Correlation between copy number variation genes and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1ZP444M
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Uterine Corpus Endometrioid Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ZP444M
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 98 peak regions and 10 molecular subtypes across 492 patients, 581 significant findings detected with Q value < 0.25.

  • Amp Peak 1(1p35.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 2(1p34.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 3(1p22.3) cnvs correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 4(1q21.3) cnvs correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 5(1q22) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 6(1q42.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 7(2p23.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 8(2q13) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 9(3p25.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 10(3p14.1) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 11(3q26.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 12(3q26.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 13(4p16.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 14(5p15.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 15(5q35.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 16(6p24.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 17(6q25.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 18(7q22.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 19(8p11.21) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 20(8q24.21) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • Amp Peak 22(9p24.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 23(9q34.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 24(10q22.2) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 25(11p11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 26(11q13.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 27(12p12.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 28(12q13.11) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 29(12q13.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 30(13q34) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 31(14q24.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 32(14q32.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 33(16p11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 34(17q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 35(17q12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 36(17q25.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 37(18p11.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 38(18q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 39(19p13.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 40(19p13.11) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 41(19q12) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 42(20p13) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 43(20q11.21) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 44(20q13.12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 45(20q13.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 46(22q12.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 47(Xp11.23) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 48(Xq28) cnvs correlated to 'CN_CNMF'.

  • Del Peak 1(1p36.21) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 2(1p36.11) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 4(2p25.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 5(2q22.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 6(2q37.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 7(3p14.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 8(3q13.31) cnvs correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 9(4p16.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 10(4p15.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 11(4q22.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 12(4q34.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 13(5q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 14(6q26) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 15(7p22.3) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 16(7q11.22) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 17(7q31.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 18(7q36.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 19(8p23.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 20(9p23) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 21(9q34.11) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 22(10q23.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 23(11p15.5) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 24(11q14.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 25(11q25) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 26(12q23.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 27(12q24.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 28(13q11) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 29(13q14.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 30(14q13.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 31(15q15.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 32(15q23) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 33(16p13.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 34(16q21) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 35(16q23.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 36(17p13.3) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 37(17p12) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 38(17p11.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 39(17q11.2) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 40(17q21.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 41(18q23) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 42(19p13.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 43(19p12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 44(19q13.43) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 45(20p12.1) cnvs correlated to 'CN_CNMF'.

  • Del Peak 46(22q11.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 47(22q12.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 48(22q13.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 49(22q13.32) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 50(Xp21.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 98 regions and 10 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
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Chi-square 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 11(3q26 2) 0 (0%) 337 5.21e-06
(0.00246) 		4.74e-05
(0.0208) 		3.77e-61
(3.62e-58) 		1.95e-17
(1.56e-14) 		0.000353
(0.141) 		0.0154
(1.00) 		1.91e-25
(1.71e-22) 		3.67e-25
(3.27e-22) 		5.62e-26
(5.05e-23) 		3.4e-24
(3.02e-21)
Del Peak 21(9q34 11) 0 (0%) 370 0.000102
(0.0433) 		1.21e-05
(0.00561) 		5.04e-52
(4.79e-49) 		1.94e-11
(1.26e-08) 		0.000384
(0.153) 		0.0316
(1.00) 		1.13e-17
(9.11e-15) 		4.84e-24
(4.28e-21) 		5.09e-18
(4.14e-15) 		1.85e-16
(1.43e-13)
Del Peak 42(19p13 3) 0 (0%) 351 5.64e-07
(0.000282) 		4.25e-06
(0.00201) 		6e-78
(5.76e-75) 		7.23e-31
(6.61e-28) 		8.99e-06
(0.00419) 		0.0146
(1.00) 		4.05e-36
(3.77e-33) 		1.96e-36
(1.82e-33) 		2.67e-35
(2.48e-32) 		4.55e-37
(4.24e-34)
Amp Peak 12(3q26 2) 0 (0%) 348 2.42e-05
(0.0108) 		0.000168
(0.07) 		8.96e-60
(8.59e-57) 		8.25e-19
(6.89e-16) 		0.0015
(0.535) 		0.0249
(1.00) 		1.89e-25
(1.69e-22) 		7.53e-26
(6.75e-23) 		1.1e-23
(9.73e-21) 		9.82e-25
(8.74e-22)
Amp Peak 16(6p24 2) 0 (0%) 391 0.00043
(0.171) 		0.00524
(1.00) 		1.36e-39
(1.27e-36) 		2.35e-11
(1.52e-08) 		0.000177
(0.0734) 		0.059
(1.00) 		6.92e-16
(5.28e-13) 		1.49e-14
(1.1e-11) 		1.26e-16
(9.74e-14) 		4.77e-15
(3.57e-12)
Amp Peak 21(8q24 21) 0 (0%) 296 0.00043
(0.171) 		0.00524
(1.00) 		8.36e-35
(7.74e-32) 		1.24e-05
(0.00568) 		7.26e-07
(0.00036) 		0.141
(1.00) 		1.82e-08
(1e-05) 		1.7e-11
(1.11e-08) 		6.82e-13
(4.75e-10) 		1.25e-11
(8.3e-09)
Amp Peak 36(17q25 1) 0 (0%) 402 0.000566
(0.219) 		0.000109
(0.0458) 		4.44e-41
(4.16e-38) 		1.36e-11
(8.95e-09) 		0.00741
(1.00) 		0.193
(1.00) 		2.59e-12
(1.76e-09) 		3.88e-13
(2.73e-10) 		5.61e-17
(4.43e-14) 		7.58e-18
(6.11e-15)
Amp Peak 39(19p13 2) 0 (0%) 408 0.000102
(0.0433) 		1.21e-05
(0.00561) 		2.95e-46
(2.78e-43) 		1.22e-09
(7.24e-07) 		0.15
(1.00) 		0.0408
(1.00) 		1.09e-18
(9.09e-16) 		1.76e-18
(1.45e-15) 		1.03e-18
(8.62e-16) 		1.45e-14
(1.07e-11)
Del Peak 37(17p12) 0 (0%) 371 0.000566
(0.219) 		0.000109
(0.0458) 		2.57e-58
(2.46e-55) 		8.75e-16
(6.66e-13) 		0.00125
(0.453) 		0.681
(1.00) 		2.64e-25
(2.35e-22) 		5.65e-29
(5.13e-26) 		1.12e-20
(9.55e-18) 		1.14e-18
(9.46e-16)
Del Peak 38(17p11 2) 0 (0%) 386 0.000235
(0.0967) 		5.66e-05
(0.0247) 		3.67e-52
(3.49e-49) 		8.82e-14
(6.33e-11) 		0.0247
(1.00) 		0.378
(1.00) 		1.28e-19
(1.08e-16) 		5.19e-24
(4.59e-21) 		1.15e-16
(8.91e-14) 		9.38e-14
(6.71e-11)
Del Peak 40(17q21 2) 0 (0%) 391 0.000102
(0.0433) 		1.21e-05
(0.00561) 		2.03e-48
(1.91e-45) 		1.41e-09
(8.25e-07) 		0.00327
(1.00) 		0.168
(1.00) 		1.38e-14
(1.02e-11) 		7.99e-19
(6.69e-16) 		1.7e-12
(1.17e-09) 		2.46e-11
(1.59e-08)
Del Peak 48(22q13 31) 0 (0%) 370 1.8e-05
(0.00821) 		2.4e-06
(0.00116) 		9.61e-55
(9.17e-52) 		4.79e-13
(3.36e-10) 		0.0018
(0.627) 		0.153
(1.00) 		8.88e-20
(7.51e-17) 		1.44e-23
(1.27e-20) 		4.73e-18
(3.85e-15) 		1.64e-18
(1.36e-15)
Del Peak 49(22q13 32) 0 (0%) 364 0.000102
(0.0433) 		1.21e-05
(0.00561) 		4.93e-53
(4.7e-50) 		2.04e-12
(1.39e-09) 		0.00148
(0.531) 		0.0786
(1.00) 		2.93e-18
(2.4e-15) 		1.21e-21
(1.04e-18) 		3.27e-17
(2.61e-14) 		7.13e-18
(5.76e-15)
Amp Peak 1(1p35 2) 0 (0%) 442 0.0191
(1.00) 		0.0435
(1.00) 		3.5e-20
(2.99e-17) 		4.77e-07
(0.000241) 		0.0001
(0.0426) 		0.267
(1.00) 		1.22e-09
(7.24e-07) 		8.4e-12
(5.6e-09) 		6.89e-08
(3.65e-05) 		2.68e-09
(1.54e-06)
Amp Peak 20(8q24 21) 0 (0%) 304 0.00236
(0.811) 		0.028
(1.00) 		1.54e-35
(1.43e-32) 		6.2e-07
(0.000309) 		8.75e-05
(0.0376) 		0.504
(1.00) 		3.35e-09
(1.93e-06) 		1.26e-11
(8.35e-09) 		3.45e-11
(2.21e-08) 		4.25e-12
(2.88e-09)
Amp Peak 26(11q13 2) 0 (0%) 424 0.000235
(0.0967) 		0.00101
(0.377) 		5.92e-22
(5.14e-19) 		0.000204
(0.0839) 		0.0148
(1.00) 		1
(1.00) 		9.44e-06
(0.00439) 		5.58e-08
(2.97e-05) 		1.11e-07
(5.82e-05) 		5.46e-07
(0.000273)
Amp Peak 40(19p13 11) 0 (0%) 409 0.000235
(0.0967) 		0.00101
(0.377) 		1.47e-45
(1.38e-42) 		5.98e-12
(4.01e-09) 		0.199
(1.00) 		0.309
(1.00) 		5e-17
(3.96e-14) 		5.37e-18
(4.35e-15) 		2.77e-18
(2.27e-15) 		3.22e-18
(2.63e-15)
Amp Peak 41(19q12) 0 (0%) 391 0.000566
(0.219) 		0.00261
(0.886) 		9.02e-49
(8.52e-46) 		5.85e-17
(4.62e-14) 		0.00289
(0.978) 		0.212
(1.00) 		2.87e-21
(2.47e-18) 		2.66e-20
(2.27e-17) 		1.15e-26
(1.04e-23) 		2.06e-24
(1.83e-21)
Amp Peak 43(20q11 21) 0 (0%) 362 0.000496
(0.194) 		0.000861
(0.324) 		6.65e-49
(6.3e-46) 		5.01e-12
(3.38e-09) 		0.00156
(0.546) 		0.205
(1.00) 		5.71e-16
(4.38e-13) 		1.02e-14
(7.54e-12) 		3.5e-19
(2.95e-16) 		2.62e-15
(1.98e-12)
Del Peak 15(7p22 3) 0 (0%) 424 0.0015
(0.535) 		0.000248
(0.101) 		4.17e-31
(3.82e-28) 		2.43e-10
(1.48e-07) 		0.0312
(1.00) 		0.0935
(1.00) 		5.12e-14
(3.7e-11) 		4.07e-15
(3.06e-12) 		1.35e-14
(9.99e-12) 		1.5e-13
(1.07e-10)
Del Peak 18(7q36 3) 0 (0%) 435 0.0882
(1.00) 		0.257
(1.00) 		9.35e-30
(8.53e-27) 		1.75e-10
(1.08e-07) 		0.0187
(1.00) 		0.000655
(0.25) 		1.29e-18
(1.07e-15) 		5.93e-16
(4.55e-13) 		6.2e-15
(4.62e-12) 		1.81e-15
(1.37e-12)
Del Peak 34(16q21) 0 (0%) 352 0.00197
(0.684) 		0.000451
(0.179) 		1.05e-56
(1e-53) 		2.95e-18
(2.41e-15) 		0.0797
(1.00) 		1
(1.00) 		9.4e-18
(7.56e-15) 		6.63e-16
(5.07e-13) 		1.85e-17
(1.48e-14) 		1.85e-18
(1.53e-15)
Del Peak 35(16q23 1) 0 (0%) 342 0.00942
(1.00) 		0.000168
(0.07) 		2.34e-57
(2.24e-54) 		2.43e-17
(1.94e-14) 		0.0275
(1.00) 		0.369
(1.00) 		7.07e-19
(5.93e-16) 		1.83e-14
(1.34e-11) 		1.7e-18
(1.4e-15) 		7.37e-21
(6.32e-18)
Del Peak 36(17p13 3) 0 (0%) 386 0.00197
(0.684) 		0.000451
(0.179) 		7.29e-49
(6.9e-46) 		2.59e-11
(1.67e-08) 		0.000824
(0.311) 		0.665
(1.00) 		7.12e-17
(5.6e-14) 		1.58e-19
(1.34e-16) 		1.4e-15
(1.06e-12) 		1.99e-12
(1.36e-09)
Del Peak 39(17q11 2) 0 (0%) 396 0.0015
(0.535) 		0.000248
(0.101) 		6.26e-44
(5.88e-41) 		1.13e-07
(5.92e-05) 		0.013
(1.00) 		0.647
(1.00) 		2.47e-14
(1.8e-11) 		4.51e-17
(3.58e-14) 		2.74e-10
(1.66e-07) 		5.88e-10
(3.53e-07)
Del Peak 44(19q13 43) 0 (0%) 432 0.00197
(0.684) 		0.000451
(0.179) 		2.7e-23
(2.36e-20) 		2.56e-09
(1.48e-06) 		0.0782
(1.00) 		0.56
(1.00) 		1.28e-09
(7.58e-07) 		2.47e-09
(1.43e-06) 		1.68e-11
(1.1e-08) 		2.15e-14
(1.57e-11)
Del Peak 50(Xp21 1) 0 (0%) 411 0.0015
(0.535) 		0.000248
(0.101) 		4.23e-33
(3.9e-30) 		3.85e-09
(2.2e-06) 		0.00541
(1.00) 		0.244
(1.00) 		1.34e-10
(8.32e-08) 		3.09e-11
(1.99e-08) 		7.15e-12
(4.77e-09) 		4.61e-13
(3.24e-10)
Amp Peak 2(1p34 2) 0 (0%) 429 0.0015
(0.535) 		0.00379
(1.00) 		2.06e-28
(1.86e-25) 		1.36e-08
(7.6e-06) 		0.00924
(1.00) 		0.56
(1.00) 		7.8e-12
(5.2e-09) 		4.95e-14
(3.58e-11) 		1.27e-15
(9.63e-13) 		9.99e-16
(7.59e-13)
Amp Peak 7(2p23 2) 0 (0%) 381 0.465
(1.00) 		0.497
(1.00) 		5.04e-28
(4.56e-25) 		1.59e-10
(9.82e-08) 		0.00451
(1.00) 		0.558
(1.00) 		3.63e-06
(0.00173) 		5.02e-06
(0.00237) 		1.18e-09
(7.02e-07) 		3.91e-10
(2.36e-07)
Amp Peak 8(2q13) 0 (0%) 385 0.0698
(1.00) 		0.18
(1.00) 		2.77e-33
(2.56e-30) 		1.95e-12
(1.34e-09) 		0.0025
(0.853) 		0.153
(1.00) 		8.42e-11
(5.32e-08) 		1.53e-10
(9.48e-08) 		2.47e-18
(2.03e-15) 		1.16e-17
(9.33e-15)
Amp Peak 9(3p25 1) 0 (0%) 422 0.0403
(1.00) 		0.212
(1.00) 		4.11e-24
(3.64e-21) 		3.75e-06
(0.00178) 		0.075
(1.00) 		0.438
(1.00) 		6.49e-08
(3.45e-05) 		1.78e-08
(9.84e-06) 		1.06e-06
(0.000523) 		1.45e-06
(0.00071)
Amp Peak 13(4p16 3) 0 (0%) 447 0.00677
(1.00) 		0.0133
(1.00) 		1.64e-21
(1.41e-18) 		0.000532
(0.207) 		0.0898
(1.00) 		0.00285
(0.966) 		5.2e-10
(3.13e-07) 		6.95e-11
(4.4e-08) 		6.4e-09
(3.62e-06) 		5.5e-08
(2.94e-05)
Amp Peak 14(5p15 33) 0 (0%) 415 0.112
(1.00) 		0.16
(1.00) 		4.71e-32
(4.33e-29) 		3.4e-12
(2.3e-09) 		0.221
(1.00) 		0.612
(1.00) 		3.21e-14
(2.33e-11) 		2.37e-12
(1.61e-09) 		2.73e-13
(1.93e-10) 		7.09e-14
(5.11e-11)
Amp Peak 15(5q35 3) 0 (0%) 444 0.176
(1.00) 		0.0543
(1.00) 		8.67e-20
(7.35e-17) 		0.000639
(0.244) 		0.237
(1.00) 		0.731
(1.00) 		3.18e-07
(0.000162) 		6.98e-05
(0.0302) 		1.92e-07
(9.86e-05) 		2.69e-06
(0.00129)
Amp Peak 17(6q25 1) 0 (0%) 416 0.563
(1.00) 		0.539
(1.00) 		7.52e-22
(6.51e-19) 		2.64e-06
(0.00127) 		0.318
(1.00) 		0.0698
(1.00) 		4.97e-07
(0.000249) 		1.03e-08
(5.78e-06) 		8.25e-06
(0.00386) 		8.96e-06
(0.00419)
Amp Peak 22(9p24 2) 0 (0%) 435 0.0831
(1.00) 		0.0503
(1.00) 		2.87e-22
(2.5e-19) 		4.87e-07
(0.000244) 		0.000874
(0.328) 		0.00457
(1.00) 		2.97e-09
(1.71e-06) 		1.17e-10
(7.3e-08) 		6.29e-12
(4.21e-09) 		1.84e-11
(1.19e-08)
Amp Peak 23(9q34 3) 0 (0%) 460 0.208
(1.00) 		0.185
(1.00) 		3.79e-12
(2.57e-09) 		9.56e-05
(0.0408) 		0.336
(1.00) 		0.507
(1.00) 		2.14e-05
(0.00969) 		3.98e-06
(0.00189) 		0.000604
(0.231) 		0.00012
(0.0501)
Amp Peak 25(11p11 2) 0 (0%) 447 0.00677
(1.00) 		0.00103
(0.378) 		1.32e-16
(1.02e-13) 		5.97e-05
(0.026) 		0.0122
(1.00) 		0.789
(1.00) 		2.37e-05
(0.0106) 		9.28e-05
(0.0397) 		1.16e-07
(6.05e-05) 		3.31e-06
(0.00158)
Amp Peak 27(12p12 1) 0 (0%) 411 0.541
(1.00) 		0.407
(1.00) 		5.1e-15
(3.81e-12) 		1.13e-07
(5.9e-05) 		0.536
(1.00) 		0.659
(1.00) 		4.17e-05
(0.0183) 		2.11e-05
(0.00958) 		8.04e-08
(4.23e-05) 		1.05e-09
(6.27e-07)
Amp Peak 28(12q13 11) 0 (0%) 413 0.32
(1.00) 		0.342
(1.00) 		6.74e-17
(5.3e-14) 		3.67e-08
(2e-05) 		0.449
(1.00) 		0.157
(1.00) 		2.19e-06
(0.00106) 		1.95e-06
(0.000952) 		1.61e-08
(8.95e-06) 		4.08e-09
(2.32e-06)
Amp Peak 29(12q13 2) 0 (0%) 405 0.155
(1.00) 		0.335
(1.00) 		1.75e-17
(1.4e-14) 		1.94e-07
(9.9e-05) 		0.315
(1.00) 		0.36
(1.00) 		1.66e-08
(9.19e-06) 		6.54e-08
(3.46e-05) 		2.24e-08
(1.23e-05) 		1.83e-10
(1.12e-07)
Amp Peak 30(13q34) 0 (0%) 443 0.176
(1.00) 		0.371
(1.00) 		4.18e-20
(3.56e-17) 		1.98e-06
(0.000962) 		0.241
(1.00) 		0.0546
(1.00) 		8.41e-12
(5.6e-09) 		1.37e-07
(7.1e-05) 		4.78e-11
(3.04e-08) 		2.36e-10
(1.44e-07)
Amp Peak 31(14q24 3) 0 (0%) 436 0.112
(1.00) 		0.0414
(1.00) 		6.04e-18
(4.89e-15) 		1.7e-05
(0.00777) 		0.153
(1.00) 		0.393
(1.00) 		4.85e-08
(2.61e-05) 		1.14e-10
(7.17e-08) 		3.83e-08
(2.07e-05) 		1.56e-08
(8.66e-06)
Amp Peak 32(14q32 33) 0 (0%) 422 0.491
(1.00) 		0.407
(1.00) 		4.26e-22
(3.7e-19) 		1.04e-06
(0.000515) 		0.426
(1.00) 		0.789
(1.00) 		3.54e-05
(0.0156) 		4.77e-08
(2.58e-05) 		3.19e-08
(1.74e-05) 		2.09e-09
(1.21e-06)
Amp Peak 33(16p11 2) 0 (0%) 437 0.0191
(1.00) 		0.00403
(1.00) 		5.49e-21
(4.71e-18) 		3.26e-05
(0.0145) 		0.138
(1.00) 		0.126
(1.00) 		1.31e-09
(7.71e-07) 		1.78e-09
(1.04e-06) 		4.87e-10
(2.93e-07) 		3.63e-09
(2.08e-06)
Amp Peak 34(17q11 2) 0 (0%) 429 0.0191
(1.00) 		0.0435
(1.00) 		1.72e-26
(1.55e-23) 		2.13e-11
(1.38e-08) 		0.0201
(1.00) 		0.0052
(1.00) 		1.25e-10
(7.81e-08) 		4.81e-10
(2.9e-07) 		2.32e-16
(1.79e-13) 		1.28e-12
(8.88e-10)
Amp Peak 35(17q12) 0 (0%) 428 0.193
(1.00) 		0.0648
(1.00) 		5.56e-23
(4.86e-20) 		1.42e-12
(9.8e-10) 		0.0111
(1.00) 		0.438
(1.00) 		3.77e-13
(2.65e-10) 		2.74e-10
(1.66e-07) 		6.27e-16
(4.8e-13) 		8.88e-17
(6.94e-14)
Amp Peak 37(18p11 31) 0 (0%) 411 0.0244
(1.00) 		0.128
(1.00) 		2.43e-33
(2.25e-30) 		5.53e-12
(3.71e-09) 		0.0101
(1.00) 		0.0197
(1.00) 		1.45e-11
(9.5e-09) 		1.9e-13
(1.35e-10) 		1.28e-17
(1.02e-14) 		3.02e-19
(2.54e-16)
Amp Peak 38(18q11 2) 0 (0%) 430 0.193
(1.00) 		0.0648
(1.00) 		4.94e-27
(4.46e-24) 		3.19e-10
(1.93e-07) 		0.156
(1.00) 		0.0444
(1.00) 		1.17e-07
(6.09e-05) 		4.53e-08
(2.45e-05) 		2.27e-14
(1.66e-11) 		9.48e-17
(7.39e-14)
Amp Peak 42(20p13) 0 (0%) 388 0.0191
(1.00) 		0.0435
(1.00) 		1.63e-33
(1.51e-30) 		1.8e-09
(1.05e-06) 		0.0828
(1.00) 		0.386
(1.00) 		3.74e-11
(2.39e-08) 		6.9e-11
(4.38e-08) 		1.52e-12
(1.05e-09) 		1.15e-10
(7.21e-08)
Amp Peak 44(20q13 12) 0 (0%) 356 0.0227
(1.00) 		0.00379
(1.00) 		2.71e-49
(2.57e-46) 		1.81e-13
(1.29e-10) 		0.00478
(1.00) 		0.105
(1.00) 		3.32e-15
(2.5e-12) 		5.03e-15
(3.76e-12) 		5.09e-18
(4.14e-15) 		9.74e-15
(7.23e-12)
Amp Peak 45(20q13 33) 0 (0%) 358 0.00538
(1.00) 		0.0108
(1.00) 		1.54e-46
(1.45e-43) 		1.43e-10
(8.84e-08) 		0.0674
(1.00) 		0.686
(1.00) 		5.7e-13
(3.99e-10) 		8.5e-14
(6.12e-11) 		5.18e-17
(4.1e-14) 		8.14e-13
(5.66e-10)
Amp Peak 46(22q12 2) 0 (0%) 438 0.0591
(1.00) 		0.133
(1.00) 		2.31e-18
(1.89e-15) 		1.88e-14
(1.38e-11) 		0.181
(1.00) 		0.0546
(1.00) 		6.35e-13
(4.43e-10) 		8.42e-11
(5.32e-08) 		1.93e-19
(1.63e-16) 		7.32e-18
(5.91e-15)
Del Peak 1(1p36 21) 0 (0%) 427 0.00538
(1.00) 		0.0108
(1.00) 		1.79e-23
(1.57e-20) 		3.67e-07
(0.000186) 		0.00518
(1.00) 		0.267
(1.00) 		1.55e-11
(1.02e-08) 		7.33e-09
(4.13e-06) 		5.45e-09
(3.08e-06) 		1.53e-10
(9.46e-08)
Del Peak 2(1p36 11) 0 (0%) 414 0.0729
(1.00) 		0.0133
(1.00) 		9.91e-33
(9.11e-30) 		6.98e-11
(4.42e-08) 		0.0339
(1.00) 		0.393
(1.00) 		1.96e-12
(1.34e-09) 		3.18e-11
(2.04e-08) 		1.66e-14
(1.22e-11) 		8.64e-16
(6.58e-13)
Del Peak 5(2q22 1) 0 (0%) 448 0.0191
(1.00) 		0.00403
(1.00) 		2.7e-20
(2.3e-17) 		0.000179
(0.0743) 		0.0907
(1.00) 		0.0831
(1.00) 		1.55e-08
(8.63e-06) 		7.77e-08
(4.1e-05) 		1.62e-07
(8.38e-05) 		2.01e-05
(0.00916)
Del Peak 6(2q37 3) 0 (0%) 443 7.94e-17
(6.22e-14) 		4.56e-05
(0.02) 		0.276
(1.00) 		0.507
(1.00) 		1.36e-05
(0.00624) 		1.43e-06
(0.000702) 		0.000248
(0.101) 		0.000461
(0.181)
Del Peak 7(3p14 2) 0 (0%) 423 0.00677
(1.00) 		0.0133
(1.00) 		5.91e-31
(5.41e-28) 		1.22e-09
(7.23e-07) 		0.000952
(0.356) 		0.0197
(1.00) 		3.77e-15
(2.83e-12) 		1.8e-14
(1.32e-11) 		1.39e-13
(9.97e-11) 		1.98e-12
(1.35e-09)
Del Peak 9(4p16 3) 0 (0%) 405 0.0227
(1.00) 		0.00379
(1.00) 		1.41e-30
(1.29e-27) 		1.74e-12
(1.2e-09) 		0.0096
(1.00) 		0.244
(1.00) 		1.57e-10
(9.7e-08) 		9.13e-11
(5.74e-08) 		4.73e-15
(3.54e-12) 		6.11e-13
(4.27e-10)
Del Peak 10(4p15 31) 0 (0%) 402 0.0227
(1.00) 		0.00379
(1.00) 		4.15e-35
(3.85e-32) 		9.13e-14
(6.54e-11) 		0.0203
(1.00) 		0.346
(1.00) 		3.81e-11
(2.43e-08) 		4.36e-11
(2.78e-08) 		1.18e-18
(9.81e-16) 		3.21e-16
(2.47e-13)
Del Peak 11(4q22 1) 0 (0%) 393 0.00538
(1.00) 		0.00101
(0.377) 		1.04e-46
(9.79e-44) 		2.05e-18
(1.69e-15) 		0.0252
(1.00) 		0.102
(1.00) 		1.1e-16
(8.6e-14) 		1.16e-18
(9.69e-16) 		2.6e-24
(2.31e-21) 		6.82e-24
(6.01e-21)
Del Peak 12(4q34 3) 0 (0%) 377 0.00538
(1.00) 		0.00101
(0.377) 		1.43e-51
(1.36e-48) 		2.7e-15
(2.04e-12) 		0.0599
(1.00) 		0.521
(1.00) 		1.31e-18
(1.09e-15) 		8.83e-20
(7.48e-17) 		1.45e-21
(1.25e-18) 		3.27e-23
(2.86e-20)
Del Peak 13(5q11 2) 0 (0%) 392 0.0227
(1.00) 		0.00379
(1.00) 		8.55e-49
(8.09e-46) 		1.18e-16
(9.2e-14) 		0.000858
(0.324) 		0.01
(1.00) 		7.39e-17
(5.8e-14) 		3.24e-17
(2.58e-14) 		3.5e-19
(2.95e-16) 		3.56e-18
(2.9e-15)
Del Peak 14(6q26) 0 (0%) 448 0.352
(1.00) 		0.133
(1.00) 		9.63e-15
(7.16e-12) 		5.19e-08
(2.78e-05) 		0.675
(1.00) 		0.301
(1.00) 		2.29e-06
(0.00111) 		7.75e-05
(0.0335) 		6.15e-08
(3.27e-05) 		1.36e-10
(8.46e-08)
Del Peak 16(7q11 22) 0 (0%) 453 3.24e-21
(2.79e-18) 		2.35e-07
(0.00012) 		0.0668
(1.00) 		0.00669
(1.00) 		4.89e-09
(2.77e-06) 		1.5e-09
(8.77e-07) 		2.32e-08
(1.27e-05) 		5.09e-08
(2.74e-05)
Del Peak 17(7q31 1) 0 (0%) 444 0.176
(1.00) 		0.0543
(1.00) 		5.75e-27
(5.19e-24) 		2.41e-09
(1.4e-06) 		0.0899
(1.00) 		0.0192
(1.00) 		3.26e-14
(2.36e-11) 		3.17e-13
(2.24e-10) 		1.27e-11
(8.43e-09) 		1.47e-11
(9.64e-09)
Del Peak 19(8p23 2) 0 (0%) 389 0.00677
(1.00) 		0.00103
(0.378) 		1.03e-40
(9.66e-38) 		1.24e-21
(1.07e-18) 		0.0469
(1.00) 		0.378
(1.00) 		6.45e-17
(5.08e-14) 		5.05e-19
(4.23e-16) 		3.02e-26
(2.71e-23) 		6.04e-29
(5.47e-26)
Del Peak 20(9p23) 0 (0%) 427 0.352
(1.00) 		0.133
(1.00) 		1.01e-22
(8.85e-20) 		1.84e-06
(0.000902) 		0.0369
(1.00) 		0.295
(1.00) 		1.93e-07
(9.9e-05) 		1.29e-09
(7.62e-07) 		8.17e-08
(4.3e-05) 		1.89e-06
(0.000923)
Del Peak 22(10q23 31) 0 (0%) 422 0.176
(1.00) 		0.0543
(1.00) 		1.2e-29
(1.09e-26) 		5.19e-08
(2.78e-05) 		0.116
(1.00) 		0.796
(1.00) 		3.39e-07
(0.000172) 		1.88e-07
(9.68e-05) 		1.78e-10
(1.09e-07) 		3.84e-09
(2.2e-06)
Del Peak 23(11p15 5) 0 (0%) 399 0.352
(1.00) 		0.133
(1.00) 		7.81e-40
(7.3e-37) 		3.91e-17
(3.1e-14) 		0.452
(1.00) 		0.309
(1.00) 		4.92e-14
(3.56e-11) 		4.77e-16
(3.67e-13) 		1.21e-16
(9.36e-14) 		8.65e-17
(6.78e-14)
Del Peak 24(11q14 1) 0 (0%) 429 7.36e-22
(6.38e-19) 		1.39e-09
(8.19e-07) 		0.328
(1.00) 		0.393
(1.00) 		2.82e-08
(1.54e-05) 		2.31e-10
(1.41e-07) 		2.34e-10
(1.43e-07) 		1.32e-11
(8.69e-09)
Del Peak 25(11q25) 0 (0%) 408 4.75e-28
(4.3e-25) 		1.41e-13
(1.01e-10) 		0.134
(1.00) 		0.804
(1.00) 		3.31e-08
(1.8e-05) 		5.43e-12
(3.66e-09) 		1.14e-12
(7.89e-10) 		1.84e-13
(1.31e-10)
Del Peak 26(12q23 1) 0 (0%) 444 2.41e-20
(2.06e-17) 		8.82e-11
(5.56e-08) 		0.0349
(1.00) 		0.00949
(1.00) 		3.97e-07
(0.000201) 		1.13e-07
(5.9e-05) 		6.08e-10
(3.64e-07) 		3.6e-13
(2.54e-10)
Del Peak 27(12q24 33) 0 (0%) 433 1.03e-25
(9.27e-23) 		2.32e-11
(1.5e-08) 		0.0355
(1.00) 		0.106
(1.00) 		1.07e-11
(7.07e-09) 		2.32e-09
(1.35e-06) 		6.67e-13
(4.65e-10) 		2.94e-14
(2.14e-11)
Del Peak 28(13q11) 0 (0%) 406 0.455
(1.00) 		0.0133
(1.00) 		1.94e-29
(1.76e-26) 		3.97e-09
(2.26e-06) 		0.162
(1.00) 		0.126
(1.00) 		4.78e-07
(0.000241) 		1.7e-11
(1.11e-08) 		1.01e-09
(6.03e-07) 		3.6e-09
(2.07e-06)
Del Peak 29(13q14 2) 0 (0%) 398 0.687
(1.00) 		0.0435
(1.00) 		2.43e-32
(2.23e-29) 		5.16e-08
(2.77e-05) 		0.0746
(1.00) 		0.102
(1.00) 		1.16e-06
(0.000574) 		9.57e-11
(6.01e-08) 		3.77e-08
(2.05e-05) 		1.02e-08
(5.7e-06)
Del Peak 30(14q13 1) 0 (0%) 430 0.0191
(1.00) 		0.00403
(1.00) 		1.28e-22
(1.12e-19) 		1.27e-10
(7.94e-08) 		0.0681
(1.00) 		0.106
(1.00) 		7.68e-09
(4.32e-06) 		1.63e-10
(1e-07) 		1.33e-09
(7.82e-07) 		6.18e-12
(4.14e-09)
Del Peak 31(15q15 1) 0 (0%) 368 0.0227
(1.00) 		0.00379
(1.00) 		1.37e-55
(1.31e-52) 		1.41e-18
(1.17e-15) 		0.00247
(0.846) 		0.205
(1.00) 		3.76e-17
(2.99e-14) 		8.64e-22
(7.47e-19) 		1.16e-23
(1.02e-20) 		2.75e-22
(2.4e-19)
Del Peak 32(15q23) 0 (0%) 392 0.00677
(1.00) 		0.00103
(0.378) 		7.28e-42
(6.83e-39) 		1.94e-18
(1.6e-15) 		0.104
(1.00) 		0.812
(1.00) 		1.46e-12
(1.01e-09) 		9.7e-15
(7.21e-12) 		1.26e-16
(9.74e-14) 		5.94e-18
(4.81e-15)
Del Peak 33(16p13 3) 0 (0%) 411 0.0015
(0.535) 		0.00379
(1.00) 		1.59e-37
(1.48e-34) 		1.53e-14
(1.12e-11) 		0.0547
(1.00) 		0.176
(1.00) 		8.49e-14
(6.12e-11) 		1.28e-11
(8.46e-09) 		4.79e-16
(3.68e-13) 		9.41e-17
(7.35e-14)
Del Peak 41(18q23) 0 (0%) 401 0.193
(1.00) 		0.504
(1.00) 		6.45e-34
(5.96e-31) 		4.64e-12
(3.13e-09) 		0.0427
(1.00) 		0.0354
(1.00) 		4.88e-11
(3.1e-08) 		2.72e-13
(1.93e-10) 		1.6e-12
(1.1e-09) 		4.5e-14
(3.26e-11)
Del Peak 43(19p12) 0 (0%) 443 1.3e-15
(9.89e-13) 		6.64e-07
(0.00033) 		0.21
(1.00) 		0.507
(1.00) 		2.14e-05
(0.00969) 		3.98e-06
(0.00189) 		3.04e-06
(0.00145) 		1.98e-06
(0.000962)
Del Peak 46(22q11 1) 0 (0%) 411 0.00677
(1.00) 		0.00103
(0.378) 		2.26e-29
(2.06e-26) 		0.000115
(0.0481) 		0.451
(1.00) 		0.796
(1.00) 		1.25e-07
(6.48e-05) 		1.85e-09
(1.08e-06) 		4.79e-07
(0.000241) 		5.37e-05
(0.0234)
Del Peak 47(22q12 1) 0 (0%) 405 0.00677
(1.00) 		0.00103
(0.378) 		1.54e-31
(1.41e-28) 		2.1e-05
(0.00955) 		0.267
(1.00) 		0.627
(1.00) 		4.79e-09
(2.72e-06) 		1.31e-11
(8.6e-09) 		1.24e-08
(6.95e-06) 		1.54e-07
(7.94e-05)
Amp Peak 10(3p14 1) 0 (0%) 436 0.86
(1.00) 		0.623
(1.00) 		7.51e-20
(6.38e-17) 		0.000802
(0.304) 		0.0521
(1.00) 		0.373
(1.00) 		3.18e-05
(0.0141) 		2.55e-05
(0.0114) 		0.000503
(0.197) 		0.000576
(0.221)
Amp Peak 19(8p11 21) 0 (0%) 346 0.00161
(0.562) 		0.0161
(1.00) 		1.7e-23
(1.5e-20) 		0.011
(1.00) 		0.00111
(0.402) 		0.719
(1.00) 		0.000553
(0.215) 		2.25e-05
(0.0101) 		6.37e-05
(0.0276) 		0.000301
(0.121)
Amp Peak 5(1q22) 0 (0%) 260 0.0177
(1.00) 		0.0229
(1.00) 		4.26e-15
(3.2e-12) 		0.000289
(0.116) 		0.132
(1.00) 		0.179
(1.00) 		0.0112
(1.00) 		0.0445
(1.00) 		3.55e-05
(0.0157) 		2.29e-05
(0.0103)
Del Peak 4(2p25 3) 0 (0%) 468 6.48e-09
(3.65e-06) 		0.00054
(0.21) 		0.268
(1.00) 		0.652
(1.00) 		8.8e-05
(0.0378) 		0.000323
(0.129) 		0.00149
(0.532) 		0.00247
(0.846)
Del Peak 8(3q13 31) 0 (0%) 464 0.0591
(1.00) 		0.133
(1.00) 		1.44e-12
(9.92e-10) 		0.00461
(1.00) 		0.0559
(1.00) 		1
(1.00) 		0.000246
(0.1) 		0.000744
(0.283) 		2.07e-06
(0.001) 		7.27e-06
(0.00341)
Amp Peak 3(1p22 3) 0 (0%) 411 0.0238
(1.00) 		0.115
(1.00) 		1.91e-08
(1.05e-05) 		0.0153
(1.00) 		0.737
(1.00) 		0.28
(1.00) 		0.00612
(1.00) 		0.0107
(1.00) 		5.96e-06
(0.0028) 		2.27e-05
(0.0102)
Amp Peak 4(1q21 3) 0 (0%) 272 0.0177
(1.00) 		0.0229
(1.00) 		1.7e-13
(1.21e-10) 		0.00951
(1.00) 		0.317
(1.00) 		0.135
(1.00) 		0.011
(1.00) 		0.0901
(1.00) 		2.19e-05
(0.00986) 		8.35e-05
(0.036)
Amp Peak 6(1q42 3) 0 (0%) 289 0.0221
(1.00) 		0.0243
(1.00) 		1.74e-07
(8.95e-05) 		0.132
(1.00) 		0.631
(1.00) 		0.0696
(1.00) 		0.0321
(1.00) 		0.0775
(1.00) 		0.00119
(0.431) 		0.359
(1.00)
Amp Peak 18(7q22 1) 0 (0%) 410 0.311
(1.00) 		0.558
(1.00) 		5.12e-20
(4.35e-17) 		0.00694
(1.00) 		0.74
(1.00) 		1
(1.00) 		0.00365
(1.00) 		0.0317
(1.00) 		0.00153
(0.537) 		0.00391
(1.00)
Amp Peak 24(10q22 2) 0 (0%) 360 0.00691
(1.00) 		0.116
(1.00) 		1.77e-08
(9.78e-06) 		0.389
(1.00) 		0.273
(1.00) 		0.414
(1.00) 		0.276
(1.00) 		0.0148
(1.00) 		0.325
(1.00) 		0.198
(1.00)
Amp Peak 47(Xp11 23) 0 (0%) 408 0.491
(1.00) 		0.407
(1.00) 		1.88e-25
(1.68e-22) 		0.00847
(1.00) 		0.783
(1.00) 		0.399
(1.00) 		0.155
(1.00) 		0.134
(1.00) 		0.000995
(0.371) 		0.00856
(1.00)
Amp Peak 48(Xq28) 0 (0%) 407 0.0698
(1.00) 		0.18
(1.00) 		4.98e-24
(4.4e-21) 		0.0269
(1.00) 		0.128
(1.00) 		0.535
(1.00) 		0.118
(1.00) 		0.202
(1.00) 		0.00332
(1.00) 		0.0421
(1.00)
Del Peak 45(20p12 1) 0 (0%) 462 1
(1.00) 		1
(1.00) 		0.000182
(0.0751) 		0.0794
(1.00) 		0.0877
(1.00) 		0.507
(1.00) 		0.101
(1.00) 		0.00996
(1.00) 		0.0183
(1.00) 		0.0258
(1.00)
Del Peak 3(1q43) 0 (0%) 483 0.00131
(0.472) 		0.174
(1.00) 		0.376
(1.00) 		0.00486
(1.00) 		0.0431
(1.00) 		0.172
(1.00) 		0.115
(1.00)
'Amp Peak 1(1p35.2)' versus 'CN_CNMF'

