Correlation between copy number variation genes and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1S46Q7P
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/C1S46Q7P
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 70 peak regions and 12 molecular subtypes across 985 patients, 621 significant findings detected with Q value < 0.25.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • Del Peak 4(3p14.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

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

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

  • Del Peak 16(9p23) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Del Peak 17(9p21.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 18(9q21.11) cnvs correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 19(9q34.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 20(10q23.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 21(10q26.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 22(11p15.5) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 23(11q13.1) cnvs correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • Del Peak 24(11q23.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • Del Peak 26(12p13.1) cnvs correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 27(12q24.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 28(13q11) 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 29(13q14.2) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 30(14q24.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 31(15q13.1) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 32(16q24.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 33(17p12) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Del Peak 34(17q21.31) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 35(18q23) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • Del Peak 36(19p13.3) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 37(19q13.32) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 38(20p13) cnvs correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • Del Peak 39(21q11.2) cnvs correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • Del Peak 40(22q11.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • Del Peak 41(22q13.31) cnvs correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 70 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 621 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Chi-square test Fisher's exact test Chi-square test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
Amp Peak 1(1p22 3) 0 (0%) 763 4.05e-14
(2.51e-11) 		3.63e-12
(2.08e-09) 		2.66e-17
(1.79e-14) 		1.09e-18
(7.51e-16) 		0.000139
(0.036) 		1.28e-07
(5.46e-05) 		8.31e-24
(6.3e-21) 		1.79e-19
(1.27e-16) 		4.18e-20
(3e-17) 		2.15e-20
(1.55e-17) 		4.39e-14
(2.72e-11) 		3.56e-12
(2.04e-09)
Amp Peak 5(3q26 32) 0 (0%) 675 5.51e-11
(2.91e-08) 		4.13e-11
(2.2e-08) 		8.19e-38
(6.64e-35) 		1.06e-19
(7.56e-17) 		7.16e-07
(0.000277) 		2.92e-06
(0.00102) 		1.78e-27
(1.39e-24) 		1.61e-24
(1.23e-21) 		9.56e-27
(7.42e-24) 		9.78e-24
(7.41e-21) 		1.08e-18
(7.46e-16) 		6.44e-16
(4.22e-13)
Amp Peak 8(6p23) 0 (0%) 719 1.79e-07
(7.46e-05) 		1.45e-07
(6.09e-05) 		1.67e-38
(1.36e-35) 		2.46e-21
(1.8e-18) 		9.24e-07
(0.000352) 		4.4e-05
(0.0126) 		1.52e-20
(1.1e-17) 		1.54e-14
(9.62e-12) 		7.78e-20
(5.56e-17) 		2.05e-19
(1.45e-16) 		2.13e-13
(1.28e-10) 		7.19e-10
(3.6e-07)
Amp Peak 9(6q21) 0 (0%) 798 1.24e-13
(7.53e-11) 		5.33e-10
(2.7e-07) 		9.77e-49
(8.08e-46) 		6.63e-19
(4.61e-16) 		1.04e-08
(4.82e-06) 		4.64e-07
(0.000185) 		1.03e-28
(8.14e-26) 		6.84e-24
(5.2e-21) 		4.59e-26
(3.54e-23) 		2.41e-24
(1.83e-21) 		2.4e-18
(1.64e-15) 		5.36e-19
(3.74e-16)
Amp Peak 12(8q24 21) 0 (0%) 359 6.27e-16
(4.11e-13) 		1.89e-08
(8.5e-06) 		2.15e-50
(1.78e-47) 		1.15e-27
(9.05e-25) 		4.58e-08
(2e-05) 		9.36e-07
(0.000356) 		5.29e-30
(4.19e-27) 		9.61e-24
(7.29e-21) 		1.28e-28
(1e-25) 		2.62e-26
(2.03e-23) 		9.97e-24
(7.54e-21) 		1.04e-15
(6.74e-13)
Amp Peak 13(10p15 1) 0 (0%) 708 2.47e-21
(1.8e-18) 		5.89e-19
(4.1e-16) 		1.09e-43
(8.94e-41) 		1.53e-27
(1.2e-24) 		7e-11
(3.67e-08) 		2.33e-12
(1.35e-09) 		3.38e-37
(2.74e-34) 		6.77e-33
(5.38e-30) 		2.75e-33
(2.2e-30) 		5.26e-33
(4.19e-30) 		1.41e-18
(9.7e-16) 		4.98e-21
(3.62e-18)
Amp Peak 18(12p13 33) 0 (0%) 728 6.85e-12
(3.85e-09) 		9.63e-12
(5.38e-09) 		9.92e-34
(7.93e-31) 		2.38e-21
(1.74e-18) 		2.7e-08
(1.21e-05) 		2.37e-07
(9.69e-05) 		5.31e-27
(4.12e-24) 		2.66e-20
(1.91e-17) 		3.78e-22
(2.8e-19) 		1.21e-21
(8.88e-19) 		3.64e-20
(2.61e-17) 		5.94e-14
(3.66e-11)
Amp Peak 21(13q34) 0 (0%) 819 1.45e-09
(7.11e-07) 		2.67e-09
(1.29e-06) 		2.61e-19
(1.83e-16) 		6.52e-14
(4e-11) 		8.21e-06
(0.0027) 		5.1e-08
(2.22e-05) 		4.72e-20
(3.38e-17) 		7.98e-21
(5.8e-18) 		1.31e-22
(9.82e-20) 		1.69e-23
(1.28e-20) 		2.53e-11
(1.38e-08) 		4.44e-14
(2.74e-11)
Amp Peak 27(19q12) 0 (0%) 734 4.35e-12
(2.48e-09) 		9.44e-11
(4.92e-08) 		1.88e-27
(1.47e-24) 		1.29e-12
(7.54e-10) 		6.19e-07
(0.000242) 		9.68e-07
(0.000364) 		4.73e-23
(3.54e-20) 		1.94e-18
(1.33e-15) 		4.21e-18
(2.86e-15) 		6.62e-18
(4.49e-15) 		1.54e-12
(8.97e-10) 		1.31e-11
(7.22e-09)
Del Peak 3(2q37 3) 0 (0%) 702 1.51e-06
(0.000552) 		3.28e-09
(1.57e-06) 		2.31e-22
(1.72e-19) 		2.98e-11
(1.62e-08) 		1.03e-08
(4.78e-06) 		1.11e-07
(4.73e-05) 		1.63e-11
(9e-09) 		1.29e-11
(7.13e-09) 		6.95e-11
(3.65e-08) 		5.85e-10
(2.94e-07) 		1.73e-13
(1.05e-10) 		1.06e-05
(0.0034)
Del Peak 4(3p14 3) 0 (0%) 685 3.85e-11
(2.07e-08) 		5.41e-08
(2.34e-05) 		7.55e-35
(6.05e-32) 		3.98e-16
(2.62e-13) 		2.51e-09
(1.22e-06) 		1.08e-05
(0.00348) 		1.56e-19
(1.11e-16) 		3.75e-13
(2.25e-10) 		2.75e-16
(1.81e-13) 		3.92e-15
(2.48e-12) 		7.21e-11
(3.77e-08) 		2.58e-10
(1.32e-07)
Del Peak 5(4p16 3) 0 (0%) 679 2.7e-11
(1.47e-08) 		2.23e-11
(1.22e-08) 		3.94e-31
(3.13e-28) 		9.99e-13
(5.95e-10) 		4.6e-07
(0.000184) 		1.62e-06
(0.000591) 		2.63e-23
(1.98e-20) 		4.16e-23
(3.12e-20) 		1.56e-18
(1.07e-15) 		1.96e-18
(1.34e-15) 		3.36e-15
(2.14e-12) 		5.39e-15
(3.4e-12)
Del Peak 6(4q35 2) 0 (0%) 675 1.17e-06
(0.000436) 		1.24e-06
(0.00046) 		4.27e-40
(3.49e-37) 		6.31e-14
(3.87e-11) 		1.51e-08
(6.91e-06) 		1.78e-06
(0.000642) 		3.21e-23
(2.41e-20) 		6.74e-19
(4.68e-16) 		5.94e-19
(4.13e-16) 		1.19e-19
(8.46e-17) 		4.2e-15
(2.66e-12) 		2e-13
(1.21e-10)
Del Peak 7(5q11 2) 0 (0%) 729 2.5e-27
(1.95e-24) 		6.92e-25
(5.29e-22) 		3.86e-75
(3.24e-72) 		4.36e-44
(3.59e-41) 		3.33e-16
(2.19e-13) 		7.43e-19
(5.15e-16) 		7.27e-58
(6.07e-55) 		6.03e-54
(5.02e-51) 		1.55e-50
(1.28e-47) 		3.59e-55
(2.99e-52) 		3.49e-35
(2.8e-32) 		3.08e-36
(2.48e-33)
Del Peak 8(5q21 3) 0 (0%) 739 3.82e-29
(3.01e-26) 		2.12e-26
(1.64e-23) 		1.48e-87
(1.24e-84) 		8.44e-53
(7.01e-50) 		2.6e-15
(1.66e-12) 		8.97e-16
(5.82e-13) 		2.08e-66
(1.74e-63) 		1.21e-58
(1.01e-55) 		4.12e-56
(3.43e-53) 		2.13e-63
(1.78e-60) 		1.16e-39
(9.46e-37) 		5.97e-44
(4.92e-41)
Del Peak 19(9q34 2) 0 (0%) 720 1.35e-07
(5.7e-05) 		4.43e-08
(1.94e-05) 		1.98e-35
(1.6e-32) 		3.68e-22
(2.73e-19) 		2.47e-05
(0.00749) 		0.000733
(0.167) 		6.46e-26
(4.97e-23) 		1.02e-18
(7.04e-16) 		2.4e-23
(1.81e-20) 		3.26e-26
(2.52e-23) 		1.07e-16
(7.08e-14) 		6.17e-17
(4.11e-14)
Del Peak 20(10q23 31) 0 (0%) 702 2.45e-05
(0.00746) 		5.63e-05
(0.0158) 		4.87e-22
(3.6e-19) 		5.74e-12
(3.23e-09) 		1.9e-07
(7.88e-05) 		7.37e-05
(0.0204) 		2.1e-15
(1.34e-12) 		1.06e-12
(6.32e-10) 		3.72e-11
(2e-08) 		2.82e-14
(1.76e-11) 		7.76e-10
(3.87e-07) 		6.77e-09
(3.18e-06)
Del Peak 21(10q26 3) 0 (0%) 698 1.01e-08
(4.68e-06) 		2.75e-07
(0.000112) 		3.2e-25
(2.45e-22) 		8.14e-14
(4.98e-11) 		3.06e-08
(1.36e-05) 		8.25e-07
(0.000316) 		3.22e-20
(2.31e-17) 		1.86e-17
(1.25e-14) 		7.44e-15
(4.67e-12) 		2.12e-19
(1.49e-16) 		1.12e-12
(6.64e-10) 		5.7e-12
(3.22e-09)
Del Peak 22(11p15 5) 0 (0%) 704 3.55e-07
(0.000144) 		2.1e-07
(8.68e-05) 		1.89e-36
(1.53e-33) 		4.7e-14
(2.89e-11) 		1.27e-09
(6.26e-07) 		1.65e-06
(6e-04) 		4.07e-17
(2.73e-14) 		3.46e-15
(2.19e-12) 		1.8e-19
(1.28e-16) 		3.48e-17
(2.34e-14) 		2.07e-13
(1.25e-10) 		1.6e-12
(9.28e-10)
Del Peak 27(12q24 31) 0 (0%) 806 5.25e-10
(2.66e-07) 		8.48e-10
(4.21e-07) 		1.48e-22
(1.1e-19) 		5.16e-19
(3.61e-16) 		1.14e-05
(0.00365) 		7.45e-07
(0.000287) 		4.41e-19
(3.09e-16) 		1.84e-17
(1.24e-14) 		5.64e-12
(3.19e-09) 		2.4e-13
(1.45e-10) 		1.41e-09
(6.9e-07) 		7.62e-11
(3.98e-08)
Del Peak 30(14q24 1) 0 (0%) 674 1.18e-13
(7.18e-11) 		1.61e-08
(7.36e-06) 		2.98e-40
(2.43e-37) 		9.21e-19
(6.37e-16) 		4.19e-07
(0.000168) 		3.69e-06
(0.00126) 		2.75e-33
(2.2e-30) 		2.53e-21
(1.84e-18) 		6.54e-22
(4.82e-19) 		4.97e-24
(3.79e-21) 		2.66e-18
(1.81e-15) 		1.14e-14
(7.11e-12)
Del Peak 31(15q13 1) 0 (0%) 649 4.93e-07
(0.000196) 		1.62e-07
(6.81e-05) 		1.24e-42
(1.02e-39) 		2.91e-14
(1.81e-11) 		0.000193
(0.0487) 		2.32e-05
(0.0071) 		1.6e-21
(1.17e-18) 		2.48e-20
(1.79e-17) 		8.06e-21
(5.84e-18) 		1.89e-21
(1.39e-18) 		2.65e-17
(1.78e-14) 		7.67e-16
(4.99e-13)
Del Peak 32(16q24 3) 0 (0%) 352 9.32e-17
(6.21e-14) 		2.67e-14
(1.67e-11) 		1.26e-12
(7.38e-10) 		3.67e-12
(2.1e-09) 		1.14e-09
(5.67e-07) 		3.45e-11
(1.86e-08) 		2.38e-29
(1.88e-26) 		1.35e-24
(1.03e-21) 		1.43e-18
(9.85e-16) 		4.01e-22
(2.96e-19) 		2.6e-12
(1.5e-09) 		6.38e-13
(3.81e-10)
Del Peak 34(17q21 31) 0 (0%) 645 1.97e-15
(1.26e-12) 		2.29e-07
(9.4e-05) 		1.64e-26
(1.27e-23) 		8.14e-14
(4.98e-11) 		1.86e-11
(1.02e-08) 		3.12e-11
(1.7e-08) 		2.01e-35
(1.61e-32) 		8.06e-21
(5.84e-18) 		4.9e-15
(3.1e-12) 		1.5e-12
(8.75e-10) 		1.24e-12
(7.28e-10) 		3.07e-12
(1.76e-09)
Del Peak 36(19p13 3) 0 (0%) 660 5.5e-11
(2.91e-08) 		2.25e-08
(1.01e-05) 		1.92e-48
(1.59e-45) 		1.44e-21
(1.06e-18) 		4.63e-06
(0.00156) 		2.02e-05
(0.00624) 		3.43e-27
(2.67e-24) 		3.27e-19
(2.3e-16) 		1.01e-25
(7.78e-23) 		3.83e-28
(3e-25) 		5.14e-17
(3.43e-14) 		7.53e-12
(4.22e-09)
Del Peak 37(19q13 32) 0 (0%) 792 8.89e-07
(0.00034) 		1.37e-05
(0.00426) 		2.29e-21
(1.68e-18) 		6.73e-11
(3.54e-08) 		0.000783
(0.176) 		4.95e-05
(0.0141) 		6.95e-15
(4.38e-12) 		1.03e-12
(6.12e-10) 		2.97e-14
(1.84e-11) 		8.49e-16
(5.52e-13) 		5.55e-12
(3.14e-09) 		7.55e-10
(3.77e-07)
Amp Peak 26(19p13 12) 0 (0%) 778 6.52e-06
(0.00217) 		5.01e-05
(0.0142) 		1.96e-15
(1.26e-12) 		2.18e-06
(0.000775) 		0.000125
(0.0329) 		0.00163
(0.348) 		4.1e-11
(2.19e-08) 		6.64e-08
(2.87e-05) 		1.62e-08
(7.38e-06) 		3.58e-10
(1.82e-07) 		4.53e-06
(0.00154) 		7.44e-06
(0.00246)
Amp Peak 29(20q13 2) 0 (0%) 488 1.81e-10
(9.33e-08) 		3.67e-05
(0.0107) 		4.55e-51
(3.78e-48) 		3.2e-23
(2.4e-20) 		0.000604
(0.141) 		0.0154
(1.00) 		1.88e-18
(1.29e-15) 		1.57e-12
(9.16e-10) 		1.19e-12
(7.04e-10) 		3.96e-11
(2.12e-08) 		3.08e-08
(1.37e-05) 		0.000451
(0.107)
Amp Peak 6(4q13 3) 0 (0%) 835 3.22e-05
(0.00948) 		4.19e-05
(0.0121) 		1.7e-17
(1.15e-14) 		3.03e-05
(0.00893) 		0.0313
(1.00) 		0.424
(1.00) 		3.3e-11
(1.78e-08) 		3.72e-07
(0.00015) 		4.34e-08
(1.9e-05) 		3.86e-11
(2.07e-08) 		5.52e-05
(0.0155) 		9.68e-05
(0.0259)
Del Peak 12(7p22 3) 0 (0%) 860 0.00104
(0.23) 		7.95e-05
(0.0215) 		1.52e-15
(9.81e-13) 		1.63e-08
(7.42e-06) 		0.0214
(1.00) 		0.00553
(1.00) 		3.96e-10
(2.01e-07) 		5.97e-10
(3e-07) 		1.24e-12
(7.29e-10) 		1.1e-12
(6.54e-10) 		3.51e-09
(1.68e-06) 		5.25e-06
(0.00176)
Del Peak 14(8p23 2) 0 (0%) 473 1.61e-09
(7.87e-07) 		9.89e-06
(0.0032) 		1.02e-33
(8.18e-31) 		2.07e-13
(1.25e-10) 		0.00955
(1.00) 		0.0341
(1.00) 		1.9e-19
(1.34e-16) 		2.61e-12
(1.5e-09) 		1.11e-12
(6.56e-10) 		1.37e-15
(8.85e-13) 		3.98e-08
(1.75e-05) 		2.97e-07
(0.000121)
Del Peak 17(9p21 3) 0 (0%) 658 2e-06
(0.000716) 		4.31e-05
(0.0124) 		3.26e-38
(2.65e-35) 		1.01e-16
(6.75e-14) 		0.00341
(0.672) 		0.444
(1.00) 		1.5e-16
(9.9e-14) 		1.74e-10
(8.98e-08) 		1.22e-10
(6.32e-08) 		2.47e-13
(1.49e-10) 		1.17e-05
(0.00372) 		8.14e-05
(0.0219)
Del Peak 18(9q21 11) 0 (0%) 722 0.0061
(1.00) 		2.17e-05
(0.00667) 		3.73e-22
(2.76e-19) 		1.3e-11
(7.18e-09) 		1.04e-05
(0.00336) 		0.00653
(1.00) 		5.21e-11
(2.76e-08) 		6.26e-09
(2.95e-06) 		4.95e-12
(2.81e-09) 		7.39e-15
(4.65e-12) 		5.32e-07
(0.000209) 		9.63e-07
(0.000363)
Del Peak 28(13q11) 0 (0%) 595 9.2e-05
(0.0246) 		0.000958
(0.215) 		4.27e-31
(3.39e-28) 		6.93e-09
(3.25e-06) 		0.14
(1.00) 		0.171
(1.00) 		7.18e-09
(3.35e-06) 		1.23e-09
(6.07e-07) 		1.66e-06
(0.000602) 		2.15e-06
(0.000768) 		2.66e-08
(1.19e-05) 		4.51e-06
(0.00153)
Del Peak 29(13q14 2) 0 (0%) 538 6.7e-05
(0.0186) 		2.5e-05
(0.00756) 		7.35e-41
(6.03e-38) 		1.31e-08
(6e-06) 		0.538
(1.00) 		0.111
(1.00) 		7.76e-10
(3.87e-07) 		1.15e-09
(5.7e-07) 		1.99e-09
(9.71e-07) 		5.25e-09
(2.5e-06) 		8.03e-10
(3.99e-07) 		2.39e-06
(0.000847)
Del Peak 38(20p13) 0 (0%) 841 4.49e-06
(0.00153) 		6.53e-05
(0.0182) 		2.38e-16
(1.57e-13) 		4.52e-13
(2.7e-10) 		0.00154
(0.329) 		0.0119
(1.00) 		3.18e-15
(2.03e-12) 		1.07e-10
(5.55e-08) 		8.71e-15
(5.46e-12) 		1.36e-17
(9.2e-15) 		1.59e-10
(8.25e-08) 		5.8e-10
(2.92e-07)
Amp Peak 4(3p26 1) 0 (0%) 784 0.00647
(1.00) 		0.00103
(0.229) 		1.21e-16
(8.01e-14) 		7.63e-07
(0.000294) 		0.00573
(1.00) 		0.00869
(1.00) 		3.15e-08
(1.39e-05) 		3.08e-09
(1.48e-06) 		5.07e-11
(2.7e-08) 		5.89e-09
(2.79e-06) 		9.02e-06
(0.00294) 		0.000753
(0.171)
Amp Peak 23(15q26 3) 0 (0%) 808 4.52e-07
(0.000181) 		0.00285
(0.571) 		5.4e-16
(3.55e-13) 		0.000123
(0.0325) 		0.00028
(0.0689) 		0.0593
(1.00) 		6.56e-09
(3.09e-06) 		1.19e-06
(0.000442) 		1.02e-08
(4.75e-06) 		1.62e-10
(8.36e-08) 		0.00145
(0.312) 		0.000401
(0.0966)
Del Peak 16(9p23) 0 (0%) 691 6.98e-08
(3e-05) 		8.19e-06
(0.0027) 		6.67e-38
(5.42e-35) 		1.92e-19
(1.35e-16) 		0.0111
(1.00) 		0.446
(1.00) 		1.72e-19
(1.22e-16) 		1.09e-08
(5e-06) 		6.56e-07
(0.000256) 		2.34e-12
(1.35e-09) 		0.000127
(0.0331) 		0.0101
(1.00)
Amp Peak 7(5p15 33) 0 (0%) 628 0.012
(1.00) 		0.00281
(0.569) 		3.22e-22
(2.4e-19) 		7.05e-09
(3.3e-06) 		0.082
(1.00) 		0.581
(1.00) 		1.99e-06
(0.000713) 		3.03e-09
(1.47e-06) 		1.38e-07
(5.81e-05) 		7.8e-07
(0.000299) 		1.58e-05
(0.0049) 		3.63e-06
(0.00125)
Amp Peak 15(11p13) 0 (0%) 781 0.0761
(1.00) 		0.0212
(1.00) 		4.68e-17
(3.13e-14) 		5.19e-07
(0.000205) 		0.0728
(1.00) 		0.112
(1.00) 		2.26e-10
(1.16e-07) 		5.17e-07
(0.000205) 		3.84e-09
(1.83e-06) 		1.1e-11
(6.14e-09) 		7.39e-06
(0.00245) 		0.00011
(0.0291)
Amp Peak 17(11q14 1) 0 (0%) 739 0.007
(1.00) 		0.0697
(1.00) 		4.39e-19
(3.08e-16) 		0.000127
(0.0331) 		0.148
(1.00) 		0.199
(1.00) 		1.92e-06
(0.000691) 		8.31e-06
(0.00273) 		3.88e-07
(0.000156) 		1.4e-07
(5.88e-05) 		0.000146
(0.0376) 		0.000288
(0.0707)
Amp Peak 19(12q15) 0 (0%) 737 3.35e-07
(0.000136) 		5.01e-06
(0.00169) 		3.52e-29
(2.77e-26) 		1.54e-13
(9.39e-11) 		0.188
(1.00) 		0.0652
(1.00) 		1.28e-11
(7.13e-09) 		6.73e-07
(0.000262) 		3.8e-05
(0.0111) 		2.48e-06
(0.00087) 		0.00664
(1.00) 		0.00295
(0.585)
Amp Peak 25(17q23 1) 0 (0%) 588 6.72e-16
(4.4e-13) 		0.00033
(0.0802) 		1.11e-42
(9.1e-40) 		1.82e-10
(9.38e-08) 		0.191
(1.00) 		0.334
(1.00) 		4.86e-23
(3.64e-20) 		1.38e-06
(0.000505) 		3.21e-08
(1.42e-05) 		3.29e-11
(1.78e-08) 		0.00209
(0.438) 		0.037
(1.00)
Del Peak 1(1p36 13) 0 (0%) 578 7.82e-05
(0.0214) 		0.00012
(0.0319) 		7.61e-31
(6.03e-28) 		1.59e-12
(9.21e-10) 		0.00726
(1.00) 		0.0805
(1.00) 		5.3e-09
(2.52e-06) 		1.12e-06
(0.000422) 		2.49e-06
(0.00087) 		0.000166
(0.0424) 		0.00669
(1.00) 		0.119
(1.00)
Del Peak 15(8p11 21) 0 (0%) 797 0.000194
(0.0489) 		0.00476
(0.885) 		1.19e-12
(7.04e-10) 		0.0313
(1.00) 		0.0465
(1.00) 		0.0191
(1.00) 		1.79e-12
(1.04e-09) 		4.61e-05
(0.0131) 		9.37e-07
(0.000356) 		1.74e-07
(7.28e-05) 		1.32e-06
(0.000485) 		4.15e-05
(0.0121)
Del Peak 33(17p12) 0 (0%) 394 1.95e-11
(1.07e-08) 		0.168
(1.00) 		3.78e-27
(2.94e-24) 		1.69e-08
(7.65e-06) 		8.07e-05
(0.0218) 		0.00775
(1.00) 		6.36e-18
(4.32e-15) 		0.00257
(0.53) 		2.3e-06
(0.000818) 		9e-06
(0.00294) 		0.000325
(0.0792) 		0.00485
(0.897)
Del Peak 35(18q23) 0 (0%) 664 0.000183
(0.0464) 		0.0629
(1.00) 		7.46e-16
(4.86e-13) 		2.54e-10
(1.3e-07) 		0.00413
(0.788) 		0.581
(1.00) 		4.43e-12
(2.52e-09) 		7.5e-05
(0.0205) 		2.83e-05
(0.00845) 		2.01e-05
(0.00623) 		6.08e-07
(0.000238) 		0.00135
(0.293)
Amp Peak 14(10q22 3) 0 (0%) 846 9.27e-06
(0.00301) 		0.143
(1.00) 		2.25e-09
(1.1e-06) 		0.00276
(0.563) 		0.0025
(0.518) 		0.0211
(1.00) 		1.21e-11
(6.72e-09) 		5.46e-07
(0.000215) 		3.04e-06
(0.00105) 		0.00702
(1.00) 		1.18e-05
(0.00374) 		0.00066
(0.152)
Amp Peak 16(11q13 3) 0 (0%) 621 0.000715
(0.165) 		0.0117
(1.00) 		1.57e-40
(1.29e-37) 		2.92e-10
(1.49e-07) 		0.966
(1.00) 		0.146
(1.00) 		5.57e-10
(2.81e-07) 		0.000983
(0.219) 		0.000222
(0.0553) 		2.6e-05
(0.00781) 		0.0197
(1.00) 		0.272
(1.00)
Amp Peak 24(17q12) 0 (0%) 674 1.1e-15
(7.11e-13) 		1.34e-05
(0.00417) 		3.76e-36
(3.03e-33) 		7.95e-09
(3.7e-06) 		0.049
(1.00) 		0.00821
(1.00) 		8.01e-26
(6.16e-23) 		2.4e-05
(0.00732) 		0.00443
(0.837) 		3.76e-07
(0.000152) 		0.0487
(1.00) 		0.162
(1.00)
Amp Peak 28(19q13 42) 0 (0%) 736 0.00013
(0.0337) 		0.00267
(0.548) 		3.23e-15
(2.06e-12) 		3.02e-06
(0.00105) 		0.000605
(0.141) 		0.0197
(1.00) 		1.47e-06
(0.000537) 		0.00555
(1.00) 		0.000126
(0.0331) 		0.000427
(0.102) 		0.191
(1.00) 		0.46
(1.00)
Del Peak 13(7q36 1) 0 (0%) 801 0.00992
(1.00) 		0.022
(1.00) 		5.11e-11
(2.71e-08) 		0.0733
(1.00) 		0.551
(1.00) 		0.0562
(1.00) 		2.92e-05
(0.00867) 		0.00023
(0.0571) 		1.39e-08
(6.37e-06) 		1.33e-07
(5.63e-05) 		9.61e-07
(0.000363) 		2.43e-06
(0.000856)
Amp Peak 2(1q21 3) 0 (0%) 275 1.25e-06
(0.000462) 		0.000537
(0.127) 		5.14e-08
(2.23e-05) 		2.2e-07
(9.06e-05) 		0.0586
(1.00) 		0.00703
(1.00) 		2.9e-09
(1.4e-06) 		0.00468
(0.88) 		0.00171
(0.362) 		2.51e-05
(0.00756) 		0.00972
(1.00) 		0.0365
(1.00)
Amp Peak 22(14q21 1) 0 (0%) 786 7.91e-05
(0.0215) 		0.00208
(0.437) 		4.07e-13
(2.44e-10) 		2.93e-05
(0.00868) 		0.0823
(1.00) 		0.0385
(1.00) 		2.73e-08
(1.22e-05) 		1.11e-05
(0.00356) 		2.82e-05
(0.00842) 		0.0301
(1.00) 		0.098
(1.00) 		0.347
(1.00)
Del Peak 10(6q15) 0 (0%) 670 2.42e-06
(0.000856) 		0.00128
(0.281) 		4.52e-35
(3.63e-32) 		3.06e-09
(1.48e-06) 		0.456
(1.00) 		0.0875
(1.00) 		3.2e-11
(1.74e-08) 		4.15e-05
(0.0121) 		0.00187
(0.395) 		3.16e-06
(0.00109) 		0.0106
(1.00) 		0.00134
(0.293)
Del Peak 24(11q23 2) 0 (0%) 497 1.86e-07
(7.72e-05) 		0.0146
(1.00) 		5.01e-39
(4.08e-36) 		2.95e-14
(1.83e-11) 		0.992
(1.00) 		0.475
(1.00) 		1.68e-15
(1.08e-12) 		0.000753
(0.171) 		0.0172
(1.00) 		7.06e-07
(0.000274) 		0.0259
(1.00) 		0.11
(1.00)
Amp Peak 3(1q44) 0 (0%) 275 1.22e-05
(0.00384) 		0.102
(1.00) 		6.67e-08
(2.88e-05) 		1.17e-06
(0.000437) 		0.864
(1.00) 		0.324
(1.00) 		1.05e-08
(4.84e-06) 		0.924
(1.00) 		0.685
(1.00) 		0.000564
(0.133) 		0.27
(1.00) 		0.0664
(1.00)
Amp Peak 10(8p11 23) 0 (0%) 611 1.27e-06
(0.000468) 		0.00415
(0.789) 		3.96e-25
(3.03e-22) 		5.89e-11
(3.11e-08) 		0.0399
(1.00) 		0.00473
(0.884) 		8.74e-12
(4.9e-09) 		7.67e-08
(3.29e-05) 		0.342
(1.00) 		0.0292
(1.00) 		0.694
(1.00) 		0.276
(1.00)
Amp Peak 20(13q12 3) 0 (0%) 851 0.0686
(1.00) 		0.0395
(1.00) 		1.19e-05
(0.00374) 		0.0272
(1.00) 		0.0155
(1.00) 		0.142
(1.00) 		6.49e-06
(0.00217) 		4.48e-05
(0.0128) 		1.15e-05
(0.00366) 		5.11e-05
(0.0144) 		0.11
(1.00) 		0.127
(1.00)
Del Peak 2(1p22 1) 0 (0%) 660 0.00343
(0.672) 		0.000233
(0.0574) 		8.39e-21
(6.07e-18) 		1.31e-07
(5.58e-05) 		0.0231
(1.00) 		0.049
(1.00) 		3.47e-09
(1.66e-06) 		1.8e-08
(8.14e-06) 		0.00234
(0.486) 		0.00385
(0.747) 		0.368
(1.00) 		0.445
(1.00)
Del Peak 25(11q25) 0 (0%) 531 0.00072
(0.165) 		0.634
(1.00) 		2.14e-36
(1.73e-33) 		2.17e-11
(1.19e-08) 		0.126
(1.00) 		0.707
(1.00) 		1.37e-11
(7.58e-09) 		0.137
(1.00) 		0.0834
(1.00) 		7.44e-05
(0.0205) 		0.265
(1.00) 		0.337
(1.00)
Amp Peak 11(8p11 21) 0 (0%) 603 0.0516
(1.00) 		0.067
(1.00) 		1.79e-22
(1.33e-19) 		9.23e-08
(3.95e-05) 		0.791
(1.00) 		0.633
(1.00) 		2.27e-08
(1.02e-05) 		2.09e-07
(8.67e-05) 		0.0391
(1.00) 		0.00769
(1.00) 		0.00403
(0.774) 		0.0165
(1.00)
Del Peak 23(11q13 1) 0 (0%) 777 0.00395
(0.762) 		0.0958
(1.00) 		6.75e-16
(4.4e-13) 		4.04e-08
(1.77e-05) 		0.331
(1.00) 		0.393
(1.00) 		6.01e-09
(2.84e-06) 		0.000219
(0.0549) 		0.199
(1.00) 		0.091
(1.00) 		0.123
(1.00) 		0.13
(1.00)
Del Peak 26(12p13 1) 0 (0%) 818 0.0315
(1.00) 		0.0843
(1.00) 		0.0002
(0.0503) 		0.0175
(1.00) 		0.222
(1.00) 		0.042
(1.00) 		0.00902
(1.00) 		0.00285
(0.571) 		7.45e-05
(0.0205) 		4.48e-06
(0.00153) 		0.00142
(0.306) 		0.000504
(0.12)
Del Peak 39(21q11 2) 0 (0%) 793 0.000341
(0.0825) 		0.0505
(1.00) 		4.09e-12
(2.33e-09) 		1.32e-05
(0.00413) 		0.225
(1.00) 		0.502
(1.00) 		5.67e-06
(0.0019) 		0.023
(1.00) 		0.00364
(0.711) 		0.00284
(0.571) 		0.0271
(1.00) 		0.513
(1.00)
Del Peak 9(6p25 3) 0 (0%) 799 0.347
(1.00) 		0.449
(1.00) 		3.08e-08
(1.37e-05) 		0.000166
(0.0424) 		0.439
(1.00) 		0.597
(1.00) 		0.000615
(0.143) 		0.0281
(1.00) 		0.0578
(1.00) 		0.0845
(1.00) 		0.0185
(1.00) 		0.0151
(1.00)
Del Peak 11(6q27) 0 (0%) 653 0.0354
(1.00) 		0.368
(1.00) 		9.1e-16
(5.9e-13) 		0.00282
(0.57) 		0.0678
(1.00) 		0.675
(1.00) 		0.00108
(0.237) 		0.68
(1.00) 		0.111
(1.00) 		0.0324
(1.00) 		0.0649
(1.00) 		0.475
(1.00)
Del Peak 40(22q11 1) 0 (0%) 567 0.333
(1.00) 		0.314
(1.00) 		3.04e-06
(0.00105) 		0.000449
(0.107) 		0.226
(1.00) 		0.14
(1.00) 		0.299
(1.00) 		0.0129
(1.00) 		0.156
(1.00) 		0.55
(1.00) 		0.816
(1.00) 		0.793
(1.00)
Del Peak 41(22q13 31) 0 (0%) 532 0.21
(1.00) 		0.181
(1.00) 		2.21e-07
(9.07e-05) 		0.00531
(0.976) 		0.186
(1.00) 		0.0714
(1.00) 		0.0994
(1.00) 		0.0167
(1.00) 		0.063
(1.00) 		0.502
(1.00) 		0.661
(1.00) 		0.747
(1.00)
'Amp Peak 1(1p22.3)' versus 'MRNA_CNMF'

