Correlation between copy number variation genes and molecular subtypes

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 64 peak regions and 10 molecular subtypes across 913 patients, 463 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', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 2(1q21.3) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Amp Peak 3(1q44) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', and 'METHLYATION_CNMF'.
Amp Peak 4(3p26.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_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', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 6(4q13.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 7(6p23) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 8(6q21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 9(8p11.23) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 10(8p11.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 11(8q24.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 12(10p15.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 13(10q22.3) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 14(11p13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 15(11q13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
Amp Peak 16(11q14.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 17(12p13.33) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 18(12q15) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 19(13q12.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 20(13q34) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 21(14q21.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Amp Peak 22(15q26.3) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 23(17q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 24(17q23.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 25(19q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 26(19q13.42) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
Amp Peak 27(20q13.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_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', and 'MIRSEQ_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', and 'MIRSEQ_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', and 'MIRSEQ_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', and 'MIRSEQ_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', and 'MIRSEQ_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', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 9(6p25.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 10(6q15) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 11(6q27) cnvs correlated to 'CN_CNMF'.
Del Peak 12(7p22.3) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 13(7q36.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 14(8p23.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 15(8p11.21) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 16(9p21.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 17(9q21.11) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 18(10q23.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 19(10q26.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 20(11p15.5) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 21(11q13.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 22(11q23.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 23(11q25) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', and 'METHLYATION_CNMF'.
Del Peak 24(12p13.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 25(12q24.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 26(13q14.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 27(14q24.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 28(15q13.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 29(16q24.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 30(17p12) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 31(17q21.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 32(18q23) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 33(19p13.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 34(19q13.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 35(20p13) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 36(21q11.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', and 'METHLYATION_CNMF'.
Del Peak 37(22q13.32) cnvs correlated to 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 64 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 463 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Chi-square test	Fisher's exact test	Chi-square test	Chi-square test	Fisher's exact 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%)	705	1.29e-13 (6.27e-11)	6.67e-12 (3e-09)	6.61e-18 (3.63e-15)	1.95e-17 (1.06e-14)	0.000139 (0.0318)	1.28e-07 (4.5e-05)	9.25e-16 (4.88e-13)	2.4e-16 (1.28e-13)	1.36e-13 (6.57e-11)	1.36e-15 (7.14e-13)
Amp Peak 5(3q26 32)	0 (0%)	625	6.88e-11 (2.96e-08)	7.83e-10 (3.2e-07)	8.72e-36 (5.38e-33)	8.01e-17 (4.32e-14)	7.16e-07 (0.000231)	2.92e-06 (0.000863)	4.31e-22 (2.52e-19)	5.88e-21 (3.36e-18)	1.63e-15 (8.53e-13)	6.39e-24 (3.78e-21)
Amp Peak 7(6p23)	0 (0%)	670	3.59e-07 (0.00012)	1.92e-07 (6.59e-05)	5.65e-34 (3.48e-31)	2.44e-17 (1.33e-14)	1.98e-06 (0.000593)	8.42e-05 (0.0201)	1.01e-13 (4.93e-11)	3.56e-11 (1.56e-08)	1.52e-18 (8.5e-16)	2.51e-15 (1.29e-12)
Amp Peak 8(6q21)	0 (0%)	743	8.2e-14 (4.03e-11)	4.54e-10 (1.87e-07)	1.67e-39 (1.04e-36)	4.11e-13 (1.95e-10)	1.04e-08 (4e-06)	4.64e-07 (0.000153)	7.59e-22 (4.42e-19)	2.72e-18 (1.51e-15)	3.42e-19 (1.93e-16)	4.33e-23 (2.55e-20)
Amp Peak 11(8q24 21)	0 (0%)	329	1.17e-16 (6.3e-14)	2.62e-07 (8.88e-05)	2.63e-43 (1.65e-40)	1.7e-27 (1.02e-24)	4.58e-08 (1.66e-05)	9.36e-07 (0.000297)	3.47e-21 (1.99e-18)	5.54e-15 (2.83e-12)	1.31e-21 (7.6e-19)	2.37e-19 (1.34e-16)
Amp Peak 12(10p15 1)	0 (0%)	655	1.72e-21 (9.93e-19)	1.06e-18 (5.92e-16)	9.95e-35 (6.13e-32)	1.93e-26 (1.16e-23)	7e-11 (3e-08)	2.33e-12 (1.07e-09)	2.05e-28 (1.24e-25)	1.17e-28 (7.06e-26)	6.23e-28 (3.76e-25)	1.2e-30 (7.31e-28)
Amp Peak 17(12p13 33)	0 (0%)	675	1.91e-12 (8.84e-10)	2.53e-11 (1.11e-08)	1.68e-28 (1.01e-25)	7.29e-17 (3.94e-14)	2.7e-08 (9.98e-06)	2.37e-07 (8.07e-05)	1.67e-17 (9.11e-15)	1.45e-15 (7.57e-13)	9.18e-22 (5.32e-19)	5.5e-18 (3.04e-15)
Amp Peak 20(13q34)	0 (0%)	754	9.14e-10 (3.72e-07)	5.78e-09 (2.28e-06)	1.51e-17 (8.24e-15)	1.33e-14 (6.7e-12)	8.21e-06 (0.00226)	5.1e-08 (1.84e-05)	8.44e-14 (4.14e-11)	1.17e-14 (5.9e-12)	1.41e-13 (6.83e-11)	5.59e-20 (3.17e-17)
Amp Peak 25(19q12)	0 (0%)	680	2.12e-12 (9.74e-10)	9.11e-11 (3.9e-08)	1.28e-21 (7.43e-19)	4.2e-12 (1.91e-09)	6.19e-07 (0.000202)	9.68e-07 (0.000306)	1.11e-15 (5.84e-13)	2.08e-15 (1.08e-12)	6.49e-13 (3.04e-10)	2.82e-18 (1.57e-15)
Del Peak 3(2q37 3)	0 (0%)	648	1.39e-06 (0.000432)	3.78e-08 (1.38e-05)	1.57e-20 (8.99e-18)	2.61e-10 (1.09e-07)	1.03e-08 (3.96e-06)	1.11e-07 (3.92e-05)	1.81e-11 (8.04e-09)	2.03e-08 (7.56e-06)	4.66e-11 (2.02e-08)	2.63e-07 (8.9e-05)
Del Peak 4(3p14 3)	0 (0%)	635	1.06e-10 (4.51e-08)	3.11e-08 (1.14e-05)	2.93e-33 (1.8e-30)	5.78e-13 (2.72e-10)	1.18e-09 (4.77e-07)	5.21e-06 (0.00148)	4.61e-18 (2.56e-15)	4.42e-13 (2.09e-10)	2.29e-19 (1.3e-16)	2.57e-14 (1.28e-11)
Del Peak 5(4p16 3)	0 (0%)	632	5.63e-11 (2.44e-08)	6.3e-12 (2.84e-09)	1.98e-26 (1.18e-23)	8.41e-13 (3.94e-10)	4.6e-07 (0.000152)	1.62e-06 (0.000497)	9.75e-24 (5.75e-21)	2.14e-18 (1.19e-15)	9.97e-15 (5.05e-12)	4.7e-18 (2.6e-15)
Del Peak 6(4q35 2)	0 (0%)	630	3.17e-06 (0.000922)	9.81e-07 (0.000309)	2.71e-37 (1.68e-34)	1.66e-13 (8e-11)	1.51e-08 (5.71e-06)	1.78e-06 (0.000537)	2.22e-21 (1.28e-18)	3.79e-14 (1.87e-11)	2.84e-13 (1.36e-10)	6.73e-18 (3.7e-15)
Del Peak 7(5q11 2)	0 (0%)	679	1.17e-27 (7.04e-25)	6.11e-25 (3.63e-22)	5.91e-60 (3.78e-57)	1.43e-39 (8.94e-37)	3.33e-16 (1.77e-13)	7.43e-19 (4.18e-16)	1.33e-40 (8.35e-38)	1.7e-43 (1.07e-40)	8.36e-40 (5.24e-37)	5.41e-49 (3.43e-46)
Del Peak 8(5q21 3)	0 (0%)	688	1.36e-29 (8.28e-27)	1e-26 (5.98e-24)	6.13e-70 (3.92e-67)	3.25e-51 (2.07e-48)	2.6e-15 (1.34e-12)	8.97e-16 (4.75e-13)	5.88e-48 (3.73e-45)	1.06e-47 (6.73e-45)	1.28e-39 (8.02e-37)	1.67e-54 (1.07e-51)
Del Peak 18(10q23 31)	0 (0%)	652	4.09e-05 (0.0103)	9.57e-05 (0.0225)	3.83e-20 (2.18e-17)	4.75e-12 (2.16e-09)	1.9e-07 (6.53e-05)	7.37e-05 (0.0178)	1.06e-11 (4.75e-09)	6.91e-09 (2.69e-06)	5.47e-09 (2.17e-06)	3.97e-09 (1.58e-06)
Del Peak 19(10q26 3)	0 (0%)	649	2.88e-08 (1.06e-05)	1.49e-07 (5.2e-05)	2.23e-22 (1.31e-19)	2.07e-12 (9.53e-10)	3.06e-08 (1.13e-05)	8.25e-07 (0.000264)	1.77e-15 (9.22e-13)	1.17e-12 (5.44e-10)	7.81e-12 (3.5e-09)	3.48e-15 (1.79e-12)
Del Peak 20(11p15 5)	0 (0%)	651	1.34e-06 (0.000418)	1.62e-07 (5.62e-05)	5.01e-36 (3.1e-33)	1.96e-12 (9.01e-10)	1.27e-09 (5.13e-07)	1.65e-06 (0.000502)	8.07e-18 (4.42e-15)	5.07e-13 (2.39e-10)	3.87e-15 (1.98e-12)	1.42e-16 (7.61e-14)
Del Peak 25(12q24 21)	0 (0%)	739	9.6e-11 (4.1e-08)	2.5e-10 (1.04e-07)	2.33e-15 (1.2e-12)	2.68e-14 (1.33e-11)	0.000209 (0.0458)	1.05e-06 (0.00033)	6.55e-16 (3.47e-13)	3.47e-13 (1.65e-10)	1.17e-08 (4.46e-06)	3.27e-13 (1.56e-10)
Del Peak 27(14q24 3)	0 (0%)	619	4e-13 (1.9e-10)	1.56e-08 (5.89e-06)	8.6e-37 (5.32e-34)	3.5e-14 (1.73e-11)	5.29e-07 (0.000174)	5.53e-06 (0.00157)	3.86e-15 (1.98e-12)	3.04e-13 (1.45e-10)	5.44e-18 (3.01e-15)	1.52e-16 (8.14e-14)
Del Peak 28(15q13 1)	0 (0%)	598	3.46e-07 (0.000116)	7.57e-08 (2.69e-05)	6.74e-31 (4.12e-28)	1.2e-11 (5.33e-09)	0.000193 (0.0427)	2.32e-05 (0.0061)	6.07e-15 (3.09e-12)	2.32e-14 (1.16e-11)	6.32e-19 (3.56e-16)	1.96e-18 (1.1e-15)
Del Peak 29(16q24 3)	0 (0%)	326	1.6e-16 (8.57e-14)	2.51e-14 (1.25e-11)	1.66e-14 (8.33e-12)	4.47e-13 (2.11e-10)	1.14e-09 (4.64e-07)	3.45e-11 (1.51e-08)	2.82e-16 (1.5e-13)	4.62e-21 (2.65e-18)	9.22e-15 (4.68e-12)	8.49e-22 (4.93e-19)
Del Peak 31(17q21 31)	0 (0%)	598	1.07e-14 (5.4e-12)	3.91e-07 (0.00013)	5.42e-22 (3.17e-19)	1.19e-11 (5.32e-09)	1.86e-11 (8.21e-09)	3.12e-11 (1.37e-08)	2.86e-21 (1.64e-18)	8.32e-17 (4.48e-14)	1.14e-12 (5.32e-10)	1.76e-11 (7.82e-09)
Del Peak 33(19p13 3)	0 (0%)	608	5.99e-11 (2.59e-08)	4.57e-08 (1.66e-05)	1.25e-44 (7.91e-42)	6.53e-18 (3.6e-15)	3.03e-06 (0.000888)	3.39e-05 (0.00861)	1.19e-12 (5.53e-10)	5.4e-10 (2.22e-07)	9.67e-16 (5.1e-13)	6.54e-17 (3.55e-14)
Del Peak 34(19q13 32)	0 (0%)	730	1.57e-06 (0.000484)	8.8e-05 (0.0208)	4.48e-20 (2.55e-17)	1.52e-10 (6.42e-08)	0.000783 (0.144)	4.95e-05 (0.0122)	5.28e-09 (2.1e-06)	6.75e-09 (2.64e-06)	3.6e-10 (1.5e-07)	5.78e-12 (2.61e-09)
Amp Peak 27(20q13 2)	0 (0%)	448	1.35e-09 (5.42e-07)	0.000278 (0.0581)	9.78e-50 (6.22e-47)	5.18e-25 (3.07e-22)	0.000604 (0.117)	0.0154 (1.00)	6.68e-09 (2.62e-06)	2.14e-07 (7.31e-05)	7.41e-10 (3.03e-07)	1.16e-06 (0.000364)
Amp Peak 6(4q13 3)	0 (0%)	770	5.63e-05 (0.0137)	0.00023 (0.0495)	7.87e-14 (3.87e-11)	3.97e-07 (0.000131)	0.0471 (1.00)	0.524 (1.00)	7e-06 (0.00195)	2.4e-05 (0.00628)	0.00138 (0.246)	1.11e-07 (3.92e-05)
Amp Peak 18(12q15)	0 (0%)	678	1.81e-08 (6.79e-06)	0.000131 (0.0301)	1.86e-25 (1.11e-22)	1.49e-13 (7.21e-11)	0.188 (1.00)	0.0652 (1.00)	6.02e-06 (0.00169)	1.71e-05 (0.00456)	9.16e-08 (3.25e-05)	0.000644 (0.124)
Amp Peak 22(15q26 3)	0 (0%)	747	3.31e-07 (0.000111)	0.00679 (0.978)	1.88e-15 (9.76e-13)	0.000326 (0.0669)	0.000153 (0.0345)	0.0384 (1.00)	2.07e-08 (7.72e-06)	7.98e-06 (0.0022)	5.92e-08 (2.11e-05)	7.56e-09 (2.93e-06)
Del Peak 1(1p36 13)	0 (0%)	533	3.27e-05 (0.00837)	0.000651 (0.124)	6.02e-32 (3.68e-29)	2.81e-09 (1.12e-06)	0.00726 (1.00)	0.0805 (1.00)	1.11e-05 (0.00299)	6.02e-05 (0.0146)	2.37e-07 (8.07e-05)	0.00056 (0.11)
Del Peak 14(8p23 2)	0 (0%)	432	1.08e-09 (4.4e-07)	2.53e-05 (0.00661)	7.63e-31 (4.65e-28)	1.19e-13 (5.8e-11)	0.00955 (1.00)	0.0341 (1.00)	2.05e-11 (9.03e-09)	3.71e-08 (1.36e-05)	5.68e-06 (0.00161)	4.79e-12 (2.17e-09)
Del Peak 16(9p21 3)	0 (0%)	606	2.43e-06 (0.000721)	0.00076 (0.141)	1.11e-29 (6.76e-27)	2.21e-15 (1.14e-12)	0.00341 (0.543)	0.444 (1.00)	7.31e-07 (0.000235)	2.64e-07 (8.9e-05)	4.02e-06 (0.00116)	4.15e-12 (1.89e-09)
Del Peak 17(9q21 11)	0 (0%)	667	0.00255 (0.426)	0.00029 (0.0603)	3.41e-16 (1.81e-13)	1.19e-10 (5.06e-08)	1.04e-05 (0.00281)	0.00653 (0.954)	2.41e-06 (0.000718)	8.3e-06 (0.00227)	1.41e-08 (5.34e-06)	9.33e-13 (4.36e-10)
Del Peak 26(13q14 2)	0 (0%)	500	2.15e-05 (0.00572)	4.23e-05 (0.0106)	7.07e-28 (4.25e-25)	1.81e-08 (6.79e-06)	0.538 (1.00)	0.111 (1.00)	1.55e-07 (5.38e-05)	6.39e-06 (0.00178)	3.86e-10 (1.6e-07)	1.12e-07 (3.93e-05)
Del Peak 35(20p13)	0 (0%)	779	8.81e-06 (0.0024)	0.000158 (0.0354)	2.59e-13 (1.24e-10)	7.15e-09 (2.78e-06)	0.00154 (0.269)	0.0119 (1.00)	2.44e-10 (1.02e-07)	7.06e-10 (2.89e-07)	2.69e-12 (1.23e-09)	1.91e-13 (9.17e-11)
Amp Peak 13(10q22 3)	0 (0%)	781	2.2e-05 (0.00582)	0.0681 (1.00)	8.18e-09 (3.16e-06)	0.000149 (0.0337)	0.0025 (0.423)	0.0211 (1.00)	1.83e-07 (6.31e-05)	0.000689 (0.129)	3.75e-05 (0.00949)	0.000675 (0.127)
Del Peak 10(6q15)	0 (0%)	612	1.55e-06 (0.000478)	0.00137 (0.246)	6.83e-28 (4.11e-25)	3.78e-08 (1.38e-05)	0.456 (1.00)	0.0875 (1.00)	2.69e-05 (0.00692)	0.000262 (0.055)	0.0136 (1.00)	5.04e-05 (0.0124)
Del Peak 12(7p22 3)	0 (0%)	795	0.00298 (0.482)	0.000366 (0.0742)	2.06e-15 (1.07e-12)	5.89e-07 (0.000193)	0.0214 (1.00)	0.00553 (0.829)	8.07e-09 (3.12e-06)	5.39e-08 (1.93e-05)	3.96e-11 (1.72e-08)	1.38e-10 (5.86e-08)
Del Peak 30(17p12)	0 (0%)	367	2.14e-10 (8.99e-08)	0.166 (1.00)	9.33e-23 (5.49e-20)	7.4e-07 (0.000238)	8.07e-05 (0.0194)	0.00775 (1.00)	0.000586 (0.114)	0.121 (1.00)	0.000255 (0.0541)	0.000127 (0.0293)
Amp Peak 2(1q21 3)	0 (0%)	254	1.54e-07 (5.37e-05)	0.00185 (0.322)	6.45e-09 (2.54e-06)	1.66e-06 (0.000504)	0.0586 (1.00)	0.00703 (1.00)	0.000167 (0.0373)	0.000205 (0.045)	0.00102 (0.184)	0.00262 (0.434)
Amp Peak 4(3p26 1)	0 (0%)	725	0.0124 (1.00)	0.00803 (1.00)	1.01e-13 (4.93e-11)	2.95e-06 (0.000868)	0.00573 (0.848)	0.00869 (1.00)	5.11e-09 (2.03e-06)	6.57e-07 (0.000213)	5.97e-06 (0.00168)	1.18e-08 (4.49e-06)
Amp Peak 21(14q21 1)	0 (0%)	732	0.000259 (0.0547)	0.00478 (0.721)	1.97e-09 (7.89e-07)	5.16e-05 (0.0127)	0.0823 (1.00)	0.0385 (1.00)	3.92e-05 (0.00987)	2.45e-06 (0.000725)	1.94e-06 (0.000584)	0.0693 (1.00)
Amp Peak 23(17q12)	0 (0%)	618	1.49e-14 (7.49e-12)	0.0003 (0.0618)	7.29e-34 (4.48e-31)	5.76e-09 (2.28e-06)	0.049 (1.00)	0.00821 (1.00)	0.000101 (0.0237)	0.000454 (0.0903)	0.0148 (1.00)	0.0196 (1.00)
Amp Peak 24(17q23 1)	0 (0%)	539	2.42e-14 (1.21e-11)	0.00149 (0.263)	6.19e-38 (3.84e-35)	1.45e-10 (6.12e-08)	0.191 (1.00)	0.334 (1.00)	0.000644 (0.124)	0.00575 (0.848)	3.1e-07 (0.000104)	3.57e-06 (0.00103)
Del Peak 32(18q23)	0 (0%)	620	0.000347 (0.0709)	0.149 (1.00)	1.32e-15 (6.95e-13)	1.2e-08 (4.56e-06)	0.00413 (0.64)	0.581 (1.00)	2.54e-05 (0.00661)	0.00371 (0.585)	0.000375 (0.0757)	0.000143 (0.0324)
Amp Peak 9(8p11 23)	0 (0%)	567	1.64e-06 (0.000501)	0.00561 (0.836)	1.44e-24 (8.5e-22)	1.22e-12 (5.64e-10)	0.0399 (1.00)	0.00473 (0.718)	0.000227 (0.049)	3.34e-05 (0.00851)	0.0447 (1.00)	0.0332 (1.00)
Amp Peak 14(11p13)	0 (0%)	721	0.311 (1.00)	0.148 (1.00)	1.84e-10 (7.73e-08)	4.84e-05 (0.012)	0.105 (1.00)	0.229 (1.00)	2.61e-05 (0.00675)	0.0204 (1.00)	1.33e-06 (0.000417)	1.91e-08 (7.15e-06)
Amp Peak 16(11q14 1)	0 (0%)	679	0.12 (1.00)	0.101 (1.00)	1.8e-19 (1.02e-16)	7.93e-06 (0.0022)	0.148 (1.00)	0.199 (1.00)	8.57e-05 (0.0203)	0.00146 (0.259)	8.98e-07 (0.000285)	1.39e-05 (0.00372)
Del Peak 2(1p22 1)	0 (0%)	608	0.00234 (0.4)	8.39e-05 (0.0201)	5.77e-22 (3.36e-19)	0.00103 (0.186)	0.0231 (1.00)	0.049 (1.00)	0.000574 (0.113)	3.06e-06 (0.000892)	0.0125 (1.00)	0.0329 (1.00)
Del Peak 13(7q36 1)	0 (0%)	739	0.0129 (1.00)	0.043 (1.00)	5.25e-10 (2.16e-07)	0.0897 (1.00)	0.551 (1.00)	0.0562 (1.00)	0.000414 (0.0831)	0.000496 (0.0983)	5.26e-08 (1.89e-05)	1.6e-06 (0.000491)
Del Peak 15(8p11 21)	0 (0%)	740	0.000126 (0.0292)	0.0141 (1.00)	6.19e-11 (2.67e-08)	0.0474 (1.00)	0.0465 (1.00)	0.0191 (1.00)	0.000593 (0.115)	0.000914 (0.167)	0.00401 (0.625)	6.26e-06 (0.00175)
Amp Peak 10(8p11 21)	0 (0%)	559	0.0144 (1.00)	0.0422 (1.00)	1.01e-22 (5.92e-20)	4.03e-08 (1.46e-05)	0.791 (1.00)	0.633 (1.00)	0.000224 (0.0487)	0.000104 (0.0242)	0.0361 (1.00)	0.0215 (1.00)
Amp Peak 19(13q12 3)	0 (0%)	785	0.0708 (1.00)	0.0557 (1.00)	2.22e-05 (0.00586)	0.00895 (1.00)	0.0155 (1.00)	0.142 (1.00)	2.63e-05 (0.00679)	0.00269 (0.441)	0.000196 (0.0433)	0.00043 (0.086)
Amp Peak 26(19q13 42)	0 (0%)	678	0.000775 (0.143)	0.0212 (1.00)	2.5e-14 (1.25e-11)	6.23e-07 (0.000202)	0.00233 (0.4)	0.0549 (1.00)	0.00264 (0.436)	0.029 (1.00)	4.27e-06 (0.00123)	0.00441 (0.675)
Del Peak 22(11q23 2)	0 (0%)	464	2.08e-08 (7.72e-06)	0.0296 (1.00)	3.22e-42 (2.02e-39)	7.68e-12 (3.45e-09)	0.975 (1.00)	0.475 (1.00)	0.00305 (0.491)	0.00254 (0.426)	0.0196 (1.00)	0.000137 (0.0314)
Del Peak 24(12p13 1)	0 (0%)	756	0.0439 (1.00)	0.14 (1.00)	0.000979 (0.178)	0.0149 (1.00)	0.222 (1.00)	0.042 (1.00)	0.00021 (0.0458)	0.0137 (1.00)	8.03e-05 (0.0194)	8.68e-06 (0.00237)
Amp Peak 3(1q44)	0 (0%)	258	3.9e-06 (0.00113)	0.263 (1.00)	1.37e-07 (4.8e-05)	9.22e-06 (0.0025)	0.864 (1.00)	0.324 (1.00)	0.206 (1.00)	0.383 (1.00)	0.711 (1.00)	0.0277 (1.00)
Amp Peak 15(11q13 3)	0 (0%)	564	0.00319 (0.511)	0.0336 (1.00)	4.91e-41 (3.08e-38)	4e-10 (1.66e-07)	0.966 (1.00)	0.146 (1.00)	0.0453 (1.00)	0.168 (1.00)	0.000292 (0.0604)	0.0396 (1.00)
Del Peak 23(11q25)	0 (0%)	492	0.000243 (0.052)	0.96 (1.00)	6.15e-38 (3.83e-35)	9.89e-09 (3.81e-06)	0.126 (1.00)	0.707 (1.00)	0.355 (1.00)	0.351 (1.00)	0.093 (1.00)	0.0331 (1.00)
Del Peak 36(21q11 2)	0 (0%)	731	0.000252 (0.0538)	0.0342 (1.00)	4.31e-11 (1.87e-08)	2.01e-06 (0.000602)	0.225 (1.00)	0.502 (1.00)	0.0581 (1.00)	0.197 (1.00)	0.0142 (1.00)	0.0194 (1.00)
Del Peak 9(6p25 3)	0 (0%)	743	0.318 (1.00)	0.522 (1.00)	8.51e-07 (0.000271)	4.71e-05 (0.0117)	0.439 (1.00)	0.597 (1.00)	0.00292 (0.477)	0.00786 (1.00)	0.299 (1.00)	0.0417 (1.00)
Del Peak 21(11q13 1)	0 (0%)	719	0.00185 (0.322)	0.0584 (1.00)	3.51e-17 (1.91e-14)	4.39e-06 (0.00125)	0.331 (1.00)	0.393 (1.00)	0.00823 (1.00)	0.0169 (1.00)	0.596 (1.00)	0.0297 (1.00)
Del Peak 11(6q27)	0 (0%)	599	0.0183 (1.00)	0.61 (1.00)	2.87e-14 (1.42e-11)	0.00375 (0.589)	0.113 (1.00)	0.796 (1.00)	0.341 (1.00)	0.561 (1.00)	0.393 (1.00)	0.115 (1.00)
Del Peak 37(22q13 32)	0 (0%)	503	0.164 (1.00)	0.0438 (1.00)	0.063 (1.00)	0.000674 (0.127)	0.121 (1.00)	0.0218 (1.00)	0.00661 (0.959)	0.00247 (0.419)	0.00438 (0.674)	0.492 (1.00)