P value = 3.5e-20 (Chi-square test), Q value = 3e-17

Table S1.  Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 1(1P35.2) CNV 0 7 42 1 0
AMP PEAK 1(1P35.2) WILD-TYPE 290 33 97 16 6

Figure S1.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 1(1p35.2)' versus 'METHLYATION_CNMF'

P value = 4.77e-07 (Fisher's exact test), Q value = 0.00024

Table S2.  Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 1(1P35.2) CNV 31 4 5
AMP PEAK 1(1P35.2) WILD-TYPE 112 81 144

Figure S2.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 1(1p35.2)' versus 'RPPA_CNMF'

P value = 1e-04 (Chi-square test), Q value = 0.043

Table S3.  Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 1(1P35.2) CNV 1 10 2 0 0 2
AMP PEAK 1(1P35.2) WILD-TYPE 40 27 37 12 41 22

Figure S3.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 1(1p35.2)' versus 'MRNASEQ_CNMF'

P value = 1.22e-09 (Fisher's exact test), Q value = 7.2e-07

Table S4.  Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 1(1P35.2) CNV 27 1 1
AMP PEAK 1(1P35.2) WILD-TYPE 115 106 112

Figure S4.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 1(1p35.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.4e-12 (Fisher's exact test), Q value = 5.6e-09

Table S5.  Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 1(1P35.2) CNV 0 0 0 29
AMP PEAK 1(1P35.2) WILD-TYPE 65 92 65 111

Figure S5.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 1(1p35.2)' versus 'MIRSEQ_CNMF'

P value = 6.89e-08 (Fisher's exact test), Q value = 3.6e-05

Table S6.  Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 1(1P35.2) CNV 39 6 3
AMP PEAK 1(1P35.2) WILD-TYPE 168 138 129

Figure S6.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 1(1p35.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.68e-09 (Fisher's exact test), Q value = 1.5e-06

Table S7.  Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 1(1P35.2) CNV 5 2 2 39
AMP PEAK 1(1P35.2) WILD-TYPE 188 77 25 145

Figure S7.  Get High-res Image Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 2(1p34.2)' versus 'CN_CNMF'

P value = 2.06e-28 (Chi-square test), Q value = 1.9e-25

Table S8.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 2(1P34.2) CNV 1 5 56 1 0
AMP PEAK 2(1P34.2) WILD-TYPE 289 35 83 16 6

Figure S8.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(1p34.2)' versus 'METHLYATION_CNMF'

P value = 1.36e-08 (Fisher's exact test), Q value = 7.6e-06

Table S9.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 2(1P34.2) CNV 37 12 4
AMP PEAK 2(1P34.2) WILD-TYPE 106 73 145

Figure S9.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 2(1p34.2)' versus 'MRNASEQ_CNMF'

P value = 7.8e-12 (Fisher's exact test), Q value = 5.2e-09

Table S10.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 2(1P34.2) CNV 34 2 1
AMP PEAK 2(1P34.2) WILD-TYPE 108 105 112

Figure S10.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 2(1p34.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.95e-14 (Fisher's exact test), Q value = 3.6e-11

Table S11.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 2(1P34.2) CNV 0 0 1 36
AMP PEAK 2(1P34.2) WILD-TYPE 65 92 64 104

Figure S11.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(1p34.2)' versus 'MIRSEQ_CNMF'

P value = 1.27e-15 (Fisher's exact test), Q value = 9.6e-13

Table S12.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 2(1P34.2) CNV 55 4 2
AMP PEAK 2(1P34.2) WILD-TYPE 152 140 130

Figure S12.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 2(1p34.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.99e-16 (Fisher's exact test), Q value = 7.6e-13

Table S13.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 2(1P34.2) CNV 4 2 2 53
AMP PEAK 2(1P34.2) WILD-TYPE 189 77 25 131

Figure S13.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.91e-08 (Chi-square test), Q value = 1e-05

Table S14.  Gene #3: 'Amp Peak 3(1p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 3(1P22.3) CNV 30 5 39 2 5
AMP PEAK 3(1P22.3) WILD-TYPE 260 35 100 15 1

Figure S14.  Get High-res Image Gene #3: 'Amp Peak 3(1p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 5.96e-06 (Fisher's exact test), Q value = 0.0028

Table S15.  Gene #3: 'Amp Peak 3(1p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 3(1P22.3) CNV 46 7 27
AMP PEAK 3(1P22.3) WILD-TYPE 161 137 105

Figure S15.  Get High-res Image Gene #3: 'Amp Peak 3(1p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 2.27e-05 (Fisher's exact test), Q value = 0.01

Table S16.  Gene #3: 'Amp Peak 3(1p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 3(1P22.3) CNV 18 18 0 44
AMP PEAK 3(1P22.3) WILD-TYPE 175 61 27 140

Figure S16.  Get High-res Image Gene #3: 'Amp Peak 3(1p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 4(1q21.3)' versus 'CN_CNMF'

P value = 1.7e-13 (Chi-square test), Q value = 1.2e-10

Table S17.  Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 4(1Q21.3) CNV 87 26 88 13 6
AMP PEAK 4(1Q21.3) WILD-TYPE 203 14 51 4 0

Figure S17.  Get High-res Image Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(1q21.3)' versus 'MIRSEQ_CNMF'

P value = 2.19e-05 (Fisher's exact test), Q value = 0.0099

Table S18.  Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 4(1Q21.3) CNV 110 42 65
AMP PEAK 4(1Q21.3) WILD-TYPE 97 102 67

Figure S18.  Get High-res Image Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 4(1q21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.35e-05 (Fisher's exact test), Q value = 0.036

Table S19.  Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 4(1Q21.3) CNV 71 33 7 106
AMP PEAK 4(1Q21.3) WILD-TYPE 122 46 20 78

Figure S19.  Get High-res Image Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 5(1q22)' versus 'CN_CNMF'

P value = 4.26e-15 (Chi-square test), Q value = 3.2e-12

Table S20.  Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 5(1Q22) CNV 91 26 96 13 6
AMP PEAK 5(1Q22) WILD-TYPE 199 14 43 4 0

Figure S20.  Get High-res Image Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 5(1q22)' versus 'METHLYATION_CNMF'

P value = 0.000289 (Fisher's exact test), Q value = 0.12

Table S21.  Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 5(1Q22) CNV 84 34 54
AMP PEAK 5(1Q22) WILD-TYPE 59 51 95

Figure S21.  Get High-res Image Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 5(1q22)' versus 'MIRSEQ_CNMF'

P value = 3.55e-05 (Fisher's exact test), Q value = 0.016

Table S22.  Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 5(1Q22) CNV 115 46 68
AMP PEAK 5(1Q22) WILD-TYPE 92 98 64

Figure S22.  Get High-res Image Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 5(1q22)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.29e-05 (Fisher's exact test), Q value = 0.01

Table S23.  Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 5(1Q22) CNV 76 34 7 112
AMP PEAK 5(1Q22) WILD-TYPE 117 45 20 72

Figure S23.  Get High-res Image Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(1q42.3)' versus 'CN_CNMF'

P value = 1.74e-07 (Chi-square test), Q value = 9e-05

Table S24.  Gene #6: 'Amp Peak 6(1q42.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 6(1Q42.3) CNV 90 24 72 11 6
AMP PEAK 6(1Q42.3) WILD-TYPE 200 16 67 6 0

Figure S24.  Get High-res Image Gene #6: 'Amp Peak 6(1q42.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(2p23.2)' versus 'CN_CNMF'

P value = 5.04e-28 (Chi-square test), Q value = 4.6e-25

Table S25.  Gene #7: 'Amp Peak 7(2p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 7(2P23.2) CNV 14 23 67 6 1
AMP PEAK 7(2P23.2) WILD-TYPE 276 17 72 11 5

Figure S25.  Get High-res Image Gene #7: 'Amp Peak 7(2p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(2p23.2)' versus 'METHLYATION_CNMF'

P value = 1.59e-10 (Fisher's exact test), Q value = 9.8e-08

Table S26.  Gene #7: 'Amp Peak 7(2p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 7(2P23.2) CNV 59 13 14
AMP PEAK 7(2P23.2) WILD-TYPE 84 72 135

Figure S26.  Get High-res Image Gene #7: 'Amp Peak 7(2p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 7(2p23.2)' versus 'MRNASEQ_CNMF'

P value = 3.63e-06 (Fisher's exact test), Q value = 0.0017

Table S27.  Gene #7: 'Amp Peak 7(2p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 7(2P23.2) CNV 46 10 14
AMP PEAK 7(2P23.2) WILD-TYPE 96 97 99

Figure S27.  Get High-res Image Gene #7: 'Amp Peak 7(2p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 7(2p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.02e-06 (Fisher's exact test), Q value = 0.0024

Table S28.  Gene #7: 'Amp Peak 7(2p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 7(2P23.2) CNV 8 7 9 46
AMP PEAK 7(2P23.2) WILD-TYPE 57 85 56 94

Figure S28.  Get High-res Image Gene #7: 'Amp Peak 7(2p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(2p23.2)' versus 'MIRSEQ_CNMF'

P value = 1.18e-09 (Fisher's exact test), Q value = 7e-07

Table S29.  Gene #7: 'Amp Peak 7(2p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 7(2P23.2) CNV 76 17 16
AMP PEAK 7(2P23.2) WILD-TYPE 131 127 116

Figure S29.  Get High-res Image Gene #7: 'Amp Peak 7(2p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 7(2p23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.91e-10 (Fisher's exact test), Q value = 2.4e-07

Table S30.  Gene #7: 'Amp Peak 7(2p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 7(2P23.2) CNV 22 10 5 72
AMP PEAK 7(2P23.2) WILD-TYPE 171 69 22 112

Figure S30.  Get High-res Image Gene #7: 'Amp Peak 7(2p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 8(2q13)' versus 'CN_CNMF'

P value = 2.77e-33 (Chi-square test), Q value = 2.6e-30

Table S31.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 8(2Q13) CNV 8 19 74 5 1
AMP PEAK 8(2Q13) WILD-TYPE 282 21 65 12 5

Figure S31.  Get High-res Image Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 8(2q13)' versus 'METHLYATION_CNMF'

P value = 1.95e-12 (Fisher's exact test), Q value = 1.3e-09

Table S32.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 8(2Q13) CNV 58 16 9
AMP PEAK 8(2Q13) WILD-TYPE 85 69 140

Figure S32.  Get High-res Image Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 8(2q13)' versus 'MRNASEQ_CNMF'

P value = 8.42e-11 (Fisher's exact test), Q value = 5.3e-08

Table S33.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 8(2Q13) CNV 50 7 8
AMP PEAK 8(2Q13) WILD-TYPE 92 100 105

Figure S33.  Get High-res Image Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 8(2q13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.53e-10 (Fisher's exact test), Q value = 9.5e-08

Table S34.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 8(2Q13) CNV 6 5 4 50
AMP PEAK 8(2Q13) WILD-TYPE 59 87 61 90

Figure S34.  Get High-res Image Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 8(2q13)' versus 'MIRSEQ_CNMF'

P value = 2.47e-18 (Fisher's exact test), Q value = 2e-15

Table S35.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 8(2Q13) CNV 85 10 10
AMP PEAK 8(2Q13) WILD-TYPE 122 134 122

Figure S35.  Get High-res Image Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 8(2q13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.16e-17 (Fisher's exact test), Q value = 9.3e-15

Table S36.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 8(2Q13) CNV 15 8 2 80
AMP PEAK 8(2Q13) WILD-TYPE 178 71 25 104

Figure S36.  Get High-res Image Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 9(3p25.1)' versus 'CN_CNMF'

P value = 4.11e-24 (Chi-square test), Q value = 3.6e-21

Table S37.  Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 9(3P25.1) CNV 4 5 50 9 2
AMP PEAK 9(3P25.1) WILD-TYPE 286 35 89 8 4

Figure S37.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(3p25.1)' versus 'METHLYATION_CNMF'

P value = 3.75e-06 (Fisher's exact test), Q value = 0.0018

Table S38.  Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 9(3P25.1) CNV 35 14 7
AMP PEAK 9(3P25.1) WILD-TYPE 108 71 142

Figure S38.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 9(3p25.1)' versus 'MRNASEQ_CNMF'

P value = 6.49e-08 (Fisher's exact test), Q value = 3.4e-05

Table S39.  Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 9(3P25.1) CNV 35 7 3
AMP PEAK 9(3P25.1) WILD-TYPE 107 100 110

Figure S39.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 9(3p25.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.78e-08 (Fisher's exact test), Q value = 9.8e-06

Table S40.  Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 9(3P25.1) CNV 0 3 8 34
AMP PEAK 9(3P25.1) WILD-TYPE 65 89 57 106

Figure S40.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 9(3p25.1)' versus 'MIRSEQ_CNMF'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00052

Table S41.  Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 9(3P25.1) CNV 49 11 8
AMP PEAK 9(3P25.1) WILD-TYPE 158 133 124

Figure S41.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 9(3p25.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.45e-06 (Fisher's exact test), Q value = 0.00071

Table S42.  Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 9(3P25.1) CNV 12 6 5 45
AMP PEAK 9(3P25.1) WILD-TYPE 181 73 22 139

Figure S42.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 10(3p14.1)' versus 'CN_CNMF'

P value = 7.51e-20 (Chi-square test), Q value = 6.4e-17

Table S43.  Gene #10: 'Amp Peak 10(3p14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 10(3P14.1) CNV 4 5 35 10 2
AMP PEAK 10(3P14.1) WILD-TYPE 286 35 104 7 4

Figure S43.  Get High-res Image Gene #10: 'Amp Peak 10(3p14.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 10(3p14.1)' versus 'MRNASEQ_CNMF'

P value = 3.18e-05 (Fisher's exact test), Q value = 0.014

Table S44.  Gene #10: 'Amp Peak 10(3p14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 10(3P14.1) CNV 25 7 2
AMP PEAK 10(3P14.1) WILD-TYPE 117 100 111

Figure S44.  Get High-res Image Gene #10: 'Amp Peak 10(3p14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 10(3p14.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.55e-05 (Fisher's exact test), Q value = 0.011

Table S45.  Gene #10: 'Amp Peak 10(3p14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 10(3P14.1) CNV 0 3 7 24
AMP PEAK 10(3P14.1) WILD-TYPE 65 89 58 116

Figure S45.  Get High-res Image Gene #10: 'Amp Peak 10(3p14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 10(3p14.1)' versus 'MIRSEQ_CNMF'

P value = 0.000503 (Fisher's exact test), Q value = 0.2

Table S46.  Gene #10: 'Amp Peak 10(3p14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 10(3P14.1) CNV 37 11 7
AMP PEAK 10(3P14.1) WILD-TYPE 170 133 125

Figure S46.  Get High-res Image Gene #10: 'Amp Peak 10(3p14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 10(3p14.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000576 (Fisher's exact test), Q value = 0.22

Table S47.  Gene #10: 'Amp Peak 10(3p14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 10(3P14.1) CNV 12 5 3 35
AMP PEAK 10(3P14.1) WILD-TYPE 181 74 24 149

Figure S47.  Get High-res Image Gene #10: 'Amp Peak 10(3p14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 11(3q26.2)' versus 'MRNA_CNMF'

P value = 5.21e-06 (Fisher's exact test), Q value = 0.0025

Table S48.  Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 11(3Q26.2) CNV 0 12 1 0
AMP PEAK 11(3Q26.2) WILD-TYPE 13 6 13 8

Figure S48.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 11(3q26.2)' versus 'MRNA_CHIERARCHICAL'

P value = 4.74e-05 (Fisher's exact test), Q value = 0.021

Table S49.  Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
AMP PEAK 11(3Q26.2) CNV 1 1 11
AMP PEAK 11(3Q26.2) WILD-TYPE 19 14 7

Figure S49.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 11(3q26.2)' versus 'CN_CNMF'

P value = 3.77e-61 (Chi-square test), Q value = 3.6e-58

Table S50.  Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 11(3Q26.2) CNV 13 10 116 12 4
AMP PEAK 11(3Q26.2) WILD-TYPE 277 30 23 5 2

Figure S50.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(3q26.2)' versus 'METHLYATION_CNMF'

P value = 1.95e-17 (Fisher's exact test), Q value = 1.6e-14

Table S51.  Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 11(3Q26.2) CNV 86 24 19
AMP PEAK 11(3Q26.2) WILD-TYPE 57 61 130

Figure S51.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 11(3q26.2)' versus 'RPPA_CNMF'

P value = 0.000353 (Chi-square test), Q value = 0.14

Table S52.  Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 11(3Q26.2) CNV 11 15 4 1 1 6
AMP PEAK 11(3Q26.2) WILD-TYPE 30 22 35 11 40 18

Figure S52.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 11(3q26.2)' versus 'MRNASEQ_CNMF'

P value = 1.91e-25 (Fisher's exact test), Q value = 1.7e-22

Table S53.  Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 11(3Q26.2) CNV 80 12 4
AMP PEAK 11(3Q26.2) WILD-TYPE 62 95 109

Figure S53.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 11(3q26.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.67e-25 (Fisher's exact test), Q value = 3.3e-22

Table S54.  Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 11(3Q26.2) CNV 0 6 12 78
AMP PEAK 11(3Q26.2) WILD-TYPE 65 86 53 62

Figure S54.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(3q26.2)' versus 'MIRSEQ_CNMF'

P value = 5.62e-26 (Fisher's exact test), Q value = 5e-23

Table S55.  Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 11(3Q26.2) CNV 118 21 12
AMP PEAK 11(3Q26.2) WILD-TYPE 89 123 120

Figure S55.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 11(3q26.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.4e-24 (Fisher's exact test), Q value = 3e-21

Table S56.  Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 11(3Q26.2) CNV 25 10 7 109
AMP PEAK 11(3Q26.2) WILD-TYPE 168 69 20 75

Figure S56.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 12(3q26.2)' versus 'MRNA_CNMF'

P value = 2.42e-05 (Fisher's exact test), Q value = 0.011

Table S57.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 12(3Q26.2) CNV 0 11 1 0
AMP PEAK 12(3Q26.2) WILD-TYPE 13 7 13 8

