(1P22.3) WILD-TYPE 72 73 184 110 190 49 15

Figure S7.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 1(1p22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.95e-21 (Fisher's exact test), Q value = 3.5e-18

Table S8.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 1(1P22.3) CNV 105 21 80
AMP PEAK 1(1P22.3) WILD-TYPE 121 194 378

Figure S8.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 1(1p22.3)' versus 'MIRSEQ_CNMF'

P value = 1.36e-13 (Fisher's exact test), Q value = 8.2e-11

Table S9.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 1(1P22.3) CNV 39 59 103
AMP PEAK 1(1P22.3) WILD-TYPE 195 333 152

Figure S9.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 1(1p22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.36e-15 (Fisher's exact test), Q value = 8.7e-13

Table S10.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 1(1P22.3) CNV 54 46 101
AMP PEAK 1(1P22.3) WILD-TYPE 308 238 134

Figure S10.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 1(1p22.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.2e-12 (Fisher's exact test), Q value = 7e-10

Table S11.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 1(1P22.3) CNV 31 23 76
AMP PEAK 1(1P22.3) WILD-TYPE 182 156 102

Figure S11.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 1(1p22.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-10 (Fisher's exact test), Q value = 2e-07

Table S12.  Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 1(1P22.3) CNV 24 13 62 31
AMP PEAK 1(1P22.3) WILD-TYPE 97 109 80 154

Figure S12.  Get High-res Image Gene #1: 'Amp Peak 1(1p22.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 2(1q21.3)' versus 'MRNA_CNMF'

P value = 1.25e-06 (Chi-square test), Q value = 0.00046

Table S13.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 2(1Q21.3) CNV 16 19 75 88 88 54 10 29
AMP PEAK 2(1Q21.3) WILD-TYPE 5 17 44 8 21 18 10 11

Figure S13.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 2(1q21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000537 (Fisher's exact test), Q value = 0.12

Table S14.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 2(1Q21.3) CNV 76 105 198
AMP PEAK 2(1Q21.3) WILD-TYPE 46 20 68

Figure S14.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 2(1q21.3)' versus 'CN_CNMF'

P value = 2.02e-11 (Chi-square test), Q value = 1.1e-08

Table S15.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 2(1Q21.3) CNV 217 166 71 182 35
AMP PEAK 2(1Q21.3) WILD-TYPE 139 46 0 59 19

Figure S15.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(1q21.3)' versus 'METHLYATION_CNMF'

P value = 3.07e-05 (Chi-square test), Q value = 0.0094

Table S16.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 2(1Q21.3) CNV 87 117 77 79 21 54
AMP PEAK 2(1Q21.3) WILD-TYPE 18 34 22 39 17 42

Figure S16.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 2(1q21.3)' versus 'MRNASEQ_CNMF'

P value = 2.35e-09 (Chi-square test), Q value = 1.1e-06

Table S17.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 2(1Q21.3) CNV 138 43 180 110 135 34 11
AMP PEAK 2(1Q21.3) WILD-TYPE 20 38 48 36 82 19 5

Figure S17.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 2(1q21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000103 (Fisher's exact test), Q value = 0.028

Table S18.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 2(1Q21.3) CNV 182 134 335
AMP PEAK 2(1Q21.3) WILD-TYPE 44 81 123

Figure S18.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(1q21.3)' versus 'MIRSEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.22

Table S19.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 2(1Q21.3) CNV 153 277 204
AMP PEAK 2(1Q21.3) WILD-TYPE 81 115 51

Figure S19.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 3(1q44)' versus 'MRNA_CNMF'

P value = 1.22e-05 (Chi-square test), Q value = 0.0039

Table S20.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 3(1Q44) CNV 16 19 69 78 90 57 11 32
AMP PEAK 3(1Q44) WILD-TYPE 5 17 50 18 19 15 9 8

Figure S20.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 3(1q44)' versus 'CN_CNMF'

P value = 8.74e-10 (Chi-square test), Q value = 4.3e-07

Table S21.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 3(1Q44) CNV 226 165 71 176 32
AMP PEAK 3(1Q44) WILD-TYPE 130 47 0 65 22

Figure S21.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 3(1q44)' versus 'METHLYATION_CNMF'

P value = 0.000361 (Chi-square test), Q value = 0.087

Table S22.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 3(1Q44) CNV 76 120 81 75 24 56
AMP PEAK 3(1Q44) WILD-TYPE 29 31 18 43 14 40

Figure S22.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 3(1q44)' versus 'MRNASEQ_CNMF'

P value = 6.43e-08 (Chi-square test), Q value = 2.8e-05

Table S23.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 3(1Q44) CNV 122 49 185 114 124 40 13
AMP PEAK 3(1Q44) WILD-TYPE 36 32 43 32 93 13 3

Figure S23.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 3(1q44)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000603 (Fisher's exact test), Q value = 0.14

Table S24.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 3(1Q44) CNV 92 67 106 137
AMP PEAK 3(1Q44) WILD-TYPE 29 55 36 48

Figure S24.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 4(3p26.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.22

Table S25.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 4(3P26.1) CNV 15 35 75
AMP PEAK 4(3P26.1) WILD-TYPE 107 90 191

Figure S25.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 4(3p26.1)' versus 'CN_CNMF'

P value = 1.21e-14 (Chi-square test), Q value = 7.4e-12

Table S26.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 4(3P26.1) CNV 24 56 20 79 14
AMP PEAK 4(3P26.1) WILD-TYPE 332 156 51 162 40

Figure S26.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(3p26.1)' versus 'METHLYATION_CNMF'

P value = 1.61e-07 (Chi-square test), Q value = 6.7e-05

Table S27.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 4(3P26.1) CNV 32 8 23 29 2 12
AMP PEAK 4(3P26.1) WILD-TYPE 73 143 76 89 36 84

Figure S27.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 4(3p26.1)' versus 'MRNASEQ_CNMF'

P value = 3.19e-08 (Chi-square test), Q value = 1.4e-05

Table S28.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 4(3P26.1) CNV 46 6 29 44 51 3 7
AMP PEAK 4(3P26.1) WILD-TYPE 112 75 199 102 166 50 9

Figure S28.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 4(3p26.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.4e-07 (Fisher's exact test), Q value = 0.00021

Table S29.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 4(3P26.1) CNV 65 20 101
AMP PEAK 4(3P26.1) WILD-TYPE 161 195 357

Figure S29.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 4(3p26.1)' versus 'MIRSEQ_CNMF'

P value = 5.97e-06 (Fisher's exact test), Q value = 0.002

Table S30.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 4(3P26.1) CNV 30 71 77
AMP PEAK 4(3P26.1) WILD-TYPE 204 321 178

Figure S30.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 4(3p26.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.18e-08 (Fisher's exact test), Q value = 5.4e-06

Table S31.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 4(3P26.1) CNV 71 31 76
AMP PEAK 4(3P26.1) WILD-TYPE 291 253 159

Figure S31.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 4(3p26.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.1e-07 (Fisher's exact test), Q value = 8.6e-05

Table S32.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 4(3P26.1) CNV 39 14 54
AMP PEAK 4(3P26.1) WILD-TYPE 174 165 124

Figure S32.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 5(3q26.32)' versus 'MRNA_CNMF'

P value = 5.51e-11 (Chi-square test), Q value = 2.9e-08

Table S33.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 5(3Q26.32) CNV 5 11 39 58 18 34 9 4
AMP PEAK 5(3Q26.32) WILD-TYPE 16 25 80 38 91 38 11 36

Figure S33.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 5(3q26.32)' versus 'MRNA_CHIERARCHICAL'

P value = 4.13e-11 (Fisher's exact test), Q value = 2.2e-08

Table S34.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 5(3Q26.32) CNV 19 71 88
AMP PEAK 5(3Q26.32) WILD-TYPE 103 54 178

Figure S34.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 5(3q26.32)' versus 'CN_CNMF'

P value = 1.51e-38 (Chi-square test), Q value = 1.2e-35

Table S35.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 5(3Q26.32) CNV 32 76 24 147 15
AMP PEAK 5(3Q26.32) WILD-TYPE 324 136 47 94 39

Figure S35.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 5(3q26.32)' versus 'METHLYATION_CNMF'

P value = 2.77e-16 (Chi-square test), Q value = 1.8e-13

Table S36.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 5(3Q26.32) CNV 64 17 32 35 8 18
AMP PEAK 5(3Q26.32) WILD-TYPE 41 134 67 83 30 78

Figure S36.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 5(3q26.32)' versus 'RPPA_CNMF'

P value = 7.16e-07 (Fisher's exact test), Q value = 0.00027

Table S37.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 5(3Q26.32) CNV 76 35 28
AMP PEAK 5(3Q26.32) WILD-TYPE 71 98 89

Figure S37.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 5(3q26.32)' versus 'RPPA_CHIERARCHICAL'

P value = 2.92e-06 (Fisher's exact test), Q value = 0.001

Table S38.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 5(3Q26.32) CNV 48 25 66
AMP PEAK 5(3Q26.32) WILD-TYPE 113 85 60

Figure S38.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 5(3q26.32)' versus 'MRNASEQ_CNMF'

P value = 1.94e-25 (Chi-square test), Q value = 1.4e-22

Table S39.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 5(3Q26.32) CNV 100 12 43 61 57 4 9
AMP PEAK 5(3Q26.32) WILD-TYPE 58 69 185 85 160 49 7

Figure S39.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 5(3q26.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.17e-22 (Fisher's exact test), Q value = 3e-19

Table S40.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 5(3Q26.32) CNV 128 30 128
AMP PEAK 5(3Q26.32) WILD-TYPE 98 185 330

Figure S40.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 5(3q26.32)' versus 'MIRSEQ_CNMF'

P value = 1.63e-15 (Fisher's exact test), Q value = 1e-12

Table S41.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 5(3Q26.32) CNV 46 100 132
AMP PEAK 5(3Q26.32) WILD-TYPE 188 292 123

Figure S41.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 5(3q26.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.39e-24 (Fisher's exact test), Q value = 4.7e-21

Table S42.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 5(3Q26.32) CNV 95 47 136
AMP PEAK 5(3Q26.32) WILD-TYPE 267 237 99

Figure S42.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 5(3q26.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.3e-17 (Fisher's exact test), Q value = 8.7e-15

Table S43.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 5(3Q26.32) CNV 50 21 94
AMP PEAK 5(3Q26.32) WILD-TYPE 163 158 84

Figure S43.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 5(3q26.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.23e-10 (Fisher's exact test), Q value = 2.6e-07

Table S44.  Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 5(3Q26.32) CNV 26 32 73 34
AMP PEAK 5(3Q26.32) WILD-TYPE 95 90 69 151

Figure S44.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 6(4q13.3)' versus 'MRNA_CNMF'

P value = 3.63e-05 (Chi-square test), Q value = 0.011

Table S45.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 6(4Q13.3) CNV 4 2 30 19 3 18 4 3
AMP PEAK 6(4Q13.3) WILD-TYPE 17 34 89 77 106 54 16 37

Figure S45.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 6(4q13.3)' versus 'MRNA_CHIERARCHICAL'

P value = 6.73e-05 (Fisher's exact test), Q value = 0.019

Table S46.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 6(4Q13.3) CNV 6 29 48
AMP PEAK 6(4Q13.3) WILD-TYPE 116 96 218

Figure S46.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 6(4q13.3)' versus 'CN_CNMF'

P value = 5.19e-14 (Chi-square test), Q value = 3.1e-11

Table S47.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 6(4Q13.3) CNV 21 58 2 57 8
AMP PEAK 6(4Q13.3) WILD-TYPE 335 154 69 184 46

Figure S47.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(4q13.3)' versus 'METHLYATION_CNMF'

P value = 7.16e-06 (Chi-square test), Q value = 0.0024

Table S48.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 6(4Q13.3) CNV 26 7 16 26 2 9
AMP PEAK 6(4Q13.3) WILD-TYPE 79 144 83 92 36 87

Figure S48.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 6(4q13.3)' versus 'MRNASEQ_CNMF'

P value = 5.44e-10 (Chi-square test), Q value = 2.7e-07

Table S49.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 6(4Q13.3) CNV 35 3 13 35 51 2 4
AMP PEAK 6(4Q13.3) WILD-TYPE 123 78 215 111 166 51 12

Figure S49.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 6(4q13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.0038

Table S50.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 6(4Q13.3) CNV 57 19 67
AMP PEAK 6(4Q13.3) WILD-TYPE 169 196 391

Figure S50.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 6(4q13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.11e-07 (Fisher's exact test), Q value = 4.7e-05

Table S51.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 6(4Q13.3) CNV 55 23 62
AMP PEAK 6(4Q13.3) WILD-TYPE 307 261 173

Figure S51.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(4q13.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.43e-05 (Fisher's exact test), Q value = 0.01

Table S52.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 6(4Q13.3) CNV 33 12 42
AMP PEAK 6(4Q13.3) WILD-TYPE 180 167 136

Figure S52.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 6(4q13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000127 (Fisher's exact test), Q value = 0.034

Table S53.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 6(4Q13.3) CNV 13 21 37 16
AMP PEAK 6(4Q13.3) WILD-TYPE 108 101 105 169

Figure S53.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 7(5p15.33)' versus 'CN_CNMF'

P value = 3.36e-22 (Chi-square test), Q value = 2.4e-19

Table S54.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 7(5P15.33) CNV 59 95 39 128 18
AMP PEAK 7(5P15.33) WILD-TYPE 297 117 32 113 36

Figure S54.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(5p15.33)' versus 'METHLYATION_CNMF'

P value = 4.17e-06 (Chi-square test), Q value = 0.0014

Table S55.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 7(5P15.33) CNV 55 37 44 41 8 24
AMP PEAK 7(5P15.33) WILD-TYPE 50 114 55 77 30 72

Figure S55.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 7(5p15.33)' versus 'MRNASEQ_CNMF'

P value = 3.62e-06 (Chi-square test), Q value = 0.0012

Table S56.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 7(5P15.33) CNV 78 16 74 62 74 10 9
AMP PEAK 7(5P15.33) WILD-TYPE 80 65 154 84 143 43 7

Figure S56.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 7(5p15.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.6e-07 (Fisher's exact test), Q value = 0.00018

Table S57.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 7(5P15.33) CNV 111 53 159
AMP PEAK 7(5P15.33) WILD-TYPE 115 162 299

Figure S57.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(5p15.33)' versus 'MIRSEQ_CNMF'

P value = 2.07e-05 (Fisher's exact test), Q value = 0.0064

Table S58.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 7(5P15.33) CNV 64 129 119
AMP PEAK 7(5P15.33) WILD-TYPE 170 263 136

Figure S58.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 7(5p15.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.0085

Table S59.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 7(5P15.33) CNV 116 84 112
AMP PEAK 7(5P15.33) WILD-TYPE 246 200 123

Figure S59.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 7(5p15.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.11e-06 (Fisher's exact test), Q value = 0.00075

Table S60.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 7(5P15.33) CNV 79 37 81
AMP PEAK 7(5P15.33) WILD-TYPE 134 142 97

Figure S60.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 7(5p15.33)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000378 (Fisher's exact test), Q value = 0.09

Table S61.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 7(5P15.33) CNV 26 42 66 63
AMP PEAK 7(5P15.33) WILD-TYPE 95 80 76 122

Figure S61.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 8(6p23)' versus 'MRNA_CNMF'

P value = 1.79e-07 (Chi-square test), Q value = 7.4e-05

Table S62.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 8(6P23) CNV 3 6 30 49 18 27 8 6
AMP PEAK 8(6P23) WILD-TYPE 18 30 89 47 91 45 12 34

Figure S62.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 8(6p23)' versus 'MRNA_CHIERARCHICAL'

P value = 1.45e-07 (Fisher's exact test), Q value = 6e-05

Table S63.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 8(6P23) CNV 19 59 69
AMP PEAK 8(6P23) WILD-TYPE 103 66 197

Figure S63.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 8(6p23)' versus 'CN_CNMF'

P value = 3.57e-34 (Chi-square test), Q value = 2.7e-31

Table S64.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 8(6P23) CNV 25 57 20 130 18
AMP PEAK 8(6P23) WILD-TYPE 331 155 51 111 36

Figure S64.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 8(6p23)' versus 'METHLYATION_CNMF'

P value = 6.83e-18 (Chi-square test), Q value = 4.6e-15

Table S65.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 8(6P23) CNV 56 12 25 43 2 14
AMP PEAK 8(6P23) WILD-TYPE 49 139 74 75 36 82

Figure S65.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 8(6p23)' versus 'RPPA_CNMF'

P value = 9.24e-07 (Fisher's exact test), Q value = 0.00035

Table S66.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 8(6P23) CNV 65 25 23
AMP PEAK 8(6P23) WILD-TYPE 82 108 94

Figure S66.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 8(6p23)' versus 'RPPA_CHIERARCHICAL'

P value = 4.4e-05 (Fisher's exact test), Q value = 0.013

Table S67.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 8(6P23) CNV 34 24 55
AMP PEAK 8(6P23) WILD-TYPE 127 86 71

Figure S67.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 8(6p23)' versus 'MRNASEQ_CNMF'

P value = 2.75e-19 (Chi-square test), Q value = 1.9e-16

Table S68.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 8(6P23) CNV 86 9 34 45 55 6 8
AMP PEAK 8(6P23) WILD-TYPE 72 72 194 101 162 47 8

Figure S68.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 8(6p23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.14e-13 (Fisher's exact test), Q value = 1.3e-10

Table S69.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 8(6P23) CNV 104 32 107
AMP PEAK 8(6P23) WILD-TYPE 122 183 351

Figure S69.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 8(6p23)' versus 'MIRSEQ_CNMF'

P value = 1.52e-18 (Fisher's exact test), Q value = 1e-15

Table S70.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 8(6P23) CNV 31 76 119
AMP PEAK 8(6P23) WILD-TYPE 203 316 136

Figure S70.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 8(6p23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.51e-15 (Fisher's exact test), Q value = 1.6e-12

Table S71.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 8(6P23) CNV 88 35 103
AMP PEAK 8(6P23) WILD-TYPE 274 249 132

Figure S71.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 8(6p23)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.97e-13 (Fisher's exact test), Q value = 1.8e-10

Table S72.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 8(6P23) CNV 40 18 77
AMP PEAK 8(6P23) WILD-TYPE 173 161 101

Figure S72.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 8(6p23)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.89e-10 (Fisher's exact test), Q value = 9.7e-08

Table S73.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 8(6P23) CNV 15 30 63 27
AMP PEAK 8(6P23) WILD-TYPE 106 92 79 158

Figure S73.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 9(6q21)' versus 'MRNA_CNMF'

P value = 1.24e-13 (Chi-square test), Q value = 7.5e-11

Table S74.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 9(6Q21) CNV 4 1 11 41 11 25 9 2
AMP PEAK 9(6Q21) WILD-TYPE 17 35 108 55 98 47 11 38

Figure S74.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 9(6q21)' versus 'MRNA_CHIERARCHICAL'

P value = 5.33e-10 (Fisher's exact test), Q value = 2.7e-07

Table S75.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 9(6Q21) CNV 9 50 45
AMP PEAK 9(6Q21) WILD-TYPE 113 75 221

Figure S75.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 9(6q21)' versus 'CN_CNMF'

P value = 2.98e-39 (Chi-square test), Q value = 2.3e-36

Table S76.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 9(6Q21) CNV 18 22 16 114 5
AMP PEAK 9(6Q21) WILD-TYPE 338 190 55 127 49

Figure S76.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(6q21)' versus 'METHLYATION_CNMF'

P value = 2.48e-13 (Chi-square test), Q value = 1.5e-10

Table S77.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 9(6Q21) CNV 43 5 17 17 2 17
AMP PEAK 9(6Q21) WILD-TYPE 62 146 82 101 36 79

Figure S77.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 9(6q21)' versus 'RPPA_CNMF'

P value = 1.04e-08 (Fisher's exact test), Q value = 4.8e-06

Table S78.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 9(6Q21) CNV 54 12 16
AMP PEAK 9(6Q21) WILD-TYPE 93 121 101

Figure S78.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 9(6q21)' versus 'RPPA_CHIERARCHICAL'

P value = 4.64e-07 (Fisher's exact test), Q value = 0.00018

Table S79.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 9(6Q21) CNV 20 15 47
AMP PEAK 9(6Q21) WILD-TYPE 141 95 79

Figure S79.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 9(6q21)' versus 'MRNASEQ_CNMF'

P value = 1.44e-23 (Chi-square test), Q value = 1e-20

Table S80.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 9(6Q21) CNV 70 5 22 40 21 3 7
AMP PEAK 9(6Q21) WILD-TYPE 88 76 206 106 196 50 9

Figure S80.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 9(6q21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.6e-20 (Fisher's exact test), Q value = 3.2e-17

Table S81.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 9(6Q21) CNV 91 15 62
AMP PEAK 9(6Q21) WILD-TYPE 135 200 396

Figure S81.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 9(6q21)' versus 'MIRSEQ_CNMF'