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

P value = 1.29e-13 (Chi-square test), Q value = 6.3e-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	124	36	23	95	72	20	103	40
AMP PEAK 1(1P22.3) CNV	16	2	3	51	16	2	24	2
AMP PEAK 1(1P22.3) WILD-TYPE	108	34	20	44	56	18	79	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 = 6.67e-12 (Fisher's exact test), Q value = 3e-09

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 1(1P22.3) CNV	13	57	46
AMP PEAK 1(1P22.3) WILD-TYPE	127	68	202

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 = 6.61e-18 (Chi-square test), Q value = 3.6e-15

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	347	222	72	223	49
AMP PEAK 1(1P22.3) CNV	47	26	29	90	16
AMP PEAK 1(1P22.3) WILD-TYPE	300	196	43	133	33

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 = 1.95e-17 (Chi-square test), Q value = 1.1e-14

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 1(1P22.3) CNV	57	21	22	17	2	17
AMP PEAK 1(1P22.3) WILD-TYPE	44	118	71	120	38	80

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 = 0.032

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 = 4.5e-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 = 9.25e-16 (Fisher's exact test), Q value = 4.9e-13

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 1(1P22.3) CNV	96	13	73
AMP PEAK 1(1P22.3) WILD-TYPE	138	135	373

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 = 2.4e-16 (Fisher's exact test), Q value = 1.3e-13

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 1(1P22.3) CNV	23	70	89
AMP PEAK 1(1P22.3) WILD-TYPE	193	338	115

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

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

P value = 1.36e-13 (Fisher's exact test), Q value = 6.6e-11

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

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

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

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

P value = 1.36e-15 (Fisher's exact test), Q value = 7.1e-13

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

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

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

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

P value = 1.54e-07 (Chi-square test), Q value = 5.4e-05

Table S11. 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	124	36	23	95	72	20	103	40
AMP PEAK 2(1Q21.3) CNV	77	19	16	88	54	10	85	30
AMP PEAK 2(1Q21.3) WILD-TYPE	47	17	7	7	18	10	18	10

Figure S11. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 6.45e-09 (Chi-square test), Q value = 2.5e-06

Table S12. 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	347	222	72	223	49
AMP PEAK 2(1Q21.3) CNV	219	167	72	167	34
AMP PEAK 2(1Q21.3) WILD-TYPE	128	55	0	56	15

Figure S12. 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 = 1.66e-06 (Chi-square test), Q value = 5e-04

Table S13. 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	101	139	93	137	40	97
AMP PEAK 2(1Q21.3) CNV	85	110	74	90	21	55
AMP PEAK 2(1Q21.3) WILD-TYPE	16	29	19	47	19	42

Figure S13. 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 = 0.000167 (Fisher's exact test), Q value = 0.037

Table S14. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 2(1Q21.3) CNV	191	94	313
AMP PEAK 2(1Q21.3) WILD-TYPE	43	54	133

Figure S14. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 0.000205 (Fisher's exact test), Q value = 0.045

Table S15. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 2(1Q21.3) CNV	137	295	166
AMP PEAK 2(1Q21.3) WILD-TYPE	79	113	38

Figure S15. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.00102 (Fisher's exact test), Q value = 0.18

Table S16. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

Figure S16. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 3.9e-06 (Chi-square test), Q value = 0.0011

Table S17. 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	124	36	23	95	72	20	103	40
AMP PEAK 3(1Q44) CNV	72	19	16	78	57	11	86	33
AMP PEAK 3(1Q44) WILD-TYPE	52	17	7	17	15	9	17	7

Figure S17. 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 = 1.37e-07 (Chi-square test), Q value = 4.8e-05

Table S18. Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 3(1Q44) CNV	226	165	72	160	32
AMP PEAK 3(1Q44) WILD-TYPE	121	57	0	63	17

Figure S18. 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 = 9.22e-06 (Chi-square test), Q value = 0.0025

Table S19. 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	101	139	93	137	40	97
AMP PEAK 3(1Q44) CNV	74	113	79	85	24	57
AMP PEAK 3(1Q44) WILD-TYPE	27	26	14	52	16	40

Figure S19. Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 1.01e-13 (Chi-square test), Q value = 4.9e-11

Table S20. 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	347	222	72	223	49
AMP PEAK 4(3P26.1) CNV	25	55	20	75	13
AMP PEAK 4(3P26.1) WILD-TYPE	322	167	52	148	36

Figure S20. 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 = 2.95e-06 (Chi-square test), Q value = 0.00087