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

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

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

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

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

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

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

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

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

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

P value = 2.66e-17 (Chi-square test), Q value = 1.8e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 1(1P22.3) CNV 48 31 26 101 16
AMP PEAK 1(1P22.3) WILD-TYPE 326 201 53 151 32

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

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

P value = 1.09e-18 (Chi-square test), Q value = 7.5e-16

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 1(1P22.3) CNV 61 25 24 16 2 19
AMP PEAK 1(1P22.3) WILD-TYPE 48 130 82 120 42 94

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

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

P value = 0.000139 (Fisher's exact test), Q value = 0.036

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

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

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

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

P value = 1.28e-07 (Fisher's exact test), Q value = 5.5e-05

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

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

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

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

P value = 8.31e-24 (Chi-square test), Q value = 6.3e-21

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 1(1P22.3) CNV 90 11 47 37 27 5 1
AMP PEAK 1(1P22.3) WILD-TYPE 85 128 170 117 197 42 14

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

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

P value = 1.79e-19 (Fisher's exact test), Q value = 1.3e-16

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 1(1P22.3) CNV 32 108 78
AMP PEAK 1(1P22.3) WILD-TYPE 259 138 356

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

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

P value = 4.18e-20 (Fisher's exact test), Q value = 3e-17

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 1(1P22.3) CNV 38 60 121
AMP PEAK 1(1P22.3) WILD-TYPE 236 353 158

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

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

P value = 2.15e-20 (Fisher's exact test), Q value = 1.6e-17

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 1(1P22.3) CNV 104 71 44
AMP PEAK 1(1P22.3) WILD-TYPE 121 305 321

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

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

P value = 4.39e-14 (Fisher's exact test), Q value = 2.7e-11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 1(1P22.3) CNV 34 30 84
AMP PEAK 1(1P22.3) WILD-TYPE 216 180 112

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

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

P value = 3.56e-12 (Fisher's exact test), Q value = 2e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 1(1P22.3) CNV 25 45 78
AMP PEAK 1(1P22.3) WILD-TYPE 135 266 107

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

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

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

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

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

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

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

P value = 0.000537 (Fisher's exact test), Q value = 0.13

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

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

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

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

P value = 5.14e-08 (Chi-square test), Q value = 2.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 2(1Q21.3) CNV 238 171 76 193 32
AMP PEAK 2(1Q21.3) WILD-TYPE 136 61 3 59 16

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

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

P value = 2.2e-07 (Chi-square test), Q value = 9.1e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 2(1Q21.3) CNV 92 125 82 86 27 62
AMP PEAK 2(1Q21.3) WILD-TYPE 17 30 24 50 17 51

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

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

P value = 2.9e-09 (Chi-square test), Q value = 1.4e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 2(1Q21.3) CNV 150 83 177 113 137 31 10
AMP PEAK 2(1Q21.3) WILD-TYPE 25 56 40 41 87 16 5

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

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

P value = 2.51e-05 (Fisher's exact test), Q value = 0.0076

Table S18.  Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 2(1Q21.3) CNV 185 271 237
AMP PEAK 2(1Q21.3) WILD-TYPE 40 105 128

Figure S18.  Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.22e-05 (Chi-square test), Q value = 0.0038

Table S19.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S19.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 6.67e-08 (Chi-square test), Q value = 2.9e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 3(1Q44) CNV 247 167 79 186 31
AMP PEAK 3(1Q44) WILD-TYPE 127 65 0 66 17

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

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

P value = 1.17e-06 (Chi-square test), Q value = 0.00044

Table S21.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 3(1Q44) CNV 82 128 88 81 29 67
AMP PEAK 3(1Q44) WILD-TYPE 27 27 18 55 15 46

Figure S21.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 1.05e-08 (Chi-square test), Q value = 4.8e-06

Table S22.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 3(1Q44) CNV 134 92 182 117 127 37 12
AMP PEAK 3(1Q44) WILD-TYPE 41 47 35 37 97 10 3

Figure S22.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 0.000564 (Fisher's exact test), Q value = 0.13

Table S23.  Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 3(1Q44) CNV 169 289 236
AMP PEAK 3(1Q44) WILD-TYPE 56 87 129

Figure S23.  Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.00103 (Fisher's exact test), Q value = 0.23

Table S24.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S24.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.21e-16 (Chi-square test), Q value = 8e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 4(3P26.1) CNV 22 64 20 81 14
AMP PEAK 4(3P26.1) WILD-TYPE 352 168 59 171 34

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

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

P value = 7.63e-07 (Chi-square test), Q value = 0.00029

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 4(3P26.1) CNV 32 11 26 32 3 12
AMP PEAK 4(3P26.1) WILD-TYPE 77 144 80 104 41 101

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

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

P value = 3.15e-08 (Chi-square test), Q value = 1.4e-05

Table S27.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 4(3P26.1) CNV 50 10 30 44 55 3 6
AMP PEAK 4(3P26.1) WILD-TYPE 125 129 187 110 169 44 9

Figure S27.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 3.08e-09 (Fisher's exact test), Q value = 1.5e-06

Table S28.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 4(3P26.1) CNV 26 69 103
AMP PEAK 4(3P26.1) WILD-TYPE 265 177 331

Figure S28.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 5.07e-11 (Fisher's exact test), Q value = 2.7e-08

Table S29.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 4(3P26.1) CNV 25 79 90
AMP PEAK 4(3P26.1) WILD-TYPE 249 334 189

Figure S29.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 5.89e-09 (Fisher's exact test), Q value = 2.8e-06

Table S30.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 4(3P26.1) CNV 70 42 82
AMP PEAK 4(3P26.1) WILD-TYPE 155 334 283

Figure S30.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 9.02e-06 (Fisher's exact test), Q value = 0.0029

Table S31.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 4(3P26.1) CNV 43 23 58
AMP PEAK 4(3P26.1) WILD-TYPE 207 187 138

Figure S31.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 0.000753 (Fisher's exact test), Q value = 0.17

Table S32.  Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 4(3P26.1) CNV 19 54 51
AMP PEAK 4(3P26.1) WILD-TYPE 141 257 134

Figure S32.  Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

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

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

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

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

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

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

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

P value = 8.19e-38 (Chi-square test), Q value = 6.6e-35

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 5(3Q26.32) CNV 35 85 26 150 14
AMP PEAK 5(3Q26.32) WILD-TYPE 339 147 53 102 34

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

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

P value = 1.06e-19 (Chi-square test), Q value = 7.6e-17

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 5(3Q26.32) CNV 70 18 34 39 10 19
AMP PEAK 5(3Q26.32) WILD-TYPE 39 137 72 97 34 94

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

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

P value = 7.16e-07 (Fisher's exact test), Q value = 0.00028

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

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

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

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

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

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

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

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

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

P value = 1.78e-27 (Chi-square test), Q value = 1.4e-24

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 5(3Q26.32) CNV 111 19 44 61 58 4 8
AMP PEAK 5(3Q26.32) WILD-TYPE 64 120 173 93 166 43 7

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

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

P value = 1.61e-24 (Fisher's exact test), Q value = 1.2e-21

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 5(3Q26.32) CNV 42 138 125
AMP PEAK 5(3Q26.32) WILD-TYPE 249 108 309

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

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

P value = 9.56e-27 (Fisher's exact test), Q value = 7.4e-24

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 5(3Q26.32) CNV 35 113 153
AMP PEAK 5(3Q26.32) WILD-TYPE 239 300 126

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

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

P value = 9.78e-24 (Fisher's exact test), Q value = 7.4e-21

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 5(3Q26.32) CNV 130 65 106
AMP PEAK 5(3Q26.32) WILD-TYPE 95 311 259

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

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

P value = 1.08e-18 (Fisher's exact test), Q value = 7.5e-16

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 5(3Q26.32) CNV 53 31 105
AMP PEAK 5(3Q26.32) WILD-TYPE 197 179 91

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

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

P value = 6.44e-16 (Fisher's exact test), Q value = 4.2e-13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 5(3Q26.32) CNV 28 63 98
AMP PEAK 5(3Q26.32) WILD-TYPE 132 248 87

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

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

P value = 3.22e-05 (Chi-square test), Q value = 0.0095

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 6(4Q13.3) CNV 4 2 30 20 3 18 4 3
AMP PEAK 6(4Q13.3) WILD-TYPE 17 34 89 76 106 54 16 37

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

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

P value = 4.19e-05 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 6(4Q13.3) CNV 6 30 48
AMP PEAK 6(4Q13.3) WILD-TYPE 116 95 218

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

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

P value = 1.7e-17 (Chi-square test), Q value = 1.2e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 6(4Q13.3) CNV 17 64 2 60 7
AMP PEAK 6(4Q13.3) WILD-TYPE 357 168 77 192 41

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

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

P value = 3.03e-05 (Chi-square test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 6(4Q13.3) CNV 24 8 15 31 3 11
AMP PEAK 6(4Q13.3) WILD-TYPE 85 147 91 105 41 102

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

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

P value = 3.3e-11 (Chi-square test), Q value = 1.8e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 6(4Q13.3) CNV 38 6 11 34 54 2 4
AMP PEAK 6(4Q13.3) WILD-TYPE 137 133 206 120 170 45 11

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

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

P value = 3.72e-07 (Fisher's exact test), Q value = 0.00015

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 6(4Q13.3) CNV 22 60 67
AMP PEAK 6(4Q13.3) WILD-TYPE 269 186 367

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

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

P value = 4.34e-08 (Fisher's exact test), Q value = 1.9e-05

Table S51.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 6(4Q13.3) CNV 18 63 67
AMP PEAK 6(4Q13.3) WILD-TYPE 256 350 212

Figure S51.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 3.86e-11 (Fisher's exact test), Q value = 2.1e-08

Table S52.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 6(4Q13.3) CNV 61 25 62
AMP PEAK 6(4Q13.3) WILD-TYPE 164 351 303

Figure S52.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.52e-05 (Fisher's exact test), Q value = 0.016

Table S53.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 6(4Q13.3) CNV 36 15 44
AMP PEAK 6(4Q13.3) WILD-TYPE 214 195 152

Figure S53.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 9.68e-05 (Fisher's exact test), Q value = 0.026

Table S54.  Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 6(4Q13.3) CNV 13 38 44
AMP PEAK 6(4Q13.3) WILD-TYPE 147 273 141

Figure S54.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 3.22e-22 (Chi-square test), Q value = 2.4e-19

Table S55.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 7(5P15.33) CNV 62 106 41 131 17
AMP PEAK 7(5P15.33) WILD-TYPE 312 126 38 121 31

Figure S55.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 7.05e-09 (Chi-square test), Q value = 3.3e-06

Table S56.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 7(5P15.33) CNV 62 41 50 45 8 27
AMP PEAK 7(5P15.33) WILD-TYPE 47 114 56 91 36 86

Figure S56.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 1.99e-06 (Chi-square test), Q value = 0.00071

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 7(5P15.33) CNV 89 34 66 62 83 9 8
AMP PEAK 7(5P15.33) WILD-TYPE 86 105 151 92 141 38 7

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

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

P value = 3.03e-09 (Fisher's exact test), Q value = 1.5e-06

Table S58.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 7(5P15.33) CNV 70 123 158
AMP PEAK 7(5P15.33) WILD-TYPE 221 123 276

Figure S58.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.38e-07 (Fisher's exact test), Q value = 5.8e-05

Table S59.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 7(5P15.33) CNV 68 146 133
AMP PEAK 7(5P15.33) WILD-TYPE 206 267 146

Figure S59.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 7.8e-07 (Fisher's exact test), Q value = 3e-04

Table S60.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 7(5P15.33) CNV 112 106 129
AMP PEAK 7(5P15.33) WILD-TYPE 113 270 236

Figure S60.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 1.58e-05 (Fisher's exact test), Q value = 0.0049

Table S61.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 7(5P15.33) CNV 91 51 91
AMP PEAK 7(5P15.33) WILD-TYPE 159 159 105

Figure S61.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 3.63e-06 (Fisher's exact test), Q value = 0.0012

Table S62.  Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 7(5P15.33) CNV 37 106 90
AMP PEAK 7(5P15.33) WILD-TYPE 123 205 95

Figure S62.  Get High-res Image Gene #7: 'Amp Peak 7(5p15.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 1.79e-07 (Chi-square test), Q value = 7.5e-05

Table S63.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S63.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 1.45e-07 (Fisher's exact test), Q value = 6.1e-05

Table S64.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S64.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.67e-38 (Chi-square test), Q value = 1.4e-35

Table S65.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 8(6P23) CNV 24 70 17 138 17
AMP PEAK 8(6P23) WILD-TYPE 350 162 62 114 31

Figure S65.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.46e-21 (Chi-square test), Q value = 1.8e-18

Table S66.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 8(6P23) CNV 62 11 28 49 3 17
AMP PEAK 8(6P23) WILD-TYPE 47 144 78 87 41 96

Figure S66.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

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

Table S67.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S67.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

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

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

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

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

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

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

P value = 1.52e-20 (Chi-square test), Q value = 1.1e-17

Table S69.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 8(6P23) CNV 94 19 30 49 56 7 8
AMP PEAK 8(6P23) WILD-TYPE 81 120 187 105 168 40 7

Figure S69.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 1.54e-14 (Fisher's exact test), Q value = 9.6e-12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 8(6P23) CNV 41 110 112
AMP PEAK 8(6P23) WILD-TYPE 250 136 322

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

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

P value = 7.78e-20 (Fisher's exact test), Q value = 5.6e-17

Table S71.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 8(6P23) CNV 33 92 129
AMP PEAK 8(6P23) WILD-TYPE 241 321 150

Figure S71.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 2.05e-19 (Fisher's exact test), Q value = 1.4e-16

Table S72.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 8(6P23) CNV 108 50 96
AMP PEAK 8(6P23) WILD-TYPE 117 326 269

Figure S72.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.13e-13 (Fisher's exact test), Q value = 1.3e-10

Table S73.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 8(6P23) CNV 46 29 88
AMP PEAK 8(6P23) WILD-TYPE 204 181 108

Figure S73.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 7.19e-10 (Fisher's exact test), Q value = 3.6e-07

Table S74.  Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 8(6P23) CNV 25 59 79
AMP PEAK 8(6P23) WILD-TYPE 135 252 106

Figure S74.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S75.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S75.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

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

Table S76.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S76.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 9.77e-49 (Chi-square test), Q value = 8.1e-46

Table S77.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 9(6Q21) CNV 18 22 14 128 5
AMP PEAK 9(6Q21) WILD-TYPE 356 210 65 124 43

Figure S77.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 6.63e-19 (Chi-square test), Q value = 4.6e-16

Table S78.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 9(6Q21) CNV 51 5 19 18 2 19
AMP PEAK 9(6Q21) WILD-TYPE 58 150 87 118 42 94

Figure S78.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

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

Table S79.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S79.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #5: 'RPPA_CNMF'

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

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

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

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

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

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

P value = 1.03e-28 (Chi-square test), Q value = 8.1e-26

Table S81.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 9(6Q21) CNV 80 8 19 44 23 3 7
AMP PEAK 9(6Q21) WILD-TYPE 95 131 198 110 201 44 8

Figure S81.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 6.84e-24 (Fisher's exact test), Q value = 5.2e-21

Table S82.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 9(6Q21) CNV 16 99 69
AMP PEAK 9(6Q21) WILD-TYPE 275 147 365

Figure S82.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 4.59e-26 (Fisher's exact test), Q value = 3.5e-23

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 9(6Q21) CNV 15 52 110
AMP PEAK 9(6Q21) WILD-TYPE 259 361 169

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

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

P value = 2.41e-24 (Fisher's exact test), Q value = 1.8e-21

Table S84.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 9(6Q21) CNV 96 30 51
AMP PEAK 9(6Q21) WILD-TYPE 129 346 314

Figure S84.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.4e-18 (Fisher's exact test), Q value = 1.6e-15

Table S85.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 9(6Q21) CNV 29 14 78
AMP PEAK 9(6Q21) WILD-TYPE 221 196 118

Figure S85.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 5.36e-19 (Fisher's exact test), Q value = 3.7e-16

Table S86.  Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 9(6Q21) CNV 13 31 77
AMP PEAK 9(6Q21) WILD-TYPE 147 280 108

