Correlation between copy number variation genes and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1ZW1JB6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ZW1JB6
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 12 molecular subtypes across 504 patients, 590 significant findings detected with Q value < 0.25.

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

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

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

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

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

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

  • Amp Peak 7(2p24.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • Amp Peak 10(3p14.1) cnvs correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

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

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

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

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

  • Amp Peak 26(11q13.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • Amp Peak 27(11q14.1) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 28(12p12.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 29(12q13.11) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 30(12q13.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 31(13q34) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 32(14q24.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Amp Peak 33(15q26.3) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 34(16p11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 35(17q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 36(17q12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 37(17q25.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 38(18p11.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 39(18q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 40(19p13.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 41(19p13.11) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 42(19q12) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 43(20p13) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 44(20q11.21) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 45(20q13.12) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 46(20q13.33) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 47(22q12.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Amp Peak 48(Xp11.23) cnvs correlated to 'CN_CNMF'.

  • Amp Peak 49(Xq28) cnvs correlated to 'CN_CNMF'.

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

  • Del Peak 2(2p25.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • Del Peak 3(2q22.1) cnvs correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 4(2q37.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 5(3p14.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 6(3q13.31) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • Del Peak 7(4p16.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 8(4p15.31) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 9(4q22.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 10(4q34.3) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 11(5q11.2) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 12(6q26) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 13(7p22.3) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 14(7q11.22) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 15(7q31.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 16(7q36.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 17(8p23.2) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 18(8p21.2) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 19(9p23) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 20(9q21.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • Del Peak 37(17p11.2) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • Del Peak 41(18q23) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • Del Peak 46(22q12.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Del Peak 47(22q13.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 48(22q13.32) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 49(Xp21.1) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 98 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 590 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type 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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
Amp Peak 11(3q26 2) 0 (0%) 344 5.91e-05
(0.0383) 		5.43e-05
(0.0353) 		6.29e-61
(7.27e-58) 		3.15e-17
(3.27e-14) 		0.000353
(0.203) 		0.0154
(1.00) 		0.000139
(0.085) 		0.000367
(0.21) 		2.49e-22
(2.71e-19) 		5.69e-16
(5.85e-13) 		3.02e-07
(0.000243) 		5.65e-10
(5.09e-07)
Del Peak 42(19p13 3) 0 (0%) 359 9.09e-06
(0.00662) 		1.96e-07
(0.000159) 		1.78e-78
(2.06e-75) 		5.06e-30
(5.6e-27) 		8.99e-06
(0.00655) 		0.0146
(1.00) 		6.31e-08
(5.26e-05) 		3.57e-07
(0.000286) 		2.53e-32
(2.82e-29) 		2.65e-24
(2.9e-21) 		4.29e-11
(4.03e-08) 		2.52e-17
(2.63e-14)
Amp Peak 12(3q26 2) 0 (0%) 355 0.000342
(0.198) 		0.000377
(0.216) 		9.76e-61
(1.13e-57) 		1.71e-18
(1.81e-15) 		0.0015
(0.763) 		0.0249
(1.00) 		3.3e-05
(0.0221) 		0.000123
(0.0758) 		1.13e-21
(1.23e-18) 		6.51e-18
(6.84e-15) 		5.02e-08
(4.22e-05) 		6.52e-12
(6.28e-09)
Amp Peak 40(19p13 2) 0 (0%) 418 2.35e-05
(0.0161) 		1.13e-06
(0.000876) 		1.34e-44
(1.52e-41) 		1.89e-09
(1.67e-06) 		0.15
(1.00) 		0.0408
(1.00) 		1.18e-06
(0.000909) 		2e-08
(1.71e-05) 		2.79e-17
(2.91e-14) 		1.28e-08
(1.11e-05) 		0.000215
(0.128) 		4.67e-06
(0.00347)
Del Peak 38(17p11 2) 0 (0%) 393 0.000111
(0.0688) 		7.26e-06
(0.00535) 		1.39e-52
(1.59e-49) 		5.35e-13
(5.28e-10) 		0.0247
(1.00) 		0.378
(1.00) 		7.44e-07
(0.000586) 		0.000144
(0.0875) 		1.38e-16
(1.42e-13) 		3.22e-10
(2.93e-07) 		0.000203
(0.122) 		8.02e-06
(0.00589)
Amp Peak 16(6p24 2) 0 (0%) 401 0.00296
(1.00) 		0.000377
(0.216) 		4.01e-39
(4.52e-36) 		6.89e-10
(6.17e-07) 		0.000177
(0.107) 		0.059
(1.00) 		1.07e-05
(0.00775) 		0.000975
(0.516) 		3.42e-12
(3.34e-09) 		2.51e-11
(2.37e-08) 		7.83e-05
(0.0499) 		2.58e-07
(0.000208)
Amp Peak 37(17q25 1) 0 (0%) 410 0.000187
(0.113) 		1.94e-05
(0.0135) 		5.41e-39
(6.09e-36) 		2.73e-10
(2.48e-07) 		0.00741
(1.00) 		0.193
(1.00) 		3.24e-06
(0.00244) 		0.0119
(1.00) 		9.58e-15
(9.7e-12) 		3.91e-12
(3.82e-09) 		0.000112
(0.069) 		1.14e-06
(0.000882)
Amp Peak 42(19q12) 0 (0%) 397 0.00518
(1.00) 		0.000132
(0.0811) 		5.42e-52
(6.2e-49) 		2e-15
(2.04e-12) 		0.00289
(1.00) 		0.212
(1.00) 		3.96e-05
(0.0263) 		7.1e-05
(0.0454) 		1.33e-18
(1.41e-15) 		4.38e-15
(4.47e-12) 		5.57e-07
(0.00044) 		2.34e-10
(2.14e-07)
Del Peak 17(8p23 2) 0 (0%) 397 0.00202
(0.987) 		0.000218
(0.13) 		5.48e-47
(6.22e-44) 		3.64e-21
(3.93e-18) 		0.0469
(1.00) 		0.378
(1.00) 		1.01e-05
(0.00732) 		1.03e-06
(0.000806) 		2.22e-23
(2.43e-20) 		2.94e-20
(3.16e-17) 		1.23e-11
(1.17e-08) 		6.89e-15
(7e-12)
Del Peak 18(8p21 2) 0 (0%) 398 0.00202
(0.987) 		0.000218
(0.13) 		6.98e-51
(7.96e-48) 		4.72e-27
(5.2e-24) 		0.017
(1.00) 		0.168
(1.00) 		8.4e-07
(0.000658) 		9.4e-09
(8.17e-06) 		2.27e-27
(2.5e-24) 		7.44e-25
(8.16e-22) 		1.33e-15
(1.37e-12) 		8.68e-19
(9.22e-16)
Del Peak 21(9q34 11) 0 (0%) 378 2.35e-05
(0.0161) 		1.13e-06
(0.000876) 		4.9e-54
(5.62e-51) 		1.92e-10
(1.77e-07) 		0.000384
(0.219) 		0.0316
(1.00) 		0.00141
(0.727) 		0.0257
(1.00) 		3.18e-19
(3.39e-16) 		5.15e-12
(4.99e-09) 		7.97e-05
(0.0508) 		5.49e-07
(0.000434)
Del Peak 32(15q23) 0 (0%) 398 0.00202
(0.987) 		0.000218
(0.13) 		2.43e-43
(2.75e-40) 		1.32e-17
(1.38e-14) 		0.104
(1.00) 		0.812
(1.00) 		4.34e-10
(3.92e-07) 		8.4e-08
(6.97e-05) 		1.65e-19
(1.76e-16) 		9.27e-15
(9.4e-12) 		1.77e-08
(1.52e-05) 		3.82e-10
(3.47e-07)
Del Peak 34(16q21) 0 (0%) 361 0.000771
(0.419) 		9.8e-05
(0.0615) 		7.21e-54
(8.25e-51) 		4.16e-17
(4.32e-14) 		0.0797
(1.00) 		1
(1.00) 		7.11e-07
(0.000561) 		5.04e-07
(0.000401) 		1.12e-19
(1.19e-16) 		1.61e-13
(1.59e-10) 		3.25e-07
(0.000261) 		1.42e-10
(1.31e-07)
Del Peak 35(16q23 1) 0 (0%) 350 0.00296
(1.00) 		0.000377
(0.216) 		6.89e-54
(7.9e-51) 		3.63e-18
(3.83e-15) 		0.0275
(1.00) 		0.369
(1.00) 		6.31e-08
(5.26e-05) 		1.74e-07
(0.000142) 		1.06e-18
(1.12e-15) 		2.49e-16
(2.57e-13) 		8.89e-08
(7.36e-05) 		1.24e-11
(1.18e-08)
Del Peak 47(22q13 31) 0 (0%) 378 3.62e-06
(0.00271) 		1.54e-07
(0.000126) 		2.19e-57
(2.52e-54) 		1.79e-12
(1.76e-09) 		0.0018
(0.906) 		0.153
(1.00) 		0.000897
(0.477) 		0.000438
(0.249) 		1.11e-18
(1.17e-15) 		3.86e-12
(3.76e-09) 		0.000267
(0.157) 		1.42e-06
(0.00109)
Del Peak 48(22q13 32) 0 (0%) 372 2.35e-05
(0.0161) 		1.13e-06
(0.000876) 		1.3e-55
(1.5e-52) 		2.52e-11
(2.38e-08) 		0.00148
(0.754) 		0.0786
(1.00) 		0.00269
(1.00) 		0.000311
(0.181) 		2.51e-19
(2.68e-16) 		7.53e-12
(7.23e-09) 		0.000428
(0.243) 		4.89e-06
(0.00362)
Amp Peak 8(2q13) 0 (0%) 393 0.159
(1.00) 		0.0339
(1.00) 		5.79e-41
(6.54e-38) 		1.47e-12
(1.45e-09) 		0.0025
(1.00) 		0.153
(1.00) 		0.000272
(0.159) 		0.000279
(0.163) 		7.96e-12
(7.63e-09) 		8.58e-14
(8.58e-11) 		6.21e-08
(5.19e-05) 		6.95e-11
(6.46e-08)
Amp Peak 14(5p15 33) 0 (0%) 425 0.231
(1.00) 		0.0213
(1.00) 		2.08e-31
(2.31e-28) 		4.65e-13
(4.59e-10) 		0.221
(1.00) 		0.612
(1.00) 		8.26e-06
(0.00605) 		1.33e-05
(0.00946) 		6.71e-10
(6.01e-07) 		7.07e-11
(6.56e-08) 		4.03e-07
(0.00032) 		1.23e-08
(1.06e-05)
Amp Peak 28(12p12 1) 0 (0%) 422 0.327
(1.00) 		0.683
(1.00) 		5.27e-14
(5.31e-11) 		3.36e-08
(2.84e-05) 		0.536
(1.00) 		0.659
(1.00) 		6.76e-05
(0.0436) 		3.62e-05
(0.0241) 		3.94e-06
(0.00294) 		1.21e-07
(9.98e-05) 		0.000172
(0.104) 		9.69e-06
(0.00705)
Amp Peak 39(18q11 2) 0 (0%) 440 0.108
(1.00) 		0.0272
(1.00) 		1.01e-25
(1.11e-22) 		4.8e-10
(4.33e-07) 		0.156
(1.00) 		0.0444
(1.00) 		4.39e-08
(3.69e-05) 		2.84e-05
(0.0193) 		4.03e-14
(4.06e-11) 		3.09e-12
(3.03e-09) 		1.8e-08
(1.54e-05) 		1.34e-10
(1.24e-07)
Amp Peak 41(19p13 11) 0 (0%) 417 0.00381
(1.00) 		0.000454
(0.256) 		2.73e-45
(3.09e-42) 		5.05e-11
(4.73e-08) 		0.199
(1.00) 		0.309
(1.00) 		1.17e-09
(1.04e-06) 		3.08e-09
(2.71e-06) 		4.46e-17
(4.63e-14) 		2.66e-10
(2.43e-07) 		1.2e-05
(0.00863) 		3.47e-07
(0.000278)
Amp Peak 44(20q11 21) 0 (0%) 371 0.00253
(1.00) 		0.000132
(0.0811) 		3.25e-54
(3.73e-51) 		5.48e-12
(5.31e-09) 		0.00156
(0.79) 		0.205
(1.00) 		1.85e-05
(0.0129) 		0.00221
(1.00) 		9.05e-14
(9.04e-11) 		6.57e-12
(6.33e-09) 		1.17e-05
(0.00838) 		1.13e-08
(9.74e-06)
Del Peak 8(4p15 31) 0 (0%) 412 0.0129
(1.00) 		0.00193
(0.963) 		2.39e-35
(2.69e-32) 		1.41e-13
(1.4e-10) 		0.0203
(1.00) 		0.346
(1.00) 		6.3e-06
(0.00466) 		1.07e-06
(0.000829) 		7.15e-17
(7.41e-14) 		1.17e-13
(1.17e-10) 		1.47e-06
(0.00112) 		1.53e-08
(1.31e-05)
Del Peak 10(4q34 3) 0 (0%) 385 0.00381
(1.00) 		0.000454
(0.256) 		2.05e-48
(2.34e-45) 		7.93e-14
(7.96e-11) 		0.0599
(1.00) 		0.521
(1.00) 		2.19e-07
(0.000177) 		1.76e-06
(0.00134) 		6.7e-18
(7.03e-15) 		3.06e-19
(3.27e-16) 		6.89e-09
(6e-06) 		2.23e-12
(2.19e-09)
Del Peak 11(5q11 2) 0 (0%) 400 0.0129
(1.00) 		0.00193
(0.963) 		7.69e-48
(8.73e-45) 		1.48e-15
(1.52e-12) 		0.000858
(0.461) 		0.01
(1.00) 		1.45e-05
(0.0103) 		0.000249
(0.147) 		1.52e-15
(1.56e-12) 		7.93e-14
(7.96e-11) 		1.19e-06
(0.000914) 		4.61e-08
(3.88e-05)
Del Peak 12(6q26) 0 (0%) 459 0.379
(1.00) 		0.0902
(1.00) 		1.11e-13
(1.11e-10) 		1.94e-08
(1.66e-05) 		0.675
(1.00) 		0.301
(1.00) 		5.42e-05
(0.0353) 		3.67e-08
(3.1e-05) 		2.15e-08
(1.83e-05) 		8.48e-09
(7.38e-06) 		0.000213
(0.127) 		1.62e-05
(0.0114)
Del Peak 22(10q23 31) 0 (0%) 432 0.137
(1.00) 		0.0194
(1.00) 		1.36e-26
(1.5e-23) 		1.1e-07
(9.06e-05) 		0.116
(1.00) 		0.796
(1.00) 		1.42e-05
(0.0101) 		2.89e-07
(0.000232) 		2.01e-11
(1.9e-08) 		1.38e-08
(1.19e-05) 		0.000146
(0.0884) 		4.14e-06
(0.00309)
Del Peak 27(12q24 33) 0 (0%) 443 8.32e-26
(9.14e-23) 		5.68e-11
(5.29e-08) 		0.0355
(1.00) 		0.106
(1.00) 		3.86e-05
(0.0257) 		9.03e-05
(0.0571) 		1.12e-11
(1.07e-08) 		1.33e-11
(1.26e-08) 		1.92e-07
(0.000156) 		1.53e-07
(0.000125)
Del Peak 31(15q15 1) 0 (0%) 375 0.0129
(1.00) 		0.00193
(0.963) 		1.6e-55
(1.84e-52) 		1.4e-16
(1.45e-13) 		0.00247
(1.00) 		0.205
(1.00) 		6.98e-10
(6.23e-07) 		2.72e-08
(2.32e-05) 		3.58e-22
(3.88e-19) 		1.43e-17
(1.49e-14) 		1.88e-07
(0.000153) 		6.96e-09
(6.06e-06)
Del Peak 33(16p13 3) 0 (0%) 421 0.0129
(1.00) 		0.00193
(0.963) 		1.91e-34
(2.14e-31) 		3.67e-14
(3.7e-11) 		0.0547
(1.00) 		0.176
(1.00) 		1.83e-05
(0.0128) 		8.93e-06
(0.00652) 		5.62e-16
(5.79e-13) 		2.52e-14
(2.55e-11) 		2.86e-05
(0.0194) 		1.58e-07
(0.000129)
Del Peak 37(17p11 2) 0 (0%) 383 0.000771
(0.419) 		9.8e-05
(0.0615) 		9.94e-57
(1.15e-53) 		1.26e-13
(1.25e-10) 		0.00226
(1.00) 		0.521
(1.00) 		3.38e-06
(0.00254) 		3e-05
(0.0202) 		8.33e-19
(8.85e-16) 		8.01e-12
(7.67e-09) 		0.000588
(0.325) 		1.42e-05
(0.0101)
Amp Peak 2(1p34 2) 0 (0%) 437 0.0129
(1.00) 		0.00193
(0.963) 		1.68e-30
(1.86e-27) 		1.19e-07
(9.8e-05) 		0.00924
(1.00) 		0.56
(1.00) 		7.23e-05
(0.0462) 		0.00451
(1.00) 		2.23e-18
(2.35e-15) 		7.53e-11
(6.99e-08) 		1.03e-05
(0.00747) 		1.63e-07
(0.000133)
Amp Peak 20(8q24 21) 0 (0%) 312 0.0121
(1.00) 		0.0358
(1.00) 		1.54e-34
(1.73e-31) 		1.33e-06
(0.00102) 		8.75e-05
(0.0554) 		0.504
(1.00) 		0.00362
(1.00) 		0.0853
(1.00) 		8.62e-11
(8e-08) 		6.36e-10
(5.71e-07) 		9.48e-05
(0.0597) 		5.95e-05
(0.0385)
Amp Peak 21(8q24 21) 0 (0%) 304 0.00296
(1.00) 		0.00397
(1.00) 		8.33e-34
(9.33e-31) 		1.53e-05
(0.0108) 		7.26e-07
(0.000572) 		0.141
(1.00) 		0.00188
(0.938) 		0.0527
(1.00) 		3.63e-11
(3.41e-08) 		1.1e-08
(9.53e-06) 		9.21e-05
(0.0581) 		0.000132
(0.081)
Amp Peak 29(12q13 11) 0 (0%) 423 0.377
(1.00) 		0.59
(1.00) 		2.56e-17
(2.67e-14) 		5.06e-08
(4.24e-05) 		0.449
(1.00) 		0.157
(1.00) 		0.0299
(1.00) 		0.000357
(0.205) 		5.3e-07
(0.00042) 		5.36e-07
(0.000425) 		2.91e-05
(0.0197) 		1.55e-05
(0.0109)
Amp Peak 31(13q34) 0 (0%) 453 0.689
(1.00) 		0.272
(1.00) 		6.11e-18
(6.44e-15) 		4.02e-07
(0.00032) 		0.241
(1.00) 		0.0546
(1.00) 		0.000349
(0.202) 		0.00315
(1.00) 		2.18e-07
(0.000176) 		8.89e-08
(7.36e-05) 		9.8e-05
(0.0615) 		1.84e-05
(0.0128)
Amp Peak 36(17q12) 0 (0%) 438 0.108
(1.00) 		0.0272
(1.00) 		3.12e-23
(3.4e-20) 		1.32e-13
(1.31e-10) 		0.0111
(1.00) 		0.438
(1.00) 		0.000245
(0.144) 		0.00643
(1.00) 		4.07e-12
(3.96e-09) 		1.25e-12
(1.23e-09) 		1.26e-05
(0.00902) 		1.56e-09
(1.38e-06)
Amp Peak 38(18p11 31) 0 (0%) 421 0.154
(1.00) 		0.0276
(1.00) 		2.25e-31
(2.5e-28) 		9.71e-12
(9.26e-09) 		0.0101
(1.00) 		0.0197
(1.00) 		0.000351
(0.202) 		0.00146
(0.745) 		6.84e-15
(6.96e-12) 		2.83e-13
(2.8e-10) 		8.84e-07
(0.00069) 		2.16e-10
(1.98e-07)
Amp Peak 45(20q13 12) 0 (0%) 364 0.0129
(1.00) 		0.00193
(0.963) 		1.08e-55
(1.25e-52) 		8.23e-14
(8.24e-11) 		0.00478
(1.00) 		0.105
(1.00) 		2.92e-05
(0.0197) 		0.00293
(1.00) 		2.26e-15
(2.31e-12) 		4.24e-12
(4.12e-09) 		1.7e-05
(0.012) 		1e-09
(8.94e-07)
Del Peak 1(1p36 11) 0 (0%) 425 0.0515
(1.00) 		0.00755
(1.00) 		1.05e-33
(1.18e-30) 		2.72e-10
(2.48e-07) 		0.0339
(1.00) 		0.393
(1.00) 		0.00276
(1.00) 		0.000282
(0.165) 		2.88e-12
(2.82e-09) 		1.23e-13
(1.23e-10) 		2.84e-05
(0.0193) 		8.76e-07
(0.000685)
Del Peak 5(3p14 2) 0 (0%) 432 0.0515
(1.00) 		0.00755
(1.00) 		1.4e-31
(1.56e-28) 		1.14e-09
(1.01e-06) 		0.000952
(0.505) 		0.0197
(1.00) 		0.000102
(0.0633) 		0.00529
(1.00) 		5.81e-11
(5.41e-08) 		6.41e-10
(5.75e-07) 		2.11e-05
(0.0146) 		7.76e-07
(0.000609)
Del Peak 9(4q22 1) 0 (0%) 404 0.00381
(1.00) 		0.000454
(0.256) 		2.26e-42
(2.56e-39) 		1.36e-17
(1.43e-14) 		0.0252
(1.00) 		0.102
(1.00) 		0.00235
(1.00) 		1.94e-05
(0.0135) 		4.06e-16
(4.18e-13) 		6.49e-18
(6.83e-15) 		1.3e-08
(1.12e-05) 		5.63e-11
(5.26e-08)
Del Peak 13(7p22 3) 0 (0%) 434 0.000567
(0.315) 		4.17e-05
(0.0277) 		3.87e-29
(4.28e-26) 		4.33e-10
(3.92e-07) 		0.0312
(1.00) 		0.0935
(1.00) 		0.0115
(1.00) 		0.0392
(1.00) 		7.68e-12
(7.36e-09) 		4.49e-10
(4.06e-07) 		6.29e-05
(0.0406) 		2.96e-07
(0.000238)
Del Peak 20(9q21 2) 0 (0%) 386 2.35e-05
(0.0161) 		1.13e-06
(0.000876) 		1.48e-50
(1.68e-47) 		1.02e-10
(9.39e-08) 		0.000759
(0.413) 		0.205
(1.00) 		0.000689
(0.378) 		0.0139
(1.00) 		8.86e-21
(9.54e-18) 		9e-12
(8.59e-09) 		0.00109
(0.568) 		1.68e-05
(0.0118)
Del Peak 36(17p13 3) 0 (0%) 391 0.000771
(0.419) 		9.8e-05
(0.0615) 		3.27e-48
(3.72e-45) 		4.12e-10
(3.74e-07) 		0.00158
(0.8) 		0.521
(1.00) 		2.07e-07
(0.000168) 		0.00183
(0.918) 		3.16e-14
(3.19e-11) 		4.48e-09
(3.92e-06) 		0.0021
(1.00) 		4.38e-05
(0.0288)
Del Peak 44(19q13 43) 0 (0%) 444 0.000771
(0.419) 		9.8e-05
(0.0615) 		3.38e-20
(3.63e-17) 		7.49e-10
(6.68e-07) 		0.0782
(1.00) 		0.56
(1.00) 		0.00685
(1.00) 		0.000812
(0.438) 		1.23e-10
(1.14e-07) 		3.22e-11
(3.02e-08) 		3.16e-05
(0.0213) 		1.1e-06
(0.000857)
Del Peak 49(Xp21 1) 0 (0%) 419 0.000567
(0.315) 		4.17e-05
(0.0277) 		8.78e-34
(9.83e-31) 		2.03e-08
(1.74e-05) 		0.00541
(1.00) 		0.244
(1.00) 		0.00024
(0.141) 		0.00794
(1.00) 		2.62e-13
(2.6e-10) 		1.4e-09
(1.24e-06) 		0.00196
(0.966) 		2.2e-05
(0.0153)
Amp Peak 5(1q22) 0 (0%) 266 0.0223
(1.00) 		0.0543
(1.00) 		6.8e-15
(6.93e-12) 		0.00014
(0.0852) 		0.132
(1.00) 		0.179
(1.00) 		0.000302
(0.176) 		0.00785
(1.00) 		8.03e-06
(0.00589) 		1.13e-05
(0.00811) 		0.162
(1.00) 		3e-05
(0.0202)
Amp Peak 30(12q13 2) 0 (0%) 415 0.181
(1.00) 		0.254
(1.00) 		1.14e-17
(1.2e-14) 		9.93e-07
(0.000774) 		0.315
(1.00) 		0.36
(1.00) 		0.247
(1.00) 		0.223
(1.00) 		6.82e-06
(0.00504) 		4.23e-06
(0.00315) 		5.23e-05
(0.0341) 		1.5e-05
(0.0106)
Amp Peak 35(17q11 2) 0 (0%) 439 0.151
(1.00) 		0.0272
(1.00) 		4.48e-25
(4.92e-22) 		1.29e-11
(1.23e-08) 		0.0201
(1.00) 		0.0052
(1.00) 		0.00282
(1.00) 		0.00411
(1.00) 		5.66e-12
(5.47e-09) 		3.59e-12
(3.5e-09) 		1.25e-05
(0.00895) 		3.35e-08
(2.84e-05)
Amp Peak 43(20p13) 0 (0%) 397 0.151
(1.00) 		0.0272
(1.00) 		1.95e-38
(2.19e-35) 		7.81e-10
(6.96e-07) 		0.0828
(1.00) 		0.386
(1.00) 		0.00144
(0.736) 		0.00299
(1.00) 		4.08e-09
(3.57e-06) 		4.64e-10
(4.19e-07) 		4.38e-05
(0.0288) 		3.58e-07
(0.000286)
Amp Peak 46(20q13 33) 0 (0%) 367 0.0243
(1.00) 		0.00409
(1.00) 		4.94e-51
(5.64e-48) 		5.45e-11
(5.09e-08) 		0.0674
(1.00) 		0.686
(1.00) 		0.000519
(0.291) 		0.0238
(1.00) 		2.85e-13
(2.82e-10) 		8.8e-11
(8.15e-08) 		0.000192
(0.116) 		7.75e-08
(6.44e-05)
Amp Peak 47(22q12 2) 0 (0%) 448 0.379
(1.00) 		0.0902
(1.00) 		5.61e-18
(5.92e-15) 		6.36e-16
(6.53e-13) 		0.181
(1.00) 		0.0546
(1.00) 		0.00268
(1.00) 		0.00122
(0.632) 		4e-12
(3.89e-09) 		2.45e-14
(2.47e-11) 		5.88e-10
(5.29e-07) 		9.49e-13
(9.35e-10)
Del Peak 7(4p16 3) 0 (0%) 415 0.0129
(1.00) 		0.00193
(0.963) 		1.58e-31
(1.76e-28) 		7.52e-12
(7.22e-09) 		0.0096
(1.00) 		0.244
(1.00) 		0.00339
(1.00) 		0.000462
(0.259) 		8.1e-14
(8.12e-11) 		1.34e-11
(1.26e-08) 		4.81e-05
(0.0315) 		1.06e-07
(8.74e-05)
Del Peak 15(7q31 1) 0 (0%) 453 0.137
(1.00) 		0.0194
(1.00) 		8.86e-25
(9.69e-22) 		3.99e-09
(3.51e-06) 		0.0899
(1.00) 		0.0192
(1.00) 		0.00458
(1.00) 		0.0119
(1.00) 		5.42e-12
(5.25e-09) 		5.19e-08
(4.35e-05) 		0.000215
(0.128) 		3.2e-06
(0.00241)
Del Peak 16(7q36 1) 0 (0%) 443 0.333
(1.00) 		0.0623
(1.00) 		7.33e-28
(8.09e-25) 		5.69e-12
(5.49e-09) 		0.0198
(1.00) 		0.00216
(1.00) 		0.00458
(1.00) 		0.00489
(1.00) 		3.18e-15
(3.25e-12) 		2.18e-11
(2.06e-08) 		1.97e-05
(0.0137) 		3.7e-09
(3.25e-06)
Del Peak 23(11p15 5) 0 (0%) 411 0.379
(1.00) 		0.0902
(1.00) 		5.06e-39
(5.7e-36) 		6.9e-14
(6.94e-11) 		0.461
(1.00) 		0.612
(1.00) 		0.000984
(0.52) 		0.0269
(1.00) 		4.25e-16
(4.38e-13) 		6.91e-10
(6.17e-07) 		4.19e-06
(0.00312) 		1.6e-09
(1.41e-06)
Del Peak 24(11q14 1) 0 (0%) 440 9.41e-23
(1.02e-19) 		1.96e-10
(1.8e-07) 		0.328
(1.00) 		0.393
(1.00) 		0.00574
(1.00) 		0.0532
(1.00) 		3.26e-09
(2.87e-06) 		1.88e-09
(1.66e-06) 		0.000391
(0.223) 		3.07e-08
(2.6e-05)
Del Peak 25(11q25) 0 (0%) 416 8.68e-30
(9.6e-27) 		4.12e-12
(4e-09) 		0.134
(1.00) 		0.804
(1.00) 		0.0193
(1.00) 		0.0724
(1.00) 		4.14e-09
(3.63e-06) 		7.34e-12
(7.06e-09) 		2.31e-05
(0.0159) 		5.64e-08
(4.71e-05)
Del Peak 26(12q23 1) 0 (0%) 452 7.34e-21
(7.9e-18) 		3.21e-10
(2.92e-07) 		0.0349
(1.00) 		0.00949
(1.00) 		0.00644
(1.00) 		0.00118
(0.613) 		2.67e-07
(0.000215) 		2.1e-11
(1.98e-08) 		2.36e-05
(0.0161) 		1.21e-06
(0.000927)
Del Peak 30(14q13 1) 0 (0%) 439 0.00809
(1.00) 		0.00105
(0.549) 		3.4e-24
(3.71e-21) 		2.7e-10
(2.47e-07) 		0.0681
(1.00) 		0.106
(1.00) 		0.00897
(1.00) 		0.158
(1.00) 		7.68e-08
(6.39e-05) 		1.37e-10
(1.26e-07) 		3.24e-05
(0.0218) 		7.23e-06
(0.00534)
Del Peak 40(17q21 2) 0 (0%) 400 2.35e-05
(0.0161) 		1.13e-06
(0.000876) 		2.56e-49
(2.91e-46) 		2.96e-08
(2.52e-05) 		0.00327
(1.00) 		0.168
(1.00) 		0.000747
(0.408) 		0.000663
(0.364) 		5.41e-15
(5.51e-12) 		2.12e-07
(0.000172) 		0.00445
(1.00) 		0.00254
(1.00)
Amp Peak 1(1p35 2) 0 (0%) 450 0.151
(1.00) 		0.0272
(1.00) 		6.44e-22
(6.97e-19) 		1.21e-05
(0.00869) 		0.0001
(0.0624) 		0.267
(1.00) 		0.0993
(1.00) 		0.119
(1.00) 		5.17e-07
(0.000411) 		1.56e-06
(0.00119) 		0.000988
(0.52) 		0.000442
(0.25)
Amp Peak 4(1q21 3) 0 (0%) 278 0.0223
(1.00) 		0.0543
(1.00) 		1.02e-12
(1e-09) 		0.00538
(1.00) 		0.317
(1.00) 		0.135
(1.00) 		5.73e-05
(0.0372) 		0.00137
(0.704) 		4.1e-06
(0.00306) 		6.84e-05
(0.044) 		0.111
(1.00) 		2.26e-05
(0.0156)
Amp Peak 7(2p24 3) 0 (0%) 391 0.682
(1.00) 		0.434
(1.00) 		7.78e-32
(8.67e-29) 		3.92e-07
(0.000313) 		0.0386
(1.00) 		0.695
(1.00) 		0.000555
(0.31) 		0.013
(1.00) 		3.46e-05
(0.0231) 		7.9e-06
(0.00581) 		0.000609
(0.336) 		2.5e-05
(0.017)
Amp Peak 9(3p25 1) 0 (0%) 433 0.188
(1.00) 		0.247
(1.00) 		2.48e-23
(2.7e-20) 		1.66e-06
(0.00126) 		0.075
(1.00) 		0.438
(1.00) 		0.00153
(0.776) 		0.0058
(1.00) 		4.65e-05
(0.0305) 		4.03e-05
(0.0268) 		0.00333
(1.00) 		9.02e-05
(0.0571)
Amp Peak 22(9p24 2) 0 (0%) 445 0.129
(1.00) 		0.0606
(1.00) 		3.85e-21
(4.16e-18) 		2.1e-06
(0.00159) 		0.000874
(0.467) 		0.00457
(1.00) 		0.0273
(1.00) 		0.00196
(0.966) 		5.94e-12
(5.73e-09) 		1.38e-07
(0.000113) 		0.00128
(0.663) 		0.000221
(0.131)
Amp Peak 32(14q24 3) 0 (0%) 446 0.0605
(1.00) 		0.0951
(1.00) 		3.66e-16
(3.77e-13) 		1.76e-05
(0.0123) 		0.153
(1.00) 		0.393
(1.00) 		0.000339
(0.197) 		0.00112
(0.586) 		2.47e-06
(0.00188) 		2.73e-06
(0.00206) 		0.0507
(1.00) 		0.00588
(1.00)
Amp Peak 34(16p11 2) 0 (0%) 447 0.00809
(1.00) 		0.00105
(0.549) 		3.87e-20
(4.15e-17) 		8.01e-06
(0.00589) 		0.138
(1.00) 		0.126
(1.00) 		0.00458
(1.00) 		0.0119
(1.00) 		1.09e-09
(9.71e-07) 		1.54e-05
(0.0109) 		0.00209
(1.00) 		0.00013
(0.0798)
Del Peak 14(7q11 22) 0 (0%) 463 4.86e-19
(5.18e-16) 		8.11e-07
(0.000636) 		0.0668
(1.00) 		0.00669
(1.00) 		0.0804
(1.00) 		0.0977
(1.00) 		5.63e-09
(4.92e-06) 		2.23e-05
(0.0154) 		0.0016
(0.804) 		0.000115
(0.0712)
Del Peak 39(17q11 2) 0 (0%) 406 0.000567
(0.315) 		4.17e-05
(0.0277) 		2.65e-42
(3e-39) 		1.18e-06
(0.000905) 		0.013
(1.00) 		0.647
(1.00) 		0.00298
(1.00) 		0.000452
(0.255) 		8.12e-12
(7.76e-09) 		8.81e-06
(0.00644) 		0.00471
(1.00) 		0.00701
(1.00)
Del Peak 41(18q23) 0 (0%) 412 0.617
(1.00) 		0.173
(1.00) 		6.53e-33
(7.29e-30) 		5.64e-11
(5.26e-08) 		0.0427
(1.00) 		0.0354
(1.00) 		0.0184
(1.00) 		0.0213
(1.00) 		3.05e-11
(2.87e-08) 		5.93e-10
(5.33e-07) 		0.000903
(0.479) 		7.07e-05
(0.0453)
Del Peak 43(19p12) 0 (0%) 453 4.55e-17
(4.72e-14) 		1.21e-07
(9.98e-05) 		0.21
(1.00) 		0.507
(1.00) 		0.0217
(1.00) 		0.0136
(1.00) 		5.16e-06
(0.00382) 		8.44e-08
(6.99e-05) 		0.00232
(1.00) 		4.18e-05
(0.0277)
Del Peak 46(22q12 1) 0 (0%) 415 0.00202
(0.987) 		0.000218
(0.13) 		1.72e-33
(1.92e-30) 		8.49e-05
(0.0539) 		0.267
(1.00) 		0.627
(1.00) 		0.0549
(1.00) 		0.0148
(1.00) 		4.51e-11
(4.23e-08) 		5.19e-05
(0.0339) 		0.217
(1.00) 		0.0638
(1.00)
Amp Peak 3(1p22 3) 0 (0%) 420 0.0196
(1.00) 		0.0156
(1.00) 		0.000107
(0.0666) 		0.0103
(1.00) 		0.737
(1.00) 		0.28
(1.00) 		0.0217
(1.00) 		0.234
(1.00) 		1.27e-06
(0.000975) 		6.36e-05
(0.041) 		0.00205
(0.993) 		3.39e-06
(0.00254)
Amp Peak 15(5q35 3) 0 (0%) 456 0.137
(1.00) 		0.0194
(1.00) 		2.47e-17
(2.58e-14) 		0.000531
(0.297) 		0.237
(1.00) 		0.731
(1.00) 		0.00799
(1.00) 		0.00666
(1.00) 		1.12e-05
(0.00805) 		9.63e-05
(0.0605) 		0.0199
(1.00) 		0.000145
(0.0882)
Amp Peak 17(6q25 1) 0 (0%) 425 0.284
(1.00) 		0.312
(1.00) 		7.75e-26
(8.53e-23) 		1.01e-05
(0.00733) 		0.318
(1.00) 		0.0698
(1.00) 		0.137
(1.00) 		0.161
(1.00) 		5.18e-05
(0.0339) 		3.14e-06
(0.00237) 		0.00536
(1.00) 		0.00088
(0.469)
Amp Peak 25(11p11 2) 0 (0%) 458 0.00202
(0.987) 		0.00755
(1.00) 		1.79e-14
(1.82e-11) 		0.000158
(0.0959) 		0.0122
(1.00) 		0.789
(1.00) 		0.0356
(1.00) 		0.0197
(1.00) 		2.27e-05
(0.0156) 		3.25e-05
(0.0218) 		0.0294
(1.00) 		0.00969
(1.00)
Del Peak 19(9p23) 0 (0%) 436 0.379
(1.00) 		0.0902
(1.00) 		3.54e-23
(3.85e-20) 		2.48e-06
(0.00188) 		0.0369
(1.00) 		0.295
(1.00) 		0.165
(1.00) 		0.866
(1.00) 		1.5e-05
(0.0106) 		1.12e-05
(0.00805) 		0.0541
(1.00) 		0.00726
(1.00)
Del Peak 28(13q11) 0 (0%) 414 0.333
(1.00) 		0.158
(1.00) 		3.76e-30
(4.16e-27) 		3.45e-08
(2.92e-05) 		0.162
(1.00) 		0.126
(1.00) 		0.000984
(0.52) 		0.00259
(1.00) 		5.13e-08
(4.3e-05) 		2.95e-08
(2.51e-05) 		0.00826
(1.00) 		0.00132
(0.684)
Del Peak 29(13q14 2) 0 (0%) 406 0.617
(1.00) 		0.301
(1.00) 		2.46e-33
(2.75e-30) 		7.57e-07
(0.000595) 		0.0746
(1.00) 		0.102
(1.00) 		0.0141
(1.00) 		0.0411
(1.00) 		1.06e-08
(9.17e-06) 		4.38e-08
(3.69e-05) 		0.0622
(1.00) 		0.0179
(1.00)
Amp Peak 13(4p16 3) 0 (0%) 458 0.0515
(1.00) 		0.00755
(1.00) 		4.34e-19
(4.63e-16) 		0.000867
(0.464) 		0.0898
(1.00) 		0.00285
(1.00) 		0.00421
(1.00) 		0.0179
(1.00) 		1.43e-08
(1.23e-05) 		2.69e-06
(0.00204) 		0.0083
(1.00) 		0.00331
(1.00)
Amp Peak 19(8p11 21) 0 (0%) 355 0.0106
(1.00) 		0.0143
(1.00) 		8.07e-22
(8.73e-19) 		0.0175
(1.00) 		0.00111
(0.578) 		0.719
(1.00) 		0.0644
(1.00) 		0.861
(1.00) 		4.63e-05
(0.0304) 		0.000206
(0.123) 		0.00595
(1.00) 		0.00226
(1.00)
Amp Peak 23(9q34 3) 0 (0%) 471 0.243
(1.00) 		0.158
(1.00) 		9.4e-11
(8.69e-08) 		7.97e-05
(0.0508) 		0.336
(1.00) 		0.507
(1.00) 		0.0835
(1.00) 		0.00402
(1.00) 		0.0157
(1.00) 		0.000103
(0.0637) 		0.0239
(1.00) 		0.0788
(1.00)
Del Peak 3(2q22 1) 0 (0%) 458 0.0391
(1.00) 		0.00466
(1.00) 		8.28e-20
(8.88e-17) 		0.0015
(0.763) 		0.0823
(1.00) 		0.155
(1.00) 		0.0217
(1.00) 		0.2
(1.00) 		1.01e-08
(8.8e-06) 		1.16e-05
(0.00837) 		0.0163
(1.00) 		0.0178
(1.00)
Amp Peak 26(11q13 2) 0 (0%) 434 0.00381
(1.00) 		0.00829
(1.00) 		7.02e-21
(7.57e-18) 		0.00336
(1.00) 		0.0148
(1.00) 		1
(1.00) 		0.176
(1.00) 		0.119
(1.00) 		0.000175
(0.106) 		0.000857
(0.461) 		0.0695
(1.00) 		0.0414
(1.00)
Del Peak 2(2p25 3) 0 (0%) 479 6.1e-09
(5.32e-06) 		0.000558
(0.311) 		0.268
(1.00) 		0.652
(1.00) 		0.069
(1.00) 		0.465
(1.00) 		0.00032
(0.186) 		0.00513
(1.00) 		0.34
(1.00) 		0.205
(1.00)
Del Peak 4(2q37 3) 0 (0%) 454 1.35e-17
(1.42e-14) 		6.89e-05
(0.0442) 		0.276
(1.00) 		0.507
(1.00) 		0.0324
(1.00) 		0.229
(1.00) 		0.000864
(0.463) 		0.000597
(0.33) 		0.0344
(1.00) 		0.0389
(1.00)
Del Peak 6(3q13 31) 0 (0%) 474 0.379
(1.00) 		0.0902
(1.00) 		1.27e-11
(1.2e-08) 		0.0289
(1.00) 		0.0559
(1.00) 		1
(1.00) 		0.0732
(1.00) 		0.0591
(1.00) 		2.33e-05
(0.016) 		0.00074
(0.405) 		0.224
(1.00) 		0.0773
(1.00)
Amp Peak 6(1q42 3) 0 (0%) 296 0.0502
(1.00) 		0.186
(1.00) 		1.5e-07
(0.000123) 		0.0712
(1.00) 		0.631
(1.00) 		0.0696
(1.00) 		0.0656
(1.00) 		0.285
(1.00) 		0.0252
(1.00) 		0.0838
(1.00) 		0.816
(1.00) 		0.118
(1.00)
Amp Peak 10(3p14 1) 0 (0%) 448 0.536
(1.00) 		1
(1.00) 		2.16e-18
(2.28e-15) 		0.00267
(1.00) 		0.0521
(1.00) 		0.373
(1.00) 		0.551
(1.00) 		0.479
(1.00) 		0.0175
(1.00) 		0.00201
(0.985) 		0.0751
(1.00) 		0.0338
(1.00)
Amp Peak 18(7q22 1) 0 (0%) 419 0.678
(1.00) 		0.744
(1.00) 		5.72e-19
(6.09e-16) 		0.00783
(1.00) 		0.74
(1.00) 		1
(1.00) 		0.0186
(1.00) 		0.077
(1.00) 		0.0422
(1.00) 		0.00333
(1.00) 		0.0379
(1.00) 		0.00371
(1.00)
Amp Peak 24(10q22 2) 0 (0%) 371 0.0321
(1.00) 		0.0871
(1.00) 		2.56e-10
(2.35e-07) 		0.351
(1.00) 		0.273
(1.00) 		0.414
(1.00) 		0.289
(1.00) 		0.623
(1.00) 		0.224
(1.00) 		0.454
(1.00) 		0.084
(1.00) 		0.184
(1.00)
Amp Peak 27(11q14 1) 0 (0%) 451 0.379
(1.00) 		0.667
(1.00) 		6.93e-15
(7.03e-12) 		0.0227
(1.00) 		0.414
(1.00) 		0.258
(1.00) 		0.025
(1.00) 		0.039
(1.00) 		0.00136
(0.7) 		0.00333
(1.00) 		0.0565
(1.00) 		0.0806
(1.00)
Amp Peak 33(15q26 3) 0 (0%) 469 1.8e-08
(1.55e-05) 		0.0378
(1.00) 		0.218
(1.00) 		0.155
(1.00) 		0.0576
(1.00) 		0.0454
(1.00) 		0.00145
(0.743) 		0.000759
(0.413) 		0.0146
(1.00) 		0.0207
(1.00)
Amp Peak 48(Xp11 23) 0 (0%) 419 0.355
(1.00) 		0.683
(1.00) 		5.87e-24
(6.4e-21) 		0.00465
(1.00) 		0.783
(1.00) 		0.399
(1.00) 		0.00325
(1.00) 		0.00185
(0.926) 		0.00702
(1.00) 		0.0107
(1.00) 		0.0208
(1.00) 		0.0365
(1.00)
Amp Peak 49(Xq28) 0 (0%) 417 0.159
(1.00) 		0.0339
(1.00) 		7.84e-25
(8.58e-22) 		0.0523
(1.00) 		0.128
(1.00) 		0.535
(1.00) 		0.308
(1.00) 		0.158
(1.00) 		0.139
(1.00) 		0.0569
(1.00) 		0.0994
(1.00) 		0.287
(1.00)
Del Peak 45(20p12 1) 0 (0%) 472 3.56e-05
(0.0238) 		0.0913
(1.00) 		0.285
(1.00) 		0.301
(1.00) 		0.343
(1.00) 		1
(1.00) 		0.000637
(0.35) 		0.0653
(1.00) 		0.411
(1.00) 		0.29
(1.00)
'Amp Peak 1(1p35.2)' versus 'CN_CNMF'