Figure S57.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 12(3q26.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000168 (Fisher's exact test), Q value = 0.07

Table S58.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
AMP PEAK 12(3Q26.2) CNV 1 1 10
AMP PEAK 12(3Q26.2) WILD-TYPE 19 14 8

Figure S58.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 12(3q26.2)' versus 'CN_CNMF'

P value = 8.96e-60 (Chi-square test), Q value = 8.6e-57

Table S59.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 12(3Q26.2) CNV 9 9 110 12 4
AMP PEAK 12(3Q26.2) WILD-TYPE 281 31 29 5 2

Figure S59.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(3q26.2)' versus 'METHLYATION_CNMF'

P value = 8.25e-19 (Fisher's exact test), Q value = 6.9e-16

Table S60.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 12(3Q26.2) CNV 84 20 16
AMP PEAK 12(3Q26.2) WILD-TYPE 59 65 133

Figure S60.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 12(3q26.2)' versus 'MRNASEQ_CNMF'

P value = 1.89e-25 (Fisher's exact test), Q value = 1.7e-22

Table S61.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 12(3Q26.2) CNV 78 10 4
AMP PEAK 12(3Q26.2) WILD-TYPE 64 97 109

Figure S61.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(3q26.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.53e-26 (Fisher's exact test), Q value = 6.8e-23

Table S62.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 12(3Q26.2) CNV 0 5 10 77
AMP PEAK 12(3Q26.2) WILD-TYPE 65 87 55 63

Figure S62.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(3q26.2)' versus 'MIRSEQ_CNMF'

P value = 1.1e-23 (Fisher's exact test), Q value = 9.7e-21

Table S63.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 12(3Q26.2) CNV 110 18 12
AMP PEAK 12(3Q26.2) WILD-TYPE 97 126 120

Figure S63.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 12(3q26.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.82e-25 (Fisher's exact test), Q value = 8.7e-22

Table S64.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 12(3Q26.2) CNV 20 9 7 104
AMP PEAK 12(3Q26.2) WILD-TYPE 173 70 20 80

Figure S64.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 13(4p16.3)' versus 'CN_CNMF'

P value = 1.64e-21 (Chi-square test), Q value = 1.4e-18

Table S65.  Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 13(4P16.3) CNV 2 1 42 0 0
AMP PEAK 13(4P16.3) WILD-TYPE 288 39 97 17 6

Figure S65.  Get High-res Image Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(4p16.3)' versus 'METHLYATION_CNMF'

P value = 0.000532 (Fisher's exact test), Q value = 0.21

Table S66.  Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 13(4P16.3) CNV 21 10 4
AMP PEAK 13(4P16.3) WILD-TYPE 122 75 145

Figure S66.  Get High-res Image Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 13(4p16.3)' versus 'MRNASEQ_CNMF'

P value = 5.2e-10 (Fisher's exact test), Q value = 3.1e-07

Table S67.  Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 13(4P16.3) CNV 28 1 1
AMP PEAK 13(4P16.3) WILD-TYPE 114 106 112

Figure S67.  Get High-res Image Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 13(4p16.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.95e-11 (Fisher's exact test), Q value = 4.4e-08

Table S68.  Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 13(4P16.3) CNV 1 0 0 29
AMP PEAK 13(4P16.3) WILD-TYPE 64 92 65 111

Figure S68.  Get High-res Image Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(4p16.3)' versus 'MIRSEQ_CNMF'

P value = 6.4e-09 (Fisher's exact test), Q value = 3.6e-06

Table S69.  Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 13(4P16.3) CNV 37 4 2
AMP PEAK 13(4P16.3) WILD-TYPE 170 140 130

Figure S69.  Get High-res Image Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 13(4p16.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.5e-08 (Fisher's exact test), Q value = 2.9e-05

Table S70.  Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 13(4P16.3) CNV 5 2 1 35
AMP PEAK 13(4P16.3) WILD-TYPE 188 77 26 149

Figure S70.  Get High-res Image Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 14(5p15.33)' versus 'CN_CNMF'

P value = 4.71e-32 (Chi-square test), Q value = 4.3e-29

Table S71.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 14(5P15.33) CNV 4 5 66 1 1
AMP PEAK 14(5P15.33) WILD-TYPE 286 35 73 16 5

Figure S71.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 14(5p15.33)' versus 'METHLYATION_CNMF'

P value = 3.4e-12 (Fisher's exact test), Q value = 2.3e-09

Table S72.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 14(5P15.33) CNV 47 12 4
AMP PEAK 14(5P15.33) WILD-TYPE 96 73 145

Figure S72.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 14(5p15.33)' versus 'MRNASEQ_CNMF'

P value = 3.21e-14 (Fisher's exact test), Q value = 2.3e-11

Table S73.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 14(5P15.33) CNV 42 0 6
AMP PEAK 14(5P15.33) WILD-TYPE 100 107 107

Figure S73.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 14(5p15.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.37e-12 (Fisher's exact test), Q value = 1.6e-09

Table S74.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 14(5P15.33) CNV 3 0 4 41
AMP PEAK 14(5P15.33) WILD-TYPE 62 92 61 99

Figure S74.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(5p15.33)' versus 'MIRSEQ_CNMF'

P value = 2.73e-13 (Fisher's exact test), Q value = 1.9e-10

Table S75.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 14(5P15.33) CNV 62 5 9
AMP PEAK 14(5P15.33) WILD-TYPE 145 139 123

Figure S75.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 14(5p15.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.09e-14 (Fisher's exact test), Q value = 5.1e-11

Table S76.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 14(5P15.33) CNV 7 6 4 59
AMP PEAK 14(5P15.33) WILD-TYPE 186 73 23 125

Figure S76.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 15(5q35.3)' versus 'CN_CNMF'

P value = 8.67e-20 (Chi-square test), Q value = 7.4e-17

Table S77.  Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 15(5Q35.3) CNV 2 3 42 0 1
AMP PEAK 15(5Q35.3) WILD-TYPE 288 37 97 17 5

Figure S77.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(5q35.3)' versus 'METHLYATION_CNMF'

P value = 0.000639 (Fisher's exact test), Q value = 0.24

Table S78.  Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 15(5Q35.3) CNV 25 10 6
AMP PEAK 15(5Q35.3) WILD-TYPE 118 75 143

Figure S78.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 15(5q35.3)' versus 'MRNASEQ_CNMF'

P value = 3.18e-07 (Fisher's exact test), Q value = 0.00016

Table S79.  Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 15(5Q35.3) CNV 23 0 4
AMP PEAK 15(5Q35.3) WILD-TYPE 119 107 109

Figure S79.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 15(5q35.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.98e-05 (Fisher's exact test), Q value = 0.03

Table S80.  Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 15(5Q35.3) CNV 2 0 5 20
AMP PEAK 15(5Q35.3) WILD-TYPE 63 92 60 120

Figure S80.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 15(5q35.3)' versus 'MIRSEQ_CNMF'

P value = 1.92e-07 (Fisher's exact test), Q value = 9.9e-05

Table S81.  Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 15(5Q35.3) CNV 38 4 5
AMP PEAK 15(5Q35.3) WILD-TYPE 169 140 127

Figure S81.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 15(5q35.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.69e-06 (Fisher's exact test), Q value = 0.0013

Table S82.  Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 15(5Q35.3) CNV 8 4 0 35
AMP PEAK 15(5Q35.3) WILD-TYPE 185 75 27 149

Figure S82.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 16(6p24.2)' versus 'MRNA_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.17

Table S83.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 16(6P24.2) CNV 0 10 2 0
AMP PEAK 16(6P24.2) WILD-TYPE 13 8 12 8

Figure S83.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 16(6p24.2)' versus 'CN_CNMF'

P value = 1.36e-39 (Chi-square test), Q value = 1.3e-36

Table S84.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 16(6P24.2) CNV 8 3 80 9 1
AMP PEAK 16(6P24.2) WILD-TYPE 282 37 59 8 5

Figure S84.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(6p24.2)' versus 'METHLYATION_CNMF'

P value = 2.35e-11 (Fisher's exact test), Q value = 1.5e-08

Table S85.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 16(6P24.2) CNV 57 17 10
AMP PEAK 16(6P24.2) WILD-TYPE 86 68 139

Figure S85.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 16(6p24.2)' versus 'RPPA_CNMF'

P value = 0.000177 (Chi-square test), Q value = 0.073

Table S86.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 16(6P24.2) CNV 4 12 2 1 0 2
AMP PEAK 16(6P24.2) WILD-TYPE 37 25 37 11 41 22

Figure S86.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 16(6p24.2)' versus 'MRNASEQ_CNMF'

P value = 6.92e-16 (Fisher's exact test), Q value = 5.3e-13

Table S87.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 16(6P24.2) CNV 52 7 2
AMP PEAK 16(6P24.2) WILD-TYPE 90 100 111

Figure S87.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 16(6p24.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.49e-14 (Fisher's exact test), Q value = 1.1e-11

Table S88.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 16(6P24.2) CNV 0 6 4 51
AMP PEAK 16(6P24.2) WILD-TYPE 65 86 61 89

Figure S88.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 16(6p24.2)' versus 'MIRSEQ_CNMF'

P value = 1.26e-16 (Fisher's exact test), Q value = 9.7e-14

Table S89.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 16(6P24.2) CNV 79 11 8
AMP PEAK 16(6P24.2) WILD-TYPE 128 133 124

Figure S89.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 16(6p24.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.77e-15 (Fisher's exact test), Q value = 3.6e-12

Table S90.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 16(6P24.2) CNV 14 7 4 73
AMP PEAK 16(6P24.2) WILD-TYPE 179 72 23 111

Figure S90.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 17(6q25.1)' versus 'CN_CNMF'

P value = 7.52e-22 (Chi-square test), Q value = 6.5e-19

Table S91.  Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 17(6Q25.1) CNV 8 5 53 8 2
AMP PEAK 17(6Q25.1) WILD-TYPE 282 35 86 9 4

Figure S91.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 17(6q25.1)' versus 'METHLYATION_CNMF'

P value = 2.64e-06 (Fisher's exact test), Q value = 0.0013

Table S92.  Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 17(6Q25.1) CNV 43 11 12
AMP PEAK 17(6Q25.1) WILD-TYPE 100 74 137

Figure S92.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 17(6q25.1)' versus 'MRNASEQ_CNMF'

P value = 4.97e-07 (Fisher's exact test), Q value = 0.00025

Table S93.  Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 17(6Q25.1) CNV 36 7 5
AMP PEAK 17(6Q25.1) WILD-TYPE 106 100 108

Figure S93.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 17(6q25.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.03e-08 (Fisher's exact test), Q value = 5.8e-06

Table S94.  Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 17(6Q25.1) CNV 0 5 6 37
AMP PEAK 17(6Q25.1) WILD-TYPE 65 87 59 103

Figure S94.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 17(6q25.1)' versus 'MIRSEQ_CNMF'

P value = 8.25e-06 (Fisher's exact test), Q value = 0.0039

Table S95.  Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 17(6Q25.1) CNV 52 13 11
AMP PEAK 17(6Q25.1) WILD-TYPE 155 131 121

Figure S95.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 17(6q25.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.96e-06 (Fisher's exact test), Q value = 0.0042

Table S96.  Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 17(6Q25.1) CNV 16 8 3 49
AMP PEAK 17(6Q25.1) WILD-TYPE 177 71 24 135

Figure S96.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 18(7q22.1)' versus 'CN_CNMF'

P value = 5.12e-20 (Chi-square test), Q value = 4.4e-17

Table S97.  Gene #18: 'Amp Peak 18(7q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 18(7Q22.1) CNV 12 22 39 7 2
AMP PEAK 18(7Q22.1) WILD-TYPE 278 18 100 10 4

Figure S97.  Get High-res Image Gene #18: 'Amp Peak 18(7q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(8p11.21)' versus 'CN_CNMF'

P value = 1.7e-23 (Chi-square test), Q value = 1.5e-20

Table S98.  Gene #19: 'Amp Peak 19(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 19(8P11.21) CNV 38 20 69 17 2
AMP PEAK 19(8P11.21) WILD-TYPE 252 20 70 0 4

Figure S98.  Get High-res Image Gene #19: 'Amp Peak 19(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(8p11.21)' versus 'MRNASEQ_CNMF'

P value = 0.000553 (Fisher's exact test), Q value = 0.21

Table S99.  Gene #19: 'Amp Peak 19(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 19(8P11.21) CNV 54 19 24
AMP PEAK 19(8P11.21) WILD-TYPE 88 88 89

Figure S99.  Get High-res Image Gene #19: 'Amp Peak 19(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 19(8p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.01

Table S100.  Gene #19: 'Amp Peak 19(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 19(8P11.21) CNV 12 15 12 58
AMP PEAK 19(8P11.21) WILD-TYPE 53 77 53 82

Figure S100.  Get High-res Image Gene #19: 'Amp Peak 19(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 19(8p11.21)' versus 'MIRSEQ_CNMF'

P value = 6.37e-05 (Fisher's exact test), Q value = 0.028

Table S101.  Gene #19: 'Amp Peak 19(8p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 19(8P11.21) CNV 83 29 31
AMP PEAK 19(8P11.21) WILD-TYPE 124 115 101

Figure S101.  Get High-res Image Gene #19: 'Amp Peak 19(8p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 19(8p11.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000301 (Fisher's exact test), Q value = 0.12

Table S102.  Gene #19: 'Amp Peak 19(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 19(8P11.21) CNV 39 21 12 71
AMP PEAK 19(8P11.21) WILD-TYPE 154 58 15 113

Figure S102.  Get High-res Image Gene #19: 'Amp Peak 19(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 20(8q24.21)' versus 'CN_CNMF'

P value = 1.54e-35 (Chi-square test), Q value = 1.4e-32

Table S103.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 20(8Q24.21) CNV 44 23 101 17 3
AMP PEAK 20(8Q24.21) WILD-TYPE 246 17 38 0 3

Figure S103.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(8q24.21)' versus 'METHLYATION_CNMF'

P value = 6.2e-07 (Fisher's exact test), Q value = 0.00031

Table S104.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 20(8Q24.21) CNV 84 33 42
AMP PEAK 20(8Q24.21) WILD-TYPE 59 52 107

Figure S104.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 20(8q24.21)' versus 'RPPA_CNMF'

P value = 8.75e-05 (Chi-square test), Q value = 0.038

Table S105.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 20(8Q24.21) CNV 12 14 8 2 2 14
AMP PEAK 20(8Q24.21) WILD-TYPE 29 23 31 10 39 10

Figure S105.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 20(8q24.21)' versus 'MRNASEQ_CNMF'

P value = 3.35e-09 (Fisher's exact test), Q value = 1.9e-06

Table S106.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 20(8Q24.21) CNV 74 20 25
AMP PEAK 20(8Q24.21) WILD-TYPE 68 87 88

Figure S106.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 20(8q24.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-11 (Fisher's exact test), Q value = 8.3e-09

Table S107.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 20(8Q24.21) CNV 13 15 13 78
AMP PEAK 20(8Q24.21) WILD-TYPE 52 77 52 62

Figure S107.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 20(8q24.21)' versus 'MIRSEQ_CNMF'

P value = 3.45e-11 (Fisher's exact test), Q value = 2.2e-08

Table S108.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 20(8Q24.21) CNV 116 36 33
AMP PEAK 20(8Q24.21) WILD-TYPE 91 108 99

Figure S108.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 20(8q24.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.25e-12 (Fisher's exact test), Q value = 2.9e-09

Table S109.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 20(8Q24.21) CNV 43 23 12 107
AMP PEAK 20(8Q24.21) WILD-TYPE 150 56 15 77

Figure S109.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.00043 (Fisher's exact test), Q value = 0.17

Table S110.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 21(8Q24.21) CNV 0 10 2 0
AMP PEAK 21(8Q24.21) WILD-TYPE 13 8 12 8

Figure S110.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 8.36e-35 (Chi-square test), Q value = 7.7e-32

Table S111.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 21(8Q24.21) CNV 49 23 104 17 3
AMP PEAK 21(8Q24.21) WILD-TYPE 241 17 35 0 3

Figure S111.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0057

Table S112.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 21(8Q24.21) CNV 84 34 47
AMP PEAK 21(8Q24.21) WILD-TYPE 59 51 102

Figure S112.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 7.26e-07 (Chi-square test), Q value = 0.00036

Table S113.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
AMP PEAK 21(8Q24.21) CNV 12 17 7 2 2 16
AMP PEAK 21(8Q24.21) WILD-TYPE 29 20 32 10 39 8

Figure S113.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

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

P value = 1.82e-08 (Fisher's exact test), Q value = 1e-05

Table S114.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 21(8Q24.21) CNV 76 25 25
AMP PEAK 21(8Q24.21) WILD-TYPE 66 82 88

Figure S114.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 1.7e-11 (Fisher's exact test), Q value = 1.1e-08

Table S115.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 21(8Q24.21) CNV 13 20 12 81
AMP PEAK 21(8Q24.21) WILD-TYPE 52 72 53 59

Figure S115.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 6.82e-13 (Fisher's exact test), Q value = 4.7e-10

Table S116.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 21(8Q24.21) CNV 122 37 33
AMP PEAK 21(8Q24.21) WILD-TYPE 85 107 99

Figure S116.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 1.25e-11 (Fisher's exact test), Q value = 8.3e-09

Table S117.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 21(8Q24.21) CNV 47 23 13 109
AMP PEAK 21(8Q24.21) WILD-TYPE 146 56 14 75

Figure S117.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 22(9p24.2)' versus 'CN_CNMF'

P value = 2.87e-22 (Chi-square test), Q value = 2.5e-19

Table S118.  Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 22(9P24.2) CNV 5 3 49 0 0
AMP PEAK 22(9P24.2) WILD-TYPE 285 37 90 17 6

Figure S118.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(9p24.2)' versus 'METHLYATION_CNMF'

P value = 4.87e-07 (Fisher's exact test), Q value = 0.00024

Table S119.  Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 22(9P24.2) CNV 33 7 5
AMP PEAK 22(9P24.2) WILD-TYPE 110 78 144

Figure S119.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 22(9p24.2)' versus 'MRNASEQ_CNMF'

P value = 2.97e-09 (Fisher's exact test), Q value = 1.7e-06

Table S120.  Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 22(9P24.2) CNV 32 2 3
AMP PEAK 22(9P24.2) WILD-TYPE 110 105 110

Figure S120.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 22(9p24.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-10 (Fisher's exact test), Q value = 7.3e-08

Table S121.  Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 22(9P24.2) CNV 0 0 5 32
AMP PEAK 22(9P24.2) WILD-TYPE 65 92 60 108

Figure S121.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(9p24.2)' versus 'MIRSEQ_CNMF'

P value = 6.29e-12 (Fisher's exact test), Q value = 4.2e-09

Table S122.  Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 22(9P24.2) CNV 48 2 6
AMP PEAK 22(9P24.2) WILD-TYPE 159 142 126

Figure S122.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 22(9p24.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.84e-11 (Fisher's exact test), Q value = 1.2e-08

Table S123.  Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 22(9P24.2) CNV 5 3 2 46
AMP PEAK 22(9P24.2) WILD-TYPE 188 76 25 138

Figure S123.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 23(9q34.3)' versus 'CN_CNMF'

P value = 3.79e-12 (Chi-square test), Q value = 2.6e-09

Table S124.  Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 23(9Q34.3) CNV 3 1 28 0 0
AMP PEAK 23(9Q34.3) WILD-TYPE 287 39 111 17 6

Figure S124.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(9q34.3)' versus 'METHLYATION_CNMF'

P value = 9.56e-05 (Fisher's exact test), Q value = 0.041

Table S125.  Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 23(9Q34.3) CNV 17 5 1
AMP PEAK 23(9Q34.3) WILD-TYPE 126 80 148

Figure S125.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(9q34.3)' versus 'MRNASEQ_CNMF'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.0097

Table S126.  Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 23(9Q34.3) CNV 20 1 3
AMP PEAK 23(9Q34.3) WILD-TYPE 122 106 110

Figure S126.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 23(9q34.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.98e-06 (Fisher's exact test), Q value = 0.0019

Table S127.  Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 23(9Q34.3) CNV 2 0 1 21
AMP PEAK 23(9Q34.3) WILD-TYPE 63 92 64 119

Figure S127.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 23(9q34.3)' versus 'MIRSEQ_CNMF'

P value = 0.000604 (Fisher's exact test), Q value = 0.23

Table S128.  Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 23(9Q34.3) CNV 22 3 3
AMP PEAK 23(9Q34.3) WILD-TYPE 185 141 129

Figure S128.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 23(9q34.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.05

Table S129.  Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 23(9Q34.3) CNV 3 3 0 22
AMP PEAK 23(9Q34.3) WILD-TYPE 190 76 27 162

Figure S129.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 24(10q22.2)' versus 'CN_CNMF'

P value = 1.77e-08 (Chi-square test), Q value = 9.8e-06

Table S130.  Gene #24: 'Amp Peak 24(10q22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 24(10Q22.2) CNV 48 18 53 10 3
AMP PEAK 24(10Q22.2) WILD-TYPE 242 22 86 7 3

Figure S130.  Get High-res Image Gene #24: 'Amp Peak 24(10q22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(11p11.2)' versus 'CN_CNMF'

P value = 1.32e-16 (Chi-square test), Q value = 1e-13

Table S131.  Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 25(11P11.2) CNV 1 6 37 1 0
AMP PEAK 25(11P11.2) WILD-TYPE 289 34 102 16 6

Figure S131.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(11p11.2)' versus 'METHLYATION_CNMF'

P value = 5.97e-05 (Fisher's exact test), Q value = 0.026

Table S132.  Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 25(11P11.2) CNV 21 12 3
AMP PEAK 25(11P11.2) WILD-TYPE 122 73 146

Figure S132.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 25(11p11.2)' versus 'MRNASEQ_CNMF'

P value = 2.37e-05 (Fisher's exact test), Q value = 0.011

Table S133.  Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 25(11P11.2) CNV 23 4 2
AMP PEAK 25(11P11.2) WILD-TYPE 119 103 111

Figure S133.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 25(11p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.28e-05 (Fisher's exact test), Q value = 0.04

Table S134.  Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 25(11P11.2) CNV 1 3 2 23
AMP PEAK 25(11P11.2) WILD-TYPE 64 89 63 117

Figure S134.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(11p11.2)' versus 'MIRSEQ_CNMF'

P value = 1.16e-07 (Fisher's exact test), Q value = 6e-05

Table S135.  Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 25(11P11.2) CNV 36 6 2
AMP PEAK 25(11P11.2) WILD-TYPE 171 138 130

Figure S135.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 25(11p11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.31e-06 (Fisher's exact test), Q value = 0.0016

Table S136.  Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 25(11P11.2) CNV 7 2 2 33
AMP PEAK 25(11P11.2) WILD-TYPE 186 77 25 151

Figure S136.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 26(11q13.2)' versus 'MRNA_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.097

Table S137.  Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 26(11Q13.2) CNV 0 8 0 0
AMP PEAK 26(11Q13.2) WILD-TYPE 13 10 14 8

Figure S137.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 26(11q13.2)' versus 'CN_CNMF'

P value = 5.92e-22 (Chi-square test), Q value = 5.1e-19

Table S138.  Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 26(11Q13.2) CNV 6 8 53 1 0
AMP PEAK 26(11Q13.2) WILD-TYPE 284 32 86 16 6

Figure S138.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 26(11q13.2)' versus 'METHLYATION_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.084

Table S139.  Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 26(11Q13.2) CNV 32 13 9
AMP PEAK 26(11Q13.2) WILD-TYPE 111 72 140

Figure S139.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 26(11q13.2)' versus 'MRNASEQ_CNMF'

P value = 9.44e-06 (Fisher's exact test), Q value = 0.0044

Table S140.  Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 26(11Q13.2) CNV 32 7 5
AMP PEAK 26(11Q13.2) WILD-TYPE 110 100 108

Figure S140.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 26(11q13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.58e-08 (Fisher's exact test), Q value = 3e-05

Table S141.  Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 26(11Q13.2) CNV 1 6 2 35
AMP PEAK 26(11Q13.2) WILD-TYPE 64 86 63 105

Figure S141.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(11q13.2)' versus 'MIRSEQ_CNMF'

P value = 1.11e-07 (Fisher's exact test), Q value = 5.8e-05

Table S142.  Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 26(11Q13.2) CNV 47 13 4
AMP PEAK 26(11Q13.2) WILD-TYPE 160 131 128

Figure S142.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 26(11q13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.46e-07 (Fisher's exact test), Q value = 0.00027

Table S143.  Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 26(11Q13.2) CNV 15 2 3 44
AMP PEAK 26(11Q13.2) WILD-TYPE 178 77 24 140

Figure S143.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 27(12p12.1)' versus 'CN_CNMF'

P value = 5.1e-15 (Chi-square test), Q value = 3.8e-12

Table S144.  Gene #27: 'Amp Peak 27(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 27(12P12.1) CNV 15 12 49 2 3
AMP PEAK 27(12P12.1) WILD-TYPE 275 28 90 15 3

Figure S144.  Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(12p12.1)' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Fisher's exact test), Q value = 5.9e-05

Table S145.  Gene #27: 'Amp Peak 27(12p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 27(12P12.1) CNV 44 13 9
AMP PEAK 27(12P12.1) WILD-TYPE 99 72 140

Figure S145.  Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 27(12p12.1)' versus 'MRNASEQ_CNMF'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.018

Table S146.  Gene #27: 'Amp Peak 27(12p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 27(12P12.1) CNV 33 9 6
AMP PEAK 27(12P12.1) WILD-TYPE 109 98 107

Figure S146.  Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 27(12p12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.11e-05 (Fisher's exact test), Q value = 0.0096

Table S147.  Gene #27: 'Amp Peak 27(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 27(12P12.1) CNV 1 8 6 33
AMP PEAK 27(12P12.1) WILD-TYPE 64 84 59 107

Figure S147.  Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(12p12.1)' versus 'MIRSEQ_CNMF'

P value = 8.04e-08 (Fisher's exact test), Q value = 4.2e-05

Table S148.  Gene #27: 'Amp Peak 27(12p12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 27(12P12.1) CNV 58 11 12
AMP PEAK 27(12P12.1) WILD-TYPE 149 133 120

Figure S148.  Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 27(12p12.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.05e-09 (Fisher's exact test), Q value = 6.3e-07

Table S149.  Gene #27: 'Amp Peak 27(12p12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 27(12P12.1) CNV 19 5 0 57
AMP PEAK 27(12P12.1) WILD-TYPE 174 74 27 127

Figure S149.  Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(12q13.11)' versus 'CN_CNMF'

P value = 6.74e-17 (Chi-square test), Q value = 5.3e-14

Table S150.  Gene #28: 'Amp Peak 28(12q13.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 28(12Q13.11) CNV 12 13 49 2 3
AMP PEAK 28(12Q13.11) WILD-TYPE 278 27 90 15 3

Figure S150.  Get High-res Image Gene #28: 'Amp Peak 28(12q13.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 28(12q13.11)' versus 'METHLYATION_CNMF'

P value = 3.67e-08 (Fisher's exact test), Q value = 2e-05

Table S151.  Gene #28: 'Amp Peak 28(12q13.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 28(12Q13.11) CNV 42 15 7
AMP PEAK 28(12Q13.11) WILD-TYPE 101 70 142

Figure S151.  Get High-res Image Gene #28: 'Amp Peak 28(12q13.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 28(12q13.11)' versus 'MRNASEQ_CNMF'

P value = 2.19e-06 (Fisher's exact test), Q value = 0.0011

Table S152.  Gene #28: 'Amp Peak 28(12q13.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 28(12Q13.11) CNV 34 7 5
AMP PEAK 28(12Q13.11) WILD-TYPE 108 100 108

Figure S152.  Get High-res Image Gene #28: 'Amp Peak 28(12q13.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 28(12q13.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.95e-06 (Fisher's exact test), Q value = 0.00095

Table S153.  Gene #28: 'Amp Peak 28(12q13.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 28(12Q13.11) CNV 1 6 5 34
AMP PEAK 28(12Q13.11) WILD-TYPE 64 86 60 106

Figure S153.  Get High-res Image Gene #28: 'Amp Peak 28(12q13.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 28(12q13.11)' versus 'MIRSEQ_CNMF'

P value = 1.61e-08 (Fisher's exact test), Q value = 8.9e-06

Table S154.  Gene #28: 'Amp Peak 28(12q13.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 28(12Q13.11) CNV 58 10 11
AMP PEAK 28(12Q13.11) WILD-TYPE 149 134 121

Figure S154.  Get High-res Image Gene #28: 'Amp Peak 28(12q13.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 28(12q13.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.08e-09 (Fisher's exact test), Q value = 2.3e-06

Table S155.  Gene #28: 'Amp Peak 28(12q13.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 28(12Q13.11) CNV 16 6 1 56
AMP PEAK 28(12Q13.11) WILD-TYPE 177 73 26 128

Figure S155.  Get High-res Image Gene #28: 'Amp Peak 28(12q13.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 29(12q13.2)' versus 'CN_CNMF'

P value = 1.75e-17 (Chi-square test), Q value = 1.4e-14

Table S156.  Gene #29: 'Amp Peak 29(12q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 29(12Q13.2) CNV 15 13 54 2 3
AMP PEAK 29(12Q13.2) WILD-TYPE 275 27 85 15 3

Figure S156.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(12q13.2)' versus 'METHLYATION_CNMF'

P value = 1.94e-07 (Fisher's exact test), Q value = 9.9e-05

Table S157.  Gene #29: 'Amp Peak 29(12q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 29(12Q13.2) CNV 46 13 11
AMP PEAK 29(12Q13.2) WILD-TYPE 97 72 138

Figure S157.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 29(12q13.2)' versus 'MRNASEQ_CNMF'