Figure S86.  Get High-res Image Gene #9: 'Amp Peak 9(6q21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S87.  Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S87.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 3.96e-25 (Chi-square test), Q value = 3e-22

Table S88.  Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 10(8P11.23) CNV 101 119 35 72 47
AMP PEAK 10(8P11.23) WILD-TYPE 273 113 44 180 1

Figure S88.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 5.89e-11 (Chi-square test), Q value = 3.1e-08

Table S89.  Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 10(8P11.23) CNV 37 36 42 86 14 33
AMP PEAK 10(8P11.23) WILD-TYPE 72 119 64 50 30 80

Figure S89.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 8.74e-12 (Chi-square test), Q value = 4.9e-09

Table S90.  Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 10(8P11.23) CNV 56 48 69 45 135 11 5
AMP PEAK 10(8P11.23) WILD-TYPE 119 91 148 109 89 36 10

Figure S90.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 7.67e-08 (Fisher's exact test), Q value = 3.3e-05

Table S91.  Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 10(8P11.23) CNV 86 75 208
AMP PEAK 10(8P11.23) WILD-TYPE 205 171 226

Figure S91.  Get High-res Image Gene #10: 'Amp Peak 10(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.79e-22 (Chi-square test), Q value = 1.3e-19

Table S92.  Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 11(8P11.21) CNV 97 102 39 96 48
AMP PEAK 11(8P11.21) WILD-TYPE 277 130 40 156 0

Figure S92.  Get High-res Image Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 9.23e-08 (Chi-square test), Q value = 3.9e-05

Table S93.  Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 11(8P11.21) CNV 59 36 39 71 14 35
AMP PEAK 11(8P11.21) WILD-TYPE 50 119 67 65 30 78

Figure S93.  Get High-res Image Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 2.27e-08 (Chi-square test), Q value = 1e-05

Table S94.  Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 11(8P11.21) CNV 89 40 72 47 115 9 5
AMP PEAK 11(8P11.21) WILD-TYPE 86 99 145 107 109 38 10

Figure S94.  Get High-res Image Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 2.09e-07 (Fisher's exact test), Q value = 8.7e-05

Table S95.  Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 11(8P11.21) CNV 75 109 193
AMP PEAK 11(8P11.21) WILD-TYPE 216 137 241

Figure S95.  Get High-res Image Gene #11: 'Amp Peak 11(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

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

Table S96.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S96.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

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

Table S97.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S97.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 2.15e-50 (Chi-square test), Q value = 1.8e-47

Table S98.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 12(8Q24.21) CNV 136 178 40 226 46
AMP PEAK 12(8Q24.21) WILD-TYPE 238 54 39 26 2

Figure S98.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.15e-27 (Chi-square test), Q value = 9e-25

Table S99.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 12(8Q24.21) CNV 100 45 70 105 17 61
AMP PEAK 12(8Q24.21) WILD-TYPE 9 110 36 31 27 52

Figure S99.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

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

Table S100.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S100.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

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

P value = 9.36e-07 (Fisher's exact test), Q value = 0.00036

Table S101.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S101.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

P value = 5.29e-30 (Chi-square test), Q value = 4.2e-27

Table S102.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 12(8Q24.21) CNV 155 63 90 109 169 16 13
AMP PEAK 12(8Q24.21) WILD-TYPE 20 76 127 45 55 31 2

Figure S102.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 9.61e-24 (Fisher's exact test), Q value = 7.3e-21

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 12(8Q24.21) CNV 123 207 285
AMP PEAK 12(8Q24.21) WILD-TYPE 168 39 149

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

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

P value = 1.28e-28 (Fisher's exact test), Q value = 1e-25

Table S104.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 12(8Q24.21) CNV 117 250 243
AMP PEAK 12(8Q24.21) WILD-TYPE 157 163 36

Figure S104.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 2.62e-26 (Fisher's exact test), Q value = 2e-23

Table S105.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 12(8Q24.21) CNV 199 174 237
AMP PEAK 12(8Q24.21) WILD-TYPE 26 202 128

Figure S105.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 9.97e-24 (Fisher's exact test), Q value = 7.5e-21

Table S106.  Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 12(8Q24.21) CNV 136 87 172
AMP PEAK 12(8Q24.21) WILD-TYPE 114 123 24

Figure S106.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 1.04e-15 (Fisher's exact test), Q value = 6.7e-13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 12(8Q24.21) CNV 71 169 155
AMP PEAK 12(8Q24.21) WILD-TYPE 89 142 30

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

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

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

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

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

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

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

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

Table S109.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S109.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.09e-43 (Chi-square test), Q value = 8.9e-41

Table S110.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 13(10P15.1) CNV 33 62 17 154 11
AMP PEAK 13(10P15.1) WILD-TYPE 341 170 62 98 37

Figure S110.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.53e-27 (Chi-square test), Q value = 1.2e-24

Table S111.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 13(10P15.1) CNV 73 10 27 30 3 29
AMP PEAK 13(10P15.1) WILD-TYPE 36 145 79 106 41 84

Figure S111.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

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

Table S112.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S112.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

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

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

Table S113.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S113.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

P value = 3.38e-37 (Chi-square test), Q value = 2.7e-34

Table S114.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 13(10P15.1) CNV 113 16 23 58 51 6 7
AMP PEAK 13(10P15.1) WILD-TYPE 62 123 194 96 173 41 8

Figure S114.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 6.77e-33 (Fisher's exact test), Q value = 5.4e-30

Table S115.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 13(10P15.1) CNV 35 143 96
AMP PEAK 13(10P15.1) WILD-TYPE 256 103 338

Figure S115.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.75e-33 (Fisher's exact test), Q value = 2.2e-30

Table S116.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 13(10P15.1) CNV 32 82 155
AMP PEAK 13(10P15.1) WILD-TYPE 242 331 124

Figure S116.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 5.26e-33 (Fisher's exact test), Q value = 4.2e-30

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 13(10P15.1) CNV 135 52 82
AMP PEAK 13(10P15.1) WILD-TYPE 90 324 283

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

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

P value = 1.41e-18 (Fisher's exact test), Q value = 9.7e-16

Table S118.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 13(10P15.1) CNV 47 27 99
AMP PEAK 13(10P15.1) WILD-TYPE 203 183 97

Figure S118.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 4.98e-21 (Fisher's exact test), Q value = 3.6e-18

Table S119.  Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 13(10P15.1) CNV 20 54 99
AMP PEAK 13(10P15.1) WILD-TYPE 140 257 86

Figure S119.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S120.  Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S120.  Get High-res Image Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 2.25e-09 (Chi-square test), Q value = 1.1e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 14(10Q22.3) CNV 22 35 13 63 6
AMP PEAK 14(10Q22.3) WILD-TYPE 352 197 66 189 42

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

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

P value = 1.21e-11 (Chi-square test), Q value = 6.7e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 14(10Q22.3) CNV 33 10 19 40 25 2 9
AMP PEAK 14(10Q22.3) WILD-TYPE 142 129 198 114 199 45 6

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

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

P value = 5.46e-07 (Fisher's exact test), Q value = 0.00021

Table S123.  Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 14(10Q22.3) CNV 18 53 67
AMP PEAK 14(10Q22.3) WILD-TYPE 273 193 367

Figure S123.  Get High-res Image Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.04e-06 (Fisher's exact test), Q value = 0.0011

Table S124.  Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 14(10Q22.3) CNV 18 58 59
AMP PEAK 14(10Q22.3) WILD-TYPE 256 355 220

Figure S124.  Get High-res Image Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0037

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 14(10Q22.3) CNV 37 11 40
AMP PEAK 14(10Q22.3) WILD-TYPE 213 199 156

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

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

P value = 0.00066 (Fisher's exact test), Q value = 0.15

Table S126.  Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 14(10Q22.3) CNV 9 44 35
AMP PEAK 14(10Q22.3) WILD-TYPE 151 267 150

Figure S126.  Get High-res Image Gene #14: 'Amp Peak 14(10q22.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 4.68e-17 (Chi-square test), Q value = 3.1e-14

Table S127.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 15(11P13) CNV 26 63 14 89 12
AMP PEAK 15(11P13) WILD-TYPE 348 169 65 163 36

Figure S127.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 5.19e-07 (Chi-square test), Q value = 0.00021

Table S128.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 15(11P13) CNV 38 19 16 39 3 15
AMP PEAK 15(11P13) WILD-TYPE 71 136 90 97 41 98

Figure S128.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 2.26e-10 (Chi-square test), Q value = 1.2e-07

Table S129.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 15(11P13) CNV 63 11 24 38 58 7 3
AMP PEAK 15(11P13) WILD-TYPE 112 128 193 116 166 40 12

Figure S129.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 5.17e-07 (Fisher's exact test), Q value = 2e-04

Table S130.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 15(11P13) CNV 37 78 89
AMP PEAK 15(11P13) WILD-TYPE 254 168 345

Figure S130.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.84e-09 (Fisher's exact test), Q value = 1.8e-06

Table S131.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 15(11P13) CNV 27 86 86
AMP PEAK 15(11P13) WILD-TYPE 247 327 193

Figure S131.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 1.1e-11 (Fisher's exact test), Q value = 6.1e-09

Table S132.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 15(11P13) CNV 74 38 87
AMP PEAK 15(11P13) WILD-TYPE 151 338 278

Figure S132.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 7.39e-06 (Fisher's exact test), Q value = 0.0025

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 15(11P13) CNV 48 20 55
AMP PEAK 15(11P13) WILD-TYPE 202 190 141

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

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

P value = 0.00011 (Fisher's exact test), Q value = 0.029

Table S134.  Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 15(11P13) CNV 15 58 50
AMP PEAK 15(11P13) WILD-TYPE 145 253 135

Figure S134.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S135.  Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S135.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 1.57e-40 (Chi-square test), Q value = 1.3e-37

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 16(11Q13.3) CNV 59 166 25 97 17
AMP PEAK 16(11Q13.3) WILD-TYPE 315 66 54 155 31

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

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

P value = 2.92e-10 (Chi-square test), Q value = 1.5e-07

Table S137.  Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 16(11Q13.3) CNV 39 37 50 72 11 19
AMP PEAK 16(11Q13.3) WILD-TYPE 70 118 56 64 33 94

Figure S137.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 5.57e-10 (Chi-square test), Q value = 2.8e-07

Table S138.  Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 16(11Q13.3) CNV 59 40 53 69 121 13 8
AMP PEAK 16(11Q13.3) WILD-TYPE 116 99 164 85 103 34 7

Figure S138.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 0.000983 (Fisher's exact test), Q value = 0.22

Table S139.  Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 16(11Q13.3) CNV 87 88 188
AMP PEAK 16(11Q13.3) WILD-TYPE 204 158 246

Figure S139.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.000222 (Fisher's exact test), Q value = 0.055

Table S140.  Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 16(11Q13.3) CNV 74 173 109
AMP PEAK 16(11Q13.3) WILD-TYPE 200 240 170

Figure S140.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 2.6e-05 (Fisher's exact test), Q value = 0.0078

Table S141.  Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 16(11Q13.3) CNV 84 108 164
AMP PEAK 16(11Q13.3) WILD-TYPE 141 268 201

Figure S141.  Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.39e-19 (Chi-square test), Q value = 3.1e-16

Table S142.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 17(11Q14.1) CNV 35 89 16 94 12
AMP PEAK 17(11Q14.1) WILD-TYPE 339 143 63 158 36

Figure S142.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000127 (Chi-square test), Q value = 0.033

Table S143.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 17(11Q14.1) CNV 38 24 33 31 9 14
AMP PEAK 17(11Q14.1) WILD-TYPE 71 131 73 105 35 99

Figure S143.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 1.92e-06 (Chi-square test), Q value = 0.00069

Table S144.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 17(11Q14.1) CNV 61 24 33 48 69 5 4
AMP PEAK 17(11Q14.1) WILD-TYPE 114 115 184 106 155 42 11

Figure S144.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 8.31e-06 (Fisher's exact test), Q value = 0.0027

Table S145.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 17(11Q14.1) CNV 48 85 111
AMP PEAK 17(11Q14.1) WILD-TYPE 243 161 323

Figure S145.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.88e-07 (Fisher's exact test), Q value = 0.00016

Table S146.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 17(11Q14.1) CNV 41 102 97
AMP PEAK 17(11Q14.1) WILD-TYPE 233 311 182

Figure S146.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 1.4e-07 (Fisher's exact test), Q value = 5.9e-05

Table S147.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 17(11Q14.1) CNV 78 59 103
AMP PEAK 17(11Q14.1) WILD-TYPE 147 317 262

Figure S147.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.000146 (Fisher's exact test), Q value = 0.038

Table S148.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 17(11Q14.1) CNV 53 33 65
AMP PEAK 17(11Q14.1) WILD-TYPE 197 177 131

Figure S148.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 0.000288 (Fisher's exact test), Q value = 0.071

Table S149.  Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 17(11Q14.1) CNV 26 63 62
AMP PEAK 17(11Q14.1) WILD-TYPE 134 248 123

Figure S149.  Get High-res Image Gene #17: 'Amp Peak 17(11q14.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

Table S150.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S150.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 9.63e-12 (Fisher's exact test), Q value = 5.4e-09

Table S151.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 18(12P13.33) CNV 11 61 74
AMP PEAK 18(12P13.33) WILD-TYPE 111 64 192

Figure S151.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 9.92e-34 (Chi-square test), Q value = 7.9e-31

Table S152.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 18(12P13.33) CNV 21 73 25 126 12
AMP PEAK 18(12P13.33) WILD-TYPE 353 159 54 126 36

Figure S152.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.38e-21 (Chi-square test), Q value = 1.7e-18

Table S153.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 18(12P13.33) CNV 63 15 23 42 3 13
AMP PEAK 18(12P13.33) WILD-TYPE 46 140 83 94 41 100

Figure S153.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 2.7e-08 (Fisher's exact test), Q value = 1.2e-05

Table S154.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 18(12P13.33) CNV 69 31 18
AMP PEAK 18(12P13.33) WILD-TYPE 78 102 99

Figure S154.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #5: 'RPPA_CNMF'

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

P value = 2.37e-07 (Fisher's exact test), Q value = 9.7e-05

Table S155.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 18(12P13.33) CNV 43 16 59
AMP PEAK 18(12P13.33) WILD-TYPE 118 94 67

Figure S155.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

P value = 5.31e-27 (Chi-square test), Q value = 4.1e-24

Table S156.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 18(12P13.33) CNV 100 16 25 45 61 4 2
AMP PEAK 18(12P13.33) WILD-TYPE 75 123 192 109 163 43 13

Figure S156.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 2.66e-20 (Fisher's exact test), Q value = 1.9e-17

Table S157.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 18(12P13.33) CNV 34 117 102
AMP PEAK 18(12P13.33) WILD-TYPE 257 129 332

Figure S157.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 3.78e-22 (Fisher's exact test), Q value = 2.8e-19

Table S158.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 18(12P13.33) CNV 35 80 133
AMP PEAK 18(12P13.33) WILD-TYPE 239 333 146

Figure S158.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 1.21e-21 (Fisher's exact test), Q value = 8.9e-19

Table S159.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 18(12P13.33) CNV 114 53 81
AMP PEAK 18(12P13.33) WILD-TYPE 111 323 284

Figure S159.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 3.64e-20 (Fisher's exact test), Q value = 2.6e-17

Table S160.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 18(12P13.33) CNV 37 25 96
AMP PEAK 18(12P13.33) WILD-TYPE 213 185 100

Figure S160.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

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

P value = 5.94e-14 (Fisher's exact test), Q value = 3.7e-11

Table S161.  Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 18(12P13.33) CNV 21 53 84
AMP PEAK 18(12P13.33) WILD-TYPE 139 258 101

Figure S161.  Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 19(12q15)' versus 'MRNA_CNMF'

P value = 3.35e-07 (Chi-square test), Q value = 0.00014

Table S162.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 19(12Q15) CNV 4 6 52 21 19 35 7 6
AMP PEAK 19(12Q15) WILD-TYPE 17 30 67 75 90 37 13 34

Figure S162.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 19(12q15)' versus 'MRNA_CHIERARCHICAL'

P value = 5.01e-06 (Fisher's exact test), Q value = 0.0017

Table S163.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 19(12Q15) CNV 19 29 102
AMP PEAK 19(12Q15) WILD-TYPE 103 96 164

Figure S163.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 19(12q15)' versus 'CN_CNMF'

P value = 3.52e-29 (Chi-square test), Q value = 2.8e-26

Table S164.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 19(12Q15) CNV 29 116 27 64 12
AMP PEAK 19(12Q15) WILD-TYPE 345 116 52 188 36

Figure S164.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(12q15)' versus 'METHLYATION_CNMF'

P value = 1.54e-13 (Chi-square test), Q value = 9.4e-11

Table S165.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 19(12Q15) CNV 19 22 24 65 6 12
AMP PEAK 19(12Q15) WILD-TYPE 90 133 82 71 38 101

Figure S165.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 19(12q15)' versus 'MRNASEQ_CNMF'

P value = 1.28e-11 (Chi-square test), Q value = 7.1e-09

Table S166.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 19(12Q15) CNV 31 19 36 57 90 9 3
AMP PEAK 19(12Q15) WILD-TYPE 144 120 181 97 134 38 12

Figure S166.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 19(12q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.73e-07 (Fisher's exact test), Q value = 0.00026

Table S167.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 19(12Q15) CNV 50 50 145
AMP PEAK 19(12Q15) WILD-TYPE 241 196 289

Figure S167.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 19(12q15)' versus 'MIRSEQ_CNMF'

P value = 3.8e-05 (Fisher's exact test), Q value = 0.011

Table S168.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 19(12Q15) CNV 43 126 73
AMP PEAK 19(12Q15) WILD-TYPE 231 287 206

Figure S168.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 19(12q15)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.48e-06 (Fisher's exact test), Q value = 0.00087

Table S169.  Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 19(12Q15) CNV 50 68 124
AMP PEAK 19(12Q15) WILD-TYPE 175 308 241

Figure S169.  Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 20(13q12.3)' versus 'CN_CNMF'

P value = 1.19e-05 (Chi-square test), Q value = 0.0037

Table S170.  Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 20(13Q12.3) CNV 24 41 11 49 9
AMP PEAK 20(13Q12.3) WILD-TYPE 350 191 68 203 39

Figure S170.  Get High-res Image Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(13q12.3)' versus 'MRNASEQ_CNMF'

P value = 6.49e-06 (Chi-square test), Q value = 0.0022

Table S171.  Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 20(13Q12.3) CNV 25 9 20 39 36 1 2
AMP PEAK 20(13Q12.3) WILD-TYPE 150 130 197 115 188 46 13

Figure S171.  Get High-res Image Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 20(13q12.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.48e-05 (Fisher's exact test), Q value = 0.013

Table S172.  Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 20(13Q12.3) CNV 19 38 75
AMP PEAK 20(13Q12.3) WILD-TYPE 272 208 359

Figure S172.  Get High-res Image Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 20(13q12.3)' versus 'MIRSEQ_CNMF'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0037

Table S173.  Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 20(13Q12.3) CNV 17 60 54
AMP PEAK 20(13Q12.3) WILD-TYPE 257 353 225

Figure S173.  Get High-res Image Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 20(13q12.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.11e-05 (Fisher's exact test), Q value = 0.014

Table S174.  Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 20(13Q12.3) CNV 42 29 60
AMP PEAK 20(13Q12.3) WILD-TYPE 183 347 305

Figure S174.  Get High-res Image Gene #20: 'Amp Peak 20(13q12.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 21(13q34)' versus 'MRNA_CNMF'

P value = 1.45e-09 (Chi-square test), Q value = 7.1e-07

Table S175.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 21(13Q34) CNV 3 3 19 42 15 10 4 0
AMP PEAK 21(13Q34) WILD-TYPE 18 33 100 54 94 62 16 40

Figure S175.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 21(13q34)' versus 'MRNA_CHIERARCHICAL'

P value = 2.67e-09 (Fisher's exact test), Q value = 1.3e-06

Table S176.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 21(13Q34) CNV 9 47 40
AMP PEAK 21(13Q34) WILD-TYPE 113 78 226

Figure S176.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 21(13q34)' versus 'CN_CNMF'

P value = 2.61e-19 (Chi-square test), Q value = 1.8e-16

Table S177.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 21(13Q34) CNV 30 31 7 91 7
AMP PEAK 21(13Q34) WILD-TYPE 344 201 72 161 41

Figure S177.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(13q34)' versus 'METHLYATION_CNMF'

P value = 6.52e-14 (Chi-square test), Q value = 4e-11

Table S178.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 21(13Q34) CNV 45 11 14 20 2 11
AMP PEAK 21(13Q34) WILD-TYPE 64 144 92 116 42 102

Figure S178.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 21(13q34)' versus 'RPPA_CNMF'

P value = 8.21e-06 (Fisher's exact test), Q value = 0.0027

Table S179.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 21(13Q34) CNV 48 22 11
AMP PEAK 21(13Q34) WILD-TYPE 99 111 106

Figure S179.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 21(13q34)' versus 'RPPA_CHIERARCHICAL'

P value = 5.1e-08 (Fisher's exact test), Q value = 2.2e-05

Table S180.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 21(13Q34) CNV 25 9 47
AMP PEAK 21(13Q34) WILD-TYPE 136 101 79

Figure S180.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 21(13q34)' versus 'MRNASEQ_CNMF'

P value = 4.72e-20 (Chi-square test), Q value = 3.4e-17

Table S181.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 21(13Q34) CNV 71 8 17 30 34 1 3
AMP PEAK 21(13Q34) WILD-TYPE 104 131 200 124 190 46 12

Figure S181.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(13q34)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.98e-21 (Fisher's exact test), Q value = 5.8e-18

Table S182.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 21(13Q34) CNV 14 88 62
AMP PEAK 21(13Q34) WILD-TYPE 277 158 372

Figure S182.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 21(13q34)' versus 'MIRSEQ_CNMF'

P value = 1.31e-22 (Fisher's exact test), Q value = 9.8e-20

Table S183.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 21(13Q34) CNV 16 46 101
AMP PEAK 21(13Q34) WILD-TYPE 258 367 178

Figure S183.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 21(13q34)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.69e-23 (Fisher's exact test), Q value = 1.3e-20

Table S184.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 21(13Q34) CNV 89 24 50
AMP PEAK 21(13Q34) WILD-TYPE 136 352 315

Figure S184.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 21(13q34)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.53e-11 (Fisher's exact test), Q value = 1.4e-08

Table S185.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 21(13Q34) CNV 24 15 60
AMP PEAK 21(13Q34) WILD-TYPE 226 195 136

Figure S185.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 21(13q34)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.44e-14 (Fisher's exact test), Q value = 2.7e-11

Table S186.  Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 21(13Q34) CNV 13 24 62
AMP PEAK 21(13Q34) WILD-TYPE 147 287 123

Figure S186.  Get High-res Image Gene #21: 'Amp Peak 21(13q34)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 22(14q21.1)' versus 'MRNA_CNMF'

P value = 7.91e-05 (Chi-square test), Q value = 0.022

Table S187.  Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 22(14Q21.1) CNV 5 8 34 11 21 26 6 0
AMP PEAK 22(14Q21.1) WILD-TYPE 16 28 85 85 88 46 14 40

Figure S187.  Get High-res Image Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 22(14q21.1)' versus 'CN_CNMF'

P value = 4.07e-13 (Chi-square test), Q value = 2.4e-10

Table S188.  Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 22(14Q21.1) CNV 37 83 23 46 10
AMP PEAK 22(14Q21.1) WILD-TYPE 337 149 56 206 38

Figure S188.  Get High-res Image Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(14q21.1)' versus 'METHLYATION_CNMF'

P value = 2.93e-05 (Chi-square test), Q value = 0.0087

Table S189.  Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 22(14Q21.1) CNV 12 23 26 42 4 13
AMP PEAK 22(14Q21.1) WILD-TYPE 97 132 80 94 40 100

Figure S189.  Get High-res Image Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 22(14q21.1)' versus 'MRNASEQ_CNMF'

P value = 2.73e-08 (Chi-square test), Q value = 1.2e-05

Table S190.  Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 22(14Q21.1) CNV 19 19 37 51 63 3 5
AMP PEAK 22(14Q21.1) WILD-TYPE 156 120 180 103 161 44 10

Figure S190.  Get High-res Image Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 22(14q21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0036

Table S191.  Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 22(14Q21.1) CNV 43 36 118
AMP PEAK 22(14Q21.1) WILD-TYPE 248 210 316

Figure S191.  Get High-res Image Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(14q21.1)' versus 'MIRSEQ_CNMF'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.0084

Table S192.  Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 22(14Q21.1) CNV 32 106 55
AMP PEAK 22(14Q21.1) WILD-TYPE 242 307 224

Figure S192.  Get High-res Image Gene #22: 'Amp Peak 22(14q21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 23(15q26.3)' versus 'MRNA_CNMF'

P value = 4.52e-07 (Chi-square test), Q value = 0.00018

Table S193.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 23(15Q26.3) CNV 3 7 30 32 4 16 8 2
AMP PEAK 23(15Q26.3) WILD-TYPE 18 29 89 64 105 56 12 38

Figure S193.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 23(15q26.3)' versus 'CN_CNMF'

P value = 5.4e-16 (Chi-square test), Q value = 3.6e-13

Table S194.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 23(15Q26.3) CNV 29 56 7 82 3
AMP PEAK 23(15Q26.3) WILD-TYPE 345 176 72 170 45

Figure S194.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(15q26.3)' versus 'METHLYATION_CNMF'

P value = 0.000123 (Chi-square test), Q value = 0.032

Table S195.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 23(15Q26.3) CNV 29 8 17 28 7 16
AMP PEAK 23(15Q26.3) WILD-TYPE 80 147 89 108 37 97

Figure S195.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(15q26.3)' versus 'RPPA_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.069

Table S196.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 23(15Q26.3) CNV 46 18 17
AMP PEAK 23(15Q26.3) WILD-TYPE 101 115 100