P value = 6.44e-22 (Chi-square test), Q value = 7e-19

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 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 1(1P35.2) CNV 0 3 48 1 2 0
AMP PEAK 1(1P35.2) WILD-TYPE 294 6 106 12 20 12

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 = 1.21e-05 (Fisher's exact test), Q value = 0.0087

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 1(1P35.2) CNV 31 6 7
AMP PEAK 1(1P35.2) WILD-TYPE 115 83 148

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 = 0.062

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 'MIRSEQ_CNMF'

P value = 5.17e-07 (Chi-square test), Q value = 0.00041

Table S4.  Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 1(1P35.2) CNV 34 5 3 3 7
AMP PEAK 1(1P35.2) WILD-TYPE 115 124 46 50 108

Figure S4.  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 = 1.56e-06 (Fisher's exact test), Q value = 0.0012

Table S5.  Gene #1: 'Amp Peak 1(1p35.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 1(1P35.2) CNV 3 7 42
AMP PEAK 1(1P35.2) WILD-TYPE 24 215 204

Figure S5.  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 = 1.68e-30 (Chi-square test), Q value = 1.9e-27

Table S6.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 2(1P34.2) CNV 0 3 62 0 2 0
AMP PEAK 2(1P34.2) WILD-TYPE 294 6 92 13 20 12

Figure S6.  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 = 1.19e-07 (Fisher's exact test), Q value = 9.8e-05

Table S7.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 2(1P34.2) CNV 38 13 6
AMP PEAK 2(1P34.2) WILD-TYPE 108 76 149

Figure S7.  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 = 7.23e-05 (Fisher's exact test), Q value = 0.046

Table S8.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 2(1P34.2) CNV 21 2 4
AMP PEAK 2(1P34.2) WILD-TYPE 28 34 29

Figure S8.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 2.23e-18 (Chi-square test), Q value = 2.3e-15

Table S9.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 2(1P34.2) CNV 52 4 1 3 5
AMP PEAK 2(1P34.2) WILD-TYPE 97 125 48 50 110

Figure S9.  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 = 7.53e-11 (Fisher's exact test), Q value = 7e-08

Table S10.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 2(1P34.2) CNV 3 6 56
AMP PEAK 2(1P34.2) WILD-TYPE 24 216 190

Figure S10.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.03e-05 (Fisher's exact test), Q value = 0.0075

Table S11.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 2(1P34.2) CNV 41 6 8
AMP PEAK 2(1P34.2) WILD-TYPE 128 109 80

Figure S11.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 1.63e-07 (Fisher's exact test), Q value = 0.00013

Table S12.  Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 2(1P34.2) CNV 13 7 34 1
AMP PEAK 2(1P34.2) WILD-TYPE 86 131 76 24

Figure S12.  Get High-res Image Gene #2: 'Amp Peak 2(1p34.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 0.000107 (Chi-square test), Q value = 0.067

Table S13.  Gene #3: 'Amp Peak 3(1p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 3(1P22.3) CNV 30 2 43 4 4 1
AMP PEAK 3(1P22.3) WILD-TYPE 264 7 111 9 18 11

Figure S13.  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 = 1.27e-06 (Chi-square test), Q value = 0.00097

Table S14.  Gene #3: 'Amp Peak 3(1p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 3(1P22.3) CNV 43 8 3 13 16
AMP PEAK 3(1P22.3) WILD-TYPE 106 121 46 40 99

Figure S14.  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 = 6.36e-05 (Fisher's exact test), Q value = 0.041

Table S15.  Gene #3: 'Amp Peak 3(1p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 3(1P22.3) CNV 1 23 59
AMP PEAK 3(1P22.3) WILD-TYPE 26 199 187

Figure S15.  Get High-res Image Gene #3: 'Amp Peak 3(1p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 3.39e-06 (Fisher's exact test), Q value = 0.0025

Table S16.  Gene #3: 'Amp Peak 3(1p22.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 3(1P22.3) CNV 12 12 37 3
AMP PEAK 3(1P22.3) WILD-TYPE 87 126 73 22

Figure S16.  Get High-res Image Gene #3: 'Amp Peak 3(1p22.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 1.02e-12 (Chi-square test), Q value = 1e-09

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 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 4(1Q21.3) CNV 89 8 100 9 11 9
AMP PEAK 4(1Q21.3) WILD-TYPE 205 1 54 4 11 3

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 'MRNASEQ_CNMF'

P value = 5.73e-05 (Fisher's exact test), Q value = 0.037

Table S18.  Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 4(1Q21.3) CNV 38 12 14
AMP PEAK 4(1Q21.3) WILD-TYPE 11 24 19

Figure S18.  Get High-res Image Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 4.1e-06 (Chi-square test), Q value = 0.0031

Table S19.  Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 4(1Q21.3) CNV 91 41 17 29 45
AMP PEAK 4(1Q21.3) WILD-TYPE 58 88 32 24 70

Figure S19.  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 = 6.84e-05 (Fisher's exact test), Q value = 0.044

Table S20.  Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 4(1Q21.3) CNV 9 79 135
AMP PEAK 4(1Q21.3) WILD-TYPE 18 143 111

Figure S20.  Get High-res Image Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.26e-05 (Fisher's exact test), Q value = 0.016

Table S21.  Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 4(1Q21.3) CNV 45 48 70 7
AMP PEAK 4(1Q21.3) WILD-TYPE 54 90 40 18

Figure S21.  Get High-res Image Gene #4: 'Amp Peak 4(1q21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 6.8e-15 (Chi-square test), Q value = 6.9e-12

Table S22.  Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 5(1Q22) CNV 93 9 107 9 11 9
AMP PEAK 5(1Q22) WILD-TYPE 201 0 47 4 11 3

Figure S22.  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 = 0.00014 (Fisher's exact test), Q value = 0.085

Table S23.  Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 5(1Q22) CNV 87 35 57
AMP PEAK 5(1Q22) WILD-TYPE 59 54 98

Figure S23.  Get High-res Image Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000302 (Fisher's exact test), Q value = 0.18

Table S24.  Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 5(1Q22) CNV 38 13 16
AMP PEAK 5(1Q22) WILD-TYPE 11 23 17

Figure S24.  Get High-res Image Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 8.03e-06 (Chi-square test), Q value = 0.0059

Table S25.  Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 5(1Q22) CNV 95 45 18 29 48
AMP PEAK 5(1Q22) WILD-TYPE 54 84 31 24 67

Figure S25.  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 = 1.13e-05 (Fisher's exact test), Q value = 0.0081

Table S26.  Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 5(1Q22) CNV 9 83 143
AMP PEAK 5(1Q22) WILD-TYPE 18 139 103

Figure S26.  Get High-res Image Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S27.  Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 5(1Q22) CNV 49 52 72 7
AMP PEAK 5(1Q22) WILD-TYPE 50 86 38 18

Figure S27.  Get High-res Image Gene #5: 'Amp Peak 5(1q22)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 1.5e-07 (Chi-square test), Q value = 0.00012

Table S28.  Gene #6: 'Amp Peak 6(1q42.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 6(1Q42.3) CNV 92 8 79 9 10 10
AMP PEAK 6(1Q42.3) WILD-TYPE 202 1 75 4 12 2

Figure S28.  Get High-res Image Gene #6: 'Amp Peak 6(1q42.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(2p24.3)' versus 'CN_CNMF'

P value = 7.78e-32 (Chi-square test), Q value = 8.7e-29

Table S29.  Gene #7: 'Amp Peak 7(2p24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 7(2P24.3) CNV 14 9 67 11 7 5
AMP PEAK 7(2P24.3) WILD-TYPE 280 0 87 2 15 7

Figure S29.  Get High-res Image Gene #7: 'Amp Peak 7(2p24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(2p24.3)' versus 'METHLYATION_CNMF'

P value = 3.92e-07 (Fisher's exact test), Q value = 0.00031

Table S30.  Gene #7: 'Amp Peak 7(2p24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 7(2P24.3) CNV 55 13 20
AMP PEAK 7(2P24.3) WILD-TYPE 91 76 135

Figure S30.  Get High-res Image Gene #7: 'Amp Peak 7(2p24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 7(2p24.3)' versus 'MIRSEQ_CNMF'

P value = 3.46e-05 (Chi-square test), Q value = 0.023

Table S31.  Gene #7: 'Amp Peak 7(2p24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 7(2P24.3) CNV 54 17 11 11 18
AMP PEAK 7(2P24.3) WILD-TYPE 95 112 38 42 97

Figure S31.  Get High-res Image Gene #7: 'Amp Peak 7(2p24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 7(2p24.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.9e-06 (Fisher's exact test), Q value = 0.0058

Table S32.  Gene #7: 'Amp Peak 7(2p24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 7(2P24.3) CNV 5 29 77
AMP PEAK 7(2P24.3) WILD-TYPE 22 193 169

Figure S32.  Get High-res Image Gene #7: 'Amp Peak 7(2p24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 7(2p24.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.5e-05 (Fisher's exact test), Q value = 0.017

Table S33.  Gene #7: 'Amp Peak 7(2p24.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 7(2P24.3) CNV 24 16 41 4
AMP PEAK 7(2P24.3) WILD-TYPE 75 122 69 21

Figure S33.  Get High-res Image Gene #7: 'Amp Peak 7(2p24.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 5.79e-41 (Chi-square test), Q value = 6.5e-38

Table S34.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 8(2Q13) CNV 6 8 79 11 4 3
AMP PEAK 8(2Q13) WILD-TYPE 288 1 75 2 18 9

Figure S34.  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 = 1.47e-12 (Fisher's exact test), Q value = 1.4e-09

Table S35.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 8(2Q13) CNV 61 16 11
AMP PEAK 8(2Q13) WILD-TYPE 85 73 144

Figure S35.  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 = 0.000272 (Fisher's exact test), Q value = 0.16

Table S36.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 8(2Q13) CNV 26 7 5
AMP PEAK 8(2Q13) WILD-TYPE 23 29 28

Figure S36.  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 = 0.000279 (Fisher's exact test), Q value = 0.16

Table S37.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
AMP PEAK 8(2Q13) CNV 24 10 4
AMP PEAK 8(2Q13) WILD-TYPE 22 26 32

Figure S37.  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 = 7.96e-12 (Chi-square test), Q value = 7.6e-09

Table S38.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 8(2Q13) CNV 63 9 12 7 18
AMP PEAK 8(2Q13) WILD-TYPE 86 120 37 46 97

Figure S38.  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 = 8.58e-14 (Fisher's exact test), Q value = 8.6e-11