P value = 3.42e-19 (Fisher's exact test), Q value = 2.4e-16

Table S82.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 9(6Q21) CNV 21 41 95
AMP PEAK 9(6Q21) WILD-TYPE 213 351 160

Figure S82.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 9(6q21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.33e-23 (Fisher's exact test), Q value = 3.1e-20

Table S83.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 9(6Q21) CNV 41 21 95
AMP PEAK 9(6Q21) WILD-TYPE 321 263 140

Figure S83.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 9(6q21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.65e-17 (Fisher's exact test), Q value = 1.1e-14

Table S84.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 9(6Q21) CNV 23 9 69
AMP PEAK 9(6Q21) WILD-TYPE 190 170 109

Figure S84.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 9(6q21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.51e-15 (Fisher's exact test), Q value = 2.2e-12

Table S85.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 9(6Q21) CNV 11 15 60 15
AMP PEAK 9(6Q21) WILD-TYPE 110 107 82 170

Figure S85.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 10(8p11.23)' versus 'MRNA_CNMF'

P value = 1.27e-06 (Chi-square test), Q value = 0.00047

Table S86.  Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 10(8P11.23) CNV 11 17 74 31 36 23 5 9
AMP PEAK 10(8P11.23) WILD-TYPE 10 19 45 65 73 49 15 31

Figure S86.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 10(8p11.23)' versus 'CN_CNMF'

P value = 4.33e-25 (Chi-square test), Q value = 3.2e-22

Table S87.  Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 10(8P11.23) CNV 96 105 30 72 53
AMP PEAK 10(8P11.23) WILD-TYPE 260 107 41 169 1

Figure S87.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 10(8p11.23)' versus 'METHLYATION_CNMF'

P value = 3.45e-10 (Chi-square test), Q value = 1.8e-07

Table S88.  Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 10(8P11.23) CNV 34 36 39 76 13 28
AMP PEAK 10(8P11.23) WILD-TYPE 71 115 60 42 25 68

Figure S88.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 10(8p11.23)' versus 'MRNASEQ_CNMF'

P value = 8.28e-12 (Chi-square test), Q value = 4.6e-09

Table S89.  Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 10(8P11.23) CNV 49 29 74 43 131 11 6
AMP PEAK 10(8P11.23) WILD-TYPE 109 52 154 103 86 42 10

Figure S89.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 10(8p11.23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.82e-08 (Fisher's exact test), Q value = 8.2e-06

Table S90.  Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 10(8P11.23) CNV 66 59 218
AMP PEAK 10(8P11.23) WILD-TYPE 160 156 240

Figure S90.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(8p11.21)' versus 'CN_CNMF'

P value = 1.22e-22 (Chi-square test), Q value = 8.8e-20

Table S91.  Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 11(8P11.21) CNV 94 88 37 92 53
AMP PEAK 11(8P11.21) WILD-TYPE 262 124 34 149 1

Figure S91.  Get High-res Image Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(8p11.21)' versus 'METHLYATION_CNMF'

P value = 2.79e-06 (Chi-square test), Q value = 0.00098

Table S92.  Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 11(8P11.21) CNV 53 37 36 63 10 32
AMP PEAK 11(8P11.21) WILD-TYPE 52 114 63 55 28 64

Figure S92.  Get High-res Image Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 11(8p11.21)' versus 'MRNASEQ_CNMF'

P value = 7.54e-08 (Chi-square test), Q value = 3.3e-05

Table S93.  Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 11(8P11.21) CNV 78 29 78 43 111 7 5
AMP PEAK 11(8P11.21) WILD-TYPE 80 52 150 103 106 46 11

Figure S93.  Get High-res Image Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 11(8p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.07e-08 (Fisher's exact test), Q value = 2.2e-05

Table S94.  Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 11(8P11.21) CNV 95 49 207
AMP PEAK 11(8P11.21) WILD-TYPE 131 166 251

Figure S94.  Get High-res Image Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(8q24.21)' versus 'MRNA_CNMF'

P value = 6.27e-16 (Chi-square test), Q value = 4.1e-13

Table S95.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 12(8Q24.21) CNV 17 20 96 84 46 56 17 15
AMP PEAK 12(8Q24.21) WILD-TYPE 4 16 23 12 63 16 3 25

Figure S95.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 12(8q24.21)' versus 'MRNA_CHIERARCHICAL'

P value = 1.89e-08 (Fisher's exact test), Q value = 8.5e-06

Table S96.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 12(8Q24.21) CNV 59 104 188
AMP PEAK 12(8Q24.21) WILD-TYPE 63 21 78

Figure S96.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 12(8q24.21)' versus 'CN_CNMF'

P value = 8.45e-49 (Chi-square test), Q value = 6.6e-46

Table S97.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 12(8Q24.21) CNV 130 159 38 220 51
AMP PEAK 12(8Q24.21) WILD-TYPE 226 53 33 21 3

Figure S97.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(8q24.21)' versus 'METHLYATION_CNMF'

P value = 3.89e-25 (Chi-square test), Q value = 2.9e-22

Table S98.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 12(8Q24.21) CNV 95 45 65 93 16 50
AMP PEAK 12(8Q24.21) WILD-TYPE 10 106 34 25 22 46

Figure S98.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 12(8q24.21)' versus 'RPPA_CNMF'

P value = 4.58e-08 (Fisher's exact test), Q value = 2e-05

Table S99.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 12(8Q24.21) CNV 125 72 76
AMP PEAK 12(8Q24.21) WILD-TYPE 22 61 41

Figure S99.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 12(8q24.21)' versus 'RPPA_CHIERARCHICAL'

P value = 9.36e-07 (Fisher's exact test), Q value = 0.00035

Table S100.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 12(8Q24.21) CNV 102 63 108
AMP PEAK 12(8Q24.21) WILD-TYPE 59 47 18

Figure S100.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 12(8q24.21)' versus 'MRNASEQ_CNMF'

P value = 1.07e-26 (Chi-square test), Q value = 7.9e-24

Table S101.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 12(8Q24.21) CNV 140 40 102 104 161 14 14
AMP PEAK 12(8Q24.21) WILD-TYPE 18 41 126 42 56 39 2

Figure S101.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(8q24.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.28e-18 (Fisher's exact test), Q value = 3.6e-15

Table S102.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 12(8Q24.21) CNV 190 95 290
AMP PEAK 12(8Q24.21) WILD-TYPE 36 120 168

Figure S102.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(8q24.21)' versus 'MIRSEQ_CNMF'

P value = 1.31e-21 (Fisher's exact test), Q value = 9.4e-19

Table S103.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 12(8Q24.21) CNV 111 233 221
AMP PEAK 12(8Q24.21) WILD-TYPE 123 159 34

Figure S103.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 12(8q24.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.37e-19 (Fisher's exact test), Q value = 1.7e-16

Table S104.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 12(8Q24.21) CNV 222 140 203
AMP PEAK 12(8Q24.21) WILD-TYPE 140 144 32

Figure S104.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 12(8q24.21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.68e-19 (Fisher's exact test), Q value = 1.2e-16

Table S105.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 12(8Q24.21) CNV 119 76 155
AMP PEAK 12(8Q24.21) WILD-TYPE 94 103 23

Figure S105.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 12(8q24.21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.96e-16 (Fisher's exact test), Q value = 5.8e-13

Table S106.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 12(8Q24.21) CNV 59 75 126 90
AMP PEAK 12(8Q24.21) WILD-TYPE 62 47 16 95

Figure S106.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 13(10p15.1)' versus 'MRNA_CNMF'

P value = 2.47e-21 (Chi-square test), Q value = 1.8e-18

Table S107.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 13(10P15.1) CNV 6 3 26 67 12 34 6 7
AMP PEAK 13(10P15.1) WILD-TYPE 15 33 93 29 97 38 14 33

Figure S107.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 13(10p15.1)' versus 'MRNA_CHIERARCHICAL'

P value = 5.89e-19 (Fisher's exact test), Q value = 4.1e-16

Table S108.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 13(10P15.1) CNV 19 81 61
AMP PEAK 13(10P15.1) WILD-TYPE 103 44 205

Figure S108.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 13(10p15.1)' versus 'CN_CNMF'

P value = 5.83e-38 (Chi-square test), Q value = 4.5e-35

Table S109.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 13(10P15.1) CNV 37 57 16 145 10
AMP PEAK 13(10P15.1) WILD-TYPE 319 155 55 96 44

Figure S109.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(10p15.1)' versus 'METHLYATION_CNMF'

P value = 8.61e-28 (Chi-square test), Q value = 6.4e-25

Table S110.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 13(10P15.1) CNV 69 6 26 28 1 25
AMP PEAK 13(10P15.1) WILD-TYPE 36 145 73 90 37 71

Figure S110.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 13(10p15.1)' versus 'RPPA_CNMF'

P value = 7e-11 (Fisher's exact test), Q value = 3.7e-08

Table S111.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 13(10P15.1) CNV 78 22 29
AMP PEAK 13(10P15.1) WILD-TYPE 69 111 88

Figure S111.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 13(10p15.1)' versus 'RPPA_CHIERARCHICAL'

P value = 2.33e-12 (Fisher's exact test), Q value = 1.3e-09

Table S112.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 13(10P15.1) CNV 30 26 73
AMP PEAK 13(10P15.1) WILD-TYPE 131 84 53

Figure S112.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 13(10p15.1)' versus 'MRNASEQ_CNMF'

P value = 1.69e-35 (Chi-square test), Q value = 1.3e-32

Table S113.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 13(10P15.1) CNV 103 9 26 59 46 5 7
AMP PEAK 13(10P15.1) WILD-TYPE 55 72 202 87 171 48 9

Figure S113.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 13(10p15.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.03e-29 (Fisher's exact test), Q value = 5.2e-26

Table S114.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 13(10P15.1) CNV 133 35 87
AMP PEAK 13(10P15.1) WILD-TYPE 93 180 371

Figure S114.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(10p15.1)' versus 'MIRSEQ_CNMF'

P value = 6.23e-28 (Fisher's exact test), Q value = 4.6e-25

Table S115.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 13(10P15.1) CNV 38 68 141
AMP PEAK 13(10P15.1) WILD-TYPE 196 324 114

Figure S115.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 13(10p15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.2e-30 (Fisher's exact test), Q value = 9.1e-28

Table S116.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 13(10P15.1) CNV 73 38 136
AMP PEAK 13(10P15.1) WILD-TYPE 289 246 99

Figure S116.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 13(10p15.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.49e-20 (Fisher's exact test), Q value = 6e-17

Table S117.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 13(10P15.1) CNV 33 24 94
AMP PEAK 13(10P15.1) WILD-TYPE 180 155 84

Figure S117.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 13(10p15.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.54e-17 (Fisher's exact test), Q value = 2.4e-14

Table S118.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 13(10P15.1) CNV 20 21 80 30
AMP PEAK 13(10P15.1) WILD-TYPE 101 101 62 155

Figure S118.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 14(10q22.3)' versus 'MRNA_CNMF'

P value = 9.27e-06 (Chi-square test), Q value = 0.003

Table S119.  Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 14(10Q22.3) CNV 6 2 15 18 9 23 8 3
AMP PEAK 14(10Q22.3) WILD-TYPE 15 34 104 78 100 49 12 37

Figure S119.  Get High-res Image Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 14(10q22.3)' versus 'CN_CNMF'

P value = 1.7e-09 (Chi-square test), Q value = 8.1e-07

Table S120.  Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 14(10Q22.3) CNV 22 31 12 63 7
AMP PEAK 14(10Q22.3) WILD-TYPE 334 181 59 178 47

Figure S120.  Get High-res Image Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 14(10q22.3)' versus 'METHLYATION_CNMF'

P value = 0.000151 (Chi-square test), Q value = 0.04

Table S121.  Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 14(10Q22.3) CNV 24 6 16 19 2 10
AMP PEAK 14(10Q22.3) WILD-TYPE 81 145 83 99 36 86

Figure S121.  Get High-res Image Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 14(10q22.3)' versus 'MRNASEQ_CNMF'

P value = 1.46e-12 (Chi-square test), Q value = 8.4e-10

Table S122.  Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 14(10Q22.3) CNV 30 4 22 42 22 2 9
AMP PEAK 14(10Q22.3) WILD-TYPE 128 77 206 104 195 51 7

Figure S122.  Get High-res Image Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 14(10q22.3)' versus 'MIRSEQ_CNMF'

P value = 3.75e-05 (Fisher's exact test), Q value = 0.011

Table S123.  Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 14(10Q22.3) CNV 21 48 58
AMP PEAK 14(10Q22.3) WILD-TYPE 213 344 197

Figure S123.  Get High-res Image Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 14(10q22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000675 (Fisher's exact test), Q value = 0.15

Table S124.  Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 14(10Q22.3) CNV 48 28 51
AMP PEAK 14(10Q22.3) WILD-TYPE 314 256 184

Figure S124.  Get High-res Image Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 14(10q22.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.14

Table S125.  Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 14(10Q22.3) CNV 29 13 38
AMP PEAK 14(10Q22.3) WILD-TYPE 184 166 140

Figure S125.  Get High-res Image Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 15(11p13)' versus 'CN_CNMF'

P value = 8.69e-11 (Chi-square test), Q value = 4.6e-08

Table S126.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 15(11P13) CNV 32 62 14 73 13
AMP PEAK 15(11P13) WILD-TYPE 324 150 57 168 41

Figure S126.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(11p13)' versus 'METHLYATION_CNMF'

P value = 0.000117 (Chi-square test), Q value = 0.032

Table S127.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 15(11P13) CNV 30 18 18 37 3 15
AMP PEAK 15(11P13) WILD-TYPE 75 133 81 81 35 81

Figure S127.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 15(11p13)' versus 'MRNASEQ_CNMF'

P value = 3.47e-06 (Chi-square test), Q value = 0.0012

Table S128.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 15(11P13) CNV 48 6 29 38 60 8 3
AMP PEAK 15(11P13) WILD-TYPE 110 75 199 108 157 45 13

Figure S128.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 15(11p13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000422 (Fisher's exact test), Q value = 0.099

Table S129.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 15(11P13) CNV 65 29 98
AMP PEAK 15(11P13) WILD-TYPE 161 186 360

Figure S129.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(11p13)' versus 'MIRSEQ_CNMF'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00049

Table S130.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 15(11P13) CNV 29 77 80
AMP PEAK 15(11P13) WILD-TYPE 205 315 175

Figure S130.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 15(11p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.91e-08 (Fisher's exact test), Q value = 8.6e-06

Table S131.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 15(11P13) CNV 80 31 75
AMP PEAK 15(11P13) WILD-TYPE 282 253 160

Figure S131.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 15(11p13)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000103 (Fisher's exact test), Q value = 0.028

Table S132.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 15(11P13) CNV 47 17 46
AMP PEAK 15(11P13) WILD-TYPE 166 162 132

Figure S132.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 15(11p13)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.22

Table S133.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 15(11P13) CNV 13 30 39 28
AMP PEAK 15(11P13) WILD-TYPE 108 92 103 157

Figure S133.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 16(11q13.3)' versus 'MRNA_CNMF'

P value = 0.000715 (Chi-square test), Q value = 0.16

Table S134.  Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 16(11Q13.3) CNV 13 17 61 29 33 37 11 13
AMP PEAK 16(11Q13.3) WILD-TYPE 8 19 58 67 76 35 9 27

Figure S134.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 16(11q13.3)' versus 'CN_CNMF'

P value = 2.12e-42 (Chi-square test), Q value = 1.6e-39

Table S135.  Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 16(11Q13.3) CNV 55 159 25 94 19
AMP PEAK 16(11Q13.3) WILD-TYPE 301 53 46 147 35

Figure S135.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(11q13.3)' versus 'METHLYATION_CNMF'

P value = 3.21e-10 (Chi-square test), Q value = 1.6e-07

Table S136.  Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 16(11Q13.3) CNV 39 35 49 66 10 18
AMP PEAK 16(11Q13.3) WILD-TYPE 66 116 50 52 28 78

Figure S136.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 16(11q13.3)' versus 'MRNASEQ_CNMF'

P value = 4.75e-10 (Chi-square test), Q value = 2.4e-07

Table S137.  Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 16(11Q13.3) CNV 53 22 58 71 119 17 8
AMP PEAK 16(11Q13.3) WILD-TYPE 105 59 170 75 98 36 8

Figure S137.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 16(11q13.3)' versus 'MIRSEQ_CNMF'

P value = 0.000292 (Fisher's exact test), Q value = 0.071

Table S138.  Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 16(11Q13.3) CNV 64 160 111
AMP PEAK 16(11Q13.3) WILD-TYPE 170 232 144

Figure S138.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 17(11q14.1)' versus 'CN_CNMF'

P value = 1.22e-19 (Chi-square test), Q value = 8.5e-17

Table S139.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 17(11Q14.1) CNV 34 88 15 90 12
AMP PEAK 17(11Q14.1) WILD-TYPE 322 124 56 151 42

Figure S139.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 17(11q14.1)' versus 'METHLYATION_CNMF'

P value = 6.78e-06 (Chi-square test), Q value = 0.0022

Table S140.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 17(11Q14.1) CNV 40 20 32 29 7 13
AMP PEAK 17(11Q14.1) WILD-TYPE 65 131 67 89 31 83

Figure S140.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 17(11q14.1)' versus 'MRNASEQ_CNMF'

P value = 1.18e-05 (Chi-square test), Q value = 0.0038

Table S141.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 17(11Q14.1) CNV 56 13 39 48 66 6 4
AMP PEAK 17(11Q14.1) WILD-TYPE 102 68 189 98 151 47 12

Figure S141.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 17(11q14.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.74e-05 (Fisher's exact test), Q value = 0.019

Table S142.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 17(11Q14.1) CNV 80 37 115
AMP PEAK 17(11Q14.1) WILD-TYPE 146 178 343

Figure S142.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 17(11q14.1)' versus 'MIRSEQ_CNMF'

P value = 8.98e-07 (Fisher's exact test), Q value = 0.00034

Table S143.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 17(11Q14.1) CNV 40 90 95
AMP PEAK 17(11Q14.1) WILD-TYPE 194 302 160

Figure S143.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 17(11q14.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.39e-05 (Fisher's exact test), Q value = 0.0044

Table S144.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 17(11Q14.1) CNV 89 51 85
AMP PEAK 17(11Q14.1) WILD-TYPE 273 233 150

Figure S144.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 17(11q14.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.91e-05 (Fisher's exact test), Q value = 0.025

Table S145.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 17(11Q14.1) CNV 46 28 62
AMP PEAK 17(11Q14.1) WILD-TYPE 167 151 116

Figure S145.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 18(12p13.33)' versus 'MRNA_CNMF'

P value = 6.85e-12 (Chi-square test), Q value = 3.8e-09

Table S146.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 18(12P13.33) CNV 3 4 35 53 16 29 3 3
AMP PEAK 18(12P13.33) WILD-TYPE 18 32 84 43 93 43 17 37

Figure S146.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 18(12p13.33)' versus 'MRNA_CHIERARCHICAL'

P value = 9.63e-12 (Fisher's exact test), Q value = 5.3e-09

Table S147.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 18(12P13.33) CNV 11 61 74
AMP PEAK 18(12P13.33) WILD-TYPE 111 64 192

Figure S147.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 18(12p13.33)' versus 'CN_CNMF'

P value = 1.54e-30 (Chi-square test), Q value = 1.2e-27

Table S148.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 18(12P13.33) CNV 21 66 24 118 14
AMP PEAK 18(12P13.33) WILD-TYPE 335 146 47 123 40

Figure S148.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 18(12p13.33)' versus 'METHLYATION_CNMF'

P value = 1.37e-16 (Chi-square test), Q value = 9e-14

Table S149.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 18(12P13.33) CNV 55 15 22 39 1 13
AMP PEAK 18(12P13.33) WILD-TYPE 50 136 77 79 37 83

Figure S149.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 18(12p13.33)' versus 'RPPA_CNMF'

P value = 2.7e-08 (Fisher's exact test), Q value = 1.2e-05

Table S150.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 18(12P13.33) CNV 69 31 18
AMP PEAK 18(12P13.33) WILD-TYPE 78 102 99

Figure S150.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 18(12p13.33)' versus 'RPPA_CHIERARCHICAL'

P value = 2.37e-07 (Fisher's exact test), Q value = 9.6e-05

Table S151.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 18(12P13.33) CNV 43 16 59
AMP PEAK 18(12P13.33) WILD-TYPE 118 94 67

Figure S151.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 18(12p13.33)' versus 'MRNASEQ_CNMF'

P value = 9.08e-24 (Chi-square test), Q value = 6.6e-21

Table S152.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 18(12P13.33) CNV 89 6 29 46 56 5 3
AMP PEAK 18(12P13.33) WILD-TYPE 69 75 199 100 161 48 13

Figure S152.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 18(12p13.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-19 (Fisher's exact test), Q value = 2.8e-16

Table S153.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 18(12P13.33) CNV 106 20 108
AMP PEAK 18(12P13.33) WILD-TYPE 120 195 350