Figure S196.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 23(15q26.3)' versus 'MRNASEQ_CNMF'

P value = 6.56e-09 (Chi-square test), Q value = 3.1e-06

Table S197.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 23(15Q26.3) CNV 55 15 18 26 52 3 3
AMP PEAK 23(15Q26.3) WILD-TYPE 120 124 199 128 172 44 12

Figure S197.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 23(15q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00044

Table S198.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 23(15Q26.3) CNV 29 67 76
AMP PEAK 23(15Q26.3) WILD-TYPE 262 179 358

Figure S198.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 23(15q26.3)' versus 'MIRSEQ_CNMF'

P value = 1.02e-08 (Fisher's exact test), Q value = 4.8e-06

Table S199.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 23(15Q26.3) CNV 27 62 81
AMP PEAK 23(15Q26.3) WILD-TYPE 247 351 198

Figure S199.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 23(15q26.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.62e-10 (Fisher's exact test), Q value = 8.4e-08

Table S200.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 23(15Q26.3) CNV 70 35 65
AMP PEAK 23(15Q26.3) WILD-TYPE 155 341 300

Figure S200.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 23(15q26.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000401 (Fisher's exact test), Q value = 0.097

Table S201.  Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 23(15Q26.3) CNV 15 52 47
AMP PEAK 23(15Q26.3) WILD-TYPE 145 259 138

Figure S201.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 24(17q12)' versus 'MRNA_CNMF'

P value = 1.1e-15 (Chi-square test), Q value = 7.1e-13

Table S202.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 24(17Q12) CNV 9 11 52 19 14 49 7 4
AMP PEAK 24(17Q12) WILD-TYPE 12 25 67 77 95 23 13 36

Figure S202.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 24(17q12)' versus 'MRNA_CHIERARCHICAL'

P value = 1.34e-05 (Fisher's exact test), Q value = 0.0042

Table S203.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 24(17Q12) CNV 20 39 106
AMP PEAK 24(17Q12) WILD-TYPE 102 86 160

Figure S203.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(17q12)' versus 'CN_CNMF'

P value = 3.76e-36 (Chi-square test), Q value = 3e-33

Table S204.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 24(17Q12) CNV 60 152 19 64 16
AMP PEAK 24(17Q12) WILD-TYPE 314 80 60 188 32

Figure S204.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(17q12)' versus 'METHLYATION_CNMF'

P value = 7.95e-09 (Chi-square test), Q value = 3.7e-06

Table S205.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 24(17Q12) CNV 28 30 48 66 10 25
AMP PEAK 24(17Q12) WILD-TYPE 81 125 58 70 34 88

Figure S205.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(17q12)' versus 'MRNASEQ_CNMF'

P value = 8.01e-26 (Chi-square test), Q value = 6.2e-23

Table S206.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 24(17Q12) CNV 34 28 39 96 101 7 4
AMP PEAK 24(17Q12) WILD-TYPE 141 111 178 58 123 40 11

Figure S206.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(17q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.4e-05 (Fisher's exact test), Q value = 0.0073

Table S207.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 24(17Q12) CNV 63 84 162
AMP PEAK 24(17Q12) WILD-TYPE 228 162 272

Figure S207.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(17q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.76e-07 (Fisher's exact test), Q value = 0.00015

Table S208.  Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 24(17Q12) CNV 64 88 152
AMP PEAK 24(17Q12) WILD-TYPE 161 288 213

Figure S208.  Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 25(17q23.1)' versus 'MRNA_CNMF'

P value = 6.72e-16 (Chi-square test), Q value = 4.4e-13

Table S209.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 25(17Q23.1) CNV 9 17 80 30 16 43 11 9
AMP PEAK 25(17Q23.1) WILD-TYPE 12 19 39 66 93 29 9 31

Figure S209.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 25(17q23.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.08

Table S210.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 25(17Q23.1) CNV 35 48 132
AMP PEAK 25(17Q23.1) WILD-TYPE 87 77 134

Figure S210.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 25(17q23.1)' versus 'CN_CNMF'

P value = 1.11e-42 (Chi-square test), Q value = 9.1e-40

Table S211.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 25(17Q23.1) CNV 69 176 22 110 20
AMP PEAK 25(17Q23.1) WILD-TYPE 305 56 57 142 28

Figure S211.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(17q23.1)' versus 'METHLYATION_CNMF'

P value = 1.82e-10 (Chi-square test), Q value = 9.4e-08

Table S212.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 25(17Q23.1) CNV 45 37 49 84 14 31
AMP PEAK 25(17Q23.1) WILD-TYPE 64 118 57 52 30 82

Figure S212.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 25(17q23.1)' versus 'MRNASEQ_CNMF'

P value = 4.86e-23 (Chi-square test), Q value = 3.6e-20

Table S213.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 25(17Q23.1) CNV 62 39 43 83 144 13 8
AMP PEAK 25(17Q23.1) WILD-TYPE 113 100 174 71 80 34 7

Figure S213.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 25(17q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.38e-06 (Fisher's exact test), Q value = 5e-04

Table S214.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 25(17Q23.1) CNV 86 95 211
AMP PEAK 25(17Q23.1) WILD-TYPE 205 151 223

Figure S214.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(17q23.1)' versus 'MIRSEQ_CNMF'

P value = 3.21e-08 (Fisher's exact test), Q value = 1.4e-05

Table S215.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 25(17Q23.1) CNV 71 185 133
AMP PEAK 25(17Q23.1) WILD-TYPE 203 228 146

Figure S215.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 25(17q23.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.29e-11 (Fisher's exact test), Q value = 1.8e-08

Table S216.  Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 25(17Q23.1) CNV 96 103 190
AMP PEAK 25(17Q23.1) WILD-TYPE 129 273 175

Figure S216.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 26(19p13.12)' versus 'MRNA_CNMF'

P value = 6.52e-06 (Chi-square test), Q value = 0.0022

Table S217.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 26(19P13.12) CNV 5 5 22 41 16 11 6 4
AMP PEAK 26(19P13.12) WILD-TYPE 16 31 97 55 93 61 14 36

Figure S217.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 26(19p13.12)' versus 'MRNA_CHIERARCHICAL'

P value = 5.01e-05 (Fisher's exact test), Q value = 0.014

Table S218.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 26(19P13.12) CNV 18 45 47
AMP PEAK 26(19P13.12) WILD-TYPE 104 80 219

Figure S218.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 26(19p13.12)' versus 'CN_CNMF'

P value = 1.96e-15 (Chi-square test), Q value = 1.3e-12

Table S219.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 26(19P13.12) CNV 37 40 26 93 11
AMP PEAK 26(19P13.12) WILD-TYPE 337 192 53 159 37

Figure S219.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 26(19p13.12)' versus 'METHLYATION_CNMF'

P value = 2.18e-06 (Chi-square test), Q value = 0.00077

Table S220.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 26(19P13.12) CNV 43 18 20 24 6 22
AMP PEAK 26(19P13.12) WILD-TYPE 66 137 86 112 38 91

Figure S220.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 26(19p13.12)' versus 'RPPA_CNMF'

P value = 0.000125 (Fisher's exact test), Q value = 0.033

Table S221.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 26(19P13.12) CNV 51 25 16
AMP PEAK 26(19P13.12) WILD-TYPE 96 108 101

Figure S221.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 26(19p13.12)' versus 'MRNASEQ_CNMF'

P value = 4.1e-11 (Chi-square test), Q value = 2.2e-08

Table S222.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 26(19P13.12) CNV 71 27 28 28 38 4 6
AMP PEAK 26(19P13.12) WILD-TYPE 104 112 189 126 186 43 9

Figure S222.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 26(19p13.12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.64e-08 (Fisher's exact test), Q value = 2.9e-05

Table S223.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 26(19P13.12) CNV 41 83 78
AMP PEAK 26(19P13.12) WILD-TYPE 250 163 356

Figure S223.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 26(19p13.12)' versus 'MIRSEQ_CNMF'

P value = 1.62e-08 (Fisher's exact test), Q value = 7.4e-06

Table S224.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 26(19P13.12) CNV 44 63 93
AMP PEAK 26(19P13.12) WILD-TYPE 230 350 186

Figure S224.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 26(19p13.12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.58e-10 (Fisher's exact test), Q value = 1.8e-07

Table S225.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 26(19P13.12) CNV 83 55 62
AMP PEAK 26(19P13.12) WILD-TYPE 142 321 303

Figure S225.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 26(19p13.12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.53e-06 (Fisher's exact test), Q value = 0.0015

Table S226.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 26(19P13.12) CNV 37 37 66
AMP PEAK 26(19P13.12) WILD-TYPE 213 173 130

Figure S226.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 26(19p13.12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.44e-06 (Fisher's exact test), Q value = 0.0025

Table S227.  Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 26(19P13.12) CNV 24 53 63
AMP PEAK 26(19P13.12) WILD-TYPE 136 258 122

Figure S227.  Get High-res Image Gene #26: 'Amp Peak 26(19p13.12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'MRNA_CNMF'

P value = 4.35e-12 (Chi-square test), Q value = 2.5e-09

Table S228.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 27(19Q12) CNV 4 4 29 56 15 20 7 5
AMP PEAK 27(19Q12) WILD-TYPE 17 32 90 40 94 52 13 35

Figure S228.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 27(19q12)' versus 'MRNA_CHIERARCHICAL'

P value = 9.44e-11 (Fisher's exact test), Q value = 4.9e-08

Table S229.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 27(19Q12) CNV 19 64 57
AMP PEAK 27(19Q12) WILD-TYPE 103 61 209

Figure S229.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'CN_CNMF'

P value = 1.88e-27 (Chi-square test), Q value = 1.5e-24

Table S230.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 27(19Q12) CNV 37 47 29 124 14
AMP PEAK 27(19Q12) WILD-TYPE 337 185 50 128 34

Figure S230.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(19q12)' versus 'METHLYATION_CNMF'

P value = 1.29e-12 (Chi-square test), Q value = 7.5e-10

Table S231.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 27(19Q12) CNV 57 19 24 34 4 24
AMP PEAK 27(19Q12) WILD-TYPE 52 136 82 102 40 89

Figure S231.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 27(19q12)' versus 'RPPA_CNMF'

P value = 6.19e-07 (Fisher's exact test), Q value = 0.00024

Table S232.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 27(19Q12) CNV 64 23 23
AMP PEAK 27(19Q12) WILD-TYPE 83 110 94

Figure S232.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 27(19q12)' versus 'RPPA_CHIERARCHICAL'

P value = 9.68e-07 (Fisher's exact test), Q value = 0.00036

Table S233.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
AMP PEAK 27(19Q12) CNV 29 24 57
AMP PEAK 27(19Q12) WILD-TYPE 132 86 69

Figure S233.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'MRNASEQ_CNMF'

P value = 4.73e-23 (Chi-square test), Q value = 3.5e-20

Table S234.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 27(19Q12) CNV 97 24 27 40 48 5 7
AMP PEAK 27(19Q12) WILD-TYPE 78 115 190 114 176 42 8

Figure S234.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 27(19q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.94e-18 (Fisher's exact test), Q value = 1.3e-15

Table S235.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 27(19Q12) CNV 43 117 88
AMP PEAK 27(19Q12) WILD-TYPE 248 129 346

Figure S235.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'MIRSEQ_CNMF'

P value = 4.21e-18 (Fisher's exact test), Q value = 2.9e-15

Table S236.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 27(19Q12) CNV 41 78 127
AMP PEAK 27(19Q12) WILD-TYPE 233 335 152

Figure S236.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 27(19q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.62e-18 (Fisher's exact test), Q value = 4.5e-15

Table S237.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 27(19Q12) CNV 109 59 78
AMP PEAK 27(19Q12) WILD-TYPE 116 317 287

Figure S237.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.54e-12 (Fisher's exact test), Q value = 9e-10

Table S238.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 27(19Q12) CNV 42 37 89
AMP PEAK 27(19Q12) WILD-TYPE 208 173 107

Figure S238.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 27(19q12)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.31e-11 (Fisher's exact test), Q value = 7.2e-09

Table S239.  Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 27(19Q12) CNV 26 58 84
AMP PEAK 27(19Q12) WILD-TYPE 134 253 101

Figure S239.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 28(19q13.42)' versus 'MRNA_CNMF'

P value = 0.00013 (Chi-square test), Q value = 0.034

Table S240.  Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 28(19Q13.42) CNV 5 8 36 41 16 21 10 6
AMP PEAK 28(19Q13.42) WILD-TYPE 16 28 83 55 93 51 10 34

Figure S240.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 28(19q13.42)' versus 'CN_CNMF'

P value = 3.23e-15 (Chi-square test), Q value = 2.1e-12

Table S241.  Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 28(19Q13.42) CNV 40 67 30 96 16
AMP PEAK 28(19Q13.42) WILD-TYPE 334 165 49 156 32

Figure S241.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 28(19q13.42)' versus 'METHLYATION_CNMF'

P value = 3.02e-06 (Chi-square test), Q value = 0.0011

Table S242.  Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 28(19Q13.42) CNV 35 21 27 49 5 17
AMP PEAK 28(19Q13.42) WILD-TYPE 74 134 79 87 39 96

Figure S242.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 28(19q13.42)' versus 'RPPA_CNMF'

P value = 0.000605 (Fisher's exact test), Q value = 0.14

Table S243.  Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 28(19Q13.42) CNV 58 28 25
AMP PEAK 28(19Q13.42) WILD-TYPE 89 105 92

Figure S243.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 28(19q13.42)' versus 'MRNASEQ_CNMF'

P value = 1.47e-06 (Chi-square test), Q value = 0.00054

Table S244.  Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 28(19Q13.42) CNV 62 32 30 41 66 6 8
AMP PEAK 28(19Q13.42) WILD-TYPE 113 107 187 113 158 41 7

Figure S244.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 28(19q13.42)' versus 'MIRSEQ_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.033

Table S245.  Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 28(19Q13.42) CNV 51 98 95
AMP PEAK 28(19Q13.42) WILD-TYPE 223 315 184

Figure S245.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 28(19q13.42)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000427 (Fisher's exact test), Q value = 0.1

Table S246.  Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 28(19Q13.42) CNV 77 74 93
AMP PEAK 28(19Q13.42) WILD-TYPE 148 302 272

Figure S246.  Get High-res Image Gene #28: 'Amp Peak 28(19q13.42)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 29(20q13.2)' versus 'MRNA_CNMF'

P value = 1.81e-10 (Chi-square test), Q value = 9.3e-08

Table S247.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
AMP PEAK 29(20Q13.2) CNV 12 18 84 52 35 49 15 9
AMP PEAK 29(20Q13.2) WILD-TYPE 9 18 35 44 74 23 5 31

Figure S247.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 29(20q13.2)' versus 'MRNA_CHIERARCHICAL'

P value = 3.67e-05 (Fisher's exact test), Q value = 0.011

Table S248.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
AMP PEAK 29(20Q13.2) CNV 44 69 161
AMP PEAK 29(20Q13.2) WILD-TYPE 78 56 105

Figure S248.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 29(20q13.2)' versus 'CN_CNMF'

P value = 4.55e-51 (Chi-square test), Q value = 3.8e-48

Table S249.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
AMP PEAK 29(20Q13.2) CNV 76 185 43 167 26
AMP PEAK 29(20Q13.2) WILD-TYPE 298 47 36 85 22

Figure S249.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 29(20q13.2)' versus 'METHLYATION_CNMF'

P value = 3.2e-23 (Chi-square test), Q value = 2.4e-20

Table S250.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
AMP PEAK 29(20Q13.2) CNV 65 37 59 107 12 36
AMP PEAK 29(20Q13.2) WILD-TYPE 44 118 47 29 32 77

Figure S250.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 29(20q13.2)' versus 'RPPA_CNMF'

P value = 0.000604 (Fisher's exact test), Q value = 0.14

Table S251.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
AMP PEAK 29(20Q13.2) CNV 99 67 53
AMP PEAK 29(20Q13.2) WILD-TYPE 48 66 64

Figure S251.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 29(20q13.2)' versus 'MRNASEQ_CNMF'

P value = 1.88e-18 (Chi-square test), Q value = 1.3e-15

Table S252.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
AMP PEAK 29(20Q13.2) CNV 95 46 71 98 156 15 9
AMP PEAK 29(20Q13.2) WILD-TYPE 80 93 146 56 68 32 6

Figure S252.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 29(20q13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.57e-12 (Fisher's exact test), Q value = 9.2e-10

Table S253.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
AMP PEAK 29(20Q13.2) CNV 95 137 258
AMP PEAK 29(20Q13.2) WILD-TYPE 196 109 176

Figure S253.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 29(20q13.2)' versus 'MIRSEQ_CNMF'

P value = 1.19e-12 (Fisher's exact test), Q value = 7e-10

Table S254.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
AMP PEAK 29(20Q13.2) CNV 88 233 169
AMP PEAK 29(20Q13.2) WILD-TYPE 186 180 110

Figure S254.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 29(20q13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.96e-11 (Fisher's exact test), Q value = 2.1e-08

Table S255.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
AMP PEAK 29(20Q13.2) CNV 128 139 223
AMP PEAK 29(20Q13.2) WILD-TYPE 97 237 142

Figure S255.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 29(20q13.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.08e-08 (Fisher's exact test), Q value = 1.4e-05

Table S256.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
AMP PEAK 29(20Q13.2) CNV 137 71 120
AMP PEAK 29(20Q13.2) WILD-TYPE 113 139 76

Figure S256.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 29(20q13.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000451 (Fisher's exact test), Q value = 0.11

Table S257.  Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
AMP PEAK 29(20Q13.2) CNV 59 164 105
AMP PEAK 29(20Q13.2) WILD-TYPE 101 147 80

Figure S257.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'MRNA_CNMF'

P value = 7.82e-05 (Chi-square test), Q value = 0.021

Table S258.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 1(1P36.13) CNV 8 12 61 41 31 46 7 12
DEL PEAK 1(1P36.13) WILD-TYPE 13 24 58 55 78 26 13 28

Figure S258.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.032

Table S259.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 1(1P36.13) CNV 34 50 134
DEL PEAK 1(1P36.13) WILD-TYPE 88 75 132

Figure S259.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'CN_CNMF'

P value = 7.61e-31 (Chi-square test), Q value = 6e-28

Table S260.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 1(1P36.13) CNV 67 142 49 130 19
DEL PEAK 1(1P36.13) WILD-TYPE 307 90 30 122 29

Figure S260.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.13)' versus 'METHLYATION_CNMF'

P value = 1.59e-12 (Chi-square test), Q value = 9.2e-10

Table S261.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 1(1P36.13) CNV 50 35 64 74 13 28
DEL PEAK 1(1P36.13) WILD-TYPE 59 120 42 62 31 85

Figure S261.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNASEQ_CNMF'

P value = 5.3e-09 (Chi-square test), Q value = 2.5e-06

Table S262.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 1(1P36.13) CNV 71 33 73 85 117 14 8
DEL PEAK 1(1P36.13) WILD-TYPE 104 106 144 69 107 33 7

Figure S262.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00042

Table S263.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 1(1P36.13) CNV 89 96 216
DEL PEAK 1(1P36.13) WILD-TYPE 202 150 218

Figure S263.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'MIRSEQ_CNMF'

P value = 2.49e-06 (Fisher's exact test), Q value = 0.00087

Table S264.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 1(1P36.13) CNV 77 187 129
DEL PEAK 1(1P36.13) WILD-TYPE 197 226 150

Figure S264.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000166 (Fisher's exact test), Q value = 0.042

Table S265.  Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 1(1P36.13) CNV 97 123 173
DEL PEAK 1(1P36.13) WILD-TYPE 128 253 192

Figure S265.  Get High-res Image Gene #30: 'Del Peak 1(1p36.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 2(1p22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000233 (Fisher's exact test), Q value = 0.057

Table S266.  Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 2(1P22.1) CNV 35 30 115
DEL PEAK 2(1P22.1) WILD-TYPE 87 95 151

Figure S266.  Get High-res Image Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p22.1)' versus 'CN_CNMF'

P value = 8.39e-21 (Chi-square test), Q value = 6.1e-18

Table S267.  Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 2(1P22.1) CNV 69 117 49 79 11
DEL PEAK 2(1P22.1) WILD-TYPE 305 115 30 173 37

Figure S267.  Get High-res Image Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p22.1)' versus 'METHLYATION_CNMF'

P value = 1.31e-07 (Chi-square test), Q value = 5.6e-05

Table S268.  Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 2(1P22.1) CNV 25 37 53 57 11 22
DEL PEAK 2(1P22.1) WILD-TYPE 84 118 53 79 33 91

Figure S268.  Get High-res Image Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 2(1p22.1)' versus 'MRNASEQ_CNMF'

P value = 3.47e-09 (Chi-square test), Q value = 1.7e-06

Table S269.  Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 2(1P22.1) CNV 36 31 71 75 96 9 4
DEL PEAK 2(1P22.1) WILD-TYPE 139 108 146 79 128 38 11

Figure S269.  Get High-res Image Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.8e-08 (Fisher's exact test), Q value = 8.1e-06

Table S270.  Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 2(1P22.1) CNV 78 57 187
DEL PEAK 2(1P22.1) WILD-TYPE 213 189 247

Figure S270.  Get High-res Image Gene #31: 'Del Peak 2(1p22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MRNA_CNMF'

P value = 1.51e-06 (Chi-square test), Q value = 0.00055

Table S271.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 3(2Q37.3) CNV 5 10 40 47 24 28 6 0
DEL PEAK 3(2Q37.3) WILD-TYPE 16 26 79 49 85 44 14 40

Figure S271.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 3(2q37.3)' versus 'MRNA_CHIERARCHICAL'

P value = 3.28e-09 (Fisher's exact test), Q value = 1.6e-06

Table S272.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 3(2Q37.3) CNV 14 58 88
DEL PEAK 3(2Q37.3) WILD-TYPE 108 67 178

Figure S272.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'CN_CNMF'

P value = 2.31e-22 (Chi-square test), Q value = 1.7e-19

Table S273.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 3(2Q37.3) CNV 39 82 29 117 16
DEL PEAK 3(2Q37.3) WILD-TYPE 335 150 50 135 32

Figure S273.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 3(2q37.3)' versus 'METHLYATION_CNMF'

P value = 2.98e-11 (Chi-square test), Q value = 1.6e-08

Table S274.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 3(2Q37.3) CNV 48 21 28 52 5 14
DEL PEAK 3(2Q37.3) WILD-TYPE 61 134 78 84 39 99

Figure S274.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 3(2q37.3)' versus 'RPPA_CNMF'

P value = 1.03e-08 (Fisher's exact test), Q value = 4.8e-06

Table S275.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 3(2Q37.3) CNV 70 38 16
DEL PEAK 3(2Q37.3) WILD-TYPE 77 95 101

Figure S275.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 3(2q37.3)' versus 'RPPA_CHIERARCHICAL'

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

Table S276.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 3(2Q37.3) CNV 56 13 55
DEL PEAK 3(2Q37.3) WILD-TYPE 105 97 71

Figure S276.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MRNASEQ_CNMF'

P value = 1.63e-11 (Chi-square test), Q value = 9e-09

Table S277.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 3(2Q37.3) CNV 78 20 44 54 74 2 4
DEL PEAK 3(2Q37.3) WILD-TYPE 97 119 173 100 150 45 11

Figure S277.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 3(2q37.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.29e-11 (Fisher's exact test), Q value = 7.1e-09

Table S278.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 3(2Q37.3) CNV 44 104 128
DEL PEAK 3(2Q37.3) WILD-TYPE 247 142 306

Figure S278.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MIRSEQ_CNMF'

P value = 6.95e-11 (Fisher's exact test), Q value = 3.7e-08

Table S279.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 3(2Q37.3) CNV 42 118 115
DEL PEAK 3(2Q37.3) WILD-TYPE 232 295 164

Figure S279.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 3(2q37.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.85e-10 (Fisher's exact test), Q value = 2.9e-07

Table S280.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 3(2Q37.3) CNV 94 67 114
DEL PEAK 3(2Q37.3) WILD-TYPE 131 309 251

Figure S280.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.73e-13 (Fisher's exact test), Q value = 1e-10

Table S281.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 3(2Q37.3) CNV 63 26 90
DEL PEAK 3(2Q37.3) WILD-TYPE 187 184 106

Figure S281.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 3(2q37.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0034

Table S282.  Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 3(2Q37.3) CNV 27 79 73
DEL PEAK 3(2Q37.3) WILD-TYPE 133 232 112

Figure S282.  Get High-res Image Gene #32: 'Del Peak 3(2q37.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'MRNA_CNMF'

P value = 3.85e-11 (Chi-square test), Q value = 2.1e-08

Table S283.  Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 4(3P14.3) CNV 5 12 39 49 7 34 9 7
DEL PEAK 4(3P14.3) WILD-TYPE 16 24 80 47 102 38 11 33

Figure S283.  Get High-res Image Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 4(3p14.3)' versus 'MRNA_CHIERARCHICAL'

P value = 5.41e-08 (Fisher's exact test), Q value = 2.3e-05

Table S284.  Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 4(3P14.3) CNV 27 66 69
DEL PEAK 4(3P14.3) WILD-TYPE 95 59 197

Figure S284.  Get High-res Image Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'CN_CNMF'

P value = 7.55e-35 (Chi-square test), Q value = 6e-32

Table S285.  Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 4(3P14.3) CNV 48 81 16 149 6
DEL PEAK 4(3P14.3) WILD-TYPE 326 151 63 103 42

Figure S285.  Get High-res Image Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(3p14.3)' versus 'METHLYATION_CNMF'

P value = 3.98e-16 (Chi-square test), Q value = 2.6e-13

Table S286.  Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 4(3P14.3) CNV 56 11 46 48 10 22
DEL PEAK 4(3P14.3) WILD-TYPE 53 144 60 88 34 91

Figure S286.  Get High-res Image Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 4(3p14.3)' versus 'RPPA_CNMF'