Table S21. 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	101	139	93	137	40	97
AMP PEAK 4(3P26.1) CNV	31	9	22	30	3	11
AMP PEAK 4(3P26.1) WILD-TYPE	70	130	71	107	37	86

Figure S21. 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 = 5.11e-09 (Fisher's exact test), Q value = 2e-06

Table S22. Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 4(3P26.1) CNV	75	10	90
AMP PEAK 4(3P26.1) WILD-TYPE	159	138	356

Figure S22. 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 = 6.57e-07 (Fisher's exact test), Q value = 0.00021

Table S23. Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 4(3P26.1) CNV	21	94	60
AMP PEAK 4(3P26.1) WILD-TYPE	195	314	144

Figure S23. Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 5.97e-06 (Fisher's exact test), Q value = 0.0017

Table S24. Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

Figure S24. Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 1.18e-08 (Fisher's exact test), Q value = 4.5e-06

Table S25. Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

Figure S25. Get High-res Image Gene #4: 'Amp Peak 4(3p26.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 6.88e-11 (Chi-square test), Q value = 3e-08

Table S26. 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	124	36	23	95	72	20	103	40
AMP PEAK 5(3Q26.32) CNV	39	11	4	58	34	9	19	4
AMP PEAK 5(3Q26.32) WILD-TYPE	85	25	19	37	38	11	84	36

Figure S26. 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 = 7.83e-10 (Fisher's exact test), Q value = 3.2e-07

Table S27. Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 5(3Q26.32) CNV	27	71	80
AMP PEAK 5(3Q26.32) WILD-TYPE	113	54	168

Figure S27. 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 = 8.72e-36 (Chi-square test), Q value = 5.4e-33

Table S28. 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	347	222	72	223	49
AMP PEAK 5(3Q26.32) CNV	35	77	24	138	14
AMP PEAK 5(3Q26.32) WILD-TYPE	312	145	48	85	35

Figure S28. 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 = 8.01e-17 (Chi-square test), Q value = 4.3e-14

Table S29. 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	101	139	93	137	40	97
AMP PEAK 5(3Q26.32) CNV	63	15	29	41	9	17
AMP PEAK 5(3Q26.32) WILD-TYPE	38	124	64	96	31	80

Figure S29. 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 = 0.00023

Table S30. 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 S30. 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 = 0.00086

Table S31. 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 S31. 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 = 4.31e-22 (Fisher's exact test), Q value = 2.5e-19

Table S32. Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 5(3Q26.32) CNV	136	21	117
AMP PEAK 5(3Q26.32) WILD-TYPE	98	127	329

Figure S32. 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 = 5.88e-21 (Fisher's exact test), Q value = 3.4e-18

Table S33. Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 5(3Q26.32) CNV	35	118	121
AMP PEAK 5(3Q26.32) WILD-TYPE	181	290	83

Figure S33. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.63e-15 (Fisher's exact test), Q value = 8.5e-13

Table S34. Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

Figure S34. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 6.39e-24 (Fisher's exact test), Q value = 3.8e-21

Table S35. Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

Figure S35. Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.63e-05 (Chi-square test), Q value = 0.014

Table S36. 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	124	36	23	95	72	20	103	40
AMP PEAK 6(4Q13.3) CNV	31	2	3	19	18	4	3	3
AMP PEAK 6(4Q13.3) WILD-TYPE	93	34	20	76	54	16	100	37

Figure S36. 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 = 0.00023 (Fisher's exact test), Q value = 0.049

Table S37. Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 6(4Q13.3) CNV	9	29	45
AMP PEAK 6(4Q13.3) WILD-TYPE	131	96	203

Figure S37. 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 = 7.87e-14 (Chi-square test), Q value = 3.9e-11

Table S38. 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	347	222	72	223	49
AMP PEAK 6(4Q13.3) CNV	21	59	2	55	6
AMP PEAK 6(4Q13.3) WILD-TYPE	326	163	70	168	43

Figure S38. 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 = 3.97e-07 (Chi-square test), Q value = 0.00013

Table S39. 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	101	139	93	137	40	97
AMP PEAK 6(4Q13.3) CNV	24	4	11	34	4	9
AMP PEAK 6(4Q13.3) WILD-TYPE	77	135	82	103	36	88

Figure S39. 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 = 7e-06 (Fisher's exact test), Q value = 0.0019

Table S40. Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 6(4Q13.3) CNV	57	9	71
AMP PEAK 6(4Q13.3) WILD-TYPE	177	139	375

Figure S40. 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 = 2.4e-05 (Fisher's exact test), Q value = 0.0063

Table S41. Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 6(4Q13.3) CNV	20	64	53
AMP PEAK 6(4Q13.3) WILD-TYPE	196	344	151

Figure S41. 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 = 0.00138 (Fisher's exact test), Q value = 0.25

Table S42. Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 6(4Q13.3) CNV	26	56	58
AMP PEAK 6(4Q13.3) WILD-TYPE	208	336	197

Figure S42. 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 = 1.11e-07 (Fisher's exact test), Q value = 3.9e-05

Table S43. Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

Figure S43. Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 7(6p23)' versus 'MRNA_CNMF'

P value = 3.59e-07 (Chi-square test), Q value = 0.00012

Table S44. Gene #7: 'Amp Peak 7(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	124	36	23	95	72	20	103	40
AMP PEAK 7(6P23) CNV	30	6	3	48	27	8	18	6
AMP PEAK 7(6P23) WILD-TYPE	94	30	20	47	45	12	85	34

Figure S44. Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 7(6p23)' versus 'MRNA_CHIERARCHICAL'

P value = 1.92e-07 (Fisher's exact test), Q value = 6.6e-05

Table S45. Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 7(6P23) CNV	22	58	66
AMP PEAK 7(6P23) WILD-TYPE	118	67	182

Figure S45. Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 7(6p23)' versus 'CN_CNMF'

P value = 5.65e-34 (Chi-square test), Q value = 3.5e-31

Table S46. Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 7(6P23) CNV	25	57	21	123	17
AMP PEAK 7(6P23) WILD-TYPE	322	165	51	100	32

Figure S46. Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(6p23)' versus 'METHLYATION_CNMF'

P value = 2.44e-17 (Chi-square test), Q value = 1.3e-14

Table S47. Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 7(6P23) CNV	54	11	22	48	2	14
AMP PEAK 7(6P23) WILD-TYPE	47	128	71	89	38	83

Figure S47. Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 7(6p23)' versus 'RPPA_CNMF'

P value = 1.98e-06 (Fisher's exact test), Q value = 0.00059

Table S48. Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
AMP PEAK 7(6P23) CNV	64	25	23
AMP PEAK 7(6P23) WILD-TYPE	83	108	94

Figure S48. Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 7(6p23)' versus 'RPPA_CHIERARCHICAL'

P value = 8.42e-05 (Fisher's exact test), Q value = 0.02

Table S49. Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
AMP PEAK 7(6P23) CNV	34	24	54
AMP PEAK 7(6P23) WILD-TYPE	127	86	72

Figure S49. Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 7(6p23)' versus 'MRNASEQ_CNMF'

P value = 1.01e-13 (Fisher's exact test), Q value = 4.9e-11

Table S50. Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 7(6P23) CNV	105	17	101
AMP PEAK 7(6P23) WILD-TYPE	129	131	345

Figure S50. Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 7(6p23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.56e-11 (Fisher's exact test), Q value = 1.6e-08

Table S51. Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 7(6P23) CNV	31	102	90
AMP PEAK 7(6P23) WILD-TYPE	185	306	114

Figure S51. Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(6p23)' versus 'MIRSEQ_CNMF'

P value = 1.52e-18 (Fisher's exact test), Q value = 8.5e-16

Table S52. Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 7(6P23) CNV	31	76	119
AMP PEAK 7(6P23) WILD-TYPE	203	316	136

Figure S52. Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 7(6p23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.51e-15 (Fisher's exact test), Q value = 1.3e-12

Table S53. Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 7(6P23) CNV	88	35	103
AMP PEAK 7(6P23) WILD-TYPE	274	249	132

Figure S53. Get High-res Image Gene #7: 'Amp Peak 7(6p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 8(6q21)' versus 'MRNA_CNMF'

P value = 8.2e-14 (Chi-square test), Q value = 4e-11

Table S54. Gene #8: 'Amp Peak 8(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	124	36	23	95	72	20	103	40
AMP PEAK 8(6Q21) CNV	11	1	4	41	25	9	11	2
AMP PEAK 8(6Q21) WILD-TYPE	113	35	19	54	47	11	92	38

Figure S54. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 8(6q21)' versus 'MRNA_CHIERARCHICAL'

P value = 4.54e-10 (Fisher's exact test), Q value = 1.9e-07

Table S55. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 8(6Q21) CNV	11	50	43
AMP PEAK 8(6Q21) WILD-TYPE	129	75	205

Figure S55. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 8(6q21)' versus 'CN_CNMF'

P value = 1.67e-39 (Chi-square test), Q value = 1e-36

Table S56. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 8(6Q21) CNV	20	20	15	109	6
AMP PEAK 8(6Q21) WILD-TYPE	327	202	57	114	43

Figure S56. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 8(6q21)' versus 'METHLYATION_CNMF'

P value = 4.11e-13 (Chi-square test), Q value = 2e-10

Table S57. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 8(6Q21) CNV	42	5	16	19	2	17
AMP PEAK 8(6Q21) WILD-TYPE	59	134	77	118	38	80

Figure S57. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 8(6q21)' versus 'RPPA_CNMF'

P value = 1.04e-08 (Fisher's exact test), Q value = 4e-06

Table S58. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
AMP PEAK 8(6Q21) CNV	54	12	16
AMP PEAK 8(6Q21) WILD-TYPE	93	121	101

Figure S58. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 8(6q21)' versus 'RPPA_CHIERARCHICAL'

P value = 4.64e-07 (Fisher's exact test), Q value = 0.00015

Table S59. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
AMP PEAK 8(6Q21) CNV	20	15	47
AMP PEAK 8(6Q21) WILD-TYPE	141	95	79

Figure S59. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 8(6q21)' versus 'MRNASEQ_CNMF'

P value = 7.59e-22 (Fisher's exact test), Q value = 4.4e-19

Table S60. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 8(6Q21) CNV	95	9	51
AMP PEAK 8(6Q21) WILD-TYPE	139	139	395

Figure S60. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 8(6q21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.72e-18 (Fisher's exact test), Q value = 1.5e-15

Table S61. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 8(6Q21) CNV	15	58	82
AMP PEAK 8(6Q21) WILD-TYPE	201	350	122

Figure S61. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 8(6q21)' versus 'MIRSEQ_CNMF'

P value = 3.42e-19 (Fisher's exact test), Q value = 1.9e-16

Table S62. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 8(6Q21) CNV	21	41	95
AMP PEAK 8(6Q21) WILD-TYPE	213	351	160

Figure S62. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 8(6q21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.33e-23 (Fisher's exact test), Q value = 2.6e-20

Table S63. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 8(6Q21) CNV	41	21	95
AMP PEAK 8(6Q21) WILD-TYPE	321	263	140

Figure S63. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 9(8p11.23)' versus 'MRNA_CNMF'

P value = 1.64e-06 (Chi-square test), Q value = 5e-04

Table S64. Gene #9: 'Amp Peak 9(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	124	36	23	95	72	20	103	40
AMP PEAK 9(8P11.23) CNV	76	17	12	30	23	5	34	9
AMP PEAK 9(8P11.23) WILD-TYPE	48	19	11	65	49	15	69	31

Figure S64. Get High-res Image Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 9(8p11.23)' versus 'CN_CNMF'

P value = 1.44e-24 (Chi-square test), Q value = 8.5e-22

Table S65. Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 9(8P11.23) CNV	94	111	32	61	48
AMP PEAK 9(8P11.23) WILD-TYPE	253	111	40	162	1

Figure S65. Get High-res Image Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(8p11.23)' versus 'METHLYATION_CNMF'

P value = 1.22e-12 (Chi-square test), Q value = 5.6e-10

Table S66. Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 9(8P11.23) CNV	32	28	37	88	12	29
AMP PEAK 9(8P11.23) WILD-TYPE	69	111	56	49	28	68

Figure S66. Get High-res Image Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 9(8p11.23)' versus 'MRNASEQ_CNMF'

P value = 0.000227 (Fisher's exact test), Q value = 0.049

Table S67. Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 9(8P11.23) CNV	78	43	202
AMP PEAK 9(8P11.23) WILD-TYPE	156	105	244

Figure S67. Get High-res Image Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 9(8p11.23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.0085

Table S68. Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 9(8P11.23) CNV	67	191	65
AMP PEAK 9(8P11.23) WILD-TYPE	149	217	139

Figure S68. Get High-res Image Gene #9: 'Amp Peak 9(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 10(8p11.21)' versus 'CN_CNMF'

P value = 1.01e-22 (Chi-square test), Q value = 5.9e-20

Table S69. Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 10(8P11.21) CNV	91	94	39	81	49
AMP PEAK 10(8P11.21) WILD-TYPE	256	128	33	142	0

Figure S69. Get High-res Image Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 10(8p11.21)' versus 'METHLYATION_CNMF'

P value = 4.03e-08 (Chi-square test), Q value = 1.5e-05

Table S70. Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 10(8P11.21) CNV	51	29	35	74	10	32
AMP PEAK 10(8P11.21) WILD-TYPE	50	110	58	63	30	65

Figure S70. Get High-res Image Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 10(8p11.21)' versus 'MRNASEQ_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.049

Table S71. Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 10(8P11.21) CNV	104	37	185
AMP PEAK 10(8P11.21) WILD-TYPE	130	111	261

Figure S71. Get High-res Image Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 10(8p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.024

Table S72. Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 10(8P11.21) CNV	59	179	88
AMP PEAK 10(8P11.21) WILD-TYPE	157	229	116

Figure S72. Get High-res Image Gene #10: 'Amp Peak 10(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(8q24.21)' versus 'MRNA_CNMF'

P value = 1.17e-16 (Chi-square test), Q value = 6.3e-14

Table S73. Gene #11: 'Amp Peak 11(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	124	36	23	95	72	20	103	40
AMP PEAK 11(8Q24.21) CNV	101	21	17	83	56	17	42	14
AMP PEAK 11(8Q24.21) WILD-TYPE	23	15	6	12	16	3	61	26

Figure S73. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 11(8q24.21)' versus 'MRNA_CHIERARCHICAL'

P value = 2.62e-07 (Fisher's exact test), Q value = 8.9e-05

Table S74. Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 11(8Q24.21) CNV	73	104	174
AMP PEAK 11(8Q24.21) WILD-TYPE	67	21	74

Figure S74. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 11(8q24.21)' versus 'CN_CNMF'

P value = 2.63e-43 (Chi-square test), Q value = 1.7e-40

Table S75. Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 11(8Q24.21) CNV	132	163	39	203	47
AMP PEAK 11(8Q24.21) WILD-TYPE	215	59	33	20	2

Figure S75. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(8q24.21)' versus 'METHLYATION_CNMF'

P value = 1.7e-27 (Chi-square test), Q value = 1e-24

Table S76. Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 11(8Q24.21) CNV	91	36	62	108	17	50
AMP PEAK 11(8Q24.21) WILD-TYPE	10	103	31	29	23	47

Figure S76. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 11(8q24.21)' versus 'RPPA_CNMF'

P value = 4.58e-08 (Fisher's exact test), Q value = 1.7e-05

Table S77. Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
AMP PEAK 11(8Q24.21) CNV	125	72	76
AMP PEAK 11(8Q24.21) WILD-TYPE	22	61	41

Figure S77. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 11(8q24.21)' versus 'RPPA_CHIERARCHICAL'

P value = 9.36e-07 (Fisher's exact test), Q value = 3e-04

Table S78. Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
AMP PEAK 11(8Q24.21) CNV	102	63	108
AMP PEAK 11(8Q24.21) WILD-TYPE	59	47	18

Figure S78. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 11(8q24.21)' versus 'MRNASEQ_CNMF'