P value = 1.66e-08 (Fisher's exact test), Q value = 9.2e-06

Table S158.  Gene #29: 'Amp Peak 29(12q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 29(12Q13.2) CNV 40 7 5
AMP PEAK 29(12Q13.2) WILD-TYPE 102 100 108

Figure S158.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 29(12q13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.54e-08 (Fisher's exact test), Q value = 3.5e-05

Table S159.  Gene #29: 'Amp Peak 29(12q13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 29(12Q13.2) CNV 1 6 6 39
AMP PEAK 29(12Q13.2) WILD-TYPE 64 86 59 101

Figure S159.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 29(12q13.2)' versus 'MIRSEQ_CNMF'

P value = 2.24e-08 (Fisher's exact test), Q value = 1.2e-05

Table S160.  Gene #29: 'Amp Peak 29(12q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 29(12Q13.2) CNV 61 14 10
AMP PEAK 29(12Q13.2) WILD-TYPE 146 130 122

Figure S160.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 29(12q13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.83e-10 (Fisher's exact test), Q value = 1.1e-07

Table S161.  Gene #29: 'Amp Peak 29(12q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 29(12Q13.2) CNV 20 5 0 60
AMP PEAK 29(12Q13.2) WILD-TYPE 173 74 27 124

Figure S161.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 30(13q34)' versus 'CN_CNMF'

P value = 4.18e-20 (Chi-square test), Q value = 3.6e-17

Table S162.  Gene #30: 'Amp Peak 30(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 30(13Q34) CNV 4 0 43 1 1
AMP PEAK 30(13Q34) WILD-TYPE 286 40 96 16 5

Figure S162.  Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 30(13q34)' versus 'METHLYATION_CNMF'

P value = 1.98e-06 (Fisher's exact test), Q value = 0.00096

Table S163.  Gene #30: 'Amp Peak 30(13q34)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 30(13Q34) CNV 30 10 4
AMP PEAK 30(13Q34) WILD-TYPE 113 75 145

Figure S163.  Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 30(13q34)' versus 'MRNASEQ_CNMF'

P value = 8.41e-12 (Fisher's exact test), Q value = 5.6e-09

Table S164.  Gene #30: 'Amp Peak 30(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 30(13Q34) CNV 31 2 0
AMP PEAK 30(13Q34) WILD-TYPE 111 105 113

Figure S164.  Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 30(13q34)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-07 (Fisher's exact test), Q value = 7.1e-05

Table S165.  Gene #30: 'Amp Peak 30(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 30(13Q34) CNV 0 2 3 28
AMP PEAK 30(13Q34) WILD-TYPE 65 90 62 112

Figure S165.  Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 30(13q34)' versus 'MIRSEQ_CNMF'

P value = 4.78e-11 (Fisher's exact test), Q value = 3e-08

Table S166.  Gene #30: 'Amp Peak 30(13q34)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 30(13Q34) CNV 43 4 2
AMP PEAK 30(13Q34) WILD-TYPE 164 140 130

Figure S166.  Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 30(13q34)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.36e-10 (Fisher's exact test), Q value = 1.4e-07

Table S167.  Gene #30: 'Amp Peak 30(13q34)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 30(13Q34) CNV 6 1 1 41
AMP PEAK 30(13Q34) WILD-TYPE 187 78 26 143

Figure S167.  Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 31(14q24.3)' versus 'CN_CNMF'

P value = 6.04e-18 (Chi-square test), Q value = 4.9e-15

Table S168.  Gene #31: 'Amp Peak 31(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 31(14Q24.3) CNV 4 5 44 3 0
AMP PEAK 31(14Q24.3) WILD-TYPE 286 35 95 14 6

Figure S168.  Get High-res Image Gene #31: 'Amp Peak 31(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 31(14q24.3)' versus 'METHLYATION_CNMF'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.0078

Table S169.  Gene #31: 'Amp Peak 31(14q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 31(14Q24.3) CNV 31 9 6
AMP PEAK 31(14Q24.3) WILD-TYPE 112 76 143

Figure S169.  Get High-res Image Gene #31: 'Amp Peak 31(14q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 31(14q24.3)' versus 'MRNASEQ_CNMF'

P value = 4.85e-08 (Fisher's exact test), Q value = 2.6e-05

Table S170.  Gene #31: 'Amp Peak 31(14q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 31(14Q24.3) CNV 29 5 1
AMP PEAK 31(14Q24.3) WILD-TYPE 113 102 112

Figure S170.  Get High-res Image Gene #31: 'Amp Peak 31(14q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 31(14q24.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.14e-10 (Fisher's exact test), Q value = 7.2e-08

Table S171.  Gene #31: 'Amp Peak 31(14q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 31(14Q24.3) CNV 0 3 0 32
AMP PEAK 31(14Q24.3) WILD-TYPE 65 89 65 108

Figure S171.  Get High-res Image Gene #31: 'Amp Peak 31(14q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 31(14q24.3)' versus 'MIRSEQ_CNMF'

P value = 3.83e-08 (Fisher's exact test), Q value = 2.1e-05

Table S172.  Gene #31: 'Amp Peak 31(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 31(14Q24.3) CNV 43 7 4
AMP PEAK 31(14Q24.3) WILD-TYPE 164 137 128

Figure S172.  Get High-res Image Gene #31: 'Amp Peak 31(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 31(14q24.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.56e-08 (Fisher's exact test), Q value = 8.7e-06

Table S173.  Gene #31: 'Amp Peak 31(14q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 31(14Q24.3) CNV 8 3 1 42
AMP PEAK 31(14Q24.3) WILD-TYPE 185 76 26 142

Figure S173.  Get High-res Image Gene #31: 'Amp Peak 31(14q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 32(14q32.33)' versus 'CN_CNMF'

P value = 4.26e-22 (Chi-square test), Q value = 3.7e-19

Table S174.  Gene #32: 'Amp Peak 32(14q32.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 32(14Q32.33) CNV 6 6 54 4 0
AMP PEAK 32(14Q32.33) WILD-TYPE 284 34 85 13 6

Figure S174.  Get High-res Image Gene #32: 'Amp Peak 32(14q32.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 32(14q32.33)' versus 'METHLYATION_CNMF'

P value = 1.04e-06 (Fisher's exact test), Q value = 0.00051

Table S175.  Gene #32: 'Amp Peak 32(14q32.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 32(14Q32.33) CNV 37 14 7
AMP PEAK 32(14Q32.33) WILD-TYPE 106 71 142

Figure S175.  Get High-res Image Gene #32: 'Amp Peak 32(14q32.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 32(14q32.33)' versus 'MRNASEQ_CNMF'

P value = 3.54e-05 (Fisher's exact test), Q value = 0.016

Table S176.  Gene #32: 'Amp Peak 32(14q32.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 32(14Q32.33) CNV 28 6 4
AMP PEAK 32(14Q32.33) WILD-TYPE 114 101 109

Figure S176.  Get High-res Image Gene #32: 'Amp Peak 32(14q32.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 32(14q32.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.77e-08 (Fisher's exact test), Q value = 2.6e-05

Table S177.  Gene #32: 'Amp Peak 32(14q32.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 32(14Q32.33) CNV 1 3 2 32
AMP PEAK 32(14Q32.33) WILD-TYPE 64 89 63 108

Figure S177.  Get High-res Image Gene #32: 'Amp Peak 32(14q32.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 32(14q32.33)' versus 'MIRSEQ_CNMF'

P value = 3.19e-08 (Fisher's exact test), Q value = 1.7e-05

Table S178.  Gene #32: 'Amp Peak 32(14q32.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 32(14Q32.33) CNV 51 13 5
AMP PEAK 32(14Q32.33) WILD-TYPE 156 131 127

Figure S178.  Get High-res Image Gene #32: 'Amp Peak 32(14q32.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 32(14q32.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.09e-09 (Fisher's exact test), Q value = 1.2e-06

Table S179.  Gene #32: 'Amp Peak 32(14q32.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 32(14Q32.33) CNV 13 3 2 51
AMP PEAK 32(14Q32.33) WILD-TYPE 180 76 25 133

Figure S179.  Get High-res Image Gene #32: 'Amp Peak 32(14q32.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 33(16p11.2)' versus 'CN_CNMF'

P value = 5.49e-21 (Chi-square test), Q value = 4.7e-18

Table S180.  Gene #33: 'Amp Peak 33(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 33(16P11.2) CNV 2 6 46 1 0
AMP PEAK 33(16P11.2) WILD-TYPE 288 34 93 16 6

Figure S180.  Get High-res Image Gene #33: 'Amp Peak 33(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 33(16p11.2)' versus 'METHLYATION_CNMF'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.014

Table S181.  Gene #33: 'Amp Peak 33(16p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 33(16P11.2) CNV 30 10 6
AMP PEAK 33(16P11.2) WILD-TYPE 113 75 143

Figure S181.  Get High-res Image Gene #33: 'Amp Peak 33(16p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 33(16p11.2)' versus 'MRNASEQ_CNMF'

P value = 1.31e-09 (Fisher's exact test), Q value = 7.7e-07

Table S182.  Gene #33: 'Amp Peak 33(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 33(16P11.2) CNV 32 1 4
AMP PEAK 33(16P11.2) WILD-TYPE 110 106 109

Figure S182.  Get High-res Image Gene #33: 'Amp Peak 33(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 33(16p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.78e-09 (Fisher's exact test), Q value = 1e-06

Table S183.  Gene #33: 'Amp Peak 33(16p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 33(16P11.2) CNV 3 0 2 32
AMP PEAK 33(16P11.2) WILD-TYPE 62 92 63 108

Figure S183.  Get High-res Image Gene #33: 'Amp Peak 33(16p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 33(16p11.2)' versus 'MIRSEQ_CNMF'

P value = 4.87e-10 (Fisher's exact test), Q value = 2.9e-07

Table S184.  Gene #33: 'Amp Peak 33(16p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 33(16P11.2) CNV 44 4 4
AMP PEAK 33(16P11.2) WILD-TYPE 163 140 128

Figure S184.  Get High-res Image Gene #33: 'Amp Peak 33(16p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 33(16p11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.63e-09 (Fisher's exact test), Q value = 2.1e-06

Table S185.  Gene #33: 'Amp Peak 33(16p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 33(16P11.2) CNV 8 1 2 41
AMP PEAK 33(16P11.2) WILD-TYPE 185 78 25 143

Figure S185.  Get High-res Image Gene #33: 'Amp Peak 33(16p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 34(17q11.2)' versus 'CN_CNMF'

P value = 1.72e-26 (Chi-square test), Q value = 1.5e-23

Table S186.  Gene #34: 'Amp Peak 34(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 34(17Q11.2) CNV 4 1 55 2 1
AMP PEAK 34(17Q11.2) WILD-TYPE 286 39 84 15 5

Figure S186.  Get High-res Image Gene #34: 'Amp Peak 34(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 34(17q11.2)' versus 'METHLYATION_CNMF'

P value = 2.13e-11 (Fisher's exact test), Q value = 1.4e-08

Table S187.  Gene #34: 'Amp Peak 34(17q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 34(17Q11.2) CNV 42 9 3
AMP PEAK 34(17Q11.2) WILD-TYPE 101 76 146

Figure S187.  Get High-res Image Gene #34: 'Amp Peak 34(17q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 34(17q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.25e-10 (Fisher's exact test), Q value = 7.8e-08

Table S188.  Gene #34: 'Amp Peak 34(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 34(17Q11.2) CNV 31 2 1
AMP PEAK 34(17Q11.2) WILD-TYPE 111 105 112

Figure S188.  Get High-res Image Gene #34: 'Amp Peak 34(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 34(17q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.81e-10 (Fisher's exact test), Q value = 2.9e-07

Table S189.  Gene #34: 'Amp Peak 34(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 34(17Q11.2) CNV 0 0 4 30
AMP PEAK 34(17Q11.2) WILD-TYPE 65 92 61 110

Figure S189.  Get High-res Image Gene #34: 'Amp Peak 34(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 34(17q11.2)' versus 'MIRSEQ_CNMF'

P value = 2.32e-16 (Fisher's exact test), Q value = 1.8e-13

Table S190.  Gene #34: 'Amp Peak 34(17q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 34(17Q11.2) CNV 55 2 3
AMP PEAK 34(17Q11.2) WILD-TYPE 152 142 129

Figure S190.  Get High-res Image Gene #34: 'Amp Peak 34(17q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 34(17q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.28e-12 (Fisher's exact test), Q value = 8.9e-10

Table S191.  Gene #34: 'Amp Peak 34(17q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 34(17Q11.2) CNV 4 5 2 49
AMP PEAK 34(17Q11.2) WILD-TYPE 189 74 25 135

Figure S191.  Get High-res Image Gene #34: 'Amp Peak 34(17q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 35(17q12)' versus 'CN_CNMF'

P value = 5.56e-23 (Chi-square test), Q value = 4.9e-20

Table S192.  Gene #35: 'Amp Peak 35(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 35(17Q12) CNV 6 2 53 2 1
AMP PEAK 35(17Q12) WILD-TYPE 284 38 86 15 5

Figure S192.  Get High-res Image Gene #35: 'Amp Peak 35(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 35(17q12)' versus 'METHLYATION_CNMF'

P value = 1.42e-12 (Fisher's exact test), Q value = 9.8e-10

Table S193.  Gene #35: 'Amp Peak 35(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 35(17Q12) CNV 42 8 2
AMP PEAK 35(17Q12) WILD-TYPE 101 77 147

Figure S193.  Get High-res Image Gene #35: 'Amp Peak 35(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 35(17q12)' versus 'MRNASEQ_CNMF'

P value = 3.77e-13 (Fisher's exact test), Q value = 2.7e-10

Table S194.  Gene #35: 'Amp Peak 35(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 35(17Q12) CNV 37 2 1
AMP PEAK 35(17Q12) WILD-TYPE 105 105 112

Figure S194.  Get High-res Image Gene #35: 'Amp Peak 35(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 35(17q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.74e-10 (Fisher's exact test), Q value = 1.7e-07

Table S195.  Gene #35: 'Amp Peak 35(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 35(17Q12) CNV 0 1 5 34
AMP PEAK 35(17Q12) WILD-TYPE 65 91 60 106

Figure S195.  Get High-res Image Gene #35: 'Amp Peak 35(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 35(17q12)' versus 'MIRSEQ_CNMF'

P value = 6.27e-16 (Fisher's exact test), Q value = 4.8e-13

Table S196.  Gene #35: 'Amp Peak 35(17q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 35(17Q12) CNV 56 3 3
AMP PEAK 35(17Q12) WILD-TYPE 151 141 129

Figure S196.  Get High-res Image Gene #35: 'Amp Peak 35(17q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 35(17q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.88e-17 (Fisher's exact test), Q value = 6.9e-14

Table S197.  Gene #35: 'Amp Peak 35(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 35(17Q12) CNV 5 2 0 55
AMP PEAK 35(17Q12) WILD-TYPE 188 77 27 129

Figure S197.  Get High-res Image Gene #35: 'Amp Peak 35(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 36(17q25.1)' versus 'MRNA_CNMF'

P value = 0.000566 (Fisher's exact test), Q value = 0.22

Table S198.  Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 36(17Q25.1) CNV 0 9 1 0
AMP PEAK 36(17Q25.1) WILD-TYPE 13 9 13 8

Figure S198.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 36(17q25.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000109 (Fisher's exact test), Q value = 0.046

Table S199.  Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
AMP PEAK 36(17Q25.1) CNV 1 0 9
AMP PEAK 36(17Q25.1) WILD-TYPE 19 15 9

Figure S199.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 36(17q25.1)' versus 'CN_CNMF'

P value = 4.44e-41 (Chi-square test), Q value = 4.2e-38

Table S200.  Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 36(17Q25.1) CNV 5 4 79 1 1
AMP PEAK 36(17Q25.1) WILD-TYPE 285 36 60 16 5

Figure S200.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 36(17q25.1)' versus 'METHLYATION_CNMF'

P value = 1.36e-11 (Fisher's exact test), Q value = 8.9e-09

Table S201.  Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 36(17Q25.1) CNV 48 16 5
AMP PEAK 36(17Q25.1) WILD-TYPE 95 69 144

Figure S201.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 36(17q25.1)' versus 'MRNASEQ_CNMF'

P value = 2.59e-12 (Fisher's exact test), Q value = 1.8e-09

Table S202.  Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 36(17Q25.1) CNV 44 3 5
AMP PEAK 36(17Q25.1) WILD-TYPE 98 104 108

Figure S202.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 36(17q25.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.88e-13 (Fisher's exact test), Q value = 2.7e-10

Table S203.  Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 36(17Q25.1) CNV 1 1 6 44
AMP PEAK 36(17Q25.1) WILD-TYPE 64 91 59 96

Figure S203.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 36(17q25.1)' versus 'MIRSEQ_CNMF'

P value = 5.61e-17 (Fisher's exact test), Q value = 4.4e-14

Table S204.  Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 36(17Q25.1) CNV 72 9 5
AMP PEAK 36(17Q25.1) WILD-TYPE 135 135 127

Figure S204.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 36(17q25.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.58e-18 (Fisher's exact test), Q value = 6.1e-15

Table S205.  Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 36(17Q25.1) CNV 10 4 2 70
AMP PEAK 36(17Q25.1) WILD-TYPE 183 75 25 114

Figure S205.  Get High-res Image Gene #36: 'Amp Peak 36(17q25.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 37(18p11.31)' versus 'CN_CNMF'

P value = 2.43e-33 (Chi-square test), Q value = 2.2e-30

Table S206.  Gene #37: 'Amp Peak 37(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 37(18P11.31) CNV 5 5 69 2 0
AMP PEAK 37(18P11.31) WILD-TYPE 285 35 70 15 6

Figure S206.  Get High-res Image Gene #37: 'Amp Peak 37(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 37(18p11.31)' versus 'METHLYATION_CNMF'

P value = 5.53e-12 (Fisher's exact test), Q value = 3.7e-09

Table S207.  Gene #37: 'Amp Peak 37(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 37(18P11.31) CNV 49 15 5
AMP PEAK 37(18P11.31) WILD-TYPE 94 70 144

Figure S207.  Get High-res Image Gene #37: 'Amp Peak 37(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 37(18p11.31)' versus 'MRNASEQ_CNMF'

P value = 1.45e-11 (Fisher's exact test), Q value = 9.5e-09

Table S208.  Gene #37: 'Amp Peak 37(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 37(18P11.31) CNV 41 4 3
AMP PEAK 37(18P11.31) WILD-TYPE 101 103 110

Figure S208.  Get High-res Image Gene #37: 'Amp Peak 37(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 37(18p11.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.9e-13 (Fisher's exact test), Q value = 1.4e-10

Table S209.  Gene #37: 'Amp Peak 37(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 37(18P11.31) CNV 1 3 1 43
AMP PEAK 37(18P11.31) WILD-TYPE 64 89 64 97

Figure S209.  Get High-res Image Gene #37: 'Amp Peak 37(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 37(18p11.31)' versus 'MIRSEQ_CNMF'

P value = 1.28e-17 (Fisher's exact test), Q value = 1e-14

Table S210.  Gene #37: 'Amp Peak 37(18p11.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 37(18P11.31) CNV 69 7 4
AMP PEAK 37(18P11.31) WILD-TYPE 138 137 128

Figure S210.  Get High-res Image Gene #37: 'Amp Peak 37(18p11.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 37(18p11.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.02e-19 (Fisher's exact test), Q value = 2.5e-16

Table S211.  Gene #37: 'Amp Peak 37(18p11.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 37(18P11.31) CNV 8 3 1 68
AMP PEAK 37(18P11.31) WILD-TYPE 185 76 26 116

Figure S211.  Get High-res Image Gene #37: 'Amp Peak 37(18p11.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 38(18q11.2)' versus 'CN_CNMF'

P value = 4.94e-27 (Chi-square test), Q value = 4.5e-24

Table S212.  Gene #38: 'Amp Peak 38(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 38(18Q11.2) CNV 3 3 55 1 0
AMP PEAK 38(18Q11.2) WILD-TYPE 287 37 84 16 6

Figure S212.  Get High-res Image Gene #38: 'Amp Peak 38(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 38(18q11.2)' versus 'METHLYATION_CNMF'

P value = 3.19e-10 (Fisher's exact test), Q value = 1.9e-07

Table S213.  Gene #38: 'Amp Peak 38(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 38(18Q11.2) CNV 36 15 2
AMP PEAK 38(18Q11.2) WILD-TYPE 107 70 147

Figure S213.  Get High-res Image Gene #38: 'Amp Peak 38(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 38(18q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.17e-07 (Fisher's exact test), Q value = 6.1e-05

Table S214.  Gene #38: 'Amp Peak 38(18q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 38(18Q11.2) CNV 28 2 3
AMP PEAK 38(18Q11.2) WILD-TYPE 114 105 110

Figure S214.  Get High-res Image Gene #38: 'Amp Peak 38(18q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 38(18q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.53e-08 (Fisher's exact test), Q value = 2.4e-05

Table S215.  Gene #38: 'Amp Peak 38(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 38(18Q11.2) CNV 1 2 1 29
AMP PEAK 38(18Q11.2) WILD-TYPE 64 90 64 111

Figure S215.  Get High-res Image Gene #38: 'Amp Peak 38(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 38(18q11.2)' versus 'MIRSEQ_CNMF'

P value = 2.27e-14 (Fisher's exact test), Q value = 1.7e-11

Table S216.  Gene #38: 'Amp Peak 38(18q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 38(18Q11.2) CNV 54 3 4
AMP PEAK 38(18Q11.2) WILD-TYPE 153 141 128

Figure S216.  Get High-res Image Gene #38: 'Amp Peak 38(18q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 38(18q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.48e-17 (Fisher's exact test), Q value = 7.4e-14

Table S217.  Gene #38: 'Amp Peak 38(18q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 38(18Q11.2) CNV 3 3 1 54
AMP PEAK 38(18Q11.2) WILD-TYPE 190 76 26 130

Figure S217.  Get High-res Image Gene #38: 'Amp Peak 38(18q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 39(19p13.2)' versus 'MRNA_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.043

Table S218.  Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 39(19P13.2) CNV 0 9 0 0
AMP PEAK 39(19P13.2) WILD-TYPE 13 9 14 8

Figure S218.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 39(19p13.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0056

Table S219.  Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
AMP PEAK 39(19P13.2) CNV 0 0 9
AMP PEAK 39(19P13.2) WILD-TYPE 20 15 9

Figure S219.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 39(19p13.2)' versus 'CN_CNMF'

P value = 2.95e-46 (Chi-square test), Q value = 2.8e-43

Table S220.  Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 39(19P13.2) CNV 0 3 79 2 0
AMP PEAK 39(19P13.2) WILD-TYPE 290 37 60 15 6

Figure S220.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 39(19p13.2)' versus 'METHLYATION_CNMF'

P value = 1.22e-09 (Fisher's exact test), Q value = 7.2e-07

Table S221.  Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 39(19P13.2) CNV 46 19 7
AMP PEAK 39(19P13.2) WILD-TYPE 97 66 142

Figure S221.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 39(19p13.2)' versus 'MRNASEQ_CNMF'

P value = 1.09e-18 (Fisher's exact test), Q value = 9.1e-16

Table S222.  Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 39(19P13.2) CNV 49 1 2
AMP PEAK 39(19P13.2) WILD-TYPE 93 106 111

Figure S222.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 39(19p13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.76e-18 (Fisher's exact test), Q value = 1.4e-15

Table S223.  Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 39(19P13.2) CNV 1 0 2 49
AMP PEAK 39(19P13.2) WILD-TYPE 64 92 63 91

Figure S223.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 39(19p13.2)' versus 'MIRSEQ_CNMF'

P value = 1.03e-18 (Fisher's exact test), Q value = 8.6e-16

Table S224.  Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 39(19P13.2) CNV 70 9 2
AMP PEAK 39(19P13.2) WILD-TYPE 137 135 130

Figure S224.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 39(19p13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.45e-14 (Fisher's exact test), Q value = 1.1e-11

Table S225.  Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 39(19P13.2) CNV 11 3 4 63
AMP PEAK 39(19P13.2) WILD-TYPE 182 76 23 121

Figure S225.  Get High-res Image Gene #39: 'Amp Peak 39(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 40(19p13.11)' versus 'MRNA_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.097

Table S226.  Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 40(19P13.11) CNV 0 8 0 0
AMP PEAK 40(19P13.11) WILD-TYPE 13 10 14 8

Figure S226.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 40(19p13.11)' versus 'CN_CNMF'

P value = 1.47e-45 (Chi-square test), Q value = 1.4e-42

Table S227.  Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 40(19P13.11) CNV 0 2 78 2 1
AMP PEAK 40(19P13.11) WILD-TYPE 290 38 61 15 5

Figure S227.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 40(19p13.11)' versus 'METHLYATION_CNMF'

P value = 5.98e-12 (Fisher's exact test), Q value = 4e-09

Table S228.  Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 40(19P13.11) CNV 49 16 5
AMP PEAK 40(19P13.11) WILD-TYPE 94 69 144

Figure S228.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 40(19p13.11)' versus 'MRNASEQ_CNMF'

P value = 5e-17 (Fisher's exact test), Q value = 4e-14

Table S229.  Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 40(19P13.11) CNV 47 1 3
AMP PEAK 40(19P13.11) WILD-TYPE 95 106 110

Figure S229.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 40(19p13.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.37e-18 (Fisher's exact test), Q value = 4.4e-15

Table S230.  Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 40(19P13.11) CNV 1 0 2 48
AMP PEAK 40(19P13.11) WILD-TYPE 64 92 63 92

Figure S230.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 40(19p13.11)' versus 'MIRSEQ_CNMF'

P value = 2.77e-18 (Fisher's exact test), Q value = 2.3e-15

Table S231.  Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 40(19P13.11) CNV 70 8 3
AMP PEAK 40(19P13.11) WILD-TYPE 137 136 129

Figure S231.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 40(19p13.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.22e-18 (Fisher's exact test), Q value = 2.6e-15

Table S232.  Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 40(19P13.11) CNV 9 2 3 67
AMP PEAK 40(19P13.11) WILD-TYPE 184 77 24 117

Figure S232.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 41(19q12)' versus 'MRNA_CNMF'

P value = 0.000566 (Fisher's exact test), Q value = 0.22

Table S233.  Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 41(19Q12) CNV 0 9 1 0
AMP PEAK 41(19Q12) WILD-TYPE 13 9 13 8

Figure S233.  Get High-res Image Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 41(19q12)' versus 'CN_CNMF'

P value = 9.02e-49 (Chi-square test), Q value = 8.5e-46

Table S234.  Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 41(19Q12) CNV 4 4 89 4 0
AMP PEAK 41(19Q12) WILD-TYPE 286 36 50 13 6

Figure S234.  Get High-res Image Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 41(19q12)' versus 'METHLYATION_CNMF'

P value = 5.85e-17 (Fisher's exact test), Q value = 4.6e-14

Table S235.  Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 41(19Q12) CNV 62 19 5
AMP PEAK 41(19Q12) WILD-TYPE 81 66 144

Figure S235.  Get High-res Image Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 41(19q12)' versus 'MRNASEQ_CNMF'

P value = 2.87e-21 (Fisher's exact test), Q value = 2.5e-18

Table S236.  Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 41(19Q12) CNV 56 2 2
AMP PEAK 41(19Q12) WILD-TYPE 86 105 111

Figure S236.  Get High-res Image Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 41(19q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.66e-20 (Fisher's exact test), Q value = 2.3e-17

Table S237.  Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 41(19Q12) CNV 1 0 4 55
AMP PEAK 41(19Q12) WILD-TYPE 64 92 61 85

Figure S237.  Get High-res Image Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 41(19q12)' versus 'MIRSEQ_CNMF'

P value = 1.15e-26 (Fisher's exact test), Q value = 1e-23

Table S238.  Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 41(19Q12) CNV 87 8 2
AMP PEAK 41(19Q12) WILD-TYPE 120 136 130

Figure S238.  Get High-res Image Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 41(19q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.06e-24 (Fisher's exact test), Q value = 1.8e-21

Table S239.  Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 41(19Q12) CNV 11 2 2 82
AMP PEAK 41(19Q12) WILD-TYPE 182 77 25 102

Figure S239.  Get High-res Image Gene #41: 'Amp Peak 41(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 42(20p13)' versus 'CN_CNMF'

P value = 1.63e-33 (Chi-square test), Q value = 1.5e-30

Table S240.  Gene #42: 'Amp Peak 42(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 42(20P13) CNV 8 18 74 2 2
AMP PEAK 42(20P13) WILD-TYPE 282 22 65 15 4

Figure S240.  Get High-res Image Gene #42: 'Amp Peak 42(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 42(20p13)' versus 'METHLYATION_CNMF'

P value = 1.8e-09 (Fisher's exact test), Q value = 1.1e-06

Table S241.  Gene #42: 'Amp Peak 42(20p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 42(20P13) CNV 59 17 15
AMP PEAK 42(20P13) WILD-TYPE 84 68 134

Figure S241.  Get High-res Image Gene #42: 'Amp Peak 42(20p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 42(20p13)' versus 'MRNASEQ_CNMF'

P value = 3.74e-11 (Fisher's exact test), Q value = 2.4e-08

Table S242.  Gene #42: 'Amp Peak 42(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 42(20P13) CNV 52 7 9
AMP PEAK 42(20P13) WILD-TYPE 90 100 104

Figure S242.  Get High-res Image Gene #42: 'Amp Peak 42(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 42(20p13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.9e-11 (Fisher's exact test), Q value = 4.4e-08

Table S243.  Gene #42: 'Amp Peak 42(20p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 42(20P13) CNV 6 5 5 52
AMP PEAK 42(20P13) WILD-TYPE 59 87 60 88

Figure S243.  Get High-res Image Gene #42: 'Amp Peak 42(20p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 42(20p13)' versus 'MIRSEQ_CNMF'