P value = 2.51e-09 (Fisher's exact test), Q value = 1.2e-06

Table S287.  Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 4(3P14.3) CNV 78 25 32
DEL PEAK 4(3P14.3) WILD-TYPE 69 108 85

Figure S287.  Get High-res Image Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 4(3p14.3)' versus 'RPPA_CHIERARCHICAL'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0035

Table S288.  Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 4(3P14.3) CNV 40 31 64
DEL PEAK 4(3P14.3) WILD-TYPE 121 79 62

Figure S288.  Get High-res Image Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'MRNASEQ_CNMF'

P value = 1.56e-19 (Chi-square test), Q value = 1.1e-16

Table S289.  Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 4(3P14.3) CNV 87 29 22 68 71 8 8
DEL PEAK 4(3P14.3) WILD-TYPE 88 110 195 86 153 39 7

Figure S289.  Get High-res Image Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 4(3p14.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.75e-13 (Fisher's exact test), Q value = 2.3e-10

Table S290.  Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 4(3P14.3) CNV 56 120 117
DEL PEAK 4(3P14.3) WILD-TYPE 235 126 317

Figure S290.  Get High-res Image Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'MIRSEQ_CNMF'

P value = 2.75e-16 (Fisher's exact test), Q value = 1.8e-13

Table S291.  Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 4(3P14.3) CNV 45 111 136
DEL PEAK 4(3P14.3) WILD-TYPE 229 302 143

Figure S291.  Get High-res Image Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 4(3p14.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.92e-15 (Fisher's exact test), Q value = 2.5e-12

Table S292.  Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 4(3P14.3) CNV 110 66 116
DEL PEAK 4(3P14.3) WILD-TYPE 115 310 249

Figure S292.  Get High-res Image Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.21e-11 (Fisher's exact test), Q value = 3.8e-08

Table S293.  Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 4(3P14.3) CNV 62 39 95
DEL PEAK 4(3P14.3) WILD-TYPE 188 171 101

Figure S293.  Get High-res Image Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 4(3p14.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.58e-10 (Fisher's exact test), Q value = 1.3e-07

Table S294.  Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 4(3P14.3) CNV 33 72 91
DEL PEAK 4(3P14.3) WILD-TYPE 127 239 94

Figure S294.  Get High-res Image Gene #33: 'Del Peak 4(3p14.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MRNA_CNMF'

P value = 2.7e-11 (Chi-square test), Q value = 1.5e-08

Table S295.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 5(4P16.3) CNV 3 10 26 56 22 37 7 6
DEL PEAK 5(4P16.3) WILD-TYPE 18 26 93 40 87 35 13 34

Figure S295.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 5(4p16.3)' versus 'MRNA_CHIERARCHICAL'

P value = 2.23e-11 (Fisher's exact test), Q value = 1.2e-08

Table S296.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 5(4P16.3) CNV 22 72 73
DEL PEAK 5(4P16.3) WILD-TYPE 100 53 193

Figure S296.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'CN_CNMF'

P value = 3.94e-31 (Chi-square test), Q value = 3.1e-28

Table S297.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 5(4P16.3) CNV 55 54 34 148 15
DEL PEAK 5(4P16.3) WILD-TYPE 319 178 45 104 33

Figure S297.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(4p16.3)' versus 'METHLYATION_CNMF'

P value = 9.99e-13 (Chi-square test), Q value = 6e-10

Table S298.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 5(4P16.3) CNV 65 32 33 29 5 31
DEL PEAK 5(4P16.3) WILD-TYPE 44 123 73 107 39 82

Figure S298.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(4p16.3)' versus 'RPPA_CNMF'

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

Table S299.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 5(4P16.3) CNV 75 39 24
DEL PEAK 5(4P16.3) WILD-TYPE 72 94 93

Figure S299.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 5(4p16.3)' versus 'RPPA_CHIERARCHICAL'

P value = 1.62e-06 (Fisher's exact test), Q value = 0.00059

Table S300.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 5(4P16.3) CNV 48 24 66
DEL PEAK 5(4P16.3) WILD-TYPE 113 86 60

Figure S300.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MRNASEQ_CNMF'

P value = 2.63e-23 (Chi-square test), Q value = 2e-20

Table S301.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 5(4P16.3) CNV 102 19 49 67 47 7 8
DEL PEAK 5(4P16.3) WILD-TYPE 73 120 168 87 177 40 7

Figure S301.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(4p16.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.16e-23 (Fisher's exact test), Q value = 3.1e-20

Table S302.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 5(4P16.3) CNV 48 138 113
DEL PEAK 5(4P16.3) WILD-TYPE 243 108 321

Figure S302.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MIRSEQ_CNMF'

P value = 1.56e-18 (Fisher's exact test), Q value = 1.1e-15

Table S303.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 5(4P16.3) CNV 42 114 140
DEL PEAK 5(4P16.3) WILD-TYPE 232 299 139

Figure S303.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 5(4p16.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.96e-18 (Fisher's exact test), Q value = 1.3e-15

Table S304.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 5(4P16.3) CNV 121 69 106
DEL PEAK 5(4P16.3) WILD-TYPE 104 307 259

Figure S304.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.36e-15 (Fisher's exact test), Q value = 2.1e-12

Table S305.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 5(4P16.3) CNV 64 34 103
DEL PEAK 5(4P16.3) WILD-TYPE 186 176 93

Figure S305.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 5(4p16.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.39e-15 (Fisher's exact test), Q value = 3.4e-12

Table S306.  Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 5(4P16.3) CNV 28 73 100
DEL PEAK 5(4P16.3) WILD-TYPE 132 238 85

Figure S306.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MRNA_CNMF'

P value = 1.17e-06 (Chi-square test), Q value = 0.00044

Table S307.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 6(4Q35.2) CNV 7 10 25 51 23 30 10 9
DEL PEAK 6(4Q35.2) WILD-TYPE 14 26 94 45 86 42 10 31

Figure S307.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 6(4q35.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.24e-06 (Fisher's exact test), Q value = 0.00046

Table S308.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 6(4Q35.2) CNV 25 63 77
DEL PEAK 6(4Q35.2) WILD-TYPE 97 62 189

Figure S308.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'CN_CNMF'

P value = 4.27e-40 (Chi-square test), Q value = 3.5e-37

Table S309.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 6(4Q35.2) CNV 54 47 39 158 12
DEL PEAK 6(4Q35.2) WILD-TYPE 320 185 40 94 36

Figure S309.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(4q35.2)' versus 'METHLYATION_CNMF'

P value = 6.31e-14 (Chi-square test), Q value = 3.9e-11

Table S310.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 6(4Q35.2) CNV 68 31 29 28 8 34
DEL PEAK 6(4Q35.2) WILD-TYPE 41 124 77 108 36 79

Figure S310.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(4q35.2)' versus 'RPPA_CNMF'

P value = 1.51e-08 (Fisher's exact test), Q value = 6.9e-06

Table S311.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 6(4Q35.2) CNV 78 35 24
DEL PEAK 6(4Q35.2) WILD-TYPE 69 98 93

Figure S311.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 6(4q35.2)' versus 'RPPA_CHIERARCHICAL'

P value = 1.78e-06 (Fisher's exact test), Q value = 0.00064

Table S312.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 6(4Q35.2) CNV 46 25 66
DEL PEAK 6(4Q35.2) WILD-TYPE 115 85 60

Figure S312.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MRNASEQ_CNMF'

P value = 3.21e-23 (Chi-square test), Q value = 2.4e-20

Table S313.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 6(4Q35.2) CNV 105 20 52 64 46 8 8
DEL PEAK 6(4Q35.2) WILD-TYPE 70 119 165 90 178 39 7

Figure S313.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 6(4q35.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.74e-19 (Fisher's exact test), Q value = 4.7e-16

Table S314.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 6(4Q35.2) CNV 51 132 120
DEL PEAK 6(4Q35.2) WILD-TYPE 240 114 314

Figure S314.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MIRSEQ_CNMF'

P value = 5.94e-19 (Fisher's exact test), Q value = 4.1e-16

Table S315.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 6(4Q35.2) CNV 45 109 143
DEL PEAK 6(4Q35.2) WILD-TYPE 229 304 136

Figure S315.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 6(4q35.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.19e-19 (Fisher's exact test), Q value = 8.5e-17

Table S316.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 6(4Q35.2) CNV 125 72 100
DEL PEAK 6(4Q35.2) WILD-TYPE 100 304 265

Figure S316.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.2e-15 (Fisher's exact test), Q value = 2.7e-12

Table S317.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 6(4Q35.2) CNV 62 35 103
DEL PEAK 6(4Q35.2) WILD-TYPE 188 175 93

Figure S317.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 6(4q35.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-13 (Fisher's exact test), Q value = 1.2e-10

Table S318.  Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 6(4Q35.2) CNV 28 75 97
DEL PEAK 6(4Q35.2) WILD-TYPE 132 236 88

Figure S318.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MRNA_CNMF'

P value = 2.5e-27 (Chi-square test), Q value = 1.9e-24

Table S319.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 7(5Q11.2) CNV 3 5 19 68 7 25 3 4
DEL PEAK 7(5Q11.2) WILD-TYPE 18 31 100 28 102 47 17 36

Figure S319.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 7(5q11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 6.92e-25 (Fisher's exact test), Q value = 5.3e-22

Table S320.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 7(5Q11.2) CNV 12 79 43
DEL PEAK 7(5Q11.2) WILD-TYPE 110 46 223

Figure S320.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'CN_CNMF'

P value = 3.86e-75 (Chi-square test), Q value = 3.2e-72

Table S321.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 7(5Q11.2) CNV 26 34 8 177 11
DEL PEAK 7(5Q11.2) WILD-TYPE 348 198 71 75 37

Figure S321.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(5q11.2)' versus 'METHLYATION_CNMF'

P value = 4.36e-44 (Chi-square test), Q value = 3.6e-41

Table S322.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 7(5Q11.2) CNV 86 4 18 30 6 27
DEL PEAK 7(5Q11.2) WILD-TYPE 23 151 88 106 38 86

Figure S322.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 7(5q11.2)' versus 'RPPA_CNMF'

P value = 3.33e-16 (Fisher's exact test), Q value = 2.2e-13

Table S323.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 7(5Q11.2) CNV 78 13 23
DEL PEAK 7(5Q11.2) WILD-TYPE 69 120 94

Figure S323.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 7(5q11.2)' versus 'RPPA_CHIERARCHICAL'

P value = 7.43e-19 (Fisher's exact test), Q value = 5.2e-16

Table S324.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 7(5Q11.2) CNV 26 13 75
DEL PEAK 7(5Q11.2) WILD-TYPE 135 97 51

Figure S324.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MRNASEQ_CNMF'

P value = 7.27e-58 (Chi-square test), Q value = 6.1e-55

Table S325.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 7(5Q11.2) CNV 127 7 16 51 44 5 4
DEL PEAK 7(5Q11.2) WILD-TYPE 48 132 201 103 180 42 11

Figure S325.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 7(5q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.03e-54 (Fisher's exact test), Q value = 5e-51

Table S326.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 7(5Q11.2) CNV 21 158 75
DEL PEAK 7(5Q11.2) WILD-TYPE 270 88 359

Figure S326.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MIRSEQ_CNMF'

P value = 1.55e-50 (Fisher's exact test), Q value = 1.3e-47

Table S327.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 7(5Q11.2) CNV 17 64 163
DEL PEAK 7(5Q11.2) WILD-TYPE 257 349 116

Figure S327.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 7(5q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.59e-55 (Fisher's exact test), Q value = 3e-52

Table S328.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 7(5Q11.2) CNV 148 29 67
DEL PEAK 7(5Q11.2) WILD-TYPE 77 347 298

Figure S328.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.49e-35 (Fisher's exact test), Q value = 2.8e-32

Table S329.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 7(5Q11.2) CNV 41 14 115
DEL PEAK 7(5Q11.2) WILD-TYPE 209 196 81

Figure S329.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 7(5q11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.08e-36 (Fisher's exact test), Q value = 2.5e-33

Table S330.  Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 7(5Q11.2) CNV 14 42 114
DEL PEAK 7(5Q11.2) WILD-TYPE 146 269 71

Figure S330.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MRNA_CNMF'

P value = 3.82e-29 (Chi-square test), Q value = 3e-26

Table S331.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 8(5Q21.3) CNV 2 5 19 69 7 24 5 2
DEL PEAK 8(5Q21.3) WILD-TYPE 19 31 100 27 102 48 15 38

Figure S331.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 8(5q21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 2.12e-26 (Fisher's exact test), Q value = 1.6e-23

Table S332.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 8(5Q21.3) CNV 11 80 42
DEL PEAK 8(5Q21.3) WILD-TYPE 111 45 224

Figure S332.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'CN_CNMF'

P value = 1.48e-87 (Chi-square test), Q value = 1.2e-84

Table S333.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 8(5Q21.3) CNV 20 27 7 182 10
DEL PEAK 8(5Q21.3) WILD-TYPE 354 205 72 70 38

Figure S333.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(5q21.3)' versus 'METHLYATION_CNMF'

P value = 8.44e-53 (Chi-square test), Q value = 7e-50

Table S334.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 8(5Q21.3) CNV 90 4 14 26 4 25
DEL PEAK 8(5Q21.3) WILD-TYPE 19 151 92 110 40 88

Figure S334.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 8(5q21.3)' versus 'RPPA_CNMF'

P value = 2.6e-15 (Fisher's exact test), Q value = 1.7e-12

Table S335.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 8(5Q21.3) CNV 76 13 23
DEL PEAK 8(5Q21.3) WILD-TYPE 71 120 94

Figure S335.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 8(5q21.3)' versus 'RPPA_CHIERARCHICAL'

P value = 8.97e-16 (Fisher's exact test), Q value = 5.8e-13

Table S336.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 8(5Q21.3) CNV 26 15 71
DEL PEAK 8(5Q21.3) WILD-TYPE 135 95 55

Figure S336.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MRNASEQ_CNMF'

P value = 2.08e-66 (Chi-square test), Q value = 1.7e-63

Table S337.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 8(5Q21.3) CNV 130 7 12 47 36 4 6
DEL PEAK 8(5Q21.3) WILD-TYPE 45 132 205 107 188 43 9

Figure S337.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 8(5q21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.21e-58 (Fisher's exact test), Q value = 1e-55

Table S338.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 8(5Q21.3) CNV 17 158 67
DEL PEAK 8(5Q21.3) WILD-TYPE 274 88 367

Figure S338.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MIRSEQ_CNMF'

P value = 4.12e-56 (Fisher's exact test), Q value = 3.4e-53

Table S339.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 8(5Q21.3) CNV 12 60 164
DEL PEAK 8(5Q21.3) WILD-TYPE 262 353 115

Figure S339.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 8(5q21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.13e-63 (Fisher's exact test), Q value = 1.8e-60

Table S340.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 8(5Q21.3) CNV 152 23 61
DEL PEAK 8(5Q21.3) WILD-TYPE 73 353 304

Figure S340.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.16e-39 (Fisher's exact test), Q value = 9.5e-37

Table S341.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 8(5Q21.3) CNV 31 12 115
DEL PEAK 8(5Q21.3) WILD-TYPE 219 198 81

Figure S341.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 8(5q21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.97e-44 (Fisher's exact test), Q value = 4.9e-41

Table S342.  Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 8(5Q21.3) CNV 10 32 116
DEL PEAK 8(5Q21.3) WILD-TYPE 150 279 69

Figure S342.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 9(6p25.3)' versus 'CN_CNMF'

P value = 3.08e-08 (Chi-square test), Q value = 1.4e-05

Table S343.  Gene #38: 'Del Peak 9(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 9(6P25.3) CNV 36 69 15 55 11
DEL PEAK 9(6P25.3) WILD-TYPE 338 163 64 197 37

Figure S343.  Get High-res Image Gene #38: 'Del Peak 9(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(6p25.3)' versus 'METHLYATION_CNMF'

P value = 0.000166 (Chi-square test), Q value = 0.042

Table S344.  Gene #38: 'Del Peak 9(6p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 9(6P25.3) CNV 26 16 21 41 5 15
DEL PEAK 9(6P25.3) WILD-TYPE 83 139 85 95 39 98

Figure S344.  Get High-res Image Gene #38: 'Del Peak 9(6p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 9(6p25.3)' versus 'MRNASEQ_CNMF'

P value = 0.000615 (Chi-square test), Q value = 0.14

Table S345.  Gene #38: 'Del Peak 9(6p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 9(6P25.3) CNV 40 14 36 24 61 6 1
DEL PEAK 9(6P25.3) WILD-TYPE 135 125 181 130 163 41 14

Figure S345.  Get High-res Image Gene #38: 'Del Peak 9(6p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(6q15)' versus 'MRNA_CNMF'

P value = 2.42e-06 (Chi-square test), Q value = 0.00086

Table S346.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 10(6Q15) CNV 6 13 62 18 24 29 4 16
DEL PEAK 10(6Q15) WILD-TYPE 15 23 57 78 85 43 16 24

Figure S346.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 10(6q15)' versus 'CN_CNMF'

P value = 4.52e-35 (Chi-square test), Q value = 3.6e-32

Table S347.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 10(6Q15) CNV 76 143 22 43 31
DEL PEAK 10(6Q15) WILD-TYPE 298 89 57 209 17

Figure S347.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(6q15)' versus 'METHLYATION_CNMF'

P value = 3.06e-09 (Chi-square test), Q value = 1.5e-06

Table S348.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 10(6Q15) CNV 19 47 39 69 6 23
DEL PEAK 10(6Q15) WILD-TYPE 90 108 67 67 38 90

Figure S348.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(6q15)' versus 'MRNASEQ_CNMF'

P value = 3.2e-11 (Chi-square test), Q value = 1.7e-08

Table S349.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 10(6Q15) CNV 29 38 62 53 114 12 3
DEL PEAK 10(6Q15) WILD-TYPE 146 101 155 101 110 35 12

Figure S349.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(6q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.15e-05 (Fisher's exact test), Q value = 0.012

Table S350.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 10(6Q15) CNV 86 56 169
DEL PEAK 10(6Q15) WILD-TYPE 205 190 265

Figure S350.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(6q15)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.16e-06 (Fisher's exact test), Q value = 0.0011

Table S351.  Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 10(6Q15) CNV 49 113 150
DEL PEAK 10(6Q15) WILD-TYPE 176 263 215

Figure S351.  Get High-res Image Gene #39: 'Del Peak 10(6q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(6q27)' versus 'CN_CNMF'

P value = 9.1e-16 (Chi-square test), Q value = 5.9e-13

Table S352.  Gene #40: 'Del Peak 11(6q27)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 11(6Q27) CNV 84 120 19 79 30
DEL PEAK 11(6Q27) WILD-TYPE 290 112 60 173 18

Figure S352.  Get High-res Image Gene #40: 'Del Peak 11(6q27)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(6q27)' versus 'MRNASEQ_CNMF'

P value = 0.00108 (Chi-square test), Q value = 0.24

Table S353.  Gene #40: 'Del Peak 11(6q27)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 11(6Q27) CNV 58 43 54 56 100 12 4
DEL PEAK 11(6Q27) WILD-TYPE 117 96 163 98 124 35 11

Figure S353.  Get High-res Image Gene #40: 'Del Peak 11(6q27)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNA_CNMF'

P value = 0.00104 (Chi-square test), Q value = 0.23

Table S354.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 12(7P22.3) CNV 4 3 25 22 3 12 2 4
DEL PEAK 12(7P22.3) WILD-TYPE 17 33 94 74 106 60 18 36

Figure S354.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNA_CHIERARCHICAL'

P value = 7.95e-05 (Fisher's exact test), Q value = 0.022

Table S355.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 12(7P22.3) CNV 5 27 43
DEL PEAK 12(7P22.3) WILD-TYPE 117 98 223

Figure S355.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 12(7p22.3)' versus 'CN_CNMF'

P value = 1.52e-15 (Chi-square test), Q value = 9.8e-13

Table S356.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 12(7P22.3) CNV 11 46 5 60 3
DEL PEAK 12(7P22.3) WILD-TYPE 363 186 74 192 45

Figure S356.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(7p22.3)' versus 'METHLYATION_CNMF'

P value = 1.63e-08 (Chi-square test), Q value = 7.4e-06

Table S357.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 12(7P22.3) CNV 28 7 15 16 1 3
DEL PEAK 12(7P22.3) WILD-TYPE 81 148 91 120 43 110

Figure S357.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNASEQ_CNMF'

P value = 3.96e-10 (Chi-square test), Q value = 2e-07

Table S358.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 12(7P22.3) CNV 45 7 10 25 35 1 1
DEL PEAK 12(7P22.3) WILD-TYPE 130 132 207 129 189 46 14

Figure S358.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.97e-10 (Fisher's exact test), Q value = 3e-07

Table S359.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 12(7P22.3) CNV 12 55 57
DEL PEAK 12(7P22.3) WILD-TYPE 279 191 377

Figure S359.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(7p22.3)' versus 'MIRSEQ_CNMF'

P value = 1.24e-12 (Fisher's exact test), Q value = 7.3e-10

Table S360.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 12(7P22.3) CNV 7 53 62
DEL PEAK 12(7P22.3) WILD-TYPE 267 360 217

Figure S360.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(7p22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.1e-12 (Fisher's exact test), Q value = 6.5e-10

Table S361.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 12(7P22.3) CNV 53 15 54
DEL PEAK 12(7P22.3) WILD-TYPE 172 361 311

Figure S361.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(7p22.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.51e-09 (Fisher's exact test), Q value = 1.7e-06

Table S362.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 12(7P22.3) CNV 23 5 41
DEL PEAK 12(7P22.3) WILD-TYPE 227 205 155

Figure S362.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(7p22.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.25e-06 (Fisher's exact test), Q value = 0.0018

Table S363.  Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 12(7P22.3) CNV 7 25 37
DEL PEAK 12(7P22.3) WILD-TYPE 153 286 148

Figure S363.  Get High-res Image Gene #41: 'Del Peak 12(7p22.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(7q36.1)' versus 'CN_CNMF'

P value = 5.11e-11 (Chi-square test), Q value = 2.7e-08

Table S364.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 13(7Q36.1) CNV 32 61 13 73 5
DEL PEAK 13(7Q36.1) WILD-TYPE 342 171 66 179 43

Figure S364.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(7q36.1)' versus 'MRNASEQ_CNMF'

P value = 2.92e-05 (Chi-square test), Q value = 0.0087

Table S365.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 13(7Q36.1) CNV 42 15 29 47 42 5 1
DEL PEAK 13(7Q36.1) WILD-TYPE 133 124 188 107 182 42 14

Figure S365.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(7q36.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.057

Table S366.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 13(7Q36.1) CNV 33 59 89
DEL PEAK 13(7Q36.1) WILD-TYPE 258 187 345

Figure S366.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(7q36.1)' versus 'MIRSEQ_CNMF'

P value = 1.39e-08 (Fisher's exact test), Q value = 6.4e-06

Table S367.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 13(7Q36.1) CNV 22 82 75
DEL PEAK 13(7Q36.1) WILD-TYPE 252 331 204

Figure S367.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 13(7q36.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.33e-07 (Fisher's exact test), Q value = 5.6e-05

Table S368.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 13(7Q36.1) CNV 58 38 83
DEL PEAK 13(7Q36.1) WILD-TYPE 167 338 282

Figure S368.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(7q36.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.61e-07 (Fisher's exact test), Q value = 0.00036

Table S369.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 13(7Q36.1) CNV 49 16 52
DEL PEAK 13(7Q36.1) WILD-TYPE 201 194 144

Figure S369.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 13(7q36.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.00086

Table S370.  Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 13(7Q36.1) CNV 12 53 52
DEL PEAK 13(7Q36.1) WILD-TYPE 148 258 133

Figure S370.  Get High-res Image Gene #42: 'Del Peak 13(7q36.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'MRNA_CNMF'

P value = 1.61e-09 (Chi-square test), Q value = 7.9e-07

Table S371.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 14(8P23.2) CNV 12 15 78 65 29 47 13 18
DEL PEAK 14(8P23.2) WILD-TYPE 9 21 41 31 80 25 7 22

Figure S371.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNA_CHIERARCHICAL'

P value = 9.89e-06 (Fisher's exact test), Q value = 0.0032

Table S372.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 14(8P23.2) CNV 47 86 144
DEL PEAK 14(8P23.2) WILD-TYPE 75 39 122

Figure S372.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'CN_CNMF'

P value = 1.02e-33 (Chi-square test), Q value = 8.2e-31

Table S373.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 14(8P23.2) CNV 118 156 20 178 40
DEL PEAK 14(8P23.2) WILD-TYPE 256 76 59 74 8

Figure S373.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(8p23.2)' versus 'METHLYATION_CNMF'

P value = 2.07e-13 (Chi-square test), Q value = 1.3e-10

Table S374.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 14(8P23.2) CNV 72 42 55 94 16 50
DEL PEAK 14(8P23.2) WILD-TYPE 37 113 51 42 28 63

Figure S374.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNASEQ_CNMF'

P value = 1.9e-19 (Chi-square test), Q value = 1.3e-16

Table S375.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 14(8P23.2) CNV 109 51 68 108 141 17 13
DEL PEAK 14(8P23.2) WILD-TYPE 66 88 149 46 83 30 2

Figure S375.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.61e-12 (Fisher's exact test), Q value = 1.5e-09

Table S376.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 14(8P23.2) CNV 104 163 240
DEL PEAK 14(8P23.2) WILD-TYPE 187 83 194

Figure S376.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'MIRSEQ_CNMF'

P value = 1.11e-12 (Fisher's exact test), Q value = 6.6e-10

Table S377.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 14(8P23.2) CNV 97 217 186
DEL PEAK 14(8P23.2) WILD-TYPE 177 196 93

Figure S377.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 14(8p23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.37e-15 (Fisher's exact test), Q value = 8.9e-13

Table S378.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 14(8P23.2) CNV 155 136 209
DEL PEAK 14(8P23.2) WILD-TYPE 70 240 156