Figure S153.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 18(12p13.33)' versus 'MIRSEQ_CNMF'

P value = 9.18e-22 (Fisher's exact test), Q value = 6.6e-19

Table S154.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 18(12P13.33) CNV 27 76 123
AMP PEAK 18(12P13.33) WILD-TYPE 207 316 132

Figure S154.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 18(12p13.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.5e-18 (Fisher's exact test), Q value = 3.7e-15

Table S155.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 18(12P13.33) CNV 73 41 112
AMP PEAK 18(12P13.33) WILD-TYPE 289 243 123

Figure S155.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 18(12p13.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.01e-18 (Fisher's exact test), Q value = 6.1e-15

Table S156.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 18(12P13.33) CNV 36 16 84
AMP PEAK 18(12P13.33) WILD-TYPE 177 163 94

Figure S156.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 18(12p13.33)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.85e-12 (Fisher's exact test), Q value = 1.6e-09

Table S157.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 18(12P13.33) CNV 16 24 68 28
AMP PEAK 18(12P13.33) WILD-TYPE 105 98 74 157

Figure S157.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 19(12q15)' versus 'MRNA_CNMF'

P value = 3.35e-07 (Chi-square test), Q value = 0.00013

Table S158.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 19(12Q15) CNV 4 6 52 21 19 35 7 6
AMP PEAK 19(12Q15) WILD-TYPE 17 30 67 75 90 37 13 34

Figure S158.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 19(12q15)' versus 'MRNA_CHIERARCHICAL'

P value = 5.01e-06 (Fisher's exact test), Q value = 0.0017

Table S159.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 19(12Q15) CNV 19 29 102
AMP PEAK 19(12Q15) WILD-TYPE 103 96 164

Figure S159.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 19(12q15)' versus 'CN_CNMF'

P value = 2.45e-30 (Chi-square test), Q value = 1.8e-27

Table S160.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 19(12Q15) CNV 24 108 27 68 12
AMP PEAK 19(12Q15) WILD-TYPE 332 104 44 173 42

Figure S160.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(12q15)' versus 'METHLYATION_CNMF'

P value = 1.27e-14 (Chi-square test), Q value = 7.8e-12

Table S161.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 19(12Q15) CNV 18 21 21 61 4 12
AMP PEAK 19(12Q15) WILD-TYPE 87 130 78 57 34 84

Figure S161.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 19(12q15)' versus 'MRNASEQ_CNMF'

P value = 3.95e-10 (Chi-square test), Q value = 2e-07

Table S162.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 19(12Q15) CNV 29 9 40 58 83 10 4
AMP PEAK 19(12Q15) WILD-TYPE 129 72 188 88 134 43 12

Figure S162.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 19(12q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.68e-06 (Fisher's exact test), Q value = 0.0016

Table S163.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 19(12Q15) CNV 48 35 150
AMP PEAK 19(12Q15) WILD-TYPE 178 180 308

Figure S163.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 19(12q15)' versus 'MIRSEQ_CNMF'

P value = 9.16e-08 (Fisher's exact test), Q value = 3.9e-05

Table S164.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 19(12Q15) CNV 29 118 79
AMP PEAK 19(12Q15) WILD-TYPE 205 274 176

Figure S164.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 19(12q15)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000644 (Fisher's exact test), Q value = 0.14

Table S165.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 19(12Q15) CNV 112 51 63
AMP PEAK 19(12Q15) WILD-TYPE 250 233 172

Figure S165.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 19(12q15)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.18e-05 (Fisher's exact test), Q value = 0.0097

Table S166.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 19(12Q15) CNV 68 23 38
AMP PEAK 19(12Q15) WILD-TYPE 145 156 140

Figure S166.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 20(13q12.3)' versus 'CN_CNMF'

P value = 2.34e-06 (Chi-square test), Q value = 0.00083

Table S167.  Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 20(13Q12.3) CNV 21 36 14 49 9
AMP PEAK 20(13Q12.3) WILD-TYPE 335 176 57 192 45

Figure S167.  Get High-res Image Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(13q12.3)' versus 'MRNASEQ_CNMF'

P value = 5.88e-06 (Chi-square test), Q value = 0.002

Table S168.  Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 20(13Q12.3) CNV 23 5 22 39 34 1 2
AMP PEAK 20(13Q12.3) WILD-TYPE 135 76 206 107 183 52 14

Figure S168.  Get High-res Image Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 20(13q12.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000614 (Fisher's exact test), Q value = 0.14

Table S169.  Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 20(13Q12.3) CNV 37 14 75
AMP PEAK 20(13Q12.3) WILD-TYPE 189 201 383

Figure S169.  Get High-res Image Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 20(13q12.3)' versus 'MIRSEQ_CNMF'

P value = 0.000196 (Fisher's exact test), Q value = 0.05

Table S170.  Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 20(13Q12.3) CNV 17 55 51
AMP PEAK 20(13Q12.3) WILD-TYPE 217 337 204

Figure S170.  Get High-res Image Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 20(13q12.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.1

Table S171.  Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 20(13Q12.3) CNV 51 24 48
AMP PEAK 20(13Q12.3) WILD-TYPE 311 260 187

Figure S171.  Get High-res Image Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 21(13q34)' versus 'MRNA_CNMF'

P value = 1.45e-09 (Chi-square test), Q value = 7e-07

Table S172.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 21(13Q34) CNV 3 3 19 42 15 10 4 0
AMP PEAK 21(13Q34) WILD-TYPE 18 33 100 54 94 62 16 40

Figure S172.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 21(13q34)' versus 'MRNA_CHIERARCHICAL'

P value = 2.67e-09 (Fisher's exact test), Q value = 1.3e-06

Table S173.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 21(13Q34) CNV 9 47 40
AMP PEAK 21(13Q34) WILD-TYPE 113 78 226

Figure S173.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 21(13q34)' versus 'CN_CNMF'

P value = 6.6e-19 (Chi-square test), Q value = 4.5e-16

Table S174.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 21(13Q34) CNV 25 32 10 88 6
AMP PEAK 21(13Q34) WILD-TYPE 331 180 61 153 48

Figure S174.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(13q34)' versus 'METHLYATION_CNMF'

P value = 3.17e-14 (Chi-square test), Q value = 1.9e-11

Table S175.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 21(13Q34) CNV 45 10 13 17 1 12
AMP PEAK 21(13Q34) WILD-TYPE 60 141 86 101 37 84

Figure S175.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 21(13q34)' versus 'RPPA_CNMF'

P value = 8.21e-06 (Fisher's exact test), Q value = 0.0027

Table S176.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 21(13Q34) CNV 48 22 11
AMP PEAK 21(13Q34) WILD-TYPE 99 111 106

Figure S176.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 21(13q34)' versus 'RPPA_CHIERARCHICAL'

P value = 5.1e-08 (Fisher's exact test), Q value = 2.2e-05

Table S177.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 21(13Q34) CNV 25 9 47
AMP PEAK 21(13Q34) WILD-TYPE 136 101 79

Figure S177.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 21(13q34)' versus 'MRNASEQ_CNMF'

P value = 5.14e-19 (Chi-square test), Q value = 3.6e-16

Table S178.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 21(13Q34) CNV 66 3 20 31 33 1 3
AMP PEAK 21(13Q34) WILD-TYPE 92 78 208 115 184 52 13

Figure S178.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(13q34)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.26e-18 (Fisher's exact test), Q value = 2.2e-15

Table S179.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 21(13Q34) CNV 84 13 60
AMP PEAK 21(13Q34) WILD-TYPE 142 202 398

Figure S179.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 21(13q34)' versus 'MIRSEQ_CNMF'

P value = 1.41e-13 (Fisher's exact test), Q value = 8.5e-11

Table S180.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 21(13Q34) CNV 25 44 86
AMP PEAK 21(13Q34) WILD-TYPE 209 348 169

Figure S180.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 21(13q34)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.59e-20 (Fisher's exact test), Q value = 3.9e-17

Table S181.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 21(13Q34) CNV 47 19 89
AMP PEAK 21(13Q34) WILD-TYPE 315 265 146

Figure S181.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 21(13q34)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.47e-12 (Fisher's exact test), Q value = 8.5e-10

Table S182.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 21(13Q34) CNV 21 11 59
AMP PEAK 21(13Q34) WILD-TYPE 192 168 119

Figure S182.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 21(13q34)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.49e-10 (Fisher's exact test), Q value = 1.8e-07

Table S183.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 21(13Q34) CNV 15 15 49 12
AMP PEAK 21(13Q34) WILD-TYPE 106 107 93 173

Figure S183.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 22(14q21.1)' versus 'MRNA_CNMF'

P value = 7.91e-05 (Chi-square test), Q value = 0.022

Table S184.  Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 22(14Q21.1) CNV 5 8 34 11 21 26 6 0
AMP PEAK 22(14Q21.1) WILD-TYPE 16 28 85 85 88 46 14 40

Figure S184.  Get High-res Image Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 22(14q21.1)' versus 'CN_CNMF'

P value = 3.55e-09 (Chi-square test), Q value = 1.7e-06

Table S185.  Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 22(14Q21.1) CNV 36 70 16 53 11
AMP PEAK 22(14Q21.1) WILD-TYPE 320 142 55 188 43

Figure S185.  Get High-res Image Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(14q21.1)' versus 'METHLYATION_CNMF'

P value = 5.89e-05 (Chi-square test), Q value = 0.017

Table S186.  Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 22(14Q21.1) CNV 15 19 25 36 5 8
AMP PEAK 22(14Q21.1) WILD-TYPE 90 132 74 82 33 88

Figure S186.  Get High-res Image Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 22(14q21.1)' versus 'MRNASEQ_CNMF'

P value = 9.88e-11 (Chi-square test), Q value = 5.2e-08

Table S187.  Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 22(14Q21.1) CNV 17 9 37 49 63 0 6
AMP PEAK 22(14Q21.1) WILD-TYPE 141 72 191 97 154 53 10

Figure S187.  Get High-res Image Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 22(14q21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.0052

Table S188.  Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 22(14Q21.1) CNV 34 27 120
AMP PEAK 22(14Q21.1) WILD-TYPE 192 188 338

Figure S188.  Get High-res Image Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(14q21.1)' versus 'MIRSEQ_CNMF'

P value = 1.94e-06 (Fisher's exact test), Q value = 0.00069

Table S189.  Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 22(14Q21.1) CNV 21 95 58
AMP PEAK 22(14Q21.1) WILD-TYPE 213 297 197

Figure S189.  Get High-res Image Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 23(15q26.3)' versus 'MRNA_CNMF'

P value = 2.4e-07 (Chi-square test), Q value = 9.7e-05

Table S190.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 23(15Q26.3) CNV 3 7 30 33 4 16 8 2
AMP PEAK 23(15Q26.3) WILD-TYPE 18 29 89 63 105 56 12 38

Figure S190.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 23(15q26.3)' versus 'CN_CNMF'

P value = 5.72e-17 (Chi-square test), Q value = 3.8e-14

Table S191.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 23(15Q26.3) CNV 30 48 5 84 3
AMP PEAK 23(15Q26.3) WILD-TYPE 326 164 66 157 51

Figure S191.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(15q26.3)' versus 'METHLYATION_CNMF'

P value = 6.68e-05 (Chi-square test), Q value = 0.019

Table S192.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 23(15Q26.3) CNV 27 6 17 25 6 14
AMP PEAK 23(15Q26.3) WILD-TYPE 78 145 82 93 32 82

Figure S192.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(15q26.3)' versus 'RPPA_CNMF'

P value = 0.000153 (Fisher's exact test), Q value = 0.04

Table S193.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 23(15Q26.3) CNV 47 18 17
AMP PEAK 23(15Q26.3) WILD-TYPE 100 115 100

Figure S193.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 23(15q26.3)' versus 'MRNASEQ_CNMF'

P value = 1.72e-09 (Chi-square test), Q value = 8.2e-07

Table S194.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 23(15Q26.3) CNV 53 11 18 27 47 2 3
AMP PEAK 23(15Q26.3) WILD-TYPE 105 70 210 119 170 51 13

Figure S194.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 23(15q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.61e-06 (Fisher's exact test), Q value = 0.00058

Table S195.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 23(15Q26.3) CNV 65 22 74
AMP PEAK 23(15Q26.3) WILD-TYPE 161 193 384

Figure S195.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 23(15q26.3)' versus 'MIRSEQ_CNMF'

P value = 5.92e-08 (Fisher's exact test), Q value = 2.6e-05

Table S196.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 23(15Q26.3) CNV 31 51 77
AMP PEAK 23(15Q26.3) WILD-TYPE 203 341 178

Figure S196.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 23(15q26.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.56e-09 (Fisher's exact test), Q value = 3.5e-06

Table S197.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 23(15Q26.3) CNV 59 28 72
AMP PEAK 23(15Q26.3) WILD-TYPE 303 256 163

Figure S197.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 23(15q26.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000152 (Fisher's exact test), Q value = 0.04

Table S198.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 23(15Q26.3) CNV 35 19 49
AMP PEAK 23(15Q26.3) WILD-TYPE 178 160 129

Figure S198.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 23(15q26.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000257 (Fisher's exact test), Q value = 0.063

Table S199.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 23(15Q26.3) CNV 15 27 40 21
AMP PEAK 23(15Q26.3) WILD-TYPE 106 95 102 164

Figure S199.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 24(17q12)' versus 'MRNA_CNMF'

P value = 1.1e-15 (Chi-square test), Q value = 7.1e-13

Table S200.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 24(17Q12) CNV 9 11 52 19 14 49 7 4
AMP PEAK 24(17Q12) WILD-TYPE 12 25 67 77 95 23 13 36

Figure S200.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 24(17q12)' versus 'MRNA_CHIERARCHICAL'

P value = 1.34e-05 (Fisher's exact test), Q value = 0.0042

Table S201.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 24(17Q12) CNV 20 39 106
AMP PEAK 24(17Q12) WILD-TYPE 102 86 160

Figure S201.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(17q12)' versus 'CN_CNMF'

P value = 1.26e-35 (Chi-square test), Q value = 9.6e-33

Table S202.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 24(17Q12) CNV 57 143 20 61 19
AMP PEAK 24(17Q12) WILD-TYPE 299 69 51 180 35

Figure S202.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(17q12)' versus 'METHLYATION_CNMF'

P value = 2.43e-09 (Chi-square test), Q value = 1.1e-06

Table S203.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 24(17Q12) CNV 28 28 42 63 9 22
AMP PEAK 24(17Q12) WILD-TYPE 77 123 57 55 29 74

Figure S203.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(17q12)' versus 'MRNASEQ_CNMF'

P value = 1.11e-26 (Chi-square test), Q value = 8.2e-24

Table S204.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 24(17Q12) CNV 31 16 41 96 97 8 5
AMP PEAK 24(17Q12) WILD-TYPE 127 65 187 50 120 45 11

Figure S204.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(17q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.36e-05 (Fisher's exact test), Q value = 0.01

Table S205.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 24(17Q12) CNV 79 44 171
AMP PEAK 24(17Q12) WILD-TYPE 147 171 287

Figure S205.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(17q23.1)' versus 'MRNA_CNMF'

P value = 6.72e-16 (Chi-square test), Q value = 4.4e-13

Table S206.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 25(17Q23.1) CNV 9 17 80 30 16 43 11 9
AMP PEAK 25(17Q23.1) WILD-TYPE 12 19 39 66 93 29 9 31

Figure S206.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 25(17q23.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.08

Table S207.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 25(17Q23.1) CNV 35 48 132
AMP PEAK 25(17Q23.1) WILD-TYPE 87 77 134

Figure S207.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 25(17q23.1)' versus 'CN_CNMF'

P value = 1.8e-38 (Chi-square test), Q value = 1.4e-35

Table S208.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 25(17Q23.1) CNV 69 161 20 110 24
AMP PEAK 25(17Q23.1) WILD-TYPE 287 51 51 131 30

Figure S208.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(17q23.1)' versus 'METHLYATION_CNMF'

P value = 5.4e-11 (Chi-square test), Q value = 2.9e-08

Table S209.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 25(17Q23.1) CNV 43 35 44 77 15 26
AMP PEAK 25(17Q23.1) WILD-TYPE 62 116 55 41 23 70

Figure S209.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 25(17q23.1)' versus 'MRNASEQ_CNMF'

P value = 1.28e-24 (Chi-square test), Q value = 9.4e-22

Table S210.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 25(17Q23.1) CNV 56 22 46 83 142 13 9
AMP PEAK 25(17Q23.1) WILD-TYPE 102 59 182 63 75 40 7

Figure S210.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 25(17q23.1)' versus 'MIRSEQ_CNMF'

P value = 3.1e-07 (Fisher's exact test), Q value = 0.00012

Table S211.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 25(17Q23.1) CNV 65 167 132
AMP PEAK 25(17Q23.1) WILD-TYPE 169 225 123

Figure S211.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 25(17q23.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.57e-06 (Fisher's exact test), Q value = 0.0012

Table S212.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 25(17Q23.1) CNV 175 84 105
AMP PEAK 25(17Q23.1) WILD-TYPE 187 200 130

Figure S212.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 25(17q23.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000384 (Fisher's exact test), Q value = 0.091

Table S213.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 25(17Q23.1) CNV 37 65 63 61
AMP PEAK 25(17Q23.1) WILD-TYPE 84 57 79 124

Figure S213.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 26(19p13.12)' versus 'MRNA_CNMF'

P value = 6.52e-06 (Chi-square test), Q value = 0.0022

Table S214.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 26(19P13.12) CNV 5 5 22 41 16 11 6 4
AMP PEAK 26(19P13.12) WILD-TYPE 16 31 97 55 93 61 14 36

Figure S214.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 26(19p13.12)' versus 'MRNA_CHIERARCHICAL'

P value = 5.01e-05 (Fisher's exact test), Q value = 0.015

Table S215.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 26(19P13.12) CNV 18 45 47
AMP PEAK 26(19P13.12) WILD-TYPE 104 80 219

Figure S215.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 26(19p13.12)' versus 'CN_CNMF'

P value = 3.88e-15 (Chi-square test), Q value = 2.4e-12

Table S216.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 26(19P13.12) CNV 36 36 23 91 11
AMP PEAK 26(19P13.12) WILD-TYPE 320 176 48 150 43

Figure S216.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 26(19p13.12)' versus 'METHLYATION_CNMF'

P value = 3.53e-07 (Chi-square test), Q value = 0.00014

Table S217.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 26(19P13.12) CNV 41 15 20 20 3 22
AMP PEAK 26(19P13.12) WILD-TYPE 64 136 79 98 35 74

Figure S217.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 26(19p13.12)' versus 'RPPA_CNMF'

P value = 0.000125 (Fisher's exact test), Q value = 0.034

Table S218.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 26(19P13.12) CNV 51 25 16
AMP PEAK 26(19P13.12) WILD-TYPE 96 108 101

Figure S218.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 26(19p13.12)' versus 'MRNASEQ_CNMF'

P value = 2.42e-11 (Chi-square test), Q value = 1.3e-08

Table S219.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 26(19P13.12) CNV 66 13 33 30 34 5 7
AMP PEAK 26(19P13.12) WILD-TYPE 92 68 195 116 183 48 9

Figure S219.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 26(19p13.12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.79e-08 (Fisher's exact test), Q value = 2.5e-05

Table S220.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 26(19P13.12) CNV 79 34 75
AMP PEAK 26(19P13.12) WILD-TYPE 147 181 383

Figure S220.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(19p13.12)' versus 'MIRSEQ_CNMF'

P value = 7.66e-08 (Fisher's exact test), Q value = 3.3e-05

Table S221.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 26(19P13.12) CNV 45 55 84
AMP PEAK 26(19P13.12) WILD-TYPE 189 337 171

Figure S221.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 26(19p13.12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.77e-11 (Fisher's exact test), Q value = 2.5e-08

Table S222.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 26(19P13.12) CNV 50 47 87
AMP PEAK 26(19P13.12) WILD-TYPE 312 237 148

Figure S222.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 26(19p13.12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.41e-08 (Fisher's exact test), Q value = 3.6e-05

Table S223.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 26(19P13.12) CNV 29 29 65
AMP PEAK 26(19P13.12) WILD-TYPE 184 150 113

Figure S223.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 26(19p13.12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.17e-06 (Fisher's exact test), Q value = 0.0011

Table S224.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 26(19P13.12) CNV 21 21 54 27
AMP PEAK 26(19P13.12) WILD-TYPE 100 101 88 158

Figure S224.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'MRNA_CNMF'

P value = 4.35e-12 (Chi-square test), Q value = 2.5e-09

Table S225.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 27(19Q12) CNV 4 4 29 56 15 20 7 5
AMP PEAK 27(19Q12) WILD-TYPE 17 32 90 40 94 52 13 35

Figure S225.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 27(19q12)' versus 'MRNA_CHIERARCHICAL'

P value = 9.44e-11 (Fisher's exact test), Q value = 5e-08

Table S226.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 27(19Q12) CNV 19 64 57
AMP PEAK 27(19Q12) WILD-TYPE 103 61 209