P value = 3.47e-21 (Fisher's exact test), Q value = 2e-18

Table S79. Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 11(8Q24.21) CNV	202	59	278
AMP PEAK 11(8Q24.21) WILD-TYPE	32	89	168

Figure S79. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 11(8q24.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.54e-15 (Fisher's exact test), Q value = 2.8e-12

Table S80. Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 11(8Q24.21) CNV	101	267	171
AMP PEAK 11(8Q24.21) WILD-TYPE	115	141	33

Figure S80. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 11(8q24.21)' versus 'MIRSEQ_CNMF'

P value = 1.31e-21 (Fisher's exact test), Q value = 7.6e-19

Table S81. Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 11(8Q24.21) CNV	111	233	221
AMP PEAK 11(8Q24.21) WILD-TYPE	123	159	34

Figure S81. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 11(8q24.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.37e-19 (Fisher's exact test), Q value = 1.3e-16

Table S82. Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 11(8Q24.21) CNV	222	140	203
AMP PEAK 11(8Q24.21) WILD-TYPE	140	144	32

Figure S82. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 12(10p15.1)' versus 'MRNA_CNMF'

P value = 1.72e-21 (Chi-square test), Q value = 9.9e-19

Table S83. Gene #12: 'Amp Peak 12(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	124	36	23	95	72	20	103	40
AMP PEAK 12(10P15.1) CNV	28	4	4	67	34	6	11	7
AMP PEAK 12(10P15.1) WILD-TYPE	96	32	19	28	38	14	92	33

Figure S83. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 12(10p15.1)' versus 'MRNA_CHIERARCHICAL'

P value = 1.06e-18 (Fisher's exact test), Q value = 5.9e-16

Table S84. Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 12(10P15.1) CNV	24	81	56
AMP PEAK 12(10P15.1) WILD-TYPE	116	44	192

Figure S84. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 12(10p15.1)' versus 'CN_CNMF'

P value = 9.95e-35 (Chi-square test), Q value = 6.1e-32

Table S85. Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 12(10P15.1) CNV	40	55	17	135	11
AMP PEAK 12(10P15.1) WILD-TYPE	307	167	55	88	38

Figure S85. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(10p15.1)' versus 'METHLYATION_CNMF'

P value = 1.93e-26 (Chi-square test), Q value = 1.2e-23

Table S86. Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 12(10P15.1) CNV	67	6	23	33	2	24
AMP PEAK 12(10P15.1) WILD-TYPE	34	133	70	104	38	73

Figure S86. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 12(10p15.1)' versus 'RPPA_CNMF'

P value = 7e-11 (Fisher's exact test), Q value = 3e-08

Table S87. Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
AMP PEAK 12(10P15.1) CNV	78	22	29
AMP PEAK 12(10P15.1) WILD-TYPE	69	111	88

Figure S87. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 12(10p15.1)' versus 'RPPA_CHIERARCHICAL'

P value = 2.33e-12 (Fisher's exact test), Q value = 1.1e-09

Table S88. Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
AMP PEAK 12(10P15.1) CNV	30	26	73
AMP PEAK 12(10P15.1) WILD-TYPE	131	84	53

Figure S88. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 12(10p15.1)' versus 'MRNASEQ_CNMF'

P value = 2.05e-28 (Fisher's exact test), Q value = 1.2e-25

Table S89. Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 12(10P15.1) CNV	135	22	81
AMP PEAK 12(10P15.1) WILD-TYPE	99	126	365

Figure S89. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(10p15.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-28 (Fisher's exact test), Q value = 7.1e-26

Table S90. Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 12(10P15.1) CNV	33	81	124
AMP PEAK 12(10P15.1) WILD-TYPE	183	327	80

Figure S90. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(10p15.1)' versus 'MIRSEQ_CNMF'

P value = 6.23e-28 (Fisher's exact test), Q value = 3.8e-25

Table S91. Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 12(10P15.1) CNV	38	68	141
AMP PEAK 12(10P15.1) WILD-TYPE	196	324	114

Figure S91. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 12(10p15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.2e-30 (Fisher's exact test), Q value = 7.3e-28

Table S92. Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 12(10P15.1) CNV	73	38	136
AMP PEAK 12(10P15.1) WILD-TYPE	289	246	99

Figure S92. Get High-res Image Gene #12: 'Amp Peak 12(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 13(10q22.3)' versus 'MRNA_CNMF'

P value = 2.2e-05 (Chi-square test), Q value = 0.0058

Table S93. Gene #13: 'Amp Peak 13(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	124	36	23	95	72	20	103	40
AMP PEAK 13(10Q22.3) CNV	17	2	5	18	23	8	8	3
AMP PEAK 13(10Q22.3) WILD-TYPE	107	34	18	77	49	12	95	37

Figure S93. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 13(10q22.3)' versus 'CN_CNMF'

P value = 8.18e-09 (Chi-square test), Q value = 3.2e-06

Table S94. Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 13(10Q22.3) CNV	23	31	12	59	7
AMP PEAK 13(10Q22.3) WILD-TYPE	324	191	60	164	42

Figure S94. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(10q22.3)' versus 'METHLYATION_CNMF'

P value = 0.000149 (Chi-square test), Q value = 0.034

Table S95. Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 13(10Q22.3) CNV	23	5	16	21	2	10
AMP PEAK 13(10Q22.3) WILD-TYPE	78	134	77	116	38	87

Figure S95. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 13(10q22.3)' versus 'MRNASEQ_CNMF'

P value = 1.83e-07 (Fisher's exact test), Q value = 6.3e-05

Table S96. Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 13(10Q22.3) CNV	61	11	52
AMP PEAK 13(10Q22.3) WILD-TYPE	173	137	394

Figure S96. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 13(10q22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000689 (Fisher's exact test), Q value = 0.13

Table S97. Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 13(10Q22.3) CNV	20	58	46
AMP PEAK 13(10Q22.3) WILD-TYPE	196	350	158

Figure S97. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(10q22.3)' versus 'MIRSEQ_CNMF'

P value = 3.75e-05 (Fisher's exact test), Q value = 0.0095

Table S98. Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 13(10Q22.3) CNV	21	48	58
AMP PEAK 13(10Q22.3) WILD-TYPE	213	344	197

Figure S98. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 13(10q22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000675 (Fisher's exact test), Q value = 0.13

Table S99. Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 13(10Q22.3) CNV	48	28	51
AMP PEAK 13(10Q22.3) WILD-TYPE	314	256	184

Figure S99. Get High-res Image Gene #13: 'Amp Peak 13(10q22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 14(11p13)' versus 'CN_CNMF'

P value = 1.84e-10 (Chi-square test), Q value = 7.7e-08

Table S100. Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 14(11P13) CNV	33	68	13	67	11
AMP PEAK 14(11P13) WILD-TYPE	314	154	59	156	38

Figure S100. Get High-res Image Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 14(11p13)' versus 'METHLYATION_CNMF'

P value = 4.84e-05 (Chi-square test), Q value = 0.012

Table S101. Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 14(11P13) CNV	27	16	16	44	3	15
AMP PEAK 14(11P13) WILD-TYPE	74	123	77	93	37	82

Figure S101. Get High-res Image Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 14(11p13)' versus 'MRNASEQ_CNMF'

P value = 2.61e-05 (Fisher's exact test), Q value = 0.0067

Table S102. Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 14(11P13) CNV	69	15	99
AMP PEAK 14(11P13) WILD-TYPE	165	133	347

Figure S102. Get High-res Image Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 14(11p13)' versus 'MIRSEQ_CNMF'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00042

Table S103. Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 14(11P13) CNV	29	77	80
AMP PEAK 14(11P13) WILD-TYPE	205	315	175

Figure S103. Get High-res Image Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 14(11p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.91e-08 (Fisher's exact test), Q value = 7.2e-06

Table S104. Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 14(11P13) CNV	80	31	75
AMP PEAK 14(11P13) WILD-TYPE	282	253	160

Figure S104. Get High-res Image Gene #14: 'Amp Peak 14(11p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 15(11q13.3)' versus 'CN_CNMF'

P value = 4.91e-41 (Chi-square test), Q value = 3.1e-38

Table S105. Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 15(11Q13.3) CNV	53	163	28	89	16
AMP PEAK 15(11Q13.3) WILD-TYPE	294	59	44	134	33

Figure S105. Get High-res Image Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(11q13.3)' versus 'METHLYATION_CNMF'

P value = 4e-10 (Chi-square test), Q value = 1.7e-07

Table S106. Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 15(11Q13.3) CNV	37	31	45	75	11	18
AMP PEAK 15(11Q13.3) WILD-TYPE	64	108	48	62	29	79

Figure S106. Get High-res Image Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 15(11q13.3)' versus 'MIRSEQ_CNMF'

P value = 0.000292 (Fisher's exact test), Q value = 0.06

Table S107. Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 15(11Q13.3) CNV	64	160	111
AMP PEAK 15(11Q13.3) WILD-TYPE	170	232	144

Figure S107. Get High-res Image Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 16(11q14.1)' versus 'CN_CNMF'

P value = 1.8e-19 (Chi-square test), Q value = 1e-16

Table S108. Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 16(11Q14.1) CNV	31	89	19	85	10
AMP PEAK 16(11Q14.1) WILD-TYPE	316	133	53	138	39

Figure S108. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(11q14.1)' versus 'METHLYATION_CNMF'

P value = 7.93e-06 (Chi-square test), Q value = 0.0022

Table S109. Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 16(11Q14.1) CNV	38	19	32	32	7	13
AMP PEAK 16(11Q14.1) WILD-TYPE	63	120	61	105	33	84

Figure S109. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 16(11q14.1)' versus 'MRNASEQ_CNMF'

P value = 8.57e-05 (Fisher's exact test), Q value = 0.02

Table S110. Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 16(11Q14.1) CNV	86	27	107
AMP PEAK 16(11Q14.1) WILD-TYPE	148	121	339

Figure S110. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 16(11q14.1)' versus 'MIRSEQ_CNMF'

P value = 8.98e-07 (Fisher's exact test), Q value = 0.00029

Table S111. Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 16(11Q14.1) CNV	40	90	95
AMP PEAK 16(11Q14.1) WILD-TYPE	194	302	160

Figure S111. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 16(11q14.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.39e-05 (Fisher's exact test), Q value = 0.0037

Table S112. Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 16(11Q14.1) CNV	89	51	85
AMP PEAK 16(11Q14.1) WILD-TYPE	273	233	150

Figure S112. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 17(12p13.33)' versus 'MRNA_CNMF'

P value = 1.91e-12 (Chi-square test), Q value = 8.8e-10

Table S113. Gene #17: 'Amp Peak 17(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	124	36	23	95	72	20	103	40
AMP PEAK 17(12P13.33) CNV	37	5	3	53	29	3	13	3
AMP PEAK 17(12P13.33) WILD-TYPE	87	31	20	42	43	17	90	37

Figure S113. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 17(12p13.33)' versus 'MRNA_CHIERARCHICAL'

P value = 2.53e-11 (Fisher's exact test), Q value = 1.1e-08

Table S114. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 17(12P13.33) CNV	15	61	70
AMP PEAK 17(12P13.33) WILD-TYPE	125	64	178

Figure S114. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 17(12p13.33)' versus 'CN_CNMF'

P value = 1.68e-28 (Chi-square test), Q value = 1e-25

Table S115. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 17(12P13.33) CNV	23	68	22	111	14
AMP PEAK 17(12P13.33) WILD-TYPE	324	154	50	112	35

Figure S115. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 17(12p13.33)' versus 'METHLYATION_CNMF'

P value = 7.29e-17 (Chi-square test), Q value = 3.9e-14

Table S116. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 17(12P13.33) CNV	54	13	20	44	2	12
AMP PEAK 17(12P13.33) WILD-TYPE	47	126	73	93	38	85

Figure S116. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 17(12p13.33)' versus 'RPPA_CNMF'

P value = 2.7e-08 (Fisher's exact test), Q value = 1e-05

Table S117. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
AMP PEAK 17(12P13.33) CNV	69	31	18
AMP PEAK 17(12P13.33) WILD-TYPE	78	102	99

Figure S117. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 17(12p13.33)' versus 'RPPA_CHIERARCHICAL'

P value = 2.37e-07 (Fisher's exact test), Q value = 8.1e-05

Table S118. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
AMP PEAK 17(12P13.33) CNV	43	16	59
AMP PEAK 17(12P13.33) WILD-TYPE	118	94	67

Figure S118. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 17(12p13.33)' versus 'MRNASEQ_CNMF'

P value = 1.67e-17 (Fisher's exact test), Q value = 9.1e-15

Table S119. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 17(12P13.33) CNV	107	12	96
AMP PEAK 17(12P13.33) WILD-TYPE	127	136	350

Figure S119. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 17(12p13.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.45e-15 (Fisher's exact test), Q value = 7.6e-13

Table S120. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 17(12P13.33) CNV	24	97	94
AMP PEAK 17(12P13.33) WILD-TYPE	192	311	110

Figure S120. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 17(12p13.33)' versus 'MIRSEQ_CNMF'

P value = 9.18e-22 (Fisher's exact test), Q value = 5.3e-19

Table S121. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 17(12P13.33) CNV	27	76	123
AMP PEAK 17(12P13.33) WILD-TYPE	207	316	132

Figure S121. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 17(12p13.33)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.5e-18 (Fisher's exact test), Q value = 3e-15

Table S122. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 17(12P13.33) CNV	73	41	112
AMP PEAK 17(12P13.33) WILD-TYPE	289	243	123

Figure S122. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 18(12q15)' versus 'MRNA_CNMF'

P value = 1.81e-08 (Chi-square test), Q value = 6.8e-06

Table S123. Gene #18: 'Amp Peak 18(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	124	36	23	95	72	20	103	40
AMP PEAK 18(12Q15) CNV	56	7	3	20	35	7	16	6
AMP PEAK 18(12Q15) WILD-TYPE	68	29	20	75	37	13	87	34

Figure S123. Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 18(12q15)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000131 (Fisher's exact test), Q value = 0.03

Table S124. Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 18(12Q15) CNV	27	29	94
AMP PEAK 18(12Q15) WILD-TYPE	113	96	154

Figure S124. Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 18(12q15)' versus 'CN_CNMF'

P value = 1.86e-25 (Chi-square test), Q value = 1.1e-22

Table S125. Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 18(12Q15) CNV	26	106	26	65	12
AMP PEAK 18(12Q15) WILD-TYPE	321	116	46	158	37

Figure S125. Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 18(12q15)' versus 'METHLYATION_CNMF'

P value = 1.49e-13 (Chi-square test), Q value = 7.2e-11

Table S126. Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 18(12Q15) CNV	17	18	19	66	6	11
AMP PEAK 18(12Q15) WILD-TYPE	84	121	74	71	34	86

Figure S126. Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 18(12q15)' versus 'MRNASEQ_CNMF'

P value = 6.02e-06 (Fisher's exact test), Q value = 0.0017

Table S127. Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 18(12Q15) CNV	63	18	142
AMP PEAK 18(12Q15) WILD-TYPE	171	130	304

Figure S127. Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 18(12q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.0046

Table S128. Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 18(12Q15) CNV	37	138	48
AMP PEAK 18(12Q15) WILD-TYPE	179	270	156

Figure S128. Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 18(12q15)' versus 'MIRSEQ_CNMF'

P value = 9.16e-08 (Fisher's exact test), Q value = 3.3e-05

Table S129. Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 18(12Q15) CNV	29	118	79
AMP PEAK 18(12Q15) WILD-TYPE	205	274	176

Figure S129. Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 18(12q15)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000644 (Fisher's exact test), Q value = 0.12

Table S130. Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 18(12Q15) CNV	112	51	63
AMP PEAK 18(12Q15) WILD-TYPE	250	233	172

Figure S130. Get High-res Image Gene #18: 'Amp Peak 18(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 19(13q12.3)' versus 'CN_CNMF'