Figure S378.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.98e-08 (Fisher's exact test), Q value = 1.8e-05

Table S379.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 14(8P23.2) CNV 124 79 130
DEL PEAK 14(8P23.2) WILD-TYPE 126 131 66

Figure S379.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 14(8p23.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.97e-07 (Fisher's exact test), Q value = 0.00012

Table S380.  Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 14(8P23.2) CNV 67 141 125
DEL PEAK 14(8P23.2) WILD-TYPE 93 170 60

Figure S380.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 15(8p11.21)' versus 'MRNA_CNMF'

P value = 0.000194 (Chi-square test), Q value = 0.049

Table S381.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 15(8P11.21) CNV 4 4 23 21 9 27 7 7
DEL PEAK 15(8P11.21) WILD-TYPE 17 32 96 75 100 45 13 33

Figure S381.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 15(8p11.21)' versus 'CN_CNMF'

P value = 1.19e-12 (Chi-square test), Q value = 7e-10

Table S382.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 15(8P11.21) CNV 44 53 8 83 0
DEL PEAK 15(8P11.21) WILD-TYPE 330 179 71 169 48

Figure S382.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(8p11.21)' versus 'MRNASEQ_CNMF'

P value = 1.79e-12 (Chi-square test), Q value = 1e-09

Table S383.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 15(8P11.21) CNV 35 19 23 63 34 7 6
DEL PEAK 15(8P11.21) WILD-TYPE 140 120 194 91 190 40 9

Figure S383.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 15(8p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.61e-05 (Fisher's exact test), Q value = 0.013

Table S384.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 15(8P11.21) CNV 36 68 83
DEL PEAK 15(8P11.21) WILD-TYPE 255 178 351

Figure S384.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(8p11.21)' versus 'MIRSEQ_CNMF'

P value = 9.37e-07 (Fisher's exact test), Q value = 0.00036

Table S385.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 15(8P11.21) CNV 26 88 72
DEL PEAK 15(8P11.21) WILD-TYPE 248 325 207

Figure S385.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 15(8p11.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.74e-07 (Fisher's exact test), Q value = 7.3e-05

Table S386.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 15(8P11.21) CNV 62 41 83
DEL PEAK 15(8P11.21) WILD-TYPE 163 335 282

Figure S386.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(8p11.21)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00049

Table S387.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 15(8P11.21) CNV 57 19 55
DEL PEAK 15(8P11.21) WILD-TYPE 193 191 141

Figure S387.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 15(8p11.21)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.15e-05 (Fisher's exact test), Q value = 0.012

Table S388.  Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 15(8P11.21) CNV 18 57 56
DEL PEAK 15(8P11.21) WILD-TYPE 142 254 129

Figure S388.  Get High-res Image Gene #44: 'Del Peak 15(8p11.21)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 16(9p23)' versus 'MRNA_CNMF'

P value = 6.98e-08 (Chi-square test), Q value = 3e-05

Table S389.  Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 16(9P23) CNV 9 15 56 19 21 34 10 5
DEL PEAK 16(9P23) WILD-TYPE 12 21 63 77 88 38 10 35

Figure S389.  Get High-res Image Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 16(9p23)' versus 'MRNA_CHIERARCHICAL'

P value = 8.19e-06 (Fisher's exact test), Q value = 0.0027

Table S390.  Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 16(9P23) CNV 25 31 113
DEL PEAK 16(9P23) WILD-TYPE 97 94 153

Figure S390.  Get High-res Image Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 16(9p23)' versus 'CN_CNMF'

P value = 6.67e-38 (Chi-square test), Q value = 5.4e-35

Table S391.  Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 16(9P23) CNV 40 139 12 92 11
DEL PEAK 16(9P23) WILD-TYPE 334 93 67 160 37

Figure S391.  Get High-res Image Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(9p23)' versus 'METHLYATION_CNMF'

P value = 1.92e-19 (Chi-square test), Q value = 1.4e-16

Table S392.  Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 16(9P23) CNV 25 17 46 74 7 16
DEL PEAK 16(9P23) WILD-TYPE 84 138 60 62 37 97

Figure S392.  Get High-res Image Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(9p23)' versus 'MRNASEQ_CNMF'

P value = 1.72e-19 (Chi-square test), Q value = 1.2e-16

Table S393.  Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 16(9P23) CNV 34 25 38 69 110 6 8
DEL PEAK 16(9P23) WILD-TYPE 141 114 179 85 114 41 7

Figure S393.  Get High-res Image Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 16(9p23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-08 (Fisher's exact test), Q value = 5e-06

Table S394.  Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 16(9P23) CNV 52 71 167
DEL PEAK 16(9P23) WILD-TYPE 239 175 267

Figure S394.  Get High-res Image Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(9p23)' versus 'MIRSEQ_CNMF'

P value = 6.56e-07 (Fisher's exact test), Q value = 0.00026

Table S395.  Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 16(9P23) CNV 49 149 89
DEL PEAK 16(9P23) WILD-TYPE 225 264 190

Figure S395.  Get High-res Image Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 16(9p23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.34e-12 (Fisher's exact test), Q value = 1.4e-09

Table S396.  Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 16(9P23) CNV 66 67 154
DEL PEAK 16(9P23) WILD-TYPE 159 309 211

Figure S396.  Get High-res Image Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 16(9p23)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.033

Table S397.  Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 16(9P23) CNV 79 36 66
DEL PEAK 16(9P23) WILD-TYPE 171 174 130

Figure S397.  Get High-res Image Gene #45: 'Del Peak 16(9p23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 17(9p21.3)' versus 'MRNA_CNMF'

P value = 2e-06 (Chi-square test), Q value = 0.00072

Table S398.  Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 17(9P21.3) CNV 9 13 60 30 23 38 8 6
DEL PEAK 17(9P21.3) WILD-TYPE 12 23 59 66 86 34 12 34

Figure S398.  Get High-res Image Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 17(9p21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.012

Table S399.  Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 17(9P21.3) CNV 26 43 118
DEL PEAK 17(9P21.3) WILD-TYPE 96 82 148

Figure S399.  Get High-res Image Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 17(9p21.3)' versus 'CN_CNMF'

P value = 3.26e-38 (Chi-square test), Q value = 2.6e-35

Table S400.  Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 17(9P21.3) CNV 45 142 15 113 12
DEL PEAK 17(9P21.3) WILD-TYPE 329 90 64 139 36

Figure S400.  Get High-res Image Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(9p21.3)' versus 'METHLYATION_CNMF'

P value = 1.01e-16 (Chi-square test), Q value = 6.7e-14

Table S401.  Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 17(9P21.3) CNV 36 20 44 75 6 19
DEL PEAK 17(9P21.3) WILD-TYPE 73 135 62 61 38 94

Figure S401.  Get High-res Image Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 1.5e-16 (Chi-square test), Q value = 9.9e-14

Table S402.  Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 17(9P21.3) CNV 54 26 42 73 113 6 7
DEL PEAK 17(9P21.3) WILD-TYPE 121 113 175 81 111 41 8

Figure S402.  Get High-res Image Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.74e-10 (Fisher's exact test), Q value = 9e-08

Table S403.  Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 17(9P21.3) CNV 53 91 177
DEL PEAK 17(9P21.3) WILD-TYPE 238 155 257

Figure S403.  Get High-res Image Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(9p21.3)' versus 'MIRSEQ_CNMF'

P value = 1.22e-10 (Fisher's exact test), Q value = 6.3e-08

Table S404.  Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 17(9P21.3) CNV 47 161 109
DEL PEAK 17(9P21.3) WILD-TYPE 227 252 170

Figure S404.  Get High-res Image Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 17(9p21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.47e-13 (Fisher's exact test), Q value = 1.5e-10

Table S405.  Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 17(9P21.3) CNV 87 71 159
DEL PEAK 17(9P21.3) WILD-TYPE 138 305 206

Figure S405.  Get High-res Image Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(9p21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0037

Table S406.  Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 17(9P21.3) CNV 82 39 77
DEL PEAK 17(9P21.3) WILD-TYPE 168 171 119

Figure S406.  Get High-res Image Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 17(9p21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.14e-05 (Fisher's exact test), Q value = 0.022

Table S407.  Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 17(9P21.3) CNV 30 94 74
DEL PEAK 17(9P21.3) WILD-TYPE 130 217 111

Figure S407.  Get High-res Image Gene #46: 'Del Peak 17(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 18(9q21.11)' versus 'MRNA_CHIERARCHICAL'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.0067

Table S408.  Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 18(9Q21.11) CNV 17 47 88
DEL PEAK 18(9Q21.11) WILD-TYPE 105 78 178

Figure S408.  Get High-res Image Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 18(9q21.11)' versus 'CN_CNMF'

P value = 3.73e-22 (Chi-square test), Q value = 2.8e-19

Table S409.  Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 18(9Q21.11) CNV 37 92 15 106 13
DEL PEAK 18(9Q21.11) WILD-TYPE 337 140 64 146 35

Figure S409.  Get High-res Image Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(9q21.11)' versus 'METHLYATION_CNMF'

P value = 1.3e-11 (Chi-square test), Q value = 7.2e-09

Table S410.  Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 18(9Q21.11) CNV 44 14 24 55 5 21
DEL PEAK 18(9Q21.11) WILD-TYPE 65 141 82 81 39 92

Figure S410.  Get High-res Image Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(9q21.11)' versus 'RPPA_CNMF'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0034

Table S411.  Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 18(9Q21.11) CNV 65 32 22
DEL PEAK 18(9Q21.11) WILD-TYPE 82 101 95

Figure S411.  Get High-res Image Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 18(9q21.11)' versus 'MRNASEQ_CNMF'

P value = 5.21e-11 (Chi-square test), Q value = 2.8e-08

Table S412.  Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 18(9Q21.11) CNV 66 16 36 48 83 6 7
DEL PEAK 18(9Q21.11) WILD-TYPE 109 123 181 106 141 41 8

Figure S412.  Get High-res Image Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 18(9q21.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.26e-09 (Fisher's exact test), Q value = 3e-06

Table S413.  Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 18(9Q21.11) CNV 43 91 128
DEL PEAK 18(9Q21.11) WILD-TYPE 248 155 306

Figure S413.  Get High-res Image Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(9q21.11)' versus 'MIRSEQ_CNMF'

P value = 4.95e-12 (Fisher's exact test), Q value = 2.8e-09

Table S414.  Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 18(9Q21.11) CNV 36 109 111
DEL PEAK 18(9Q21.11) WILD-TYPE 238 304 168

Figure S414.  Get High-res Image Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 18(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.39e-15 (Fisher's exact test), Q value = 4.7e-12

Table S415.  Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 18(9Q21.11) CNV 98 53 105
DEL PEAK 18(9Q21.11) WILD-TYPE 127 323 260

Figure S415.  Get High-res Image Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(9q21.11)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.32e-07 (Fisher's exact test), Q value = 0.00021

Table S416.  Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 18(9Q21.11) CNV 54 33 75
DEL PEAK 18(9Q21.11) WILD-TYPE 196 177 121

Figure S416.  Get High-res Image Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 18(9q21.11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.63e-07 (Fisher's exact test), Q value = 0.00036

Table S417.  Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 18(9Q21.11) CNV 26 64 72
DEL PEAK 18(9Q21.11) WILD-TYPE 134 247 113

Figure S417.  Get High-res Image Gene #47: 'Del Peak 18(9q21.11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 19(9q34.2)' versus 'MRNA_CNMF'

P value = 1.35e-07 (Chi-square test), Q value = 5.7e-05

Table S418.  Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 19(9Q34.2) CNV 6 5 38 52 23 17 7 4
DEL PEAK 19(9Q34.2) WILD-TYPE 15 31 81 44 86 55 13 36

Figure S418.  Get High-res Image Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 19(9q34.2)' versus 'MRNA_CHIERARCHICAL'

P value = 4.43e-08 (Fisher's exact test), Q value = 1.9e-05

Table S419.  Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 19(9Q34.2) CNV 16 58 78
DEL PEAK 19(9Q34.2) WILD-TYPE 106 67 188

Figure S419.  Get High-res Image Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 19(9q34.2)' versus 'CN_CNMF'

P value = 1.98e-35 (Chi-square test), Q value = 1.6e-32

Table S420.  Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 19(9Q34.2) CNV 26 83 12 130 14
DEL PEAK 19(9Q34.2) WILD-TYPE 348 149 67 122 34

Figure S420.  Get High-res Image Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(9q34.2)' versus 'METHLYATION_CNMF'

P value = 3.68e-22 (Chi-square test), Q value = 2.7e-19

Table S421.  Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 19(9Q34.2) CNV 65 12 26 42 4 16
DEL PEAK 19(9Q34.2) WILD-TYPE 44 143 80 94 40 97

Figure S421.  Get High-res Image Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(9q34.2)' versus 'RPPA_CNMF'

P value = 2.47e-05 (Fisher's exact test), Q value = 0.0075

Table S422.  Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 19(9Q34.2) CNV 63 33 21
DEL PEAK 19(9Q34.2) WILD-TYPE 84 100 96

Figure S422.  Get High-res Image Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 19(9q34.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000733 (Fisher's exact test), Q value = 0.17

Table S423.  Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 19(9Q34.2) CNV 44 21 52
DEL PEAK 19(9Q34.2) WILD-TYPE 117 89 74

Figure S423.  Get High-res Image Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(9q34.2)' versus 'MRNASEQ_CNMF'

P value = 6.46e-26 (Chi-square test), Q value = 5e-23

Table S424.  Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 19(9Q34.2) CNV 96 10 33 36 75 3 7
DEL PEAK 19(9Q34.2) WILD-TYPE 79 129 184 118 149 44 8

Figure S424.  Get High-res Image Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 19(9q34.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.02e-18 (Fisher's exact test), Q value = 7e-16

Table S425.  Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 19(9Q34.2) CNV 35 115 110
DEL PEAK 19(9Q34.2) WILD-TYPE 256 131 324

Figure S425.  Get High-res Image Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(9q34.2)' versus 'MIRSEQ_CNMF'

P value = 2.4e-23 (Fisher's exact test), Q value = 1.8e-20

Table S426.  Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 19(9Q34.2) CNV 26 99 131
DEL PEAK 19(9Q34.2) WILD-TYPE 248 314 148

Figure S426.  Get High-res Image Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 19(9q34.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.26e-26 (Fisher's exact test), Q value = 2.5e-23

Table S427.  Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 19(9Q34.2) CNV 116 42 98
DEL PEAK 19(9Q34.2) WILD-TYPE 109 334 267

Figure S427.  Get High-res Image Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 19(9q34.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.07e-16 (Fisher's exact test), Q value = 7.1e-14

Table S428.  Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 19(9Q34.2) CNV 47 25 93
DEL PEAK 19(9Q34.2) WILD-TYPE 203 185 103

Figure S428.  Get High-res Image Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 19(9q34.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.17e-17 (Fisher's exact test), Q value = 4.1e-14

Table S429.  Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 19(9Q34.2) CNV 18 57 90
DEL PEAK 19(9Q34.2) WILD-TYPE 142 254 95

Figure S429.  Get High-res Image Gene #48: 'Del Peak 19(9q34.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 20(10q23.31)' versus 'MRNA_CNMF'

P value = 2.45e-05 (Chi-square test), Q value = 0.0075

Table S430.  Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 20(10Q23.31) CNV 7 7 35 46 21 20 7 3
DEL PEAK 20(10Q23.31) WILD-TYPE 14 29 84 50 88 52 13 37

Figure S430.  Get High-res Image Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 20(10q23.31)' versus 'MRNA_CHIERARCHICAL'

P value = 5.63e-05 (Fisher's exact test), Q value = 0.016

Table S431.  Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 20(10Q23.31) CNV 21 53 72
DEL PEAK 20(10Q23.31) WILD-TYPE 101 72 194

Figure S431.  Get High-res Image Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 20(10q23.31)' versus 'CN_CNMF'

P value = 4.87e-22 (Chi-square test), Q value = 3.6e-19

Table S432.  Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 20(10Q23.31) CNV 44 78 21 123 17
DEL PEAK 20(10Q23.31) WILD-TYPE 330 154 58 129 31

Figure S432.  Get High-res Image Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 20(10q23.31)' versus 'METHLYATION_CNMF'

P value = 5.74e-12 (Chi-square test), Q value = 3.2e-09

Table S433.  Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 20(10Q23.31) CNV 60 24 31 50 11 19
DEL PEAK 20(10Q23.31) WILD-TYPE 49 131 75 86 33 94

Figure S433.  Get High-res Image Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 20(10q23.31)' versus 'RPPA_CNMF'

P value = 1.9e-07 (Fisher's exact test), Q value = 7.9e-05

Table S434.  Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 20(10Q23.31) CNV 67 30 19
DEL PEAK 20(10Q23.31) WILD-TYPE 80 103 98

Figure S434.  Get High-res Image Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 20(10q23.31)' versus 'RPPA_CHIERARCHICAL'

P value = 7.37e-05 (Fisher's exact test), Q value = 0.02

Table S435.  Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 20(10Q23.31) CNV 45 18 53
DEL PEAK 20(10Q23.31) WILD-TYPE 116 92 73

Figure S435.  Get High-res Image Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 20(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 2.1e-15 (Chi-square test), Q value = 1.3e-12

Table S436.  Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 20(10Q23.31) CNV 87 23 37 54 73 2 3
DEL PEAK 20(10Q23.31) WILD-TYPE 88 116 180 100 151 45 12

Figure S436.  Get High-res Image Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 20(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-12 (Fisher's exact test), Q value = 6.3e-10

Table S437.  Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 20(10Q23.31) CNV 48 112 119
DEL PEAK 20(10Q23.31) WILD-TYPE 243 134 315

Figure S437.  Get High-res Image Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(10q23.31)' versus 'MIRSEQ_CNMF'

P value = 3.72e-11 (Fisher's exact test), Q value = 2e-08

Table S438.  Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 20(10Q23.31) CNV 52 99 123
DEL PEAK 20(10Q23.31) WILD-TYPE 222 314 156

Figure S438.  Get High-res Image Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 20(10q23.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.82e-14 (Fisher's exact test), Q value = 1.8e-11

Table S439.  Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 20(10Q23.31) CNV 109 68 97
DEL PEAK 20(10Q23.31) WILD-TYPE 116 308 268

Figure S439.  Get High-res Image Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 20(10q23.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.76e-10 (Fisher's exact test), Q value = 3.9e-07

Table S440.  Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 20(10Q23.31) CNV 56 38 89
DEL PEAK 20(10Q23.31) WILD-TYPE 194 172 107

Figure S440.  Get High-res Image Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 20(10q23.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.77e-09 (Fisher's exact test), Q value = 3.2e-06

Table S441.  Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 20(10Q23.31) CNV 31 68 84
DEL PEAK 20(10Q23.31) WILD-TYPE 129 243 101

Figure S441.  Get High-res Image Gene #49: 'Del Peak 20(10q23.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 21(10q26.3)' versus 'MRNA_CNMF'

P value = 1.01e-08 (Chi-square test), Q value = 4.7e-06

Table S442.  Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 21(10Q26.3) CNV 8 8 37 53 16 21 6 4
DEL PEAK 21(10Q26.3) WILD-TYPE 13 28 82 43 93 51 14 36

Figure S442.  Get High-res Image Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 21(10q26.3)' versus 'MRNA_CHIERARCHICAL'

P value = 2.75e-07 (Fisher's exact test), Q value = 0.00011

Table S443.  Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 21(10Q26.3) CNV 19 59 75
DEL PEAK 21(10Q26.3) WILD-TYPE 103 66 191

Figure S443.  Get High-res Image Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 21(10q26.3)' versus 'CN_CNMF'

P value = 3.2e-25 (Chi-square test), Q value = 2.5e-22

Table S444.  Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 21(10Q26.3) CNV 43 82 19 129 14
DEL PEAK 21(10Q26.3) WILD-TYPE 331 150 60 123 34

Figure S444.  Get High-res Image Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(10q26.3)' versus 'METHLYATION_CNMF'

P value = 8.14e-14 (Chi-square test), Q value = 5e-11

Table S445.  Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 21(10Q26.3) CNV 62 20 38 43 11 20
DEL PEAK 21(10Q26.3) WILD-TYPE 47 135 68 93 33 93

Figure S445.  Get High-res Image Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 21(10q26.3)' versus 'RPPA_CNMF'

P value = 3.06e-08 (Fisher's exact test), Q value = 1.4e-05

Table S446.  Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 21(10Q26.3) CNV 72 27 24
DEL PEAK 21(10Q26.3) WILD-TYPE 75 106 93

Figure S446.  Get High-res Image Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 21(10q26.3)' versus 'RPPA_CHIERARCHICAL'

P value = 8.25e-07 (Fisher's exact test), Q value = 0.00032

Table S447.  Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 21(10Q26.3) CNV 45 18 60
DEL PEAK 21(10Q26.3) WILD-TYPE 116 92 66

Figure S447.  Get High-res Image Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 21(10q26.3)' versus 'MRNASEQ_CNMF'

P value = 3.22e-20 (Chi-square test), Q value = 2.3e-17

Table S448.  Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 21(10Q26.3) CNV 93 18 32 60 71 6 2
DEL PEAK 21(10Q26.3) WILD-TYPE 82 121 185 94 153 41 13

Figure S448.  Get High-res Image Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 21(10q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.86e-17 (Fisher's exact test), Q value = 1.3e-14

Table S449.  Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 21(10Q26.3) CNV 42 120 120
DEL PEAK 21(10Q26.3) WILD-TYPE 249 126 314

Figure S449.  Get High-res Image Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 21(10q26.3)' versus 'MIRSEQ_CNMF'

P value = 7.44e-15 (Fisher's exact test), Q value = 4.7e-12

Table S450.  Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 21(10Q26.3) CNV 44 103 129
DEL PEAK 21(10Q26.3) WILD-TYPE 230 310 150

Figure S450.  Get High-res Image Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 21(10q26.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.12e-19 (Fisher's exact test), Q value = 1.5e-16

Table S451.  Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 21(10Q26.3) CNV 114 57 105
DEL PEAK 21(10Q26.3) WILD-TYPE 111 319 260

Figure S451.  Get High-res Image Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 21(10q26.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.12e-12 (Fisher's exact test), Q value = 6.6e-10

Table S452.  Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 21(10Q26.3) CNV 62 32 94
DEL PEAK 21(10Q26.3) WILD-TYPE 188 178 102

Figure S452.  Get High-res Image Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 21(10q26.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.7e-12 (Fisher's exact test), Q value = 3.2e-09

Table S453.  Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 21(10Q26.3) CNV 25 73 90
DEL PEAK 21(10Q26.3) WILD-TYPE 135 238 95

Figure S453.  Get High-res Image Gene #50: 'Del Peak 21(10q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 22(11p15.5)' versus 'MRNA_CNMF'

P value = 3.55e-07 (Chi-square test), Q value = 0.00014

Table S454.  Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 22(11P15.5) CNV 3 8 32 46 14 32 7 9
DEL PEAK 22(11P15.5) WILD-TYPE 18 28 87 50 95 40 13 31

Figure S454.  Get High-res Image Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 22(11p15.5)' versus 'MRNA_CHIERARCHICAL'

P value = 2.1e-07 (Fisher's exact test), Q value = 8.7e-05

Table S455.  Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 22(11P15.5) CNV 26 62 63
DEL PEAK 22(11P15.5) WILD-TYPE 96 63 203

Figure S455.  Get High-res Image Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 22(11p15.5)' versus 'CN_CNMF'

P value = 1.89e-36 (Chi-square test), Q value = 1.5e-33

Table S456.  Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 22(11P15.5) CNV 34 76 20 143 8
DEL PEAK 22(11P15.5) WILD-TYPE 340 156 59 109 40

Figure S456.  Get High-res Image Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(11p15.5)' versus 'METHLYATION_CNMF'

P value = 4.7e-14 (Chi-square test), Q value = 2.9e-11

Table S457.  Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 22(11P15.5) CNV 57 14 33 45 9 19
DEL PEAK 22(11P15.5) WILD-TYPE 52 141 73 91 35 94

Figure S457.  Get High-res Image Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 22(11p15.5)' versus 'RPPA_CNMF'

P value = 1.27e-09 (Fisher's exact test), Q value = 6.3e-07

Table S458.  Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 22(11P15.5) CNV 76 26 25
DEL PEAK 22(11P15.5) WILD-TYPE 71 107 92

Figure S458.  Get High-res Image Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 22(11p15.5)' versus 'RPPA_CHIERARCHICAL'

P value = 1.65e-06 (Fisher's exact test), Q value = 6e-04

Table S459.  Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 22(11P15.5) CNV 38 26 63
DEL PEAK 22(11P15.5) WILD-TYPE 123 84 63

Figure S459.  Get High-res Image Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 22(11p15.5)' versus 'MRNASEQ_CNMF'

P value = 4.07e-17 (Chi-square test), Q value = 2.7e-14

Table S460.  Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 22(11P15.5) CNV 84 21 26 64 67 9 5
DEL PEAK 22(11P15.5) WILD-TYPE 91 118 191 90 157 38 10

Figure S460.  Get High-res Image Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 22(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.46e-15 (Fisher's exact test), Q value = 2.2e-12

Table S461.  Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 22(11P15.5) CNV 50 119 107
DEL PEAK 22(11P15.5) WILD-TYPE 241 127 327

Figure S461.  Get High-res Image Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 22(11p15.5)' versus 'MIRSEQ_CNMF'

P value = 1.8e-19 (Fisher's exact test), Q value = 1.3e-16

Table S462.  Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 22(11P15.5) CNV 44 91 138
DEL PEAK 22(11P15.5) WILD-TYPE 230 322 141

Figure S462.  Get High-res Image Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 22(11p15.5)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.48e-17 (Fisher's exact test), Q value = 2.3e-14

Table S463.  Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 22(11P15.5) CNV 113 63 97
DEL PEAK 22(11P15.5) WILD-TYPE 112 313 268

Figure S463.  Get High-res Image Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 22(11p15.5)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.07e-13 (Fisher's exact test), Q value = 1.2e-10

Table S464.  Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 22(11P15.5) CNV 53 33 94
DEL PEAK 22(11P15.5) WILD-TYPE 197 177 102