Table S39.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 8(2Q13) CNV 2 18 89
AMP PEAK 8(2Q13) WILD-TYPE 25 204 157

Figure S39.  Get High-res Image Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 6.21e-08 (Fisher's exact test), Q value = 5.2e-05

Table S40.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 8(2Q13) CNV 56 7 23
AMP PEAK 8(2Q13) WILD-TYPE 113 108 65

Figure S40.  Get High-res Image Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 6.95e-11 (Fisher's exact test), Q value = 6.5e-08

Table S41.  Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 8(2Q13) CNV 31 9 44 2
AMP PEAK 8(2Q13) WILD-TYPE 68 129 66 23

Figure S41.  Get High-res Image Gene #8: 'Amp Peak 8(2q13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 2.48e-23 (Chi-square test), Q value = 2.7e-20

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 9(3P25.1) CNV 5 0 52 2 4 8
AMP PEAK 9(3P25.1) WILD-TYPE 289 9 102 11 18 4

Figure S42.  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 = 1.66e-06 (Fisher's exact test), Q value = 0.0013

Table S43.  Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 9(3P25.1) CNV 36 14 7
AMP PEAK 9(3P25.1) WILD-TYPE 110 75 148

Figure S43.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 4.65e-05 (Chi-square test), Q value = 0.03

Table S44.  Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 9(3P25.1) CNV 38 10 7 4 10
AMP PEAK 9(3P25.1) WILD-TYPE 111 119 42 49 105

Figure S44.  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 = 4.03e-05 (Fisher's exact test), Q value = 0.027

Table S45.  Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 9(3P25.1) CNV 3 15 51
AMP PEAK 9(3P25.1) WILD-TYPE 24 207 195

Figure S45.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 9.02e-05 (Fisher's exact test), Q value = 0.057

Table S46.  Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 9(3P25.1) CNV 16 8 29 4
AMP PEAK 9(3P25.1) WILD-TYPE 83 130 81 21

Figure S46.  Get High-res Image Gene #9: 'Amp Peak 9(3p25.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 2.16e-18 (Chi-square test), Q value = 2.3e-15

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 10(3P14.1) CNV 5 0 37 2 4 8
AMP PEAK 10(3P14.1) WILD-TYPE 289 9 117 11 18 4

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

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

P value = 5.91e-05 (Fisher's exact test), Q value = 0.038

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 14 17 12 10
AMP PEAK 11(3Q26.2) CNV 1 11 1 0
AMP PEAK 11(3Q26.2) WILD-TYPE 13 6 11 10

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 = 5.43e-05 (Fisher's exact test), Q value = 0.035

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 11(3Q26.2) CNV 2 1 10
AMP PEAK 11(3Q26.2) WILD-TYPE 17 18 5

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 = 6.29e-61 (Chi-square test), Q value = 7.3e-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 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 11(3Q26.2) CNV 13 1 126 4 7 9
AMP PEAK 11(3Q26.2) WILD-TYPE 281 8 28 9 15 3

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 = 3.15e-17 (Fisher's exact test), Q value = 3.3e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 11(3Q26.2) CNV 88 26 21
AMP PEAK 11(3Q26.2) WILD-TYPE 58 63 134

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 = 0.2

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 = 0.000139 (Fisher's exact test), Q value = 0.085

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 11(3Q26.2) CNV 33 8 14
AMP PEAK 11(3Q26.2) WILD-TYPE 16 28 19

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 = 0.000367 (Fisher's exact test), Q value = 0.21

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
AMP PEAK 11(3Q26.2) CNV 32 12 11
AMP PEAK 11(3Q26.2) WILD-TYPE 14 24 25

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 = 2.49e-22 (Chi-square test), Q value = 2.7e-19

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 11(3Q26.2) CNV 95 19 15 7 20
AMP PEAK 11(3Q26.2) WILD-TYPE 54 110 34 46 95

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 = 5.69e-16 (Fisher's exact test), Q value = 5.9e-13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 11(3Q26.2) CNV 7 30 119
AMP PEAK 11(3Q26.2) WILD-TYPE 20 192 127

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

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

P value = 3.02e-07 (Fisher's exact test), Q value = 0.00024

Table S57.  Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 11(3Q26.2) CNV 83 21 28
AMP PEAK 11(3Q26.2) WILD-TYPE 86 94 60

Figure S57.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 5.65e-10 (Fisher's exact test), Q value = 5.1e-07

Table S58.  Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 11(3Q26.2) CNV 39 24 63 6
AMP PEAK 11(3Q26.2) WILD-TYPE 60 114 47 19

Figure S58.  Get High-res Image Gene #11: 'Amp Peak 11(3q26.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 0.000342 (Fisher's exact test), Q value = 0.2

Table S59.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 12(3Q26.2) CNV 1 10 1 0
AMP PEAK 12(3Q26.2) WILD-TYPE 13 7 11 10

Figure S59.  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 = 0.000377 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 12(3Q26.2) CNV 2 1 9
AMP PEAK 12(3Q26.2) WILD-TYPE 17 18 6

Figure S60.  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 = 9.76e-61 (Chi-square test), Q value = 1.1e-57

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 12(3Q26.2) CNV 9 1 120 4 5 10
AMP PEAK 12(3Q26.2) WILD-TYPE 285 8 34 9 17 2

Figure S61.  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 = 1.71e-18 (Fisher's exact test), Q value = 1.8e-15

Table S62.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 12(3Q26.2) CNV 86 22 18
AMP PEAK 12(3Q26.2) WILD-TYPE 60 67 137

Figure S62.  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 = 3.3e-05 (Fisher's exact test), Q value = 0.022

Table S63.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 12(3Q26.2) CNV 32 7 10
AMP PEAK 12(3Q26.2) WILD-TYPE 17 29 23

Figure S63.  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 = 0.000123 (Fisher's exact test), Q value = 0.076

Table S64.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
AMP PEAK 12(3Q26.2) CNV 30 11 8
AMP PEAK 12(3Q26.2) WILD-TYPE 16 25 28

Figure S64.  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 = 1.13e-21 (Chi-square test), Q value = 1.2e-18

Table S65.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 12(3Q26.2) CNV 90 17 14 6 18
AMP PEAK 12(3Q26.2) WILD-TYPE 59 112 35 47 97

Figure S65.  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 = 6.51e-18 (Fisher's exact test), Q value = 6.8e-15

Table S66.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 12(3Q26.2) CNV 8 23 114
AMP PEAK 12(3Q26.2) WILD-TYPE 19 199 132

Figure S66.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.02e-08 (Fisher's exact test), Q value = 4.2e-05

Table S67.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 12(3Q26.2) CNV 79 17 26
AMP PEAK 12(3Q26.2) WILD-TYPE 90 98 62

Figure S67.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 6.52e-12 (Fisher's exact test), Q value = 6.3e-09

Table S68.  Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 12(3Q26.2) CNV 38 19 61 4
AMP PEAK 12(3Q26.2) WILD-TYPE 61 119 49 21

Figure S68.  Get High-res Image Gene #12: 'Amp Peak 12(3q26.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 4.34e-19 (Chi-square test), Q value = 4.6e-16

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 13(4P16.3) CNV 1 0 43 1 1 0
AMP PEAK 13(4P16.3) WILD-TYPE 293 9 111 12 21 12

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

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

P value = 1.43e-08 (Chi-square test), Q value = 1.2e-05

Table S70.  Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 13(4P16.3) CNV 32 4 3 1 4
AMP PEAK 13(4P16.3) WILD-TYPE 117 125 46 52 111

Figure S70.  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 = 2.69e-06 (Fisher's exact test), Q value = 0.002

Table S71.  Gene #13: 'Amp Peak 13(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 13(4P16.3) CNV 3 5 36
AMP PEAK 13(4P16.3) WILD-TYPE 24 217 210

Figure S71.  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 = 2.08e-31 (Chi-square test), Q value = 2.3e-28

Table S72.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 14(5P15.33) CNV 4 1 70 0 4 0
AMP PEAK 14(5P15.33) WILD-TYPE 290 8 84 13 18 12

Figure S72.  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 = 4.65e-13 (Fisher's exact test), Q value = 4.6e-10

Table S73.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 14(5P15.33) CNV 49 13 4
AMP PEAK 14(5P15.33) WILD-TYPE 97 76 151

Figure S73.  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 = 8.26e-06 (Fisher's exact test), Q value = 0.006

Table S74.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 14(5P15.33) CNV 22 2 3
AMP PEAK 14(5P15.33) WILD-TYPE 27 34 30

Figure S74.  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 = 1.33e-05 (Fisher's exact test), Q value = 0.0095

Table S75.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
AMP PEAK 14(5P15.33) CNV 21 4 2
AMP PEAK 14(5P15.33) WILD-TYPE 25 32 34

Figure S75.  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 = 6.71e-10 (Chi-square test), Q value = 6e-07

Table S76.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 14(5P15.33) CNV 48 5 8 7 10
AMP PEAK 14(5P15.33) WILD-TYPE 101 124 41 46 105

Figure S76.  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 = 7.07e-11 (Fisher's exact test), Q value = 6.6e-08

Table S77.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 14(5P15.33) CNV 3 10 65
AMP PEAK 14(5P15.33) WILD-TYPE 24 212 181

Figure S77.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.03e-07 (Fisher's exact test), Q value = 0.00032

Table S78.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 14(5P15.33) CNV 47 5 13
AMP PEAK 14(5P15.33) WILD-TYPE 122 110 75

Figure S78.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 1.23e-08 (Fisher's exact test), Q value = 1.1e-05

Table S79.  Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 14(5P15.33) CNV 20 5 35 5
AMP PEAK 14(5P15.33) WILD-TYPE 79 133 75 20

Figure S79.  Get High-res Image Gene #14: 'Amp Peak 14(5p15.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 2.47e-17 (Chi-square test), Q value = 2.6e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 15(5Q35.3) CNV 2 2 42 0 2 0
AMP PEAK 15(5Q35.3) WILD-TYPE 292 7 112 13 20 12

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

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

P value = 1.12e-05 (Chi-square test), Q value = 0.0081

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 15(5Q35.3) CNV 29 4 5 5 4
AMP PEAK 15(5Q35.3) WILD-TYPE 120 125 44 48 111

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 = 9.63e-05 (Fisher's exact test), Q value = 0.061

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 15(5Q35.3) CNV 0 10 37
AMP PEAK 15(5Q35.3) WILD-TYPE 27 212 209

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

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

P value = 0.000145 (Fisher's exact test), Q value = 0.088

Table S83.  Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 15(5Q35.3) CNV 13 5 21 0
AMP PEAK 15(5Q35.3) WILD-TYPE 86 133 89 25

Figure S83.  Get High-res Image Gene #15: 'Amp Peak 15(5q35.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 0.000377 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 16(6P24.2) CNV 1 2 9
AMP PEAK 16(6P24.2) WILD-TYPE 18 17 6

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

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

P value = 4.01e-39 (Chi-square test), Q value = 4.5e-36

Table S85.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 16(6P24.2) CNV 8 1 83 1 1 9
AMP PEAK 16(6P24.2) WILD-TYPE 286 8 71 12 21 3

Figure S85.  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 = 6.89e-10 (Fisher's exact test), Q value = 6.2e-07

Table S86.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 16(6P24.2) CNV 57 17 13
AMP PEAK 16(6P24.2) WILD-TYPE 89 72 142

Figure S86.  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 = 0.11

Table S87.  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 S87.  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 = 1.07e-05 (Fisher's exact test), Q value = 0.0077

Table S88.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 16(6P24.2) CNV 27 3 8
AMP PEAK 16(6P24.2) WILD-TYPE 22 33 25

Figure S88.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 3.42e-12 (Chi-square test), Q value = 3.3e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 16(6P24.2) CNV 59 12 14 5 10
AMP PEAK 16(6P24.2) WILD-TYPE 90 117 35 48 105

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 = 2.51e-11 (Fisher's exact test), Q value = 2.4e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 16(6P24.2) CNV 5 16 79
AMP PEAK 16(6P24.2) WILD-TYPE 22 206 167

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

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

P value = 7.83e-05 (Fisher's exact test), Q value = 0.05

Table S91.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 16(6P24.2) CNV 54 12 20
AMP PEAK 16(6P24.2) WILD-TYPE 115 103 68

Figure S91.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 2.58e-07 (Fisher's exact test), Q value = 0.00021

Table S92.  Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 16(6P24.2) CNV 28 13 42 3
AMP PEAK 16(6P24.2) WILD-TYPE 71 125 68 22

Figure S92.  Get High-res Image Gene #16: 'Amp Peak 16(6p24.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 7.75e-26 (Chi-square test), Q value = 8.5e-23

Table S93.  Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 17(6Q25.1) CNV 7 1 60 1 2 8
AMP PEAK 17(6Q25.1) WILD-TYPE 287 8 94 12 20 4

Figure S93.  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 = 1.01e-05 (Fisher's exact test), Q value = 0.0073

Table S94.  Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 17(6Q25.1) CNV 44 11 15
AMP PEAK 17(6Q25.1) WILD-TYPE 102 78 140

Figure S94.  Get High-res Image Gene #17: 'Amp Peak 17(6q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 5.18e-05 (Chi-square test), Q value = 0.034

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 17(6Q25.1) CNV 40 12 11 7 9
AMP PEAK 17(6Q25.1) WILD-TYPE 109 117 38 46 106

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 = 3.14e-06 (Fisher's exact test), Q value = 0.0024

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 17(6Q25.1) CNV 5 16 58
AMP PEAK 17(6Q25.1) WILD-TYPE 22 206 188

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 = 5.72e-19 (Chi-square test), Q value = 6.1e-16

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 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 18(7Q22.1) CNV 15 8 43 6 9 4
AMP PEAK 18(7Q22.1) WILD-TYPE 279 1 111 7 13 8

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 = 8.07e-22 (Chi-square test), Q value = 8.7e-19

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 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 19(8P11.21) CNV 40 4 75 3 15 12
AMP PEAK 19(8P11.21) WILD-TYPE 254 5 79 10 7 0

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 'MIRSEQ_CNMF'

P value = 4.63e-05 (Chi-square test), Q value = 0.03

Table S99.  Gene #19: 'Amp Peak 19(8p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 19(8P11.21) CNV 64 29 14 19 20
AMP PEAK 19(8P11.21) WILD-TYPE 85 100 35 34 95

Figure S99.  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 = 0.000206 (Fisher's exact test), Q value = 0.12

Table S100.  Gene #19: 'Amp Peak 19(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 19(8P11.21) CNV 10 45 91
AMP PEAK 19(8P11.21) WILD-TYPE 17 177 155

Figure S100.  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-34 (Chi-square test), Q value = 1.7e-31

Table S101.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 20(8Q24.21) CNV 46 5 110 3 16 12
AMP PEAK 20(8Q24.21) WILD-TYPE 248 4 44 10 6 0

Figure S101.  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 = 1.33e-06 (Fisher's exact test), Q value = 0.001

Table S102.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 20(8Q24.21) CNV 85 34 45
AMP PEAK 20(8Q24.21) WILD-TYPE 61 55 110

Figure S102.  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 = 0.055

Table S103.  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 S103.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

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

P value = 8.62e-11 (Chi-square test), Q value = 8e-08

Table S104.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 20(8Q24.21) CNV 91 35 18 20 25
AMP PEAK 20(8Q24.21) WILD-TYPE 58 94 31 33 90

Figure S104.  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 = 6.36e-10 (Fisher's exact test), Q value = 5.7e-07

Table S105.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 20(8Q24.21) CNV 11 51 127
AMP PEAK 20(8Q24.21) WILD-TYPE 16 171 119

Figure S105.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 9.48e-05 (Fisher's exact test), Q value = 0.06

Table S106.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 20(8Q24.21) CNV 90 32 35
AMP PEAK 20(8Q24.21) WILD-TYPE 79 83 53

Figure S106.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 5.95e-05 (Fisher's exact test), Q value = 0.039

Table S107.  Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 20(8Q24.21) CNV 46 40 63 8
AMP PEAK 20(8Q24.21) WILD-TYPE 53 98 47 17

Figure S107.  Get High-res Image Gene #20: 'Amp Peak 20(8q24.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 8.33e-34 (Chi-square test), Q value = 9.3e-31

Table S108.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 21(8Q24.21) CNV 51 5 113 3 16 12
AMP PEAK 21(8Q24.21) WILD-TYPE 243 4 41 10 6 0

Figure S108.  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 = 1.53e-05 (Fisher's exact test), Q value = 0.011

Table S109.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 21(8Q24.21) CNV 85 36 49
AMP PEAK 21(8Q24.21) WILD-TYPE 61 53 106

Figure S109.  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 = 0.00057

Table S110.  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 S110.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

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

P value = 3.63e-11 (Chi-square test), Q value = 3.4e-08

Table S111.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 21(8Q24.21) CNV 94 37 19 20 26
AMP PEAK 21(8Q24.21) WILD-TYPE 55 92 30 33 89

Figure S111.  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 = 1.1e-08 (Fisher's exact test), Q value = 9.5e-06

Table S112.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 21(8Q24.21) CNV 12 56 128
AMP PEAK 21(8Q24.21) WILD-TYPE 15 166 118

Figure S112.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 9.21e-05 (Fisher's exact test), Q value = 0.058

Table S113.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 21(8Q24.21) CNV 94 35 35
AMP PEAK 21(8Q24.21) WILD-TYPE 75 80 53

Figure S113.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 0.000132 (Fisher's exact test), Q value = 0.081

Table S114.  Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 21(8Q24.21) CNV 45 44 66 9
AMP PEAK 21(8Q24.21) WILD-TYPE 54 94 44 16

Figure S114.  Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 3.85e-21 (Chi-square test), Q value = 4.2e-18

Table S115.  Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 22(9P24.2) CNV 5 1 52 0 1 0
AMP PEAK 22(9P24.2) WILD-TYPE 289 8 102 13 21 12

Figure S115.  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 = 2.1e-06 (Fisher's exact test), Q value = 0.0016

Table S116.  Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 22(9P24.2) CNV 34 7 7
AMP PEAK 22(9P24.2) WILD-TYPE 112 82 148

Figure S116.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 5.94e-12 (Chi-square test), Q value = 5.7e-09

Table S117.  Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 22(9P24.2) CNV 42 2 2 5 7
AMP PEAK 22(9P24.2) WILD-TYPE 107 127 47 48 108

Figure S117.  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 = 1.38e-07 (Fisher's exact test), Q value = 0.00011

Table S118.  Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 22(9P24.2) CNV 2 8 48
AMP PEAK 22(9P24.2) WILD-TYPE 25 214 198

Figure S118.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000221 (Fisher's exact test), Q value = 0.13

Table S119.  Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 22(9P24.2) CNV 14 7 25 1
AMP PEAK 22(9P24.2) WILD-TYPE 85 131 85 24

Figure S119.  Get High-res Image Gene #22: 'Amp Peak 22(9p24.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 9.4e-11 (Chi-square test), Q value = 8.7e-08

Table S120.  Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 23(9Q34.3) CNV 3 0 29 1 0 0
AMP PEAK 23(9Q34.3) WILD-TYPE 291 9 125 12 22 12

Figure S120.  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 = 7.97e-05 (Fisher's exact test), Q value = 0.051

Table S121.  Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 23(9Q34.3) CNV 17 6 1
AMP PEAK 23(9Q34.3) WILD-TYPE 129 83 154

Figure S121.  Get High-res Image Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 0.000103 (Fisher's exact test), Q value = 0.064

Table S122.  Gene #23: 'Amp Peak 23(9q34.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 23(9Q34.3) CNV 1 3 25
AMP PEAK 23(9Q34.3) WILD-TYPE 26 219 221

Figure S122.  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 = 2.56e-10 (Chi-square test), Q value = 2.3e-07

Table S123.  Gene #24: 'Amp Peak 24(10q22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 24(10Q22.2) CNV 46 4 58 10 8 7
AMP PEAK 24(10Q22.2) WILD-TYPE 248 5 96 3 14 5

Figure S123.  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 = 1.79e-14 (Chi-square test), Q value = 1.8e-11

Table S124.  Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 25(11P11.2) CNV 2 1 38 1 4 0
AMP PEAK 25(11P11.2) WILD-TYPE 292 8 116 12 18 12

Figure S124.  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 = 0.000158 (Fisher's exact test), Q value = 0.096

Table S125.  Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 25(11P11.2) CNV 22 12 4
AMP PEAK 25(11P11.2) WILD-TYPE 124 77 151

Figure S125.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 2.27e-05 (Chi-square test), Q value = 0.016

Table S126.  Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 25(11P11.2) CNV 28 6 5 3 3
AMP PEAK 25(11P11.2) WILD-TYPE 121 123 44 50 112

Figure S126.  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 = 3.25e-05 (Fisher's exact test), Q value = 0.022

Table S127.  Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 25(11P11.2) CNV 2 7 36
AMP PEAK 25(11P11.2) WILD-TYPE 25 215 210

Figure S127.  Get High-res Image Gene #25: 'Amp Peak 25(11p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 7.02e-21 (Chi-square test), Q value = 7.6e-18

Table S128.  Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 26(11Q13.2) CNV 7 1 57 1 4 0
AMP PEAK 26(11Q13.2) WILD-TYPE 287 8 97 12 18 12

Figure S128.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000175 (Chi-square test), Q value = 0.11

Table S129.  Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 26(11Q13.2) CNV 36 13 5 4 8
AMP PEAK 26(11Q13.2) WILD-TYPE 113 116 44 49 107

Figure S129.  Get High-res Image Gene #26: 'Amp Peak 26(11q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 27(11q14.1)' versus 'CN_CNMF'

P value = 6.93e-15 (Chi-square test), Q value = 7e-12

Table S130.  Gene #27: 'Amp Peak 27(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 27(11Q14.1) CNV 5 1 43 1 3 0
AMP PEAK 27(11Q14.1) WILD-TYPE 289 8 111 12 19 12

Figure S130.  Get High-res Image Gene #27: 'Amp Peak 27(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 28(12p12.1)' versus 'CN_CNMF'

P value = 5.27e-14 (Chi-square test), Q value = 5.3e-11

Table S131.  Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 28(12P12.1) CNV 14 3 50 5 8 2
AMP PEAK 28(12P12.1) WILD-TYPE 280 6 104 8 14 10

Figure S131.  Get High-res Image Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 28(12p12.1)' versus 'METHLYATION_CNMF'

P value = 3.36e-08 (Fisher's exact test), Q value = 2.8e-05

Table S132.  Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 28(12P12.1) CNV 45 13 9
AMP PEAK 28(12P12.1) WILD-TYPE 101 76 146

Figure S132.  Get High-res Image Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 28(12p12.1)' versus 'MRNASEQ_CNMF'

P value = 6.76e-05 (Fisher's exact test), Q value = 0.044

Table S133.  Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 28(12P12.1) CNV 18 7 0
AMP PEAK 28(12P12.1) WILD-TYPE 31 29 33

Figure S133.  Get High-res Image Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 28(12p12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.62e-05 (Fisher's exact test), Q value = 0.024

Table S134.  Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
AMP PEAK 28(12P12.1) CNV 17 8 0
AMP PEAK 28(12P12.1) WILD-TYPE 29 28 36

Figure S134.  Get High-res Image Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 28(12p12.1)' versus 'MIRSEQ_CNMF'

P value = 3.94e-06 (Chi-square test), Q value = 0.0029

Table S135.  Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 28(12P12.1) CNV 42 10 13 6 11
AMP PEAK 28(12P12.1) WILD-TYPE 107 119 36 47 104

Figure S135.  Get High-res Image Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 28(12p12.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.21e-07 (Fisher's exact test), Q value = 1e-04

Table S136.  Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 28(12P12.1) CNV 0 19 63
AMP PEAK 28(12P12.1) WILD-TYPE 27 203 183

Figure S136.  Get High-res Image Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(12p12.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000172 (Fisher's exact test), Q value = 0.1

Table S137.  Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 28(12P12.1) CNV 43 8 14
AMP PEAK 28(12P12.1) WILD-TYPE 126 107 74

Figure S137.  Get High-res Image Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 28(12p12.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.69e-06 (Fisher's exact test), Q value = 0.007

Table S138.  Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 28(12P12.1) CNV 19 10 34 2
AMP PEAK 28(12P12.1) WILD-TYPE 80 128 76 23

Figure S138.  Get High-res Image Gene #28: 'Amp Peak 28(12p12.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 29(12q13.11)' versus 'CN_CNMF'

P value = 2.56e-17 (Chi-square test), Q value = 2.7e-14

Table S139.  Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 29(12Q13.11) CNV 11 2 53 5 9 1
AMP PEAK 29(12Q13.11) WILD-TYPE 283 7 101 8 13 11

Figure S139.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(12q13.11)' versus 'METHLYATION_CNMF'

P value = 5.06e-08 (Fisher's exact test), Q value = 4.2e-05

Table S140.  Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 29(12Q13.11) CNV 43 15 8
AMP PEAK 29(12Q13.11) WILD-TYPE 103 74 147

Figure S140.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 29(12q13.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000357 (Fisher's exact test), Q value = 0.21

Table S141.  Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
AMP PEAK 29(12Q13.11) CNV 17 7 1
AMP PEAK 29(12Q13.11) WILD-TYPE 29 29 35

Figure S141.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 29(12q13.11)' versus 'MIRSEQ_CNMF'

P value = 5.3e-07 (Chi-square test), Q value = 0.00042

Table S142.  Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 29(12Q13.11) CNV 46 10 8 5 12
AMP PEAK 29(12Q13.11) WILD-TYPE 103 119 41 48 103

Figure S142.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 29(12q13.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.36e-07 (Fisher's exact test), Q value = 0.00042

Table S143.  Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 29(12Q13.11) CNV 2 17 62
AMP PEAK 29(12Q13.11) WILD-TYPE 25 205 184

Figure S143.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 29(12q13.11)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.91e-05 (Fisher's exact test), Q value = 0.02

Table S144.  Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 29(12Q13.11) CNV 42 6 14
AMP PEAK 29(12Q13.11) WILD-TYPE 127 109 74

Figure S144.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 29(12q13.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.55e-05 (Fisher's exact test), Q value = 0.011

Table S145.  Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 29(12Q13.11) CNV 16 9 33 4
AMP PEAK 29(12Q13.11) WILD-TYPE 83 129 77 21

Figure S145.  Get High-res Image Gene #29: 'Amp Peak 29(12q13.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 30(12q13.2)' versus 'CN_CNMF'

P value = 1.14e-17 (Chi-square test), Q value = 1.2e-14

Table S146.  Gene #30: 'Amp Peak 30(12q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 30(12Q13.2) CNV 14 2 58 5 9 1
AMP PEAK 30(12Q13.2) WILD-TYPE 280 7 96 8 13 11

Figure S146.  Get High-res Image Gene #30: 'Amp Peak 30(12q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 30(12q13.2)' versus 'METHLYATION_CNMF'

P value = 9.93e-07 (Fisher's exact test), Q value = 0.00077

Table S147.  Gene #30: 'Amp Peak 30(12q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 30(12Q13.2) CNV 46 13 13
AMP PEAK 30(12Q13.2) WILD-TYPE 100 76 142

Figure S147.  Get High-res Image Gene #30: 'Amp Peak 30(12q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 30(12q13.2)' versus 'MIRSEQ_CNMF'

P value = 6.82e-06 (Chi-square test), Q value = 0.005

Table S148.  Gene #30: 'Amp Peak 30(12q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 30(12Q13.2) CNV 46 12 10 5 14
AMP PEAK 30(12Q13.2) WILD-TYPE 103 117 39 48 101

Figure S148.  Get High-res Image Gene #30: 'Amp Peak 30(12q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 30(12q13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.23e-06 (Fisher's exact test), Q value = 0.0031

Table S149.  Gene #30: 'Amp Peak 30(12q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 30(12Q13.2) CNV 2 21 64
AMP PEAK 30(12Q13.2) WILD-TYPE 25 201 182

Figure S149.  Get High-res Image Gene #30: 'Amp Peak 30(12q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 30(12q13.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.23e-05 (Fisher's exact test), Q value = 0.034

Table S150.  Gene #30: 'Amp Peak 30(12q13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 30(12Q13.2) CNV 48 10 12
AMP PEAK 30(12Q13.2) WILD-TYPE 121 105 76

Figure S150.  Get High-res Image Gene #30: 'Amp Peak 30(12q13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 30(12q13.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.5e-05 (Fisher's exact test), Q value = 0.011