P value = 2.22e-05 (Chi-square test), Q value = 0.0059

Table S131. Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 19(13Q12.3) CNV	23	38	13	46	8
AMP PEAK 19(13Q12.3) WILD-TYPE	324	184	59	177	41

Figure S131. Get High-res Image Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(13q12.3)' versus 'MRNASEQ_CNMF'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.0068

Table S132. Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 19(13Q12.3) CNV	45	6	70
AMP PEAK 19(13Q12.3) WILD-TYPE	189	142	376

Figure S132. Get High-res Image Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 19(13q12.3)' versus 'MIRSEQ_CNMF'

P value = 0.000196 (Fisher's exact test), Q value = 0.043

Table S133. Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 19(13Q12.3) CNV	17	55	51
AMP PEAK 19(13Q12.3) WILD-TYPE	217	337	204

Figure S133. Get High-res Image Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 19(13q12.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.086

Table S134. Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 19(13Q12.3) CNV	51	24	48
AMP PEAK 19(13Q12.3) WILD-TYPE	311	260	187

Figure S134. Get High-res Image Gene #19: 'Amp Peak 19(13q12.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 20(13q34)' versus 'MRNA_CNMF'

P value = 9.14e-10 (Chi-square test), Q value = 3.7e-07

Table S135. Gene #20: 'Amp Peak 20(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	124	36	23	95	72	20	103	40
AMP PEAK 20(13Q34) CNV	19	3	3	42	10	4	15	0
AMP PEAK 20(13Q34) WILD-TYPE	105	33	20	53	62	16	88	40

Figure S135. Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 20(13q34)' versus 'MRNA_CHIERARCHICAL'

P value = 5.78e-09 (Fisher's exact test), Q value = 2.3e-06

Table S136. Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 20(13Q34) CNV	12	47	37
AMP PEAK 20(13Q34) WILD-TYPE	128	78	211

Figure S136. Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 20(13q34)' versus 'CN_CNMF'

P value = 1.51e-17 (Chi-square test), Q value = 8.2e-15

Table S137. Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 20(13Q34) CNV	28	33	9	83	6
AMP PEAK 20(13Q34) WILD-TYPE	319	189	63	140	43

Figure S137. Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(13q34)' versus 'METHLYATION_CNMF'

P value = 1.33e-14 (Chi-square test), Q value = 6.7e-12

Table S138. Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 20(13Q34) CNV	44	8	13	20	1	12
AMP PEAK 20(13Q34) WILD-TYPE	57	131	80	117	39	85

Figure S138. Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 20(13q34)' versus 'RPPA_CNMF'

P value = 8.21e-06 (Fisher's exact test), Q value = 0.0023

Table S139. Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
AMP PEAK 20(13Q34) CNV	48	22	11
AMP PEAK 20(13Q34) WILD-TYPE	99	111	106

Figure S139. Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 20(13q34)' versus 'RPPA_CHIERARCHICAL'

P value = 5.1e-08 (Fisher's exact test), Q value = 1.8e-05

Table S140. Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
AMP PEAK 20(13Q34) CNV	25	9	47
AMP PEAK 20(13Q34) WILD-TYPE	136	101	79

Figure S140. Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 20(13q34)' versus 'MRNASEQ_CNMF'

P value = 8.44e-14 (Fisher's exact test), Q value = 4.1e-11

Table S141. Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 20(13Q34) CNV	77	7	59
AMP PEAK 20(13Q34) WILD-TYPE	157	141	387

Figure S141. Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 20(13q34)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-14 (Fisher's exact test), Q value = 5.9e-12

Table S142. Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 20(13Q34) CNV	15	55	73
AMP PEAK 20(13Q34) WILD-TYPE	201	353	131

Figure S142. Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 20(13q34)' versus 'MIRSEQ_CNMF'

P value = 1.41e-13 (Fisher's exact test), Q value = 6.8e-11

Table S143. Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 20(13Q34) CNV	25	44	86
AMP PEAK 20(13Q34) WILD-TYPE	209	348	169

Figure S143. Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 20(13q34)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.59e-20 (Fisher's exact test), Q value = 3.2e-17

Table S144. Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 20(13Q34) CNV	47	19	89
AMP PEAK 20(13Q34) WILD-TYPE	315	265	146

Figure S144. Get High-res Image Gene #20: 'Amp Peak 20(13q34)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 21(14q21.1)' versus 'MRNA_CNMF'

P value = 0.000259 (Chi-square test), Q value = 0.055

Table S145. Gene #21: 'Amp Peak 21(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	124	36	23	95	72	20	103	40
AMP PEAK 21(14Q21.1) CNV	35	7	5	11	26	6	20	1
AMP PEAK 21(14Q21.1) WILD-TYPE	89	29	18	84	46	14	83	39

Figure S145. Get High-res Image Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 21(14q21.1)' versus 'CN_CNMF'

P value = 1.97e-09 (Chi-square test), Q value = 7.9e-07

Table S146. Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 21(14Q21.1) CNV	34	73	15	49	10
AMP PEAK 21(14Q21.1) WILD-TYPE	313	149	57	174	39

Figure S146. Get High-res Image Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(14q21.1)' versus 'METHLYATION_CNMF'

P value = 5.16e-05 (Chi-square test), Q value = 0.013

Table S147. Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 21(14Q21.1) CNV	13	18	23	41	4	9
AMP PEAK 21(14Q21.1) WILD-TYPE	88	121	70	96	36	88

Figure S147. Get High-res Image Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 21(14q21.1)' versus 'MRNASEQ_CNMF'

P value = 3.92e-05 (Fisher's exact test), Q value = 0.0099

Table S148. Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 21(14Q21.1) CNV	42	15	117
AMP PEAK 21(14Q21.1) WILD-TYPE	192	133	329

Figure S148. Get High-res Image Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(14q21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.45e-06 (Fisher's exact test), Q value = 0.00072

Table S149. Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 21(14Q21.1) CNV	27	115	32
AMP PEAK 21(14Q21.1) WILD-TYPE	189	293	172

Figure S149. Get High-res Image Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 21(14q21.1)' versus 'MIRSEQ_CNMF'

P value = 1.94e-06 (Fisher's exact test), Q value = 0.00058

Table S150. Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 21(14Q21.1) CNV	21	95	58
AMP PEAK 21(14Q21.1) WILD-TYPE	213	297	197

Figure S150. Get High-res Image Gene #21: 'Amp Peak 21(14q21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 22(15q26.3)' versus 'MRNA_CNMF'

P value = 3.31e-07 (Chi-square test), Q value = 0.00011

Table S151. Gene #22: 'Amp Peak 22(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	124	36	23	95	72	20	103	40
AMP PEAK 22(15Q26.3) CNV	32	7	2	32	16	8	4	2
AMP PEAK 22(15Q26.3) WILD-TYPE	92	29	21	63	56	12	99	38

Figure S151. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 22(15q26.3)' versus 'CN_CNMF'

P value = 1.88e-15 (Chi-square test), Q value = 9.8e-13

Table S152. Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 22(15Q26.3) CNV	30	47	6	79	4
AMP PEAK 22(15Q26.3) WILD-TYPE	317	175	66	144	45

Figure S152. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(15q26.3)' versus 'METHLYATION_CNMF'

P value = 0.000326 (Chi-square test), Q value = 0.067

Table S153. Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 22(15Q26.3) CNV	26	6	17	26	6	14
AMP PEAK 22(15Q26.3) WILD-TYPE	75	133	76	111	34	83

Figure S153. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 22(15q26.3)' versus 'RPPA_CNMF'

P value = 0.000153 (Fisher's exact test), Q value = 0.035

Table S154. Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
AMP PEAK 22(15Q26.3) CNV	47	18	17
AMP PEAK 22(15Q26.3) WILD-TYPE	100	115	100

Figure S154. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 22(15q26.3)' versus 'MRNASEQ_CNMF'

P value = 2.07e-08 (Fisher's exact test), Q value = 7.7e-06

Table S155. Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 22(15Q26.3) CNV	70	10	74
AMP PEAK 22(15Q26.3) WILD-TYPE	164	138	372

Figure S155. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 22(15q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.98e-06 (Fisher's exact test), Q value = 0.0022

Table S156. Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 22(15Q26.3) CNV	24	70	60
AMP PEAK 22(15Q26.3) WILD-TYPE	192	338	144

Figure S156. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(15q26.3)' versus 'MIRSEQ_CNMF'

P value = 5.92e-08 (Fisher's exact test), Q value = 2.1e-05

Table S157. Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 22(15Q26.3) CNV	31	51	77
AMP PEAK 22(15Q26.3) WILD-TYPE	203	341	178

Figure S157. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 22(15q26.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.56e-09 (Fisher's exact test), Q value = 2.9e-06

Table S158. Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 22(15Q26.3) CNV	59	28	72
AMP PEAK 22(15Q26.3) WILD-TYPE	303	256	163

Figure S158. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 23(17q12)' versus 'MRNA_CNMF'

P value = 1.49e-14 (Chi-square test), Q value = 7.5e-12

Table S159. Gene #23: 'Amp Peak 23(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	124	36	23	95	72	20	103	40
AMP PEAK 23(17Q12) CNV	52	12	8	19	49	7	14	4
AMP PEAK 23(17Q12) WILD-TYPE	72	24	15	76	23	13	89	36

Figure S159. Get High-res Image Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 23(17q12)' versus 'MRNA_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.062

Table S160. Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 23(17Q12) CNV	28	39	98
AMP PEAK 23(17Q12) WILD-TYPE	112	86	150

Figure S160. Get High-res Image Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 23(17q12)' versus 'CN_CNMF'

P value = 7.29e-34 (Chi-square test), Q value = 4.5e-31

Table S161. Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 23(17Q12) CNV	55	146	22	57	15
AMP PEAK 23(17Q12) WILD-TYPE	292	76	50	166	34

Figure S161. Get High-res Image Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(17q12)' versus 'METHLYATION_CNMF'

P value = 5.76e-09 (Chi-square test), Q value = 2.3e-06

Table S162. Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 23(17Q12) CNV	27	24	40	69	11	21
AMP PEAK 23(17Q12) WILD-TYPE	74	115	53	68	29	76

Figure S162. Get High-res Image Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(17q12)' versus 'MRNASEQ_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.024

Table S163. Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 23(17Q12) CNV	89	28	159
AMP PEAK 23(17Q12) WILD-TYPE	145	120	287

Figure S163. Get High-res Image Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 23(17q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000454 (Fisher's exact test), Q value = 0.09

Table S164. Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 23(17Q12) CNV	50	157	69
AMP PEAK 23(17Q12) WILD-TYPE	166	251	135

Figure S164. Get High-res Image Gene #23: 'Amp Peak 23(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(17q23.1)' versus 'MRNA_CNMF'

P value = 2.42e-14 (Chi-square test), Q value = 1.2e-11

Table S165. Gene #24: 'Amp Peak 24(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	124	36	23	95	72	20	103	40
AMP PEAK 24(17Q23.1) CNV	81	17	8	29	43	11	16	10
AMP PEAK 24(17Q23.1) WILD-TYPE	43	19	15	66	29	9	87	30

Figure S165. Get High-res Image Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 24(17q23.1)' versus 'CN_CNMF'

P value = 6.19e-38 (Chi-square test), Q value = 3.8e-35

Table S166. Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 24(17Q23.1) CNV	66	166	21	102	19
AMP PEAK 24(17Q23.1) WILD-TYPE	281	56	51	121	30

Figure S166. Get High-res Image Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(17q23.1)' versus 'METHLYATION_CNMF'

P value = 1.45e-10 (Chi-square test), Q value = 6.1e-08

Table S167. Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 24(17Q23.1) CNV	42	31	40	85	17	25
AMP PEAK 24(17Q23.1) WILD-TYPE	59	108	53	52	23	72

Figure S167. Get High-res Image Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(17q23.1)' versus 'MRNASEQ_CNMF'

P value = 0.000644 (Fisher's exact test), Q value = 0.12

Table S168. Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 24(17Q23.1) CNV	99	43	209
AMP PEAK 24(17Q23.1) WILD-TYPE	135	105	237

Figure S168. Get High-res Image Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(17q23.1)' versus 'MIRSEQ_CNMF'

P value = 3.1e-07 (Fisher's exact test), Q value = 1e-04

Table S169. Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 24(17Q23.1) CNV	65	167	132
AMP PEAK 24(17Q23.1) WILD-TYPE	169	225	123

Figure S169. Get High-res Image Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 24(17q23.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.57e-06 (Fisher's exact test), Q value = 0.001

Table S170. Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 24(17Q23.1) CNV	175	84	105
AMP PEAK 24(17Q23.1) WILD-TYPE	187	200	130

Figure S170. Get High-res Image Gene #24: 'Amp Peak 24(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 25(19q12)' versus 'MRNA_CNMF'

P value = 2.12e-12 (Chi-square test), Q value = 9.7e-10

Table S171. Gene #25: 'Amp Peak 25(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	124	36	23	95	72	20	103	40
AMP PEAK 25(19Q12) CNV	30	4	4	56	20	7	14	5
AMP PEAK 25(19Q12) WILD-TYPE	94	32	19	39	52	13	89	35

Figure S171. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 25(19q12)' versus 'MRNA_CHIERARCHICAL'

P value = 9.11e-11 (Fisher's exact test), Q value = 3.9e-08

Table S172. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 25(19Q12) CNV	22	64	54
AMP PEAK 25(19Q12) WILD-TYPE	118	61	194

Figure S172. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 25(19q12)' versus 'CN_CNMF'

P value = 1.28e-21 (Chi-square test), Q value = 7.4e-19

Table S173. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 25(19Q12) CNV	41	44	26	108	14
AMP PEAK 25(19Q12) WILD-TYPE	306	178	46	115	35

Figure S173. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 25(19q12)' versus 'METHLYATION_CNMF'

P value = 4.2e-12 (Chi-square test), Q value = 1.9e-09

Table S174. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 25(19Q12) CNV	53	15	20	34	4	22
AMP PEAK 25(19Q12) WILD-TYPE	48	124	73	103	36	75

Figure S174. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 25(19q12)' versus 'RPPA_CNMF'

P value = 6.19e-07 (Fisher's exact test), Q value = 2e-04

Table S175. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
AMP PEAK 25(19Q12) CNV	64	23	23
AMP PEAK 25(19Q12) WILD-TYPE	83	110	94

Figure S175. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 25(19q12)' versus 'RPPA_CHIERARCHICAL'

P value = 9.68e-07 (Fisher's exact test), Q value = 0.00031

Table S176. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
AMP PEAK 25(19Q12) CNV	29	24	57
AMP PEAK 25(19Q12) WILD-TYPE	132	86	69

Figure S176. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 25(19q12)' versus 'MRNASEQ_CNMF'

P value = 1.11e-15 (Fisher's exact test), Q value = 5.8e-13

Table S177. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 25(19Q12) CNV	109	26	79
AMP PEAK 25(19Q12) WILD-TYPE	125	122	367

Figure S177. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 25(19q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.08e-15 (Fisher's exact test), Q value = 1.1e-12

Table S178. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 25(19Q12) CNV	37	78	99
AMP PEAK 25(19Q12) WILD-TYPE	179	330	105

Figure S178. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(19q12)' versus 'MIRSEQ_CNMF'

P value = 6.49e-13 (Fisher's exact test), Q value = 3e-10

Table S179. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 25(19Q12) CNV	45	71	111
AMP PEAK 25(19Q12) WILD-TYPE	189	321	144

Figure S179. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 25(19q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.82e-18 (Fisher's exact test), Q value = 1.6e-15

Table S180. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 25(19Q12) CNV	65	48	114
AMP PEAK 25(19Q12) WILD-TYPE	297	236	121

Figure S180. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 26(19q13.42)' versus 'MRNA_CNMF'

P value = 0.000775 (Chi-square test), Q value = 0.14

Table S181. Gene #26: 'Amp Peak 26(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	124	36	23	95	72	20	103	40
AMP PEAK 26(19Q13.42) CNV	38	8	5	37	22	10	15	6
AMP PEAK 26(19Q13.42) WILD-TYPE	86	28	18	58	50	10	88	34