Figure S226.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'CN_CNMF'

P value = 8.25e-25 (Chi-square test), Q value = 6e-22

Table S227.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 27(19Q12) CNV 37 43 27 117 14
AMP PEAK 27(19Q12) WILD-TYPE 319 169 44 124 40

Figure S227.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(19q12)' versus 'METHLYATION_CNMF'

P value = 3.98e-12 (Chi-square test), Q value = 2.2e-09

Table S228.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 27(19Q12) CNV 54 18 22 30 2 22
AMP PEAK 27(19Q12) WILD-TYPE 51 133 77 88 36 74

Figure S228.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 27(19q12)' versus 'RPPA_CNMF'

P value = 6.19e-07 (Fisher's exact test), Q value = 0.00024

Table S229.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 27(19Q12) CNV 64 23 23
AMP PEAK 27(19Q12) WILD-TYPE 83 110 94

Figure S229.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 27(19q12)' versus 'RPPA_CHIERARCHICAL'

P value = 9.68e-07 (Fisher's exact test), Q value = 0.00036

Table S230.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 27(19Q12) CNV 29 24 57
AMP PEAK 27(19Q12) WILD-TYPE 132 86 69

Figure S230.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'MRNASEQ_CNMF'

P value = 2e-21 (Chi-square test), Q value = 1.4e-18

Table S231.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 27(19Q12) CNV 88 11 32 42 46 5 7
AMP PEAK 27(19Q12) WILD-TYPE 70 70 196 104 171 48 9

Figure S231.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 27(19q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.4e-17 (Fisher's exact test), Q value = 3.6e-14

Table S232.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 27(19Q12) CNV 109 36 86
AMP PEAK 27(19Q12) WILD-TYPE 117 179 372

Figure S232.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'MIRSEQ_CNMF'

P value = 6.49e-13 (Fisher's exact test), Q value = 3.8e-10

Table S233.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 27(19Q12) CNV 45 71 111
AMP PEAK 27(19Q12) WILD-TYPE 189 321 144

Figure S233.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 27(19q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.82e-18 (Fisher's exact test), Q value = 1.9e-15

Table S234.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 27(19Q12) CNV 65 48 114
AMP PEAK 27(19Q12) WILD-TYPE 297 236 121

Figure S234.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.58e-11 (Fisher's exact test), Q value = 5e-08

Table S235.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 27(19Q12) CNV 37 31 80
AMP PEAK 27(19Q12) WILD-TYPE 176 148 98

Figure S235.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 27(19q12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.3e-10 (Fisher's exact test), Q value = 3.1e-07

Table S236.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 27(19Q12) CNV 26 25 68 29
AMP PEAK 27(19Q12) WILD-TYPE 95 97 74 156

Figure S236.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 28(19q13.42)' versus 'MRNA_CNMF'

P value = 0.000812 (Chi-square test), Q value = 0.18

Table S237.  Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 28(19Q13.42) CNV 5 8 37 37 16 22 10 6
AMP PEAK 28(19Q13.42) WILD-TYPE 16 28 82 59 93 50 10 34

Figure S237.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 28(19q13.42)' versus 'CN_CNMF'

P value = 9.78e-16 (Chi-square test), Q value = 6.3e-13

Table S238.  Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 28(19Q13.42) CNV 38 61 27 97 17
AMP PEAK 28(19Q13.42) WILD-TYPE 318 151 44 144 37

Figure S238.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 28(19q13.42)' versus 'METHLYATION_CNMF'

P value = 1.65e-06 (Chi-square test), Q value = 6e-04

Table S239.  Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 28(19Q13.42) CNV 34 20 28 45 3 17
AMP PEAK 28(19Q13.42) WILD-TYPE 71 131 71 73 35 79

Figure S239.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 28(19q13.42)' versus 'MRNASEQ_CNMF'

P value = 1.65e-06 (Chi-square test), Q value = 6e-04

Table S240.  Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 28(19Q13.42) CNV 53 13 37 46 69 6 8
AMP PEAK 28(19Q13.42) WILD-TYPE 105 68 191 100 148 47 8

Figure S240.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 28(19q13.42)' versus 'MIRSEQ_CNMF'

P value = 4.27e-06 (Fisher's exact test), Q value = 0.0015

Table S241.  Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 28(19Q13.42) CNV 43 91 95
AMP PEAK 28(19Q13.42) WILD-TYPE 191 301 160

Figure S241.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 29(20q13.2)' versus 'MRNA_CNMF'

P value = 1.81e-10 (Chi-square test), Q value = 9.3e-08

Table S242.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 29(20Q13.2) CNV 12 18 84 52 35 49 15 9
AMP PEAK 29(20Q13.2) WILD-TYPE 9 18 35 44 74 23 5 31

Figure S242.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 29(20q13.2)' versus 'MRNA_CHIERARCHICAL'

P value = 3.67e-05 (Fisher's exact test), Q value = 0.011

Table S243.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 29(20Q13.2) CNV 44 69 161
AMP PEAK 29(20Q13.2) WILD-TYPE 78 56 105

Figure S243.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 29(20q13.2)' versus 'CN_CNMF'

P value = 4.27e-52 (Chi-square test), Q value = 3.4e-49

Table S244.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
AMP PEAK 29(20Q13.2) CNV 68 168 42 166 31
AMP PEAK 29(20Q13.2) WILD-TYPE 288 44 29 75 23

Figure S244.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(20q13.2)' versus 'METHLYATION_CNMF'

P value = 3e-22 (Chi-square test), Q value = 2.2e-19

Table S245.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
AMP PEAK 29(20Q13.2) CNV 65 35 54 95 12 31
AMP PEAK 29(20Q13.2) WILD-TYPE 40 116 45 23 26 65

Figure S245.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 29(20q13.2)' versus 'RPPA_CNMF'

P value = 0.000604 (Fisher's exact test), Q value = 0.14

Table S246.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 29(20Q13.2) CNV 99 67 53
AMP PEAK 29(20Q13.2) WILD-TYPE 48 66 64

Figure S246.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 29(20q13.2)' versus 'MRNASEQ_CNMF'

P value = 1.91e-20 (Chi-square test), Q value = 1.3e-17

Table S247.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
AMP PEAK 29(20Q13.2) CNV 87 25 77 95 154 12 10
AMP PEAK 29(20Q13.2) WILD-TYPE 71 56 151 51 63 41 6

Figure S247.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 29(20q13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.59e-07 (Fisher's exact test), Q value = 1e-04

Table S248.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
AMP PEAK 29(20Q13.2) CNV 125 75 260
AMP PEAK 29(20Q13.2) WILD-TYPE 101 140 198

Figure S248.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 29(20q13.2)' versus 'MIRSEQ_CNMF'

P value = 7.41e-10 (Fisher's exact test), Q value = 3.7e-07

Table S249.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
AMP PEAK 29(20Q13.2) CNV 80 214 159
AMP PEAK 29(20Q13.2) WILD-TYPE 154 178 96

Figure S249.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 29(20q13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00043

Table S250.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
AMP PEAK 29(20Q13.2) CNV 205 110 138
AMP PEAK 29(20Q13.2) WILD-TYPE 157 174 97

Figure S250.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 29(20q13.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.83e-08 (Fisher's exact test), Q value = 3e-05

Table S251.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
AMP PEAK 29(20Q13.2) CNV 120 60 110
AMP PEAK 29(20Q13.2) WILD-TYPE 93 119 68

Figure S251.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 29(20q13.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0034

Table S252.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
AMP PEAK 29(20Q13.2) CNV 41 74 87 88
AMP PEAK 29(20Q13.2) WILD-TYPE 80 48 55 97

Figure S252.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'MRNA_CNMF'

P value = 7.82e-05 (Chi-square test), Q value = 0.022

Table S253.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 1(1P36.13) CNV 8 12 61 41 31 46 7 12
DEL PEAK 1(1P36.13) WILD-TYPE 13 24 58 55 78 26 13 28

Figure S253.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.033

Table S254.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 1(1P36.13) CNV 34 50 134
DEL PEAK 1(1P36.13) WILD-TYPE 88 75 132

Figure S254.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'CN_CNMF'

P value = 3.3e-31 (Chi-square test), Q value = 2.5e-28

Table S255.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 1(1P36.13) CNV 62 132 45 127 23
DEL PEAK 1(1P36.13) WILD-TYPE 294 80 26 114 31

Figure S255.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.13)' versus 'METHLYATION_CNMF'

P value = 1.19e-10 (Chi-square test), Q value = 6.2e-08

Table S256.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 1(1P36.13) CNV 48 36 57 66 9 25
DEL PEAK 1(1P36.13) WILD-TYPE 57 115 42 52 29 71

Figure S256.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNASEQ_CNMF'

P value = 4.32e-11 (Chi-square test), Q value = 2.3e-08

Table S257.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 1(1P36.13) CNV 67 17 75 81 116 9 9
DEL PEAK 1(1P36.13) WILD-TYPE 91 64 153 65 101 44 7

Figure S257.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.61e-07 (Fisher's exact test), Q value = 0.00033

Table S258.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 1(1P36.13) CNV 92 59 223
DEL PEAK 1(1P36.13) WILD-TYPE 134 156 235

Figure S258.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'MIRSEQ_CNMF'

P value = 2.37e-07 (Fisher's exact test), Q value = 9.6e-05

Table S259.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 1(1P36.13) CNV 64 168 131
DEL PEAK 1(1P36.13) WILD-TYPE 170 224 124

Figure S259.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.13

Table S260.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 1(1P36.13) CNV 168 91 104
DEL PEAK 1(1P36.13) WILD-TYPE 194 193 131

Figure S260.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.07e-05 (Fisher's exact test), Q value = 0.023

Table S261.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 1(1P36.13) CNV 95 46 79
DEL PEAK 1(1P36.13) WILD-TYPE 118 133 99

Figure S261.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 2(1p22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000233 (Fisher's exact test), Q value = 0.058

Table S262.  Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 2(1P22.1) CNV 35 30 115
DEL PEAK 2(1P22.1) WILD-TYPE 87 95 151

Figure S262.  Get High-res Image Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p22.1)' versus 'CN_CNMF'

P value = 4.81e-22 (Chi-square test), Q value = 3.4e-19

Table S263.  Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 2(1P22.1) CNV 62 113 44 76 15
DEL PEAK 2(1P22.1) WILD-TYPE 294 99 27 165 39

Figure S263.  Get High-res Image Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p22.1)' versus 'METHLYATION_CNMF'

P value = 0.000103 (Chi-square test), Q value = 0.028

Table S264.  Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 2(1P22.1) CNV 28 36 46 49 10 21
DEL PEAK 2(1P22.1) WILD-TYPE 77 115 53 69 28 75

Figure S264.  Get High-res Image Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 2(1p22.1)' versus 'MRNASEQ_CNMF'

P value = 1.6e-07 (Chi-square test), Q value = 6.6e-05

Table S265.  Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 2(1P22.1) CNV 33 19 75 69 93 9 5
DEL PEAK 2(1P22.1) WILD-TYPE 125 62 153 77 124 44 11

Figure S265.  Get High-res Image Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.52e-06 (Fisher's exact test), Q value = 0.0019

Table S266.  Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 2(1P22.1) CNV 53 62 188
DEL PEAK 2(1P22.1) WILD-TYPE 173 153 270

Figure S266.  Get High-res Image Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MRNA_CNMF'

P value = 1.51e-06 (Chi-square test), Q value = 0.00055

Table S267.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 3(2Q37.3) CNV 5 10 40 47 24 28 6 0
DEL PEAK 3(2Q37.3) WILD-TYPE 16 26 79 49 85 44 14 40

Figure S267.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 3(2q37.3)' versus 'MRNA_CHIERARCHICAL'

P value = 3.28e-09 (Fisher's exact test), Q value = 1.5e-06

Table S268.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 3(2Q37.3) CNV 14 58 88
DEL PEAK 3(2Q37.3) WILD-TYPE 108 67 178

Figure S268.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'CN_CNMF'

P value = 1.25e-20 (Chi-square test), Q value = 8.8e-18

Table S269.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 3(2Q37.3) CNV 40 71 26 114 20
DEL PEAK 3(2Q37.3) WILD-TYPE 316 141 45 127 34

Figure S269.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 3(2q37.3)' versus 'METHLYATION_CNMF'

P value = 1.75e-09 (Chi-square test), Q value = 8.3e-07

Table S270.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 3(2Q37.3) CNV 46 23 27 45 4 12
DEL PEAK 3(2Q37.3) WILD-TYPE 59 128 72 73 34 84

Figure S270.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 3(2q37.3)' versus 'RPPA_CNMF'

P value = 1.03e-08 (Fisher's exact test), Q value = 4.7e-06

Table S271.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 3(2Q37.3) CNV 70 38 16
DEL PEAK 3(2Q37.3) WILD-TYPE 77 95 101

Figure S271.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 3(2q37.3)' versus 'RPPA_CHIERARCHICAL'

P value = 1.11e-07 (Fisher's exact test), Q value = 4.7e-05

Table S272.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 3(2Q37.3) CNV 56 13 55
DEL PEAK 3(2Q37.3) WILD-TYPE 105 97 71

Figure S272.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MRNASEQ_CNMF'

P value = 2.43e-10 (Chi-square test), Q value = 1.2e-07

Table S273.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 3(2Q37.3) CNV 70 12 48 51 72 1 5
DEL PEAK 3(2Q37.3) WILD-TYPE 88 69 180 95 145 52 11

Figure S273.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 3(2q37.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.39e-10 (Fisher's exact test), Q value = 1.7e-07

Table S274.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 3(2Q37.3) CNV 90 28 141
DEL PEAK 3(2Q37.3) WILD-TYPE 136 187 317

Figure S274.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MIRSEQ_CNMF'

P value = 4.66e-11 (Fisher's exact test), Q value = 2.5e-08

Table S275.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 3(2Q37.3) CNV 43 99 116
DEL PEAK 3(2Q37.3) WILD-TYPE 191 293 139

Figure S275.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 3(2q37.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.63e-07 (Fisher's exact test), Q value = 0.00011

Table S276.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 3(2Q37.3) CNV 110 53 95
DEL PEAK 3(2Q37.3) WILD-TYPE 252 231 140

Figure S276.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.84e-10 (Fisher's exact test), Q value = 4.8e-07

Table S277.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 3(2Q37.3) CNV 58 25 79
DEL PEAK 3(2Q37.3) WILD-TYPE 155 154 99

Figure S277.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 3(2q37.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.0045

Table S278.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 3(2Q37.3) CNV 21 40 60 41
DEL PEAK 3(2Q37.3) WILD-TYPE 100 82 82 144

Figure S278.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 4(3p21.31)' versus 'MRNA_CNMF'

P value = 2.91e-11 (Chi-square test), Q value = 1.6e-08

Table S279.  Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 4(3P21.31) CNV 4 15 38 50 8 34 8 7
DEL PEAK 4(3P21.31) WILD-TYPE 17 21 81 46 101 38 12 33

Figure S279.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 4(3p21.31)' versus 'MRNA_CHIERARCHICAL'

P value = 4.45e-08 (Fisher's exact test), Q value = 2e-05

Table S280.  Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 4(3P21.31) CNV 30 67 67
DEL PEAK 4(3P21.31) WILD-TYPE 92 58 199

Figure S280.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 4(3p21.31)' versus 'CN_CNMF'

P value = 4.55e-36 (Chi-square test), Q value = 3.5e-33

Table S281.  Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 4(3P21.31) CNV 49 76 11 148 7
DEL PEAK 4(3P21.31) WILD-TYPE 307 136 60 93 47

Figure S281.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(3p21.31)' versus 'METHLYATION_CNMF'

P value = 1.2e-13 (Chi-square test), Q value = 7.3e-11

Table S282.  Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 4(3P21.31) CNV 52 13 43 42 9 18
DEL PEAK 4(3P21.31) WILD-TYPE 53 138 56 76 29 78

Figure S282.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 4(3p21.31)' versus 'RPPA_CNMF'

P value = 2.03e-08 (Fisher's exact test), Q value = 9.1e-06

Table S283.  Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 4(3P21.31) CNV 78 27 34
DEL PEAK 4(3P21.31) WILD-TYPE 69 106 83

Figure S283.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 4(3p21.31)' versus 'RPPA_CHIERARCHICAL'

P value = 6.18e-06 (Fisher's exact test), Q value = 0.0021

Table S284.  Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 4(3P21.31) CNV 42 31 66
DEL PEAK 4(3P21.31) WILD-TYPE 119 79 60

Figure S284.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 4(3p21.31)' versus 'MRNASEQ_CNMF'

P value = 1.72e-19 (Chi-square test), Q value = 1.2e-16

Table S285.  Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 4(3P21.31) CNV 80 16 27 68 73 6 7
DEL PEAK 4(3P21.31) WILD-TYPE 78 65 201 78 144 47 9

Figure S285.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 4(3p21.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.03e-12 (Fisher's exact test), Q value = 3.4e-09

Table S286.  Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 4(3P21.31) CNV 113 45 119
DEL PEAK 4(3P21.31) WILD-TYPE 113 170 339

Figure S286.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 4(3p21.31)' versus 'MIRSEQ_CNMF'

P value = 3.86e-18 (Fisher's exact test), Q value = 2.6e-15

Table S287.  Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 4(3P21.31) CNV 47 91 136
DEL PEAK 4(3P21.31) WILD-TYPE 187 301 119

Figure S287.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 4(3p21.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.17e-12 (Fisher's exact test), Q value = 6.8e-10

Table S288.  Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 4(3P21.31) CNV 103 55 116
DEL PEAK 4(3P21.31) WILD-TYPE 259 229 119

Figure S288.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(3p21.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.82e-13 (Fisher's exact test), Q value = 1.1e-10

Table S289.  Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 4(3P21.31) CNV 53 29 93
DEL PEAK 4(3P21.31) WILD-TYPE 160 150 85

Figure S289.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 4(3p21.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.3e-10 (Fisher's exact test), Q value = 4.5e-07

Table S290.  Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 4(3P21.31) CNV 26 41 73 35
DEL PEAK 4(3P21.31) WILD-TYPE 95 81 69 150

Figure S290.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MRNA_CNMF'

P value = 2.7e-11 (Chi-square test), Q value = 1.5e-08

Table S291.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 5(4P16.3) CNV 3 10 26 56 22 37 7 6
DEL PEAK 5(4P16.3) WILD-TYPE 18 26 93 40 87 35 13 34

Figure S291.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 5(4p16.3)' versus 'MRNA_CHIERARCHICAL'

P value = 2.23e-11 (Fisher's exact test), Q value = 1.2e-08

Table S292.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 5(4P16.3) CNV 22 72 73
DEL PEAK 5(4P16.3) WILD-TYPE 100 53 193

Figure S292.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'CN_CNMF'

P value = 1.07e-29 (Chi-square test), Q value = 8e-27

Table S293.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 5(4P16.3) CNV 51 50 33 139 13
DEL PEAK 5(4P16.3) WILD-TYPE 305 162 38 102 41

Figure S293.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(4p16.3)' versus 'METHLYATION_CNMF'

P value = 8.23e-14 (Chi-square test), Q value = 5e-11

Table S294.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 5(4P16.3) CNV 65 30 28 24 5 25
DEL PEAK 5(4P16.3) WILD-TYPE 40 121 71 94 33 71

Figure S294.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(4p16.3)' versus 'RPPA_CNMF'

P value = 4.6e-07 (Fisher's exact test), Q value = 0.00018

Table S295.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 5(4P16.3) CNV 75 39 24
DEL PEAK 5(4P16.3) WILD-TYPE 72 94 93

Figure S295.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 5(4p16.3)' versus 'RPPA_CHIERARCHICAL'

P value = 1.62e-06 (Fisher's exact test), Q value = 0.00059

Table S296.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 5(4P16.3) CNV 48 24 66
DEL PEAK 5(4P16.3) WILD-TYPE 113 86 60

Figure S296.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MRNASEQ_CNMF'

P value = 2.51e-22 (Chi-square test), Q value = 1.8e-19

Table S297.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 5(4P16.3) CNV 92 13 47 65 42 7 9
DEL PEAK 5(4P16.3) WILD-TYPE 66 68 181 81 175 46 7

Figure S297.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(4p16.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.85e-20 (Fisher's exact test), Q value = 3.4e-17

Table S298.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 5(4P16.3) CNV 125 35 115
DEL PEAK 5(4P16.3) WILD-TYPE 101 180 343

Figure S298.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MIRSEQ_CNMF'

P value = 9.97e-15 (Fisher's exact test), Q value = 6.1e-12

Table S299.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 5(4P16.3) CNV 48 94 129
DEL PEAK 5(4P16.3) WILD-TYPE 186 298 126

Figure S299.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 5(4p16.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.7e-18 (Fisher's exact test), Q value = 3.2e-15

Table S300.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 5(4P16.3) CNV 93 52 126
DEL PEAK 5(4P16.3) WILD-TYPE 269 232 109

Figure S300.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.76e-15 (Fisher's exact test), Q value = 3e-12