Table S151.  Gene #30: 'Amp Peak 30(12q13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 30(12Q13.2) CNV 18 13 37 2
AMP PEAK 30(12Q13.2) WILD-TYPE 81 125 73 23

Figure S151.  Get High-res Image Gene #30: 'Amp Peak 30(12q13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 31(13q34)' versus 'CN_CNMF'

P value = 6.11e-18 (Chi-square test), Q value = 6.4e-15

Table S152.  Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 31(13Q34) CNV 4 0 45 1 0 1
AMP PEAK 31(13Q34) WILD-TYPE 290 9 109 12 22 11

Figure S152.  Get High-res Image Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 31(13q34)' versus 'METHLYATION_CNMF'

P value = 4.02e-07 (Fisher's exact test), Q value = 0.00032

Table S153.  Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 31(13Q34) CNV 32 10 4
AMP PEAK 31(13Q34) WILD-TYPE 114 79 151

Figure S153.  Get High-res Image Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 31(13q34)' versus 'MRNASEQ_CNMF'

P value = 0.000349 (Fisher's exact test), Q value = 0.2

Table S154.  Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 31(13Q34) CNV 13 0 2
AMP PEAK 31(13Q34) WILD-TYPE 36 36 31

Figure S154.  Get High-res Image Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 31(13q34)' versus 'MIRSEQ_CNMF'

P value = 2.18e-07 (Chi-square test), Q value = 0.00018

Table S155.  Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 31(13Q34) CNV 32 3 8 2 6
AMP PEAK 31(13Q34) WILD-TYPE 117 126 41 51 109

Figure S155.  Get High-res Image Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 31(13q34)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.89e-08 (Fisher's exact test), Q value = 7.4e-05

Table S156.  Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 31(13Q34) CNV 1 6 44
AMP PEAK 31(13Q34) WILD-TYPE 26 216 202

Figure S156.  Get High-res Image Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 31(13q34)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.062

Table S157.  Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 31(13Q34) CNV 31 3 11
AMP PEAK 31(13Q34) WILD-TYPE 138 112 77

Figure S157.  Get High-res Image Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 31(13q34)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.84e-05 (Fisher's exact test), Q value = 0.013

Table S158.  Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 31(13Q34) CNV 15 4 24 2
AMP PEAK 31(13Q34) WILD-TYPE 84 134 86 23

Figure S158.  Get High-res Image Gene #31: 'Amp Peak 31(13q34)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 32(14q24.3)' versus 'CN_CNMF'

P value = 3.66e-16 (Chi-square test), Q value = 3.8e-13

Table S159.  Gene #32: 'Amp Peak 32(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 32(14Q24.3) CNV 5 1 46 0 4 2
AMP PEAK 32(14Q24.3) WILD-TYPE 289 8 108 13 18 10

Figure S159.  Get High-res Image Gene #32: 'Amp Peak 32(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 32(14q24.3)' versus 'METHLYATION_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.012

Table S160.  Gene #32: 'Amp Peak 32(14q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 32(14Q24.3) CNV 32 9 7
AMP PEAK 32(14Q24.3) WILD-TYPE 114 80 148

Figure S160.  Get High-res Image Gene #32: 'Amp Peak 32(14q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 32(14q24.3)' versus 'MRNASEQ_CNMF'

P value = 0.000339 (Fisher's exact test), Q value = 0.2

Table S161.  Gene #32: 'Amp Peak 32(14q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 32(14Q24.3) CNV 17 2 2
AMP PEAK 32(14Q24.3) WILD-TYPE 32 34 31

Figure S161.  Get High-res Image Gene #32: 'Amp Peak 32(14q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 32(14q24.3)' versus 'MIRSEQ_CNMF'

P value = 2.47e-06 (Chi-square test), Q value = 0.0019

Table S162.  Gene #32: 'Amp Peak 32(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 32(14Q24.3) CNV 33 8 8 4 3
AMP PEAK 32(14Q24.3) WILD-TYPE 116 121 41 49 112

Figure S162.  Get High-res Image Gene #32: 'Amp Peak 32(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 32(14q24.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.73e-06 (Fisher's exact test), Q value = 0.0021

Table S163.  Gene #32: 'Amp Peak 32(14q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 32(14Q24.3) CNV 2 9 45
AMP PEAK 32(14Q24.3) WILD-TYPE 25 213 201

Figure S163.  Get High-res Image Gene #32: 'Amp Peak 32(14q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 33(15q26.3)' versus 'CN_CNMF'

P value = 1.8e-08 (Chi-square test), Q value = 1.5e-05

Table S164.  Gene #33: 'Amp Peak 33(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 33(15Q26.3) CNV 4 1 27 0 3 0
AMP PEAK 33(15Q26.3) WILD-TYPE 290 8 127 13 19 12

Figure S164.  Get High-res Image Gene #33: 'Amp Peak 33(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 34(16p11.2)' versus 'CN_CNMF'

P value = 3.87e-20 (Chi-square test), Q value = 4.2e-17

Table S165.  Gene #34: 'Amp Peak 34(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 34(16P11.2) CNV 2 2 49 0 3 1
AMP PEAK 34(16P11.2) WILD-TYPE 292 7 105 13 19 11

Figure S165.  Get High-res Image Gene #34: 'Amp Peak 34(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 34(16p11.2)' versus 'METHLYATION_CNMF'

P value = 8.01e-06 (Fisher's exact test), Q value = 0.0059

Table S166.  Gene #34: 'Amp Peak 34(16p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 34(16P11.2) CNV 32 11 6
AMP PEAK 34(16P11.2) WILD-TYPE 114 78 149

Figure S166.  Get High-res Image Gene #34: 'Amp Peak 34(16p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 34(16p11.2)' versus 'MIRSEQ_CNMF'

P value = 1.09e-09 (Chi-square test), Q value = 9.7e-07

Table S167.  Gene #34: 'Amp Peak 34(16p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 34(16P11.2) CNV 37 4 7 2 4
AMP PEAK 34(16P11.2) WILD-TYPE 112 125 42 51 111

Figure S167.  Get High-res Image Gene #34: 'Amp Peak 34(16p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 34(16p11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.54e-05 (Fisher's exact test), Q value = 0.011

Table S168.  Gene #34: 'Amp Peak 34(16p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 34(16P11.2) CNV 1 10 43
AMP PEAK 34(16P11.2) WILD-TYPE 26 212 203

Figure S168.  Get High-res Image Gene #34: 'Amp Peak 34(16p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 34(16p11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.08

Table S169.  Gene #34: 'Amp Peak 34(16p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 34(16P11.2) CNV 15 6 24 1
AMP PEAK 34(16P11.2) WILD-TYPE 84 132 86 24

Figure S169.  Get High-res Image Gene #34: 'Amp Peak 34(16p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 35(17q11.2)' versus 'CN_CNMF'

P value = 4.48e-25 (Chi-square test), Q value = 4.9e-22

Table S170.  Gene #35: 'Amp Peak 35(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 35(17Q11.2) CNV 3 0 58 2 1 1
AMP PEAK 35(17Q11.2) WILD-TYPE 291 9 96 11 21 11

Figure S170.  Get High-res Image Gene #35: 'Amp Peak 35(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 35(17q11.2)' versus 'METHLYATION_CNMF'

P value = 1.29e-11 (Fisher's exact test), Q value = 1.2e-08

Table S171.  Gene #35: 'Amp Peak 35(17q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 35(17Q11.2) CNV 44 9 4
AMP PEAK 35(17Q11.2) WILD-TYPE 102 80 151

Figure S171.  Get High-res Image Gene #35: 'Amp Peak 35(17q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 35(17q11.2)' versus 'MIRSEQ_CNMF'

P value = 5.66e-12 (Chi-square test), Q value = 5.5e-09

Table S172.  Gene #35: 'Amp Peak 35(17q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 35(17Q11.2) CNV 44 3 5 4 6
AMP PEAK 35(17Q11.2) WILD-TYPE 105 126 44 49 109

Figure S172.  Get High-res Image Gene #35: 'Amp Peak 35(17q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 35(17q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.59e-12 (Fisher's exact test), Q value = 3.5e-09

Table S173.  Gene #35: 'Amp Peak 35(17q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 35(17Q11.2) CNV 3 4 55
AMP PEAK 35(17Q11.2) WILD-TYPE 24 218 191

Figure S173.  Get High-res Image Gene #35: 'Amp Peak 35(17q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 35(17q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.25e-05 (Fisher's exact test), Q value = 0.009

Table S174.  Gene #35: 'Amp Peak 35(17q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 35(17Q11.2) CNV 38 4 12
AMP PEAK 35(17Q11.2) WILD-TYPE 131 111 76

Figure S174.  Get High-res Image Gene #35: 'Amp Peak 35(17q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 35(17q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.35e-08 (Fisher's exact test), Q value = 2.8e-05

Table S175.  Gene #35: 'Amp Peak 35(17q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 35(17Q11.2) CNV 16 4 32 2
AMP PEAK 35(17Q11.2) WILD-TYPE 83 134 78 23

Figure S175.  Get High-res Image Gene #35: 'Amp Peak 35(17q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 36(17q12)' versus 'CN_CNMF'

P value = 3.12e-23 (Chi-square test), Q value = 3.4e-20

Table S176.  Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 36(17Q12) CNV 5 0 56 4 0 1
AMP PEAK 36(17Q12) WILD-TYPE 289 9 98 9 22 11

Figure S176.  Get High-res Image Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 36(17q12)' versus 'METHLYATION_CNMF'

P value = 1.32e-13 (Fisher's exact test), Q value = 1.3e-10

Table S177.  Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 36(17Q12) CNV 44 8 2
AMP PEAK 36(17Q12) WILD-TYPE 102 81 153

Figure S177.  Get High-res Image Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 36(17q12)' versus 'MRNASEQ_CNMF'

P value = 0.000245 (Fisher's exact test), Q value = 0.14

Table S178.  Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 36(17Q12) CNV 17 3 1
AMP PEAK 36(17Q12) WILD-TYPE 32 33 32

Figure S178.  Get High-res Image Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 36(17q12)' versus 'MIRSEQ_CNMF'

P value = 4.07e-12 (Chi-square test), Q value = 4e-09

Table S179.  Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 36(17Q12) CNV 45 3 5 2 9
AMP PEAK 36(17Q12) WILD-TYPE 104 126 44 51 106

Figure S179.  Get High-res Image Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 36(17q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-12 (Fisher's exact test), Q value = 1.2e-09

Table S180.  Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 36(17Q12) CNV 1 5 58
AMP PEAK 36(17Q12) WILD-TYPE 26 217 188

Figure S180.  Get High-res Image Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 36(17q12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.009

Table S181.  Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 36(17Q12) CNV 34 3 15
AMP PEAK 36(17Q12) WILD-TYPE 135 112 73

Figure S181.  Get High-res Image Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 36(17q12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.56e-09 (Fisher's exact test), Q value = 1.4e-06

Table S182.  Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 36(17Q12) CNV 19 3 30 0
AMP PEAK 36(17Q12) WILD-TYPE 80 135 80 25

Figure S182.  Get High-res Image Gene #36: 'Amp Peak 36(17q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 37(17q25.1)' versus 'MRNA_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.11

Table S183.  Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 37(17Q25.1) CNV 0 9 1 0
AMP PEAK 37(17Q25.1) WILD-TYPE 14 8 11 10

Figure S183.  Get High-res Image Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 37(17q25.1)' versus 'MRNA_CHIERARCHICAL'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.014

Table S184.  Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 37(17Q25.1) CNV 1 0 9
AMP PEAK 37(17Q25.1) WILD-TYPE 18 19 6

Figure S184.  Get High-res Image Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 37(17q25.1)' versus 'CN_CNMF'

P value = 5.41e-39 (Chi-square test), Q value = 6.1e-36

Table S185.  Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 37(17Q25.1) CNV 4 1 83 4 1 1
AMP PEAK 37(17Q25.1) WILD-TYPE 290 8 71 9 21 11

Figure S185.  Get High-res Image Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 37(17q25.1)' versus 'METHLYATION_CNMF'

P value = 2.73e-10 (Fisher's exact test), Q value = 2.5e-07

Table S186.  Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 37(17Q25.1) CNV 50 16 8
AMP PEAK 37(17Q25.1) WILD-TYPE 96 73 147

Figure S186.  Get High-res Image Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 37(17q25.1)' versus 'MRNASEQ_CNMF'

P value = 3.24e-06 (Fisher's exact test), Q value = 0.0024

Table S187.  Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 37(17Q25.1) CNV 26 2 7
AMP PEAK 37(17Q25.1) WILD-TYPE 23 34 26

Figure S187.  Get High-res Image Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 37(17q25.1)' versus 'MIRSEQ_CNMF'

P value = 9.58e-15 (Chi-square test), Q value = 9.7e-12

Table S188.  Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 37(17Q25.1) CNV 60 8 7 6 9
AMP PEAK 37(17Q25.1) WILD-TYPE 89 121 42 47 106

Figure S188.  Get High-res Image Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 37(17q25.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.91e-12 (Fisher's exact test), Q value = 3.8e-09

Table S189.  Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 37(17Q25.1) CNV 4 12 74
AMP PEAK 37(17Q25.1) WILD-TYPE 23 210 172

Figure S189.  Get High-res Image Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 37(17q25.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000112 (Fisher's exact test), Q value = 0.069

Table S190.  Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 37(17Q25.1) CNV 44 8 18
AMP PEAK 37(17Q25.1) WILD-TYPE 125 107 70

Figure S190.  Get High-res Image Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 37(17q25.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00088

Table S191.  Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 37(17Q25.1) CNV 27 9 32 2
AMP PEAK 37(17Q25.1) WILD-TYPE 72 129 78 23

Figure S191.  Get High-res Image Gene #37: 'Amp Peak 37(17q25.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 38(18p11.31)' versus 'CN_CNMF'

P value = 2.25e-31 (Chi-square test), Q value = 2.5e-28

Table S192.  Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 38(18P11.31) CNV 5 4 71 1 1 1
AMP PEAK 38(18P11.31) WILD-TYPE 289 5 83 12 21 11

Figure S192.  Get High-res Image Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 38(18p11.31)' versus 'METHLYATION_CNMF'

P value = 9.71e-12 (Fisher's exact test), Q value = 9.3e-09

Table S193.  Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 38(18P11.31) CNV 50 16 6
AMP PEAK 38(18P11.31) WILD-TYPE 96 73 149

Figure S193.  Get High-res Image Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 38(18p11.31)' versus 'MRNASEQ_CNMF'

P value = 0.000351 (Fisher's exact test), Q value = 0.2

Table S194.  Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 38(18P11.31) CNV 23 5 4
AMP PEAK 38(18P11.31) WILD-TYPE 26 31 29

Figure S194.  Get High-res Image Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 38(18p11.31)' versus 'MIRSEQ_CNMF'

P value = 6.84e-15 (Chi-square test), Q value = 7e-12

Table S195.  Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 38(18P11.31) CNV 54 5 12 6 5
AMP PEAK 38(18P11.31) WILD-TYPE 95 124 37 47 110

Figure S195.  Get High-res Image Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 38(18p11.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.83e-13 (Fisher's exact test), Q value = 2.8e-10

Table S196.  Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 38(18P11.31) CNV 1 10 71
AMP PEAK 38(18P11.31) WILD-TYPE 26 212 175

Figure S196.  Get High-res Image Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 38(18p11.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.84e-07 (Fisher's exact test), Q value = 0.00069

Table S197.  Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 38(18P11.31) CNV 45 5 20
AMP PEAK 38(18P11.31) WILD-TYPE 124 110 68

Figure S197.  Get High-res Image Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 38(18p11.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.16e-10 (Fisher's exact test), Q value = 2e-07

Table S198.  Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 38(18P11.31) CNV 26 5 37 2
AMP PEAK 38(18P11.31) WILD-TYPE 73 133 73 23

Figure S198.  Get High-res Image Gene #38: 'Amp Peak 38(18p11.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 39(18q11.2)' versus 'CN_CNMF'

P value = 1.01e-25 (Chi-square test), Q value = 1.1e-22

Table S199.  Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 39(18Q11.2) CNV 3 3 57 0 0 1
AMP PEAK 39(18Q11.2) WILD-TYPE 291 6 97 13 22 11

Figure S199.  Get High-res Image Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 39(18q11.2)' versus 'METHLYATION_CNMF'

P value = 4.8e-10 (Fisher's exact test), Q value = 4.3e-07

Table S200.  Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 39(18Q11.2) CNV 38 15 3
AMP PEAK 39(18Q11.2) WILD-TYPE 108 74 152

Figure S200.  Get High-res Image Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 39(18q11.2)' versus 'MRNASEQ_CNMF'

P value = 4.39e-08 (Fisher's exact test), Q value = 3.7e-05

Table S201.  Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 39(18Q11.2) CNV 24 2 1
AMP PEAK 39(18Q11.2) WILD-TYPE 25 34 32

Figure S201.  Get High-res Image Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 39(18q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.84e-05 (Fisher's exact test), Q value = 0.019

Table S202.  Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
AMP PEAK 39(18Q11.2) CNV 20 6 1
AMP PEAK 39(18Q11.2) WILD-TYPE 26 30 35

Figure S202.  Get High-res Image Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 39(18q11.2)' versus 'MIRSEQ_CNMF'

P value = 4.03e-14 (Chi-square test), Q value = 4.1e-11

Table S203.  Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 39(18Q11.2) CNV 45 1 8 6 3
AMP PEAK 39(18Q11.2) WILD-TYPE 104 128 41 47 112

Figure S203.  Get High-res Image Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 39(18q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.09e-12 (Fisher's exact test), Q value = 3e-09

Table S204.  Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 39(18Q11.2) CNV 1 5 57
AMP PEAK 39(18Q11.2) WILD-TYPE 26 217 189

Figure S204.  Get High-res Image Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 39(18q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.8e-08 (Fisher's exact test), Q value = 1.5e-05

Table S205.  Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 39(18Q11.2) CNV 39 1 13
AMP PEAK 39(18Q11.2) WILD-TYPE 130 114 75

Figure S205.  Get High-res Image Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 39(18q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.34e-10 (Fisher's exact test), Q value = 1.2e-07

Table S206.  Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 39(18Q11.2) CNV 21 1 29 2
AMP PEAK 39(18Q11.2) WILD-TYPE 78 137 81 23

Figure S206.  Get High-res Image Gene #39: 'Amp Peak 39(18q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 40(19p13.2)' versus 'MRNA_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.016

Table S207.  Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
AMP PEAK 40(19P13.2) CNV 0 9 0 0
AMP PEAK 40(19P13.2) WILD-TYPE 14 8 12 10

Figure S207.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 40(19p13.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00088

Table S208.  Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 40(19P13.2) CNV 0 0 9
AMP PEAK 40(19P13.2) WILD-TYPE 19 19 6

Figure S208.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 40(19p13.2)' versus 'CN_CNMF'

P value = 1.34e-44 (Chi-square test), Q value = 1.5e-41

Table S209.  Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 40(19P13.2) CNV 0 1 83 0 0 2
AMP PEAK 40(19P13.2) WILD-TYPE 294 8 71 13 22 10

Figure S209.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 40(19p13.2)' versus 'METHLYATION_CNMF'

P value = 1.89e-09 (Fisher's exact test), Q value = 1.7e-06

Table S210.  Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 40(19P13.2) CNV 47 20 8
AMP PEAK 40(19P13.2) WILD-TYPE 99 69 147

Figure S210.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 40(19p13.2)' versus 'MRNASEQ_CNMF'

P value = 1.18e-06 (Fisher's exact test), Q value = 0.00091

Table S211.  Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 40(19P13.2) CNV 22 0 8
AMP PEAK 40(19P13.2) WILD-TYPE 27 36 25

Figure S211.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 40(19p13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-08 (Fisher's exact test), Q value = 1.7e-05

Table S212.  Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
AMP PEAK 40(19P13.2) CNV 24 0 6
AMP PEAK 40(19P13.2) WILD-TYPE 22 36 30

Figure S212.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 40(19p13.2)' versus 'MIRSEQ_CNMF'

P value = 2.79e-17 (Chi-square test), Q value = 2.9e-14

Table S213.  Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 40(19P13.2) CNV 59 8 8 4 4
AMP PEAK 40(19P13.2) WILD-TYPE 90 121 41 49 111

Figure S213.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 40(19p13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.28e-08 (Fisher's exact test), Q value = 1.1e-05

Table S214.  Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 40(19P13.2) CNV 4 14 65
AMP PEAK 40(19P13.2) WILD-TYPE 23 208 181

Figure S214.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 40(19p13.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000215 (Fisher's exact test), Q value = 0.13

Table S215.  Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 40(19P13.2) CNV 45 9 17
AMP PEAK 40(19P13.2) WILD-TYPE 124 106 71

Figure S215.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 40(19p13.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.67e-06 (Fisher's exact test), Q value = 0.0035

Table S216.  Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 40(19P13.2) CNV 20 11 37 3
AMP PEAK 40(19P13.2) WILD-TYPE 79 127 73 22

Figure S216.  Get High-res Image Gene #40: 'Amp Peak 40(19p13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 41(19p13.11)' versus 'CN_CNMF'

P value = 2.73e-45 (Chi-square test), Q value = 3.1e-42

Table S217.  Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 41(19P13.11) CNV 0 1 84 0 0 2
AMP PEAK 41(19P13.11) WILD-TYPE 294 8 70 13 22 10

Figure S217.  Get High-res Image Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 41(19p13.11)' versus 'METHLYATION_CNMF'

P value = 5.05e-11 (Fisher's exact test), Q value = 4.7e-08

Table S218.  Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 41(19P13.11) CNV 50 18 7
AMP PEAK 41(19P13.11) WILD-TYPE 96 71 148

Figure S218.  Get High-res Image Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 41(19p13.11)' versus 'MRNASEQ_CNMF'

P value = 1.17e-09 (Fisher's exact test), Q value = 1e-06

Table S219.  Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 41(19P13.11) CNV 28 0 6
AMP PEAK 41(19P13.11) WILD-TYPE 21 36 27

Figure S219.  Get High-res Image Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 41(19p13.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.08e-09 (Fisher's exact test), Q value = 2.7e-06

Table S220.  Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
AMP PEAK 41(19P13.11) CNV 28 2 4
AMP PEAK 41(19P13.11) WILD-TYPE 18 34 32

Figure S220.  Get High-res Image Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 41(19p13.11)' versus 'MIRSEQ_CNMF'

P value = 4.46e-17 (Chi-square test), Q value = 4.6e-14

Table S221.  Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 41(19P13.11) CNV 59 6 10 5 5
AMP PEAK 41(19P13.11) WILD-TYPE 90 123 39 48 110

Figure S221.  Get High-res Image Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 41(19p13.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.66e-10 (Fisher's exact test), Q value = 2.4e-07

Table S222.  Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 41(19P13.11) CNV 3 13 69
AMP PEAK 41(19P13.11) WILD-TYPE 24 209 177

Figure S222.  Get High-res Image Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 41(19p13.11)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.0086

Table S223.  Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 41(19P13.11) CNV 46 7 19
AMP PEAK 41(19P13.11) WILD-TYPE 123 108 69

Figure S223.  Get High-res Image Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 41(19p13.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.47e-07 (Fisher's exact test), Q value = 0.00028

Table S224.  Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 41(19P13.11) CNV 23 9 37 3
AMP PEAK 41(19P13.11) WILD-TYPE 76 129 73 22

Figure S224.  Get High-res Image Gene #41: 'Amp Peak 41(19p13.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 42(19q12)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000132 (Fisher's exact test), Q value = 0.081

Table S225.  Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 42(19Q12) CNV 2 0 8
AMP PEAK 42(19Q12) WILD-TYPE 17 19 7

Figure S225.  Get High-res Image Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 42(19q12)' versus 'CN_CNMF'

P value = 5.42e-52 (Chi-square test), Q value = 6.2e-49

Table S226.  Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 42(19Q12) CNV 3 2 99 1 0 2
AMP PEAK 42(19Q12) WILD-TYPE 291 7 55 12 22 10

Figure S226.  Get High-res Image Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 42(19q12)' versus 'METHLYATION_CNMF'

P value = 2e-15 (Fisher's exact test), Q value = 2e-12

Table S227.  Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 42(19Q12) CNV 64 21 8
AMP PEAK 42(19Q12) WILD-TYPE 82 68 147

Figure S227.  Get High-res Image Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 42(19q12)' versus 'MRNASEQ_CNMF'

P value = 3.96e-05 (Fisher's exact test), Q value = 0.026

Table S228.  Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 42(19Q12) CNV 29 5 9
AMP PEAK 42(19Q12) WILD-TYPE 20 31 24

Figure S228.  Get High-res Image Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 42(19q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.045

Table S229.  Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
AMP PEAK 42(19Q12) CNV 28 8 7
AMP PEAK 42(19Q12) WILD-TYPE 18 28 29

Figure S229.  Get High-res Image Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 42(19q12)' versus 'MIRSEQ_CNMF'

P value = 1.33e-18 (Chi-square test), Q value = 1.4e-15

Table S230.  Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 42(19Q12) CNV 69 8 11 5 10
AMP PEAK 42(19Q12) WILD-TYPE 80 121 38 48 105

Figure S230.  Get High-res Image Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 42(19q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.38e-15 (Fisher's exact test), Q value = 4.5e-12

Table S231.  Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 42(19Q12) CNV 4 13 86
AMP PEAK 42(19Q12) WILD-TYPE 23 209 160

Figure S231.  Get High-res Image Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 42(19q12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.57e-07 (Fisher's exact test), Q value = 0.00044

Table S232.  Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 42(19Q12) CNV 57 9 24
AMP PEAK 42(19Q12) WILD-TYPE 112 106 64

Figure S232.  Get High-res Image Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 42(19q12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.34e-10 (Fisher's exact test), Q value = 2.1e-07

Table S233.  Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 42(19Q12) CNV 28 11 48 3
AMP PEAK 42(19Q12) WILD-TYPE 71 127 62 22

Figure S233.  Get High-res Image Gene #42: 'Amp Peak 42(19q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 43(20p13)' versus 'CN_CNMF'

P value = 1.95e-38 (Chi-square test), Q value = 2.2e-35

Table S234.  Gene #43: 'Amp Peak 43(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 43(20P13) CNV 8 3 78 0 17 1
AMP PEAK 43(20P13) WILD-TYPE 286 6 76 13 5 11

Figure S234.  Get High-res Image Gene #43: 'Amp Peak 43(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 43(20p13)' versus 'METHLYATION_CNMF'

P value = 7.81e-10 (Fisher's exact test), Q value = 7e-07

Table S235.  Gene #43: 'Amp Peak 43(20p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 43(20P13) CNV 61 18 16
AMP PEAK 43(20P13) WILD-TYPE 85 71 139

Figure S235.  Get High-res Image Gene #43: 'Amp Peak 43(20p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 43(20p13)' versus 'MIRSEQ_CNMF'

P value = 4.08e-09 (Chi-square test), Q value = 3.6e-06

Table S236.  Gene #43: 'Amp Peak 43(20p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 43(20P13) CNV 59 14 11 8 14
AMP PEAK 43(20P13) WILD-TYPE 90 115 38 45 101

Figure S236.  Get High-res Image Gene #43: 'Amp Peak 43(20p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 43(20p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.64e-10 (Fisher's exact test), Q value = 4.2e-07

Table S237.  Gene #43: 'Amp Peak 43(20p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 43(20P13) CNV 3 21 82
AMP PEAK 43(20P13) WILD-TYPE 24 201 164

Figure S237.  Get High-res Image Gene #43: 'Amp Peak 43(20p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 43(20p13)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.38e-05 (Fisher's exact test), Q value = 0.029

Table S238.  Gene #43: 'Amp Peak 43(20p13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 43(20P13) CNV 58 14 17
AMP PEAK 43(20P13) WILD-TYPE 111 101 71

Figure S238.  Get High-res Image Gene #43: 'Amp Peak 43(20p13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 43(20p13)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.58e-07 (Fisher's exact test), Q value = 0.00029

Table S239.  Gene #43: 'Amp Peak 43(20p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 43(20P13) CNV 23 15 46 5
AMP PEAK 43(20P13) WILD-TYPE 76 123 64 20

Figure S239.  Get High-res Image Gene #43: 'Amp Peak 43(20p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 44(20q11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000132 (Fisher's exact test), Q value = 0.081