P value = 1.52e-12 (Fisher's exact test), Q value = 1e-09

Table S244.  Gene #42: 'Amp Peak 42(20p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 42(20P13) CNV 77 14 12
AMP PEAK 42(20P13) WILD-TYPE 130 130 120

Figure S244.  Get High-res Image Gene #42: 'Amp Peak 42(20p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 42(20p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.15e-10 (Fisher's exact test), Q value = 7.2e-08

Table S245.  Gene #42: 'Amp Peak 42(20p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 42(20P13) CNV 19 11 3 70
AMP PEAK 42(20P13) WILD-TYPE 174 68 24 114

Figure S245.  Get High-res Image Gene #42: 'Amp Peak 42(20p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 43(20q11.21)' versus 'MRNA_CNMF'

P value = 0.000496 (Fisher's exact test), Q value = 0.19

Table S246.  Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
AMP PEAK 43(20Q11.21) CNV 1 9 0 0
AMP PEAK 43(20Q11.21) WILD-TYPE 12 9 14 8

Figure S246.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 43(20q11.21)' versus 'CN_CNMF'

P value = 6.65e-49 (Chi-square test), Q value = 6.3e-46

Table S247.  Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 43(20Q11.21) CNV 7 24 94 3 2
AMP PEAK 43(20Q11.21) WILD-TYPE 283 16 45 14 4

Figure S247.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 43(20q11.21)' versus 'METHLYATION_CNMF'

P value = 5.01e-12 (Fisher's exact test), Q value = 3.4e-09

Table S248.  Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 43(20Q11.21) CNV 72 20 19
AMP PEAK 43(20Q11.21) WILD-TYPE 71 65 130

Figure S248.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 43(20q11.21)' versus 'MRNASEQ_CNMF'

P value = 5.71e-16 (Fisher's exact test), Q value = 4.4e-13

Table S249.  Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 43(20Q11.21) CNV 62 8 7
AMP PEAK 43(20Q11.21) WILD-TYPE 80 99 106

Figure S249.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 43(20q11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-14 (Fisher's exact test), Q value = 7.5e-12

Table S250.  Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 43(20Q11.21) CNV 5 5 6 61
AMP PEAK 43(20Q11.21) WILD-TYPE 60 87 59 79

Figure S250.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 43(20q11.21)' versus 'MIRSEQ_CNMF'

P value = 3.5e-19 (Fisher's exact test), Q value = 2.9e-16

Table S251.  Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 43(20Q11.21) CNV 98 18 11
AMP PEAK 43(20Q11.21) WILD-TYPE 109 126 121

Figure S251.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 43(20q11.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.62e-15 (Fisher's exact test), Q value = 2e-12

Table S252.  Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 43(20Q11.21) CNV 25 12 2 88
AMP PEAK 43(20Q11.21) WILD-TYPE 168 67 25 96

Figure S252.  Get High-res Image Gene #43: 'Amp Peak 43(20q11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 44(20q13.12)' versus 'CN_CNMF'

P value = 2.71e-49 (Chi-square test), Q value = 2.6e-46

Table S253.  Gene #44: 'Amp Peak 44(20q13.12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 44(20Q13.12) CNV 9 25 96 3 3
AMP PEAK 44(20Q13.12) WILD-TYPE 281 15 43 14 3

Figure S253.  Get High-res Image Gene #44: 'Amp Peak 44(20q13.12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 44(20q13.12)' versus 'METHLYATION_CNMF'

P value = 1.81e-13 (Fisher's exact test), Q value = 1.3e-10

Table S254.  Gene #44: 'Amp Peak 44(20q13.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 44(20Q13.12) CNV 79 20 22
AMP PEAK 44(20Q13.12) WILD-TYPE 64 65 127

Figure S254.  Get High-res Image Gene #44: 'Amp Peak 44(20q13.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 44(20q13.12)' versus 'MRNASEQ_CNMF'

P value = 3.32e-15 (Fisher's exact test), Q value = 2.5e-12

Table S255.  Gene #44: 'Amp Peak 44(20q13.12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 44(20Q13.12) CNV 64 9 9
AMP PEAK 44(20Q13.12) WILD-TYPE 78 98 104

Figure S255.  Get High-res Image Gene #44: 'Amp Peak 44(20q13.12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 44(20q13.12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.03e-15 (Fisher's exact test), Q value = 3.8e-12

Table S256.  Gene #44: 'Amp Peak 44(20q13.12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 44(20Q13.12) CNV 5 6 7 64
AMP PEAK 44(20Q13.12) WILD-TYPE 60 86 58 76

Figure S256.  Get High-res Image Gene #44: 'Amp Peak 44(20q13.12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 44(20q13.12)' versus 'MIRSEQ_CNMF'

P value = 5.09e-18 (Fisher's exact test), Q value = 4.1e-15

Table S257.  Gene #44: 'Amp Peak 44(20q13.12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 44(20Q13.12) CNV 101 20 14
AMP PEAK 44(20Q13.12) WILD-TYPE 106 124 118

Figure S257.  Get High-res Image Gene #44: 'Amp Peak 44(20q13.12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 44(20q13.12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.74e-15 (Fisher's exact test), Q value = 7.2e-12

Table S258.  Gene #44: 'Amp Peak 44(20q13.12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 44(20Q13.12) CNV 26 14 4 91
AMP PEAK 44(20Q13.12) WILD-TYPE 167 65 23 93

Figure S258.  Get High-res Image Gene #44: 'Amp Peak 44(20q13.12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 45(20q13.33)' versus 'CN_CNMF'

P value = 1.54e-46 (Chi-square test), Q value = 1.4e-43

Table S259.  Gene #45: 'Amp Peak 45(20q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 45(20Q13.33) CNV 10 27 91 3 3
AMP PEAK 45(20Q13.33) WILD-TYPE 280 13 48 14 3

Figure S259.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 45(20q13.33)' versus 'METHLYATION_CNMF'

P value = 1.43e-10 (Fisher's exact test), Q value = 8.8e-08

Table S260.  Gene #45: 'Amp Peak 45(20q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 45(20Q13.33) CNV 73 21 23
AMP PEAK 45(20Q13.33) WILD-TYPE 70 64 126

Figure S260.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 45(20q13.33)' versus 'MRNASEQ_CNMF'

P value = 5.7e-13 (Fisher's exact test), Q value = 4e-10

Table S261.  Gene #45: 'Amp Peak 45(20q13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 45(20Q13.33) CNV 61 9 11
AMP PEAK 45(20Q13.33) WILD-TYPE 81 98 102

Figure S261.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 45(20q13.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.5e-14 (Fisher's exact test), Q value = 6.1e-11

Table S262.  Gene #45: 'Amp Peak 45(20q13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 45(20Q13.33) CNV 5 6 8 62
AMP PEAK 45(20Q13.33) WILD-TYPE 60 86 57 78

Figure S262.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 45(20q13.33)' versus 'MIRSEQ_CNMF'

P value = 5.18e-17 (Fisher's exact test), Q value = 4.1e-14

Table S263.  Gene #45: 'Amp Peak 45(20q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 45(20Q13.33) CNV 98 21 13
AMP PEAK 45(20Q13.33) WILD-TYPE 109 123 119

Figure S263.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 45(20q13.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.14e-13 (Fisher's exact test), Q value = 5.7e-10

Table S264.  Gene #45: 'Amp Peak 45(20q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 45(20Q13.33) CNV 27 13 5 87
AMP PEAK 45(20Q13.33) WILD-TYPE 166 66 22 97

Figure S264.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 46(22q12.2)' versus 'CN_CNMF'

P value = 2.31e-18 (Chi-square test), Q value = 1.9e-15

Table S265.  Gene #46: 'Amp Peak 46(22q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 46(22Q12.2) CNV 4 4 44 1 1
AMP PEAK 46(22Q12.2) WILD-TYPE 286 36 95 16 5

Figure S265.  Get High-res Image Gene #46: 'Amp Peak 46(22q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 46(22q12.2)' versus 'METHLYATION_CNMF'

P value = 1.88e-14 (Fisher's exact test), Q value = 1.4e-11

Table S266.  Gene #46: 'Amp Peak 46(22q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
AMP PEAK 46(22Q12.2) CNV 40 8 0
AMP PEAK 46(22Q12.2) WILD-TYPE 103 77 149

Figure S266.  Get High-res Image Gene #46: 'Amp Peak 46(22q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 46(22q12.2)' versus 'MRNASEQ_CNMF'

P value = 6.35e-13 (Fisher's exact test), Q value = 4.4e-10

Table S267.  Gene #46: 'Amp Peak 46(22q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
AMP PEAK 46(22Q12.2) CNV 32 0 1
AMP PEAK 46(22Q12.2) WILD-TYPE 110 107 112

Figure S267.  Get High-res Image Gene #46: 'Amp Peak 46(22q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 46(22q12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.42e-11 (Fisher's exact test), Q value = 5.3e-08

Table S268.  Gene #46: 'Amp Peak 46(22q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
AMP PEAK 46(22Q12.2) CNV 1 0 1 31
AMP PEAK 46(22Q12.2) WILD-TYPE 64 92 64 109

Figure S268.  Get High-res Image Gene #46: 'Amp Peak 46(22q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 46(22q12.2)' versus 'MIRSEQ_CNMF'

P value = 1.93e-19 (Fisher's exact test), Q value = 1.6e-16

Table S269.  Gene #46: 'Amp Peak 46(22q12.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
AMP PEAK 46(22Q12.2) CNV 52 0 1
AMP PEAK 46(22Q12.2) WILD-TYPE 155 144 131

Figure S269.  Get High-res Image Gene #46: 'Amp Peak 46(22q12.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 46(22q12.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.32e-18 (Fisher's exact test), Q value = 5.9e-15

Table S270.  Gene #46: 'Amp Peak 46(22q12.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
AMP PEAK 46(22Q12.2) CNV 2 1 0 50
AMP PEAK 46(22Q12.2) WILD-TYPE 191 78 27 134

Figure S270.  Get High-res Image Gene #46: 'Amp Peak 46(22q12.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 47(Xp11.23)' versus 'CN_CNMF'

P value = 1.88e-25 (Chi-square test), Q value = 1.7e-22

Table S271.  Gene #47: 'Amp Peak 47(Xp11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 47(XP11.23) CNV 10 16 42 14 2
AMP PEAK 47(XP11.23) WILD-TYPE 280 24 97 3 4

Figure S271.  Get High-res Image Gene #47: 'Amp Peak 47(Xp11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 48(Xq28)' versus 'CN_CNMF'

P value = 4.98e-24 (Chi-square test), Q value = 4.4e-21

Table S272.  Gene #48: 'Amp Peak 48(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
AMP PEAK 48(XQ28) CNV 12 16 41 14 2
AMP PEAK 48(XQ28) WILD-TYPE 278 24 98 3 4

Figure S272.  Get High-res Image Gene #48: 'Amp Peak 48(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.21)' versus 'CN_CNMF'

P value = 1.79e-23 (Chi-square test), Q value = 1.6e-20

Table S273.  Gene #49: 'Del Peak 1(1p36.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 1(1P36.21) CNV 3 7 51 1 3
DEL PEAK 1(1P36.21) WILD-TYPE 287 33 88 16 3

Figure S273.  Get High-res Image Gene #49: 'Del Peak 1(1p36.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.21)' versus 'METHLYATION_CNMF'

P value = 3.67e-07 (Fisher's exact test), Q value = 0.00019

Table S274.  Gene #49: 'Del Peak 1(1p36.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 1(1P36.21) CNV 34 15 5
DEL PEAK 1(1P36.21) WILD-TYPE 109 70 144

Figure S274.  Get High-res Image Gene #49: 'Del Peak 1(1p36.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.21)' versus 'MRNASEQ_CNMF'

P value = 1.55e-11 (Fisher's exact test), Q value = 1e-08

Table S275.  Gene #49: 'Del Peak 1(1p36.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 1(1P36.21) CNV 35 0 5
DEL PEAK 1(1P36.21) WILD-TYPE 107 107 108

Figure S275.  Get High-res Image Gene #49: 'Del Peak 1(1p36.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.33e-09 (Fisher's exact test), Q value = 4.1e-06

Table S276.  Gene #49: 'Del Peak 1(1p36.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 1(1P36.21) CNV 2 0 6 32
DEL PEAK 1(1P36.21) WILD-TYPE 63 92 59 108

Figure S276.  Get High-res Image Gene #49: 'Del Peak 1(1p36.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.21)' versus 'MIRSEQ_CNMF'

P value = 5.45e-09 (Fisher's exact test), Q value = 3.1e-06

Table S277.  Gene #49: 'Del Peak 1(1p36.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 1(1P36.21) CNV 49 7 6
DEL PEAK 1(1P36.21) WILD-TYPE 158 137 126

Figure S277.  Get High-res Image Gene #49: 'Del Peak 1(1p36.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.53e-10 (Fisher's exact test), Q value = 9.5e-08

Table S278.  Gene #49: 'Del Peak 1(1p36.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 1(1P36.21) CNV 5 7 3 47
DEL PEAK 1(1P36.21) WILD-TYPE 188 72 24 137

Figure S278.  Get High-res Image Gene #49: 'Del Peak 1(1p36.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 2(1p36.11)' versus 'CN_CNMF'

P value = 9.91e-33 (Chi-square test), Q value = 9.1e-30

Table S279.  Gene #50: 'Del Peak 2(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 2(1P36.11) CNV 2 7 65 1 3
DEL PEAK 2(1P36.11) WILD-TYPE 288 33 74 16 3

Figure S279.  Get High-res Image Gene #50: 'Del Peak 2(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p36.11)' versus 'METHLYATION_CNMF'

P value = 6.98e-11 (Fisher's exact test), Q value = 4.4e-08

Table S280.  Gene #50: 'Del Peak 2(1p36.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 2(1P36.11) CNV 48 15 6
DEL PEAK 2(1P36.11) WILD-TYPE 95 70 143

Figure S280.  Get High-res Image Gene #50: 'Del Peak 2(1p36.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 2(1p36.11)' versus 'MRNASEQ_CNMF'

P value = 1.96e-12 (Fisher's exact test), Q value = 1.3e-09

Table S281.  Gene #50: 'Del Peak 2(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 2(1P36.11) CNV 37 0 5
DEL PEAK 2(1P36.11) WILD-TYPE 105 107 108

Figure S281.  Get High-res Image Gene #50: 'Del Peak 2(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p36.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.18e-11 (Fisher's exact test), Q value = 2e-08

Table S282.  Gene #50: 'Del Peak 2(1p36.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 2(1P36.11) CNV 1 0 5 36
DEL PEAK 2(1P36.11) WILD-TYPE 64 92 60 104

Figure S282.  Get High-res Image Gene #50: 'Del Peak 2(1p36.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p36.11)' versus 'MIRSEQ_CNMF'

P value = 1.66e-14 (Fisher's exact test), Q value = 1.2e-11

Table S283.  Gene #50: 'Del Peak 2(1p36.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 2(1P36.11) CNV 63 7 5
DEL PEAK 2(1P36.11) WILD-TYPE 144 137 127

Figure S283.  Get High-res Image Gene #50: 'Del Peak 2(1p36.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 2(1p36.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.64e-16 (Fisher's exact test), Q value = 6.6e-13

Table S284.  Gene #50: 'Del Peak 2(1p36.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 2(1P36.11) CNV 5 6 4 60
DEL PEAK 2(1P36.11) WILD-TYPE 188 73 23 124

Figure S284.  Get High-res Image Gene #50: 'Del Peak 2(1p36.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(2p25.3)' versus 'CN_CNMF'

P value = 6.48e-09 (Chi-square test), Q value = 3.7e-06

Table S285.  Gene #52: 'Del Peak 4(2p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 4(2P25.3) CNV 2 1 21 0 0
DEL PEAK 4(2P25.3) WILD-TYPE 288 39 118 17 6

Figure S285.  Get High-res Image Gene #52: 'Del Peak 4(2p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(2p25.3)' versus 'METHLYATION_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.21

Table S286.  Gene #52: 'Del Peak 4(2p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 4(2P25.3) CNV 17 4 2
DEL PEAK 4(2P25.3) WILD-TYPE 126 81 147

Figure S286.  Get High-res Image Gene #52: 'Del Peak 4(2p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 4(2p25.3)' versus 'MRNASEQ_CNMF'

P value = 8.8e-05 (Fisher's exact test), Q value = 0.038

Table S287.  Gene #52: 'Del Peak 4(2p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 4(2P25.3) CNV 13 0 1
DEL PEAK 4(2P25.3) WILD-TYPE 129 107 112

Figure S287.  Get High-res Image Gene #52: 'Del Peak 4(2p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 4(2p25.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000323 (Fisher's exact test), Q value = 0.13

Table S288.  Gene #52: 'Del Peak 4(2p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 4(2P25.3) CNV 1 0 0 13
DEL PEAK 4(2P25.3) WILD-TYPE 64 92 65 127

Figure S288.  Get High-res Image Gene #52: 'Del Peak 4(2p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(2q22.1)' versus 'CN_CNMF'

P value = 2.7e-20 (Chi-square test), Q value = 2.3e-17

Table S289.  Gene #53: 'Del Peak 5(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 5(2Q22.1) CNV 0 4 40 0 0
DEL PEAK 5(2Q22.1) WILD-TYPE 290 36 99 17 6

Figure S289.  Get High-res Image Gene #53: 'Del Peak 5(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(2q22.1)' versus 'METHLYATION_CNMF'

P value = 0.000179 (Fisher's exact test), Q value = 0.074

Table S290.  Gene #53: 'Del Peak 5(2q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 5(2Q22.1) CNV 23 10 4
DEL PEAK 5(2Q22.1) WILD-TYPE 120 75 145

Figure S290.  Get High-res Image Gene #53: 'Del Peak 5(2q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(2q22.1)' versus 'MRNASEQ_CNMF'

P value = 1.55e-08 (Fisher's exact test), Q value = 8.6e-06

Table S291.  Gene #53: 'Del Peak 5(2q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 5(2Q22.1) CNV 22 1 0
DEL PEAK 5(2Q22.1) WILD-TYPE 120 106 113

Figure S291.  Get High-res Image Gene #53: 'Del Peak 5(2q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(2q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.77e-08 (Fisher's exact test), Q value = 4.1e-05

Table S292.  Gene #53: 'Del Peak 5(2q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 5(2Q22.1) CNV 0 0 1 22
DEL PEAK 5(2Q22.1) WILD-TYPE 65 92 64 118

Figure S292.  Get High-res Image Gene #53: 'Del Peak 5(2q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(2q22.1)' versus 'MIRSEQ_CNMF'

P value = 1.62e-07 (Fisher's exact test), Q value = 8.4e-05

Table S293.  Gene #53: 'Del Peak 5(2q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 5(2Q22.1) CNV 35 4 3
DEL PEAK 5(2Q22.1) WILD-TYPE 172 140 129

Figure S293.  Get High-res Image Gene #53: 'Del Peak 5(2q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 5(2q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.01e-05 (Fisher's exact test), Q value = 0.0092

Table S294.  Gene #53: 'Del Peak 5(2q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 5(2Q22.1) CNV 6 4 1 31
DEL PEAK 5(2Q22.1) WILD-TYPE 187 75 26 153

Figure S294.  Get High-res Image Gene #53: 'Del Peak 5(2q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(2q37.3)' versus 'CN_CNMF'

P value = 7.94e-17 (Chi-square test), Q value = 6.2e-14

Table S295.  Gene #54: 'Del Peak 6(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 6(2Q37.3) CNV 3 7 39 0 0
DEL PEAK 6(2Q37.3) WILD-TYPE 287 33 100 17 6

Figure S295.  Get High-res Image Gene #54: 'Del Peak 6(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(2q37.3)' versus 'METHLYATION_CNMF'

P value = 4.56e-05 (Fisher's exact test), Q value = 0.02

Table S296.  Gene #54: 'Del Peak 6(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 6(2Q37.3) CNV 31 6 8
DEL PEAK 6(2Q37.3) WILD-TYPE 112 79 141

Figure S296.  Get High-res Image Gene #54: 'Del Peak 6(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(2q37.3)' versus 'MRNASEQ_CNMF'

P value = 1.36e-05 (Fisher's exact test), Q value = 0.0062

Table S297.  Gene #54: 'Del Peak 6(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 6(2Q37.3) CNV 21 2 2
DEL PEAK 6(2Q37.3) WILD-TYPE 121 105 111

Figure S297.  Get High-res Image Gene #54: 'Del Peak 6(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 6(2q37.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.43e-06 (Fisher's exact test), Q value = 7e-04

Table S298.  Gene #54: 'Del Peak 6(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 6(2Q37.3) CNV 0 0 4 21
DEL PEAK 6(2Q37.3) WILD-TYPE 65 92 61 119

Figure S298.  Get High-res Image Gene #54: 'Del Peak 6(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(2q37.3)' versus 'MIRSEQ_CNMF'

P value = 0.000248 (Fisher's exact test), Q value = 0.1

Table S299.  Gene #54: 'Del Peak 6(2q37.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 6(2Q37.3) CNV 34 8 6
DEL PEAK 6(2Q37.3) WILD-TYPE 173 136 126

Figure S299.  Get High-res Image Gene #54: 'Del Peak 6(2q37.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 6(2q37.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000461 (Fisher's exact test), Q value = 0.18

Table S300.  Gene #54: 'Del Peak 6(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 6(2Q37.3) CNV 10 4 2 32
DEL PEAK 6(2Q37.3) WILD-TYPE 183 75 25 152

Figure S300.  Get High-res Image Gene #54: 'Del Peak 6(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(3p14.2)' versus 'CN_CNMF'

P value = 5.91e-31 (Chi-square test), Q value = 5.4e-28

Table S301.  Gene #55: 'Del Peak 7(3p14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 7(3P14.2) CNV 1 8 60 0 0
DEL PEAK 7(3P14.2) WILD-TYPE 289 32 79 17 6

Figure S301.  Get High-res Image Gene #55: 'Del Peak 7(3p14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(3p14.2)' versus 'METHLYATION_CNMF'

P value = 1.22e-09 (Fisher's exact test), Q value = 7.2e-07

Table S302.  Gene #55: 'Del Peak 7(3p14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 7(3P14.2) CNV 40 14 4
DEL PEAK 7(3P14.2) WILD-TYPE 103 71 145

Figure S302.  Get High-res Image Gene #55: 'Del Peak 7(3p14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 7(3p14.2)' versus 'MRNASEQ_CNMF'

P value = 3.77e-15 (Fisher's exact test), Q value = 2.8e-12

Table S303.  Gene #55: 'Del Peak 7(3p14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 7(3P14.2) CNV 41 2 1
DEL PEAK 7(3P14.2) WILD-TYPE 101 105 112

Figure S303.  Get High-res Image Gene #55: 'Del Peak 7(3p14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 7(3p14.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.8e-14 (Fisher's exact test), Q value = 1.3e-11

Table S304.  Gene #55: 'Del Peak 7(3p14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 7(3P14.2) CNV 0 1 2 41
DEL PEAK 7(3P14.2) WILD-TYPE 65 91 63 99

Figure S304.  Get High-res Image Gene #55: 'Del Peak 7(3p14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(3p14.2)' versus 'MIRSEQ_CNMF'

P value = 1.39e-13 (Fisher's exact test), Q value = 1e-10

Table S305.  Gene #55: 'Del Peak 7(3p14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 7(3P14.2) CNV 57 4 6
DEL PEAK 7(3P14.2) WILD-TYPE 150 140 126

Figure S305.  Get High-res Image Gene #55: 'Del Peak 7(3p14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 7(3p14.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.98e-12 (Fisher's exact test), Q value = 1.4e-09

Table S306.  Gene #55: 'Del Peak 7(3p14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 7(3P14.2) CNV 6 6 2 53
DEL PEAK 7(3P14.2) WILD-TYPE 187 73 25 131

Figure S306.  Get High-res Image Gene #55: 'Del Peak 7(3p14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(3q13.31)' versus 'CN_CNMF'

P value = 1.44e-12 (Chi-square test), Q value = 9.9e-10

Table S307.  Gene #56: 'Del Peak 8(3q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 8(3Q13.31) CNV 1 1 26 0 0
DEL PEAK 8(3Q13.31) WILD-TYPE 289 39 113 17 6

Figure S307.  Get High-res Image Gene #56: 'Del Peak 8(3q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(3q13.31)' versus 'MRNASEQ_CNMF'

P value = 0.000246 (Fisher's exact test), Q value = 0.1

Table S308.  Gene #56: 'Del Peak 8(3q13.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 8(3Q13.31) CNV 12 0 1
DEL PEAK 8(3Q13.31) WILD-TYPE 130 107 112

Figure S308.  Get High-res Image Gene #56: 'Del Peak 8(3q13.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 8(3q13.31)' versus 'MIRSEQ_CNMF'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.001

Table S309.  Gene #56: 'Del Peak 8(3q13.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 8(3Q13.31) CNV 24 2 1
DEL PEAK 8(3Q13.31) WILD-TYPE 183 142 131

Figure S309.  Get High-res Image Gene #56: 'Del Peak 8(3q13.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 8(3q13.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.27e-06 (Fisher's exact test), Q value = 0.0034

Table S310.  Gene #56: 'Del Peak 8(3q13.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 8(3Q13.31) CNV 4 0 0 23
DEL PEAK 8(3Q13.31) WILD-TYPE 189 79 27 161

Figure S310.  Get High-res Image Gene #56: 'Del Peak 8(3q13.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 9(4p16.3)' versus 'CN_CNMF'

P value = 1.41e-30 (Chi-square test), Q value = 1.3e-27

Table S311.  Gene #57: 'Del Peak 9(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 9(4P16.3) CNV 4 12 67 3 1
DEL PEAK 9(4P16.3) WILD-TYPE 286 28 72 14 5

Figure S311.  Get High-res Image Gene #57: 'Del Peak 9(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4p16.3)' versus 'METHLYATION_CNMF'

P value = 1.74e-12 (Fisher's exact test), Q value = 1.2e-09

Table S312.  Gene #57: 'Del Peak 9(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 9(4P16.3) CNV 54 14 7
DEL PEAK 9(4P16.3) WILD-TYPE 89 71 142

Figure S312.  Get High-res Image Gene #57: 'Del Peak 9(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 9(4p16.3)' versus 'MRNASEQ_CNMF'

P value = 1.57e-10 (Fisher's exact test), Q value = 9.7e-08

Table S313.  Gene #57: 'Del Peak 9(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 9(4P16.3) CNV 40 4 4
DEL PEAK 9(4P16.3) WILD-TYPE 102 103 109

Figure S313.  Get High-res Image Gene #57: 'Del Peak 9(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 9(4p16.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.13e-11 (Fisher's exact test), Q value = 5.7e-08

Table S314.  Gene #57: 'Del Peak 9(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 9(4P16.3) CNV 1 2 5 40
DEL PEAK 9(4P16.3) WILD-TYPE 64 90 60 100

Figure S314.  Get High-res Image Gene #57: 'Del Peak 9(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(4p16.3)' versus 'MIRSEQ_CNMF'

P value = 4.73e-15 (Fisher's exact test), Q value = 3.5e-12

Table S315.  Gene #57: 'Del Peak 9(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 9(4P16.3) CNV 69 9 6
DEL PEAK 9(4P16.3) WILD-TYPE 138 135 126

Figure S315.  Get High-res Image Gene #57: 'Del Peak 9(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 9(4p16.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.11e-13 (Fisher's exact test), Q value = 4.3e-10

Table S316.  Gene #57: 'Del Peak 9(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 9(4P16.3) CNV 9 9 4 62
DEL PEAK 9(4P16.3) WILD-TYPE 184 70 23 122

Figure S316.  Get High-res Image Gene #57: 'Del Peak 9(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(4p15.31)' versus 'CN_CNMF'

P value = 4.15e-35 (Chi-square test), Q value = 3.8e-32

Table S317.  Gene #58: 'Del Peak 10(4p15.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 10(4P15.31) CNV 3 12 72 3 0
DEL PEAK 10(4P15.31) WILD-TYPE 287 28 67 14 6

Figure S317.  Get High-res Image Gene #58: 'Del Peak 10(4p15.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4p15.31)' versus 'METHLYATION_CNMF'

P value = 9.13e-14 (Fisher's exact test), Q value = 6.5e-11

Table S318.  Gene #58: 'Del Peak 10(4p15.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 10(4P15.31) CNV 56 16 6
DEL PEAK 10(4P15.31) WILD-TYPE 87 69 143

Figure S318.  Get High-res Image Gene #58: 'Del Peak 10(4p15.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(4p15.31)' versus 'MRNASEQ_CNMF'

P value = 3.81e-11 (Fisher's exact test), Q value = 2.4e-08

Table S319.  Gene #58: 'Del Peak 10(4p15.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 10(4P15.31) CNV 40 3 4
DEL PEAK 10(4P15.31) WILD-TYPE 102 104 109

Figure S319.  Get High-res Image Gene #58: 'Del Peak 10(4p15.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(4p15.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.36e-11 (Fisher's exact test), Q value = 2.8e-08

Table S320.  Gene #58: 'Del Peak 10(4p15.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 10(4P15.31) CNV 1 2 4 40
DEL PEAK 10(4P15.31) WILD-TYPE 64 90 61 100

Figure S320.  Get High-res Image Gene #58: 'Del Peak 10(4p15.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(4p15.31)' versus 'MIRSEQ_CNMF'

P value = 1.18e-18 (Fisher's exact test), Q value = 9.8e-16

Table S321.  Gene #58: 'Del Peak 10(4p15.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 10(4P15.31) CNV 75 8 5
DEL PEAK 10(4P15.31) WILD-TYPE 132 136 127

Figure S321.  Get High-res Image Gene #58: 'Del Peak 10(4p15.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 10(4p15.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.21e-16 (Fisher's exact test), Q value = 2.5e-13