Table S301.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 5(4P16.3) CNV 57 25 94
DEL PEAK 5(4P16.3) WILD-TYPE 156 154 84

Figure S301.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 5(4p16.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.8e-10 (Fisher's exact test), Q value = 9.3e-08

Table S302.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 5(4P16.3) CNV 24 25 77 50
DEL PEAK 5(4P16.3) WILD-TYPE 97 97 65 135

Figure S302.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MRNA_CNMF'

P value = 1.17e-06 (Chi-square test), Q value = 0.00043

Table S303.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 6(4Q35.2) CNV 7 10 25 51 23 30 10 9
DEL PEAK 6(4Q35.2) WILD-TYPE 14 26 94 45 86 42 10 31

Figure S303.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 6(4q35.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.24e-06 (Fisher's exact test), Q value = 0.00046

Table S304.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 6(4Q35.2) CNV 25 63 77
DEL PEAK 6(4Q35.2) WILD-TYPE 97 62 189

Figure S304.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'CN_CNMF'

P value = 1.36e-38 (Chi-square test), Q value = 1e-35

Table S305.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 6(4Q35.2) CNV 50 44 36 150 11
DEL PEAK 6(4Q35.2) WILD-TYPE 306 168 35 91 43

Figure S305.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(4q35.2)' versus 'METHLYATION_CNMF'

P value = 7.49e-15 (Chi-square test), Q value = 4.7e-12

Table S306.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 6(4Q35.2) CNV 66 30 25 20 7 29
DEL PEAK 6(4Q35.2) WILD-TYPE 39 121 74 98 31 67

Figure S306.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(4q35.2)' versus 'RPPA_CNMF'

P value = 1.51e-08 (Fisher's exact test), Q value = 6.8e-06

Table S307.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 6(4Q35.2) CNV 78 35 24
DEL PEAK 6(4Q35.2) WILD-TYPE 69 98 93

Figure S307.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 6(4q35.2)' versus 'RPPA_CHIERARCHICAL'

P value = 1.78e-06 (Fisher's exact test), Q value = 0.00064

Table S308.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 6(4Q35.2) CNV 46 25 66
DEL PEAK 6(4Q35.2) WILD-TYPE 115 85 60

Figure S308.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MRNASEQ_CNMF'

P value = 6.54e-21 (Chi-square test), Q value = 4.6e-18

Table S309.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 6(4Q35.2) CNV 93 12 48 61 44 9 9
DEL PEAK 6(4Q35.2) WILD-TYPE 65 69 180 85 173 44 7

Figure S309.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 6(4q35.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.35e-15 (Fisher's exact test), Q value = 1.5e-12

Table S310.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 6(4Q35.2) CNV 118 39 119
DEL PEAK 6(4Q35.2) WILD-TYPE 108 176 339

Figure S310.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MIRSEQ_CNMF'

P value = 2.84e-13 (Fisher's exact test), Q value = 1.7e-10

Table S311.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 6(4Q35.2) CNV 48 97 126
DEL PEAK 6(4Q35.2) WILD-TYPE 186 295 129

Figure S311.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 6(4q35.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.73e-18 (Fisher's exact test), Q value = 4.5e-15

Table S312.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 6(4Q35.2) CNV 87 57 127
DEL PEAK 6(4Q35.2) WILD-TYPE 275 227 108

Figure S312.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.82e-13 (Fisher's exact test), Q value = 1.1e-10

Table S313.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 6(4Q35.2) CNV 57 26 91
DEL PEAK 6(4Q35.2) WILD-TYPE 156 153 87

Figure S313.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 6(4q35.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.64e-11 (Fisher's exact test), Q value = 9e-09

Table S314.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 6(4Q35.2) CNV 20 25 77 52
DEL PEAK 6(4Q35.2) WILD-TYPE 101 97 65 133

Figure S314.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MRNA_CNMF'

P value = 2.5e-27 (Chi-square test), Q value = 1.9e-24

Table S315.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 7(5Q11.2) CNV 3 5 19 68 7 25 3 4
DEL PEAK 7(5Q11.2) WILD-TYPE 18 31 100 28 102 47 17 36

Figure S315.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 7(5q11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 6.92e-25 (Fisher's exact test), Q value = 5.1e-22

Table S316.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 7(5Q11.2) CNV 12 79 43
DEL PEAK 7(5Q11.2) WILD-TYPE 110 46 223

Figure S316.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'CN_CNMF'

P value = 5.53e-66 (Chi-square test), Q value = 4.4e-63

Table S317.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 7(5Q11.2) CNV 33 27 7 165 9
DEL PEAK 7(5Q11.2) WILD-TYPE 323 185 64 76 45

Figure S317.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(5q11.2)' versus 'METHLYATION_CNMF'

P value = 7.27e-43 (Chi-square test), Q value = 5.7e-40

Table S318.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 7(5Q11.2) CNV 82 4 16 22 5 23
DEL PEAK 7(5Q11.2) WILD-TYPE 23 147 83 96 33 73

Figure S318.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 7(5q11.2)' versus 'RPPA_CNMF'

P value = 3.33e-16 (Fisher's exact test), Q value = 2.2e-13

Table S319.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 7(5Q11.2) CNV 78 13 23
DEL PEAK 7(5Q11.2) WILD-TYPE 69 120 94

Figure S319.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 7(5q11.2)' versus 'RPPA_CHIERARCHICAL'

P value = 7.43e-19 (Fisher's exact test), Q value = 5.1e-16

Table S320.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 7(5Q11.2) CNV 26 13 75
DEL PEAK 7(5Q11.2) WILD-TYPE 135 97 51

Figure S320.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MRNASEQ_CNMF'

P value = 2.21e-51 (Chi-square test), Q value = 1.7e-48

Table S321.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 7(5Q11.2) CNV 113 5 16 48 42 3 4
DEL PEAK 7(5Q11.2) WILD-TYPE 45 76 212 98 175 50 12

Figure S321.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 7(5q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.53e-48 (Fisher's exact test), Q value = 1.2e-45

Table S322.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 7(5Q11.2) CNV 145 19 67
DEL PEAK 7(5Q11.2) WILD-TYPE 81 196 391

Figure S322.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MIRSEQ_CNMF'

P value = 8.36e-40 (Fisher's exact test), Q value = 6.5e-37

Table S323.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 7(5Q11.2) CNV 32 45 145
DEL PEAK 7(5Q11.2) WILD-TYPE 202 347 110

Figure S323.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 7(5q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.41e-49 (Fisher's exact test), Q value = 4.2e-46

Table S324.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 7(5Q11.2) CNV 63 16 143
DEL PEAK 7(5Q11.2) WILD-TYPE 299 268 92

Figure S324.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.61e-40 (Fisher's exact test), Q value = 5.9e-37

Table S325.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 7(5Q11.2) CNV 28 9 111
DEL PEAK 7(5Q11.2) WILD-TYPE 185 170 67

Figure S325.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 7(5q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.03e-33 (Fisher's exact test), Q value = 7.8e-31

Table S326.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 7(5Q11.2) CNV 13 25 94 16
DEL PEAK 7(5Q11.2) WILD-TYPE 108 97 48 169

Figure S326.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MRNA_CNMF'

P value = 3.82e-29 (Chi-square test), Q value = 2.9e-26

Table S327.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 8(5Q21.3) CNV 2 5 19 69 7 24 5 2
DEL PEAK 8(5Q21.3) WILD-TYPE 19 31 100 27 102 48 15 38

Figure S327.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 8(5q21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 2.12e-26 (Fisher's exact test), Q value = 1.6e-23

Table S328.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 8(5Q21.3) CNV 11 80 42
DEL PEAK 8(5Q21.3) WILD-TYPE 111 45 224

Figure S328.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'CN_CNMF'

P value = 1.01e-74 (Chi-square test), Q value = 8e-72

Table S329.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 8(5Q21.3) CNV 26 23 6 167 8
DEL PEAK 8(5Q21.3) WILD-TYPE 330 189 65 74 46

Figure S329.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(5q21.3)' versus 'METHLYATION_CNMF'

P value = 5.17e-55 (Chi-square test), Q value = 4.1e-52

Table S330.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 8(5Q21.3) CNV 88 4 10 18 3 23
DEL PEAK 8(5Q21.3) WILD-TYPE 17 147 89 100 35 73

Figure S330.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 8(5q21.3)' versus 'RPPA_CNMF'

P value = 2.6e-15 (Fisher's exact test), Q value = 1.6e-12

Table S331.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 8(5Q21.3) CNV 76 13 23
DEL PEAK 8(5Q21.3) WILD-TYPE 71 120 94

Figure S331.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 8(5q21.3)' versus 'RPPA_CHIERARCHICAL'

P value = 8.97e-16 (Fisher's exact test), Q value = 5.8e-13

Table S332.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 8(5Q21.3) CNV 26 15 71
DEL PEAK 8(5Q21.3) WILD-TYPE 135 95 55

Figure S332.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MRNASEQ_CNMF'

P value = 3.05e-60 (Chi-square test), Q value = 2.4e-57

Table S333.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 8(5Q21.3) CNV 117 5 12 44 34 3 6
DEL PEAK 8(5Q21.3) WILD-TYPE 41 76 216 102 183 50 10

Figure S333.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 8(5q21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.25e-53 (Fisher's exact test), Q value = 2.6e-50

Table S334.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 8(5Q21.3) CNV 146 18 57
DEL PEAK 8(5Q21.3) WILD-TYPE 80 197 401

Figure S334.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MIRSEQ_CNMF'

P value = 1.28e-39 (Fisher's exact test), Q value = 9.9e-37

Table S335.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 8(5Q21.3) CNV 31 42 142
DEL PEAK 8(5Q21.3) WILD-TYPE 203 350 113

Figure S335.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 8(5q21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.67e-54 (Fisher's exact test), Q value = 1.3e-51

Table S336.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 8(5Q21.3) CNV 55 14 146
DEL PEAK 8(5Q21.3) WILD-TYPE 307 270 89

Figure S336.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.34e-42 (Fisher's exact test), Q value = 4.1e-39

Table S337.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 8(5Q21.3) CNV 22 7 108
DEL PEAK 8(5Q21.3) WILD-TYPE 191 172 70

Figure S337.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 8(5q21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.27e-39 (Fisher's exact test), Q value = 9.8e-37

Table S338.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 8(5Q21.3) CNV 12 16 96 13
DEL PEAK 8(5Q21.3) WILD-TYPE 109 106 46 172

Figure S338.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 9(6p25.3)' versus 'CN_CNMF'

P value = 2.64e-07 (Chi-square test), Q value = 0.00011

Table S339.  Gene #38: 'Del Peak 9(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 9(6P25.3) CNV 35 61 12 56 12
DEL PEAK 9(6P25.3) WILD-TYPE 321 151 59 185 42

Figure S339.  Get High-res Image Gene #38: 'Del Peak 9(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(6p25.3)' versus 'METHLYATION_CNMF'

P value = 8.62e-06 (Chi-square test), Q value = 0.0028

Table S340.  Gene #38: 'Del Peak 9(6p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 9(6P25.3) CNV 26 13 21 37 2 14
DEL PEAK 9(6P25.3) WILD-TYPE 79 138 78 81 36 82

Figure S340.  Get High-res Image Gene #38: 'Del Peak 9(6p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 9(6p25.3)' versus 'MRNASEQ_CNMF'

P value = 0.000205 (Chi-square test), Q value = 0.052

Table S341.  Gene #38: 'Del Peak 9(6p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 9(6P25.3) CNV 36 5 32 25 59 8 1
DEL PEAK 9(6P25.3) WILD-TYPE 122 76 196 121 158 45 15

Figure S341.  Get High-res Image Gene #38: 'Del Peak 9(6p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(6q15)' versus 'MRNA_CNMF'

P value = 2.42e-06 (Chi-square test), Q value = 0.00085

Table S342.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 10(6Q15) CNV 6 13 62 18 24 29 4 16
DEL PEAK 10(6Q15) WILD-TYPE 15 23 57 78 85 43 16 24

Figure S342.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 10(6q15)' versus 'CN_CNMF'

P value = 6.35e-28 (Chi-square test), Q value = 4.7e-25

Table S343.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 10(6Q15) CNV 76 124 20 49 37
DEL PEAK 10(6Q15) WILD-TYPE 280 88 51 192 17

Figure S343.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(6q15)' versus 'METHLYATION_CNMF'

P value = 8.08e-08 (Chi-square test), Q value = 3.5e-05

Table S344.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 10(6Q15) CNV 21 46 37 62 7 19
DEL PEAK 10(6Q15) WILD-TYPE 84 105 62 56 31 77

Figure S344.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(6q15)' versus 'MRNASEQ_CNMF'

P value = 1.35e-10 (Chi-square test), Q value = 7e-08

Table S345.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 10(6Q15) CNV 29 21 63 52 113 17 3
DEL PEAK 10(6Q15) WILD-TYPE 129 60 165 94 104 36 13

Figure S345.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(6q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000293 (Fisher's exact test), Q value = 0.071

Table S346.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 10(6Q15) CNV 54 66 178
DEL PEAK 10(6Q15) WILD-TYPE 172 149 280

Figure S346.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(6q15)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.04e-05 (Fisher's exact test), Q value = 0.015

Table S347.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 10(6Q15) CNV 150 86 58
DEL PEAK 10(6Q15) WILD-TYPE 212 198 177

Figure S347.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(6q15)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.04

Table S348.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 10(6Q15) CNV 42 55 28 63
DEL PEAK 10(6Q15) WILD-TYPE 79 67 114 122

Figure S348.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 11(6q27)' versus 'CN_CNMF'

P value = 3.77e-14 (Chi-square test), Q value = 2.3e-11

Table S349.  Gene #40: 'Del Peak 11(6q27)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 11(6Q27) CNV 78 106 19 83 34
DEL PEAK 11(6Q27) WILD-TYPE 278 106 52 158 20

Figure S349.  Get High-res Image Gene #40: 'Del Peak 11(6q27)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(6q27)' versus 'MRNASEQ_CNMF'

P value = 0.000224 (Chi-square test), Q value = 0.056

Table S350.  Gene #40: 'Del Peak 11(6q27)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 11(6Q27) CNV 56 25 54 55 99 16 4
DEL PEAK 11(6Q27) WILD-TYPE 102 56 174 91 118 37 12

Figure S350.  Get High-res Image Gene #40: 'Del Peak 11(6q27)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNA_CNMF'

P value = 0.00104 (Chi-square test), Q value = 0.22

Table S351.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 12(7P22.3) CNV 4 3 25 22 3 12 2 4
DEL PEAK 12(7P22.3) WILD-TYPE 17 33 94 74 106 60 18 36

Figure S351.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNA_CHIERARCHICAL'

P value = 7.95e-05 (Fisher's exact test), Q value = 0.022

Table S352.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 12(7P22.3) CNV 5 27 43
DEL PEAK 12(7P22.3) WILD-TYPE 117 98 223

Figure S352.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 12(7p22.3)' versus 'CN_CNMF'

P value = 8.24e-17 (Chi-square test), Q value = 5.4e-14

Table S353.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 12(7P22.3) CNV 10 44 2 60 5
DEL PEAK 12(7P22.3) WILD-TYPE 346 168 69 181 49

Figure S353.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(7p22.3)' versus 'METHLYATION_CNMF'

P value = 6.11e-07 (Chi-square test), Q value = 0.00024

Table S354.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 12(7P22.3) CNV 25 7 14 16 1 2
DEL PEAK 12(7P22.3) WILD-TYPE 80 144 85 102 37 94

Figure S354.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNASEQ_CNMF'

P value = 8.51e-08 (Chi-square test), Q value = 3.6e-05

Table S355.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 12(7P22.3) CNV 39 2 16 24 35 1 1
DEL PEAK 12(7P22.3) WILD-TYPE 119 79 212 122 182 52 15

Figure S355.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-09 (Fisher's exact test), Q value = 4.9e-07

Table S356.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 12(7P22.3) CNV 50 6 62
DEL PEAK 12(7P22.3) WILD-TYPE 176 209 396

Figure S356.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(7p22.3)' versus 'MIRSEQ_CNMF'

P value = 3.96e-11 (Fisher's exact test), Q value = 2.1e-08

Table S357.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 12(7P22.3) CNV 7 48 59
DEL PEAK 12(7P22.3) WILD-TYPE 227 344 196

Figure S357.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(7p22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.38e-10 (Fisher's exact test), Q value = 7.1e-08

Table S358.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 12(7P22.3) CNV 46 12 56
DEL PEAK 12(7P22.3) WILD-TYPE 316 272 179

Figure S358.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(7p22.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.87e-07 (Fisher's exact test), Q value = 0.00015

Table S359.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 12(7P22.3) CNV 23 4 34
DEL PEAK 12(7P22.3) WILD-TYPE 190 175 144

Figure S359.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(7p22.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000239 (Fisher's exact test), Q value = 0.06

Table S360.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 12(7P22.3) CNV 6 13 29 13
DEL PEAK 12(7P22.3) WILD-TYPE 115 109 113 172

Figure S360.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(7q36.1)' versus 'CN_CNMF'

P value = 1.23e-11 (Chi-square test), Q value = 6.8e-09

Table S361.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 13(7Q36.1) CNV 29 61 13 69 6
DEL PEAK 13(7Q36.1) WILD-TYPE 327 151 58 172 48

Figure S361.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(7q36.1)' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Chi-square test), Q value = 0.047

Table S362.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 13(7Q36.1) CNV 36 11 30 46 42 6 1
DEL PEAK 13(7Q36.1) WILD-TYPE 122 70 198 100 175 47 15

Figure S362.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(7q36.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000721 (Fisher's exact test), Q value = 0.16

Table S363.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 13(7Q36.1) CNV 52 23 97
DEL PEAK 13(7Q36.1) WILD-TYPE 174 192 361

Figure S363.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(7q36.1)' versus 'MIRSEQ_CNMF'

P value = 5.26e-08 (Fisher's exact test), Q value = 2.3e-05

Table S364.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 13(7Q36.1) CNV 23 69 77
DEL PEAK 13(7Q36.1) WILD-TYPE 211 323 178

Figure S364.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 13(7q36.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.6e-06 (Fisher's exact test), Q value = 0.00058

Table S365.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 13(7Q36.1) CNV 73 30 66
DEL PEAK 13(7Q36.1) WILD-TYPE 289 254 169

Figure S365.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(7q36.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.033

Table S366.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 13(7Q36.1) CNV 38 19 50
DEL PEAK 13(7Q36.1) WILD-TYPE 175 160 128

Figure S366.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNA_CNMF'

P value = 1.61e-09 (Chi-square test), Q value = 7.7e-07

Table S367.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 14(8P23.2) CNV 12 15 78 65 29 47 13 18
DEL PEAK 14(8P23.2) WILD-TYPE 9 21 41 31 80 25 7 22

Figure S367.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNA_CHIERARCHICAL'

P value = 9.89e-06 (Fisher's exact test), Q value = 0.0032

Table S368.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 14(8P23.2) CNV 47 86 144
DEL PEAK 14(8P23.2) WILD-TYPE 75 39 122

Figure S368.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'CN_CNMF'

P value = 1.09e-32 (Chi-square test), Q value = 8.3e-30

Table S369.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 14(8P23.2) CNV 115 145 15 172 42
DEL PEAK 14(8P23.2) WILD-TYPE 241 67 56 69 12

Figure S369.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(8p23.2)' versus 'METHLYATION_CNMF'

P value = 2.68e-10 (Chi-square test), Q value = 1.4e-07

Table S370.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 14(8P23.2) CNV 71 46 50 80 16 42
DEL PEAK 14(8P23.2) WILD-TYPE 34 105 49 38 22 54

Figure S370.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNASEQ_CNMF'

P value = 1.28e-16 (Chi-square test), Q value = 8.4e-14

Table S371.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 14(8P23.2) CNV 101 31 75 98 138 19 14
DEL PEAK 14(8P23.2) WILD-TYPE 57 50 153 48 79 34 2

Figure S371.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.97e-09 (Fisher's exact test), Q value = 1.4e-06

Table S372.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 14(8P23.2) CNV 151 80 245
DEL PEAK 14(8P23.2) WILD-TYPE 75 135 213

Figure S372.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'MIRSEQ_CNMF'

P value = 5.68e-06 (Fisher's exact test), Q value = 0.0019

Table S373.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 14(8P23.2) CNV 98 203 163
DEL PEAK 14(8P23.2) WILD-TYPE 136 189 92

Figure S373.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 14(8p23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.79e-12 (Fisher's exact test), Q value = 2.7e-09

Table S374.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 14(8P23.2) CNV 189 110 165
DEL PEAK 14(8P23.2) WILD-TYPE 173 174 70

Figure S374.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.49e-09 (Fisher's exact test), Q value = 7.1e-07

Table S375.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 14(8P23.2) CNV 114 62 121
DEL PEAK 14(8P23.2) WILD-TYPE 99 117 57

Figure S375.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 14(8p23.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.84e-07 (Fisher's exact test), Q value = 0.00019