Table S240.  Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
AMP PEAK 44(20Q11.21) CNV 2 0 8
AMP PEAK 44(20Q11.21) WILD-TYPE 17 19 7

Figure S240.  Get High-res Image Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 44(20q11.21)' versus 'CN_CNMF'

P value = 3.25e-54 (Chi-square test), Q value = 3.7e-51

Table S241.  Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 44(20Q11.21) CNV 7 5 101 0 19 1
AMP PEAK 44(20Q11.21) WILD-TYPE 287 4 53 13 3 11

Figure S241.  Get High-res Image Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 44(20q11.21)' versus 'METHLYATION_CNMF'

P value = 5.48e-12 (Fisher's exact test), Q value = 5.3e-09

Table S242.  Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 44(20Q11.21) CNV 73 22 20
AMP PEAK 44(20Q11.21) WILD-TYPE 73 67 135

Figure S242.  Get High-res Image Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 44(20q11.21)' versus 'MRNASEQ_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.013

Table S243.  Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 44(20Q11.21) CNV 32 6 11
AMP PEAK 44(20Q11.21) WILD-TYPE 17 30 22

Figure S243.  Get High-res Image Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 44(20q11.21)' versus 'MIRSEQ_CNMF'

P value = 9.05e-14 (Chi-square test), Q value = 9e-11

Table S244.  Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 44(20Q11.21) CNV 75 18 13 8 16
AMP PEAK 44(20Q11.21) WILD-TYPE 74 111 36 45 99

Figure S244.  Get High-res Image Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 44(20q11.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.57e-12 (Fisher's exact test), Q value = 6.3e-09

Table S245.  Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 44(20Q11.21) CNV 4 27 99
AMP PEAK 44(20Q11.21) WILD-TYPE 23 195 147

Figure S245.  Get High-res Image Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 44(20q11.21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0084

Table S246.  Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 44(20Q11.21) CNV 71 20 20
AMP PEAK 44(20Q11.21) WILD-TYPE 98 95 68

Figure S246.  Get High-res Image Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 44(20q11.21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.13e-08 (Fisher's exact test), Q value = 9.7e-06

Table S247.  Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 44(20Q11.21) CNV 24 23 58 6
AMP PEAK 44(20Q11.21) WILD-TYPE 75 115 52 19

Figure S247.  Get High-res Image Gene #44: 'Amp Peak 44(20q11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 45(20q13.12)' versus 'CN_CNMF'

P value = 1.08e-55 (Chi-square test), Q value = 1.2e-52

Table S248.  Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 45(20Q13.12) CNV 9 5 106 0 19 1
AMP PEAK 45(20Q13.12) WILD-TYPE 285 4 48 13 3 11

Figure S248.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 45(20q13.12)' versus 'METHLYATION_CNMF'

P value = 8.23e-14 (Fisher's exact test), Q value = 8.2e-11

Table S249.  Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 45(20Q13.12) CNV 81 22 23
AMP PEAK 45(20Q13.12) WILD-TYPE 65 67 132

Figure S249.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 45(20q13.12)' versus 'MRNASEQ_CNMF'

P value = 2.92e-05 (Fisher's exact test), Q value = 0.02

Table S250.  Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
AMP PEAK 45(20Q13.12) CNV 33 7 12
AMP PEAK 45(20Q13.12) WILD-TYPE 16 29 21

Figure S250.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 45(20q13.12)' versus 'MIRSEQ_CNMF'

P value = 2.26e-15 (Chi-square test), Q value = 2.3e-12

Table S251.  Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 45(20Q13.12) CNV 80 21 15 8 15
AMP PEAK 45(20Q13.12) WILD-TYPE 69 108 34 45 100

Figure S251.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 45(20q13.12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.24e-12 (Fisher's exact test), Q value = 4.1e-09

Table S252.  Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 45(20Q13.12) CNV 6 29 104
AMP PEAK 45(20Q13.12) WILD-TYPE 21 193 142

Figure S252.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 45(20q13.12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.012

Table S253.  Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 45(20Q13.12) CNV 75 22 23
AMP PEAK 45(20Q13.12) WILD-TYPE 94 93 65

Figure S253.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 45(20q13.12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-09 (Fisher's exact test), Q value = 8.9e-07

Table S254.  Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 45(20Q13.12) CNV 25 26 63 6
AMP PEAK 45(20Q13.12) WILD-TYPE 74 112 47 19

Figure S254.  Get High-res Image Gene #45: 'Amp Peak 45(20q13.12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 46(20q13.33)' versus 'CN_CNMF'

P value = 4.94e-51 (Chi-square test), Q value = 5.6e-48

Table S255.  Gene #46: 'Amp Peak 46(20q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 46(20Q13.33) CNV 10 6 100 1 19 1
AMP PEAK 46(20Q13.33) WILD-TYPE 284 3 54 12 3 11

Figure S255.  Get High-res Image Gene #46: 'Amp Peak 46(20q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 46(20q13.33)' versus 'METHLYATION_CNMF'

P value = 5.45e-11 (Fisher's exact test), Q value = 5.1e-08

Table S256.  Gene #46: 'Amp Peak 46(20q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 46(20Q13.33) CNV 75 22 24
AMP PEAK 46(20Q13.33) WILD-TYPE 71 67 131

Figure S256.  Get High-res Image Gene #46: 'Amp Peak 46(20q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 46(20q13.33)' versus 'MIRSEQ_CNMF'

P value = 2.85e-13 (Chi-square test), Q value = 2.8e-10

Table S257.  Gene #46: 'Amp Peak 46(20q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 46(20Q13.33) CNV 76 21 14 9 15
AMP PEAK 46(20Q13.33) WILD-TYPE 73 108 35 44 100

Figure S257.  Get High-res Image Gene #46: 'Amp Peak 46(20q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 46(20q13.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.8e-11 (Fisher's exact test), Q value = 8.2e-08

Table S258.  Gene #46: 'Amp Peak 46(20q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 46(20Q13.33) CNV 5 30 100
AMP PEAK 46(20Q13.33) WILD-TYPE 22 192 146

Figure S258.  Get High-res Image Gene #46: 'Amp Peak 46(20q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 46(20q13.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.12

Table S259.  Gene #46: 'Amp Peak 46(20q13.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 46(20Q13.33) CNV 70 22 23
AMP PEAK 46(20Q13.33) WILD-TYPE 99 93 65

Figure S259.  Get High-res Image Gene #46: 'Amp Peak 46(20q13.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 46(20q13.33)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.75e-08 (Fisher's exact test), Q value = 6.4e-05

Table S260.  Gene #46: 'Amp Peak 46(20q13.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 46(20Q13.33) CNV 26 25 58 6
AMP PEAK 46(20Q13.33) WILD-TYPE 73 113 52 19

Figure S260.  Get High-res Image Gene #46: 'Amp Peak 46(20q13.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 47(22q12.2)' versus 'CN_CNMF'

P value = 5.61e-18 (Chi-square test), Q value = 5.9e-15

Table S261.  Gene #47: 'Amp Peak 47(22q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 47(22Q12.2) CNV 4 3 46 2 1 0
AMP PEAK 47(22Q12.2) WILD-TYPE 290 6 108 11 21 12

Figure S261.  Get High-res Image Gene #47: 'Amp Peak 47(22q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 47(22q12.2)' versus 'METHLYATION_CNMF'

P value = 6.36e-16 (Fisher's exact test), Q value = 6.5e-13

Table S262.  Gene #47: 'Amp Peak 47(22q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
AMP PEAK 47(22Q12.2) CNV 43 8 0
AMP PEAK 47(22Q12.2) WILD-TYPE 103 81 155

Figure S262.  Get High-res Image Gene #47: 'Amp Peak 47(22q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 47(22q12.2)' versus 'MIRSEQ_CNMF'

P value = 4e-12 (Chi-square test), Q value = 3.9e-09

Table S263.  Gene #47: 'Amp Peak 47(22q12.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
AMP PEAK 47(22Q12.2) CNV 40 0 5 1 9
AMP PEAK 47(22Q12.2) WILD-TYPE 109 129 44 52 106

Figure S263.  Get High-res Image Gene #47: 'Amp Peak 47(22q12.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 47(22q12.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.45e-14 (Fisher's exact test), Q value = 2.5e-11

Table S264.  Gene #47: 'Amp Peak 47(22q12.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
AMP PEAK 47(22Q12.2) CNV 0 2 53
AMP PEAK 47(22Q12.2) WILD-TYPE 27 220 193

Figure S264.  Get High-res Image Gene #47: 'Amp Peak 47(22q12.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 47(22q12.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.88e-10 (Fisher's exact test), Q value = 5.3e-07

Table S265.  Gene #47: 'Amp Peak 47(22q12.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
AMP PEAK 47(22Q12.2) CNV 42 1 7
AMP PEAK 47(22Q12.2) WILD-TYPE 127 114 81

Figure S265.  Get High-res Image Gene #47: 'Amp Peak 47(22q12.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 47(22q12.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.49e-13 (Fisher's exact test), Q value = 9.4e-10

Table S266.  Gene #47: 'Amp Peak 47(22q12.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
AMP PEAK 47(22Q12.2) CNV 15 1 34 0
AMP PEAK 47(22Q12.2) WILD-TYPE 84 137 76 25

Figure S266.  Get High-res Image Gene #47: 'Amp Peak 47(22q12.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 48(Xp11.23)' versus 'CN_CNMF'

P value = 5.87e-24 (Chi-square test), Q value = 6.4e-21

Table S267.  Gene #48: 'Amp Peak 48(Xp11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 48(XP11.23) CNV 11 5 43 7 9 10
AMP PEAK 48(XP11.23) WILD-TYPE 283 4 111 6 13 2

Figure S267.  Get High-res Image Gene #48: 'Amp Peak 48(Xp11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 49(Xq28)' versus 'CN_CNMF'

P value = 7.84e-25 (Chi-square test), Q value = 8.6e-22

Table S268.  Gene #49: 'Amp Peak 49(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
AMP PEAK 49(XQ28) CNV 11 4 44 8 10 10
AMP PEAK 49(XQ28) WILD-TYPE 283 5 110 5 12 2

Figure S268.  Get High-res Image Gene #49: 'Amp Peak 49(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.11)' versus 'CN_CNMF'

P value = 1.05e-33 (Chi-square test), Q value = 1.2e-30

Table S269.  Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 1(1P36.11) CNV 2 1 71 4 1 0
DEL PEAK 1(1P36.11) WILD-TYPE 292 8 83 9 21 12

Figure S269.  Get High-res Image Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.11)' versus 'METHLYATION_CNMF'

P value = 2.72e-10 (Fisher's exact test), Q value = 2.5e-07

Table S270.  Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 1(1P36.11) CNV 48 15 7
DEL PEAK 1(1P36.11) WILD-TYPE 98 74 148

Figure S270.  Get High-res Image Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000282 (Fisher's exact test), Q value = 0.16

Table S271.  Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 1(1P36.11) CNV 20 9 2
DEL PEAK 1(1P36.11) WILD-TYPE 26 27 34

Figure S271.  Get High-res Image Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.11)' versus 'MIRSEQ_CNMF'

P value = 2.88e-12 (Chi-square test), Q value = 2.8e-09

Table S272.  Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 1(1P36.11) CNV 51 7 6 5 7
DEL PEAK 1(1P36.11) WILD-TYPE 98 122 43 48 108

Figure S272.  Get High-res Image Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.23e-13 (Fisher's exact test), Q value = 1.2e-10

Table S273.  Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 1(1P36.11) CNV 5 6 65
DEL PEAK 1(1P36.11) WILD-TYPE 22 216 181

Figure S273.  Get High-res Image Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.11)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.84e-05 (Fisher's exact test), Q value = 0.019

Table S274.  Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 1(1P36.11) CNV 44 7 19
DEL PEAK 1(1P36.11) WILD-TYPE 125 108 69

Figure S274.  Get High-res Image Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 1(1p36.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.76e-07 (Fisher's exact test), Q value = 0.00069

Table S275.  Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 1(1P36.11) CNV 22 9 36 3
DEL PEAK 1(1P36.11) WILD-TYPE 77 129 74 22

Figure S275.  Get High-res Image Gene #50: 'Del Peak 1(1p36.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 2(2p25.3)' versus 'CN_CNMF'

P value = 6.1e-09 (Chi-square test), Q value = 5.3e-06

Table S276.  Gene #51: 'Del Peak 2(2p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 2(2P25.3) CNV 2 0 23 0 0 0
DEL PEAK 2(2P25.3) WILD-TYPE 292 9 131 13 22 12

Figure S276.  Get High-res Image Gene #51: 'Del Peak 2(2p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(2p25.3)' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Chi-square test), Q value = 0.19

Table S277.  Gene #51: 'Del Peak 2(2p25.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 2(2P25.3) CNV 17 3 3 2 0
DEL PEAK 2(2P25.3) WILD-TYPE 132 126 46 51 115

Figure S277.  Get High-res Image Gene #51: 'Del Peak 2(2p25.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 3(2q22.1)' versus 'CN_CNMF'

P value = 8.28e-20 (Chi-square test), Q value = 8.9e-17

Table S278.  Gene #52: 'Del Peak 3(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 3(2Q22.1) CNV 0 0 43 0 3 0
DEL PEAK 3(2Q22.1) WILD-TYPE 294 9 111 13 19 12

Figure S278.  Get High-res Image Gene #52: 'Del Peak 3(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 3(2q22.1)' versus 'MIRSEQ_CNMF'

P value = 1.01e-08 (Chi-square test), Q value = 8.8e-06

Table S279.  Gene #52: 'Del Peak 3(2q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 3(2Q22.1) CNV 32 4 1 4 3
DEL PEAK 3(2Q22.1) WILD-TYPE 117 125 48 49 112

Figure S279.  Get High-res Image Gene #52: 'Del Peak 3(2q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 3(2q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0084

Table S280.  Gene #52: 'Del Peak 3(2q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 3(2Q22.1) CNV 2 6 36
DEL PEAK 3(2Q22.1) WILD-TYPE 25 216 210

Figure S280.  Get High-res Image Gene #52: 'Del Peak 3(2q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(2q37.3)' versus 'CN_CNMF'

P value = 1.35e-17 (Chi-square test), Q value = 1.4e-14

Table S281.  Gene #53: 'Del Peak 4(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 4(2Q37.3) CNV 2 2 43 0 3 0
DEL PEAK 4(2Q37.3) WILD-TYPE 292 7 111 13 19 12

Figure S281.  Get High-res Image Gene #53: 'Del Peak 4(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(2q37.3)' versus 'METHLYATION_CNMF'

P value = 6.89e-05 (Fisher's exact test), Q value = 0.044

Table S282.  Gene #53: 'Del Peak 4(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 4(2Q37.3) CNV 31 6 9
DEL PEAK 4(2Q37.3) WILD-TYPE 115 83 146

Figure S282.  Get High-res Image Gene #53: 'Del Peak 4(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(3p14.2)' versus 'CN_CNMF'

P value = 1.4e-31 (Chi-square test), Q value = 1.6e-28

Table S283.  Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 5(3P14.2) CNV 0 2 66 1 3 0
DEL PEAK 5(3P14.2) WILD-TYPE 294 7 88 12 19 12

Figure S283.  Get High-res Image Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(3p14.2)' versus 'METHLYATION_CNMF'

P value = 1.14e-09 (Fisher's exact test), Q value = 1e-06

Table S284.  Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 5(3P14.2) CNV 42 14 5
DEL PEAK 5(3P14.2) WILD-TYPE 104 75 150

Figure S284.  Get High-res Image Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(3p14.2)' versus 'MRNASEQ_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.063

Table S285.  Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 5(3P14.2) CNV 18 3 1
DEL PEAK 5(3P14.2) WILD-TYPE 31 33 32

Figure S285.  Get High-res Image Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(3p14.2)' versus 'MIRSEQ_CNMF'

P value = 5.81e-11 (Chi-square test), Q value = 5.4e-08

Table S286.  Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 5(3P14.2) CNV 46 4 7 6 7
DEL PEAK 5(3P14.2) WILD-TYPE 103 125 42 47 108

Figure S286.  Get High-res Image Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 5(3p14.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.41e-10 (Fisher's exact test), Q value = 5.7e-07

Table S287.  Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 5(3P14.2) CNV 2 9 59
DEL PEAK 5(3P14.2) WILD-TYPE 25 213 187

Figure S287.  Get High-res Image Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(3p14.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.11e-05 (Fisher's exact test), Q value = 0.015

Table S288.  Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 5(3P14.2) CNV 40 5 14
DEL PEAK 5(3P14.2) WILD-TYPE 129 110 74

Figure S288.  Get High-res Image Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 5(3p14.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.76e-07 (Fisher's exact test), Q value = 0.00061

Table S289.  Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 5(3P14.2) CNV 18 6 32 3
DEL PEAK 5(3P14.2) WILD-TYPE 81 132 78 22

Figure S289.  Get High-res Image Gene #54: 'Del Peak 5(3p14.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 6(3q13.31)' versus 'CN_CNMF'

P value = 1.27e-11 (Chi-square test), Q value = 1.2e-08

Table S290.  Gene #55: 'Del Peak 6(3q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 6(3Q13.31) CNV 1 0 28 0 1 0
DEL PEAK 6(3Q13.31) WILD-TYPE 293 9 126 13 21 12

Figure S290.  Get High-res Image Gene #55: 'Del Peak 6(3q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(3q13.31)' versus 'MIRSEQ_CNMF'

P value = 2.33e-05 (Chi-square test), Q value = 0.016

Table S291.  Gene #55: 'Del Peak 6(3q13.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 6(3Q13.31) CNV 21 2 2 1 3
DEL PEAK 6(3Q13.31) WILD-TYPE 128 127 47 52 112

Figure S291.  Get High-res Image Gene #55: 'Del Peak 6(3q13.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 7(4p16.3)' versus 'CN_CNMF'

P value = 1.58e-31 (Chi-square test), Q value = 1.8e-28

Table S292.  Gene #56: 'Del Peak 7(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 7(4P16.3) CNV 4 4 73 4 3 1
DEL PEAK 7(4P16.3) WILD-TYPE 290 5 81 9 19 11

Figure S292.  Get High-res Image Gene #56: 'Del Peak 7(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(4p16.3)' versus 'METHLYATION_CNMF'

P value = 7.52e-12 (Fisher's exact test), Q value = 7.2e-09

Table S293.  Gene #56: 'Del Peak 7(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 7(4P16.3) CNV 54 15 8
DEL PEAK 7(4P16.3) WILD-TYPE 92 74 147

Figure S293.  Get High-res Image Gene #56: 'Del Peak 7(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 7(4p16.3)' versus 'MIRSEQ_CNMF'

P value = 8.1e-14 (Chi-square test), Q value = 8.1e-11

Table S294.  Gene #56: 'Del Peak 7(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 7(4P16.3) CNV 55 8 11 8 4
DEL PEAK 7(4P16.3) WILD-TYPE 94 121 38 45 111

Figure S294.  Get High-res Image Gene #56: 'Del Peak 7(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 7(4p16.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.34e-11 (Fisher's exact test), Q value = 1.3e-08

Table S295.  Gene #56: 'Del Peak 7(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 7(4P16.3) CNV 5 11 70
DEL PEAK 7(4P16.3) WILD-TYPE 22 211 176

Figure S295.  Get High-res Image Gene #56: 'Del Peak 7(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(4p16.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.81e-05 (Fisher's exact test), Q value = 0.032

Table S296.  Gene #56: 'Del Peak 7(4p16.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 7(4P16.3) CNV 48 9 20
DEL PEAK 7(4P16.3) WILD-TYPE 121 106 68

Figure S296.  Get High-res Image Gene #56: 'Del Peak 7(4p16.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 7(4p16.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-07 (Fisher's exact test), Q value = 8.7e-05

Table S297.  Gene #56: 'Del Peak 7(4p16.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 7(4P16.3) CNV 21 10 41 5
DEL PEAK 7(4P16.3) WILD-TYPE 78 128 69 20

Figure S297.  Get High-res Image Gene #56: 'Del Peak 7(4p16.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 8(4p15.31)' versus 'CN_CNMF'

P value = 2.39e-35 (Chi-square test), Q value = 2.7e-32

Table S298.  Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 8(4P15.31) CNV 3 4 78 3 3 1
DEL PEAK 8(4P15.31) WILD-TYPE 291 5 76 10 19 11

Figure S298.  Get High-res Image Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(4p15.31)' versus 'METHLYATION_CNMF'

P value = 1.41e-13 (Fisher's exact test), Q value = 1.4e-10

Table S299.  Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 8(4P15.31) CNV 57 17 7
DEL PEAK 8(4P15.31) WILD-TYPE 89 72 148

Figure S299.  Get High-res Image Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 8(4p15.31)' versus 'MRNASEQ_CNMF'

P value = 6.3e-06 (Fisher's exact test), Q value = 0.0047

Table S300.  Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 8(4P15.31) CNV 30 9 4
DEL PEAK 8(4P15.31) WILD-TYPE 19 27 29

Figure S300.  Get High-res Image Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 8(4p15.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00083

Table S301.  Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 8(4P15.31) CNV 27 14 2
DEL PEAK 8(4P15.31) WILD-TYPE 19 22 34

Figure S301.  Get High-res Image Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(4p15.31)' versus 'MIRSEQ_CNMF'

P value = 7.15e-17 (Chi-square test), Q value = 7.4e-14

Table S302.  Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 8(4P15.31) CNV 61 7 10 7 5
DEL PEAK 8(4P15.31) WILD-TYPE 88 122 39 46 110

Figure S302.  Get High-res Image Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 8(4p15.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.17e-13 (Fisher's exact test), Q value = 1.2e-10

Table S303.  Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 8(4P15.31) CNV 5 10 75
DEL PEAK 8(4P15.31) WILD-TYPE 22 212 171

Figure S303.  Get High-res Image Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(4p15.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.0011

Table S304.  Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 8(4P15.31) CNV 53 8 20
DEL PEAK 8(4P15.31) WILD-TYPE 116 107 68

Figure S304.  Get High-res Image Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 8(4p15.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.53e-08 (Fisher's exact test), Q value = 1.3e-05

Table S305.  Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 8(4P15.31) CNV 26 9 41 5
DEL PEAK 8(4P15.31) WILD-TYPE 73 129 69 20

Figure S305.  Get High-res Image Gene #57: 'Del Peak 8(4p15.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 9(4q22.1)' versus 'CN_CNMF'

P value = 2.26e-42 (Chi-square test), Q value = 2.6e-39

Table S306.  Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 9(4Q22.1) CNV 2 2 88 4 3 1
DEL PEAK 9(4Q22.1) WILD-TYPE 292 7 66 9 19 11

Figure S306.  Get High-res Image Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4q22.1)' versus 'METHLYATION_CNMF'

P value = 1.36e-17 (Fisher's exact test), Q value = 1.4e-14

Table S307.  Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 9(4Q22.1) CNV 63 18 5
DEL PEAK 9(4Q22.1) WILD-TYPE 83 71 150

Figure S307.  Get High-res Image Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 9(4q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.014

Table S308.  Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 9(4Q22.1) CNV 27 10 4
DEL PEAK 9(4Q22.1) WILD-TYPE 19 26 32

Figure S308.  Get High-res Image Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(4q22.1)' versus 'MIRSEQ_CNMF'

P value = 4.06e-16 (Chi-square test), Q value = 4.2e-13

Table S309.  Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 9(4Q22.1) CNV 63 7 12 6 9
DEL PEAK 9(4Q22.1) WILD-TYPE 86 122 37 47 106

Figure S309.  Get High-res Image Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 9(4q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.49e-18 (Fisher's exact test), Q value = 6.8e-15

Table S310.  Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 9(4Q22.1) CNV 5 8 84
DEL PEAK 9(4Q22.1) WILD-TYPE 22 214 162

Figure S310.  Get High-res Image Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 9(4q22.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.3e-08 (Fisher's exact test), Q value = 1.1e-05

Table S311.  Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 9(4Q22.1) CNV 55 6 25
DEL PEAK 9(4Q22.1) WILD-TYPE 114 109 63

Figure S311.  Get High-res Image Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 9(4q22.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.63e-11 (Fisher's exact test), Q value = 5.3e-08

Table S312.  Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 9(4Q22.1) CNV 33 7 41 5
DEL PEAK 9(4Q22.1) WILD-TYPE 66 131 69 20

Figure S312.  Get High-res Image Gene #58: 'Del Peak 9(4q22.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 10(4q34.3)' versus 'CN_CNMF'

P value = 2.05e-48 (Chi-square test), Q value = 2.3e-45

Table S313.  Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 10(4Q34.3) CNV 6 3 102 3 4 1
DEL PEAK 10(4Q34.3) WILD-TYPE 288 6 52 10 18 11

Figure S313.  Get High-res Image Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4q34.3)' versus 'METHLYATION_CNMF'

P value = 7.93e-14 (Fisher's exact test), Q value = 8e-11

Table S314.  Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 10(4Q34.3) CNV 67 24 12
DEL PEAK 10(4Q34.3) WILD-TYPE 79 65 143

Figure S314.  Get High-res Image Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(4q34.3)' versus 'MRNASEQ_CNMF'

P value = 2.19e-07 (Fisher's exact test), Q value = 0.00018

Table S315.  Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 10(4Q34.3) CNV 34 7 6
DEL PEAK 10(4Q34.3) WILD-TYPE 15 29 27

Figure S315.  Get High-res Image Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(4q34.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.0013

Table S316.  Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 10(4Q34.3) CNV 31 11 5
DEL PEAK 10(4Q34.3) WILD-TYPE 15 25 31

Figure S316.  Get High-res Image Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(4q34.3)' versus 'MIRSEQ_CNMF'

P value = 6.7e-18 (Chi-square test), Q value = 7e-15

Table S317.  Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 10(4Q34.3) CNV 73 8 12 11 12
DEL PEAK 10(4Q34.3) WILD-TYPE 76 121 37 42 103

Figure S317.  Get High-res Image Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 10(4q34.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.06e-19 (Fisher's exact test), Q value = 3.3e-16

Table S318.  Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 10(4Q34.3) CNV 7 12 97
DEL PEAK 10(4Q34.3) WILD-TYPE 20 210 149

Figure S318.  Get High-res Image Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(4q34.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.89e-09 (Fisher's exact test), Q value = 6e-06

Table S319.  Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 10(4Q34.3) CNV 64 9 29
DEL PEAK 10(4Q34.3) WILD-TYPE 105 106 59

Figure S319.  Get High-res Image Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 10(4q34.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.23e-12 (Fisher's exact test), Q value = 2.2e-09

Table S320.  Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 10(4Q34.3) CNV 38 10 49 5
DEL PEAK 10(4Q34.3) WILD-TYPE 61 128 61 20

Figure S320.  Get High-res Image Gene #59: 'Del Peak 10(4q34.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 11(5q11.2)' versus 'CN_CNMF'

P value = 7.69e-48 (Chi-square test), Q value = 8.7e-45

Table S321.  Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 11(5Q11.2) CNV 0 4 93 1 5 1
DEL PEAK 11(5Q11.2) WILD-TYPE 294 5 61 12 17 11

Figure S321.  Get High-res Image Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(5q11.2)' versus 'METHLYATION_CNMF'

P value = 1.48e-15 (Fisher's exact test), Q value = 1.5e-12

Table S322.  Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 11(5Q11.2) CNV 64 18 8
DEL PEAK 11(5Q11.2) WILD-TYPE 82 71 147

Figure S322.  Get High-res Image Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 11(5q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.01

Table S323.  Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 11(5Q11.2) CNV 31 7 7
DEL PEAK 11(5Q11.2) WILD-TYPE 18 29 26

Figure S323.  Get High-res Image Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 11(5q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000249 (Fisher's exact test), Q value = 0.15

Table S324.  Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 11(5Q11.2) CNV 28 10 7
DEL PEAK 11(5Q11.2) WILD-TYPE 18 26 29

Figure S324.  Get High-res Image Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(5q11.2)' versus 'MIRSEQ_CNMF'

P value = 1.52e-15 (Chi-square test), Q value = 1.6e-12

Table S325.  Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 11(5Q11.2) CNV 64 9 14 8 8
DEL PEAK 11(5Q11.2) WILD-TYPE 85 120 35 45 107

Figure S325.  Get High-res Image Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 11(5q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.93e-14 (Fisher's exact test), Q value = 8e-11

Table S326.  Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 11(5Q11.2) CNV 5 14 84
DEL PEAK 11(5Q11.2) WILD-TYPE 22 208 162