Figure S464.  Get High-res Image Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 22(11p15.5)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.6e-12 (Fisher's exact test), Q value = 9.3e-10

Table S465.  Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 22(11P15.5) CNV 25 66 89
DEL PEAK 22(11P15.5) WILD-TYPE 135 245 96

Figure S465.  Get High-res Image Gene #51: 'Del Peak 22(11p15.5)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 23(11q13.1)' versus 'CN_CNMF'

P value = 6.75e-16 (Chi-square test), Q value = 4.4e-13

Table S466.  Gene #52: 'Del Peak 23(11q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 23(11Q13.1) CNV 34 88 25 51 10
DEL PEAK 23(11Q13.1) WILD-TYPE 340 144 54 201 38

Figure S466.  Get High-res Image Gene #52: 'Del Peak 23(11q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(11q13.1)' versus 'METHLYATION_CNMF'

P value = 4.04e-08 (Chi-square test), Q value = 1.8e-05

Table S467.  Gene #52: 'Del Peak 23(11q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 23(11Q13.1) CNV 22 18 33 47 7 9
DEL PEAK 23(11Q13.1) WILD-TYPE 87 137 73 89 37 104

Figure S467.  Get High-res Image Gene #52: 'Del Peak 23(11q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 23(11q13.1)' versus 'MRNASEQ_CNMF'

P value = 6.01e-09 (Chi-square test), Q value = 2.8e-06

Table S468.  Gene #52: 'Del Peak 23(11q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 23(11Q13.1) CNV 32 21 31 28 85 8 2
DEL PEAK 23(11Q13.1) WILD-TYPE 143 118 186 126 139 39 13

Figure S468.  Get High-res Image Gene #52: 'Del Peak 23(11q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 23(11q13.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000219 (Fisher's exact test), Q value = 0.055

Table S469.  Gene #52: 'Del Peak 23(11q13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 23(11Q13.1) CNV 44 45 118
DEL PEAK 23(11Q13.1) WILD-TYPE 247 201 316

Figure S469.  Get High-res Image Gene #52: 'Del Peak 23(11q13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 24(11q23.2)' versus 'MRNA_CNMF'

P value = 1.86e-07 (Chi-square test), Q value = 7.7e-05

Table S470.  Gene #53: 'Del Peak 24(11q23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 24(11Q23.2) CNV 12 21 87 38 36 37 12 22
DEL PEAK 24(11Q23.2) WILD-TYPE 9 15 32 58 73 35 8 18

Figure S470.  Get High-res Image Gene #53: 'Del Peak 24(11q23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 24(11q23.2)' versus 'CN_CNMF'

P value = 5.01e-39 (Chi-square test), Q value = 4.1e-36

Table S471.  Gene #53: 'Del Peak 24(11q23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 24(11Q23.2) CNV 105 196 39 130 18
DEL PEAK 24(11Q23.2) WILD-TYPE 269 36 40 122 30

Figure S471.  Get High-res Image Gene #53: 'Del Peak 24(11q23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(11q23.2)' versus 'METHLYATION_CNMF'

P value = 2.95e-14 (Chi-square test), Q value = 1.8e-11

Table S472.  Gene #53: 'Del Peak 24(11q23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 24(11Q23.2) CNV 48 52 69 99 20 35
DEL PEAK 24(11Q23.2) WILD-TYPE 61 103 37 37 24 78

Figure S472.  Get High-res Image Gene #53: 'Del Peak 24(11q23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 24(11q23.2)' versus 'MRNASEQ_CNMF'

P value = 1.68e-15 (Chi-square test), Q value = 1.1e-12

Table S473.  Gene #53: 'Del Peak 24(11q23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 24(11Q23.2) CNV 73 62 72 80 165 22 8
DEL PEAK 24(11Q23.2) WILD-TYPE 102 77 145 74 59 25 7

Figure S473.  Get High-res Image Gene #53: 'Del Peak 24(11q23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 24(11q23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000753 (Fisher's exact test), Q value = 0.17

Table S474.  Gene #53: 'Del Peak 24(11q23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 24(11Q23.2) CNV 134 104 244
DEL PEAK 24(11Q23.2) WILD-TYPE 157 142 190

Figure S474.  Get High-res Image Gene #53: 'Del Peak 24(11q23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 24(11q23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.06e-07 (Fisher's exact test), Q value = 0.00027

Table S475.  Gene #53: 'Del Peak 24(11q23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 24(11Q23.2) CNV 98 157 219
DEL PEAK 24(11Q23.2) WILD-TYPE 127 219 146

Figure S475.  Get High-res Image Gene #53: 'Del Peak 24(11q23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(11q25)' versus 'MRNA_CNMF'

P value = 0.00072 (Chi-square test), Q value = 0.16

Table S476.  Gene #54: 'Del Peak 25(11q25)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 25(11Q25) CNV 10 20 75 45 34 37 12 20
DEL PEAK 25(11Q25) WILD-TYPE 11 16 44 51 75 35 8 20

Figure S476.  Get High-res Image Gene #54: 'Del Peak 25(11q25)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 25(11q25)' versus 'CN_CNMF'

P value = 2.14e-36 (Chi-square test), Q value = 1.7e-33

Table S477.  Gene #54: 'Del Peak 25(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 25(11Q25) CNV 91 181 35 131 16
DEL PEAK 25(11Q25) WILD-TYPE 283 51 44 121 32

Figure S477.  Get High-res Image Gene #54: 'Del Peak 25(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(11q25)' versus 'METHLYATION_CNMF'

P value = 2.17e-11 (Chi-square test), Q value = 1.2e-08

Table S478.  Gene #54: 'Del Peak 25(11q25)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 25(11Q25) CNV 51 45 64 87 16 33
DEL PEAK 25(11Q25) WILD-TYPE 58 110 42 49 28 80

Figure S478.  Get High-res Image Gene #54: 'Del Peak 25(11q25)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(11q25)' versus 'MRNASEQ_CNMF'

P value = 1.37e-11 (Chi-square test), Q value = 7.6e-09

Table S479.  Gene #54: 'Del Peak 25(11q25)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 25(11Q25) CNV 82 58 62 72 147 22 6
DEL PEAK 25(11Q25) WILD-TYPE 93 81 155 82 77 25 9

Figure S479.  Get High-res Image Gene #54: 'Del Peak 25(11q25)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(11q25)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.44e-05 (Fisher's exact test), Q value = 0.021

Table S480.  Gene #54: 'Del Peak 25(11q25)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 25(11Q25) CNV 104 142 196
DEL PEAK 25(11Q25) WILD-TYPE 121 234 169

Figure S480.  Get High-res Image Gene #54: 'Del Peak 25(11q25)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(12p13.1)' versus 'CN_CNMF'

P value = 2e-04 (Chi-square test), Q value = 0.05

Table S481.  Gene #55: 'Del Peak 26(12p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 26(12P13.1) CNV 40 51 12 58 6
DEL PEAK 26(12P13.1) WILD-TYPE 334 181 67 194 42

Figure S481.  Get High-res Image Gene #55: 'Del Peak 26(12p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(12p13.1)' versus 'MIRSEQ_CNMF'

P value = 7.45e-05 (Fisher's exact test), Q value = 0.021

Table S482.  Gene #55: 'Del Peak 26(12p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 26(12P13.1) CNV 28 69 67
DEL PEAK 26(12P13.1) WILD-TYPE 246 344 212

Figure S482.  Get High-res Image Gene #55: 'Del Peak 26(12p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 26(12p13.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.48e-06 (Fisher's exact test), Q value = 0.0015

Table S483.  Gene #55: 'Del Peak 26(12p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 26(12P13.1) CNV 56 38 70
DEL PEAK 26(12P13.1) WILD-TYPE 169 338 295

Figure S483.  Get High-res Image Gene #55: 'Del Peak 26(12p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(12p13.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000504 (Fisher's exact test), Q value = 0.12

Table S484.  Gene #55: 'Del Peak 26(12p13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 26(12P13.1) CNV 19 40 47
DEL PEAK 26(12P13.1) WILD-TYPE 141 271 138

Figure S484.  Get High-res Image Gene #55: 'Del Peak 26(12p13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 27(12q24.31)' versus 'MRNA_CNMF'

P value = 5.25e-10 (Chi-square test), Q value = 2.7e-07

Table S485.  Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 27(12Q24.31) CNV 4 6 12 40 5 20 5 6
DEL PEAK 27(12Q24.31) WILD-TYPE 17 30 107 56 104 52 15 34

Figure S485.  Get High-res Image Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 27(12q24.31)' versus 'MRNA_CHIERARCHICAL'

P value = 8.48e-10 (Fisher's exact test), Q value = 4.2e-07

Table S486.  Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 27(12Q24.31) CNV 14 50 34
DEL PEAK 27(12Q24.31) WILD-TYPE 108 75 232

Figure S486.  Get High-res Image Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 27(12q24.31)' versus 'CN_CNMF'

P value = 1.48e-22 (Chi-square test), Q value = 1.1e-19

Table S487.  Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 27(12Q24.31) CNV 35 24 14 100 6
DEL PEAK 27(12Q24.31) WILD-TYPE 339 208 65 152 42

Figure S487.  Get High-res Image Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(12q24.31)' versus 'METHLYATION_CNMF'

P value = 5.16e-19 (Chi-square test), Q value = 3.6e-16

Table S488.  Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 27(12Q24.31) CNV 54 11 18 19 3 13
DEL PEAK 27(12Q24.31) WILD-TYPE 55 144 88 117 41 100

Figure S488.  Get High-res Image Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 27(12q24.31)' versus 'RPPA_CNMF'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0036

Table S489.  Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 27(12Q24.31) CNV 46 12 20
DEL PEAK 27(12Q24.31) WILD-TYPE 101 121 97

Figure S489.  Get High-res Image Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 27(12q24.31)' versus 'RPPA_CHIERARCHICAL'

P value = 7.45e-07 (Fisher's exact test), Q value = 0.00029

Table S490.  Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 27(12Q24.31) CNV 20 13 45
DEL PEAK 27(12Q24.31) WILD-TYPE 141 97 81

Figure S490.  Get High-res Image Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 27(12q24.31)' versus 'MRNASEQ_CNMF'

P value = 4.41e-19 (Chi-square test), Q value = 3.1e-16

Table S491.  Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 27(12Q24.31) CNV 72 15 17 40 24 6 2
DEL PEAK 27(12Q24.31) WILD-TYPE 103 124 200 114 200 41 13

Figure S491.  Get High-res Image Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 27(12q24.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.84e-17 (Fisher's exact test), Q value = 1.2e-14

Table S492.  Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 27(12Q24.31) CNV 32 93 51
DEL PEAK 27(12Q24.31) WILD-TYPE 259 153 383

Figure S492.  Get High-res Image Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(12q24.31)' versus 'MIRSEQ_CNMF'

P value = 5.64e-12 (Fisher's exact test), Q value = 3.2e-09

Table S493.  Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 27(12Q24.31) CNV 29 56 91
DEL PEAK 27(12Q24.31) WILD-TYPE 245 357 188

Figure S493.  Get High-res Image Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 27(12q24.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.4e-13 (Fisher's exact test), Q value = 1.4e-10

Table S494.  Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 27(12Q24.31) CNV 81 41 54
DEL PEAK 27(12Q24.31) WILD-TYPE 144 335 311

Figure S494.  Get High-res Image Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(12q24.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.41e-09 (Fisher's exact test), Q value = 6.9e-07

Table S495.  Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 27(12Q24.31) CNV 33 22 66
DEL PEAK 27(12Q24.31) WILD-TYPE 217 188 130

Figure S495.  Get High-res Image Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 27(12q24.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.62e-11 (Fisher's exact test), Q value = 4e-08

Table S496.  Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 27(12Q24.31) CNV 18 37 66
DEL PEAK 27(12Q24.31) WILD-TYPE 142 274 119

Figure S496.  Get High-res Image Gene #56: 'Del Peak 27(12q24.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 28(13q11)' versus 'MRNA_CNMF'

P value = 9.2e-05 (Chi-square test), Q value = 0.025

Table S497.  Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 28(13Q11) CNV 5 9 58 47 29 39 10 11
DEL PEAK 28(13Q11) WILD-TYPE 16 27 61 49 80 33 10 29

Figure S497.  Get High-res Image Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 28(13q11)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000958 (Fisher's exact test), Q value = 0.21

Table S498.  Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 28(13Q11) CNV 35 65 108
DEL PEAK 28(13Q11) WILD-TYPE 87 60 158

Figure S498.  Get High-res Image Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 28(13q11)' versus 'CN_CNMF'

P value = 4.27e-31 (Chi-square test), Q value = 3.4e-28

Table S499.  Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 28(13Q11) CNV 58 126 48 135 23
DEL PEAK 28(13Q11) WILD-TYPE 316 106 31 117 25

Figure S499.  Get High-res Image Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(13q11)' versus 'METHLYATION_CNMF'

P value = 6.93e-09 (Chi-square test), Q value = 3.2e-06

Table S500.  Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 28(13Q11) CNV 59 37 55 63 7 39
DEL PEAK 28(13Q11) WILD-TYPE 50 118 51 73 37 74

Figure S500.  Get High-res Image Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 28(13q11)' versus 'MRNASEQ_CNMF'

P value = 7.18e-09 (Chi-square test), Q value = 3.4e-06

Table S501.  Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 28(13Q11) CNV 96 36 62 74 97 12 7
DEL PEAK 28(13Q11) WILD-TYPE 79 103 155 80 127 35 8

Figure S501.  Get High-res Image Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 28(13q11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.23e-09 (Fisher's exact test), Q value = 6.1e-07

Table S502.  Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 28(13Q11) CNV 81 135 168
DEL PEAK 28(13Q11) WILD-TYPE 210 111 266

Figure S502.  Get High-res Image Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(13q11)' versus 'MIRSEQ_CNMF'

P value = 1.66e-06 (Fisher's exact test), Q value = 6e-04

Table S503.  Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 28(13Q11) CNV 78 164 139
DEL PEAK 28(13Q11) WILD-TYPE 196 249 140

Figure S503.  Get High-res Image Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 28(13q11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.15e-06 (Fisher's exact test), Q value = 0.00077

Table S504.  Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 28(13Q11) CNV 114 114 153
DEL PEAK 28(13Q11) WILD-TYPE 111 262 212

Figure S504.  Get High-res Image Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(13q11)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.66e-08 (Fisher's exact test), Q value = 1.2e-05

Table S505.  Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 28(13Q11) CNV 93 54 106
DEL PEAK 28(13Q11) WILD-TYPE 157 156 90

Figure S505.  Get High-res Image Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 28(13q11)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.51e-06 (Fisher's exact test), Q value = 0.0015

Table S506.  Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 28(13Q11) CNV 45 110 98
DEL PEAK 28(13Q11) WILD-TYPE 115 201 87

Figure S506.  Get High-res Image Gene #57: 'Del Peak 28(13q11)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 29(13q14.2)' versus 'MRNA_CNMF'

P value = 6.7e-05 (Chi-square test), Q value = 0.019

Table S507.  Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 29(13Q14.2) CNV 8 12 70 56 34 39 9 13
DEL PEAK 29(13Q14.2) WILD-TYPE 13 24 49 40 75 33 11 27

Figure S507.  Get High-res Image Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 29(13q14.2)' versus 'MRNA_CHIERARCHICAL'

P value = 2.5e-05 (Fisher's exact test), Q value = 0.0076

Table S508.  Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 29(13Q14.2) CNV 38 75 128
DEL PEAK 29(13Q14.2) WILD-TYPE 84 50 138

Figure S508.  Get High-res Image Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 29(13q14.2)' versus 'CN_CNMF'

P value = 7.35e-41 (Chi-square test), Q value = 6e-38

Table S509.  Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 29(13Q14.2) CNV 66 147 59 147 28
DEL PEAK 29(13Q14.2) WILD-TYPE 308 85 20 105 20

Figure S509.  Get High-res Image Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(13q14.2)' versus 'METHLYATION_CNMF'

P value = 1.31e-08 (Chi-square test), Q value = 6e-06

Table S510.  Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 29(13Q14.2) CNV 66 46 60 72 12 39
DEL PEAK 29(13Q14.2) WILD-TYPE 43 109 46 64 32 74

Figure S510.  Get High-res Image Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 29(13q14.2)' versus 'MRNASEQ_CNMF'

P value = 7.76e-10 (Chi-square test), Q value = 3.9e-07

Table S511.  Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 29(13Q14.2) CNV 107 39 79 77 118 13 8
DEL PEAK 29(13Q14.2) WILD-TYPE 68 100 138 77 106 34 7

Figure S511.  Get High-res Image Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 29(13q14.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.15e-09 (Fisher's exact test), Q value = 5.7e-07

Table S512.  Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 29(13Q14.2) CNV 93 146 202
DEL PEAK 29(13Q14.2) WILD-TYPE 198 100 232

Figure S512.  Get High-res Image Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(13q14.2)' versus 'MIRSEQ_CNMF'

P value = 1.99e-09 (Fisher's exact test), Q value = 9.7e-07

Table S513.  Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 29(13Q14.2) CNV 82 199 155
DEL PEAK 29(13Q14.2) WILD-TYPE 192 214 124

Figure S513.  Get High-res Image Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 29(13q14.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.25e-09 (Fisher's exact test), Q value = 2.5e-06

Table S514.  Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 29(13Q14.2) CNV 128 125 183
DEL PEAK 29(13Q14.2) WILD-TYPE 97 251 182

Figure S514.  Get High-res Image Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(13q14.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.03e-10 (Fisher's exact test), Q value = 4e-07

Table S515.  Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 29(13Q14.2) CNV 109 57 115
DEL PEAK 29(13Q14.2) WILD-TYPE 141 153 81

Figure S515.  Get High-res Image Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 29(13q14.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.39e-06 (Fisher's exact test), Q value = 0.00085

Table S516.  Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 29(13Q14.2) CNV 48 128 105
DEL PEAK 29(13Q14.2) WILD-TYPE 112 183 80

Figure S516.  Get High-res Image Gene #58: 'Del Peak 29(13q14.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 30(14q24.1)' versus 'MRNA_CNMF'

P value = 1.18e-13 (Chi-square test), Q value = 7.2e-11

Table S517.  Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 30(14Q24.1) CNV 4 8 46 59 10 21 10 8
DEL PEAK 30(14Q24.1) WILD-TYPE 17 28 73 37 99 51 10 32

Figure S517.  Get High-res Image Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 30(14q24.1)' versus 'MRNA_CHIERARCHICAL'

P value = 1.61e-08 (Fisher's exact test), Q value = 7.4e-06

Table S518.  Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 30(14Q24.1) CNV 27 68 71
DEL PEAK 30(14Q24.1) WILD-TYPE 95 57 195

Figure S518.  Get High-res Image Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 30(14q24.1)' versus 'CN_CNMF'

P value = 2.98e-40 (Chi-square test), Q value = 2.4e-37

Table S519.  Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 30(14Q24.1) CNV 40 78 17 157 19
DEL PEAK 30(14Q24.1) WILD-TYPE 334 154 62 95 29

Figure S519.  Get High-res Image Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(14q24.1)' versus 'METHLYATION_CNMF'

P value = 9.21e-19 (Chi-square test), Q value = 6.4e-16

Table S520.  Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 30(14Q24.1) CNV 71 21 33 50 8 22
DEL PEAK 30(14Q24.1) WILD-TYPE 38 134 73 86 36 91

Figure S520.  Get High-res Image Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 30(14q24.1)' versus 'RPPA_CNMF'

P value = 4.19e-07 (Fisher's exact test), Q value = 0.00017

Table S521.  Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 30(14Q24.1) CNV 73 27 32
DEL PEAK 30(14Q24.1) WILD-TYPE 74 106 85

Figure S521.  Get High-res Image Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 30(14q24.1)' versus 'RPPA_CHIERARCHICAL'

P value = 3.69e-06 (Fisher's exact test), Q value = 0.0013

Table S522.  Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 30(14Q24.1) CNV 42 26 64
DEL PEAK 30(14Q24.1) WILD-TYPE 119 84 62

Figure S522.  Get High-res Image Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 30(14q24.1)' versus 'MRNASEQ_CNMF'

P value = 2.75e-33 (Chi-square test), Q value = 2.2e-30

Table S523.  Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 30(14Q24.1) CNV 113 21 24 48 90 5 7
DEL PEAK 30(14Q24.1) WILD-TYPE 62 118 193 106 134 42 8

Figure S523.  Get High-res Image Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(14q24.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.53e-21 (Fisher's exact test), Q value = 1.8e-18

Table S524.  Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 30(14Q24.1) CNV 48 136 124
DEL PEAK 30(14Q24.1) WILD-TYPE 243 110 310

Figure S524.  Get High-res Image Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 30(14q24.1)' versus 'MIRSEQ_CNMF'

P value = 6.54e-22 (Fisher's exact test), Q value = 4.8e-19

Table S525.  Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 30(14Q24.1) CNV 48 102 151
DEL PEAK 30(14Q24.1) WILD-TYPE 226 311 128

Figure S525.  Get High-res Image Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 30(14q24.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.97e-24 (Fisher's exact test), Q value = 3.8e-21

Table S526.  Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 30(14Q24.1) CNV 128 61 112
DEL PEAK 30(14Q24.1) WILD-TYPE 97 315 253

Figure S526.  Get High-res Image Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(14q24.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.66e-18 (Fisher's exact test), Q value = 1.8e-15

Table S527.  Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 30(14Q24.1) CNV 66 34 111
DEL PEAK 30(14Q24.1) WILD-TYPE 184 176 85

Figure S527.  Get High-res Image Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 30(14q24.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.14e-14 (Fisher's exact test), Q value = 7.1e-12

Table S528.  Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 30(14Q24.1) CNV 28 81 102
DEL PEAK 30(14Q24.1) WILD-TYPE 132 230 83

Figure S528.  Get High-res Image Gene #59: 'Del Peak 30(14q24.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 31(15q13.1)' versus 'MRNA_CNMF'

P value = 4.93e-07 (Chi-square test), Q value = 2e-04

Table S529.  Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 31(15Q13.1) CNV 5 11 41 56 23 33 10 8
DEL PEAK 31(15Q13.1) WILD-TYPE 16 25 78 40 86 39 10 32

Figure S529.  Get High-res Image Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 31(15q13.1)' versus 'MRNA_CHIERARCHICAL'

P value = 1.62e-07 (Fisher's exact test), Q value = 6.8e-05

Table S530.  Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 31(15Q13.1) CNV 25 68 94
DEL PEAK 31(15Q13.1) WILD-TYPE 97 57 172

Figure S530.  Get High-res Image Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 31(15q13.1)' versus 'CN_CNMF'

P value = 1.24e-42 (Chi-square test), Q value = 1e-39

Table S531.  Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 31(15Q13.1) CNV 46 74 40 165 11
DEL PEAK 31(15Q13.1) WILD-TYPE 328 158 39 87 37

Figure S531.  Get High-res Image Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(15q13.1)' versus 'METHLYATION_CNMF'

P value = 2.91e-14 (Chi-square test), Q value = 1.8e-11

Table S532.  Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 31(15Q13.1) CNV 69 25 35 52 12 26
DEL PEAK 31(15Q13.1) WILD-TYPE 40 130 71 84 32 87

Figure S532.  Get High-res Image Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 31(15q13.1)' versus 'RPPA_CNMF'

P value = 0.000193 (Fisher's exact test), Q value = 0.049

Table S533.  Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 31(15Q13.1) CNV 76 39 38
DEL PEAK 31(15Q13.1) WILD-TYPE 71 94 79

Figure S533.  Get High-res Image Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 31(15q13.1)' versus 'RPPA_CHIERARCHICAL'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.0071

Table S534.  Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 31(15Q13.1) CNV 54 30 69
DEL PEAK 31(15Q13.1) WILD-TYPE 107 80 57

Figure S534.  Get High-res Image Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 31(15q13.1)' versus 'MRNASEQ_CNMF'

P value = 1.6e-21 (Chi-square test), Q value = 1.2e-18

Table S535.  Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 31(15Q13.1) CNV 109 26 46 66 73 5 7
DEL PEAK 31(15Q13.1) WILD-TYPE 66 113 171 88 151 42 8

Figure S535.  Get High-res Image Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(15q13.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.48e-20 (Fisher's exact test), Q value = 1.8e-17

Table S536.  Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 31(15Q13.1) CNV 53 140 139
DEL PEAK 31(15Q13.1) WILD-TYPE 238 106 295

Figure S536.  Get High-res Image Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q13.1)' versus 'MIRSEQ_CNMF'

P value = 8.06e-21 (Fisher's exact test), Q value = 5.8e-18

Table S537.  Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 31(15Q13.1) CNV 45 130 152
DEL PEAK 31(15Q13.1) WILD-TYPE 229 283 127

Figure S537.  Get High-res Image Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 31(15q13.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.89e-21 (Fisher's exact test), Q value = 1.4e-18

Table S538.  Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 31(15Q13.1) CNV 133 75 119
DEL PEAK 31(15Q13.1) WILD-TYPE 92 301 246

Figure S538.  Get High-res Image Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(15q13.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.65e-17 (Fisher's exact test), Q value = 1.8e-14

Table S539.  Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 31(15Q13.1) CNV 80 31 108
DEL PEAK 31(15Q13.1) WILD-TYPE 170 179 88

Figure S539.  Get High-res Image Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 31(15q13.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.67e-16 (Fisher's exact test), Q value = 5e-13

Table S540.  Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 31(15Q13.1) CNV 26 88 105
DEL PEAK 31(15Q13.1) WILD-TYPE 134 223 80

Figure S540.  Get High-res Image Gene #60: 'Del Peak 31(15q13.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 32(16q24.3)' versus 'MRNA_CNMF'

P value = 9.32e-17 (Chi-square test), Q value = 6.2e-14

Table S541.  Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 32(16Q24.3) CNV 16 25 81 27 94 45 13 35
DEL PEAK 32(16Q24.3) WILD-TYPE 5 11 38 69 15 27 7 5

Figure S541.  Get High-res Image Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 32(16q24.3)' versus 'MRNA_CHIERARCHICAL'