Table S322.  Gene #58: 'Del Peak 10(4p15.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 10(4P15.31) CNV 8 8 4 68
DEL PEAK 10(4P15.31) WILD-TYPE 185 71 23 116

Figure S322.  Get High-res Image Gene #58: 'Del Peak 10(4p15.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(4q22.1)' versus 'CN_CNMF'

P value = 1.04e-46 (Chi-square test), Q value = 9.8e-44

Table S323.  Gene #59: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 11(4Q22.1) CNV 2 9 86 1 1
DEL PEAK 11(4Q22.1) WILD-TYPE 288 31 53 16 5

Figure S323.  Get High-res Image Gene #59: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q22.1)' versus 'METHLYATION_CNMF'

P value = 2.05e-18 (Fisher's exact test), Q value = 1.7e-15

Table S324.  Gene #59: 'Del Peak 11(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 11(4Q22.1) CNV 63 17 4
DEL PEAK 11(4Q22.1) WILD-TYPE 80 68 145

Figure S324.  Get High-res Image Gene #59: 'Del Peak 11(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 11(4q22.1)' versus 'MRNASEQ_CNMF'

P value = 1.1e-16 (Fisher's exact test), Q value = 8.6e-14

Table S325.  Gene #59: 'Del Peak 11(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 11(4Q22.1) CNV 50 2 4
DEL PEAK 11(4Q22.1) WILD-TYPE 92 105 109

Figure S325.  Get High-res Image Gene #59: 'Del Peak 11(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 11(4q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.16e-18 (Fisher's exact test), Q value = 9.7e-16

Table S326.  Gene #59: 'Del Peak 11(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 11(4Q22.1) CNV 1 1 2 52
DEL PEAK 11(4Q22.1) WILD-TYPE 64 91 63 88

Figure S326.  Get High-res Image Gene #59: 'Del Peak 11(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(4q22.1)' versus 'MIRSEQ_CNMF'

P value = 2.6e-24 (Fisher's exact test), Q value = 2.3e-21

Table S327.  Gene #59: 'Del Peak 11(4q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 11(4Q22.1) CNV 85 7 4
DEL PEAK 11(4Q22.1) WILD-TYPE 122 137 128

Figure S327.  Get High-res Image Gene #59: 'Del Peak 11(4q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 11(4q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.82e-24 (Fisher's exact test), Q value = 6e-21

Table S328.  Gene #59: 'Del Peak 11(4q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 11(4Q22.1) CNV 5 7 5 79
DEL PEAK 11(4Q22.1) WILD-TYPE 188 72 22 105

Figure S328.  Get High-res Image Gene #59: 'Del Peak 11(4q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(4q34.3)' versus 'CN_CNMF'

P value = 1.43e-51 (Chi-square test), Q value = 1.4e-48

Table S329.  Gene #60: 'Del Peak 12(4q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 12(4Q34.3) CNV 6 10 97 1 1
DEL PEAK 12(4Q34.3) WILD-TYPE 284 30 42 16 5

Figure S329.  Get High-res Image Gene #60: 'Del Peak 12(4q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(4q34.3)' versus 'METHLYATION_CNMF'

P value = 2.7e-15 (Fisher's exact test), Q value = 2e-12

Table S330.  Gene #60: 'Del Peak 12(4q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 12(4Q34.3) CNV 66 23 9
DEL PEAK 12(4Q34.3) WILD-TYPE 77 62 140

Figure S330.  Get High-res Image Gene #60: 'Del Peak 12(4q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(4q34.3)' versus 'MRNASEQ_CNMF'

P value = 1.31e-18 (Fisher's exact test), Q value = 1.1e-15

Table S331.  Gene #60: 'Del Peak 12(4q34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 12(4Q34.3) CNV 59 3 6
DEL PEAK 12(4Q34.3) WILD-TYPE 83 104 107

Figure S331.  Get High-res Image Gene #60: 'Del Peak 12(4q34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(4q34.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.83e-20 (Fisher's exact test), Q value = 7.5e-17

Table S332.  Gene #60: 'Del Peak 12(4q34.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 12(4Q34.3) CNV 1 1 7 59
DEL PEAK 12(4Q34.3) WILD-TYPE 64 91 58 81

Figure S332.  Get High-res Image Gene #60: 'Del Peak 12(4q34.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(4q34.3)' versus 'MIRSEQ_CNMF'

P value = 1.45e-21 (Fisher's exact test), Q value = 1.3e-18

Table S333.  Gene #60: 'Del Peak 12(4q34.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 12(4Q34.3) CNV 92 8 12
DEL PEAK 12(4Q34.3) WILD-TYPE 115 136 120

Figure S333.  Get High-res Image Gene #60: 'Del Peak 12(4q34.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(4q34.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.27e-23 (Fisher's exact test), Q value = 2.9e-20

Table S334.  Gene #60: 'Del Peak 12(4q34.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 12(4Q34.3) CNV 9 10 6 87
DEL PEAK 12(4Q34.3) WILD-TYPE 184 69 21 97

Figure S334.  Get High-res Image Gene #60: 'Del Peak 12(4q34.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(5q11.2)' versus 'CN_CNMF'

P value = 8.55e-49 (Chi-square test), Q value = 8.1e-46

Table S335.  Gene #61: 'Del Peak 13(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 13(5Q11.2) CNV 0 11 87 2 0
DEL PEAK 13(5Q11.2) WILD-TYPE 290 29 52 15 6

Figure S335.  Get High-res Image Gene #61: 'Del Peak 13(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(5q11.2)' versus 'METHLYATION_CNMF'

P value = 1.18e-16 (Fisher's exact test), Q value = 9.2e-14

Table S336.  Gene #61: 'Del Peak 13(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 13(5Q11.2) CNV 63 16 6
DEL PEAK 13(5Q11.2) WILD-TYPE 80 69 143

Figure S336.  Get High-res Image Gene #61: 'Del Peak 13(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 13(5q11.2)' versus 'MRNASEQ_CNMF'

P value = 7.39e-17 (Fisher's exact test), Q value = 5.8e-14

Table S337.  Gene #61: 'Del Peak 13(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 13(5Q11.2) CNV 49 2 3
DEL PEAK 13(5Q11.2) WILD-TYPE 93 105 110

Figure S337.  Get High-res Image Gene #61: 'Del Peak 13(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(5q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.24e-17 (Fisher's exact test), Q value = 2.6e-14

Table S338.  Gene #61: 'Del Peak 13(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 13(5Q11.2) CNV 0 1 4 49
DEL PEAK 13(5Q11.2) WILD-TYPE 65 91 61 91

Figure S338.  Get High-res Image Gene #61: 'Del Peak 13(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(5q11.2)' versus 'MIRSEQ_CNMF'

P value = 3.5e-19 (Fisher's exact test), Q value = 2.9e-16

Table S339.  Gene #61: 'Del Peak 13(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 13(5Q11.2) CNV 82 11 6
DEL PEAK 13(5Q11.2) WILD-TYPE 125 133 126

Figure S339.  Get High-res Image Gene #61: 'Del Peak 13(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 13(5q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.56e-18 (Fisher's exact test), Q value = 2.9e-15

Table S340.  Gene #61: 'Del Peak 13(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 13(5Q11.2) CNV 10 8 5 76
DEL PEAK 13(5Q11.2) WILD-TYPE 183 71 22 108

Figure S340.  Get High-res Image Gene #61: 'Del Peak 13(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(6q26)' versus 'CN_CNMF'

P value = 9.63e-15 (Chi-square test), Q value = 7.2e-12

Table S341.  Gene #62: 'Del Peak 14(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 14(6Q26) CNV 4 4 36 0 0
DEL PEAK 14(6Q26) WILD-TYPE 286 36 103 17 6

Figure S341.  Get High-res Image Gene #62: 'Del Peak 14(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(6q26)' versus 'METHLYATION_CNMF'

P value = 5.19e-08 (Fisher's exact test), Q value = 2.8e-05

Table S342.  Gene #62: 'Del Peak 14(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 14(6Q26) CNV 27 10 1
DEL PEAK 14(6Q26) WILD-TYPE 116 75 148

Figure S342.  Get High-res Image Gene #62: 'Del Peak 14(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(6q26)' versus 'MRNASEQ_CNMF'

P value = 2.29e-06 (Fisher's exact test), Q value = 0.0011

Table S343.  Gene #62: 'Del Peak 14(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 14(6Q26) CNV 21 1 2
DEL PEAK 14(6Q26) WILD-TYPE 121 106 111

Figure S343.  Get High-res Image Gene #62: 'Del Peak 14(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 14(6q26)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.75e-05 (Fisher's exact test), Q value = 0.033

Table S344.  Gene #62: 'Del Peak 14(6q26)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 14(6Q26) CNV 2 1 1 20
DEL PEAK 14(6Q26) WILD-TYPE 63 91 64 120

Figure S344.  Get High-res Image Gene #62: 'Del Peak 14(6q26)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(6q26)' versus 'MIRSEQ_CNMF'

P value = 6.15e-08 (Fisher's exact test), Q value = 3.3e-05

Table S345.  Gene #62: 'Del Peak 14(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 14(6Q26) CNV 36 3 4
DEL PEAK 14(6Q26) WILD-TYPE 171 141 128

Figure S345.  Get High-res Image Gene #62: 'Del Peak 14(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 14(6q26)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.36e-10 (Fisher's exact test), Q value = 8.5e-08

Table S346.  Gene #62: 'Del Peak 14(6q26)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 14(6Q26) CNV 1 5 1 36
DEL PEAK 14(6Q26) WILD-TYPE 192 74 26 148

Figure S346.  Get High-res Image Gene #62: 'Del Peak 14(6q26)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(7p22.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.1

Table S347.  Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 15(7P22.3) CNV 0 0 7
DEL PEAK 15(7P22.3) WILD-TYPE 20 15 11

Figure S347.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 15(7p22.3)' versus 'CN_CNMF'

P value = 4.17e-31 (Chi-square test), Q value = 3.8e-28

Table S348.  Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 15(7P22.3) CNV 4 2 61 0 1
DEL PEAK 15(7P22.3) WILD-TYPE 286 38 78 17 5

Figure S348.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(7p22.3)' versus 'METHLYATION_CNMF'

P value = 2.43e-10 (Fisher's exact test), Q value = 1.5e-07

Table S349.  Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 15(7P22.3) CNV 42 12 4
DEL PEAK 15(7P22.3) WILD-TYPE 101 73 145

Figure S349.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 15(7p22.3)' versus 'MRNASEQ_CNMF'

P value = 5.12e-14 (Fisher's exact test), Q value = 3.7e-11

Table S350.  Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 15(7P22.3) CNV 41 2 2
DEL PEAK 15(7P22.3) WILD-TYPE 101 105 111

Figure S350.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 15(7p22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.07e-15 (Fisher's exact test), Q value = 3.1e-12

Table S351.  Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 15(7P22.3) CNV 2 0 1 42
DEL PEAK 15(7P22.3) WILD-TYPE 63 92 64 98

Figure S351.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(7p22.3)' versus 'MIRSEQ_CNMF'

P value = 1.35e-14 (Fisher's exact test), Q value = 1e-11

Table S352.  Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 15(7P22.3) CNV 58 6 3
DEL PEAK 15(7P22.3) WILD-TYPE 149 138 129

Figure S352.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 15(7p22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.5e-13 (Fisher's exact test), Q value = 1.1e-10

Table S353.  Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 15(7P22.3) CNV 5 6 2 54
DEL PEAK 15(7P22.3) WILD-TYPE 188 73 25 130

Figure S353.  Get High-res Image Gene #63: 'Del Peak 15(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 16(7q11.22)' versus 'CN_CNMF'

P value = 3.24e-21 (Chi-square test), Q value = 2.8e-18

Table S354.  Gene #64: 'Del Peak 16(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 16(7Q11.22) CNV 0 0 38 0 1
DEL PEAK 16(7Q11.22) WILD-TYPE 290 40 101 17 5

Figure S354.  Get High-res Image Gene #64: 'Del Peak 16(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(7q11.22)' versus 'METHLYATION_CNMF'

P value = 2.35e-07 (Fisher's exact test), Q value = 0.00012

Table S355.  Gene #64: 'Del Peak 16(7q11.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 16(7Q11.22) CNV 25 9 1
DEL PEAK 16(7Q11.22) WILD-TYPE 118 76 148

Figure S355.  Get High-res Image Gene #64: 'Del Peak 16(7q11.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(7q11.22)' versus 'MRNASEQ_CNMF'

P value = 4.89e-09 (Fisher's exact test), Q value = 2.8e-06

Table S356.  Gene #64: 'Del Peak 16(7q11.22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 16(7Q11.22) CNV 23 1 0
DEL PEAK 16(7Q11.22) WILD-TYPE 119 106 113

Figure S356.  Get High-res Image Gene #64: 'Del Peak 16(7q11.22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 16(7q11.22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.5e-09 (Fisher's exact test), Q value = 8.8e-07

Table S357.  Gene #64: 'Del Peak 16(7q11.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 16(7Q11.22) CNV 0 0 0 24
DEL PEAK 16(7Q11.22) WILD-TYPE 65 92 65 116

Figure S357.  Get High-res Image Gene #64: 'Del Peak 16(7q11.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(7q11.22)' versus 'MIRSEQ_CNMF'

P value = 2.32e-08 (Fisher's exact test), Q value = 1.3e-05

Table S358.  Gene #64: 'Del Peak 16(7q11.22)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 16(7Q11.22) CNV 33 4 1
DEL PEAK 16(7Q11.22) WILD-TYPE 174 140 131

Figure S358.  Get High-res Image Gene #64: 'Del Peak 16(7q11.22)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 16(7q11.22)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.09e-08 (Fisher's exact test), Q value = 2.7e-05

Table S359.  Gene #64: 'Del Peak 16(7q11.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 16(7Q11.22) CNV 4 1 1 32
DEL PEAK 16(7Q11.22) WILD-TYPE 189 78 26 152

Figure S359.  Get High-res Image Gene #64: 'Del Peak 16(7q11.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(7q31.1)' versus 'CN_CNMF'

P value = 5.75e-27 (Chi-square test), Q value = 5.2e-24

Table S360.  Gene #65: 'Del Peak 17(7q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 17(7Q31.1) CNV 0 0 47 0 1
DEL PEAK 17(7Q31.1) WILD-TYPE 290 40 92 17 5

Figure S360.  Get High-res Image Gene #65: 'Del Peak 17(7q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(7q31.1)' versus 'METHLYATION_CNMF'

P value = 2.41e-09 (Fisher's exact test), Q value = 1.4e-06

Table S361.  Gene #65: 'Del Peak 17(7q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 17(7Q31.1) CNV 31 10 1
DEL PEAK 17(7Q31.1) WILD-TYPE 112 75 148

Figure S361.  Get High-res Image Gene #65: 'Del Peak 17(7q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(7q31.1)' versus 'MRNASEQ_CNMF'

P value = 3.26e-14 (Fisher's exact test), Q value = 2.4e-11

Table S362.  Gene #65: 'Del Peak 17(7q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 17(7Q31.1) CNV 32 0 0
DEL PEAK 17(7Q31.1) WILD-TYPE 110 107 113

Figure S362.  Get High-res Image Gene #65: 'Del Peak 17(7q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(7q31.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.17e-13 (Fisher's exact test), Q value = 2.2e-10

Table S363.  Gene #65: 'Del Peak 17(7q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 17(7Q31.1) CNV 0 0 0 32
DEL PEAK 17(7Q31.1) WILD-TYPE 65 92 65 108

Figure S363.  Get High-res Image Gene #65: 'Del Peak 17(7q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(7q31.1)' versus 'MIRSEQ_CNMF'

P value = 1.27e-11 (Fisher's exact test), Q value = 8.4e-09

Table S364.  Gene #65: 'Del Peak 17(7q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 17(7Q31.1) CNV 42 4 1
DEL PEAK 17(7Q31.1) WILD-TYPE 165 140 131

Figure S364.  Get High-res Image Gene #65: 'Del Peak 17(7q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 17(7q31.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.47e-11 (Fisher's exact test), Q value = 9.6e-09

Table S365.  Gene #65: 'Del Peak 17(7q31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 17(7Q31.1) CNV 4 1 1 41
DEL PEAK 17(7Q31.1) WILD-TYPE 189 78 26 143

Figure S365.  Get High-res Image Gene #65: 'Del Peak 17(7q31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(7q36.3)' versus 'CN_CNMF'

P value = 9.35e-30 (Chi-square test), Q value = 8.5e-27

Table S366.  Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 18(7Q36.3) CNV 1 1 54 0 1
DEL PEAK 18(7Q36.3) WILD-TYPE 289 39 85 17 5

Figure S366.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(7q36.3)' versus 'METHLYATION_CNMF'

P value = 1.75e-10 (Fisher's exact test), Q value = 1.1e-07

Table S367.  Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 18(7Q36.3) CNV 34 12 1
DEL PEAK 18(7Q36.3) WILD-TYPE 109 73 148

Figure S367.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(7q36.3)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000655 (Fisher's exact test), Q value = 0.25

Table S368.  Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 73 121
DEL PEAK 18(7Q36.3) CNV 12 3
DEL PEAK 18(7Q36.3) WILD-TYPE 61 118

Figure S368.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 18(7q36.3)' versus 'MRNASEQ_CNMF'

P value = 1.29e-18 (Fisher's exact test), Q value = 1.1e-15

Table S369.  Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 18(7Q36.3) CNV 41 0 0
DEL PEAK 18(7Q36.3) WILD-TYPE 101 107 113

Figure S369.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 18(7q36.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.93e-16 (Fisher's exact test), Q value = 4.5e-13

Table S370.  Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 18(7Q36.3) CNV 0 0 1 40
DEL PEAK 18(7Q36.3) WILD-TYPE 65 92 64 100

Figure S370.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(7q36.3)' versus 'MIRSEQ_CNMF'

P value = 6.2e-15 (Fisher's exact test), Q value = 4.6e-12

Table S371.  Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 18(7Q36.3) CNV 51 4 1
DEL PEAK 18(7Q36.3) WILD-TYPE 156 140 131

Figure S371.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 18(7q36.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.81e-15 (Fisher's exact test), Q value = 1.4e-12

Table S372.  Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 18(7Q36.3) CNV 4 1 1 50
DEL PEAK 18(7Q36.3) WILD-TYPE 189 78 26 134

Figure S372.  Get High-res Image Gene #66: 'Del Peak 18(7q36.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 19(8p23.2)' versus 'CN_CNMF'

P value = 1.03e-40 (Chi-square test), Q value = 9.7e-38

Table S373.  Gene #67: 'Del Peak 19(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 19(8P23.2) CNV 9 6 85 2 1
DEL PEAK 19(8P23.2) WILD-TYPE 281 34 54 15 5

Figure S373.  Get High-res Image Gene #67: 'Del Peak 19(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(8p23.2)' versus 'METHLYATION_CNMF'

P value = 1.24e-21 (Fisher's exact test), Q value = 1.1e-18

Table S374.  Gene #67: 'Del Peak 19(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 19(8P23.2) CNV 68 18 3
DEL PEAK 19(8P23.2) WILD-TYPE 75 67 146

Figure S374.  Get High-res Image Gene #67: 'Del Peak 19(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(8p23.2)' versus 'MRNASEQ_CNMF'

P value = 6.45e-17 (Fisher's exact test), Q value = 5.1e-14

Table S375.  Gene #67: 'Del Peak 19(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 19(8P23.2) CNV 52 2 5
DEL PEAK 19(8P23.2) WILD-TYPE 90 105 108

Figure S375.  Get High-res Image Gene #67: 'Del Peak 19(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 19(8p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.05e-19 (Fisher's exact test), Q value = 4.2e-16

Table S376.  Gene #67: 'Del Peak 19(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 19(8P23.2) CNV 1 1 3 54
DEL PEAK 19(8P23.2) WILD-TYPE 64 91 62 86

Figure S376.  Get High-res Image Gene #67: 'Del Peak 19(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(8p23.2)' versus 'MIRSEQ_CNMF'

P value = 3.02e-26 (Fisher's exact test), Q value = 2.7e-23

Table S377.  Gene #67: 'Del Peak 19(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 19(8P23.2) CNV 89 7 4
DEL PEAK 19(8P23.2) WILD-TYPE 118 137 128

Figure S377.  Get High-res Image Gene #67: 'Del Peak 19(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 19(8p23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.04e-29 (Fisher's exact test), Q value = 5.5e-26

Table S378.  Gene #67: 'Del Peak 19(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 19(8P23.2) CNV 6 4 3 87
DEL PEAK 19(8P23.2) WILD-TYPE 187 75 24 97

Figure S378.  Get High-res Image Gene #67: 'Del Peak 19(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 20(9p23)' versus 'CN_CNMF'

P value = 1.01e-22 (Chi-square test), Q value = 8.9e-20

Table S379.  Gene #68: 'Del Peak 20(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 20(9P23) CNV 2 12 49 2 0
DEL PEAK 20(9P23) WILD-TYPE 288 28 90 15 6

Figure S379.  Get High-res Image Gene #68: 'Del Peak 20(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 20(9p23)' versus 'METHLYATION_CNMF'

P value = 1.84e-06 (Fisher's exact test), Q value = 9e-04

Table S380.  Gene #68: 'Del Peak 20(9p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 20(9P23) CNV 32 18 6
DEL PEAK 20(9P23) WILD-TYPE 111 67 143

Figure S380.  Get High-res Image Gene #68: 'Del Peak 20(9p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 20(9p23)' versus 'MRNASEQ_CNMF'

P value = 1.93e-07 (Fisher's exact test), Q value = 9.9e-05

Table S381.  Gene #68: 'Del Peak 20(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 20(9P23) CNV 29 3 3
DEL PEAK 20(9P23) WILD-TYPE 113 104 110

Figure S381.  Get High-res Image Gene #68: 'Del Peak 20(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 20(9p23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.29e-09 (Fisher's exact test), Q value = 7.6e-07

Table S382.  Gene #68: 'Del Peak 20(9p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 20(9P23) CNV 0 1 3 31
DEL PEAK 20(9P23) WILD-TYPE 65 91 62 109

Figure S382.  Get High-res Image Gene #68: 'Del Peak 20(9p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(9p23)' versus 'MIRSEQ_CNMF'

P value = 8.17e-08 (Fisher's exact test), Q value = 4.3e-05

Table S383.  Gene #68: 'Del Peak 20(9p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 20(9P23) CNV 46 15 3
DEL PEAK 20(9P23) WILD-TYPE 161 129 129

Figure S383.  Get High-res Image Gene #68: 'Del Peak 20(9p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 20(9p23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.89e-06 (Fisher's exact test), Q value = 0.00092

Table S384.  Gene #68: 'Del Peak 20(9p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 20(9P23) CNV 12 5 3 44
DEL PEAK 20(9P23) WILD-TYPE 181 74 24 140

Figure S384.  Get High-res Image Gene #68: 'Del Peak 20(9p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 21(9q34.11)' versus 'MRNA_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.043

Table S385.  Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 21(9Q34.11) CNV 0 9 0 0
DEL PEAK 21(9Q34.11) WILD-TYPE 13 9 14 8

Figure S385.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 21(9q34.11)' versus 'MRNA_CHIERARCHICAL'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0056

Table S386.  Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 21(9Q34.11) CNV 0 0 9
DEL PEAK 21(9Q34.11) WILD-TYPE 20 15 9

Figure S386.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 21(9q34.11)' versus 'CN_CNMF'

P value = 5.04e-52 (Chi-square test), Q value = 4.8e-49

Table S387.  Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 21(9Q34.11) CNV 5 18 97 1 1
DEL PEAK 21(9Q34.11) WILD-TYPE 285 22 42 16 5

Figure S387.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(9q34.11)' versus 'METHLYATION_CNMF'

P value = 1.94e-11 (Fisher's exact test), Q value = 1.3e-08

Table S388.  Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 21(9Q34.11) CNV 64 25 14
DEL PEAK 21(9Q34.11) WILD-TYPE 79 60 135

Figure S388.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 21(9q34.11)' versus 'RPPA_CNMF'

P value = 0.000384 (Chi-square test), Q value = 0.15

Table S389.  Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
DEL PEAK 21(9Q34.11) CNV 8 14 2 2 1 6
DEL PEAK 21(9Q34.11) WILD-TYPE 33 23 37 10 40 18

Figure S389.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 21(9q34.11)' versus 'MRNASEQ_CNMF'

P value = 1.13e-17 (Fisher's exact test), Q value = 9.1e-15

Table S390.  Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 21(9Q34.11) CNV 63 6 7
DEL PEAK 21(9Q34.11) WILD-TYPE 79 101 106

Figure S390.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 21(9q34.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.84e-24 (Fisher's exact test), Q value = 4.3e-21

Table S391.  Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 21(9Q34.11) CNV 0 2 7 67
DEL PEAK 21(9Q34.11) WILD-TYPE 65 90 58 73

Figure S391.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 21(9q34.11)' versus 'MIRSEQ_CNMF'

P value = 5.09e-18 (Fisher's exact test), Q value = 4.1e-15

Table S392.  Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 21(9Q34.11) CNV 91 19 8
DEL PEAK 21(9Q34.11) WILD-TYPE 116 125 124

Figure S392.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 21(9q34.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.85e-16 (Fisher's exact test), Q value = 1.4e-13

Table S393.  Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 21(9Q34.11) CNV 17 10 8 83
DEL PEAK 21(9Q34.11) WILD-TYPE 176 69 19 101

Figure S393.  Get High-res Image Gene #69: 'Del Peak 21(9q34.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 22(10q23.31)' versus 'CN_CNMF'

P value = 1.2e-29 (Chi-square test), Q value = 1.1e-26

Table S394.  Gene #70: 'Del Peak 22(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 22(10Q23.31) CNV 5 4 61 0 0
DEL PEAK 22(10Q23.31) WILD-TYPE 285 36 78 17 6

Figure S394.  Get High-res Image Gene #70: 'Del Peak 22(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(10q23.31)' versus 'METHLYATION_CNMF'

P value = 5.19e-08 (Fisher's exact test), Q value = 2.8e-05

Table S395.  Gene #70: 'Del Peak 22(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 22(10Q23.31) CNV 39 16 6
DEL PEAK 22(10Q23.31) WILD-TYPE 104 69 143

Figure S395.  Get High-res Image Gene #70: 'Del Peak 22(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 22(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 3.39e-07 (Fisher's exact test), Q value = 0.00017

Table S396.  Gene #70: 'Del Peak 22(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 22(10Q23.31) CNV 30 4 3
DEL PEAK 22(10Q23.31) WILD-TYPE 112 103 110

Figure S396.  Get High-res Image Gene #70: 'Del Peak 22(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 22(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.88e-07 (Fisher's exact test), Q value = 9.7e-05

Table S397.  Gene #70: 'Del Peak 22(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 22(10Q23.31) CNV 0 2 6 29
DEL PEAK 22(10Q23.31) WILD-TYPE 65 90 59 111

Figure S397.  Get High-res Image Gene #70: 'Del Peak 22(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 22(10q23.31)' versus 'MIRSEQ_CNMF'

P value = 1.78e-10 (Fisher's exact test), Q value = 1.1e-07

Table S398.  Gene #70: 'Del Peak 22(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 22(10Q23.31) CNV 55 8 6
DEL PEAK 22(10Q23.31) WILD-TYPE 152 136 126

Figure S398.  Get High-res Image Gene #70: 'Del Peak 22(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 22(10q23.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.84e-09 (Fisher's exact test), Q value = 2.2e-06

Table S399.  Gene #70: 'Del Peak 22(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 22(10Q23.31) CNV 9 7 3 50
DEL PEAK 22(10Q23.31) WILD-TYPE 184 72 24 134

Figure S399.  Get High-res Image Gene #70: 'Del Peak 22(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 23(11p15.5)' versus 'CN_CNMF'

P value = 7.81e-40 (Chi-square test), Q value = 7.3e-37

Table S400.  Gene #71: 'Del Peak 23(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 23(11P15.5) CNV 1 11 77 2 2
DEL PEAK 23(11P15.5) WILD-TYPE 289 29 62 15 4

Figure S400.  Get High-res Image Gene #71: 'Del Peak 23(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(11p15.5)' versus 'METHLYATION_CNMF'

P value = 3.91e-17 (Fisher's exact test), Q value = 3.1e-14

Table S401.  Gene #71: 'Del Peak 23(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 23(11P15.5) CNV 60 19 4
DEL PEAK 23(11P15.5) WILD-TYPE 83 66 145

Figure S401.  Get High-res Image Gene #71: 'Del Peak 23(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 23(11p15.5)' versus 'MRNASEQ_CNMF'

P value = 4.92e-14 (Fisher's exact test), Q value = 3.6e-11

Table S402.  Gene #71: 'Del Peak 23(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 23(11P15.5) CNV 43 2 3
DEL PEAK 23(11P15.5) WILD-TYPE 99 105 110

Figure S402.  Get High-res Image Gene #71: 'Del Peak 23(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 23(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.77e-16 (Fisher's exact test), Q value = 3.7e-13

Table S403.  Gene #71: 'Del Peak 23(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 23(11P15.5) CNV 1 1 1 45
DEL PEAK 23(11P15.5) WILD-TYPE 64 91 64 95

Figure S403.  Get High-res Image Gene #71: 'Del Peak 23(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 23(11p15.5)' versus 'MIRSEQ_CNMF'

P value = 1.21e-16 (Fisher's exact test), Q value = 9.4e-14

Table S404.  Gene #71: 'Del Peak 23(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 23(11P15.5) CNV 75 12 5
DEL PEAK 23(11P15.5) WILD-TYPE 132 132 127

Figure S404.  Get High-res Image Gene #71: 'Del Peak 23(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 23(11p15.5)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.65e-17 (Fisher's exact test), Q value = 6.8e-14