Table S376.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 14(8P23.2) CNV 56 72 97 72
DEL PEAK 14(8P23.2) WILD-TYPE 65 50 45 113

Figure S376.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 15(8p11.21)' versus 'MRNA_CNMF'

P value = 0.000194 (Chi-square test), Q value = 0.049

Table S377.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 15(8P11.21) CNV 4 4 23 21 9 27 7 7
DEL PEAK 15(8P11.21) WILD-TYPE 17 32 96 75 100 45 13 33

Figure S377.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 15(8p11.21)' versus 'CN_CNMF'

P value = 1.73e-12 (Chi-square test), Q value = 1e-09

Table S378.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 15(8P11.21) CNV 43 49 6 79 0
DEL PEAK 15(8P11.21) WILD-TYPE 313 163 65 162 54

Figure S378.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(8p11.21)' versus 'MRNASEQ_CNMF'

P value = 8.59e-13 (Chi-square test), Q value = 5e-10

Table S379.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 15(8P11.21) CNV 32 8 23 59 35 7 7
DEL PEAK 15(8P11.21) WILD-TYPE 126 73 205 87 182 46 9

Figure S379.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 15(8p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000438 (Fisher's exact test), Q value = 0.1

Table S380.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 15(8P11.21) CNV 62 28 81
DEL PEAK 15(8P11.21) WILD-TYPE 164 187 377

Figure S380.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(8p11.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.26e-06 (Fisher's exact test), Q value = 0.0021

Table S381.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 15(8P11.21) CNV 72 32 66
DEL PEAK 15(8P11.21) WILD-TYPE 290 252 169

Figure S381.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(8p11.21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.89e-06 (Fisher's exact test), Q value = 0.00067

Table S382.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 15(8P11.21) CNV 50 15 50
DEL PEAK 15(8P11.21) WILD-TYPE 163 164 128

Figure S382.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 15(8p11.21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000275 (Fisher's exact test), Q value = 0.068

Table S383.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 15(8P11.21) CNV 13 25 45 32
DEL PEAK 15(8P11.21) WILD-TYPE 108 97 97 153

Figure S383.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MRNA_CNMF'

P value = 2e-06 (Chi-square test), Q value = 0.00071

Table S384.  Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 16(9P21.3) CNV 9 13 60 30 23 38 8 6
DEL PEAK 16(9P21.3) WILD-TYPE 12 23 59 66 86 34 12 34

Figure S384.  Get High-res Image Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 16(9p21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.013

Table S385.  Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 16(9P21.3) CNV 26 43 118
DEL PEAK 16(9P21.3) WILD-TYPE 96 82 148

Figure S385.  Get High-res Image Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'CN_CNMF'

P value = 4.89e-30 (Chi-square test), Q value = 3.7e-27

Table S386.  Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 16(9P21.3) CNV 47 119 15 117 17
DEL PEAK 16(9P21.3) WILD-TYPE 309 93 56 124 37

Figure S386.  Get High-res Image Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(9p21.3)' versus 'METHLYATION_CNMF'

P value = 9.03e-15 (Chi-square test), Q value = 5.6e-12

Table S387.  Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 16(9P21.3) CNV 40 18 41 63 7 15
DEL PEAK 16(9P21.3) WILD-TYPE 65 133 58 55 31 81

Figure S387.  Get High-res Image Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 9.52e-15 (Chi-square test), Q value = 5.9e-12

Table S388.  Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 16(9P21.3) CNV 52 15 45 70 107 6 7
DEL PEAK 16(9P21.3) WILD-TYPE 106 66 183 76 110 47 9

Figure S388.  Get High-res Image Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 16(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.58e-07 (Fisher's exact test), Q value = 1e-04

Table S389.  Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 16(9P21.3) CNV 86 40 176
DEL PEAK 16(9P21.3) WILD-TYPE 140 175 282

Figure S389.  Get High-res Image Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_CNMF'

P value = 4.02e-06 (Fisher's exact test), Q value = 0.0014

Table S390.  Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 16(9P21.3) CNV 51 134 109
DEL PEAK 16(9P21.3) WILD-TYPE 183 258 146

Figure S390.  Get High-res Image Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.15e-12 (Fisher's exact test), Q value = 2.3e-09

Table S391.  Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 16(9P21.3) CNV 146 49 99
DEL PEAK 16(9P21.3) WILD-TYPE 216 235 136

Figure S391.  Get High-res Image Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.12e-07 (Fisher's exact test), Q value = 4.7e-05

Table S392.  Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 16(9P21.3) CNV 73 28 74
DEL PEAK 16(9P21.3) WILD-TYPE 140 151 104

Figure S392.  Get High-res Image Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.91e-07 (Fisher's exact test), Q value = 7.8e-05

Table S393.  Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 16(9P21.3) CNV 24 51 62 38
DEL PEAK 16(9P21.3) WILD-TYPE 97 71 80 147

Figure S393.  Get High-res Image Gene #45: 'Del Peak 16(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 17(9q21.11)' versus 'MRNA_CHIERARCHICAL'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.0067

Table S394.  Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 17(9Q21.11) CNV 17 47 88
DEL PEAK 17(9Q21.11) WILD-TYPE 105 78 178

Figure S394.  Get High-res Image Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 17(9q21.11)' versus 'CN_CNMF'

P value = 5.55e-18 (Chi-square test), Q value = 3.8e-15

Table S395.  Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 17(9Q21.11) CNV 40 79 16 103 15
DEL PEAK 17(9Q21.11) WILD-TYPE 316 133 55 138 39

Figure S395.  Get High-res Image Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(9q21.11)' versus 'METHLYATION_CNMF'

P value = 1.43e-09 (Chi-square test), Q value = 6.9e-07

Table S396.  Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 17(9Q21.11) CNV 41 14 23 46 4 19
DEL PEAK 17(9Q21.11) WILD-TYPE 64 137 76 72 34 77

Figure S396.  Get High-res Image Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(9q21.11)' versus 'RPPA_CNMF'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0033

Table S397.  Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 17(9Q21.11) CNV 65 32 22
DEL PEAK 17(9Q21.11) WILD-TYPE 82 101 95

Figure S397.  Get High-res Image Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 17(9q21.11)' versus 'MRNASEQ_CNMF'

P value = 8.82e-09 (Chi-square test), Q value = 4.1e-06

Table S398.  Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 17(9Q21.11) CNV 60 10 38 47 76 6 7
DEL PEAK 17(9Q21.11) WILD-TYPE 98 71 190 99 141 47 9

Figure S398.  Get High-res Image Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(9q21.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.99e-07 (Fisher's exact test), Q value = 0.00037

Table S399.  Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 17(9Q21.11) CNV 82 32 130
DEL PEAK 17(9Q21.11) WILD-TYPE 144 183 328

Figure S399.  Get High-res Image Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(9q21.11)' versus 'MIRSEQ_CNMF'

P value = 1.41e-08 (Fisher's exact test), Q value = 6.4e-06

Table S400.  Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 17(9Q21.11) CNV 39 93 102
DEL PEAK 17(9Q21.11) WILD-TYPE 195 299 153

Figure S400.  Get High-res Image Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 17(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.33e-13 (Fisher's exact test), Q value = 5.5e-10

Table S401.  Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 17(9Q21.11) CNV 102 36 96
DEL PEAK 17(9Q21.11) WILD-TYPE 260 248 139

Figure S401.  Get High-res Image Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(9q21.11)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00043

Table S402.  Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 17(9Q21.11) CNV 50 24 66
DEL PEAK 17(9Q21.11) WILD-TYPE 163 155 112

Figure S402.  Get High-res Image Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 17(9q21.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.56e-09 (Fisher's exact test), Q value = 7.4e-07

Table S403.  Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 17(9Q21.11) CNV 21 33 62 24
DEL PEAK 17(9Q21.11) WILD-TYPE 100 89 80 161

Figure S403.  Get High-res Image Gene #46: 'Del Peak 17(9q21.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'MRNA_CNMF'

P value = 2.45e-05 (Chi-square test), Q value = 0.0076

Table S404.  Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 18(10Q23.31) CNV 7 7 35 46 21 20 7 3
DEL PEAK 18(10Q23.31) WILD-TYPE 14 29 84 50 88 52 13 37

Figure S404.  Get High-res Image Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 18(10q23.31)' versus 'MRNA_CHIERARCHICAL'

P value = 5.63e-05 (Fisher's exact test), Q value = 0.016

Table S405.  Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 18(10Q23.31) CNV 21 53 72
DEL PEAK 18(10Q23.31) WILD-TYPE 101 72 194

Figure S405.  Get High-res Image Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'CN_CNMF'

P value = 2.26e-22 (Chi-square test), Q value = 1.6e-19

Table S406.  Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 18(10Q23.31) CNV 45 69 17 124 15
DEL PEAK 18(10Q23.31) WILD-TYPE 311 143 54 117 39

Figure S406.  Get High-res Image Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(10q23.31)' versus 'METHLYATION_CNMF'

P value = 3.88e-12 (Chi-square test), Q value = 2.2e-09

Table S407.  Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 18(10Q23.31) CNV 58 24 27 44 7 15
DEL PEAK 18(10Q23.31) WILD-TYPE 47 127 72 74 31 81

Figure S407.  Get High-res Image Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(10q23.31)' versus 'RPPA_CNMF'

P value = 1.9e-07 (Fisher's exact test), Q value = 7.8e-05

Table S408.  Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 18(10Q23.31) CNV 67 30 19
DEL PEAK 18(10Q23.31) WILD-TYPE 80 103 98

Figure S408.  Get High-res Image Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 18(10q23.31)' versus 'RPPA_CHIERARCHICAL'

P value = 7.37e-05 (Fisher's exact test), Q value = 0.021

Table S409.  Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 18(10Q23.31) CNV 45 18 53
DEL PEAK 18(10Q23.31) WILD-TYPE 116 92 73

Figure S409.  Get High-res Image Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 5.35e-15 (Chi-square test), Q value = 3.3e-12

Table S410.  Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 18(10Q23.31) CNV 79 11 42 52 70 1 4
DEL PEAK 18(10Q23.31) WILD-TYPE 79 70 186 94 147 52 12

Figure S410.  Get High-res Image Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 18(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-10 (Fisher's exact test), Q value = 5.3e-08

Table S411.  Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 18(10Q23.31) CNV 101 34 124
DEL PEAK 18(10Q23.31) WILD-TYPE 125 181 334

Figure S411.  Get High-res Image Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'MIRSEQ_CNMF'

P value = 5.47e-09 (Fisher's exact test), Q value = 2.5e-06

Table S412.  Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 18(10Q23.31) CNV 49 92 111
DEL PEAK 18(10Q23.31) WILD-TYPE 185 300 144

Figure S412.  Get High-res Image Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 18(10q23.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.97e-09 (Fisher's exact test), Q value = 1.8e-06

Table S413.  Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 18(10Q23.31) CNV 97 53 102
DEL PEAK 18(10Q23.31) WILD-TYPE 265 231 133

Figure S413.  Get High-res Image Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.18e-08 (Fisher's exact test), Q value = 1.4e-05

Table S414.  Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 18(10Q23.31) CNV 51 31 79
DEL PEAK 18(10Q23.31) WILD-TYPE 162 148 99

Figure S414.  Get High-res Image Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 18(10q23.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.54e-10 (Fisher's exact test), Q value = 3.7e-07

Table S415.  Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 18(10Q23.31) CNV 26 37 69 29
DEL PEAK 18(10Q23.31) WILD-TYPE 95 85 73 156

Figure S415.  Get High-res Image Gene #47: 'Del Peak 18(10q23.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'MRNA_CNMF'

P value = 1.01e-08 (Chi-square test), Q value = 4.6e-06

Table S416.  Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 19(10Q26.3) CNV 8 8 37 53 16 21 6 4
DEL PEAK 19(10Q26.3) WILD-TYPE 13 28 82 43 93 51 14 36

Figure S416.  Get High-res Image Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 19(10q26.3)' versus 'MRNA_CHIERARCHICAL'

P value = 2.75e-07 (Fisher's exact test), Q value = 0.00011

Table S417.  Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 19(10Q26.3) CNV 19 59 75
DEL PEAK 19(10Q26.3) WILD-TYPE 103 66 191

Figure S417.  Get High-res Image Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'CN_CNMF'

P value = 5.72e-24 (Chi-square test), Q value = 4.2e-21

Table S418.  Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 19(10Q26.3) CNV 46 72 15 127 13
DEL PEAK 19(10Q26.3) WILD-TYPE 310 140 56 114 41

Figure S418.  Get High-res Image Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(10q26.3)' versus 'METHLYATION_CNMF'

P value = 3.41e-12 (Chi-square test), Q value = 1.9e-09

Table S419.  Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 19(10Q26.3) CNV 59 21 31 37 8 17
DEL PEAK 19(10Q26.3) WILD-TYPE 46 130 68 81 30 79

Figure S419.  Get High-res Image Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(10q26.3)' versus 'RPPA_CNMF'

P value = 3.06e-08 (Fisher's exact test), Q value = 1.4e-05

Table S420.  Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 19(10Q26.3) CNV 72 27 24
DEL PEAK 19(10Q26.3) WILD-TYPE 75 106 93

Figure S420.  Get High-res Image Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 19(10q26.3)' versus 'RPPA_CHIERARCHICAL'

P value = 8.25e-07 (Fisher's exact test), Q value = 0.00031

Table S421.  Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 19(10Q26.3) CNV 45 18 60
DEL PEAK 19(10Q26.3) WILD-TYPE 116 92 66

Figure S421.  Get High-res Image Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'MRNASEQ_CNMF'

P value = 1.9e-19 (Chi-square test), Q value = 1.3e-16

Table S422.  Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 19(10Q26.3) CNV 84 10 34 58 69 4 2
DEL PEAK 19(10Q26.3) WILD-TYPE 74 71 194 88 148 49 14

Figure S422.  Get High-res Image Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 19(10q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.02e-15 (Fisher's exact test), Q value = 1.9e-12

Table S423.  Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 19(10Q26.3) CNV 109 29 123
DEL PEAK 19(10Q26.3) WILD-TYPE 117 186 335

Figure S423.  Get High-res Image Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'MIRSEQ_CNMF'

P value = 7.81e-12 (Fisher's exact test), Q value = 4.3e-09

Table S424.  Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 19(10Q26.3) CNV 44 92 117
DEL PEAK 19(10Q26.3) WILD-TYPE 190 300 138

Figure S424.  Get High-res Image Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 19(10q26.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.48e-15 (Fisher's exact test), Q value = 2.2e-12

Table S425.  Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 19(10Q26.3) CNV 100 42 111
DEL PEAK 19(10Q26.3) WILD-TYPE 262 242 124

Figure S425.  Get High-res Image Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.91e-11 (Fisher's exact test), Q value = 2.6e-08

Table S426.  Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 19(10Q26.3) CNV 57 25 83
DEL PEAK 19(10Q26.3) WILD-TYPE 156 154 95

Figure S426.  Get High-res Image Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 19(10q26.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.02e-12 (Fisher's exact test), Q value = 1.2e-09

Table S427.  Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 19(10Q26.3) CNV 22 39 74 30
DEL PEAK 19(10Q26.3) WILD-TYPE 99 83 68 155

Figure S427.  Get High-res Image Gene #48: 'Del Peak 19(10q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'MRNA_CNMF'

P value = 3.55e-07 (Chi-square test), Q value = 0.00014

Table S428.  Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 20(11P15.5) CNV 3 8 32 46 14 32 7 9
DEL PEAK 20(11P15.5) WILD-TYPE 18 28 87 50 95 40 13 31

Figure S428.  Get High-res Image Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 20(11p15.5)' versus 'MRNA_CHIERARCHICAL'

P value = 2.1e-07 (Fisher's exact test), Q value = 8.6e-05

Table S429.  Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 20(11P15.5) CNV 26 62 63
DEL PEAK 20(11P15.5) WILD-TYPE 96 63 203

Figure S429.  Get High-res Image Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'CN_CNMF'

P value = 1.32e-36 (Chi-square test), Q value = 1e-33

Table S430.  Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 20(11P15.5) CNV 36 69 14 141 8
DEL PEAK 20(11P15.5) WILD-TYPE 320 143 57 100 46

Figure S430.  Get High-res Image Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 20(11p15.5)' versus 'METHLYATION_CNMF'

P value = 1.47e-12 (Chi-square test), Q value = 8.5e-10

Table S431.  Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 20(11P15.5) CNV 55 16 31 37 8 15
DEL PEAK 20(11P15.5) WILD-TYPE 50 135 68 81 30 81

Figure S431.  Get High-res Image Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 20(11p15.5)' versus 'RPPA_CNMF'

P value = 1.27e-09 (Fisher's exact test), Q value = 6.1e-07

Table S432.  Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 20(11P15.5) CNV 76 26 25
DEL PEAK 20(11P15.5) WILD-TYPE 71 107 92

Figure S432.  Get High-res Image Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 20(11p15.5)' versus 'RPPA_CHIERARCHICAL'

P value = 1.65e-06 (Fisher's exact test), Q value = 6e-04

Table S433.  Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 20(11P15.5) CNV 38 26 63
DEL PEAK 20(11P15.5) WILD-TYPE 123 84 63

Figure S433.  Get High-res Image Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'MRNASEQ_CNMF'

P value = 3.49e-18 (Chi-square test), Q value = 2.4e-15

Table S434.  Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 20(11P15.5) CNV 79 11 26 60 68 8 6
DEL PEAK 20(11P15.5) WILD-TYPE 79 70 202 86 149 45 10

Figure S434.  Get High-res Image Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 20(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.86e-16 (Fisher's exact test), Q value = 3.2e-13

Table S435.  Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 20(11P15.5) CNV 114 35 109
DEL PEAK 20(11P15.5) WILD-TYPE 112 180 349

Figure S435.  Get High-res Image Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'MIRSEQ_CNMF'

P value = 3.87e-15 (Fisher's exact test), Q value = 2.4e-12

Table S436.  Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 20(11P15.5) CNV 43 85 123
DEL PEAK 20(11P15.5) WILD-TYPE 191 307 132

Figure S436.  Get High-res Image Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 20(11p15.5)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.42e-16 (Fisher's exact test), Q value = 9.3e-14

Table S437.  Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 20(11P15.5) CNV 93 43 115
DEL PEAK 20(11P15.5) WILD-TYPE 269 241 120

Figure S437.  Get High-res Image Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.71e-14 (Fisher's exact test), Q value = 1.7e-11

Table S438.  Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 20(11P15.5) CNV 46 24 88
DEL PEAK 20(11P15.5) WILD-TYPE 167 155 90

Figure S438.  Get High-res Image Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 20(11p15.5)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.09e-10 (Fisher's exact test), Q value = 4e-07

Table S439.  Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 20(11P15.5) CNV 24 35 69 30
DEL PEAK 20(11P15.5) WILD-TYPE 97 87 73 155

Figure S439.  Get High-res Image Gene #49: 'Del Peak 20(11p15.5)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 21(11q13.1)' versus 'CN_CNMF'

P value = 5.93e-19 (Chi-square test), Q value = 4.1e-16

Table S440.  Gene #50: 'Del Peak 21(11q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 21(11Q13.1) CNV 32 89 21 47 8
DEL PEAK 21(11Q13.1) WILD-TYPE 324 123 50 194 46

Figure S440.  Get High-res Image Gene #50: 'Del Peak 21(11q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(11q13.1)' versus 'METHLYATION_CNMF'

P value = 6.11e-07 (Chi-square test), Q value = 0.00024

Table S441.  Gene #50: 'Del Peak 21(11q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 21(11Q13.1) CNV 18 21 29 43 6 8
DEL PEAK 21(11Q13.1) WILD-TYPE 87 130 70 75 32 88

Figure S441.  Get High-res Image Gene #50: 'Del Peak 21(11q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 21(11q13.1)' versus 'MRNASEQ_CNMF'

P value = 1.22e-09 (Chi-square test), Q value = 5.9e-07

Table S442.  Gene #50: 'Del Peak 21(11q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 21(11Q13.1) CNV 26 11 31 29 84 9 3
DEL PEAK 21(11Q13.1) WILD-TYPE 132 70 197 117 133 44 13

Figure S442.  Get High-res Image Gene #50: 'Del Peak 21(11q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 22(11q23.2)' versus 'MRNA_CNMF'

P value = 6.71e-08 (Chi-square test), Q value = 2.9e-05

Table S443.  Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 22(11Q23.2) CNV 12 21 88 37 36 37 11 22
DEL PEAK 22(11Q23.2) WILD-TYPE 9 15 31 59 73 35 9 18

Figure S443.  Get High-res Image Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 22(11q23.2)' versus 'CN_CNMF'

P value = 7.27e-43 (Chi-square test), Q value = 5.7e-40

Table S444.  Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 22(11Q23.2) CNV 100 189 33 120 19
DEL PEAK 22(11Q23.2) WILD-TYPE 256 23 38 121 35

Figure S444.  Get High-res Image Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(11q23.2)' versus 'METHLYATION_CNMF'

P value = 2.05e-13 (Chi-square test), Q value = 1.2e-10

Table S445.  Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 22(11Q23.2) CNV 41 54 63 89 17 30
DEL PEAK 22(11Q23.2) WILD-TYPE 64 97 36 29 21 66