P value = 2.67e-14 (Fisher's exact test), Q value = 1.7e-11

Table S542.  Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 32(16Q24.3) CNV 96 45 195
DEL PEAK 32(16Q24.3) WILD-TYPE 26 80 71

Figure S542.  Get High-res Image Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 32(16q24.3)' versus 'CN_CNMF'

P value = 1.26e-12 (Chi-square test), Q value = 7.4e-10

Table S543.  Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 32(16Q24.3) CNV 268 150 64 114 37
DEL PEAK 32(16Q24.3) WILD-TYPE 106 82 15 138 11

Figure S543.  Get High-res Image Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(16q24.3)' versus 'METHLYATION_CNMF'

P value = 3.67e-12 (Chi-square test), Q value = 2.1e-09

Table S544.  Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 32(16Q24.3) CNV 42 127 79 81 23 64
DEL PEAK 32(16Q24.3) WILD-TYPE 67 28 27 55 21 49

Figure S544.  Get High-res Image Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 32(16q24.3)' versus 'RPPA_CNMF'

P value = 1.14e-09 (Fisher's exact test), Q value = 5.7e-07

Table S545.  Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 32(16Q24.3) CNV 63 103 84
DEL PEAK 32(16Q24.3) WILD-TYPE 84 30 33

Figure S545.  Get High-res Image Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 32(16q24.3)' versus 'RPPA_CHIERARCHICAL'

P value = 3.45e-11 (Fisher's exact test), Q value = 1.9e-08

Table S546.  Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 32(16Q24.3) CNV 119 83 48
DEL PEAK 32(16Q24.3) WILD-TYPE 42 27 78

Figure S546.  Get High-res Image Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 32(16q24.3)' versus 'MRNASEQ_CNMF'

P value = 2.38e-29 (Chi-square test), Q value = 1.9e-26

Table S547.  Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 32(16Q24.3) CNV 53 109 182 91 138 39 12
DEL PEAK 32(16Q24.3) WILD-TYPE 122 30 35 63 86 8 3

Figure S547.  Get High-res Image Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(16q24.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.35e-24 (Fisher's exact test), Q value = 1e-21

Table S548.  Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 32(16Q24.3) CNV 225 90 309
DEL PEAK 32(16Q24.3) WILD-TYPE 66 156 125

Figure S548.  Get High-res Image Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(16q24.3)' versus 'MIRSEQ_CNMF'

P value = 1.43e-18 (Fisher's exact test), Q value = 9.8e-16

Table S549.  Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 32(16Q24.3) CNV 208 295 118
DEL PEAK 32(16Q24.3) WILD-TYPE 66 118 161

Figure S549.  Get High-res Image Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 32(16q24.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.01e-22 (Fisher's exact test), Q value = 3e-19

Table S550.  Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 32(16Q24.3) CNV 88 298 235
DEL PEAK 32(16Q24.3) WILD-TYPE 137 78 130

Figure S550.  Get High-res Image Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(16q24.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.6e-12 (Fisher's exact test), Q value = 1.5e-09

Table S551.  Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 32(16Q24.3) CNV 172 159 83
DEL PEAK 32(16Q24.3) WILD-TYPE 78 51 113

Figure S551.  Get High-res Image Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 32(16q24.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.38e-13 (Fisher's exact test), Q value = 3.8e-10

Table S552.  Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 32(16Q24.3) CNV 126 211 77
DEL PEAK 32(16Q24.3) WILD-TYPE 34 100 108

Figure S552.  Get High-res Image Gene #61: 'Del Peak 32(16q24.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 33(17p12)' versus 'MRNA_CNMF'

P value = 1.95e-11 (Chi-square test), Q value = 1.1e-08

Table S553.  Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 33(17P12) CNV 14 27 78 61 33 60 15 24
DEL PEAK 33(17P12) WILD-TYPE 7 9 41 35 76 12 5 16

Figure S553.  Get High-res Image Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 33(17p12)' versus 'CN_CNMF'

P value = 3.78e-27 (Chi-square test), Q value = 2.9e-24

Table S554.  Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 33(17P12) CNV 147 180 43 195 26
DEL PEAK 33(17P12) WILD-TYPE 227 52 36 57 22

Figure S554.  Get High-res Image Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 33(17p12)' versus 'METHLYATION_CNMF'

P value = 1.69e-08 (Chi-square test), Q value = 7.6e-06

Table S555.  Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 33(17P12) CNV 67 66 76 102 23 55
DEL PEAK 33(17P12) WILD-TYPE 42 89 30 34 21 58

Figure S555.  Get High-res Image Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 33(17p12)' versus 'RPPA_CNMF'

P value = 8.07e-05 (Fisher's exact test), Q value = 0.022

Table S556.  Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 33(17P12) CNV 109 67 65
DEL PEAK 33(17P12) WILD-TYPE 38 66 52

Figure S556.  Get High-res Image Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 33(17p12)' versus 'MRNASEQ_CNMF'

P value = 6.36e-18 (Chi-square test), Q value = 4.3e-15

Table S557.  Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 33(17P12) CNV 107 73 82 126 159 25 12
DEL PEAK 33(17P12) WILD-TYPE 68 66 135 28 65 22 3

Figure S557.  Get High-res Image Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 33(17p12)' versus 'MIRSEQ_CNMF'

P value = 2.3e-06 (Fisher's exact test), Q value = 0.00082

Table S558.  Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 33(17P12) CNV 138 245 199
DEL PEAK 33(17P12) WILD-TYPE 136 168 80

Figure S558.  Get High-res Image Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 33(17p12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-06 (Fisher's exact test), Q value = 0.0029

Table S559.  Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 33(17P12) CNV 153 191 238
DEL PEAK 33(17P12) WILD-TYPE 72 185 127

Figure S559.  Get High-res Image Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 33(17p12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000325 (Fisher's exact test), Q value = 0.079

Table S560.  Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 33(17P12) CNV 148 106 137
DEL PEAK 33(17P12) WILD-TYPE 102 104 59

Figure S560.  Get High-res Image Gene #62: 'Del Peak 33(17p12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 34(17q21.31)' versus 'MRNA_CNMF'

P value = 1.97e-15 (Chi-square test), Q value = 1.3e-12

Table S561.  Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 34(17Q21.31) CNV 7 17 28 51 13 50 9 15
DEL PEAK 34(17Q21.31) WILD-TYPE 14 19 91 45 96 22 11 25

Figure S561.  Get High-res Image Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 34(17q21.31)' versus 'MRNA_CHIERARCHICAL'

P value = 2.29e-07 (Fisher's exact test), Q value = 9.4e-05

Table S562.  Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 34(17Q21.31) CNV 42 72 76
DEL PEAK 34(17Q21.31) WILD-TYPE 80 53 190

Figure S562.  Get High-res Image Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 34(17q21.31)' versus 'CN_CNMF'

P value = 1.64e-26 (Chi-square test), Q value = 1.3e-23

Table S563.  Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 34(17Q21.31) CNV 76 77 21 157 9
DEL PEAK 34(17Q21.31) WILD-TYPE 298 155 58 95 39

Figure S563.  Get High-res Image Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 34(17q21.31)' versus 'METHLYATION_CNMF'

P value = 8.14e-14 (Chi-square test), Q value = 5e-11

Table S564.  Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 34(17Q21.31) CNV 66 19 37 42 11 35
DEL PEAK 34(17Q21.31) WILD-TYPE 43 136 69 94 33 78

Figure S564.  Get High-res Image Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 34(17q21.31)' versus 'RPPA_CNMF'

P value = 1.86e-11 (Fisher's exact test), Q value = 1e-08

Table S565.  Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 34(17Q21.31) CNV 87 25 44
DEL PEAK 34(17Q21.31) WILD-TYPE 60 108 73

Figure S565.  Get High-res Image Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 34(17q21.31)' versus 'RPPA_CHIERARCHICAL'

P value = 3.12e-11 (Fisher's exact test), Q value = 1.7e-08

Table S566.  Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 34(17Q21.31) CNV 42 33 81
DEL PEAK 34(17Q21.31) WILD-TYPE 119 77 45

Figure S566.  Get High-res Image Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 34(17q21.31)' versus 'MRNASEQ_CNMF'

P value = 2.01e-35 (Chi-square test), Q value = 1.6e-32

Table S567.  Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 34(17Q21.31) CNV 91 35 28 109 53 13 6
DEL PEAK 34(17Q21.31) WILD-TYPE 84 104 189 45 171 34 9

Figure S567.  Get High-res Image Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 34(17q21.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.06e-21 (Fisher's exact test), Q value = 5.8e-18

Table S568.  Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 34(17Q21.31) CNV 75 148 112
DEL PEAK 34(17Q21.31) WILD-TYPE 216 98 322

Figure S568.  Get High-res Image Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(17q21.31)' versus 'MIRSEQ_CNMF'

P value = 4.9e-15 (Fisher's exact test), Q value = 3.1e-12

Table S569.  Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 34(17Q21.31) CNV 58 127 148
DEL PEAK 34(17Q21.31) WILD-TYPE 216 286 131

Figure S569.  Get High-res Image Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 34(17q21.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.5e-12 (Fisher's exact test), Q value = 8.7e-10

Table S570.  Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 34(17Q21.31) CNV 118 86 129
DEL PEAK 34(17Q21.31) WILD-TYPE 107 290 236

Figure S570.  Get High-res Image Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(17q21.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.24e-12 (Fisher's exact test), Q value = 7.3e-10

Table S571.  Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 34(17Q21.31) CNV 80 42 107
DEL PEAK 34(17Q21.31) WILD-TYPE 170 168 89

Figure S571.  Get High-res Image Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 34(17q21.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.07e-12 (Fisher's exact test), Q value = 1.8e-09

Table S572.  Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 34(17Q21.31) CNV 39 85 105
DEL PEAK 34(17Q21.31) WILD-TYPE 121 226 80

Figure S572.  Get High-res Image Gene #63: 'Del Peak 34(17q21.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 35(18q23)' versus 'MRNA_CNMF'

P value = 0.000183 (Chi-square test), Q value = 0.046

Table S573.  Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 35(18Q23) CNV 6 13 38 37 18 37 6 9
DEL PEAK 35(18Q23) WILD-TYPE 15 23 81 59 91 35 14 31

Figure S573.  Get High-res Image Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(18q23)' versus 'CN_CNMF'

P value = 7.46e-16 (Chi-square test), Q value = 4.9e-13

Table S574.  Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 35(18Q23) CNV 64 94 30 121 12
DEL PEAK 35(18Q23) WILD-TYPE 310 138 49 131 36

Figure S574.  Get High-res Image Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(18q23)' versus 'METHLYATION_CNMF'

P value = 2.54e-10 (Chi-square test), Q value = 1.3e-07

Table S575.  Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 35(18Q23) CNV 45 27 55 58 10 23
DEL PEAK 35(18Q23) WILD-TYPE 64 128 51 78 34 90

Figure S575.  Get High-res Image Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 35(18q23)' versus 'MRNASEQ_CNMF'

P value = 4.43e-12 (Chi-square test), Q value = 2.5e-09

Table S576.  Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 35(18Q23) CNV 69 27 41 82 78 12 5
DEL PEAK 35(18Q23) WILD-TYPE 106 112 176 72 146 35 10

Figure S576.  Get High-res Image Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(18q23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.5e-05 (Fisher's exact test), Q value = 0.021

Table S577.  Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 35(18Q23) CNV 73 105 136
DEL PEAK 35(18Q23) WILD-TYPE 218 141 298

Figure S577.  Get High-res Image Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(18q23)' versus 'MIRSEQ_CNMF'

P value = 2.83e-05 (Fisher's exact test), Q value = 0.0084

Table S578.  Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 35(18Q23) CNV 65 135 117
DEL PEAK 35(18Q23) WILD-TYPE 209 278 162

Figure S578.  Get High-res Image Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 35(18q23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.01e-05 (Fisher's exact test), Q value = 0.0062

Table S579.  Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 35(18Q23) CNV 98 95 124
DEL PEAK 35(18Q23) WILD-TYPE 127 281 241

Figure S579.  Get High-res Image Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 35(18q23)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.08e-07 (Fisher's exact test), Q value = 0.00024

Table S580.  Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 35(18Q23) CNV 74 44 89
DEL PEAK 35(18Q23) WILD-TYPE 176 166 107

Figure S580.  Get High-res Image Gene #64: 'Del Peak 35(18q23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 36(19p13.3)' versus 'MRNA_CNMF'

P value = 5.5e-11 (Chi-square test), Q value = 2.9e-08

Table S581.  Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 36(19P13.3) CNV 7 10 49 55 13 35 6 6
DEL PEAK 36(19P13.3) WILD-TYPE 14 26 70 41 96 37 14 34

Figure S581.  Get High-res Image Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 36(19p13.3)' versus 'MRNA_CHIERARCHICAL'

P value = 2.25e-08 (Fisher's exact test), Q value = 1e-05

Table S582.  Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 36(19P13.3) CNV 21 66 94
DEL PEAK 36(19P13.3) WILD-TYPE 101 59 172

Figure S582.  Get High-res Image Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(19p13.3)' versus 'CN_CNMF'

P value = 1.92e-48 (Chi-square test), Q value = 1.6e-45

Table S583.  Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 36(19P13.3) CNV 31 116 11 151 16
DEL PEAK 36(19P13.3) WILD-TYPE 343 116 68 101 32

Figure S583.  Get High-res Image Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 36(19p13.3)' versus 'METHLYATION_CNMF'

P value = 1.44e-21 (Chi-square test), Q value = 1.1e-18

Table S584.  Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 36(19P13.3) CNV 59 9 31 66 5 25
DEL PEAK 36(19P13.3) WILD-TYPE 50 146 75 70 39 88

Figure S584.  Get High-res Image Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 36(19p13.3)' versus 'RPPA_CNMF'

P value = 4.63e-06 (Fisher's exact test), Q value = 0.0016

Table S585.  Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 36(19P13.3) CNV 78 38 32
DEL PEAK 36(19P13.3) WILD-TYPE 69 95 85

Figure S585.  Get High-res Image Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 36(19p13.3)' versus 'RPPA_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.0062

Table S586.  Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 36(19P13.3) CNV 48 32 68
DEL PEAK 36(19P13.3) WILD-TYPE 113 78 58

Figure S586.  Get High-res Image Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 36(19p13.3)' versus 'MRNASEQ_CNMF'

P value = 3.43e-27 (Chi-square test), Q value = 2.7e-24

Table S587.  Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 36(19P13.3) CNV 97 22 21 66 96 9 9
DEL PEAK 36(19P13.3) WILD-TYPE 78 117 196 88 128 38 6

Figure S587.  Get High-res Image Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 36(19p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.27e-19 (Fisher's exact test), Q value = 2.3e-16

Table S588.  Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 36(19P13.3) CNV 43 126 151
DEL PEAK 36(19P13.3) WILD-TYPE 248 120 283

Figure S588.  Get High-res Image Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 1.01e-25 (Fisher's exact test), Q value = 7.8e-23

Table S589.  Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 36(19P13.3) CNV 33 132 150
DEL PEAK 36(19P13.3) WILD-TYPE 241 281 129

Figure S589.  Get High-res Image Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 36(19p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.83e-28 (Fisher's exact test), Q value = 3e-25

Table S590.  Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 36(19P13.3) CNV 128 53 134
DEL PEAK 36(19P13.3) WILD-TYPE 97 323 231

Figure S590.  Get High-res Image Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 36(19p13.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.14e-17 (Fisher's exact test), Q value = 3.4e-14

Table S591.  Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 36(19P13.3) CNV 70 33 108
DEL PEAK 36(19P13.3) WILD-TYPE 180 177 88

Figure S591.  Get High-res Image Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 36(19p13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.53e-12 (Fisher's exact test), Q value = 4.2e-09

Table S592.  Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 36(19P13.3) CNV 32 81 98
DEL PEAK 36(19P13.3) WILD-TYPE 128 230 87

Figure S592.  Get High-res Image Gene #65: 'Del Peak 36(19p13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 37(19q13.32)' versus 'MRNA_CNMF'

P value = 8.89e-07 (Chi-square test), Q value = 0.00034

Table S593.  Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 37(19Q13.32) CNV 4 7 22 24 7 29 1 3
DEL PEAK 37(19Q13.32) WILD-TYPE 17 29 97 72 102 43 19 37

Figure S593.  Get High-res Image Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 37(19q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.0043

Table S594.  Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 37(19Q13.32) CNV 8 36 53
DEL PEAK 37(19Q13.32) WILD-TYPE 114 89 213

Figure S594.  Get High-res Image Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 37(19q13.32)' versus 'CN_CNMF'

P value = 2.29e-21 (Chi-square test), Q value = 1.7e-18

Table S595.  Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 37(19Q13.32) CNV 22 72 5 84 10
DEL PEAK 37(19Q13.32) WILD-TYPE 352 160 74 168 38

Figure S595.  Get High-res Image Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 37(19q13.32)' versus 'METHLYATION_CNMF'

P value = 6.73e-11 (Chi-square test), Q value = 3.5e-08

Table S596.  Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 37(19Q13.32) CNV 38 6 22 42 4 17
DEL PEAK 37(19Q13.32) WILD-TYPE 71 149 84 94 40 96

Figure S596.  Get High-res Image Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(19q13.32)' versus 'RPPA_CNMF'

P value = 0.000783 (Fisher's exact test), Q value = 0.18

Table S597.  Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 147 133 117
DEL PEAK 37(19Q13.32) CNV 44 20 15
DEL PEAK 37(19Q13.32) WILD-TYPE 103 113 102

Figure S597.  Get High-res Image Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 37(19q13.32)' versus 'RPPA_CHIERARCHICAL'

P value = 4.95e-05 (Fisher's exact test), Q value = 0.014

Table S598.  Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 110 126
DEL PEAK 37(19Q13.32) CNV 27 11 41
DEL PEAK 37(19Q13.32) WILD-TYPE 134 99 85

Figure S598.  Get High-res Image Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 37(19q13.32)' versus 'MRNASEQ_CNMF'

P value = 6.95e-15 (Chi-square test), Q value = 4.4e-12

Table S599.  Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 37(19Q13.32) CNV 52 9 17 55 54 4 1
DEL PEAK 37(19Q13.32) WILD-TYPE 123 130 200 99 170 43 14

Figure S599.  Get High-res Image Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 37(19q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.03e-12 (Fisher's exact test), Q value = 6.1e-10

Table S600.  Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 37(19Q13.32) CNV 23 81 88
DEL PEAK 37(19Q13.32) WILD-TYPE 268 165 346

Figure S600.  Get High-res Image Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(19q13.32)' versus 'MIRSEQ_CNMF'

P value = 2.97e-14 (Fisher's exact test), Q value = 1.8e-11

Table S601.  Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 37(19Q13.32) CNV 16 84 86
DEL PEAK 37(19Q13.32) WILD-TYPE 258 329 193

Figure S601.  Get High-res Image Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 37(19q13.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.49e-16 (Fisher's exact test), Q value = 5.5e-13

Table S602.  Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 37(19Q13.32) CNV 68 26 92
DEL PEAK 37(19Q13.32) WILD-TYPE 157 350 273

Figure S602.  Get High-res Image Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 37(19q13.32)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.55e-12 (Fisher's exact test), Q value = 3.1e-09

Table S603.  Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 37(19Q13.32) CNV 51 13 66
DEL PEAK 37(19Q13.32) WILD-TYPE 199 197 130

Figure S603.  Get High-res Image Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 37(19q13.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.55e-10 (Fisher's exact test), Q value = 3.8e-07

Table S604.  Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 37(19Q13.32) CNV 12 54 64
DEL PEAK 37(19Q13.32) WILD-TYPE 148 257 121

Figure S604.  Get High-res Image Gene #66: 'Del Peak 37(19q13.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 38(20p13)' versus 'MRNA_CNMF'

P value = 4.49e-06 (Chi-square test), Q value = 0.0015

Table S605.  Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 38(20P13) CNV 1 3 28 24 3 16 3 1
DEL PEAK 38(20P13) WILD-TYPE 20 33 91 72 106 56 17 39

Figure S605.  Get High-res Image Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 38(20p13)' versus 'MRNA_CHIERARCHICAL'

P value = 6.53e-05 (Fisher's exact test), Q value = 0.018

Table S606.  Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 125 266
DEL PEAK 38(20P13) CNV 7 32 40
DEL PEAK 38(20P13) WILD-TYPE 115 93 226

Figure S606.  Get High-res Image Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(20p13)' versus 'CN_CNMF'

P value = 2.38e-16 (Chi-square test), Q value = 1.6e-13

Table S607.  Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 38(20P13) CNV 15 40 6 71 12
DEL PEAK 38(20P13) WILD-TYPE 359 192 73 181 36

Figure S607.  Get High-res Image Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 38(20p13)' versus 'METHLYATION_CNMF'

P value = 4.52e-13 (Chi-square test), Q value = 2.7e-10

Table S608.  Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 38(20P13) CNV 39 5 13 22 4 7
DEL PEAK 38(20P13) WILD-TYPE 70 150 93 114 40 106

Figure S608.  Get High-res Image Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 38(20p13)' versus 'MRNASEQ_CNMF'

P value = 3.18e-15 (Chi-square test), Q value = 2e-12

Table S609.  Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 38(20P13) CNV 52 7 7 27 48 1 1
DEL PEAK 38(20P13) WILD-TYPE 123 132 210 127 176 46 14

Figure S609.  Get High-res Image Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 38(20p13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-10 (Fisher's exact test), Q value = 5.5e-08

Table S610.  Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 291 246 434
DEL PEAK 38(20P13) CNV 20 68 55
DEL PEAK 38(20P13) WILD-TYPE 271 178 379

Figure S610.  Get High-res Image Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(20p13)' versus 'MIRSEQ_CNMF'

P value = 8.71e-15 (Fisher's exact test), Q value = 5.5e-12

Table S611.  Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 274 413 279
DEL PEAK 38(20P13) CNV 12 47 77
DEL PEAK 38(20P13) WILD-TYPE 262 366 202

Figure S611.  Get High-res Image Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 38(20p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.36e-17 (Fisher's exact test), Q value = 9.2e-15

Table S612.  Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 376 365
DEL PEAK 38(20P13) CNV 69 17 50
DEL PEAK 38(20P13) WILD-TYPE 156 359 315

Figure S612.  Get High-res Image Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 38(20p13)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.59e-10 (Fisher's exact test), Q value = 8.3e-08

Table S613.  Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 250 210 196
DEL PEAK 38(20P13) CNV 27 11 55
DEL PEAK 38(20P13) WILD-TYPE 223 199 141

Figure S613.  Get High-res Image Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 38(20p13)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.8e-10 (Fisher's exact test), Q value = 2.9e-07

Table S614.  Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 160 311 185
DEL PEAK 38(20P13) CNV 9 31 53
DEL PEAK 38(20P13) WILD-TYPE 151 280 132

Figure S614.  Get High-res Image Gene #67: 'Del Peak 38(20p13)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 39(21q11.2)' versus 'MRNA_CNMF'

P value = 0.000341 (Chi-square test), Q value = 0.082

Table S615.  Gene #68: 'Del Peak 39(21q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 36 119 96 109 72 20 40
DEL PEAK 39(21Q11.2) CNV 3 11 37 15 11 22 3 4
DEL PEAK 39(21Q11.2) WILD-TYPE 18 25 82 81 98 50 17 36

Figure S615.  Get High-res Image Gene #68: 'Del Peak 39(21q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 39(21q11.2)' versus 'CN_CNMF'

P value = 4.09e-12 (Chi-square test), Q value = 2.3e-09

Table S616.  Gene #68: 'Del Peak 39(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 39(21Q11.2) CNV 29 73 16 63 11
DEL PEAK 39(21Q11.2) WILD-TYPE 345 159 63 189 37

Figure S616.  Get High-res Image Gene #68: 'Del Peak 39(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 39(21q11.2)' versus 'METHLYATION_CNMF'

P value = 1.32e-05 (Chi-square test), Q value = 0.0041

Table S617.  Gene #68: 'Del Peak 39(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 39(21Q11.2) CNV 16 19 24 45 7 12
DEL PEAK 39(21Q11.2) WILD-TYPE 93 136 82 91 37 101

Figure S617.  Get High-res Image Gene #68: 'Del Peak 39(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 39(21q11.2)' versus 'MRNASEQ_CNMF'

P value = 5.67e-06 (Chi-square test), Q value = 0.0019

Table S618.  Gene #68: 'Del Peak 39(21q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 175 139 217 154 224 47 15
DEL PEAK 39(21Q11.2) CNV 28 19 27 42 65 4 2
DEL PEAK 39(21Q11.2) WILD-TYPE 147 120 190 112 159 43 13

Figure S618.  Get High-res Image Gene #68: 'Del Peak 39(21q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(22q11.1)' versus 'CN_CNMF'

P value = 3.04e-06 (Chi-square test), Q value = 0.0011

Table S619.  Gene #69: 'Del Peak 40(22q11.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 40(22Q11.1) CNV 123 114 49 110 22
DEL PEAK 40(22Q11.1) WILD-TYPE 251 118 30 142 26

Figure S619.  Get High-res Image Gene #69: 'Del Peak 40(22q11.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(22q11.1)' versus 'METHLYATION_CNMF'

P value = 0.000449 (Chi-square test), Q value = 0.11

Table S620.  Gene #69: 'Del Peak 40(22q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 109 155 106 136 44 113
DEL PEAK 40(22Q11.1) CNV 46 55 52 75 11 39
DEL PEAK 40(22Q11.1) WILD-TYPE 63 100 54 61 33 74

Figure S620.  Get High-res Image Gene #69: 'Del Peak 40(22q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 41(22q13.31)' versus 'CN_CNMF'

P value = 2.21e-07 (Chi-square test), Q value = 9.1e-05

Table S621.  Gene #70: 'Del Peak 41(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 374 232 79 252 48
DEL PEAK 41(22Q13.31) CNV 135 124 54 115 25
DEL PEAK 41(22Q13.31) WILD-TYPE 239 108 25 137 23

Figure S621.  Get High-res Image Gene #70: 'Del Peak 41(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

  • Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

  • Molecular subtype file = BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 985

  • Number of copy number variation regions = 70

  • Number of molecular subtypes = 12

  • Exclude regions that fewer than K tumors have alterations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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