Figure S326.  Get High-res Image Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(5q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00091

Table S327.  Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 11(5Q11.2) CNV 60 11 18
DEL PEAK 11(5Q11.2) WILD-TYPE 109 104 70

Figure S327.  Get High-res Image Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 11(5q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.61e-08 (Fisher's exact test), Q value = 3.9e-05

Table S328.  Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 11(5Q11.2) CNV 28 12 44 5
DEL PEAK 11(5Q11.2) WILD-TYPE 71 126 66 20

Figure S328.  Get High-res Image Gene #60: 'Del Peak 11(5q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 12(6q26)' versus 'CN_CNMF'

P value = 1.11e-13 (Chi-square test), Q value = 1.1e-10

Table S329.  Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 12(6Q26) CNV 4 2 37 2 0 0
DEL PEAK 12(6Q26) WILD-TYPE 290 7 117 11 22 12

Figure S329.  Get High-res Image Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(6q26)' versus 'METHLYATION_CNMF'

P value = 1.94e-08 (Fisher's exact test), Q value = 1.7e-05

Table S330.  Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 12(6Q26) CNV 28 10 1
DEL PEAK 12(6Q26) WILD-TYPE 118 79 154

Figure S330.  Get High-res Image Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(6q26)' versus 'MRNASEQ_CNMF'

P value = 5.42e-05 (Fisher's exact test), Q value = 0.035

Table S331.  Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 12(6Q26) CNV 17 1 2
DEL PEAK 12(6Q26) WILD-TYPE 32 35 31

Figure S331.  Get High-res Image Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(6q26)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.67e-08 (Fisher's exact test), Q value = 3.1e-05

Table S332.  Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 12(6Q26) CNV 19 1 0
DEL PEAK 12(6Q26) WILD-TYPE 27 35 36

Figure S332.  Get High-res Image Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(6q26)' versus 'MIRSEQ_CNMF'

P value = 2.15e-08 (Chi-square test), Q value = 1.8e-05

Table S333.  Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 12(6Q26) CNV 30 2 5 6 1
DEL PEAK 12(6Q26) WILD-TYPE 119 127 44 47 114

Figure S333.  Get High-res Image Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(6q26)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.48e-09 (Fisher's exact test), Q value = 7.4e-06

Table S334.  Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 12(6Q26) CNV 1 3 40
DEL PEAK 12(6Q26) WILD-TYPE 26 219 206

Figure S334.  Get High-res Image Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(6q26)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000213 (Fisher's exact test), Q value = 0.13

Table S335.  Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 12(6Q26) CNV 25 2 12
DEL PEAK 12(6Q26) WILD-TYPE 144 113 76

Figure S335.  Get High-res Image Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(6q26)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.62e-05 (Fisher's exact test), Q value = 0.011

Table S336.  Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 12(6Q26) CNV 16 2 18 3
DEL PEAK 12(6Q26) WILD-TYPE 83 136 92 22

Figure S336.  Get High-res Image Gene #61: 'Del Peak 12(6q26)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(7p22.3)' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.028

Table S337.  Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 13(7P22.3) CNV 0 0 7
DEL PEAK 13(7P22.3) WILD-TYPE 19 19 8

Figure S337.  Get High-res Image Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 13(7p22.3)' versus 'CN_CNMF'

P value = 3.87e-29 (Chi-square test), Q value = 4.3e-26

Table S338.  Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 13(7P22.3) CNV 4 1 64 1 0 0
DEL PEAK 13(7P22.3) WILD-TYPE 290 8 90 12 22 12

Figure S338.  Get High-res Image Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(7p22.3)' versus 'METHLYATION_CNMF'

P value = 4.33e-10 (Fisher's exact test), Q value = 3.9e-07

Table S339.  Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 13(7P22.3) CNV 43 13 5
DEL PEAK 13(7P22.3) WILD-TYPE 103 76 150

Figure S339.  Get High-res Image Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 13(7p22.3)' versus 'MIRSEQ_CNMF'

P value = 7.68e-12 (Chi-square test), Q value = 7.4e-09

Table S340.  Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 13(7P22.3) CNV 46 6 9 4 4
DEL PEAK 13(7P22.3) WILD-TYPE 103 123 40 49 111

Figure S340.  Get High-res Image Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 13(7p22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.49e-10 (Fisher's exact test), Q value = 4.1e-07

Table S341.  Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 13(7P22.3) CNV 3 8 58
DEL PEAK 13(7P22.3) WILD-TYPE 24 214 188

Figure S341.  Get High-res Image Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(7p22.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.29e-05 (Fisher's exact test), Q value = 0.041

Table S342.  Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 13(7P22.3) CNV 37 5 16
DEL PEAK 13(7P22.3) WILD-TYPE 132 110 72

Figure S342.  Get High-res Image Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 13(7p22.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.96e-07 (Fisher's exact test), Q value = 0.00024

Table S343.  Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 13(7P22.3) CNV 20 6 31 1
DEL PEAK 13(7P22.3) WILD-TYPE 79 132 79 24

Figure S343.  Get High-res Image Gene #62: 'Del Peak 13(7p22.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 14(7q11.22)' versus 'CN_CNMF'

P value = 4.86e-19 (Chi-square test), Q value = 5.2e-16

Table S344.  Gene #63: 'Del Peak 14(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 14(7Q11.22) CNV 0 0 40 1 0 0
DEL PEAK 14(7Q11.22) WILD-TYPE 294 9 114 12 22 12

Figure S344.  Get High-res Image Gene #63: 'Del Peak 14(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(7q11.22)' versus 'METHLYATION_CNMF'

P value = 8.11e-07 (Fisher's exact test), Q value = 0.00064

Table S345.  Gene #63: 'Del Peak 14(7q11.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 14(7Q11.22) CNV 26 10 2
DEL PEAK 14(7Q11.22) WILD-TYPE 120 79 153

Figure S345.  Get High-res Image Gene #63: 'Del Peak 14(7q11.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(7q11.22)' versus 'MIRSEQ_CNMF'

P value = 5.63e-09 (Chi-square test), Q value = 4.9e-06

Table S346.  Gene #63: 'Del Peak 14(7q11.22)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 14(7Q11.22) CNV 30 3 4 2 1
DEL PEAK 14(7Q11.22) WILD-TYPE 119 126 45 51 114

Figure S346.  Get High-res Image Gene #63: 'Del Peak 14(7q11.22)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 14(7q11.22)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.23e-05 (Fisher's exact test), Q value = 0.015

Table S347.  Gene #63: 'Del Peak 14(7q11.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 14(7Q11.22) CNV 3 5 32
DEL PEAK 14(7Q11.22) WILD-TYPE 24 217 214

Figure S347.  Get High-res Image Gene #63: 'Del Peak 14(7q11.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(7q11.22)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000115 (Fisher's exact test), Q value = 0.071

Table S348.  Gene #63: 'Del Peak 14(7q11.22)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 14(7Q11.22) CNV 12 4 20 0
DEL PEAK 14(7Q11.22) WILD-TYPE 87 134 90 25

Figure S348.  Get High-res Image Gene #63: 'Del Peak 14(7q11.22)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 15(7q31.1)' versus 'CN_CNMF'

P value = 8.86e-25 (Chi-square test), Q value = 9.7e-22

Table S349.  Gene #64: 'Del Peak 15(7q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 15(7Q31.1) CNV 0 0 50 1 0 0
DEL PEAK 15(7Q31.1) WILD-TYPE 294 9 104 12 22 12

Figure S349.  Get High-res Image Gene #64: 'Del Peak 15(7q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(7q31.1)' versus 'METHLYATION_CNMF'

P value = 3.99e-09 (Fisher's exact test), Q value = 3.5e-06

Table S350.  Gene #64: 'Del Peak 15(7q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 15(7Q31.1) CNV 33 11 2
DEL PEAK 15(7Q31.1) WILD-TYPE 113 78 153

Figure S350.  Get High-res Image Gene #64: 'Del Peak 15(7q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 15(7q31.1)' versus 'MIRSEQ_CNMF'

P value = 5.42e-12 (Chi-square test), Q value = 5.3e-09

Table S351.  Gene #64: 'Del Peak 15(7q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 15(7Q31.1) CNV 38 3 5 2 2
DEL PEAK 15(7Q31.1) WILD-TYPE 111 126 44 51 113

Figure S351.  Get High-res Image Gene #64: 'Del Peak 15(7q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 15(7q31.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.19e-08 (Fisher's exact test), Q value = 4.3e-05

Table S352.  Gene #64: 'Del Peak 15(7q31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 15(7Q31.1) CNV 2 5 43
DEL PEAK 15(7Q31.1) WILD-TYPE 25 217 203

Figure S352.  Get High-res Image Gene #64: 'Del Peak 15(7q31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(7q31.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000215 (Fisher's exact test), Q value = 0.13

Table S353.  Gene #64: 'Del Peak 15(7q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 15(7Q31.1) CNV 29 3 11
DEL PEAK 15(7Q31.1) WILD-TYPE 140 112 77

Figure S353.  Get High-res Image Gene #64: 'Del Peak 15(7q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 15(7q31.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.2e-06 (Fisher's exact test), Q value = 0.0024

Table S354.  Gene #64: 'Del Peak 15(7q31.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 15(7Q31.1) CNV 15 4 24 0
DEL PEAK 15(7Q31.1) WILD-TYPE 84 134 86 25

Figure S354.  Get High-res Image Gene #64: 'Del Peak 15(7q31.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 16(7q36.1)' versus 'CN_CNMF'

P value = 7.33e-28 (Chi-square test), Q value = 8.1e-25

Table S355.  Gene #65: 'Del Peak 16(7q36.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 16(7Q36.1) CNV 1 0 58 1 1 0
DEL PEAK 16(7Q36.1) WILD-TYPE 293 9 96 12 21 12

Figure S355.  Get High-res Image Gene #65: 'Del Peak 16(7q36.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(7q36.1)' versus 'METHLYATION_CNMF'

P value = 5.69e-12 (Fisher's exact test), Q value = 5.5e-09

Table S356.  Gene #65: 'Del Peak 16(7q36.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 16(7Q36.1) CNV 38 13 1
DEL PEAK 16(7Q36.1) WILD-TYPE 108 76 154

Figure S356.  Get High-res Image Gene #65: 'Del Peak 16(7q36.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(7q36.1)' versus 'MIRSEQ_CNMF'

P value = 3.18e-15 (Chi-square test), Q value = 3.2e-12

Table S357.  Gene #65: 'Del Peak 16(7q36.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 16(7Q36.1) CNV 46 3 6 2 3
DEL PEAK 16(7Q36.1) WILD-TYPE 103 126 43 51 112

Figure S357.  Get High-res Image Gene #65: 'Del Peak 16(7q36.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 16(7q36.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.18e-11 (Fisher's exact test), Q value = 2.1e-08

Table S358.  Gene #65: 'Del Peak 16(7q36.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 16(7Q36.1) CNV 1 5 54
DEL PEAK 16(7Q36.1) WILD-TYPE 26 217 192

Figure S358.  Get High-res Image Gene #65: 'Del Peak 16(7q36.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 16(7q36.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.014

Table S359.  Gene #65: 'Del Peak 16(7q36.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 16(7Q36.1) CNV 34 3 12
DEL PEAK 16(7Q36.1) WILD-TYPE 135 112 76

Figure S359.  Get High-res Image Gene #65: 'Del Peak 16(7q36.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 16(7q36.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.7e-09 (Fisher's exact test), Q value = 3.3e-06

Table S360.  Gene #65: 'Del Peak 16(7q36.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 16(7Q36.1) CNV 16 3 30 0
DEL PEAK 16(7Q36.1) WILD-TYPE 83 135 80 25

Figure S360.  Get High-res Image Gene #65: 'Del Peak 16(7q36.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 17(8p23.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.13

Table S361.  Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 17(8P23.2) CNV 0 0 6
DEL PEAK 17(8P23.2) WILD-TYPE 19 19 9

Figure S361.  Get High-res Image Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 17(8p23.2)' versus 'CN_CNMF'

P value = 5.48e-47 (Chi-square test), Q value = 6.2e-44

Table S362.  Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 17(8P23.2) CNV 7 4 95 1 0 0
DEL PEAK 17(8P23.2) WILD-TYPE 287 5 59 12 22 12

Figure S362.  Get High-res Image Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(8p23.2)' versus 'METHLYATION_CNMF'

P value = 3.64e-21 (Fisher's exact test), Q value = 3.9e-18

Table S363.  Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 17(8P23.2) CNV 69 20 4
DEL PEAK 17(8P23.2) WILD-TYPE 77 69 151

Figure S363.  Get High-res Image Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(8p23.2)' versus 'MRNASEQ_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0073

Table S364.  Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 17(8P23.2) CNV 29 8 4
DEL PEAK 17(8P23.2) WILD-TYPE 20 28 29

Figure S364.  Get High-res Image Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(8p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.03e-06 (Fisher's exact test), Q value = 0.00081

Table S365.  Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 17(8P23.2) CNV 27 12 2
DEL PEAK 17(8P23.2) WILD-TYPE 19 24 34

Figure S365.  Get High-res Image Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(8p23.2)' versus 'MIRSEQ_CNMF'

P value = 2.22e-23 (Chi-square test), Q value = 2.4e-20

Table S366.  Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 17(8P23.2) CNV 74 6 11 4 9
DEL PEAK 17(8P23.2) WILD-TYPE 75 123 38 49 106

Figure S366.  Get High-res Image Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 17(8p23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.94e-20 (Fisher's exact test), Q value = 3.2e-17

Table S367.  Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 17(8P23.2) CNV 5 8 91
DEL PEAK 17(8P23.2) WILD-TYPE 22 214 155

Figure S367.  Get High-res Image Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(8p23.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.23e-11 (Fisher's exact test), Q value = 1.2e-08

Table S368.  Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 17(8P23.2) CNV 62 4 22
DEL PEAK 17(8P23.2) WILD-TYPE 107 111 66

Figure S368.  Get High-res Image Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 17(8p23.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.89e-15 (Fisher's exact test), Q value = 7e-12

Table S369.  Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 17(8P23.2) CNV 31 6 49 2
DEL PEAK 17(8P23.2) WILD-TYPE 68 132 61 23

Figure S369.  Get High-res Image Gene #66: 'Del Peak 17(8p23.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 18(8p21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.13

Table S370.  Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 18(8P21.2) CNV 0 0 6
DEL PEAK 18(8P21.2) WILD-TYPE 19 19 9

Figure S370.  Get High-res Image Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 18(8p21.2)' versus 'CN_CNMF'

P value = 6.98e-51 (Chi-square test), Q value = 8e-48

Table S371.  Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 18(8P21.2) CNV 5 4 97 0 0 0
DEL PEAK 18(8P21.2) WILD-TYPE 289 5 57 13 22 12

Figure S371.  Get High-res Image Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(8p21.2)' versus 'METHLYATION_CNMF'

P value = 4.72e-27 (Fisher's exact test), Q value = 5.2e-24

Table S372.  Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 18(8P21.2) CNV 73 18 1
DEL PEAK 18(8P21.2) WILD-TYPE 73 71 154

Figure S372.  Get High-res Image Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(8p21.2)' versus 'MRNASEQ_CNMF'

P value = 8.4e-07 (Fisher's exact test), Q value = 0.00066

Table S373.  Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 18(8P21.2) CNV 30 8 3
DEL PEAK 18(8P21.2) WILD-TYPE 19 28 30

Figure S373.  Get High-res Image Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 18(8p21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.4e-09 (Fisher's exact test), Q value = 8.2e-06

Table S374.  Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 18(8P21.2) CNV 29 11 1
DEL PEAK 18(8P21.2) WILD-TYPE 17 25 35

Figure S374.  Get High-res Image Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(8p21.2)' versus 'MIRSEQ_CNMF'

P value = 2.27e-27 (Chi-square test), Q value = 2.5e-24

Table S375.  Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 18(8P21.2) CNV 77 2 10 4 10
DEL PEAK 18(8P21.2) WILD-TYPE 72 127 39 49 105

Figure S375.  Get High-res Image Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 18(8p21.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.44e-25 (Fisher's exact test), Q value = 8.2e-22

Table S376.  Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 18(8P21.2) CNV 3 5 95
DEL PEAK 18(8P21.2) WILD-TYPE 24 217 151

Figure S376.  Get High-res Image Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(8p21.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.33e-15 (Fisher's exact test), Q value = 1.4e-12

Table S377.  Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 18(8P21.2) CNV 64 1 23
DEL PEAK 18(8P21.2) WILD-TYPE 105 114 65

Figure S377.  Get High-res Image Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 18(8p21.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.68e-19 (Fisher's exact test), Q value = 9.2e-16

Table S378.  Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 18(8P21.2) CNV 32 3 51 2
DEL PEAK 18(8P21.2) WILD-TYPE 67 135 59 23

Figure S378.  Get High-res Image Gene #67: 'Del Peak 18(8p21.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 19(9p23)' versus 'CN_CNMF'

P value = 3.54e-23 (Chi-square test), Q value = 3.8e-20

Table S379.  Gene #68: 'Del Peak 19(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 19(9P23) CNV 2 3 55 2 6 0
DEL PEAK 19(9P23) WILD-TYPE 292 6 99 11 16 12

Figure S379.  Get High-res Image Gene #68: 'Del Peak 19(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(9p23)' versus 'METHLYATION_CNMF'

P value = 2.48e-06 (Fisher's exact test), Q value = 0.0019

Table S380.  Gene #68: 'Del Peak 19(9p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 19(9P23) CNV 33 19 7
DEL PEAK 19(9P23) WILD-TYPE 113 70 148

Figure S380.  Get High-res Image Gene #68: 'Del Peak 19(9p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(9p23)' versus 'MIRSEQ_CNMF'

P value = 1.5e-05 (Chi-square test), Q value = 0.011

Table S381.  Gene #68: 'Del Peak 19(9p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 19(9P23) CNV 37 12 8 5 5
DEL PEAK 19(9P23) WILD-TYPE 112 117 41 48 110

Figure S381.  Get High-res Image Gene #68: 'Del Peak 19(9p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 19(9p23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-05 (Fisher's exact test), Q value = 0.0081

Table S382.  Gene #68: 'Del Peak 19(9p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 19(9P23) CNV 4 13 50
DEL PEAK 19(9P23) WILD-TYPE 23 209 196

Figure S382.  Get High-res Image Gene #68: 'Del Peak 19(9p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 20(9q21.2)' versus 'MRNA_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.016

Table S383.  Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 20(9Q21.2) CNV 0 9 0 0
DEL PEAK 20(9Q21.2) WILD-TYPE 14 8 12 10

Figure S383.  Get High-res Image Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 20(9q21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00088

Table S384.  Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 20(9Q21.2) CNV 0 0 9
DEL PEAK 20(9Q21.2) WILD-TYPE 19 19 6

Figure S384.  Get High-res Image Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 20(9q21.2)' versus 'CN_CNMF'

P value = 1.48e-50 (Chi-square test), Q value = 1.7e-47

Table S385.  Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 20(9Q21.2) CNV 3 3 101 2 9 0
DEL PEAK 20(9Q21.2) WILD-TYPE 291 6 53 11 13 12

Figure S385.  Get High-res Image Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 20(9q21.2)' versus 'METHLYATION_CNMF'

P value = 1.02e-10 (Fisher's exact test), Q value = 9.4e-08

Table S386.  Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 20(9Q21.2) CNV 63 24 15
DEL PEAK 20(9Q21.2) WILD-TYPE 83 65 140

Figure S386.  Get High-res Image Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 20(9q21.2)' versus 'MIRSEQ_CNMF'

P value = 8.86e-21 (Chi-square test), Q value = 9.5e-18

Table S387.  Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 20(9Q21.2) CNV 76 15 12 7 5
DEL PEAK 20(9Q21.2) WILD-TYPE 73 114 37 46 110

Figure S387.  Get High-res Image Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 20(9q21.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-12 (Fisher's exact test), Q value = 8.6e-09

Table S388.  Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 20(9Q21.2) CNV 7 20 88
DEL PEAK 20(9Q21.2) WILD-TYPE 20 202 158

Figure S388.  Get High-res Image Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 20(9q21.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.012

Table S389.  Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 20(9Q21.2) CNV 31 21 45 3
DEL PEAK 20(9Q21.2) WILD-TYPE 68 117 65 22

Figure S389.  Get High-res Image Gene #69: 'Del Peak 20(9q21.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 21(9q34.11)' versus 'MRNA_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.016

Table S390.  Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 21(9Q34.11) CNV 0 9 0 0
DEL PEAK 21(9Q34.11) WILD-TYPE 14 8 12 10

Figure S390.  Get High-res Image Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 21(9q34.11)' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00088

Table S391.  Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 21(9Q34.11) CNV 0 0 9
DEL PEAK 21(9Q34.11) WILD-TYPE 19 19 6

Figure S391.  Get High-res Image Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 21(9q34.11)' versus 'CN_CNMF'

P value = 4.9e-54 (Chi-square test), Q value = 5.6e-51

Table S392.  Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 21(9Q34.11) CNV 4 4 107 2 9 0
DEL PEAK 21(9Q34.11) WILD-TYPE 290 5 47 11 13 12

Figure S392.  Get High-res Image Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(9q34.11)' versus 'METHLYATION_CNMF'

P value = 1.92e-10 (Fisher's exact test), Q value = 1.8e-07

Table S393.  Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 21(9Q34.11) CNV 65 26 17
DEL PEAK 21(9Q34.11) WILD-TYPE 81 63 138

Figure S393.  Get High-res Image Gene #70: '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 = 0.22

Table S394.  Gene #70: '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 S394.  Get High-res Image Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 21(9q34.11)' versus 'MIRSEQ_CNMF'

P value = 3.18e-19 (Chi-square test), Q value = 3.4e-16

Table S395.  Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 21(9Q34.11) CNV 77 17 13 9 6
DEL PEAK 21(9Q34.11) WILD-TYPE 72 112 36 44 109

Figure S395.  Get High-res Image Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 21(9q34.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.15e-12 (Fisher's exact test), Q value = 5e-09

Table S396.  Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 21(9Q34.11) CNV 8 22 92
DEL PEAK 21(9Q34.11) WILD-TYPE 19 200 154

Figure S396.  Get High-res Image Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 21(9q34.11)' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.97e-05 (Fisher's exact test), Q value = 0.051

Table S397.  Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 21(9Q34.11) CNV 64 17 24
DEL PEAK 21(9Q34.11) WILD-TYPE 105 98 64

Figure S397.  Get High-res Image Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 21(9q34.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.49e-07 (Fisher's exact test), Q value = 0.00043

Table S398.  Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 21(9Q34.11) CNV 27 21 52 5
DEL PEAK 21(9Q34.11) WILD-TYPE 72 117 58 20

Figure S398.  Get High-res Image Gene #70: 'Del Peak 21(9q34.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 22(10q23.31)' versus 'CN_CNMF'

P value = 1.36e-26 (Chi-square test), Q value = 1.5e-23

Table S399.  Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 22(10Q23.31) CNV 5 0 63 1 3 0
DEL PEAK 22(10Q23.31) WILD-TYPE 289 9 91 12 19 12

Figure S399.  Get High-res Image Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(10q23.31)' versus 'METHLYATION_CNMF'

P value = 1.1e-07 (Fisher's exact test), Q value = 9.1e-05

Table S400.  Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 22(10Q23.31) CNV 40 16 7
DEL PEAK 22(10Q23.31) WILD-TYPE 106 73 148

Figure S400.  Get High-res Image Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 22(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.01

Table S401.  Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 22(10Q23.31) CNV 25 3 5
DEL PEAK 22(10Q23.31) WILD-TYPE 24 33 28

Figure S401.  Get High-res Image Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 22(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.89e-07 (Fisher's exact test), Q value = 0.00023

Table S402.  Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 22(10Q23.31) CNV 26 3 4
DEL PEAK 22(10Q23.31) WILD-TYPE 20 33 32

Figure S402.  Get High-res Image Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 22(10q23.31)' versus 'MIRSEQ_CNMF'

P value = 2.01e-11 (Chi-square test), Q value = 1.9e-08

Table S403.  Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 22(10Q23.31) CNV 46 7 10 4 4
DEL PEAK 22(10Q23.31) WILD-TYPE 103 122 39 49 111

Figure S403.  Get High-res Image Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 22(10q23.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.38e-08 (Fisher's exact test), Q value = 1.2e-05

Table S404.  Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 22(10Q23.31) CNV 2 11 58
DEL PEAK 22(10Q23.31) WILD-TYPE 25 211 188

Figure S404.  Get High-res Image Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 22(10q23.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000146 (Fisher's exact test), Q value = 0.088

Table S405.  Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 22(10Q23.31) CNV 41 7 14
DEL PEAK 22(10Q23.31) WILD-TYPE 128 108 74

Figure S405.  Get High-res Image Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 22(10q23.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.14e-06 (Fisher's exact test), Q value = 0.0031

Table S406.  Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 22(10Q23.31) CNV 20 8 32 2
DEL PEAK 22(10Q23.31) WILD-TYPE 79 130 78 23

Figure S406.  Get High-res Image Gene #71: 'Del Peak 22(10q23.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 23(11p15.5)' versus 'CN_CNMF'

P value = 5.06e-39 (Chi-square test), Q value = 5.7e-36

Table S407.  Gene #72: 'Del Peak 23(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 23(11P15.5) CNV 1 4 80 5 3 0
DEL PEAK 23(11P15.5) WILD-TYPE 293 5 74 8 19 12

Figure S407.  Get High-res Image Gene #72: 'Del Peak 23(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(11p15.5)' versus 'METHLYATION_CNMF'

P value = 6.9e-14 (Fisher's exact test), Q value = 6.9e-11

Table S408.  Gene #72: 'Del Peak 23(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 23(11P15.5) CNV 58 20 7
DEL PEAK 23(11P15.5) WILD-TYPE 88 69 148

Figure S408.  Get High-res Image Gene #72: 'Del Peak 23(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 23(11p15.5)' versus 'MIRSEQ_CNMF'

P value = 4.25e-16 (Chi-square test), Q value = 4.4e-13

Table S409.  Gene #72: 'Del Peak 23(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 23(11P15.5) CNV 62 13 7 6 4
DEL PEAK 23(11P15.5) WILD-TYPE 87 116 42 47 111

Figure S409.  Get High-res Image Gene #72: 'Del Peak 23(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 23(11p15.5)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.91e-10 (Fisher's exact test), Q value = 6.2e-07

Table S410.  Gene #72: 'Del Peak 23(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 23(11P15.5) CNV 3 16 73
DEL PEAK 23(11P15.5) WILD-TYPE 24 206 173

Figure S410.  Get High-res Image Gene #72: 'Del Peak 23(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 23(11p15.5)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.19e-06 (Fisher's exact test), Q value = 0.0031

Table S411.  Gene #72: 'Del Peak 23(11p15.5)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 23(11P15.5) CNV 58 12 15
DEL PEAK 23(11P15.5) WILD-TYPE 111 103 73

Figure S411.  Get High-res Image Gene #72: 'Del Peak 23(11p15.5)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 23(11p15.5)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.6e-09 (Fisher's exact test), Q value = 1.4e-06

Table S412.  Gene #72: 'Del Peak 23(11p15.5)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 23(11P15.5) CNV 22 13 48 2
DEL PEAK 23(11P15.5) WILD-TYPE 77 125 62 23

Figure S412.  Get High-res Image Gene #72: 'Del Peak 23(11p15.5)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 24(11q14.1)' versus 'CN_CNMF'

P value = 9.41e-23 (Chi-square test), Q value = 1e-19

Table S413.  Gene #73: 'Del Peak 24(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 24(11Q14.1) CNV 1 2 52 5 4 0
DEL PEAK 24(11Q14.1) WILD-TYPE 293 7 102 8 18 12

Figure S413.  Get High-res Image Gene #73: 'Del Peak 24(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(11q14.1)' versus 'METHLYATION_CNMF'

P value = 1.96e-10 (Fisher's exact test), Q value = 1.8e-07

Table S414.  Gene #73: 'Del Peak 24(11q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 24(11Q14.1) CNV 42 13 4
DEL PEAK 24(11Q14.1) WILD-TYPE 104 76 151

Figure S414.  Get High-res Image Gene #73: 'Del Peak 24(11q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 24(11q14.1)' versus 'MIRSEQ_CNMF'