Figure S181. Get High-res Image Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 26(19q13.42)' versus 'CN_CNMF'

P value = 2.5e-14 (Chi-square test), Q value = 1.2e-11

Table S182. Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 26(19Q13.42) CNV	41	59	27	92	16
AMP PEAK 26(19Q13.42) WILD-TYPE	306	163	45	131	33

Figure S182. Get High-res Image Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 26(19q13.42)' versus 'METHLYATION_CNMF'

P value = 6.23e-07 (Chi-square test), Q value = 2e-04

Table S183. Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 26(19Q13.42) CNV	34	15	25	51	5	17
AMP PEAK 26(19Q13.42) WILD-TYPE	67	124	68	86	35	80

Figure S183. Get High-res Image Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 26(19q13.42)' versus 'MIRSEQ_CNMF'

P value = 4.27e-06 (Fisher's exact test), Q value = 0.0012

Table S184. Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 26(19Q13.42) CNV	43	91	95
AMP PEAK 26(19Q13.42) WILD-TYPE	191	301	160

Figure S184. Get High-res Image Gene #26: 'Amp Peak 26(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 27(20q13.2)' versus 'MRNA_CNMF'

P value = 1.35e-09 (Chi-square test), Q value = 5.4e-07

Table S185. Gene #27: 'Amp Peak 27(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	124	36	23	95	72	20	103	40
AMP PEAK 27(20Q13.2) CNV	87	18	10	51	49	15	34	10
AMP PEAK 27(20Q13.2) WILD-TYPE	37	18	13	44	23	5	69	30

Figure S185. Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 27(20q13.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000278 (Fisher's exact test), Q value = 0.058

Table S186. Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
AMP PEAK 27(20Q13.2) CNV	55	69	150
AMP PEAK 27(20Q13.2) WILD-TYPE	85	56	98

Figure S186. Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 27(20q13.2)' versus 'CN_CNMF'

P value = 9.78e-50 (Chi-square test), Q value = 6.2e-47

Table S187. Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
AMP PEAK 27(20Q13.2) CNV	67	170	43	158	27
AMP PEAK 27(20Q13.2) WILD-TYPE	280	52	29	65	22

Figure S187. Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 27(20q13.2)' versus 'METHLYATION_CNMF'

P value = 5.18e-25 (Chi-square test), Q value = 3.1e-22

Table S188. Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
AMP PEAK 27(20Q13.2) CNV	61	28	48	111	12	32
AMP PEAK 27(20Q13.2) WILD-TYPE	40	111	45	26	28	65

Figure S188. Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 27(20q13.2)' versus 'RPPA_CNMF'

P value = 0.000604 (Fisher's exact test), Q value = 0.12

Table S189. Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
AMP PEAK 27(20Q13.2) CNV	99	67	53
AMP PEAK 27(20Q13.2) WILD-TYPE	48	66	64

Figure S189. Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 27(20q13.2)' versus 'MRNASEQ_CNMF'

P value = 6.68e-09 (Fisher's exact test), Q value = 2.6e-06

Table S190. Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
AMP PEAK 27(20Q13.2) CNV	140	45	253
AMP PEAK 27(20Q13.2) WILD-TYPE	94	103	193

Figure S190. Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 27(20q13.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.14e-07 (Fisher's exact test), Q value = 7.3e-05

Table S191. Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
AMP PEAK 27(20Q13.2) CNV	80	245	113
AMP PEAK 27(20Q13.2) WILD-TYPE	136	163	91

Figure S191. Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(20q13.2)' versus 'MIRSEQ_CNMF'

P value = 7.41e-10 (Fisher's exact test), Q value = 3e-07

Table S192. Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
AMP PEAK 27(20Q13.2) CNV	80	214	159
AMP PEAK 27(20Q13.2) WILD-TYPE	154	178	96

Figure S192. Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 27(20q13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00036

Table S193. Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
AMP PEAK 27(20Q13.2) CNV	205	110	138
AMP PEAK 27(20Q13.2) WILD-TYPE	157	174	97

Figure S193. Get High-res Image Gene #27: 'Amp Peak 27(20q13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'MRNA_CNMF'

P value = 3.27e-05 (Chi-square test), Q value = 0.0084

Table S194. Gene #28: '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	124	36	23	95	72	20	103	40
DEL PEAK 1(1P36.13) CNV	65	11	7	40	46	7	30	12
DEL PEAK 1(1P36.13) WILD-TYPE	59	25	16	55	26	13	73	28

Figure S194. Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000651 (Fisher's exact test), Q value = 0.12

Table S195. Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 1(1P36.13) CNV	43	50	125
DEL PEAK 1(1P36.13) WILD-TYPE	97	75	123

Figure S195. Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'CN_CNMF'

P value = 6.02e-32 (Chi-square test), Q value = 3.7e-29

Table S196. Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 1(1P36.13) CNV	58	135	47	120	20
DEL PEAK 1(1P36.13) WILD-TYPE	289	87	25	103	29

Figure S196. Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.13)' versus 'METHLYATION_CNMF'

P value = 2.81e-09 (Chi-square test), Q value = 1.1e-06

Table S197. Gene #28: '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	101	139	93	137	40	97
DEL PEAK 1(1P36.13) CNV	46	33	50	76	11	25
DEL PEAK 1(1P36.13) WILD-TYPE	55	106	43	61	29	72

Figure S197. Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNASEQ_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.003

Table S198. Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 1(1P36.13) CNV	105	37	207
DEL PEAK 1(1P36.13) WILD-TYPE	129	111	239

Figure S198. Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.02e-05 (Fisher's exact test), Q value = 0.015

Table S199. Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 1(1P36.13) CNV	68	201	80
DEL PEAK 1(1P36.13) WILD-TYPE	148	207	124

Figure S199. Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.13)' versus 'MIRSEQ_CNMF'

P value = 2.37e-07 (Fisher's exact test), Q value = 8.1e-05

Table S200. Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 1(1P36.13) CNV	64	168	131
DEL PEAK 1(1P36.13) WILD-TYPE	170	224	124

Figure S200. Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.11

Table S201. Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 1(1P36.13) CNV	168	91	104
DEL PEAK 1(1P36.13) WILD-TYPE	194	193	131

Figure S201. Get High-res Image Gene #28: 'Del Peak 1(1p36.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 2(1p22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 8.39e-05 (Fisher's exact test), Q value = 0.02

Table S202. Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 2(1P22.1) CNV	40	30	110
DEL PEAK 2(1P22.1) WILD-TYPE	100	95	138

Figure S202. Get High-res Image Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p22.1)' versus 'CN_CNMF'

P value = 5.77e-22 (Chi-square test), Q value = 3.4e-19

Table S203. Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 2(1P22.1) CNV	61	117	45	70	12
DEL PEAK 2(1P22.1) WILD-TYPE	286	105	27	153	37

Figure S203. Get High-res Image Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p22.1)' versus 'METHLYATION_CNMF'

P value = 0.00103 (Chi-square test), Q value = 0.19

Table S204. Gene #29: '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	101	139	93	137	40	97
DEL PEAK 2(1P22.1) CNV	25	35	40	56	13	21
DEL PEAK 2(1P22.1) WILD-TYPE	76	104	53	81	27	76

Figure S204. Get High-res Image Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 2(1p22.1)' versus 'MRNASEQ_CNMF'

P value = 0.000574 (Fisher's exact test), Q value = 0.11

Table S205. Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 2(1P22.1) CNV	68	38	180
DEL PEAK 2(1P22.1) WILD-TYPE	166	110	266

Figure S205. Get High-res Image Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.06e-06 (Fisher's exact test), Q value = 0.00089

Table S206. Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 2(1P22.1) CNV	64	174	48
DEL PEAK 2(1P22.1) WILD-TYPE	152	234	156

Figure S206. Get High-res Image Gene #29: 'Del Peak 2(1p22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MRNA_CNMF'

P value = 1.39e-06 (Chi-square test), Q value = 0.00043

Table S207. Gene #30: '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	124	36	23	95	72	20	103	40
DEL PEAK 3(2Q37.3) CNV	43	10	5	46	28	6	22	0
DEL PEAK 3(2Q37.3) WILD-TYPE	81	26	18	49	44	14	81	40

Figure S207. Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 3(2q37.3)' versus 'MRNA_CHIERARCHICAL'

P value = 3.78e-08 (Fisher's exact test), Q value = 1.4e-05

Table S208. Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 3(2Q37.3) CNV	20	58	82
DEL PEAK 3(2Q37.3) WILD-TYPE	120	67	166

Figure S208. Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'CN_CNMF'

P value = 1.57e-20 (Chi-square test), Q value = 9e-18

Table S209. Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 3(2Q37.3) CNV	39	76	26	108	16
DEL PEAK 3(2Q37.3) WILD-TYPE	308	146	46	115	33

Figure S209. Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 3(2q37.3)' versus 'METHLYATION_CNMF'

P value = 2.61e-10 (Chi-square test), Q value = 1.1e-07

Table S210. Gene #30: '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	101	139	93	137	40	97
DEL PEAK 3(2Q37.3) CNV	44	19	25	53	4	12
DEL PEAK 3(2Q37.3) WILD-TYPE	57	120	68	84	36	85

Figure S210. Get High-res Image Gene #30: '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 = 4e-06

Table S211. Gene #30: '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 S211. Get High-res Image Gene #30: '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 = 3.9e-05

Table S212. Gene #30: '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 S212. Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MRNASEQ_CNMF'

P value = 1.81e-11 (Fisher's exact test), Q value = 8e-09

Table S213. Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 3(2Q37.3) CNV	103	17	126
DEL PEAK 3(2Q37.3) WILD-TYPE	131	131	320

Figure S213. Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 3(2q37.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.03e-08 (Fisher's exact test), Q value = 7.6e-06

Table S214. Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 3(2Q37.3) CNV	35	125	86
DEL PEAK 3(2Q37.3) WILD-TYPE	181	283	118

Figure S214. Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q37.3)' versus 'MIRSEQ_CNMF'

P value = 4.66e-11 (Fisher's exact test), Q value = 2e-08

Table S215. Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 3(2Q37.3) CNV	43	99	116
DEL PEAK 3(2Q37.3) WILD-TYPE	191	293	139

Figure S215. Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 3(2q37.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.63e-07 (Fisher's exact test), Q value = 8.9e-05

Table S216. Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 3(2Q37.3) CNV	110	53	95
DEL PEAK 3(2Q37.3) WILD-TYPE	252	231	140

Figure S216. Get High-res Image Gene #30: 'Del Peak 3(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'MRNA_CNMF'

P value = 1.06e-10 (Chi-square test), Q value = 4.5e-08

Table S217. Gene #31: '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	124	36	23	95	72	20	103	40
DEL PEAK 4(3P14.3) CNV	39	11	4	50	34	9	8	8
DEL PEAK 4(3P14.3) WILD-TYPE	85	25	19	45	38	11	95	32

Figure S217. Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 4(3p14.3)' versus 'MRNA_CHIERARCHICAL'

P value = 3.11e-08 (Fisher's exact test), Q value = 1.1e-05

Table S218. Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 4(3P14.3) CNV	36	67	60
DEL PEAK 4(3P14.3) WILD-TYPE	104	58	188

Figure S218. Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'CN_CNMF'

P value = 2.93e-33 (Chi-square test), Q value = 1.8e-30

Table S219. Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 4(3P14.3) CNV	44	80	12	134	8
DEL PEAK 4(3P14.3) WILD-TYPE	303	142	60	89	41

Figure S219. Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(3p14.3)' versus 'METHLYATION_CNMF'

P value = 5.78e-13 (Chi-square test), Q value = 2.7e-10

Table S220. Gene #31: '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	101	139	93	137	40	97
DEL PEAK 4(3P14.3) CNV	49	9	35	51	12	18
DEL PEAK 4(3P14.3) WILD-TYPE	52	130	58	86	28	79

Figure S220. Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 4(3p14.3)' versus 'RPPA_CNMF'

P value = 1.18e-09 (Fisher's exact test), Q value = 4.8e-07

Table S221. Gene #31: '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	79	25	32
DEL PEAK 4(3P14.3) WILD-TYPE	68	108	85

Figure S221. Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 4(3p14.3)' versus 'RPPA_CHIERARCHICAL'

P value = 5.21e-06 (Fisher's exact test), Q value = 0.0015

Table S222. Gene #31: '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	65
DEL PEAK 4(3P14.3) WILD-TYPE	121	79	61

Figure S222. Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'MRNASEQ_CNMF'

P value = 4.61e-18 (Fisher's exact test), Q value = 2.6e-15

Table S223. Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 4(3P14.3) CNV	127	28	102
DEL PEAK 4(3P14.3) WILD-TYPE	107	120	344

Figure S223. Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 4(3p14.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.42e-13 (Fisher's exact test), Q value = 2.1e-10

Table S224. Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 4(3P14.3) CNV	45	105	107
DEL PEAK 4(3P14.3) WILD-TYPE	171	303	97

Figure S224. Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 4(3p14.3)' versus 'MIRSEQ_CNMF'

P value = 2.29e-19 (Fisher's exact test), Q value = 1.3e-16

Table S225. Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 4(3P14.3) CNV	45	87	136
DEL PEAK 4(3P14.3) WILD-TYPE	189	305	119

Figure S225. Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 4(3p14.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.57e-14 (Fisher's exact test), Q value = 1.3e-11

Table S226. Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 4(3P14.3) CNV	100	51	117
DEL PEAK 4(3P14.3) WILD-TYPE	262	233	118

Figure S226. Get High-res Image Gene #31: 'Del Peak 4(3p14.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MRNA_CNMF'

P value = 5.63e-11 (Chi-square test), Q value = 2.4e-08

Table S227. Gene #32: '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	124	36	23	95	72	20	103	40
DEL PEAK 5(4P16.3) CNV	28	10	4	55	37	7	21	5
DEL PEAK 5(4P16.3) WILD-TYPE	96	26	19	40	35	13	82	35

Figure S227. Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 5(4p16.3)' versus 'MRNA_CHIERARCHICAL'

P value = 6.3e-12 (Fisher's exact test), Q value = 2.8e-09

Table S228. Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 5(4P16.3) CNV	24	72	71
DEL PEAK 5(4P16.3) WILD-TYPE	116	53	177

Figure S228. Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'CN_CNMF'

P value = 1.98e-26 (Chi-square test), Q value = 1.2e-23

Table S229. Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 5(4P16.3) CNV	55	52	31	130	13
DEL PEAK 5(4P16.3) WILD-TYPE	292	170	41	93	36

Figure S229. Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(4p16.3)' versus 'METHLYATION_CNMF'

P value = 8.41e-13 (Chi-square test), Q value = 3.9e-10

Table S230. Gene #32: '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	101	139	93	137	40	97
DEL PEAK 5(4P16.3) CNV	62	30	27	28	5	25
DEL PEAK 5(4P16.3) WILD-TYPE	39	109	66	109	35	72

Figure S230. Get High-res Image Gene #32: '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 = 0.00015

Table S231. Gene #32: '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 S231. Get High-res Image Gene #32: '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 = 5e-04

Table S232. Gene #32: '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 S232. Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MRNASEQ_CNMF'

P value = 9.75e-24 (Fisher's exact test), Q value = 5.8e-21

Table S233. Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 5(4P16.3) CNV	134	20	104
DEL PEAK 5(4P16.3) WILD-TYPE	100	128	342

Figure S233. Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(4p16.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.14e-18 (Fisher's exact test), Q value = 1.2e-15

Table S234. Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 5(4P16.3) CNV	38	105	115
DEL PEAK 5(4P16.3) WILD-TYPE	178	303	89

Figure S234. Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(4p16.3)' versus 'MIRSEQ_CNMF'

P value = 9.97e-15 (Fisher's exact test), Q value = 5.1e-12

Table S235. Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 5(4P16.3) CNV	48	94	129
DEL PEAK 5(4P16.3) WILD-TYPE	186	298	126