Figure S445.  Get High-res Image Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 22(11q23.2)' versus 'MRNASEQ_CNMF'

P value = 2.17e-17 (Chi-square test), Q value = 1.4e-14

Table S446.  Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 22(11Q23.2) CNV 61 32 78 77 163 23 9
DEL PEAK 22(11Q23.2) WILD-TYPE 97 49 150 69 54 30 7

Figure S446.  Get High-res Image Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 22(11q23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000521 (Fisher's exact test), Q value = 0.12

Table S447.  Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 22(11Q23.2) CNV 92 97 254
DEL PEAK 22(11Q23.2) WILD-TYPE 134 118 204

Figure S447.  Get High-res Image Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 22(11q23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000137 (Fisher's exact test), Q value = 0.037

Table S448.  Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 22(11Q23.2) CNV 209 125 100
DEL PEAK 22(11Q23.2) WILD-TYPE 153 159 135

Figure S448.  Get High-res Image Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 22(11q23.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.071

Table S449.  Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 22(11Q23.2) CNV 54 77 53 82
DEL PEAK 22(11Q23.2) WILD-TYPE 67 45 89 103

Figure S449.  Get High-res Image Gene #51: 'Del Peak 22(11q23.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 23(11q25)' versus 'MRNA_CNMF'

P value = 0.00072 (Chi-square test), Q value = 0.16

Table S450.  Gene #52: 'Del Peak 23(11q25)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 23(11Q25) CNV 10 20 75 45 34 37 12 20
DEL PEAK 23(11Q25) WILD-TYPE 11 16 44 51 75 35 8 20

Figure S450.  Get High-res Image Gene #52: 'Del Peak 23(11q25)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 23(11q25)' versus 'CN_CNMF'

P value = 1.59e-40 (Chi-square test), Q value = 1.2e-37

Table S451.  Gene #52: 'Del Peak 23(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 23(11Q25) CNV 87 176 30 124 16
DEL PEAK 23(11Q25) WILD-TYPE 269 36 41 117 38

Figure S451.  Get High-res Image Gene #52: 'Del Peak 23(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(11q25)' versus 'METHLYATION_CNMF'

P value = 9.8e-10 (Chi-square test), Q value = 4.8e-07

Table S452.  Gene #52: 'Del Peak 23(11q25)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 23(11Q25) CNV 46 47 58 78 13 29
DEL PEAK 23(11Q25) WILD-TYPE 59 104 41 40 25 67

Figure S452.  Get High-res Image Gene #52: 'Del Peak 23(11q25)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 23(11q25)' versus 'MRNASEQ_CNMF'

P value = 4.69e-12 (Chi-square test), Q value = 2.6e-09

Table S453.  Gene #52: 'Del Peak 23(11q25)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 23(11Q25) CNV 73 30 68 70 145 23 7
DEL PEAK 23(11Q25) WILD-TYPE 85 51 160 76 72 30 9

Figure S453.  Get High-res Image Gene #52: 'Del Peak 23(11q25)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 24(12p13.1)' versus 'CN_CNMF'

P value = 0.00099 (Chi-square test), Q value = 0.21

Table S454.  Gene #53: 'Del Peak 24(12p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 24(12P13.1) CNV 43 42 10 59 6
DEL PEAK 24(12P13.1) WILD-TYPE 313 170 61 182 48

Figure S454.  Get High-res Image Gene #53: 'Del Peak 24(12p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(12p13.1)' versus 'MRNASEQ_CNMF'

P value = 0.000717 (Chi-square test), Q value = 0.16

Table S455.  Gene #53: 'Del Peak 24(12p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 24(12P13.1) CNV 39 12 26 38 35 4 3
DEL PEAK 24(12P13.1) WILD-TYPE 119 69 202 108 182 49 13

Figure S455.  Get High-res Image Gene #53: 'Del Peak 24(12p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 24(12p13.1)' versus 'MIRSEQ_CNMF'

P value = 8.03e-05 (Fisher's exact test), Q value = 0.023

Table S456.  Gene #53: 'Del Peak 24(12p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 24(12P13.1) CNV 30 56 67
DEL PEAK 24(12P13.1) WILD-TYPE 204 336 188

Figure S456.  Get High-res Image Gene #53: 'Del Peak 24(12p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 24(12p13.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.68e-06 (Fisher's exact test), Q value = 0.0028

Table S457.  Gene #53: 'Del Peak 24(12p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 24(12P13.1) CNV 60 30 63
DEL PEAK 24(12P13.1) WILD-TYPE 302 254 172

Figure S457.  Get High-res Image Gene #53: 'Del Peak 24(12p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'MRNA_CNMF'

P value = 3.42e-11 (Chi-square test), Q value = 1.8e-08

Table S458.  Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 25(12Q24.21) CNV 3 5 15 42 5 22 3 5
DEL PEAK 25(12Q24.21) WILD-TYPE 18 31 104 54 104 50 17 35

Figure S458.  Get High-res Image Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 25(12q24.21)' versus 'MRNA_CHIERARCHICAL'

P value = 2.7e-10 (Fisher's exact test), Q value = 1.4e-07

Table S459.  Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 25(12Q24.21) CNV 12 51 37
DEL PEAK 25(12Q24.21) WILD-TYPE 110 74 229

Figure S459.  Get High-res Image Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'CN_CNMF'

P value = 2.64e-15 (Chi-square test), Q value = 1.7e-12

Table S460.  Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 25(12Q24.21) CNV 38 31 16 90 5
DEL PEAK 25(12Q24.21) WILD-TYPE 318 181 55 151 49

Figure S460.  Get High-res Image Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(12q24.21)' versus 'METHLYATION_CNMF'

P value = 2.94e-14 (Chi-square test), Q value = 1.8e-11

Table S461.  Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 25(12Q24.21) CNV 49 15 15 17 1 14
DEL PEAK 25(12Q24.21) WILD-TYPE 56 136 84 101 37 82

Figure S461.  Get High-res Image Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(12q24.21)' versus 'RPPA_CNMF'

P value = 0.000209 (Fisher's exact test), Q value = 0.053

Table S462.  Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 25(12Q24.21) CNV 44 14 21
DEL PEAK 25(12Q24.21) WILD-TYPE 103 119 96

Figure S462.  Get High-res Image Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 25(12q24.21)' versus 'RPPA_CHIERARCHICAL'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00039

Table S463.  Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 25(12Q24.21) CNV 22 12 45
DEL PEAK 25(12Q24.21) WILD-TYPE 139 98 81

Figure S463.  Get High-res Image Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'MRNASEQ_CNMF'

P value = 4.05e-15 (Chi-square test), Q value = 2.5e-12

Table S464.  Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 25(12Q24.21) CNV 66 11 20 37 29 7 2
DEL PEAK 25(12Q24.21) WILD-TYPE 92 70 208 109 188 46 14

Figure S464.  Get High-res Image Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(12q24.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.99e-14 (Fisher's exact test), Q value = 1.2e-11

Table S465.  Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 25(12Q24.21) CNV 86 28 58
DEL PEAK 25(12Q24.21) WILD-TYPE 140 187 400

Figure S465.  Get High-res Image Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'MIRSEQ_CNMF'

P value = 1.17e-08 (Fisher's exact test), Q value = 5.3e-06

Table S466.  Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 25(12Q24.21) CNV 32 53 81
DEL PEAK 25(12Q24.21) WILD-TYPE 202 339 174

Figure S466.  Get High-res Image Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(12q24.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.27e-13 (Fisher's exact test), Q value = 1.9e-10

Table S467.  Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 25(12Q24.21) CNV 47 34 85
DEL PEAK 25(12Q24.21) WILD-TYPE 315 250 150

Figure S467.  Get High-res Image Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.19e-07 (Fisher's exact test), Q value = 5e-05

Table S468.  Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 25(12Q24.21) CNV 32 21 61
DEL PEAK 25(12Q24.21) WILD-TYPE 181 158 117

Figure S468.  Get High-res Image Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 25(12q24.21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.37e-07 (Fisher's exact test), Q value = 0.00024

Table S469.  Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 25(12Q24.21) CNV 19 21 52 22
DEL PEAK 25(12Q24.21) WILD-TYPE 102 101 90 163

Figure S469.  Get High-res Image Gene #54: 'Del Peak 25(12q24.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 26(13q14.2)' versus 'MRNA_CNMF'

P value = 6.7e-05 (Chi-square test), Q value = 0.019

Table S470.  Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 26(13Q14.2) CNV 8 12 70 56 34 39 9 13
DEL PEAK 26(13Q14.2) WILD-TYPE 13 24 49 40 75 33 11 27

Figure S470.  Get High-res Image Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 26(13q14.2)' versus 'MRNA_CHIERARCHICAL'

P value = 2.5e-05 (Fisher's exact test), Q value = 0.0077

Table S471.  Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 26(13Q14.2) CNV 38 75 128
DEL PEAK 26(13Q14.2) WILD-TYPE 84 50 138

Figure S471.  Get High-res Image Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 26(13q14.2)' versus 'CN_CNMF'

P value = 4.2e-27 (Chi-square test), Q value = 3.1e-24

Table S472.  Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 26(13Q14.2) CNV 78 129 44 140 34
DEL PEAK 26(13Q14.2) WILD-TYPE 278 83 27 101 20

Figure S472.  Get High-res Image Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(13q14.2)' versus 'METHLYATION_CNMF'

P value = 7.87e-08 (Chi-square test), Q value = 3.4e-05

Table S473.  Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 26(13Q14.2) CNV 64 46 54 62 9 33
DEL PEAK 26(13Q14.2) WILD-TYPE 41 105 45 56 29 63

Figure S473.  Get High-res Image Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(13q14.2)' versus 'MRNASEQ_CNMF'

P value = 4.8e-10 (Chi-square test), Q value = 2.4e-07

Table S474.  Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 26(13Q14.2) CNV 97 22 76 74 117 15 8
DEL PEAK 26(13Q14.2) WILD-TYPE 61 59 152 72 100 38 8

Figure S474.  Get High-res Image Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 26(13q14.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.41e-10 (Fisher's exact test), Q value = 3.7e-07

Table S475.  Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 26(13Q14.2) CNV 132 61 216
DEL PEAK 26(13Q14.2) WILD-TYPE 94 154 242

Figure S475.  Get High-res Image Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(13q14.2)' versus 'MIRSEQ_CNMF'

P value = 3.86e-10 (Fisher's exact test), Q value = 2e-07

Table S476.  Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 26(13Q14.2) CNV 69 182 150
DEL PEAK 26(13Q14.2) WILD-TYPE 165 210 105

Figure S476.  Get High-res Image Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 26(13q14.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-07 (Fisher's exact test), Q value = 4.7e-05

Table S477.  Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 26(13Q14.2) CNV 172 94 135
DEL PEAK 26(13Q14.2) WILD-TYPE 190 190 100

Figure S477.  Get High-res Image Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(13q14.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.05e-07 (Fisher's exact test), Q value = 8.4e-05

Table S478.  Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 26(13Q14.2) CNV 98 49 99
DEL PEAK 26(13Q14.2) WILD-TYPE 115 130 79

Figure S478.  Get High-res Image Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 26(13q14.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000164 (Fisher's exact test), Q value = 0.043

Table S479.  Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 26(13Q14.2) CNV 38 56 81 71
DEL PEAK 26(13Q14.2) WILD-TYPE 83 66 61 114

Figure S479.  Get High-res Image Gene #55: 'Del Peak 26(13q14.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'MRNA_CNMF'

P value = 2.41e-13 (Chi-square test), Q value = 1.4e-10

Table S480.  Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 27(14Q24.3) CNV 4 8 49 58 10 22 10 8
DEL PEAK 27(14Q24.3) WILD-TYPE 17 28 70 38 99 50 10 32

Figure S480.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 27(14q24.3)' versus 'MRNA_CHIERARCHICAL'

P value = 8.08e-09 (Fisher's exact test), Q value = 3.7e-06

Table S481.  Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 27(14Q24.3) CNV 26 69 74
DEL PEAK 27(14Q24.3) WILD-TYPE 96 56 192

Figure S481.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'CN_CNMF'

P value = 3.07e-40 (Chi-square test), Q value = 2.4e-37

Table S482.  Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 27(14Q24.3) CNV 39 73 14 154 21
DEL PEAK 27(14Q24.3) WILD-TYPE 317 139 57 87 33

Figure S482.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(14q24.3)' versus 'METHLYATION_CNMF'

P value = 6.06e-15 (Chi-square test), Q value = 3.8e-12

Table S483.  Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 27(14Q24.3) CNV 62 17 33 46 7 22
DEL PEAK 27(14Q24.3) WILD-TYPE 43 134 66 72 31 74

Figure S483.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 27(14q24.3)' versus 'RPPA_CNMF'

P value = 5.29e-07 (Fisher's exact test), Q value = 0.00021

Table S484.  Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 27(14Q24.3) CNV 74 29 31
DEL PEAK 27(14Q24.3) WILD-TYPE 73 104 86

Figure S484.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 27(14q24.3)' versus 'RPPA_CHIERARCHICAL'

P value = 5.53e-06 (Fisher's exact test), Q value = 0.0019

Table S485.  Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 27(14Q24.3) CNV 45 25 64
DEL PEAK 27(14Q24.3) WILD-TYPE 116 85 62

Figure S485.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'MRNASEQ_CNMF'

P value = 6.41e-29 (Chi-square test), Q value = 4.8e-26

Table S486.  Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 27(14Q24.3) CNV 98 12 27 47 94 5 8
DEL PEAK 27(14Q24.3) WILD-TYPE 60 69 201 99 123 48 8

Figure S486.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 27(14q24.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.14e-16 (Fisher's exact test), Q value = 7.5e-14

Table S487.  Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 27(14Q24.3) CNV 123 38 130
DEL PEAK 27(14Q24.3) WILD-TYPE 103 177 328

Figure S487.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'MIRSEQ_CNMF'

P value = 5.44e-18 (Fisher's exact test), Q value = 3.7e-15

Table S488.  Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 27(14Q24.3) CNV 51 91 138
DEL PEAK 27(14Q24.3) WILD-TYPE 183 301 117

Figure S488.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 27(14q24.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.52e-16 (Fisher's exact test), Q value = 9.9e-14

Table S489.  Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 27(14Q24.3) CNV 102 53 125
DEL PEAK 27(14Q24.3) WILD-TYPE 260 231 110

Figure S489.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.08e-15 (Fisher's exact test), Q value = 5e-12

Table S490.  Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 27(14Q24.3) CNV 59 30 99
DEL PEAK 27(14Q24.3) WILD-TYPE 154 149 79

Figure S490.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 27(14q24.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.29e-12 (Fisher's exact test), Q value = 1.9e-09

Table S491.  Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 27(14Q24.3) CNV 24 47 79 38
DEL PEAK 27(14Q24.3) WILD-TYPE 97 75 63 147

Figure S491.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'MRNA_CNMF'

P value = 4.93e-07 (Chi-square test), Q value = 0.00019

Table S492.  Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 28(15Q13.1) CNV 5 11 41 56 23 33 10 8
DEL PEAK 28(15Q13.1) WILD-TYPE 16 25 78 40 86 39 10 32

Figure S492.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 28(15q13.1)' versus 'MRNA_CHIERARCHICAL'

P value = 1.62e-07 (Fisher's exact test), Q value = 6.7e-05

Table S493.  Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 28(15Q13.1) CNV 25 68 94
DEL PEAK 28(15Q13.1) WILD-TYPE 97 57 172

Figure S493.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'CN_CNMF'

P value = 5.79e-34 (Chi-square test), Q value = 4.4e-31

Table S494.  Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 28(15Q13.1) CNV 53 65 36 153 14
DEL PEAK 28(15Q13.1) WILD-TYPE 303 147 35 88 40

Figure S494.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(15q13.1)' versus 'METHLYATION_CNMF'

P value = 2.35e-12 (Chi-square test), Q value = 1.3e-09

Table S495.  Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 28(15Q13.1) CNV 66 27 32 45 8 25
DEL PEAK 28(15Q13.1) WILD-TYPE 39 124 67 73 30 71

Figure S495.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 28(15q13.1)' versus 'RPPA_CNMF'

P value = 0.000193 (Fisher's exact test), Q value = 0.049

Table S496.  Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 28(15Q13.1) CNV 76 39 38
DEL PEAK 28(15Q13.1) WILD-TYPE 71 94 79

Figure S496.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 28(15q13.1)' versus 'RPPA_CHIERARCHICAL'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.0072

Table S497.  Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 28(15Q13.1) CNV 54 30 69
DEL PEAK 28(15Q13.1) WILD-TYPE 107 80 57

Figure S497.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'MRNASEQ_CNMF'

P value = 3.32e-18 (Chi-square test), Q value = 2.3e-15

Table S498.  Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 28(15Q13.1) CNV 96 13 52 63 73 5 7
DEL PEAK 28(15Q13.1) WILD-TYPE 62 68 176 83 144 48 9

Figure S498.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 28(15q13.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.26e-15 (Fisher's exact test), Q value = 1.4e-12

Table S499.  Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 28(15Q13.1) CNV 126 43 140
DEL PEAK 28(15Q13.1) WILD-TYPE 100 172 318

Figure S499.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'MIRSEQ_CNMF'

P value = 6.32e-19 (Fisher's exact test), Q value = 4.4e-16

Table S500.  Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 28(15Q13.1) CNV 47 110 145
DEL PEAK 28(15Q13.1) WILD-TYPE 187 282 110

Figure S500.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 28(15q13.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.96e-18 (Fisher's exact test), Q value = 1.3e-15

Table S501.  Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 28(15Q13.1) CNV 112 56 134
DEL PEAK 28(15Q13.1) WILD-TYPE 250 228 101

Figure S501.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.64e-17 (Fisher's exact test), Q value = 1.8e-14

Table S502.  Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 28(15Q13.1) CNV 72 23 99
DEL PEAK 28(15Q13.1) WILD-TYPE 141 156 79

Figure S502.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 28(15q13.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.17e-12 (Fisher's exact test), Q value = 2.9e-09

Table S503.  Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 28(15Q13.1) CNV 19 38 82 55
DEL PEAK 28(15Q13.1) WILD-TYPE 102 84 60 130

Figure S503.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'MRNA_CNMF'

P value = 9.32e-17 (Chi-square test), Q value = 6.2e-14

Table S504.  Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 29(16Q24.3) CNV 16 25 81 27 94 45 13 35
DEL PEAK 29(16Q24.3) WILD-TYPE 5 11 38 69 15 27 7 5

Figure S504.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 29(16q24.3)' versus 'MRNA_CHIERARCHICAL'

P value = 2.67e-14 (Fisher's exact test), Q value = 1.6e-11

Table S505.  Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 29(16Q24.3) CNV 96 45 195
DEL PEAK 29(16Q24.3) WILD-TYPE 26 80 71

Figure S505.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'CN_CNMF'

P value = 6.75e-15 (Chi-square test), Q value = 4.2e-12

Table S506.  Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 29(16Q24.3) CNV 252 143 58 103 44
DEL PEAK 29(16Q24.3) WILD-TYPE 104 69 13 138 10

Figure S506.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(16q24.3)' versus 'METHLYATION_CNMF'

P value = 1.14e-11 (Chi-square test), Q value = 6.3e-09

Table S507.  Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 29(16Q24.3) CNV 41 124 74 69 19 56
DEL PEAK 29(16Q24.3) WILD-TYPE 64 27 25 49 19 40

Figure S507.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 29(16q24.3)' versus 'RPPA_CNMF'

P value = 1.14e-09 (Fisher's exact test), Q value = 5.6e-07

Table S508.  Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 29(16Q24.3) CNV 63 103 84
DEL PEAK 29(16Q24.3) WILD-TYPE 84 30 33

Figure S508.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 29(16q24.3)' versus 'RPPA_CHIERARCHICAL'

P value = 3.45e-11 (Fisher's exact test), Q value = 1.9e-08

Table S509.  Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 29(16Q24.3) CNV 119 83 48
DEL PEAK 29(16Q24.3) WILD-TYPE 42 27 78

Figure S509.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'MRNASEQ_CNMF'

P value = 1.01e-30 (Chi-square test), Q value = 7.6e-28

Table S510.  Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 29(16Q24.3) CNV 45 61 196 85 135 45 13
DEL PEAK 29(16Q24.3) WILD-TYPE 113 20 32 61 82 8 3

Figure S510.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 29(16q24.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.89e-23 (Fisher's exact test), Q value = 5e-20

Table S511.  Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 29(16Q24.3) CNV 82 162 336
DEL PEAK 29(16Q24.3) WILD-TYPE 144 53 122

Figure S511.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'MIRSEQ_CNMF'

P value = 9.22e-15 (Fisher's exact test), Q value = 5.7e-12

Table S512.  Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 29(16Q24.3) CNV 168 288 112
DEL PEAK 29(16Q24.3) WILD-TYPE 66 104 143

Figure S512.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 29(16q24.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.49e-22 (Fisher's exact test), Q value = 6.1e-19

Table S513.  Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 29(16Q24.3) CNV 239 233 96
DEL PEAK 29(16Q24.3) WILD-TYPE 123 51 139