Table S405.  Gene #71: 'Del Peak 23(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 23(11P15.5) CNV 13 4 3 72
DEL PEAK 23(11P15.5) WILD-TYPE 180 75 24 112

Figure S405.  Get High-res Image Gene #71: 'Del Peak 23(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 24(11q14.1)' versus 'CN_CNMF'

P value = 7.36e-22 (Chi-square test), Q value = 6.4e-19

Table S406.  Gene #72: 'Del Peak 24(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 24(11Q14.1) CNV 1 11 47 2 2
DEL PEAK 24(11Q14.1) WILD-TYPE 289 29 92 15 4

Figure S406.  Get High-res Image Gene #72: 'Del Peak 24(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(11q14.1)' versus 'METHLYATION_CNMF'

P value = 1.39e-09 (Fisher's exact test), Q value = 8.2e-07

Table S407.  Gene #72: 'Del Peak 24(11q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 24(11Q14.1) CNV 40 13 4
DEL PEAK 24(11Q14.1) WILD-TYPE 103 72 145

Figure S407.  Get High-res Image Gene #72: 'Del Peak 24(11q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 24(11q14.1)' versus 'MRNASEQ_CNMF'

P value = 2.82e-08 (Fisher's exact test), Q value = 1.5e-05

Table S408.  Gene #72: 'Del Peak 24(11q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 24(11Q14.1) CNV 28 2 2
DEL PEAK 24(11Q14.1) WILD-TYPE 114 105 111

Figure S408.  Get High-res Image Gene #72: 'Del Peak 24(11q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 24(11q14.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.31e-10 (Fisher's exact test), Q value = 1.4e-07

Table S409.  Gene #72: 'Del Peak 24(11q14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 24(11Q14.1) CNV 1 0 1 30
DEL PEAK 24(11Q14.1) WILD-TYPE 64 92 64 110

Figure S409.  Get High-res Image Gene #72: 'Del Peak 24(11q14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 24(11q14.1)' versus 'MIRSEQ_CNMF'

P value = 2.34e-10 (Fisher's exact test), Q value = 1.4e-07

Table S410.  Gene #72: 'Del Peak 24(11q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 24(11Q14.1) CNV 50 9 3
DEL PEAK 24(11Q14.1) WILD-TYPE 157 135 129

Figure S410.  Get High-res Image Gene #72: 'Del Peak 24(11q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 24(11q14.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.32e-11 (Fisher's exact test), Q value = 8.7e-09

Table S411.  Gene #72: 'Del Peak 24(11q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 24(11Q14.1) CNV 7 4 1 50
DEL PEAK 24(11Q14.1) WILD-TYPE 186 75 26 134

Figure S411.  Get High-res Image Gene #72: 'Del Peak 24(11q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(11q25)' versus 'CN_CNMF'

P value = 4.75e-28 (Chi-square test), Q value = 4.3e-25

Table S412.  Gene #73: 'Del Peak 25(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 25(11Q25) CNV 4 15 61 2 2
DEL PEAK 25(11Q25) WILD-TYPE 286 25 78 15 4

Figure S412.  Get High-res Image Gene #73: 'Del Peak 25(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(11q25)' versus 'METHLYATION_CNMF'

P value = 1.41e-13 (Fisher's exact test), Q value = 1e-10

Table S413.  Gene #73: 'Del Peak 25(11q25)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 25(11Q25) CNV 55 14 6
DEL PEAK 25(11Q25) WILD-TYPE 88 71 143

Figure S413.  Get High-res Image Gene #73: 'Del Peak 25(11q25)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(11q25)' versus 'MRNASEQ_CNMF'

P value = 3.31e-08 (Fisher's exact test), Q value = 1.8e-05

Table S414.  Gene #73: 'Del Peak 25(11q25)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 25(11Q25) CNV 35 3 6
DEL PEAK 25(11Q25) WILD-TYPE 107 104 107

Figure S414.  Get High-res Image Gene #73: 'Del Peak 25(11q25)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(11q25)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.43e-12 (Fisher's exact test), Q value = 3.7e-09

Table S415.  Gene #73: 'Del Peak 25(11q25)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 25(11Q25) CNV 1 1 3 39
DEL PEAK 25(11Q25) WILD-TYPE 64 91 62 101

Figure S415.  Get High-res Image Gene #73: 'Del Peak 25(11q25)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(11q25)' versus 'MIRSEQ_CNMF'

P value = 1.14e-12 (Fisher's exact test), Q value = 7.9e-10

Table S416.  Gene #73: 'Del Peak 25(11q25)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 25(11Q25) CNV 65 11 6
DEL PEAK 25(11Q25) WILD-TYPE 142 133 126

Figure S416.  Get High-res Image Gene #73: 'Del Peak 25(11q25)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(11q25)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.84e-13 (Fisher's exact test), Q value = 1.3e-10

Table S417.  Gene #73: 'Del Peak 25(11q25)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 25(11Q25) CNV 9 7 4 62
DEL PEAK 25(11Q25) WILD-TYPE 184 72 23 122

Figure S417.  Get High-res Image Gene #73: 'Del Peak 25(11q25)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(12q23.1)' versus 'CN_CNMF'

P value = 2.41e-20 (Chi-square test), Q value = 2.1e-17

Table S418.  Gene #74: 'Del Peak 26(12q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 26(12Q23.1) CNV 0 4 42 2 0
DEL PEAK 26(12Q23.1) WILD-TYPE 290 36 97 15 6

Figure S418.  Get High-res Image Gene #74: 'Del Peak 26(12q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(12q23.1)' versus 'METHLYATION_CNMF'

P value = 8.82e-11 (Fisher's exact test), Q value = 5.6e-08

Table S419.  Gene #74: 'Del Peak 26(12q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 26(12Q23.1) CNV 31 9 0
DEL PEAK 26(12Q23.1) WILD-TYPE 112 76 149

Figure S419.  Get High-res Image Gene #74: 'Del Peak 26(12q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(12q23.1)' versus 'MRNASEQ_CNMF'

P value = 3.97e-07 (Fisher's exact test), Q value = 2e-04

Table S420.  Gene #74: 'Del Peak 26(12q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 26(12Q23.1) CNV 21 1 1
DEL PEAK 26(12Q23.1) WILD-TYPE 121 106 112

Figure S420.  Get High-res Image Gene #74: 'Del Peak 26(12q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 26(12q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.13e-07 (Fisher's exact test), Q value = 5.9e-05

Table S421.  Gene #74: 'Del Peak 26(12q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 26(12Q23.1) CNV 0 1 0 22
DEL PEAK 26(12Q23.1) WILD-TYPE 65 91 65 118

Figure S421.  Get High-res Image Gene #74: 'Del Peak 26(12q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(12q23.1)' versus 'MIRSEQ_CNMF'

P value = 6.08e-10 (Fisher's exact test), Q value = 3.6e-07

Table S422.  Gene #74: 'Del Peak 26(12q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 26(12Q23.1) CNV 40 3 3
DEL PEAK 26(12Q23.1) WILD-TYPE 167 141 129

Figure S422.  Get High-res Image Gene #74: 'Del Peak 26(12q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 26(12q23.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.6e-13 (Fisher's exact test), Q value = 2.5e-10

Table S423.  Gene #74: 'Del Peak 26(12q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 26(12Q23.1) CNV 1 3 1 41
DEL PEAK 26(12Q23.1) WILD-TYPE 192 76 26 143

Figure S423.  Get High-res Image Gene #74: 'Del Peak 26(12q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(12q24.33)' versus 'CN_CNMF'

P value = 1.03e-25 (Chi-square test), Q value = 9.3e-23

Table S424.  Gene #75: 'Del Peak 27(12q24.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 27(12Q24.33) CNV 1 4 52 2 0
DEL PEAK 27(12Q24.33) WILD-TYPE 289 36 87 15 6

Figure S424.  Get High-res Image Gene #75: 'Del Peak 27(12q24.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(12q24.33)' versus 'METHLYATION_CNMF'

P value = 2.32e-11 (Fisher's exact test), Q value = 1.5e-08

Table S425.  Gene #75: 'Del Peak 27(12q24.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 27(12Q24.33) CNV 40 12 2
DEL PEAK 27(12Q24.33) WILD-TYPE 103 73 147

Figure S425.  Get High-res Image Gene #75: 'Del Peak 27(12q24.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 27(12q24.33)' versus 'MRNASEQ_CNMF'

P value = 1.07e-11 (Fisher's exact test), Q value = 7.1e-09

Table S426.  Gene #75: 'Del Peak 27(12q24.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 27(12Q24.33) CNV 29 1 0
DEL PEAK 27(12Q24.33) WILD-TYPE 113 106 113

Figure S426.  Get High-res Image Gene #75: 'Del Peak 27(12q24.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 27(12q24.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.32e-09 (Fisher's exact test), Q value = 1.3e-06

Table S427.  Gene #75: 'Del Peak 27(12q24.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 27(12Q24.33) CNV 0 1 1 28
DEL PEAK 27(12Q24.33) WILD-TYPE 65 91 64 112

Figure S427.  Get High-res Image Gene #75: 'Del Peak 27(12q24.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(12q24.33)' versus 'MIRSEQ_CNMF'

P value = 6.67e-13 (Fisher's exact test), Q value = 4.6e-10

Table S428.  Gene #75: 'Del Peak 27(12q24.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 27(12Q24.33) CNV 50 3 4
DEL PEAK 27(12Q24.33) WILD-TYPE 157 141 128

Figure S428.  Get High-res Image Gene #75: 'Del Peak 27(12q24.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 27(12q24.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.94e-14 (Fisher's exact test), Q value = 2.1e-11

Table S429.  Gene #75: 'Del Peak 27(12q24.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 27(12Q24.33) CNV 3 3 2 49
DEL PEAK 27(12Q24.33) WILD-TYPE 190 76 25 135

Figure S429.  Get High-res Image Gene #75: 'Del Peak 27(12q24.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(13q11)' versus 'CN_CNMF'

P value = 1.94e-29 (Chi-square test), Q value = 1.8e-26

Table S430.  Gene #76: 'Del Peak 28(13q11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 28(13Q11) CNV 4 17 62 2 1
DEL PEAK 28(13Q11) WILD-TYPE 286 23 77 15 5

Figure S430.  Get High-res Image Gene #76: 'Del Peak 28(13q11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(13q11)' versus 'METHLYATION_CNMF'

P value = 3.97e-09 (Fisher's exact test), Q value = 2.3e-06

Table S431.  Gene #76: 'Del Peak 28(13q11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 28(13Q11) CNV 47 17 8
DEL PEAK 28(13Q11) WILD-TYPE 96 68 141

Figure S431.  Get High-res Image Gene #76: 'Del Peak 28(13q11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 28(13q11)' versus 'MRNASEQ_CNMF'

P value = 4.78e-07 (Fisher's exact test), Q value = 0.00024

Table S432.  Gene #76: 'Del Peak 28(13q11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 28(13Q11) CNV 35 5 6
DEL PEAK 28(13Q11) WILD-TYPE 107 102 107

Figure S432.  Get High-res Image Gene #76: 'Del Peak 28(13q11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 28(13q11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.7e-11 (Fisher's exact test), Q value = 1.1e-08

Table S433.  Gene #76: 'Del Peak 28(13q11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 28(13Q11) CNV 1 2 3 40
DEL PEAK 28(13Q11) WILD-TYPE 64 90 62 100

Figure S433.  Get High-res Image Gene #76: 'Del Peak 28(13q11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(13q11)' versus 'MIRSEQ_CNMF'

P value = 1.01e-09 (Fisher's exact test), Q value = 6e-07

Table S434.  Gene #76: 'Del Peak 28(13q11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 28(13Q11) CNV 63 13 9
DEL PEAK 28(13Q11) WILD-TYPE 144 131 123

Figure S434.  Get High-res Image Gene #76: 'Del Peak 28(13q11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 28(13q11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.6e-09 (Fisher's exact test), Q value = 2.1e-06

Table S435.  Gene #76: 'Del Peak 28(13q11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 28(13Q11) CNV 13 9 6 57
DEL PEAK 28(13Q11) WILD-TYPE 180 70 21 127

Figure S435.  Get High-res Image Gene #76: 'Del Peak 28(13q11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(13q14.2)' versus 'CN_CNMF'

P value = 2.43e-32 (Chi-square test), Q value = 2.2e-29

Table S436.  Gene #77: 'Del Peak 29(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 29(13Q14.2) CNV 5 19 67 2 1
DEL PEAK 29(13Q14.2) WILD-TYPE 285 21 72 15 5

Figure S436.  Get High-res Image Gene #77: 'Del Peak 29(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(13q14.2)' versus 'METHLYATION_CNMF'

P value = 5.16e-08 (Fisher's exact test), Q value = 2.8e-05

Table S437.  Gene #77: 'Del Peak 29(13q14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 29(13Q14.2) CNV 48 21 11
DEL PEAK 29(13Q14.2) WILD-TYPE 95 64 138

Figure S437.  Get High-res Image Gene #77: 'Del Peak 29(13q14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 29(13q14.2)' versus 'MRNASEQ_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00057

Table S438.  Gene #77: 'Del Peak 29(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 29(13Q14.2) CNV 35 5 7
DEL PEAK 29(13Q14.2) WILD-TYPE 107 102 106

Figure S438.  Get High-res Image Gene #77: 'Del Peak 29(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 29(13q14.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.57e-11 (Fisher's exact test), Q value = 6e-08

Table S439.  Gene #77: 'Del Peak 29(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 29(13Q14.2) CNV 2 2 3 40
DEL PEAK 29(13Q14.2) WILD-TYPE 63 90 62 100

Figure S439.  Get High-res Image Gene #77: 'Del Peak 29(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(13q14.2)' versus 'MIRSEQ_CNMF'

P value = 3.77e-08 (Fisher's exact test), Q value = 2e-05

Table S440.  Gene #77: 'Del Peak 29(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 29(13Q14.2) CNV 65 16 12
DEL PEAK 29(13Q14.2) WILD-TYPE 142 128 120

Figure S440.  Get High-res Image Gene #77: 'Del Peak 29(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 29(13q14.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.02e-08 (Fisher's exact test), Q value = 5.7e-06

Table S441.  Gene #77: 'Del Peak 29(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 29(13Q14.2) CNV 16 10 7 60
DEL PEAK 29(13Q14.2) WILD-TYPE 177 69 20 124

Figure S441.  Get High-res Image Gene #77: 'Del Peak 29(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(14q13.1)' versus 'CN_CNMF'

P value = 1.28e-22 (Chi-square test), Q value = 1.1e-19

Table S442.  Gene #78: 'Del Peak 30(14q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 30(14Q13.1) CNV 2 6 50 2 2
DEL PEAK 30(14Q13.1) WILD-TYPE 288 34 89 15 4

Figure S442.  Get High-res Image Gene #78: 'Del Peak 30(14q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(14q13.1)' versus 'METHLYATION_CNMF'

P value = 1.27e-10 (Fisher's exact test), Q value = 7.9e-08

Table S443.  Gene #78: 'Del Peak 30(14q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 30(14Q13.1) CNV 41 7 4
DEL PEAK 30(14Q13.1) WILD-TYPE 102 78 145

Figure S443.  Get High-res Image Gene #78: 'Del Peak 30(14q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 30(14q13.1)' versus 'MRNASEQ_CNMF'

P value = 7.68e-09 (Fisher's exact test), Q value = 4.3e-06

Table S444.  Gene #78: 'Del Peak 30(14q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 30(14Q13.1) CNV 31 2 3
DEL PEAK 30(14Q13.1) WILD-TYPE 111 105 110

Figure S444.  Get High-res Image Gene #78: 'Del Peak 30(14q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(14q13.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.63e-10 (Fisher's exact test), Q value = 1e-07

Table S445.  Gene #78: 'Del Peak 30(14q13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 30(14Q13.1) CNV 1 1 1 33
DEL PEAK 30(14Q13.1) WILD-TYPE 64 91 64 107

Figure S445.  Get High-res Image Gene #78: 'Del Peak 30(14q13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(14q13.1)' versus 'MIRSEQ_CNMF'

P value = 1.33e-09 (Fisher's exact test), Q value = 7.8e-07

Table S446.  Gene #78: 'Del Peak 30(14q13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 30(14Q13.1) CNV 49 5 7
DEL PEAK 30(14Q13.1) WILD-TYPE 158 139 125

Figure S446.  Get High-res Image Gene #78: 'Del Peak 30(14q13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 30(14q13.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.18e-12 (Fisher's exact test), Q value = 4.1e-09

Table S447.  Gene #78: 'Del Peak 30(14q13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 30(14Q13.1) CNV 4 8 1 48
DEL PEAK 30(14Q13.1) WILD-TYPE 189 71 26 136

Figure S447.  Get High-res Image Gene #78: 'Del Peak 30(14q13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1)' versus 'CN_CNMF'

P value = 1.37e-55 (Chi-square test), Q value = 1.3e-52

Table S448.  Gene #79: 'Del Peak 31(15q15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 31(15Q15.1) CNV 4 17 100 0 3
DEL PEAK 31(15Q15.1) WILD-TYPE 286 23 39 17 3

Figure S448.  Get High-res Image Gene #79: 'Del Peak 31(15q15.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(15q15.1)' versus 'METHLYATION_CNMF'

P value = 1.41e-18 (Fisher's exact test), Q value = 1.2e-15

Table S449.  Gene #79: 'Del Peak 31(15q15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 31(15Q15.1) CNV 74 25 9
DEL PEAK 31(15Q15.1) WILD-TYPE 69 60 140

Figure S449.  Get High-res Image Gene #79: 'Del Peak 31(15q15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 31(15q15.1)' versus 'MRNASEQ_CNMF'

P value = 3.76e-17 (Fisher's exact test), Q value = 3e-14

Table S450.  Gene #79: 'Del Peak 31(15q15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 31(15Q15.1) CNV 60 4 8
DEL PEAK 31(15Q15.1) WILD-TYPE 82 103 105

Figure S450.  Get High-res Image Gene #79: 'Del Peak 31(15q15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(15q15.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.64e-22 (Fisher's exact test), Q value = 7.5e-19

Table S451.  Gene #79: 'Del Peak 31(15q15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 31(15Q15.1) CNV 1 1 7 63
DEL PEAK 31(15Q15.1) WILD-TYPE 64 91 58 77

Figure S451.  Get High-res Image Gene #79: 'Del Peak 31(15q15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_CNMF'

P value = 1.16e-23 (Fisher's exact test), Q value = 1e-20

Table S452.  Gene #79: 'Del Peak 31(15q15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 31(15Q15.1) CNV 100 13 9
DEL PEAK 31(15Q15.1) WILD-TYPE 107 131 123

Figure S452.  Get High-res Image Gene #79: 'Del Peak 31(15q15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.75e-22 (Fisher's exact test), Q value = 2.4e-19

Table S453.  Gene #79: 'Del Peak 31(15q15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 31(15Q15.1) CNV 12 12 7 91
DEL PEAK 31(15Q15.1) WILD-TYPE 181 67 20 93

Figure S453.  Get High-res Image Gene #79: 'Del Peak 31(15q15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(15q23)' versus 'CN_CNMF'

P value = 7.28e-42 (Chi-square test), Q value = 6.8e-39

Table S454.  Gene #80: 'Del Peak 32(15q23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 32(15Q23) CNV 3 14 79 0 4
DEL PEAK 32(15Q23) WILD-TYPE 287 26 60 17 2

Figure S454.  Get High-res Image Gene #80: 'Del Peak 32(15q23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(15q23)' versus 'METHLYATION_CNMF'

P value = 1.94e-18 (Fisher's exact test), Q value = 1.6e-15

Table S455.  Gene #80: 'Del Peak 32(15q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 32(15Q23) CNV 65 16 5
DEL PEAK 32(15Q23) WILD-TYPE 78 69 144

Figure S455.  Get High-res Image Gene #80: 'Del Peak 32(15q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 32(15q23)' versus 'MRNASEQ_CNMF'

P value = 1.46e-12 (Fisher's exact test), Q value = 1e-09

Table S456.  Gene #80: 'Del Peak 32(15q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 32(15Q23) CNV 45 2 7
DEL PEAK 32(15Q23) WILD-TYPE 97 105 106

Figure S456.  Get High-res Image Gene #80: 'Del Peak 32(15q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(15q23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.7e-15 (Fisher's exact test), Q value = 7.2e-12

Table S457.  Gene #80: 'Del Peak 32(15q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 32(15Q23) CNV 1 1 5 47
DEL PEAK 32(15Q23) WILD-TYPE 64 91 60 93

Figure S457.  Get High-res Image Gene #80: 'Del Peak 32(15q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(15q23)' versus 'MIRSEQ_CNMF'

P value = 1.26e-16 (Fisher's exact test), Q value = 9.7e-14

Table S458.  Gene #80: 'Del Peak 32(15q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 32(15Q23) CNV 79 11 8
DEL PEAK 32(15Q23) WILD-TYPE 128 133 124

Figure S458.  Get High-res Image Gene #80: 'Del Peak 32(15q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 32(15q23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.94e-18 (Fisher's exact test), Q value = 4.8e-15

Table S459.  Gene #80: 'Del Peak 32(15q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 32(15Q23) CNV 8 11 5 74
DEL PEAK 32(15Q23) WILD-TYPE 185 68 22 110

Figure S459.  Get High-res Image Gene #80: 'Del Peak 32(15q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 33(16p13.3)' versus 'CN_CNMF'

P value = 1.59e-37 (Chi-square test), Q value = 1.5e-34

Table S460.  Gene #81: 'Del Peak 33(16p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 33(16P13.3) CNV 2 8 71 0 0
DEL PEAK 33(16P13.3) WILD-TYPE 288 32 68 17 6

Figure S460.  Get High-res Image Gene #81: 'Del Peak 33(16p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 33(16p13.3)' versus 'METHLYATION_CNMF'

P value = 1.53e-14 (Fisher's exact test), Q value = 1.1e-11

Table S461.  Gene #81: 'Del Peak 33(16p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 33(16P13.3) CNV 51 17 3
DEL PEAK 33(16P13.3) WILD-TYPE 92 68 146

Figure S461.  Get High-res Image Gene #81: 'Del Peak 33(16p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 33(16p13.3)' versus 'MRNASEQ_CNMF'

P value = 8.49e-14 (Fisher's exact test), Q value = 6.1e-11

Table S462.  Gene #81: 'Del Peak 33(16p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 33(16P13.3) CNV 40 3 1
DEL PEAK 33(16P13.3) WILD-TYPE 102 104 112

Figure S462.  Get High-res Image Gene #81: 'Del Peak 33(16p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 33(16p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.28e-11 (Fisher's exact test), Q value = 8.5e-09

Table S463.  Gene #81: 'Del Peak 33(16p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 33(16P13.3) CNV 1 2 2 39
DEL PEAK 33(16P13.3) WILD-TYPE 64 90 63 101

Figure S463.  Get High-res Image Gene #81: 'Del Peak 33(16p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(16p13.3)' versus 'MIRSEQ_CNMF'

P value = 4.79e-16 (Fisher's exact test), Q value = 3.7e-13

Table S464.  Gene #81: 'Del Peak 33(16p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 33(16P13.3) CNV 67 7 5
DEL PEAK 33(16P13.3) WILD-TYPE 140 137 127

Figure S464.  Get High-res Image Gene #81: 'Del Peak 33(16p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 33(16p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.41e-17 (Fisher's exact test), Q value = 7.4e-14

Table S465.  Gene #81: 'Del Peak 33(16p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 33(16P13.3) CNV 6 6 3 64
DEL PEAK 33(16P13.3) WILD-TYPE 187 73 24 120

Figure S465.  Get High-res Image Gene #81: 'Del Peak 33(16p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(16q21)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000451 (Fisher's exact test), Q value = 0.18

Table S466.  Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 34(16Q21) CNV 1 0 8
DEL PEAK 34(16Q21) WILD-TYPE 19 15 10

Figure S466.  Get High-res Image Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 34(16q21)' versus 'CN_CNMF'

P value = 1.05e-56 (Chi-square test), Q value = 1e-53

Table S467.  Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 34(16Q21) CNV 15 14 111 0 0
DEL PEAK 34(16Q21) WILD-TYPE 275 26 28 17 6

Figure S467.  Get High-res Image Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 34(16q21)' versus 'METHLYATION_CNMF'

P value = 2.95e-18 (Fisher's exact test), Q value = 2.4e-15

Table S468.  Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 34(16Q21) CNV 80 28 13
DEL PEAK 34(16Q21) WILD-TYPE 63 57 136

Figure S468.  Get High-res Image Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 34(16q21)' versus 'MRNASEQ_CNMF'

P value = 9.4e-18 (Fisher's exact test), Q value = 7.6e-15

Table S469.  Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 34(16Q21) CNV 70 7 12
DEL PEAK 34(16Q21) WILD-TYPE 72 100 101

Figure S469.  Get High-res Image Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 34(16q21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.63e-16 (Fisher's exact test), Q value = 5.1e-13

Table S470.  Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 34(16Q21) CNV 9 5 7 68
DEL PEAK 34(16Q21) WILD-TYPE 56 87 58 72

Figure S470.  Get High-res Image Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(16q21)' versus 'MIRSEQ_CNMF'

P value = 1.85e-17 (Fisher's exact test), Q value = 1.5e-14

Table S471.  Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 34(16Q21) CNV 101 17 18
DEL PEAK 34(16Q21) WILD-TYPE 106 127 114

Figure S471.  Get High-res Image Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 34(16q21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.85e-18 (Fisher's exact test), Q value = 1.5e-15

Table S472.  Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 34(16Q21) CNV 23 12 5 96
DEL PEAK 34(16Q21) WILD-TYPE 170 67 22 88

Figure S472.  Get High-res Image Gene #82: 'Del Peak 34(16q21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 35(16q23.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000168 (Fisher's exact test), Q value = 0.07

Table S473.  Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 35(16Q23.1) CNV 1 1 10
DEL PEAK 35(16Q23.1) WILD-TYPE 19 14 8

Figure S473.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 35(16q23.1)' versus 'CN_CNMF'

P value = 2.34e-57 (Chi-square test), Q value = 2.2e-54

Table S474.  Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 35(16Q23.1) CNV 20 14 116 0 0
DEL PEAK 35(16Q23.1) WILD-TYPE 270 26 23 17 6

Figure S474.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(16q23.1)' versus 'METHLYATION_CNMF'

P value = 2.43e-17 (Fisher's exact test), Q value = 1.9e-14

Table S475.  Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 35(16Q23.1) CNV 81 29 15
DEL PEAK 35(16Q23.1) WILD-TYPE 62 56 134

Figure S475.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 35(16q23.1)' versus 'MRNASEQ_CNMF'

P value = 7.07e-19 (Fisher's exact test), Q value = 5.9e-16

Table S476.  Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 35(16Q23.1) CNV 76 9 13
DEL PEAK 35(16Q23.1) WILD-TYPE 66 98 100

Figure S476.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(16q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.83e-14 (Fisher's exact test), Q value = 1.3e-11

Table S477.  Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 35(16Q23.1) CNV 10 7 10 71
DEL PEAK 35(16Q23.1) WILD-TYPE 55 85 55 69

Figure S477.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(16q23.1)' versus 'MIRSEQ_CNMF'

P value = 1.7e-18 (Fisher's exact test), Q value = 1.4e-15

Table S478.  Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 35(16Q23.1) CNV 107 19 19
DEL PEAK 35(16Q23.1) WILD-TYPE 100 125 113

Figure S478.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 35(16q23.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.37e-21 (Fisher's exact test), Q value = 6.3e-18

Table S479.  Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 35(16Q23.1) CNV 24 13 5 103
DEL PEAK 35(16Q23.1) WILD-TYPE 169 66 22 81

Figure S479.  Get High-res Image Gene #83: 'Del Peak 35(16q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 36(17p13.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000451 (Fisher's exact test), Q value = 0.18

Table S480.  Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 36(17P13.3) CNV 1 0 8
DEL PEAK 36(17P13.3) WILD-TYPE 19 15 10

Figure S480.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(17p13.3)' versus 'CN_CNMF'

P value = 7.29e-49 (Chi-square test), Q value = 6.9e-46

Table S481.  Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 36(17P13.3) CNV 3 14 89 0 0
DEL PEAK 36(17P13.3) WILD-TYPE 287 26 50 17 6

Figure S481.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 36(17p13.3)' versus 'METHLYATION_CNMF'

P value = 2.59e-11 (Fisher's exact test), Q value = 1.7e-08

Table S482.  Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 36(17P13.3) CNV 57 21 10
DEL PEAK 36(17P13.3) WILD-TYPE 86 64 139

Figure S482.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 36(17p13.3)' versus 'MRNASEQ_CNMF'

P value = 7.12e-17 (Fisher's exact test), Q value = 5.6e-14

Table S483.  Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 36(17P13.3) CNV 54 3 5
DEL PEAK 36(17P13.3) WILD-TYPE 88 104 108

Figure S483.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 36(17p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.58e-19 (Fisher's exact test), Q value = 1.3e-16

Table S484.  Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 36(17P13.3) CNV 1 0 6 55
DEL PEAK 36(17P13.3) WILD-TYPE 64 92 59 85

Figure S484.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(17p13.3)' versus 'MIRSEQ_CNMF'

P value = 1.4e-15 (Fisher's exact test), Q value = 1.1e-12

Table S485.  Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 36(17P13.3) CNV 80 16 7
DEL PEAK 36(17P13.3) WILD-TYPE 127 128 125

Figure S485.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 36(17p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-12 (Fisher's exact test), Q value = 1.4e-09

Table S486.  Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 36(17P13.3) CNV 17 9 5 72
DEL PEAK 36(17P13.3) WILD-TYPE 176 70 22 112

Figure S486.  Get High-res Image Gene #84: 'Del Peak 36(17p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 37(17p12)' versus 'MRNA_CNMF'