Figure S235. Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 5(4p16.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.7e-18 (Fisher's exact test), Q value = 2.6e-15

Table S236. Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 5(4P16.3) CNV	93	52	126
DEL PEAK 5(4P16.3) WILD-TYPE	269	232	109

Figure S236. Get High-res Image Gene #32: 'Del Peak 5(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MRNA_CNMF'

P value = 3.17e-06 (Chi-square test), Q value = 0.00092

Table S237. Gene #33: '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	124	36	23	95	72	20	103	40
DEL PEAK 6(4Q35.2) CNV	27	10	7	50	30	10	23	8
DEL PEAK 6(4Q35.2) WILD-TYPE	97	26	16	45	42	10	80	32

Figure S237. Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 6(4q35.2)' versus 'MRNA_CHIERARCHICAL'

P value = 9.81e-07 (Fisher's exact test), Q value = 0.00031

Table S238. Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 6(4Q35.2) CNV	29	63	73
DEL PEAK 6(4Q35.2) WILD-TYPE	111	62	175

Figure S238. Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'CN_CNMF'

P value = 2.71e-37 (Chi-square test), Q value = 1.7e-34

Table S239. Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 6(4Q35.2) CNV	53	42	36	141	11
DEL PEAK 6(4Q35.2) WILD-TYPE	294	180	36	82	38

Figure S239. Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(4q35.2)' versus 'METHLYATION_CNMF'

P value = 1.66e-13 (Chi-square test), Q value = 8e-11

Table S240. Gene #33: '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	101	139	93	137	40	97
DEL PEAK 6(4Q35.2) CNV	63	29	23	26	7	29
DEL PEAK 6(4Q35.2) WILD-TYPE	38	110	70	111	33	68

Figure S240. Get High-res Image Gene #33: '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 = 5.7e-06

Table S241. Gene #33: '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 S241. Get High-res Image Gene #33: '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 = 0.00054

Table S242. Gene #33: '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 S242. Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MRNASEQ_CNMF'

P value = 2.22e-21 (Fisher's exact test), Q value = 1.3e-18

Table S243. Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 6(4Q35.2) CNV	131	21	107
DEL PEAK 6(4Q35.2) WILD-TYPE	103	127	339

Figure S243. Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 6(4q35.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.79e-14 (Fisher's exact test), Q value = 1.9e-11

Table S244. Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 6(4Q35.2) CNV	43	107	109
DEL PEAK 6(4Q35.2) WILD-TYPE	173	301	95

Figure S244. Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(4q35.2)' versus 'MIRSEQ_CNMF'

P value = 2.84e-13 (Fisher's exact test), Q value = 1.4e-10

Table S245. Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 6(4Q35.2) CNV	48	97	126
DEL PEAK 6(4Q35.2) WILD-TYPE	186	295	129

Figure S245. Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 6(4q35.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.73e-18 (Fisher's exact test), Q value = 3.7e-15

Table S246. Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 6(4Q35.2) CNV	87	57	127
DEL PEAK 6(4Q35.2) WILD-TYPE	275	227	108

Figure S246. Get High-res Image Gene #33: 'Del Peak 6(4q35.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MRNA_CNMF'

P value = 1.17e-27 (Chi-square test), Q value = 7e-25

Table S247. Gene #34: '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	124	36	23	95	72	20	103	40
DEL PEAK 7(5Q11.2) CNV	19	5	2	68	25	3	8	4
DEL PEAK 7(5Q11.2) WILD-TYPE	105	31	21	27	47	17	95	36

Figure S247. Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 7(5q11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 6.11e-25 (Fisher's exact test), Q value = 3.6e-22

Table S248. Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 7(5Q11.2) CNV	14	79	41
DEL PEAK 7(5Q11.2) WILD-TYPE	126	46	207

Figure S248. Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'CN_CNMF'

P value = 5.91e-60 (Chi-square test), Q value = 3.8e-57

Table S249. Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 7(5Q11.2) CNV	35	29	8	152	10
DEL PEAK 7(5Q11.2) WILD-TYPE	312	193	64	71	39

Figure S249. Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(5q11.2)' versus 'METHLYATION_CNMF'

P value = 1.43e-39 (Chi-square test), Q value = 8.9e-37

Table S250. Gene #34: '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	101	139	93	137	40	97
DEL PEAK 7(5Q11.2) CNV	78	4	15	28	5	22
DEL PEAK 7(5Q11.2) WILD-TYPE	23	135	78	109	35	75

Figure S250. Get High-res Image Gene #34: '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 = 1.8e-13

Table S251. Gene #34: '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 S251. Get High-res Image Gene #34: '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 = 4.2e-16

Table S252. Gene #34: '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 S252. Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MRNASEQ_CNMF'

P value = 1.33e-40 (Fisher's exact test), Q value = 8.3e-38

Table S253. Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 7(5Q11.2) CNV	140	11	67
DEL PEAK 7(5Q11.2) WILD-TYPE	94	137	379

Figure S253. Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 7(5q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.7e-43 (Fisher's exact test), Q value = 1.1e-40

Table S254. Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 7(5Q11.2) CNV	19	67	132
DEL PEAK 7(5Q11.2) WILD-TYPE	197	341	72

Figure S254. Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(5q11.2)' versus 'MIRSEQ_CNMF'

P value = 8.36e-40 (Fisher's exact test), Q value = 5.2e-37

Table S255. Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 7(5Q11.2) CNV	32	45	145
DEL PEAK 7(5Q11.2) WILD-TYPE	202	347	110

Figure S255. Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 7(5q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.41e-49 (Fisher's exact test), Q value = 3.4e-46

Table S256. Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 7(5Q11.2) CNV	63	16	143
DEL PEAK 7(5Q11.2) WILD-TYPE	299	268	92

Figure S256. Get High-res Image Gene #34: 'Del Peak 7(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MRNA_CNMF'

P value = 1.36e-29 (Chi-square test), Q value = 8.3e-27

Table S257. Gene #35: '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	124	36	23	95	72	20	103	40
DEL PEAK 8(5Q21.3) CNV	19	5	2	69	24	5	7	2
DEL PEAK 8(5Q21.3) WILD-TYPE	105	31	21	26	48	15	96	38

Figure S257. Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 8(5q21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 1e-26 (Fisher's exact test), Q value = 6e-24

Table S258. Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 8(5Q21.3) CNV	12	80	41
DEL PEAK 8(5Q21.3) WILD-TYPE	128	45	207

Figure S258. Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'CN_CNMF'

P value = 6.13e-70 (Chi-square test), Q value = 3.9e-67

Table S259. Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 8(5Q21.3) CNV	28	25	7	156	9
DEL PEAK 8(5Q21.3) WILD-TYPE	319	197	65	67	40

Figure S259. Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(5q21.3)' versus 'METHLYATION_CNMF'

P value = 3.25e-51 (Chi-square test), Q value = 2.1e-48

Table S260. Gene #35: '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	101	139	93	137	40	97
DEL PEAK 8(5Q21.3) CNV	84	4	10	23	3	22
DEL PEAK 8(5Q21.3) WILD-TYPE	17	135	83	114	37	75

Figure S260. Get High-res Image Gene #35: '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 = 1.3e-12

Table S261. Gene #35: '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 S261. Get High-res Image Gene #35: '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 = 4.7e-13

Table S262. Gene #35: '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 S262. Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MRNASEQ_CNMF'

P value = 5.88e-48 (Fisher's exact test), Q value = 3.7e-45

Table S263. Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 8(5Q21.3) CNV	143	8	57
DEL PEAK 8(5Q21.3) WILD-TYPE	91	140	389

Figure S263. Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 8(5q21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-47 (Fisher's exact test), Q value = 6.7e-45

Table S264. Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 8(5Q21.3) CNV	18	57	133
DEL PEAK 8(5Q21.3) WILD-TYPE	198	351	71

Figure S264. Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 8(5q21.3)' versus 'MIRSEQ_CNMF'

P value = 1.28e-39 (Fisher's exact test), Q value = 8e-37

Table S265. Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 8(5Q21.3) CNV	31	42	142
DEL PEAK 8(5Q21.3) WILD-TYPE	203	350	113

Figure S265. Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 8(5q21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.67e-54 (Fisher's exact test), Q value = 1.1e-51

Table S266. Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 8(5Q21.3) CNV	55	14	146
DEL PEAK 8(5Q21.3) WILD-TYPE	307	270	89

Figure S266. Get High-res Image Gene #35: 'Del Peak 8(5q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 9(6p25.3)' versus 'CN_CNMF'

P value = 8.51e-07 (Chi-square test), Q value = 0.00027

Table S267. Gene #36: 'Del Peak 9(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 9(6P25.3) CNV	35	63	12	47	13
DEL PEAK 9(6P25.3) WILD-TYPE	312	159	60	176	36

Figure S267. Get High-res Image Gene #36: 'Del Peak 9(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(6p25.3)' versus 'METHLYATION_CNMF'

P value = 4.71e-05 (Chi-square test), Q value = 0.012

Table S268. Gene #36: '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	101	139	93	137	40	97
DEL PEAK 9(6P25.3) CNV	24	13	19	41	2	14
DEL PEAK 9(6P25.3) WILD-TYPE	77	126	74	96	38	83

Figure S268. Get High-res Image Gene #36: 'Del Peak 9(6p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(6q15)' versus 'MRNA_CNMF'

P value = 1.55e-06 (Chi-square test), Q value = 0.00048

Table S269. Gene #37: '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	124	36	23	95	72	20	103	40
DEL PEAK 10(6Q15) CNV	64	13	7	17	29	4	22	16
DEL PEAK 10(6Q15) WILD-TYPE	60	23	16	78	43	16	81	24

Figure S269. Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 10(6q15)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.25

Table S270. Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 10(6Q15) CNV	49	26	97
DEL PEAK 10(6Q15) WILD-TYPE	91	99	151

Figure S270. Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 10(6q15)' versus 'CN_CNMF'

P value = 6.83e-28 (Chi-square test), Q value = 4.1e-25

Table S271. Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 10(6Q15) CNV	73	133	19	45	31
DEL PEAK 10(6Q15) WILD-TYPE	274	89	53	178	18

Figure S271. Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(6q15)' versus 'METHLYATION_CNMF'

P value = 3.78e-08 (Chi-square test), Q value = 1.4e-05

Table S272. Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 10(6Q15) CNV	19	43	34	70	7	19
DEL PEAK 10(6Q15) WILD-TYPE	82	96	59	67	33	78

Figure S272. Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 10(6q15)' versus 'MRNASEQ_CNMF'

P value = 2.69e-05 (Fisher's exact test), Q value = 0.0069

Table S273. Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 10(6Q15) CNV	56	43	181
DEL PEAK 10(6Q15) WILD-TYPE	178	105	265

Figure S273. Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(6q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000262 (Fisher's exact test), Q value = 0.055

Table S274. Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 10(6Q15) CNV	66	164	50
DEL PEAK 10(6Q15) WILD-TYPE	150	244	154

Figure S274. Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(6q15)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.04e-05 (Fisher's exact test), Q value = 0.012

Table S275. Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 10(6Q15) CNV	150	86	58
DEL PEAK 10(6Q15) WILD-TYPE	212	198	177

Figure S275. Get High-res Image Gene #37: 'Del Peak 10(6q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(6q27)' versus 'CN_CNMF'

P value = 2.87e-14 (Chi-square test), Q value = 1.4e-11

Table S276. Gene #38: 'Del Peak 11(6q27)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 11(6Q27) CNV	76	112	19	76	31
DEL PEAK 11(6Q27) WILD-TYPE	271	110	53	147	18

Figure S276. Get High-res Image Gene #38: 'Del Peak 11(6q27)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000366 (Fisher's exact test), Q value = 0.074

Table S277. Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 12(7P22.3) CNV	8	27	40
DEL PEAK 12(7P22.3) WILD-TYPE	132	98	208

Figure S277. Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 12(7p22.3)' versus 'CN_CNMF'

P value = 2.06e-15 (Chi-square test), Q value = 1.1e-12

Table S278. Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 12(7P22.3) CNV	11	47	3	54	3
DEL PEAK 12(7P22.3) WILD-TYPE	336	175	69	169	46

Figure S278. Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(7p22.3)' versus 'METHLYATION_CNMF'

P value = 5.89e-07 (Chi-square test), Q value = 0.00019

Table S279. Gene #39: '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	101	139	93	137	40	97
DEL PEAK 12(7P22.3) CNV	25	6	12	18	2	2
DEL PEAK 12(7P22.3) WILD-TYPE	76	133	81	119	38	95

Figure S279. Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNASEQ_CNMF'

P value = 8.07e-09 (Fisher's exact test), Q value = 3.1e-06

Table S280. Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 12(7P22.3) CNV	55	4	56
DEL PEAK 12(7P22.3) WILD-TYPE	179	144	390

Figure S280. Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(7p22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.39e-08 (Fisher's exact test), Q value = 1.9e-05

Table S281. Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 12(7P22.3) CNV	9	60	46
DEL PEAK 12(7P22.3) WILD-TYPE	207	348	158

Figure S281. Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(7p22.3)' versus 'MIRSEQ_CNMF'

P value = 3.96e-11 (Fisher's exact test), Q value = 1.7e-08

Table S282. Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 12(7P22.3) CNV	7	48	59
DEL PEAK 12(7P22.3) WILD-TYPE	227	344	196

Figure S282. Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(7p22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.38e-10 (Fisher's exact test), Q value = 5.9e-08

Table S283. Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 12(7P22.3) CNV	46	12	56
DEL PEAK 12(7P22.3) WILD-TYPE	316	272	179

Figure S283. Get High-res Image Gene #39: 'Del Peak 12(7p22.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(7q36.1)' versus 'CN_CNMF'

P value = 5.25e-10 (Chi-square test), Q value = 2.2e-07

Table S284. Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 13(7Q36.1) CNV	32	61	13	64	4
DEL PEAK 13(7Q36.1) WILD-TYPE	315	161	59	159	45

Figure S284. Get High-res Image Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(7q36.1)' versus 'MRNASEQ_CNMF'

P value = 0.000414 (Fisher's exact test), Q value = 0.083

Table S285. Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 13(7Q36.1) CNV	65	17	87
DEL PEAK 13(7Q36.1) WILD-TYPE	169	131	359

Figure S285. Get High-res Image Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(7q36.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000496 (Fisher's exact test), Q value = 0.098

Table S286. Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 13(7Q36.1) CNV	25	95	49
DEL PEAK 13(7Q36.1) WILD-TYPE	191	313	155

Figure S286. Get High-res Image Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(7q36.1)' versus 'MIRSEQ_CNMF'

P value = 5.26e-08 (Fisher's exact test), Q value = 1.9e-05

Table S287. Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 13(7Q36.1) CNV	23	69	77
DEL PEAK 13(7Q36.1) WILD-TYPE	211	323	178

Figure S287. Get High-res Image Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 13(7q36.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.6e-06 (Fisher's exact test), Q value = 0.00049

Table S288. Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 13(7Q36.1) CNV	73	30	66
DEL PEAK 13(7Q36.1) WILD-TYPE	289	254	169

Figure S288. Get High-res Image Gene #40: 'Del Peak 13(7q36.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'MRNA_CNMF'

P value = 1.08e-09 (Chi-square test), Q value = 4.4e-07

Table S289. Gene #41: '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	124	36	23	95	72	20	103	40
DEL PEAK 14(8P23.2) CNV	81	16	13	64	47	13	26	17
DEL PEAK 14(8P23.2) WILD-TYPE	43	20	10	31	25	7	77	23

Figure S289. Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNA_CHIERARCHICAL'

P value = 2.53e-05 (Fisher's exact test), Q value = 0.0066

Table S290. Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 14(8P23.2) CNV	57	86	134
DEL PEAK 14(8P23.2) WILD-TYPE	83	39	114

Figure S290. Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'CN_CNMF'

P value = 7.63e-31 (Chi-square test), Q value = 4.7e-28

Table S291. Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 14(8P23.2) CNV	117	148	15	161	40
DEL PEAK 14(8P23.2) WILD-TYPE	230	74	57	62	9