P value = 3.26e-09 (Chi-square test), Q value = 2.9e-06

Table S415.  Gene #73: 'Del Peak 24(11q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 24(11Q14.1) CNV 41 8 6 5 3
DEL PEAK 24(11Q14.1) WILD-TYPE 108 121 43 48 112

Figure S415.  Get High-res Image Gene #73: 'Del Peak 24(11q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 24(11q14.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.88e-09 (Fisher's exact test), Q value = 1.7e-06

Table S416.  Gene #73: 'Del Peak 24(11q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 24(11Q14.1) CNV 1 8 54
DEL PEAK 24(11Q14.1) WILD-TYPE 26 214 192

Figure S416.  Get High-res Image Gene #73: 'Del Peak 24(11q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 24(11q14.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000391 (Fisher's exact test), Q value = 0.22

Table S417.  Gene #73: 'Del Peak 24(11q14.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 24(11Q14.1) CNV 40 8 11
DEL PEAK 24(11Q14.1) WILD-TYPE 129 107 77

Figure S417.  Get High-res Image Gene #73: 'Del Peak 24(11q14.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 24(11q14.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.07e-08 (Fisher's exact test), Q value = 2.6e-05

Table S418.  Gene #73: 'Del Peak 24(11q14.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 24(11Q14.1) CNV 13 8 37 1
DEL PEAK 24(11Q14.1) WILD-TYPE 86 130 73 24

Figure S418.  Get High-res Image Gene #73: 'Del Peak 24(11q14.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 25(11q25)' versus 'CN_CNMF'

P value = 8.68e-30 (Chi-square test), Q value = 9.6e-27

Table S419.  Gene #74: 'Del Peak 25(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 25(11Q25) CNV 4 3 70 5 6 0
DEL PEAK 25(11Q25) WILD-TYPE 290 6 84 8 16 12

Figure S419.  Get High-res Image Gene #74: 'Del Peak 25(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(11q25)' versus 'METHLYATION_CNMF'

P value = 4.12e-12 (Fisher's exact test), Q value = 4e-09

Table S420.  Gene #74: 'Del Peak 25(11q25)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 25(11Q25) CNV 56 14 9
DEL PEAK 25(11Q25) WILD-TYPE 90 75 146

Figure S420.  Get High-res Image Gene #74: 'Del Peak 25(11q25)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(11q25)' versus 'MIRSEQ_CNMF'

P value = 4.14e-09 (Chi-square test), Q value = 3.6e-06

Table S421.  Gene #74: 'Del Peak 25(11q25)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 25(11Q25) CNV 50 12 9 9 6
DEL PEAK 25(11Q25) WILD-TYPE 99 117 40 44 109

Figure S421.  Get High-res Image Gene #74: 'Del Peak 25(11q25)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(11q25)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.34e-12 (Fisher's exact test), Q value = 7.1e-09

Table S422.  Gene #74: 'Del Peak 25(11q25)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 25(11Q25) CNV 4 11 71
DEL PEAK 25(11Q25) WILD-TYPE 23 211 175

Figure S422.  Get High-res Image Gene #74: 'Del Peak 25(11q25)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(11q25)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.016

Table S423.  Gene #74: 'Del Peak 25(11q25)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 25(11Q25) CNV 52 10 17
DEL PEAK 25(11Q25) WILD-TYPE 117 105 71

Figure S423.  Get High-res Image Gene #74: 'Del Peak 25(11q25)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 25(11q25)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.64e-08 (Fisher's exact test), Q value = 4.7e-05

Table S424.  Gene #74: 'Del Peak 25(11q25)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 25(11Q25) CNV 21 11 43 4
DEL PEAK 25(11Q25) WILD-TYPE 78 127 67 21

Figure S424.  Get High-res Image Gene #74: 'Del Peak 25(11q25)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 26(12q23.1)' versus 'CN_CNMF'

P value = 7.34e-21 (Chi-square test), Q value = 7.9e-18

Table S425.  Gene #75: 'Del Peak 26(12q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 26(12Q23.1) CNV 0 2 47 1 1 1
DEL PEAK 26(12Q23.1) WILD-TYPE 294 7 107 12 21 11

Figure S425.  Get High-res Image Gene #75: 'Del Peak 26(12q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(12q23.1)' versus 'METHLYATION_CNMF'

P value = 3.21e-10 (Fisher's exact test), Q value = 2.9e-07

Table S426.  Gene #75: 'Del Peak 26(12q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 26(12Q23.1) CNV 33 10 1
DEL PEAK 26(12Q23.1) WILD-TYPE 113 79 154

Figure S426.  Get High-res Image Gene #75: 'Del Peak 26(12q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(12q23.1)' versus 'MIRSEQ_CNMF'

P value = 2.67e-07 (Chi-square test), Q value = 0.00021

Table S427.  Gene #75: 'Del Peak 26(12q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 26(12Q23.1) CNV 30 2 9 5 4
DEL PEAK 26(12Q23.1) WILD-TYPE 119 127 40 48 111

Figure S427.  Get High-res Image Gene #75: 'Del Peak 26(12q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 26(12q23.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.1e-11 (Fisher's exact test), Q value = 2e-08

Table S428.  Gene #75: 'Del Peak 26(12q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 26(12Q23.1) CNV 0 3 47
DEL PEAK 26(12Q23.1) WILD-TYPE 27 219 199

Figure S428.  Get High-res Image Gene #75: 'Del Peak 26(12q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(12q23.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.36e-05 (Fisher's exact test), Q value = 0.016

Table S429.  Gene #75: 'Del Peak 26(12q23.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 26(12Q23.1) CNV 30 2 12
DEL PEAK 26(12Q23.1) WILD-TYPE 139 113 76

Figure S429.  Get High-res Image Gene #75: 'Del Peak 26(12q23.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 26(12q23.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.21e-06 (Fisher's exact test), Q value = 0.00093

Table S430.  Gene #75: 'Del Peak 26(12q23.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 26(12Q23.1) CNV 17 2 22 3
DEL PEAK 26(12Q23.1) WILD-TYPE 82 136 88 22

Figure S430.  Get High-res Image Gene #75: 'Del Peak 26(12q23.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 27(12q24.33)' versus 'CN_CNMF'

P value = 8.32e-26 (Chi-square test), Q value = 9.1e-23

Table S431.  Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 27(12Q24.33) CNV 1 2 56 0 1 1
DEL PEAK 27(12Q24.33) WILD-TYPE 293 7 98 13 21 11

Figure S431.  Get High-res Image Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(12q24.33)' versus 'METHLYATION_CNMF'

P value = 5.68e-11 (Fisher's exact test), Q value = 5.3e-08

Table S432.  Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 27(12Q24.33) CNV 41 12 3
DEL PEAK 27(12Q24.33) WILD-TYPE 105 77 152

Figure S432.  Get High-res Image Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 27(12q24.33)' versus 'MRNASEQ_CNMF'

P value = 3.86e-05 (Fisher's exact test), Q value = 0.026

Table S433.  Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 27(12Q24.33) CNV 23 3 4
DEL PEAK 27(12Q24.33) WILD-TYPE 26 33 29

Figure S433.  Get High-res Image Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 27(12q24.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.03e-05 (Fisher's exact test), Q value = 0.057

Table S434.  Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 27(12Q24.33) CNV 21 7 2
DEL PEAK 27(12Q24.33) WILD-TYPE 25 29 34

Figure S434.  Get High-res Image Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(12q24.33)' versus 'MIRSEQ_CNMF'

P value = 1.12e-11 (Chi-square test), Q value = 1.1e-08

Table S435.  Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 27(12Q24.33) CNV 41 3 8 4 3
DEL PEAK 27(12Q24.33) WILD-TYPE 108 126 41 49 112

Figure S435.  Get High-res Image Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 27(12q24.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.33e-11 (Fisher's exact test), Q value = 1.3e-08

Table S436.  Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 27(12Q24.33) CNV 2 4 53
DEL PEAK 27(12Q24.33) WILD-TYPE 25 218 193

Figure S436.  Get High-res Image Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(12q24.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.92e-07 (Fisher's exact test), Q value = 0.00016

Table S437.  Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 27(12Q24.33) CNV 42 3 11
DEL PEAK 27(12Q24.33) WILD-TYPE 127 112 77

Figure S437.  Get High-res Image Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 27(12q24.33)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.53e-07 (Fisher's exact test), Q value = 0.00013

Table S438.  Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 27(12Q24.33) CNV 17 4 30 5
DEL PEAK 27(12Q24.33) WILD-TYPE 82 134 80 20

Figure S438.  Get High-res Image Gene #76: 'Del Peak 27(12q24.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 28(13q11)' versus 'CN_CNMF'

P value = 3.76e-30 (Chi-square test), Q value = 4.2e-27

Table S439.  Gene #77: 'Del Peak 28(13q11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 28(13Q11) CNV 3 3 70 5 8 1
DEL PEAK 28(13Q11) WILD-TYPE 291 6 84 8 14 11

Figure S439.  Get High-res Image Gene #77: 'Del Peak 28(13q11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(13q11)' versus 'METHLYATION_CNMF'

P value = 3.45e-08 (Fisher's exact test), Q value = 2.9e-05

Table S440.  Gene #77: 'Del Peak 28(13q11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 28(13Q11) CNV 47 19 10
DEL PEAK 28(13Q11) WILD-TYPE 99 70 145

Figure S440.  Get High-res Image Gene #77: 'Del Peak 28(13q11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 28(13q11)' versus 'MIRSEQ_CNMF'

P value = 5.13e-08 (Chi-square test), Q value = 4.3e-05

Table S441.  Gene #77: 'Del Peak 28(13q11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 28(13Q11) CNV 49 13 11 9 7
DEL PEAK 28(13Q11) WILD-TYPE 100 116 38 44 108

Figure S441.  Get High-res Image Gene #77: 'Del Peak 28(13q11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 28(13q11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.95e-08 (Fisher's exact test), Q value = 2.5e-05

Table S442.  Gene #77: 'Del Peak 28(13q11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 28(13Q11) CNV 7 16 66
DEL PEAK 28(13Q11) WILD-TYPE 20 206 180

Figure S442.  Get High-res Image Gene #77: 'Del Peak 28(13q11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(13q14.2)' versus 'CN_CNMF'

P value = 2.46e-33 (Chi-square test), Q value = 2.7e-30

Table S443.  Gene #78: 'Del Peak 29(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 29(13Q14.2) CNV 4 5 76 4 8 1
DEL PEAK 29(13Q14.2) WILD-TYPE 290 4 78 9 14 11

Figure S443.  Get High-res Image Gene #78: 'Del Peak 29(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(13q14.2)' versus 'METHLYATION_CNMF'

P value = 7.57e-07 (Fisher's exact test), Q value = 0.00059

Table S444.  Gene #78: 'Del Peak 29(13q14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 29(13Q14.2) CNV 48 23 14
DEL PEAK 29(13Q14.2) WILD-TYPE 98 66 141

Figure S444.  Get High-res Image Gene #78: 'Del Peak 29(13q14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 29(13q14.2)' versus 'MIRSEQ_CNMF'

P value = 1.06e-08 (Chi-square test), Q value = 9.2e-06

Table S445.  Gene #78: 'Del Peak 29(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 29(13Q14.2) CNV 53 17 9 12 6
DEL PEAK 29(13Q14.2) WILD-TYPE 96 112 40 41 109

Figure S445.  Get High-res Image Gene #78: 'Del Peak 29(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 29(13q14.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.38e-08 (Fisher's exact test), Q value = 3.7e-05

Table S446.  Gene #78: 'Del Peak 29(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 29(13Q14.2) CNV 8 19 70
DEL PEAK 29(13Q14.2) WILD-TYPE 19 203 176

Figure S446.  Get High-res Image Gene #78: 'Del Peak 29(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(14q13.1)' versus 'CN_CNMF'

P value = 3.4e-24 (Chi-square test), Q value = 3.7e-21

Table S447.  Gene #79: 'Del Peak 30(14q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 30(14Q13.1) CNV 2 0 55 5 2 1
DEL PEAK 30(14Q13.1) WILD-TYPE 292 9 99 8 20 11

Figure S447.  Get High-res Image Gene #79: 'Del Peak 30(14q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(14q13.1)' versus 'METHLYATION_CNMF'

P value = 2.7e-10 (Fisher's exact test), Q value = 2.5e-07

Table S448.  Gene #79: 'Del Peak 30(14q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 30(14Q13.1) CNV 43 7 6
DEL PEAK 30(14Q13.1) WILD-TYPE 103 82 149

Figure S448.  Get High-res Image Gene #79: 'Del Peak 30(14q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 30(14q13.1)' versus 'MIRSEQ_CNMF'

P value = 7.68e-08 (Chi-square test), Q value = 6.4e-05

Table S449.  Gene #79: 'Del Peak 30(14q13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 30(14Q13.1) CNV 38 4 8 8 6
DEL PEAK 30(14Q13.1) WILD-TYPE 111 125 41 45 109

Figure S449.  Get High-res Image Gene #79: 'Del Peak 30(14q13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 30(14q13.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.37e-10 (Fisher's exact test), Q value = 1.3e-07

Table S450.  Gene #79: 'Del Peak 30(14q13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 30(14Q13.1) CNV 3 6 55
DEL PEAK 30(14Q13.1) WILD-TYPE 24 216 191

Figure S450.  Get High-res Image Gene #79: 'Del Peak 30(14q13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(14q13.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.022

Table S451.  Gene #79: 'Del Peak 30(14q13.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 30(14Q13.1) CNV 39 5 14
DEL PEAK 30(14Q13.1) WILD-TYPE 130 110 74

Figure S451.  Get High-res Image Gene #79: 'Del Peak 30(14q13.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 30(14q13.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.23e-06 (Fisher's exact test), Q value = 0.0053

Table S452.  Gene #79: 'Del Peak 30(14q13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 30(14Q13.1) CNV 16 7 31 4
DEL PEAK 30(14Q13.1) WILD-TYPE 83 131 79 21

Figure S452.  Get High-res Image Gene #79: 'Del Peak 30(14q13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 31(15q15.1)' versus 'CN_CNMF'

P value = 1.6e-55 (Chi-square test), Q value = 1.8e-52

Table S453.  Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 31(15Q15.1) CNV 4 3 110 4 8 0
DEL PEAK 31(15Q15.1) WILD-TYPE 290 6 44 9 14 12

Figure S453.  Get High-res Image Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(15q15.1)' versus 'METHLYATION_CNMF'

P value = 1.4e-16 (Fisher's exact test), Q value = 1.4e-13

Table S454.  Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 31(15Q15.1) CNV 74 27 12
DEL PEAK 31(15Q15.1) WILD-TYPE 72 62 143

Figure S454.  Get High-res Image Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 31(15q15.1)' versus 'MRNASEQ_CNMF'

P value = 6.98e-10 (Fisher's exact test), Q value = 6.2e-07

Table S455.  Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 31(15Q15.1) CNV 38 6 7
DEL PEAK 31(15Q15.1) WILD-TYPE 11 30 26

Figure S455.  Get High-res Image Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(15q15.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.72e-08 (Fisher's exact test), Q value = 2.3e-05

Table S456.  Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 31(15Q15.1) CNV 35 10 6
DEL PEAK 31(15Q15.1) WILD-TYPE 11 26 30

Figure S456.  Get High-res Image Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_CNMF'

P value = 3.58e-22 (Chi-square test), Q value = 3.9e-19

Table S457.  Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 31(15Q15.1) CNV 80 11 18 10 8
DEL PEAK 31(15Q15.1) WILD-TYPE 69 118 31 43 107

Figure S457.  Get High-res Image Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.43e-17 (Fisher's exact test), Q value = 1.5e-14

Table S458.  Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 31(15Q15.1) CNV 8 17 102
DEL PEAK 31(15Q15.1) WILD-TYPE 19 205 144

Figure S458.  Get High-res Image Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.88e-07 (Fisher's exact test), Q value = 0.00015

Table S459.  Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 31(15Q15.1) CNV 68 13 29
DEL PEAK 31(15Q15.1) WILD-TYPE 101 102 59

Figure S459.  Get High-res Image Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.96e-09 (Fisher's exact test), Q value = 6.1e-06

Table S460.  Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 31(15Q15.1) CNV 37 16 50 7
DEL PEAK 31(15Q15.1) WILD-TYPE 62 122 60 18

Figure S460.  Get High-res Image Gene #80: 'Del Peak 31(15q15.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 32(15q23)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.13

Table S461.  Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 32(15Q23) CNV 0 0 6
DEL PEAK 32(15Q23) WILD-TYPE 19 19 9

Figure S461.  Get High-res Image Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 32(15q23)' versus 'CN_CNMF'

P value = 2.43e-43 (Chi-square test), Q value = 2.8e-40

Table S462.  Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 32(15Q23) CNV 3 2 91 4 6 0
DEL PEAK 32(15Q23) WILD-TYPE 291 7 63 9 16 12

Figure S462.  Get High-res Image Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(15q23)' versus 'METHLYATION_CNMF'

P value = 1.32e-17 (Fisher's exact test), Q value = 1.4e-14

Table S463.  Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 32(15Q23) CNV 67 18 7
DEL PEAK 32(15Q23) WILD-TYPE 79 71 148

Figure S463.  Get High-res Image Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 32(15q23)' versus 'MRNASEQ_CNMF'

P value = 4.34e-10 (Fisher's exact test), Q value = 3.9e-07

Table S464.  Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 32(15Q23) CNV 36 5 5
DEL PEAK 32(15Q23) WILD-TYPE 13 31 28

Figure S464.  Get High-res Image Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(15q23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.4e-08 (Fisher's exact test), Q value = 7e-05

Table S465.  Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 32(15Q23) CNV 32 10 4
DEL PEAK 32(15Q23) WILD-TYPE 14 26 32

Figure S465.  Get High-res Image Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(15q23)' versus 'MIRSEQ_CNMF'

P value = 1.65e-19 (Chi-square test), Q value = 1.8e-16

Table S466.  Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 32(15Q23) CNV 69 8 12 10 5
DEL PEAK 32(15Q23) WILD-TYPE 80 121 37 43 110

Figure S466.  Get High-res Image Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 32(15q23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.27e-15 (Fisher's exact test), Q value = 9.4e-12

Table S467.  Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 32(15Q23) CNV 6 13 85
DEL PEAK 32(15Q23) WILD-TYPE 21 209 161

Figure S467.  Get High-res Image Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(15q23)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.77e-08 (Fisher's exact test), Q value = 1.5e-05

Table S468.  Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 32(15Q23) CNV 63 9 18
DEL PEAK 32(15Q23) WILD-TYPE 106 106 70

Figure S468.  Get High-res Image Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 32(15q23)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.82e-10 (Fisher's exact test), Q value = 3.5e-07

Table S469.  Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 32(15Q23) CNV 24 11 49 6
DEL PEAK 32(15Q23) WILD-TYPE 75 127 61 19

Figure S469.  Get High-res Image Gene #81: 'Del Peak 32(15q23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 33(16p13.3)' versus 'CN_CNMF'

P value = 1.91e-34 (Chi-square test), Q value = 2.1e-31

Table S470.  Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 33(16P13.3) CNV 2 1 74 3 3 0
DEL PEAK 33(16P13.3) WILD-TYPE 292 8 80 10 19 12

Figure S470.  Get High-res Image Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 33(16p13.3)' versus 'METHLYATION_CNMF'

P value = 3.67e-14 (Fisher's exact test), Q value = 3.7e-11

Table S471.  Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 33(16P13.3) CNV 52 18 4
DEL PEAK 33(16P13.3) WILD-TYPE 94 71 151

Figure S471.  Get High-res Image Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 33(16p13.3)' versus 'MRNASEQ_CNMF'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.013

Table S472.  Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 33(16P13.3) CNV 26 5 4
DEL PEAK 33(16P13.3) WILD-TYPE 23 31 29

Figure S472.  Get High-res Image Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 33(16p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.93e-06 (Fisher's exact test), Q value = 0.0065

Table S473.  Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 33(16P13.3) CNV 25 7 3
DEL PEAK 33(16P13.3) WILD-TYPE 21 29 33

Figure S473.  Get High-res Image Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(16p13.3)' versus 'MIRSEQ_CNMF'

P value = 5.62e-16 (Chi-square test), Q value = 5.8e-13

Table S474.  Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 33(16P13.3) CNV 57 7 7 5 5
DEL PEAK 33(16P13.3) WILD-TYPE 92 122 42 48 110

Figure S474.  Get High-res Image Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 33(16p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.52e-14 (Fisher's exact test), Q value = 2.5e-11

Table S475.  Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 33(16P13.3) CNV 4 7 70
DEL PEAK 33(16P13.3) WILD-TYPE 23 215 176

Figure S475.  Get High-res Image Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 33(16p13.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.86e-05 (Fisher's exact test), Q value = 0.019

Table S476.  Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 33(16P13.3) CNV 47 8 18
DEL PEAK 33(16P13.3) WILD-TYPE 122 107 70

Figure S476.  Get High-res Image Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 33(16p13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.58e-07 (Fisher's exact test), Q value = 0.00013

Table S477.  Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 33(16P13.3) CNV 25 8 36 4
DEL PEAK 33(16P13.3) WILD-TYPE 74 130 74 21

Figure S477.  Get High-res Image Gene #82: 'Del Peak 33(16p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 34(16q21)' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.062

Table S478.  Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 34(16Q21) CNV 0 1 8
DEL PEAK 34(16Q21) WILD-TYPE 19 18 7

Figure S478.  Get High-res Image Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 34(16q21)' versus 'CN_CNMF'

P value = 7.21e-54 (Chi-square test), Q value = 8.3e-51

Table S479.  Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 34(16Q21) CNV 14 4 117 3 5 0
DEL PEAK 34(16Q21) WILD-TYPE 280 5 37 10 17 12

Figure S479.  Get High-res Image Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 34(16q21)' versus 'METHLYATION_CNMF'

P value = 4.16e-17 (Fisher's exact test), Q value = 4.3e-14

Table S480.  Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 34(16Q21) CNV 80 29 15
DEL PEAK 34(16Q21) WILD-TYPE 66 60 140

Figure S480.  Get High-res Image Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 34(16q21)' versus 'MRNASEQ_CNMF'

P value = 7.11e-07 (Fisher's exact test), Q value = 0.00056

Table S481.  Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 34(16Q21) CNV 34 6 9
DEL PEAK 34(16Q21) WILD-TYPE 15 30 24

Figure S481.  Get High-res Image Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 34(16q21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.04e-07 (Fisher's exact test), Q value = 4e-04

Table S482.  Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 34(16Q21) CNV 33 9 7
DEL PEAK 34(16Q21) WILD-TYPE 13 27 29

Figure S482.  Get High-res Image Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(16q21)' versus 'MIRSEQ_CNMF'

P value = 1.12e-19 (Chi-square test), Q value = 1.2e-16

Table S483.  Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 34(16Q21) CNV 85 16 14 11 13
DEL PEAK 34(16Q21) WILD-TYPE 64 113 35 42 102

Figure S483.  Get High-res Image Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 34(16q21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.61e-13 (Fisher's exact test), Q value = 1.6e-10

Table S484.  Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 34(16Q21) CNV 6 27 106
DEL PEAK 34(16Q21) WILD-TYPE 21 195 140

Figure S484.  Get High-res Image Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(16q21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.25e-07 (Fisher's exact test), Q value = 0.00026

Table S485.  Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 34(16Q21) CNV 76 17 29
DEL PEAK 34(16Q21) WILD-TYPE 93 98 59

Figure S485.  Get High-res Image Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 34(16q21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.42e-10 (Fisher's exact test), Q value = 1.3e-07

Table S486.  Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 34(16Q21) CNV 34 19 60 9
DEL PEAK 34(16Q21) WILD-TYPE 65 119 50 16

Figure S486.  Get High-res Image Gene #83: 'Del Peak 34(16q21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 35(16q23.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000377 (Fisher's exact test), Q value = 0.22

Table S487.  Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 35(16Q23.1) CNV 1 2 9
DEL PEAK 35(16Q23.1) WILD-TYPE 18 17 6

Figure S487.  Get High-res Image Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 35(16q23.1)' versus 'CN_CNMF'

P value = 6.89e-54 (Chi-square test), Q value = 7.9e-51

Table S488.  Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 35(16Q23.1) CNV 19 4 122 3 6 0
DEL PEAK 35(16Q23.1) WILD-TYPE 275 5 32 10 16 12

Figure S488.  Get High-res Image Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(16q23.1)' versus 'METHLYATION_CNMF'

P value = 3.63e-18 (Fisher's exact test), Q value = 3.8e-15

Table S489.  Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 35(16Q23.1) CNV 84 30 16
DEL PEAK 35(16Q23.1) WILD-TYPE 62 59 139

Figure S489.  Get High-res Image Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 35(16q23.1)' versus 'MRNASEQ_CNMF'

P value = 6.31e-08 (Fisher's exact test), Q value = 5.3e-05

Table S490.  Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 35(16Q23.1) CNV 37 7 9
DEL PEAK 35(16Q23.1) WILD-TYPE 12 29 24

Figure S490.  Get High-res Image Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(16q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.74e-07 (Fisher's exact test), Q value = 0.00014

Table S491.  Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 35(16Q23.1) CNV 35 11 7
DEL PEAK 35(16Q23.1) WILD-TYPE 11 25 29

Figure S491.  Get High-res Image Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(16q23.1)' versus 'MIRSEQ_CNMF'

P value = 1.06e-18 (Chi-square test), Q value = 1.1e-15

Table S492.  Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 35(16Q23.1) CNV 87 17 17 12 16
DEL PEAK 35(16Q23.1) WILD-TYPE 62 112 32 41 99

Figure S492.  Get High-res Image Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 35(16q23.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.49e-16 (Fisher's exact test), Q value = 2.6e-13

Table S493.  Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 35(16Q23.1) CNV 5 28 116
DEL PEAK 35(16Q23.1) WILD-TYPE 22 194 130

Figure S493.  Get High-res Image Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 35(16q23.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.89e-08 (Fisher's exact test), Q value = 7.4e-05

Table S494.  Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 35(16Q23.1) CNV 78 17 33
DEL PEAK 35(16Q23.1) WILD-TYPE 91 98 55

Figure S494.  Get High-res Image Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 35(16q23.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.24e-11 (Fisher's exact test), Q value = 1.2e-08

Table S495.  Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 35(16Q23.1) CNV 41 18 60 9
DEL PEAK 35(16Q23.1) WILD-TYPE 58 120 50 16

Figure S495.  Get High-res Image Gene #84: 'Del Peak 35(16q23.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 36(17p13.3)' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.062

Table S496.  Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 36(17P13.3) CNV 1 0 8
DEL PEAK 36(17P13.3) WILD-TYPE 18 19 7

Figure S496.  Get High-res Image Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(17p13.3)' versus 'CN_CNMF'

P value = 3.27e-48 (Chi-square test), Q value = 3.7e-45

Table S497.  Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 36(17P13.3) CNV 3 2 98 3 7 0
DEL PEAK 36(17P13.3) WILD-TYPE 291 7 56 10 15 12

Figure S497.  Get High-res Image Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 36(17p13.3)' versus 'METHLYATION_CNMF'

P value = 4.12e-10 (Fisher's exact test), Q value = 3.7e-07

Table S498.  Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 36(17P13.3) CNV 58 23 13
DEL PEAK 36(17P13.3) WILD-TYPE 88 66 142

Figure S498.  Get High-res Image Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 36(17p13.3)' versus 'MRNASEQ_CNMF'

P value = 2.07e-07 (Fisher's exact test), Q value = 0.00017

Table S499.  Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 36(17P13.3) CNV 30 2 12
DEL PEAK 36(17P13.3) WILD-TYPE 19 34 21

Figure S499.  Get High-res Image Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 36(17p13.3)' versus 'MIRSEQ_CNMF'

P value = 3.16e-14 (Chi-square test), Q value = 3.2e-11

Table S500.  Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 36(17P13.3) CNV 67 15 11 9 8
DEL PEAK 36(17P13.3) WILD-TYPE 82 114 38 44 107

Figure S500.  Get High-res Image Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 36(17p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.48e-09 (Fisher's exact test), Q value = 3.9e-06

Table S501.  Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 36(17P13.3) CNV 8 22 80
DEL PEAK 36(17P13.3) WILD-TYPE 19 200 166

Figure S501.  Get High-res Image Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 36(17p13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.38e-05 (Fisher's exact test), Q value = 0.029