P value = 0.000566 (Fisher's exact test), Q value = 0.22

Table S487.  Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 37(17P12) CNV 0 9 1 0
DEL PEAK 37(17P12) WILD-TYPE 13 9 13 8

Figure S487.  Get High-res Image Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 37(17p12)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000109 (Fisher's exact test), Q value = 0.046

Table S488.  Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 37(17P12) CNV 1 0 9
DEL PEAK 37(17P12) WILD-TYPE 19 15 9

Figure S488.  Get High-res Image Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 37(17p12)' versus 'CN_CNMF'

P value = 2.57e-58 (Chi-square test), Q value = 2.5e-55

Table S489.  Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 37(17P12) CNV 4 13 103 0 1
DEL PEAK 37(17P12) WILD-TYPE 286 27 36 17 5

Figure S489.  Get High-res Image Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 37(17p12)' versus 'METHLYATION_CNMF'

P value = 8.75e-16 (Fisher's exact test), Q value = 6.7e-13

Table S490.  Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 37(17P12) CNV 69 23 10
DEL PEAK 37(17P12) WILD-TYPE 74 62 139

Figure S490.  Get High-res Image Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(17p12)' versus 'MRNASEQ_CNMF'

P value = 2.64e-25 (Fisher's exact test), Q value = 2.4e-22

Table S491.  Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 37(17P12) CNV 69 3 4
DEL PEAK 37(17P12) WILD-TYPE 73 104 109

Figure S491.  Get High-res Image Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 37(17p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.65e-29 (Fisher's exact test), Q value = 5.1e-26

Table S492.  Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 37(17P12) CNV 1 0 4 71
DEL PEAK 37(17P12) WILD-TYPE 64 92 61 69

Figure S492.  Get High-res Image Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(17p12)' versus 'MIRSEQ_CNMF'

P value = 1.12e-20 (Fisher's exact test), Q value = 9.6e-18

Table S493.  Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 37(17P12) CNV 93 18 6
DEL PEAK 37(17P12) WILD-TYPE 114 126 126

Figure S493.  Get High-res Image Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 37(17p12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.14e-18 (Fisher's exact test), Q value = 9.5e-16

Table S494.  Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 37(17P12) CNV 17 9 4 87
DEL PEAK 37(17P12) WILD-TYPE 176 70 23 97

Figure S494.  Get High-res Image Gene #85: 'Del Peak 37(17p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 38(17p11.2)' versus 'MRNA_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.097

Table S495.  Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 38(17P11.2) CNV 0 8 0 0
DEL PEAK 38(17P11.2) WILD-TYPE 13 10 14 8

Figure S495.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 38(17p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 5.66e-05 (Fisher's exact test), Q value = 0.025

Table S496.  Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 38(17P11.2) CNV 0 0 8
DEL PEAK 38(17P11.2) WILD-TYPE 20 15 10

Figure S496.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(17p11.2)' versus 'CN_CNMF'

P value = 3.67e-52 (Chi-square test), Q value = 3.5e-49

Table S497.  Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 38(17P11.2) CNV 2 12 92 0 0
DEL PEAK 38(17P11.2) WILD-TYPE 288 28 47 17 6

Figure S497.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 38(17p11.2)' versus 'METHLYATION_CNMF'

P value = 8.82e-14 (Fisher's exact test), Q value = 6.3e-11

Table S498.  Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 38(17P11.2) CNV 62 21 9
DEL PEAK 38(17P11.2) WILD-TYPE 81 64 140

Figure S498.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 38(17p11.2)' versus 'MRNASEQ_CNMF'

P value = 1.28e-19 (Fisher's exact test), Q value = 1.1e-16

Table S499.  Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 38(17P11.2) CNV 58 3 4
DEL PEAK 38(17P11.2) WILD-TYPE 84 104 109

Figure S499.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 38(17p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.19e-24 (Fisher's exact test), Q value = 4.6e-21

Table S500.  Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 38(17P11.2) CNV 1 0 3 61
DEL PEAK 38(17P11.2) WILD-TYPE 64 92 62 79

Figure S500.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(17p11.2)' versus 'MIRSEQ_CNMF'

P value = 1.15e-16 (Fisher's exact test), Q value = 8.9e-14

Table S501.  Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 38(17P11.2) CNV 81 16 6
DEL PEAK 38(17P11.2) WILD-TYPE 126 128 126

Figure S501.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 38(17p11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.38e-14 (Fisher's exact test), Q value = 6.7e-11

Table S502.  Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 38(17P11.2) CNV 16 9 4 74
DEL PEAK 38(17P11.2) WILD-TYPE 177 70 23 110

Figure S502.  Get High-res Image Gene #86: 'Del Peak 38(17p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 39(17q11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.1

Table S503.  Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 39(17Q11.2) CNV 0 0 7
DEL PEAK 39(17Q11.2) WILD-TYPE 20 15 11

Figure S503.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 39(17q11.2)' versus 'CN_CNMF'

P value = 6.26e-44 (Chi-square test), Q value = 5.9e-41

Table S504.  Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 39(17Q11.2) CNV 2 13 81 0 0
DEL PEAK 39(17Q11.2) WILD-TYPE 288 27 58 17 6

Figure S504.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 39(17q11.2)' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Fisher's exact test), Q value = 5.9e-05

Table S505.  Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 39(17Q11.2) CNV 49 20 12
DEL PEAK 39(17Q11.2) WILD-TYPE 94 65 137

Figure S505.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 39(17q11.2)' versus 'MRNASEQ_CNMF'

P value = 2.47e-14 (Fisher's exact test), Q value = 1.8e-11

Table S506.  Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 39(17Q11.2) CNV 50 3 6
DEL PEAK 39(17Q11.2) WILD-TYPE 92 104 107

Figure S506.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 39(17q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.51e-17 (Fisher's exact test), Q value = 3.6e-14

Table S507.  Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 39(17Q11.2) CNV 1 1 5 52
DEL PEAK 39(17Q11.2) WILD-TYPE 64 91 60 88

Figure S507.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(17q11.2)' versus 'MIRSEQ_CNMF'

P value = 2.74e-10 (Fisher's exact test), Q value = 1.7e-07

Table S508.  Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 39(17Q11.2) CNV 67 17 8
DEL PEAK 39(17Q11.2) WILD-TYPE 140 127 124

Figure S508.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 39(17q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.88e-10 (Fisher's exact test), Q value = 3.5e-07

Table S509.  Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 39(17Q11.2) CNV 18 6 5 63
DEL PEAK 39(17Q11.2) WILD-TYPE 175 73 22 121

Figure S509.  Get High-res Image Gene #87: 'Del Peak 39(17q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 40(17q21.2)' versus 'MRNA_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.043

Table S510.  Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 40(17Q21.2) CNV 0 9 0 0
DEL PEAK 40(17Q21.2) WILD-TYPE 13 9 14 8

Figure S510.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(17q21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0056

Table S511.  Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 40(17Q21.2) CNV 0 0 9
DEL PEAK 40(17Q21.2) WILD-TYPE 20 15 9

Figure S511.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(17q21.2)' versus 'CN_CNMF'

P value = 2.03e-48 (Chi-square test), Q value = 1.9e-45

Table S512.  Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 40(17Q21.2) CNV 1 12 87 1 0
DEL PEAK 40(17Q21.2) WILD-TYPE 289 28 52 16 6

Figure S512.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(17q21.2)' versus 'METHLYATION_CNMF'

P value = 1.41e-09 (Fisher's exact test), Q value = 8.2e-07

Table S513.  Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 40(17Q21.2) CNV 53 23 11
DEL PEAK 40(17Q21.2) WILD-TYPE 90 62 138

Figure S513.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 40(17q21.2)' versus 'MRNASEQ_CNMF'

P value = 1.38e-14 (Fisher's exact test), Q value = 1e-11

Table S514.  Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 40(17Q21.2) CNV 49 3 5
DEL PEAK 40(17Q21.2) WILD-TYPE 93 104 108

Figure S514.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(17q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.99e-19 (Fisher's exact test), Q value = 6.7e-16

Table S515.  Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 40(17Q21.2) CNV 1 0 4 52
DEL PEAK 40(17Q21.2) WILD-TYPE 64 92 61 88

Figure S515.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(17q21.2)' versus 'MIRSEQ_CNMF'

P value = 1.7e-12 (Fisher's exact test), Q value = 1.2e-09

Table S516.  Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 40(17Q21.2) CNV 72 17 7
DEL PEAK 40(17Q21.2) WILD-TYPE 135 127 125

Figure S516.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 40(17q21.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.46e-11 (Fisher's exact test), Q value = 1.6e-08

Table S517.  Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 40(17Q21.2) CNV 18 6 5 67
DEL PEAK 40(17Q21.2) WILD-TYPE 175 73 22 117

Figure S517.  Get High-res Image Gene #88: 'Del Peak 40(17q21.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 41(18q23)' versus 'CN_CNMF'

P value = 6.45e-34 (Chi-square test), Q value = 6e-31

Table S518.  Gene #89: 'Del Peak 41(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 41(18Q23) CNV 2 17 68 3 1
DEL PEAK 41(18Q23) WILD-TYPE 288 23 71 14 5

Figure S518.  Get High-res Image Gene #89: 'Del Peak 41(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 41(18q23)' versus 'METHLYATION_CNMF'

P value = 4.64e-12 (Fisher's exact test), Q value = 3.1e-09

Table S519.  Gene #89: 'Del Peak 41(18q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 41(18Q23) CNV 55 15 8
DEL PEAK 41(18Q23) WILD-TYPE 88 70 141

Figure S519.  Get High-res Image Gene #89: 'Del Peak 41(18q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 41(18q23)' versus 'MRNASEQ_CNMF'

P value = 4.88e-11 (Fisher's exact test), Q value = 3.1e-08

Table S520.  Gene #89: 'Del Peak 41(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 41(18Q23) CNV 41 3 5
DEL PEAK 41(18Q23) WILD-TYPE 101 104 108

Figure S520.  Get High-res Image Gene #89: 'Del Peak 41(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 41(18q23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.72e-13 (Fisher's exact test), Q value = 1.9e-10

Table S521.  Gene #89: 'Del Peak 41(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 41(18Q23) CNV 1 1 4 43
DEL PEAK 41(18Q23) WILD-TYPE 64 91 61 97

Figure S521.  Get High-res Image Gene #89: 'Del Peak 41(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 41(18q23)' versus 'MIRSEQ_CNMF'

P value = 1.6e-12 (Fisher's exact test), Q value = 1.1e-09

Table S522.  Gene #89: 'Del Peak 41(18q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 41(18Q23) CNV 69 12 8
DEL PEAK 41(18Q23) WILD-TYPE 138 132 124

Figure S522.  Get High-res Image Gene #89: 'Del Peak 41(18q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 41(18q23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.5e-14 (Fisher's exact test), Q value = 3.3e-11

Table S523.  Gene #89: 'Del Peak 41(18q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 41(18Q23) CNV 11 6 7 65
DEL PEAK 41(18Q23) WILD-TYPE 182 73 20 119

Figure S523.  Get High-res Image Gene #89: 'Del Peak 41(18q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 42(19p13.3)' versus 'MRNA_CNMF'

P value = 5.64e-07 (Fisher's exact test), Q value = 0.00028

Table S524.  Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 42(19P13.3) CNV 0 12 0 0
DEL PEAK 42(19P13.3) WILD-TYPE 13 6 14 8

Figure S524.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 42(19p13.3)' versus 'MRNA_CHIERARCHICAL'

P value = 4.25e-06 (Fisher's exact test), Q value = 0.002

Table S525.  Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 42(19P13.3) CNV 0 1 11
DEL PEAK 42(19P13.3) WILD-TYPE 20 14 7

Figure S525.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 42(19p13.3)' versus 'CN_CNMF'

P value = 6e-78 (Chi-square test), Q value = 5.8e-75

Table S526.  Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 42(19P13.3) CNV 1 13 124 2 1
DEL PEAK 42(19P13.3) WILD-TYPE 289 27 15 15 5

Figure S526.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 42(19p13.3)' versus 'METHLYATION_CNMF'

P value = 7.23e-31 (Fisher's exact test), Q value = 6.6e-28

Table S527.  Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 42(19P13.3) CNV 91 24 5
DEL PEAK 42(19P13.3) WILD-TYPE 52 61 144

Figure S527.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 42(19p13.3)' versus 'RPPA_CNMF'

P value = 8.99e-06 (Chi-square test), Q value = 0.0042

Table S528.  Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
DEL PEAK 42(19P13.3) CNV 6 15 2 0 1 7
DEL PEAK 42(19P13.3) WILD-TYPE 35 22 37 12 40 17

Figure S528.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 42(19p13.3)' versus 'MRNASEQ_CNMF'

P value = 4.05e-36 (Fisher's exact test), Q value = 3.8e-33

Table S529.  Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 42(19P13.3) CNV 82 2 2
DEL PEAK 42(19P13.3) WILD-TYPE 60 105 111

Figure S529.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 42(19p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.96e-36 (Fisher's exact test), Q value = 1.8e-33

Table S530.  Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 42(19P13.3) CNV 1 0 3 82
DEL PEAK 42(19P13.3) WILD-TYPE 64 92 62 58

Figure S530.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 2.67e-35 (Fisher's exact test), Q value = 2.5e-32

Table S531.  Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 42(19P13.3) CNV 118 12 6
DEL PEAK 42(19P13.3) WILD-TYPE 89 132 126

Figure S531.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 42(19p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.55e-37 (Fisher's exact test), Q value = 4.2e-34

Table S532.  Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 42(19P13.3) CNV 11 7 5 113
DEL PEAK 42(19P13.3) WILD-TYPE 182 72 22 71

Figure S532.  Get High-res Image Gene #90: 'Del Peak 42(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 43(19p12)' versus 'CN_CNMF'

P value = 1.3e-15 (Chi-square test), Q value = 9.9e-13

Table S533.  Gene #91: 'Del Peak 43(19p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 43(19P12) CNV 2 12 33 2 0
DEL PEAK 43(19P12) WILD-TYPE 288 28 106 15 6

Figure S533.  Get High-res Image Gene #91: 'Del Peak 43(19p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 43(19p12)' versus 'METHLYATION_CNMF'

P value = 6.64e-07 (Fisher's exact test), Q value = 0.00033

Table S534.  Gene #91: 'Del Peak 43(19p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 43(19P12) CNV 29 11 3
DEL PEAK 43(19P12) WILD-TYPE 114 74 146

Figure S534.  Get High-res Image Gene #91: 'Del Peak 43(19p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 43(19p12)' versus 'MRNASEQ_CNMF'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.0097

Table S535.  Gene #91: 'Del Peak 43(19p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 43(19P12) CNV 20 1 3
DEL PEAK 43(19P12) WILD-TYPE 122 106 110

Figure S535.  Get High-res Image Gene #91: 'Del Peak 43(19p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 43(19p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.98e-06 (Fisher's exact test), Q value = 0.0019

Table S536.  Gene #91: 'Del Peak 43(19p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 43(19P12) CNV 1 0 2 21
DEL PEAK 43(19P12) WILD-TYPE 64 92 63 119

Figure S536.  Get High-res Image Gene #91: 'Del Peak 43(19p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 43(19p12)' versus 'MIRSEQ_CNMF'

P value = 3.04e-06 (Fisher's exact test), Q value = 0.0015

Table S537.  Gene #91: 'Del Peak 43(19p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 43(19P12) CNV 37 5 6
DEL PEAK 43(19P12) WILD-TYPE 170 139 126

Figure S537.  Get High-res Image Gene #91: 'Del Peak 43(19p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 43(19p12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.98e-06 (Fisher's exact test), Q value = 0.00096

Table S538.  Gene #91: 'Del Peak 43(19p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 43(19P12) CNV 5 6 3 34
DEL PEAK 43(19P12) WILD-TYPE 188 73 24 150

Figure S538.  Get High-res Image Gene #91: 'Del Peak 43(19p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 44(19q13.43)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000451 (Fisher's exact test), Q value = 0.18

Table S539.  Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 44(19Q13.43) CNV 1 0 8
DEL PEAK 44(19Q13.43) WILD-TYPE 19 15 10

Figure S539.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 44(19q13.43)' versus 'CN_CNMF'

P value = 2.7e-23 (Chi-square test), Q value = 2.4e-20

Table S540.  Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 44(19Q13.43) CNV 2 9 49 0 0
DEL PEAK 44(19Q13.43) WILD-TYPE 288 31 90 17 6

Figure S540.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(19q13.43)' versus 'METHLYATION_CNMF'

P value = 2.56e-09 (Fisher's exact test), Q value = 1.5e-06

Table S541.  Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 44(19Q13.43) CNV 34 12 2
DEL PEAK 44(19Q13.43) WILD-TYPE 109 73 147

Figure S541.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 44(19q13.43)' versus 'MRNASEQ_CNMF'

P value = 1.28e-09 (Fisher's exact test), Q value = 7.6e-07

Table S542.  Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 44(19Q13.43) CNV 29 1 2
DEL PEAK 44(19Q13.43) WILD-TYPE 113 106 111

Figure S542.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 44(19q13.43)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.47e-09 (Fisher's exact test), Q value = 1.4e-06

Table S543.  Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 44(19Q13.43) CNV 1 0 2 29
DEL PEAK 44(19Q13.43) WILD-TYPE 64 92 63 111

Figure S543.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 44(19q13.43)' versus 'MIRSEQ_CNMF'

P value = 1.68e-11 (Fisher's exact test), Q value = 1.1e-08

Table S544.  Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 44(19Q13.43) CNV 48 5 3
DEL PEAK 44(19Q13.43) WILD-TYPE 159 139 129

Figure S544.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 44(19q13.43)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.15e-14 (Fisher's exact test), Q value = 1.6e-11

Table S545.  Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 44(19Q13.43) CNV 2 4 2 48
DEL PEAK 44(19Q13.43) WILD-TYPE 191 75 25 136

Figure S545.  Get High-res Image Gene #92: 'Del Peak 44(19q13.43)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 45(20p12.1)' versus 'CN_CNMF'

P value = 0.000182 (Chi-square test), Q value = 0.075

Table S546.  Gene #93: 'Del Peak 45(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 45(20P12.1) CNV 6 6 16 2 0
DEL PEAK 45(20P12.1) WILD-TYPE 284 34 123 15 6

Figure S546.  Get High-res Image Gene #93: 'Del Peak 45(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 46(22q11.1)' versus 'CN_CNMF'

P value = 2.26e-29 (Chi-square test), Q value = 2.1e-26

Table S547.  Gene #94: 'Del Peak 46(22q11.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 46(22Q11.1) CNV 3 15 61 1 1
DEL PEAK 46(22Q11.1) WILD-TYPE 287 25 78 16 5

Figure S547.  Get High-res Image Gene #94: 'Del Peak 46(22q11.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 46(22q11.1)' versus 'METHLYATION_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.048

Table S548.  Gene #94: 'Del Peak 46(22q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 46(22Q11.1) CNV 39 18 13
DEL PEAK 46(22Q11.1) WILD-TYPE 104 67 136

Figure S548.  Get High-res Image Gene #94: 'Del Peak 46(22q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 46(22q11.1)' versus 'MRNASEQ_CNMF'

P value = 1.25e-07 (Fisher's exact test), Q value = 6.5e-05

Table S549.  Gene #94: 'Del Peak 46(22q11.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 46(22Q11.1) CNV 34 4 5
DEL PEAK 46(22Q11.1) WILD-TYPE 108 103 108

Figure S549.  Get High-res Image Gene #94: 'Del Peak 46(22q11.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 46(22q11.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.85e-09 (Fisher's exact test), Q value = 1.1e-06

Table S550.  Gene #94: 'Del Peak 46(22q11.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 46(22Q11.1) CNV 1 2 4 36
DEL PEAK 46(22Q11.1) WILD-TYPE 64 90 61 104

Figure S550.  Get High-res Image Gene #94: 'Del Peak 46(22q11.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 46(22q11.1)' versus 'MIRSEQ_CNMF'

P value = 4.79e-07 (Fisher's exact test), Q value = 0.00024

Table S551.  Gene #94: 'Del Peak 46(22q11.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 46(22Q11.1) CNV 55 16 8
DEL PEAK 46(22Q11.1) WILD-TYPE 152 128 124

Figure S551.  Get High-res Image Gene #94: 'Del Peak 46(22q11.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 46(22q11.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.37e-05 (Fisher's exact test), Q value = 0.023

Table S552.  Gene #94: 'Del Peak 46(22q11.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 46(22Q11.1) CNV 17 9 5 48
DEL PEAK 46(22Q11.1) WILD-TYPE 176 70 22 136

Figure S552.  Get High-res Image Gene #94: 'Del Peak 46(22q11.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 47(22q12.1)' versus 'CN_CNMF'

P value = 1.54e-31 (Chi-square test), Q value = 1.4e-28

Table S553.  Gene #95: 'Del Peak 47(22q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 47(22Q12.1) CNV 4 13 67 1 2
DEL PEAK 47(22Q12.1) WILD-TYPE 286 27 72 16 4

Figure S553.  Get High-res Image Gene #95: 'Del Peak 47(22q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 47(22q12.1)' versus 'METHLYATION_CNMF'

P value = 2.1e-05 (Fisher's exact test), Q value = 0.0096

Table S554.  Gene #95: 'Del Peak 47(22q12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 47(22Q12.1) CNV 41 21 13
DEL PEAK 47(22Q12.1) WILD-TYPE 102 64 136

Figure S554.  Get High-res Image Gene #95: 'Del Peak 47(22q12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 47(22q12.1)' versus 'MRNASEQ_CNMF'

P value = 4.79e-09 (Fisher's exact test), Q value = 2.7e-06

Table S555.  Gene #95: 'Del Peak 47(22q12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 47(22Q12.1) CNV 39 4 6
DEL PEAK 47(22Q12.1) WILD-TYPE 103 103 107

Figure S555.  Get High-res Image Gene #95: 'Del Peak 47(22q12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 47(22q12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.31e-11 (Fisher's exact test), Q value = 8.6e-09

Table S556.  Gene #95: 'Del Peak 47(22q12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 47(22Q12.1) CNV 2 2 3 42
DEL PEAK 47(22Q12.1) WILD-TYPE 63 90 62 98

Figure S556.  Get High-res Image Gene #95: 'Del Peak 47(22q12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 47(22q12.1)' versus 'MIRSEQ_CNMF'

P value = 1.24e-08 (Fisher's exact test), Q value = 6.9e-06

Table S557.  Gene #95: 'Del Peak 47(22q12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 47(22Q12.1) CNV 60 18 7
DEL PEAK 47(22Q12.1) WILD-TYPE 147 126 125

Figure S557.  Get High-res Image Gene #95: 'Del Peak 47(22q12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 47(22q12.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.54e-07 (Fisher's exact test), Q value = 7.9e-05

Table S558.  Gene #95: 'Del Peak 47(22q12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 47(22Q12.1) CNV 16 8 6 55
DEL PEAK 47(22Q12.1) WILD-TYPE 177 71 21 129

Figure S558.  Get High-res Image Gene #95: 'Del Peak 47(22q12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 48(22q13.31)' versus 'MRNA_CNMF'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.0082

Table S559.  Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 48(22Q13.31) CNV 0 10 0 0
DEL PEAK 48(22Q13.31) WILD-TYPE 13 8 14 8

Figure S559.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 48(22q13.31)' versus 'MRNA_CHIERARCHICAL'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0012

Table S560.  Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 48(22Q13.31) CNV 0 0 10
DEL PEAK 48(22Q13.31) WILD-TYPE 20 15 8

Figure S560.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 48(22q13.31)' versus 'CN_CNMF'

P value = 9.61e-55 (Chi-square test), Q value = 9.2e-52

Table S561.  Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 48(22Q13.31) CNV 4 14 100 1 3
DEL PEAK 48(22Q13.31) WILD-TYPE 286 26 39 16 3

Figure S561.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 48(22q13.31)' versus 'METHLYATION_CNMF'

P value = 4.79e-13 (Fisher's exact test), Q value = 3.4e-10

Table S562.  Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 48(22Q13.31) CNV 67 24 13
DEL PEAK 48(22Q13.31) WILD-TYPE 76 61 136

Figure S562.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 48(22q13.31)' versus 'MRNASEQ_CNMF'

P value = 8.88e-20 (Fisher's exact test), Q value = 7.5e-17

Table S563.  Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 48(22Q13.31) CNV 63 4 6
DEL PEAK 48(22Q13.31) WILD-TYPE 79 103 107

Figure S563.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 48(22q13.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.44e-23 (Fisher's exact test), Q value = 1.3e-20

Table S564.  Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 48(22Q13.31) CNV 1 2 4 66
DEL PEAK 48(22Q13.31) WILD-TYPE 64 90 61 74

Figure S564.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 48(22q13.31)' versus 'MIRSEQ_CNMF'

P value = 4.73e-18 (Fisher's exact test), Q value = 3.9e-15

Table S565.  Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 48(22Q13.31) CNV 90 20 7
DEL PEAK 48(22Q13.31) WILD-TYPE 117 124 125

Figure S565.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 48(22q13.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.64e-18 (Fisher's exact test), Q value = 1.4e-15

Table S566.  Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 48(22Q13.31) CNV 16 9 6 86
DEL PEAK 48(22Q13.31) WILD-TYPE 177 70 21 98

Figure S566.  Get High-res Image Gene #96: 'Del Peak 48(22q13.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 49(22q13.32)' versus 'MRNA_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.043

Table S567.  Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 13 18 14 8
DEL PEAK 49(22Q13.32) CNV 0 9 0 0
DEL PEAK 49(22Q13.32) WILD-TYPE 13 9 14 8

Figure S567.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 49(22q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0056

Table S568.  Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 49(22Q13.32) CNV 0 0 9
DEL PEAK 49(22Q13.32) WILD-TYPE 20 15 9

Figure S568.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 49(22q13.32)' versus 'CN_CNMF'

P value = 4.93e-53 (Chi-square test), Q value = 4.7e-50

Table S569.  Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 49(22Q13.32) CNV 8 14 102 1 3
DEL PEAK 49(22Q13.32) WILD-TYPE 282 26 37 16 3

Figure S569.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 49(22q13.32)' versus 'METHLYATION_CNMF'

P value = 2.04e-12 (Fisher's exact test), Q value = 1.4e-09

Table S570.  Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 49(22Q13.32) CNV 68 28 15
DEL PEAK 49(22Q13.32) WILD-TYPE 75 57 134

Figure S570.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 49(22q13.32)' versus 'MRNASEQ_CNMF'

P value = 2.93e-18 (Fisher's exact test), Q value = 2.4e-15

Table S571.  Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 49(22Q13.32) CNV 64 5 8
DEL PEAK 49(22Q13.32) WILD-TYPE 78 102 105

Figure S571.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 49(22q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.21e-21 (Fisher's exact test), Q value = 1e-18

Table S572.  Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 49(22Q13.32) CNV 2 3 5 67
DEL PEAK 49(22Q13.32) WILD-TYPE 63 89 60 73

Figure S572.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 49(22q13.32)' versus 'MIRSEQ_CNMF'

P value = 3.27e-17 (Fisher's exact test), Q value = 2.6e-14

Table S573.  Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 49(22Q13.32) CNV 93 22 9
DEL PEAK 49(22Q13.32) WILD-TYPE 114 122 123

Figure S573.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 49(22q13.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.13e-18 (Fisher's exact test), Q value = 5.8e-15

Table S574.  Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 49(22Q13.32) CNV 19 10 6 89
DEL PEAK 49(22Q13.32) WILD-TYPE 174 69 21 95

Figure S574.  Get High-res Image Gene #97: 'Del Peak 49(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 50(Xp21.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.1

Table S575.  Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
DEL PEAK 50(XP21.1) CNV 0 0 7
DEL PEAK 50(XP21.1) WILD-TYPE 20 15 11

Figure S575.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 50(Xp21.1)' versus 'CN_CNMF'

P value = 4.23e-33 (Chi-square test), Q value = 3.9e-30

Table S576.  Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
DEL PEAK 50(XP21.1) CNV 2 10 67 2 0
DEL PEAK 50(XP21.1) WILD-TYPE 288 30 72 15 6

Figure S576.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 50(Xp21.1)' versus 'METHLYATION_CNMF'

P value = 3.85e-09 (Fisher's exact test), Q value = 2.2e-06

Table S577.  Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
DEL PEAK 50(XP21.1) CNV 45 15 7
DEL PEAK 50(XP21.1) WILD-TYPE 98 70 142

Figure S577.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 50(Xp21.1)' versus 'MRNASEQ_CNMF'

P value = 1.34e-10 (Fisher's exact test), Q value = 8.3e-08

Table S578.  Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
DEL PEAK 50(XP21.1) CNV 38 2 5
DEL PEAK 50(XP21.1) WILD-TYPE 104 105 108

Figure S578.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 50(Xp21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.09e-11 (Fisher's exact test), Q value = 2e-08

Table S579.  Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
DEL PEAK 50(XP21.1) CNV 2 1 3 39
DEL PEAK 50(XP21.1) WILD-TYPE 63 91 62 101

Figure S579.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 50(Xp21.1)' versus 'MIRSEQ_CNMF'

P value = 7.15e-12 (Fisher's exact test), Q value = 4.8e-09

Table S580.  Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
DEL PEAK 50(XP21.1) CNV 62 9 7
DEL PEAK 50(XP21.1) WILD-TYPE 145 135 125

Figure S580.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 50(Xp21.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.61e-13 (Fisher's exact test), Q value = 3.2e-10

Table S581.  Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
DEL PEAK 50(XP21.1) CNV 9 5 5 59
DEL PEAK 50(XP21.1) WILD-TYPE 184 74 22 125

Figure S581.  Get High-res Image Gene #98: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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 = UCEC-TP.transferedmergedcluster.txt

  • Number of patients = 492

  • Number of copy number variation regions = 98

  • Number of molecular subtypes = 10

  • Exclude regions that fewer than K tumors have alterations, K = 3

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

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

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] 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)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[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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