Figure S513.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.37e-13 (Fisher's exact test), Q value = 8.2e-11

Table S514.  Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 29(16Q24.3) CNV 149 139 72
DEL PEAK 29(16Q24.3) WILD-TYPE 64 40 106

Figure S514.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 29(16q24.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.13e-15 (Fisher's exact test), Q value = 7.3e-13

Table S515.  Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 29(16Q24.3) CNV 98 67 54 141
DEL PEAK 29(16Q24.3) WILD-TYPE 23 55 88 44

Figure S515.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 30(17p12)' versus 'MRNA_CNMF'

P value = 1.95e-11 (Chi-square test), Q value = 1.1e-08

Table S516.  Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 30(17P12) CNV 14 27 78 61 33 60 15 24
DEL PEAK 30(17P12) WILD-TYPE 7 9 41 35 76 12 5 16

Figure S516.  Get High-res Image Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 30(17p12)' versus 'CN_CNMF'

P value = 1.24e-23 (Chi-square test), Q value = 9e-21

Table S517.  Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 30(17P12) CNV 145 161 35 188 31
DEL PEAK 30(17P12) WILD-TYPE 211 51 36 53 23

Figure S517.  Get High-res Image Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(17p12)' versus 'METHLYATION_CNMF'

P value = 8.79e-08 (Chi-square test), Q value = 3.7e-05

Table S518.  Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 30(17P12) CNV 64 66 71 90 19 47
DEL PEAK 30(17P12) WILD-TYPE 41 85 28 28 19 49

Figure S518.  Get High-res Image Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 30(17p12)' versus 'RPPA_CNMF'

P value = 8.07e-05 (Fisher's exact test), Q value = 0.023

Table S519.  Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 30(17P12) CNV 109 67 65
DEL PEAK 30(17P12) WILD-TYPE 38 66 52

Figure S519.  Get High-res Image Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 30(17p12)' versus 'MRNASEQ_CNMF'

P value = 1.07e-15 (Chi-square test), Q value = 6.9e-13

Table S520.  Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 30(17P12) CNV 93 45 89 118 153 29 13
DEL PEAK 30(17P12) WILD-TYPE 65 36 139 28 64 24 3

Figure S520.  Get High-res Image Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(17p12)' versus 'MIRSEQ_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.063

Table S521.  Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 30(17P12) CNV 133 220 181
DEL PEAK 30(17P12) WILD-TYPE 101 172 74

Figure S521.  Get High-res Image Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 30(17p12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000127 (Fisher's exact test), Q value = 0.034

Table S522.  Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 30(17P12) CNV 219 149 166
DEL PEAK 30(17P12) WILD-TYPE 143 135 69

Figure S522.  Get High-res Image Gene #59: 'Del Peak 30(17p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'MRNA_CNMF'

P value = 1.97e-15 (Chi-square test), Q value = 1.3e-12

Table S523.  Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 31(17Q21.31) CNV 7 17 28 51 13 50 9 15
DEL PEAK 31(17Q21.31) WILD-TYPE 14 19 91 45 96 22 11 25

Figure S523.  Get High-res Image Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 31(17q21.31)' versus 'MRNA_CHIERARCHICAL'

P value = 2.29e-07 (Fisher's exact test), Q value = 9.3e-05

Table S524.  Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 31(17Q21.31) CNV 42 72 76
DEL PEAK 31(17Q21.31) WILD-TYPE 80 53 190

Figure S524.  Get High-res Image Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'CN_CNMF'

P value = 1.05e-23 (Chi-square test), Q value = 7.7e-21

Table S525.  Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 31(17Q21.31) CNV 79 67 17 149 10
DEL PEAK 31(17Q21.31) WILD-TYPE 277 145 54 92 44

Figure S525.  Get High-res Image Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(17q21.31)' versus 'METHLYATION_CNMF'

P value = 3.7e-13 (Chi-square test), Q value = 2.2e-10

Table S526.  Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 31(17Q21.31) CNV 63 18 36 36 11 29
DEL PEAK 31(17Q21.31) WILD-TYPE 42 133 63 82 27 67

Figure S526.  Get High-res Image Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 31(17q21.31)' versus 'RPPA_CNMF'

P value = 1.86e-11 (Fisher's exact test), Q value = 1e-08

Table S527.  Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 31(17Q21.31) CNV 87 25 44
DEL PEAK 31(17Q21.31) WILD-TYPE 60 108 73

Figure S527.  Get High-res Image Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 31(17q21.31)' versus 'RPPA_CHIERARCHICAL'

P value = 3.12e-11 (Fisher's exact test), Q value = 1.7e-08

Table S528.  Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 31(17Q21.31) CNV 42 33 81
DEL PEAK 31(17Q21.31) WILD-TYPE 119 77 45

Figure S528.  Get High-res Image Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'MRNASEQ_CNMF'

P value = 1.29e-32 (Chi-square test), Q value = 9.7e-30

Table S529.  Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 31(17Q21.31) CNV 80 22 27 103 56 17 6
DEL PEAK 31(17Q21.31) WILD-TYPE 78 59 201 43 161 36 10

Figure S529.  Get High-res Image Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(17q21.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.89e-17 (Fisher's exact test), Q value = 1.3e-14

Table S530.  Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 31(17Q21.31) CNV 132 68 111
DEL PEAK 31(17Q21.31) WILD-TYPE 94 147 347

Figure S530.  Get High-res Image Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'MIRSEQ_CNMF'

P value = 1.14e-12 (Fisher's exact test), Q value = 6.7e-10

Table S531.  Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 31(17Q21.31) CNV 69 102 137
DEL PEAK 31(17Q21.31) WILD-TYPE 165 290 118

Figure S531.  Get High-res Image Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 31(17q21.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.76e-11 (Fisher's exact test), Q value = 9.7e-09

Table S532.  Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 31(17Q21.31) CNV 110 72 126
DEL PEAK 31(17Q21.31) WILD-TYPE 252 212 109

Figure S532.  Get High-res Image Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.43e-10 (Fisher's exact test), Q value = 4.1e-07

Table S533.  Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 31(17Q21.31) CNV 69 39 96
DEL PEAK 31(17Q21.31) WILD-TYPE 144 140 82

Figure S533.  Get High-res Image Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 31(17q21.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.84e-06 (Fisher's exact test), Q value = 0.0026

Table S534.  Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 31(17Q21.31) CNV 38 40 76 50
DEL PEAK 31(17Q21.31) WILD-TYPE 83 82 66 135

Figure S534.  Get High-res Image Gene #60: 'Del Peak 31(17q21.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 32(18q23)' versus 'MRNA_CNMF'

P value = 0.000183 (Chi-square test), Q value = 0.047

Table S535.  Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 32(18Q23) CNV 6 13 38 37 18 37 6 9
DEL PEAK 32(18Q23) WILD-TYPE 15 23 81 59 91 35 14 31

Figure S535.  Get High-res Image Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 32(18q23)' versus 'CN_CNMF'

P value = 7.49e-15 (Chi-square test), Q value = 4.7e-12

Table S536.  Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 32(18Q23) CNV 61 87 25 115 14
DEL PEAK 32(18Q23) WILD-TYPE 295 125 46 126 40

Figure S536.  Get High-res Image Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(18q23)' versus 'METHLYATION_CNMF'

P value = 9.79e-08 (Chi-square test), Q value = 4.2e-05

Table S537.  Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 32(18Q23) CNV 43 29 50 48 9 20
DEL PEAK 32(18Q23) WILD-TYPE 62 122 49 70 29 76

Figure S537.  Get High-res Image Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 32(18q23)' versus 'MRNASEQ_CNMF'

P value = 4.31e-10 (Chi-square test), Q value = 2.2e-07

Table S538.  Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 32(18Q23) CNV 61 17 42 75 75 12 6
DEL PEAK 32(18Q23) WILD-TYPE 97 64 186 71 142 41 10

Figure S538.  Get High-res Image Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(18q23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000188 (Fisher's exact test), Q value = 0.048

Table S539.  Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 32(18Q23) CNV 93 49 146
DEL PEAK 32(18Q23) WILD-TYPE 133 166 312

Figure S539.  Get High-res Image Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(18q23)' versus 'MIRSEQ_CNMF'

P value = 0.000375 (Fisher's exact test), Q value = 0.09

Table S540.  Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 32(18Q23) CNV 60 120 107
DEL PEAK 32(18Q23) WILD-TYPE 174 272 148

Figure S540.  Get High-res Image Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 32(18q23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000143 (Fisher's exact test), Q value = 0.038

Table S541.  Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 32(18Q23) CNV 113 73 101
DEL PEAK 32(18Q23) WILD-TYPE 249 211 134

Figure S541.  Get High-res Image Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(18q23)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.044

Table S542.  Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 32(18Q23) CNV 65 38 74
DEL PEAK 32(18Q23) WILD-TYPE 148 141 104

Figure S542.  Get High-res Image Gene #61: 'Del Peak 32(18q23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 33(19p13.3)' versus 'MRNA_CNMF'

P value = 3.9e-11 (Chi-square test), Q value = 2.1e-08

Table S543.  Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 33(19P13.3) CNV 8 10 50 54 13 37 6 6
DEL PEAK 33(19P13.3) WILD-TYPE 13 26 69 42 96 35 14 34

Figure S543.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 33(19p13.3)' versus 'MRNA_CHIERARCHICAL'

P value = 1.45e-08 (Fisher's exact test), Q value = 6.6e-06

Table S544.  Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 33(19P13.3) CNV 20 65 99
DEL PEAK 33(19P13.3) WILD-TYPE 102 60 167

Figure S544.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 33(19p13.3)' versus 'CN_CNMF'

P value = 6.28e-47 (Chi-square test), Q value = 4.9e-44

Table S545.  Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 33(19P13.3) CNV 29 107 10 146 19
DEL PEAK 33(19P13.3) WILD-TYPE 327 105 61 95 35

Figure S545.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 33(19p13.3)' versus 'METHLYATION_CNMF'

P value = 6.89e-18 (Chi-square test), Q value = 4.6e-15

Table S546.  Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 33(19P13.3) CNV 55 11 27 58 5 24
DEL PEAK 33(19P13.3) WILD-TYPE 50 140 72 60 33 72

Figure S546.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 33(19p13.3)' versus 'RPPA_CNMF'

P value = 3.03e-06 (Fisher's exact test), Q value = 0.0011

Table S547.  Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 33(19P13.3) CNV 79 40 31
DEL PEAK 33(19P13.3) WILD-TYPE 68 93 86

Figure S547.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 33(19p13.3)' versus 'RPPA_CHIERARCHICAL'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.01

Table S548.  Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 33(19P13.3) CNV 51 31 68
DEL PEAK 33(19P13.3) WILD-TYPE 110 79 58

Figure S548.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 33(19p13.3)' versus 'MRNASEQ_CNMF'

P value = 6.91e-25 (Chi-square test), Q value = 5.1e-22

Table S549.  Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 33(19P13.3) CNV 84 14 24 67 94 7 10
DEL PEAK 33(19P13.3) WILD-TYPE 74 67 204 79 123 46 6

Figure S549.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 33(19p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.57e-11 (Fisher's exact test), Q value = 2.9e-08

Table S550.  Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 33(19P13.3) CNV 110 39 151
DEL PEAK 33(19P13.3) WILD-TYPE 116 176 307

Figure S550.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 9.67e-16 (Fisher's exact test), Q value = 6.2e-13

Table S551.  Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 33(19P13.3) CNV 47 111 137
DEL PEAK 33(19P13.3) WILD-TYPE 187 281 118

Figure S551.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 33(19p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.54e-17 (Fisher's exact test), Q value = 4.3e-14

Table S552.  Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 33(19P13.3) CNV 124 48 123
DEL PEAK 33(19P13.3) WILD-TYPE 238 236 112

Figure S552.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 33(19p13.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.5e-12 (Fisher's exact test), Q value = 4.2e-09

Table S553.  Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 33(19P13.3) CNV 59 34 95
DEL PEAK 33(19P13.3) WILD-TYPE 154 145 83

Figure S553.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 33(19p13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-10 (Fisher's exact test), Q value = 5.2e-08

Table S554.  Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 33(19P13.3) CNV 29 46 77 36
DEL PEAK 33(19P13.3) WILD-TYPE 92 76 65 149

Figure S554.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'MRNA_CNMF'

P value = 8.89e-07 (Chi-square test), Q value = 0.00034

Table S555.  Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 34(19Q13.32) CNV 4 7 22 24 7 29 1 3
DEL PEAK 34(19Q13.32) WILD-TYPE 17 29 97 72 102 43 19 37

Figure S555.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 34(19q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.0043

Table S556.  Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 34(19Q13.32) CNV 8 36 53
DEL PEAK 34(19Q13.32) WILD-TYPE 114 89 213

Figure S556.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'CN_CNMF'

P value = 7.77e-21 (Chi-square test), Q value = 5.5e-18

Table S557.  Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 34(19Q13.32) CNV 21 63 5 85 10
DEL PEAK 34(19Q13.32) WILD-TYPE 335 149 66 156 44

Figure S557.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 34(19q13.32)' versus 'METHLYATION_CNMF'

P value = 1.08e-10 (Chi-square test), Q value = 5.6e-08

Table S558.  Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 34(19Q13.32) CNV 40 7 21 36 5 13
DEL PEAK 34(19Q13.32) WILD-TYPE 65 144 78 82 33 83

Figure S558.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 34(19q13.32)' versus 'RPPA_CNMF'

P value = 0.000783 (Fisher's exact test), Q value = 0.17

Table S559.  Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 34(19Q13.32) CNV 44 20 15
DEL PEAK 34(19Q13.32) WILD-TYPE 103 113 102

Figure S559.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 34(19q13.32)' versus 'RPPA_CHIERARCHICAL'

P value = 4.95e-05 (Fisher's exact test), Q value = 0.015

Table S560.  Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 34(19Q13.32) CNV 27 11 41
DEL PEAK 34(19Q13.32) WILD-TYPE 134 99 85

Figure S560.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'MRNASEQ_CNMF'

P value = 1.34e-12 (Chi-square test), Q value = 7.8e-10

Table S561.  Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 34(19Q13.32) CNV 46 7 18 52 54 4 1
DEL PEAK 34(19Q13.32) WILD-TYPE 112 74 210 94 163 49 15

Figure S561.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 34(19q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.73e-09 (Fisher's exact test), Q value = 1.3e-06

Table S562.  Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 34(19Q13.32) CNV 72 18 92
DEL PEAK 34(19Q13.32) WILD-TYPE 154 197 366

Figure S562.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'MIRSEQ_CNMF'

P value = 3.6e-10 (Fisher's exact test), Q value = 1.8e-07

Table S563.  Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 34(19Q13.32) CNV 24 66 85
DEL PEAK 34(19Q13.32) WILD-TYPE 210 326 170

Figure S563.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 34(19q13.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.78e-12 (Fisher's exact test), Q value = 3.2e-09

Table S564.  Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 34(19Q13.32) CNV 78 22 75
DEL PEAK 34(19Q13.32) WILD-TYPE 284 262 160

Figure S564.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.28e-12 (Fisher's exact test), Q value = 1.9e-09

Table S565.  Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 34(19Q13.32) CNV 46 10 63
DEL PEAK 34(19Q13.32) WILD-TYPE 167 169 115

Figure S565.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 34(19q13.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.96e-08 (Fisher's exact test), Q value = 8.8e-06

Table S566.  Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 34(19Q13.32) CNV 14 40 45 20
DEL PEAK 34(19Q13.32) WILD-TYPE 107 82 97 165

Figure S566.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 35(20p13)' versus 'MRNA_CNMF'

P value = 4.49e-06 (Chi-square test), Q value = 0.0015

Table S567.  Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 35(20P13) CNV 1 3 28 24 3 16 3 1
DEL PEAK 35(20P13) WILD-TYPE 20 33 91 72 106 56 17 39

Figure S567.  Get High-res Image Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(20p13)' versus 'MRNA_CHIERARCHICAL'

P value = 6.53e-05 (Fisher's exact test), Q value = 0.019

Table S568.  Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 35(20P13) CNV 7 32 40
DEL PEAK 35(20P13) WILD-TYPE 115 93 226

Figure S568.  Get High-res Image Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 35(20p13)' versus 'CN_CNMF'

P value = 1.45e-15 (Chi-square test), Q value = 9.3e-13

Table S569.  Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 35(20P13) CNV 17 32 5 69 15
DEL PEAK 35(20P13) WILD-TYPE 339 180 66 172 39

Figure S569.  Get High-res Image Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(20p13)' versus 'METHLYATION_CNMF'

P value = 4.16e-08 (Chi-square test), Q value = 1.8e-05

Table S570.  Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 35(20P13) CNV 31 5 14 20 3 7
DEL PEAK 35(20P13) WILD-TYPE 74 146 85 98 35 89

Figure S570.  Get High-res Image Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 35(20p13)' versus 'MRNASEQ_CNMF'

P value = 4.16e-13 (Chi-square test), Q value = 2.4e-10

Table S571.  Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 35(20P13) CNV 44 3 9 26 49 1 1
DEL PEAK 35(20P13) WILD-TYPE 114 78 219 120 168 52 15

Figure S571.  Get High-res Image Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(20p13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.32e-10 (Fisher's exact test), Q value = 6.9e-08

Table S572.  Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 215 458
DEL PEAK 35(20P13) CNV 61 10 62
DEL PEAK 35(20P13) WILD-TYPE 165 205 396

Figure S572.  Get High-res Image Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(20p13)' versus 'MIRSEQ_CNMF'

P value = 2.69e-12 (Fisher's exact test), Q value = 1.5e-09

Table S573.  Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 234 392 255
DEL PEAK 35(20P13) CNV 15 40 72
DEL PEAK 35(20P13) WILD-TYPE 219 352 183

Figure S573.  Get High-res Image Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 35(20p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.91e-13 (Fisher's exact test), Q value = 1.1e-10

Table S574.  Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 362 284 235
DEL PEAK 35(20P13) CNV 48 13 66
DEL PEAK 35(20P13) WILD-TYPE 314 271 169

Figure S574.  Get High-res Image Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 35(20p13)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.67e-09 (Fisher's exact test), Q value = 1.3e-06

Table S575.  Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 179 178
DEL PEAK 35(20P13) CNV 25 9 50
DEL PEAK 35(20P13) WILD-TYPE 188 170 128

Figure S575.  Get High-res Image Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 35(20p13)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.26e-09 (Fisher's exact test), Q value = 6.1e-07

Table S576.  Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 121 122 142 185
DEL PEAK 35(20P13) CNV 9 20 44 11
DEL PEAK 35(20P13) WILD-TYPE 112 102 98 174

Figure S576.  Get High-res Image Gene #64: 'Del Peak 35(20p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 36(21q11.2)' versus 'MRNA_CNMF'

P value = 0.000341 (Chi-square test), Q value = 0.082

Table S577.  Gene #65: 'Del Peak 36(21q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 36(21Q11.2) CNV 3 11 37 15 11 22 3 4
DEL PEAK 36(21Q11.2) WILD-TYPE 18 25 82 81 98 50 17 36

Figure S577.  Get High-res Image Gene #65: 'Del Peak 36(21q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 36(21q11.2)' versus 'CN_CNMF'

P value = 9.95e-13 (Chi-square test), Q value = 5.8e-10

Table S578.  Gene #65: 'Del Peak 36(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 356 212 71 241 54
DEL PEAK 36(21Q11.2) CNV 26 65 13 68 13
DEL PEAK 36(21Q11.2) WILD-TYPE 330 147 58 173 41

Figure S578.  Get High-res Image Gene #65: 'Del Peak 36(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 36(21q11.2)' versus 'METHLYATION_CNMF'

P value = 0.000524 (Chi-square test), Q value = 0.12

Table S579.  Gene #65: 'Del Peak 36(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 36(21Q11.2) CNV 19 20 23 37 7 9
DEL PEAK 36(21Q11.2) WILD-TYPE 86 131 76 81 31 87

Figure S579.  Get High-res Image Gene #65: 'Del Peak 36(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 36(21q11.2)' versus 'MRNASEQ_CNMF'

P value = 9.01e-06 (Chi-square test), Q value = 0.0029

Table S580.  Gene #65: 'Del Peak 36(21q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 158 81 228 146 217 53 16
DEL PEAK 36(21Q11.2) CNV 25 12 29 40 64 4 3
DEL PEAK 36(21Q11.2) WILD-TYPE 133 69 199 106 153 49 13

Figure S580.  Get High-res Image Gene #65: 'Del Peak 36(21q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 37(22q11.1)' versus 'METHLYATION_CNMF'

P value = 0.000679 (Chi-square test), Q value = 0.15

Table S581.  Gene #66: 'Del Peak 37(22q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 151 99 118 38 96
DEL PEAK 37(22Q11.1) CNV 43 55 48 64 8 31
DEL PEAK 37(22Q11.1) WILD-TYPE 62 96 51 54 30 65

Figure S581.  Get High-res Image Gene #66: 'Del Peak 37(22q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

Methods & Data
Input

  • Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

  • Molecular subtype file = BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 934

  • Number of copy number variation regions = 66

  • Number of molecular subtypes = 12

  • Exclude regions that fewer than K tumors have alterations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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