Table S502.  Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 36(17P13.3) CNV 24 18 43 6
DEL PEAK 36(17P13.3) WILD-TYPE 75 120 67 19

Figure S502.  Get High-res Image Gene #85: 'Del Peak 36(17p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 37(17p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.062

Table S503.  Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 37(17P11.2) CNV 1 0 8
DEL PEAK 37(17P11.2) WILD-TYPE 18 19 7

Figure S503.  Get High-res Image Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 37(17p11.2)' versus 'CN_CNMF'

P value = 9.94e-57 (Chi-square test), Q value = 1.1e-53

Table S504.  Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 37(17P11.2) CNV 3 0 108 3 7 0
DEL PEAK 37(17P11.2) WILD-TYPE 291 9 46 10 15 12

Figure S504.  Get High-res Image Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 37(17p11.2)' versus 'METHLYATION_CNMF'

P value = 1.26e-13 (Fisher's exact test), Q value = 1.3e-10

Table S505.  Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 37(17P11.2) CNV 68 23 13
DEL PEAK 37(17P11.2) WILD-TYPE 78 66 142

Figure S505.  Get High-res Image Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(17p11.2)' versus 'MRNASEQ_CNMF'

P value = 3.38e-06 (Fisher's exact test), Q value = 0.0025

Table S506.  Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 37(17P11.2) CNV 31 4 12
DEL PEAK 37(17P11.2) WILD-TYPE 18 32 21

Figure S506.  Get High-res Image Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 37(17p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S507.  Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 37(17P11.2) CNV 30 7 10
DEL PEAK 37(17P11.2) WILD-TYPE 16 29 26

Figure S507.  Get High-res Image Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(17p11.2)' versus 'MIRSEQ_CNMF'

P value = 8.33e-19 (Chi-square test), Q value = 8.9e-16

Table S508.  Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 37(17P11.2) CNV 75 15 12 8 7
DEL PEAK 37(17P11.2) WILD-TYPE 74 114 37 45 108

Figure S508.  Get High-res Image Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 37(17p11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.01e-12 (Fisher's exact test), Q value = 7.7e-09

Table S509.  Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 37(17P11.2) CNV 6 21 90
DEL PEAK 37(17P11.2) WILD-TYPE 21 201 156

Figure S509.  Get High-res Image Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 37(17p11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.01

Table S510.  Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 37(17P11.2) CNV 31 19 45 6
DEL PEAK 37(17P11.2) WILD-TYPE 68 119 65 19

Figure S510.  Get High-res Image Gene #86: 'Del Peak 37(17p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 38(17p11.2)' versus 'MRNA_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.069

Table S511.  Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 38(17P11.2) CNV 0 8 0 0
DEL PEAK 38(17P11.2) WILD-TYPE 14 9 12 10

Figure S511.  Get High-res Image Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 38(17p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 7.26e-06 (Fisher's exact test), Q value = 0.0054

Table S512.  Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 38(17P11.2) CNV 0 0 8
DEL PEAK 38(17P11.2) WILD-TYPE 19 19 7

Figure S512.  Get High-res Image Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(17p11.2)' versus 'CN_CNMF'

P value = 1.39e-52 (Chi-square test), Q value = 1.6e-49

Table S513.  Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 38(17P11.2) CNV 1 0 100 3 7 0
DEL PEAK 38(17P11.2) WILD-TYPE 293 9 54 10 15 12

Figure S513.  Get High-res Image Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 38(17p11.2)' versus 'METHLYATION_CNMF'

P value = 5.35e-13 (Fisher's exact test), Q value = 5.3e-10

Table S514.  Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 38(17P11.2) CNV 63 23 11
DEL PEAK 38(17P11.2) WILD-TYPE 83 66 144

Figure S514.  Get High-res Image Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 38(17p11.2)' versus 'MRNASEQ_CNMF'

P value = 7.44e-07 (Fisher's exact test), Q value = 0.00059

Table S515.  Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 38(17P11.2) CNV 30 3 9
DEL PEAK 38(17P11.2) WILD-TYPE 19 33 24

Figure S515.  Get High-res Image Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 38(17p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000144 (Fisher's exact test), Q value = 0.087

Table S516.  Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 38(17P11.2) CNV 27 6 9
DEL PEAK 38(17P11.2) WILD-TYPE 19 30 27

Figure S516.  Get High-res Image Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(17p11.2)' versus 'MIRSEQ_CNMF'

P value = 1.38e-16 (Chi-square test), Q value = 1.4e-13

Table S517.  Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 38(17P11.2) CNV 69 14 11 7 7
DEL PEAK 38(17P11.2) WILD-TYPE 80 115 38 46 108

Figure S517.  Get High-res Image Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 38(17p11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.22e-10 (Fisher's exact test), Q value = 2.9e-07

Table S518.  Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 38(17P11.2) CNV 6 20 82
DEL PEAK 38(17P11.2) WILD-TYPE 21 202 164

Figure S518.  Get High-res Image Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 38(17p11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000203 (Fisher's exact test), Q value = 0.12

Table S519.  Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 38(17P11.2) CNV 58 15 22
DEL PEAK 38(17P11.2) WILD-TYPE 111 100 66

Figure S519.  Get High-res Image Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 38(17p11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.02e-06 (Fisher's exact test), Q value = 0.0059

Table S520.  Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 38(17P11.2) CNV 28 17 44 6
DEL PEAK 38(17P11.2) WILD-TYPE 71 121 66 19

Figure S520.  Get High-res Image Gene #87: 'Del Peak 38(17p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 39(17q11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.028

Table S521.  Gene #88: 'Del Peak 39(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 39(17Q11.2) CNV 0 0 7
DEL PEAK 39(17Q11.2) WILD-TYPE 19 19 8

Figure S521.  Get High-res Image Gene #88: 'Del Peak 39(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 39(17q11.2)' versus 'CN_CNMF'

P value = 2.65e-42 (Chi-square test), Q value = 3e-39

Table S522.  Gene #88: 'Del Peak 39(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 39(17Q11.2) CNV 2 1 86 1 8 0
DEL PEAK 39(17Q11.2) WILD-TYPE 292 8 68 12 14 12

Figure S522.  Get High-res Image Gene #88: 'Del Peak 39(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 39(17q11.2)' versus 'METHLYATION_CNMF'

P value = 1.18e-06 (Fisher's exact test), Q value = 0.00091

Table S523.  Gene #88: 'Del Peak 39(17q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 39(17Q11.2) CNV 48 21 14
DEL PEAK 39(17Q11.2) WILD-TYPE 98 68 141

Figure S523.  Get High-res Image Gene #88: 'Del Peak 39(17q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 39(17q11.2)' versus 'MIRSEQ_CNMF'

P value = 8.12e-12 (Chi-square test), Q value = 7.8e-09

Table S524.  Gene #88: 'Del Peak 39(17q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 39(17Q11.2) CNV 58 14 8 7 7
DEL PEAK 39(17Q11.2) WILD-TYPE 91 115 41 46 108

Figure S524.  Get High-res Image Gene #88: 'Del Peak 39(17q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 39(17q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.81e-06 (Fisher's exact test), Q value = 0.0064

Table S525.  Gene #88: 'Del Peak 39(17q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 39(17Q11.2) CNV 6 22 66
DEL PEAK 39(17Q11.2) WILD-TYPE 21 200 180

Figure S525.  Get High-res Image Gene #88: 'Del Peak 39(17q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 40(17q21.2)' versus 'MRNA_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.016

Table S526.  Gene #89: 'Del Peak 40(17q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 40(17Q21.2) CNV 0 9 0 0
DEL PEAK 40(17Q21.2) WILD-TYPE 14 8 12 10

Figure S526.  Get High-res Image Gene #89: 'Del Peak 40(17q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(17q21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00088

Table S527.  Gene #89: 'Del Peak 40(17q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 40(17Q21.2) CNV 0 0 9
DEL PEAK 40(17Q21.2) WILD-TYPE 19 19 6

Figure S527.  Get High-res Image Gene #89: 'Del Peak 40(17q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(17q21.2)' versus 'CN_CNMF'

P value = 2.56e-49 (Chi-square test), Q value = 2.9e-46

Table S528.  Gene #89: 'Del Peak 40(17q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 40(17Q21.2) CNV 1 0 94 1 8 0
DEL PEAK 40(17Q21.2) WILD-TYPE 293 9 60 12 14 12

Figure S528.  Get High-res Image Gene #89: 'Del Peak 40(17q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(17q21.2)' versus 'METHLYATION_CNMF'

P value = 2.96e-08 (Fisher's exact test), Q value = 2.5e-05

Table S529.  Gene #89: 'Del Peak 40(17q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 40(17Q21.2) CNV 53 24 14
DEL PEAK 40(17Q21.2) WILD-TYPE 93 65 141

Figure S529.  Get High-res Image Gene #89: 'Del Peak 40(17q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 40(17q21.2)' versus 'MIRSEQ_CNMF'

P value = 5.41e-15 (Chi-square test), Q value = 5.5e-12

Table S530.  Gene #89: 'Del Peak 40(17q21.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 40(17Q21.2) CNV 64 15 7 7 6
DEL PEAK 40(17Q21.2) WILD-TYPE 85 114 42 46 109

Figure S530.  Get High-res Image Gene #89: 'Del Peak 40(17q21.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 40(17q21.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.12e-07 (Fisher's exact test), Q value = 0.00017

Table S531.  Gene #89: 'Del Peak 40(17q21.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 40(17Q21.2) CNV 6 21 72
DEL PEAK 40(17Q21.2) WILD-TYPE 21 201 174

Figure S531.  Get High-res Image Gene #89: 'Del Peak 40(17q21.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 41(18q23)' versus 'CN_CNMF'

P value = 6.53e-33 (Chi-square test), Q value = 7.3e-30

Table S532.  Gene #90: 'Del Peak 41(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 41(18Q23) CNV 2 3 74 4 8 1
DEL PEAK 41(18Q23) WILD-TYPE 292 6 80 9 14 11

Figure S532.  Get High-res Image Gene #90: 'Del Peak 41(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 41(18q23)' versus 'METHLYATION_CNMF'

P value = 5.64e-11 (Fisher's exact test), Q value = 5.3e-08

Table S533.  Gene #90: 'Del Peak 41(18q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 41(18Q23) CNV 55 15 10
DEL PEAK 41(18Q23) WILD-TYPE 91 74 145

Figure S533.  Get High-res Image Gene #90: 'Del Peak 41(18q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 41(18q23)' versus 'MIRSEQ_CNMF'

P value = 3.05e-11 (Chi-square test), Q value = 2.9e-08

Table S534.  Gene #90: 'Del Peak 41(18q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 41(18Q23) CNV 55 12 10 6 7
DEL PEAK 41(18Q23) WILD-TYPE 94 117 39 47 108

Figure S534.  Get High-res Image Gene #90: 'Del Peak 41(18q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 41(18q23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.93e-10 (Fisher's exact test), Q value = 5.3e-07

Table S535.  Gene #90: 'Del Peak 41(18q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 41(18Q23) CNV 7 14 69
DEL PEAK 41(18Q23) WILD-TYPE 20 208 177

Figure S535.  Get High-res Image Gene #90: 'Del Peak 41(18q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 41(18q23)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.07e-05 (Fisher's exact test), Q value = 0.045

Table S536.  Gene #90: 'Del Peak 41(18q23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 41(18Q23) CNV 25 13 35 6
DEL PEAK 41(18Q23) WILD-TYPE 74 125 75 19

Figure S536.  Get High-res Image Gene #90: 'Del Peak 41(18q23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 42(19p13.3)' versus 'MRNA_CNMF'

P value = 9.09e-06 (Fisher's exact test), Q value = 0.0066

Table S537.  Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 42(19P13.3) CNV 1 11 0 0
DEL PEAK 42(19P13.3) WILD-TYPE 13 6 12 10

Figure S537.  Get High-res Image Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 42(19p13.3)' versus 'MRNA_CHIERARCHICAL'

P value = 1.96e-07 (Fisher's exact test), Q value = 0.00016

Table S538.  Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 42(19P13.3) CNV 1 0 11
DEL PEAK 42(19P13.3) WILD-TYPE 18 19 4

Figure S538.  Get High-res Image Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 42(19p13.3)' versus 'CN_CNMF'

P value = 1.78e-78 (Chi-square test), Q value = 2.1e-75

Table S539.  Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 42(19P13.3) CNV 0 3 133 3 6 0
DEL PEAK 42(19P13.3) WILD-TYPE 294 6 21 10 16 12

Figure S539.  Get High-res Image Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 42(19p13.3)' versus 'METHLYATION_CNMF'

P value = 5.06e-30 (Fisher's exact test), Q value = 5.6e-27

Table S540.  Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 42(19P13.3) CNV 93 25 7
DEL PEAK 42(19P13.3) WILD-TYPE 53 64 148

Figure S540.  Get High-res Image Gene #91: '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 = 0.0066

Table S541.  Gene #91: '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 S541.  Get High-res Image Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 42(19p13.3)' versus 'MRNASEQ_CNMF'

P value = 6.31e-08 (Fisher's exact test), Q value = 5.3e-05

Table S542.  Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 42(19P13.3) CNV 37 7 9
DEL PEAK 42(19P13.3) WILD-TYPE 12 29 24

Figure S542.  Get High-res Image Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 42(19p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.57e-07 (Fisher's exact test), Q value = 0.00029

Table S543.  Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 42(19P13.3) CNV 34 13 6
DEL PEAK 42(19P13.3) WILD-TYPE 12 23 30

Figure S543.  Get High-res Image Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 2.53e-32 (Chi-square test), Q value = 2.8e-29

Table S544.  Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 42(19P13.3) CNV 97 10 16 6 11
DEL PEAK 42(19P13.3) WILD-TYPE 52 119 33 47 104

Figure S544.  Get High-res Image Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 42(19p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.65e-24 (Fisher's exact test), Q value = 2.9e-21

Table S545.  Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 42(19P13.3) CNV 5 16 119
DEL PEAK 42(19P13.3) WILD-TYPE 22 206 127

Figure S545.  Get High-res Image Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 42(19p13.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.29e-11 (Fisher's exact test), Q value = 4e-08

Table S546.  Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 42(19P13.3) CNV 81 12 29
DEL PEAK 42(19P13.3) WILD-TYPE 88 103 59

Figure S546.  Get High-res Image Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 42(19p13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.52e-17 (Fisher's exact test), Q value = 2.6e-14

Table S547.  Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 42(19P13.3) CNV 36 13 67 6
DEL PEAK 42(19P13.3) WILD-TYPE 63 125 43 19

Figure S547.  Get High-res Image Gene #91: 'Del Peak 42(19p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 43(19p12)' versus 'CN_CNMF'

P value = 4.55e-17 (Chi-square test), Q value = 4.7e-14

Table S548.  Gene #92: 'Del Peak 43(19p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 43(19P12) CNV 1 4 38 3 5 0
DEL PEAK 43(19P12) WILD-TYPE 293 5 116 10 17 12

Figure S548.  Get High-res Image Gene #92: 'Del Peak 43(19p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 43(19p12)' versus 'METHLYATION_CNMF'

P value = 1.21e-07 (Fisher's exact test), Q value = 1e-04

Table S549.  Gene #92: 'Del Peak 43(19p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 43(19P12) CNV 31 11 3
DEL PEAK 43(19P12) WILD-TYPE 115 78 152

Figure S549.  Get High-res Image Gene #92: 'Del Peak 43(19p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 43(19p12)' versus 'MIRSEQ_CNMF'

P value = 5.16e-06 (Chi-square test), Q value = 0.0038

Table S550.  Gene #92: 'Del Peak 43(19p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 43(19P12) CNV 31 5 5 5 4
DEL PEAK 43(19P12) WILD-TYPE 118 124 44 48 111

Figure S550.  Get High-res Image Gene #92: 'Del Peak 43(19p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 43(19p12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.44e-08 (Fisher's exact test), Q value = 7e-05

Table S551.  Gene #92: 'Del Peak 43(19p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 43(19P12) CNV 3 5 42
DEL PEAK 43(19P12) WILD-TYPE 24 217 204

Figure S551.  Get High-res Image Gene #92: 'Del Peak 43(19p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 43(19p12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.18e-05 (Fisher's exact test), Q value = 0.028

Table S552.  Gene #92: 'Del Peak 43(19p12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 43(19P12) CNV 9 6 26 4
DEL PEAK 43(19P12) WILD-TYPE 90 132 84 21

Figure S552.  Get High-res Image Gene #92: 'Del Peak 43(19p12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 44(19q13.43)' versus 'MRNA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.062

Table S553.  Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 44(19Q13.43) CNV 1 0 8
DEL PEAK 44(19Q13.43) WILD-TYPE 18 19 7

Figure S553.  Get High-res Image Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 44(19q13.43)' versus 'CN_CNMF'

P value = 3.38e-20 (Chi-square test), Q value = 3.6e-17

Table S554.  Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 44(19Q13.43) CNV 2 2 50 2 4 0
DEL PEAK 44(19Q13.43) WILD-TYPE 292 7 104 11 18 12

Figure S554.  Get High-res Image Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(19q13.43)' versus 'METHLYATION_CNMF'

P value = 7.49e-10 (Fisher's exact test), Q value = 6.7e-07

Table S555.  Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 44(19Q13.43) CNV 35 12 2
DEL PEAK 44(19Q13.43) WILD-TYPE 111 77 153

Figure S555.  Get High-res Image Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 44(19q13.43)' versus 'MIRSEQ_CNMF'

P value = 1.23e-10 (Chi-square test), Q value = 1.1e-07

Table S556.  Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 44(19Q13.43) CNV 40 4 4 3 5
DEL PEAK 44(19Q13.43) WILD-TYPE 109 125 45 50 110

Figure S556.  Get High-res Image Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 44(19q13.43)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.22e-11 (Fisher's exact test), Q value = 3e-08

Table S557.  Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 44(19Q13.43) CNV 1 4 51
DEL PEAK 44(19Q13.43) WILD-TYPE 26 218 195

Figure S557.  Get High-res Image Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 44(19q13.43)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.16e-05 (Fisher's exact test), Q value = 0.021

Table S558.  Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 44(19Q13.43) CNV 32 3 15
DEL PEAK 44(19Q13.43) WILD-TYPE 137 112 73

Figure S558.  Get High-res Image Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 44(19q13.43)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.1e-06 (Fisher's exact test), Q value = 0.00086

Table S559.  Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 44(19Q13.43) CNV 20 3 23 4
DEL PEAK 44(19Q13.43) WILD-TYPE 79 135 87 21

Figure S559.  Get High-res Image Gene #93: 'Del Peak 44(19q13.43)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 45(20p12.1)' versus 'CN_CNMF'

P value = 3.56e-05 (Chi-square test), Q value = 0.024

Table S560.  Gene #94: 'Del Peak 45(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 45(20P12.1) CNV 5 2 20 2 2 1
DEL PEAK 45(20P12.1) WILD-TYPE 289 7 134 11 20 11

Figure S560.  Get High-res Image Gene #94: 'Del Peak 45(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 46(22q12.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.13

Table S561.  Gene #95: 'Del Peak 46(22q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 46(22Q12.1) CNV 0 0 6
DEL PEAK 46(22Q12.1) WILD-TYPE 19 19 9

Figure S561.  Get High-res Image Gene #95: 'Del Peak 46(22q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 46(22q12.1)' versus 'CN_CNMF'

P value = 1.72e-33 (Chi-square test), Q value = 1.9e-30

Table S562.  Gene #95: 'Del Peak 46(22q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 46(22Q12.1) CNV 4 0 75 3 7 0
DEL PEAK 46(22Q12.1) WILD-TYPE 290 9 79 10 15 12

Figure S562.  Get High-res Image Gene #95: 'Del Peak 46(22q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 46(22q12.1)' versus 'METHLYATION_CNMF'

P value = 8.49e-05 (Fisher's exact test), Q value = 0.054

Table S563.  Gene #95: 'Del Peak 46(22q12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 46(22Q12.1) CNV 41 22 15
DEL PEAK 46(22Q12.1) WILD-TYPE 105 67 140

Figure S563.  Get High-res Image Gene #95: 'Del Peak 46(22q12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 46(22q12.1)' versus 'MIRSEQ_CNMF'

P value = 4.51e-11 (Chi-square test), Q value = 4.2e-08

Table S564.  Gene #95: 'Del Peak 46(22q12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 46(22Q12.1) CNV 53 18 5 8 3
DEL PEAK 46(22Q12.1) WILD-TYPE 96 111 44 45 112

Figure S564.  Get High-res Image Gene #95: 'Del Peak 46(22q12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 46(22q12.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.034

Table S565.  Gene #95: 'Del Peak 46(22q12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 46(22Q12.1) CNV 6 21 60
DEL PEAK 46(22Q12.1) WILD-TYPE 21 201 186

Figure S565.  Get High-res Image Gene #95: 'Del Peak 46(22q12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 47(22q13.31)' versus 'MRNA_CNMF'

P value = 3.62e-06 (Fisher's exact test), Q value = 0.0027

Table S566.  Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 47(22Q13.31) CNV 0 10 0 0
DEL PEAK 47(22Q13.31) WILD-TYPE 14 7 12 10

Figure S566.  Get High-res Image Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 47(22q13.31)' versus 'MRNA_CHIERARCHICAL'

P value = 1.54e-07 (Fisher's exact test), Q value = 0.00013

Table S567.  Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 47(22Q13.31) CNV 0 0 10
DEL PEAK 47(22Q13.31) WILD-TYPE 19 19 5

Figure S567.  Get High-res Image Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 47(22q13.31)' versus 'CN_CNMF'

P value = 2.19e-57 (Chi-square test), Q value = 2.5e-54

Table S568.  Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 47(22Q13.31) CNV 4 1 111 3 7 0
DEL PEAK 47(22Q13.31) WILD-TYPE 290 8 43 10 15 12

Figure S568.  Get High-res Image Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 47(22q13.31)' versus 'METHLYATION_CNMF'

P value = 1.79e-12 (Fisher's exact test), Q value = 1.8e-09

Table S569.  Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 47(22Q13.31) CNV 68 26 15
DEL PEAK 47(22Q13.31) WILD-TYPE 78 63 140

Figure S569.  Get High-res Image Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 47(22q13.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000438 (Fisher's exact test), Q value = 0.25

Table S570.  Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 47(22Q13.31) CNV 29 9 10
DEL PEAK 47(22Q13.31) WILD-TYPE 17 27 26

Figure S570.  Get High-res Image Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 47(22q13.31)' versus 'MIRSEQ_CNMF'

P value = 1.11e-18 (Chi-square test), Q value = 1.2e-15

Table S571.  Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 47(22Q13.31) CNV 77 17 11 8 8
DEL PEAK 47(22Q13.31) WILD-TYPE 72 112 38 45 107

Figure S571.  Get High-res Image Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 47(22q13.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.86e-12 (Fisher's exact test), Q value = 3.8e-09

Table S572.  Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 47(22Q13.31) CNV 6 22 93
DEL PEAK 47(22Q13.31) WILD-TYPE 21 200 153

Figure S572.  Get High-res Image Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 47(22q13.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.16

Table S573.  Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 47(22Q13.31) CNV 63 18 24
DEL PEAK 47(22Q13.31) WILD-TYPE 106 97 64

Figure S573.  Get High-res Image Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 47(22q13.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.42e-06 (Fisher's exact test), Q value = 0.0011

Table S574.  Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 47(22Q13.31) CNV 30 21 50 4
DEL PEAK 47(22Q13.31) WILD-TYPE 69 117 60 21

Figure S574.  Get High-res Image Gene #96: 'Del Peak 47(22q13.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 48(22q13.32)' versus 'MRNA_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.016

Table S575.  Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 17 12 10
DEL PEAK 48(22Q13.32) CNV 0 9 0 0
DEL PEAK 48(22Q13.32) WILD-TYPE 14 8 12 10

Figure S575.  Get High-res Image Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 48(22q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00088

Table S576.  Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 48(22Q13.32) CNV 0 0 9
DEL PEAK 48(22Q13.32) WILD-TYPE 19 19 6

Figure S576.  Get High-res Image Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 48(22q13.32)' versus 'CN_CNMF'

P value = 1.3e-55 (Chi-square test), Q value = 1.5e-52

Table S577.  Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 48(22Q13.32) CNV 8 1 113 3 7 0
DEL PEAK 48(22Q13.32) WILD-TYPE 286 8 41 10 15 12

Figure S577.  Get High-res Image Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 48(22q13.32)' versus 'METHLYATION_CNMF'

P value = 2.52e-11 (Fisher's exact test), Q value = 2.4e-08

Table S578.  Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 48(22Q13.32) CNV 69 29 18
DEL PEAK 48(22Q13.32) WILD-TYPE 77 60 137

Figure S578.  Get High-res Image Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 48(22q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000311 (Fisher's exact test), Q value = 0.18

Table S579.  Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
DEL PEAK 48(22Q13.32) CNV 30 9 11
DEL PEAK 48(22Q13.32) WILD-TYPE 16 27 25

Figure S579.  Get High-res Image Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 48(22q13.32)' versus 'MIRSEQ_CNMF'

P value = 2.51e-19 (Chi-square test), Q value = 2.7e-16

Table S580.  Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 48(22Q13.32) CNV 80 19 12 10 7
DEL PEAK 48(22Q13.32) WILD-TYPE 69 110 37 43 108

Figure S580.  Get High-res Image Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 48(22q13.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.53e-12 (Fisher's exact test), Q value = 7.2e-09

Table S581.  Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 48(22Q13.32) CNV 6 25 97
DEL PEAK 48(22Q13.32) WILD-TYPE 21 197 149

Figure S581.  Get High-res Image Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 48(22q13.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000428 (Fisher's exact test), Q value = 0.24

Table S582.  Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
DEL PEAK 48(22Q13.32) CNV 67 21 24
DEL PEAK 48(22Q13.32) WILD-TYPE 102 94 64

Figure S582.  Get High-res Image Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 48(22q13.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.89e-06 (Fisher's exact test), Q value = 0.0036

Table S583.  Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 48(22Q13.32) CNV 31 24 52 5
DEL PEAK 48(22Q13.32) WILD-TYPE 68 114 58 20

Figure S583.  Get High-res Image Gene #97: 'Del Peak 48(22q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 49(Xp21.1)' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.028

Table S584.  Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
DEL PEAK 49(XP21.1) CNV 0 0 7
DEL PEAK 49(XP21.1) WILD-TYPE 19 19 8

Figure S584.  Get High-res Image Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 49(Xp21.1)' versus 'CN_CNMF'

P value = 8.78e-34 (Chi-square test), Q value = 9.8e-31

Table S585.  Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
DEL PEAK 49(XP21.1) CNV 2 2 74 2 5 0
DEL PEAK 49(XP21.1) WILD-TYPE 292 7 80 11 17 12

Figure S585.  Get High-res Image Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 49(Xp21.1)' versus 'METHLYATION_CNMF'

P value = 2.03e-08 (Fisher's exact test), Q value = 1.7e-05

Table S586.  Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
DEL PEAK 49(XP21.1) CNV 46 17 9
DEL PEAK 49(XP21.1) WILD-TYPE 100 72 146

Figure S586.  Get High-res Image Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 49(Xp21.1)' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.14

Table S587.  Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
DEL PEAK 49(XP21.1) CNV 25 5 6
DEL PEAK 49(XP21.1) WILD-TYPE 24 31 27

Figure S587.  Get High-res Image Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 49(Xp21.1)' versus 'MIRSEQ_CNMF'

P value = 2.62e-13 (Chi-square test), Q value = 2.6e-10

Table S588.  Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
DEL PEAK 49(XP21.1) CNV 55 9 6 5 7
DEL PEAK 49(XP21.1) WILD-TYPE 94 120 43 48 108

Figure S588.  Get High-res Image Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 49(Xp21.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.4e-09 (Fisher's exact test), Q value = 1.2e-06

Table S589.  Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
DEL PEAK 49(XP21.1) CNV 7 12 63
DEL PEAK 49(XP21.1) WILD-TYPE 20 210 183

Figure S589.  Get High-res Image Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 49(Xp21.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.2e-05 (Fisher's exact test), Q value = 0.015

Table S590.  Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
DEL PEAK 49(XP21.1) CNV 21 12 36 3
DEL PEAK 49(XP21.1) WILD-TYPE 78 126 74 22

Figure S590.  Get High-res Image Gene #98: 'Del Peak 49(Xp21.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_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 = 504

  • Number of copy number variation regions = 98

  • Number of molecular subtypes = 12

  • 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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