Figure S291. Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(8p23.2)' versus 'METHLYATION_CNMF'

P value = 1.19e-13 (Chi-square test), Q value = 5.8e-11

Table S292. Gene #41: '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	101	139	93	137	40	97
DEL PEAK 14(8P23.2) CNV	68	35	48	95	18	41
DEL PEAK 14(8P23.2) WILD-TYPE	33	104	45	42	22	56

Figure S292. Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNASEQ_CNMF'

P value = 2.05e-11 (Fisher's exact test), Q value = 9e-09

Table S293. Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 14(8P23.2) CNV	162	49	232
DEL PEAK 14(8P23.2) WILD-TYPE	72	99	214

Figure S293. Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 14(8p23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.71e-08 (Fisher's exact test), Q value = 1.4e-05

Table S294. Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 14(8P23.2) CNV	84	222	137
DEL PEAK 14(8P23.2) WILD-TYPE	132	186	67

Figure S294. Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'MIRSEQ_CNMF'

P value = 5.68e-06 (Fisher's exact test), Q value = 0.0016

Table S295. Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 14(8P23.2) CNV	98	203	163
DEL PEAK 14(8P23.2) WILD-TYPE	136	189	92

Figure S295. Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 14(8p23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.79e-12 (Fisher's exact test), Q value = 2.2e-09

Table S296. Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 14(8P23.2) CNV	189	110	165
DEL PEAK 14(8P23.2) WILD-TYPE	173	174	70

Figure S296. Get High-res Image Gene #41: 'Del Peak 14(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(8p11.21)' versus 'MRNA_CNMF'

P value = 0.000126 (Chi-square test), Q value = 0.029

Table S297. Gene #42: '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	124	36	23	95	72	20	103	40
DEL PEAK 15(8P11.21) CNV	24	5	4	21	27	7	7	7
DEL PEAK 15(8P11.21) WILD-TYPE	100	31	19	74	45	13	96	33

Figure S297. Get High-res Image Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 15(8p11.21)' versus 'CN_CNMF'

P value = 6.19e-11 (Chi-square test), Q value = 2.7e-08

Table S298. Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 15(8P11.21) CNV	45	47	7	74	0
DEL PEAK 15(8P11.21) WILD-TYPE	302	175	65	149	49

Figure S298. Get High-res Image Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(8p11.21)' versus 'MRNASEQ_CNMF'

P value = 0.000593 (Fisher's exact test), Q value = 0.12

Table S299. Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 15(8P11.21) CNV	64	18	79
DEL PEAK 15(8P11.21) WILD-TYPE	170	130	367

Figure S299. Get High-res Image Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 15(8p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000914 (Fisher's exact test), Q value = 0.17

Table S300. Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 15(8P11.21) CNV	28	77	56
DEL PEAK 15(8P11.21) WILD-TYPE	188	331	148

Figure S300. Get High-res Image Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(8p11.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.26e-06 (Fisher's exact test), Q value = 0.0018

Table S301. Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 15(8P11.21) CNV	72	32	66
DEL PEAK 15(8P11.21) WILD-TYPE	290	252	169

Figure S301. Get High-res Image Gene #42: 'Del Peak 15(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MRNA_CNMF'

P value = 2.43e-06 (Chi-square test), Q value = 0.00072

Table S302. Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 16(9P21.3) CNV	62	13	9	29	38	8	23	5
DEL PEAK 16(9P21.3) WILD-TYPE	62	23	14	66	34	12	80	35

Figure S302. Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 16(9p21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.14

Table S303. Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 16(9P21.3) CNV	35	43	109
DEL PEAK 16(9P21.3) WILD-TYPE	105	82	139

Figure S303. Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'CN_CNMF'

P value = 1.11e-29 (Chi-square test), Q value = 6.8e-27

Table S304. Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 16(9P21.3) CNV	44	122	17	110	14
DEL PEAK 16(9P21.3) WILD-TYPE	303	100	55	113	35

Figure S304. Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(9p21.3)' versus 'METHLYATION_CNMF'

P value = 2.21e-15 (Chi-square test), Q value = 1.1e-12

Table S305. Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 16(9P21.3) CNV	37	14	38	72	8	15
DEL PEAK 16(9P21.3) WILD-TYPE	64	125	55	65	32	82

Figure S305. Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 7.31e-07 (Fisher's exact test), Q value = 0.00024

Table S306. Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 16(9P21.3) CNV	95	25	168
DEL PEAK 16(9P21.3) WILD-TYPE	139	123	278

Figure S306. Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 16(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.64e-07 (Fisher's exact test), Q value = 8.9e-05

Table S307. Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 16(9P21.3) CNV	43	165	80
DEL PEAK 16(9P21.3) WILD-TYPE	173	243	124

Figure S307. Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_CNMF'

P value = 4.02e-06 (Fisher's exact test), Q value = 0.0012

Table S308. Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 16(9P21.3) CNV	51	134	109
DEL PEAK 16(9P21.3) WILD-TYPE	183	258	146

Figure S308. Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.15e-12 (Fisher's exact test), Q value = 1.9e-09

Table S309. Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 16(9P21.3) CNV	146	49	99
DEL PEAK 16(9P21.3) WILD-TYPE	216	235	136

Figure S309. Get High-res Image Gene #43: 'Del Peak 16(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 17(9q21.11)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.06

Table S310. Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 17(9Q21.11) CNV	24	47	81
DEL PEAK 17(9Q21.11) WILD-TYPE	116	78	167

Figure S310. Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 17(9q21.11)' versus 'CN_CNMF'

P value = 3.41e-16 (Chi-square test), Q value = 1.8e-13

Table S311. Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 17(9Q21.11) CNV	41	77	17	97	14
DEL PEAK 17(9Q21.11) WILD-TYPE	306	145	55	126	35

Figure S311. Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(9q21.11)' versus 'METHLYATION_CNMF'

P value = 1.19e-10 (Chi-square test), Q value = 5.1e-08

Table S312. Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 17(9Q21.11) CNV	38	10	23	54	4	18
DEL PEAK 17(9Q21.11) WILD-TYPE	63	129	70	83	36	79

Figure S312. Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 17(9q21.11)' versus 'RPPA_CNMF'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0028

Table S313. Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
DEL PEAK 17(9Q21.11) CNV	65	32	22
DEL PEAK 17(9Q21.11) WILD-TYPE	82	101	95

Figure S313. Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 17(9q21.11)' versus 'MRNASEQ_CNMF'

P value = 2.41e-06 (Fisher's exact test), Q value = 0.00072

Table S314. Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 17(9Q21.11) CNV	86	20	123
DEL PEAK 17(9Q21.11) WILD-TYPE	148	128	323

Figure S314. Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 17(9q21.11)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.3e-06 (Fisher's exact test), Q value = 0.0023

Table S315. Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 17(9Q21.11) CNV	35	120	74
DEL PEAK 17(9Q21.11) WILD-TYPE	181	288	130

Figure S315. Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(9q21.11)' versus 'MIRSEQ_CNMF'

P value = 1.41e-08 (Fisher's exact test), Q value = 5.3e-06

Table S316. Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 17(9Q21.11) CNV	39	93	102
DEL PEAK 17(9Q21.11) WILD-TYPE	195	299	153

Figure S316. Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 17(9q21.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.33e-13 (Fisher's exact test), Q value = 4.4e-10

Table S317. Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 17(9Q21.11) CNV	102	36	96
DEL PEAK 17(9Q21.11) WILD-TYPE	260	248	139

Figure S317. Get High-res Image Gene #44: 'Del Peak 17(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'MRNA_CNMF'

P value = 4.09e-05 (Chi-square test), Q value = 0.01

Table S318. Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 18(10Q23.31) CNV	36	7	7	45	20	7	22	2
DEL PEAK 18(10Q23.31) WILD-TYPE	88	29	16	50	52	13	81	38

Figure S318. Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 18(10q23.31)' versus 'MRNA_CHIERARCHICAL'

P value = 9.57e-05 (Fisher's exact test), Q value = 0.022

Table S319. Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 18(10Q23.31) CNV	26	53	67
DEL PEAK 18(10Q23.31) WILD-TYPE	114	72	181

Figure S319. Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'CN_CNMF'

P value = 3.83e-20 (Chi-square test), Q value = 2.2e-17

Table S320. Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 18(10Q23.31) CNV	45	72	17	113	14
DEL PEAK 18(10Q23.31) WILD-TYPE	302	150	55	110	35

Figure S320. Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(10q23.31)' versus 'METHLYATION_CNMF'

P value = 4.75e-12 (Chi-square test), Q value = 2.2e-09

Table S321. Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 18(10Q23.31) CNV	55	22	23	53	7	15
DEL PEAK 18(10Q23.31) WILD-TYPE	46	117	70	84	33	82

Figure S321. Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(10q23.31)' versus 'RPPA_CNMF'

P value = 1.9e-07 (Fisher's exact test), Q value = 6.5e-05

Table S322. Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
DEL PEAK 18(10Q23.31) CNV	67	30	19
DEL PEAK 18(10Q23.31) WILD-TYPE	80	103	98

Figure S322. Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 18(10q23.31)' versus 'RPPA_CHIERARCHICAL'

P value = 7.37e-05 (Fisher's exact test), Q value = 0.018

Table S323. Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
DEL PEAK 18(10Q23.31) CNV	45	18	53
DEL PEAK 18(10Q23.31) WILD-TYPE	116	92	73

Figure S323. Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 1.06e-11 (Fisher's exact test), Q value = 4.7e-09

Table S324. Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 18(10Q23.31) CNV	108	21	115
DEL PEAK 18(10Q23.31) WILD-TYPE	126	127	331

Figure S324. Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 18(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.91e-09 (Fisher's exact test), Q value = 2.7e-06

Table S325. Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 18(10Q23.31) CNV	39	113	92
DEL PEAK 18(10Q23.31) WILD-TYPE	177	295	112

Figure S325. Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(10q23.31)' versus 'MIRSEQ_CNMF'

P value = 5.47e-09 (Fisher's exact test), Q value = 2.2e-06

Table S326. Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 18(10Q23.31) CNV	49	92	111
DEL PEAK 18(10Q23.31) WILD-TYPE	185	300	144

Figure S326. Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 18(10q23.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.97e-09 (Fisher's exact test), Q value = 1.6e-06

Table S327. Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 18(10Q23.31) CNV	97	53	102
DEL PEAK 18(10Q23.31) WILD-TYPE	265	231	133

Figure S327. Get High-res Image Gene #45: 'Del Peak 18(10q23.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'MRNA_CNMF'

P value = 2.88e-08 (Chi-square test), Q value = 1.1e-05

Table S328. Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 19(10Q26.3) CNV	38	9	8	52	21	6	16	3
DEL PEAK 19(10Q26.3) WILD-TYPE	86	27	15	43	51	14	87	37

Figure S328. Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 19(10q26.3)' versus 'MRNA_CHIERARCHICAL'

P value = 1.49e-07 (Fisher's exact test), Q value = 5.2e-05

Table S329. Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 19(10Q26.3) CNV	22	59	72
DEL PEAK 19(10Q26.3) WILD-TYPE	118	66	176

Figure S329. Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'CN_CNMF'

P value = 2.23e-22 (Chi-square test), Q value = 1.3e-19

Table S330. Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 19(10Q26.3) CNV	45	77	15	116	11
DEL PEAK 19(10Q26.3) WILD-TYPE	302	145	57	107	38

Figure S330. Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(10q26.3)' versus 'METHLYATION_CNMF'

P value = 2.07e-12 (Chi-square test), Q value = 9.5e-10

Table S331. Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 19(10Q26.3) CNV	57	18	28	45	8	17
DEL PEAK 19(10Q26.3) WILD-TYPE	44	121	65	92	32	80

Figure S331. Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(10q26.3)' versus 'RPPA_CNMF'

P value = 3.06e-08 (Fisher's exact test), Q value = 1.1e-05

Table S332. Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
DEL PEAK 19(10Q26.3) CNV	72	27	24
DEL PEAK 19(10Q26.3) WILD-TYPE	75	106	93

Figure S332. Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 19(10q26.3)' versus 'RPPA_CHIERARCHICAL'

P value = 8.25e-07 (Fisher's exact test), Q value = 0.00026

Table S333. Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
DEL PEAK 19(10Q26.3) CNV	45	18	60
DEL PEAK 19(10Q26.3) WILD-TYPE	116	92	66

Figure S333. Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'MRNASEQ_CNMF'

P value = 1.77e-15 (Fisher's exact test), Q value = 9.2e-13

Table S334. Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 19(10Q26.3) CNV	115	18	114
DEL PEAK 19(10Q26.3) WILD-TYPE	119	130	332

Figure S334. Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 19(10q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.17e-12 (Fisher's exact test), Q value = 5.4e-10

Table S335. Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 19(10Q26.3) CNV	34	114	99
DEL PEAK 19(10Q26.3) WILD-TYPE	182	294	105

Figure S335. Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(10q26.3)' versus 'MIRSEQ_CNMF'

P value = 7.81e-12 (Fisher's exact test), Q value = 3.5e-09

Table S336. Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 19(10Q26.3) CNV	44	92	117
DEL PEAK 19(10Q26.3) WILD-TYPE	190	300	138

Figure S336. Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 19(10q26.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.48e-15 (Fisher's exact test), Q value = 1.8e-12

Table S337. Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 19(10Q26.3) CNV	100	42	111
DEL PEAK 19(10Q26.3) WILD-TYPE	262	242	124

Figure S337. Get High-res Image Gene #46: 'Del Peak 19(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'MRNA_CNMF'

P value = 1.34e-06 (Chi-square test), Q value = 0.00042

Table S338. Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 20(11P15.5) CNV	33	8	3	45	32	7	15	8
DEL PEAK 20(11P15.5) WILD-TYPE	91	28	20	50	40	13	88	32

Figure S338. Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 20(11p15.5)' versus 'MRNA_CHIERARCHICAL'

P value = 1.62e-07 (Fisher's exact test), Q value = 5.6e-05

Table S339. Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 20(11P15.5) CNV	29	62	60
DEL PEAK 20(11P15.5) WILD-TYPE	111	63	188

Figure S339. Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'CN_CNMF'

P value = 5.01e-36 (Chi-square test), Q value = 3.1e-33

Table S340. Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 20(11P15.5) CNV	35	69	15	134	9
DEL PEAK 20(11P15.5) WILD-TYPE	312	153	57	89	40

Figure S340. Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 20(11p15.5)' versus 'METHLYATION_CNMF'

P value = 1.96e-12 (Chi-square test), Q value = 9e-10

Table S341. Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 20(11P15.5) CNV	54	15	27	42	10	14
DEL PEAK 20(11P15.5) WILD-TYPE	47	124	66	95	30	83

Figure S341. Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 20(11p15.5)' versus 'RPPA_CNMF'

P value = 1.27e-09 (Fisher's exact test), Q value = 5.1e-07

Table S342. Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
DEL PEAK 20(11P15.5) CNV	76	26	25
DEL PEAK 20(11P15.5) WILD-TYPE	71	107	92

Figure S342. Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 20(11p15.5)' versus 'RPPA_CHIERARCHICAL'

P value = 1.65e-06 (Fisher's exact test), Q value = 5e-04

Table S343. Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
DEL PEAK 20(11P15.5) CNV	38	26	63
DEL PEAK 20(11P15.5) WILD-TYPE	123	84	63

Figure S343. Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'MRNASEQ_CNMF'

P value = 8.07e-18 (Fisher's exact test), Q value = 4.4e-15

Table S344. Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 20(11P15.5) CNV	121	22	100
DEL PEAK 20(11P15.5) WILD-TYPE	113	126	346

Figure S344. Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 20(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.07e-13 (Fisher's exact test), Q value = 2.4e-10

Table S345. Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 20(11P15.5) CNV	42	98	103
DEL PEAK 20(11P15.5) WILD-TYPE	174	310	101

Figure S345. Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(11p15.5)' versus 'MIRSEQ_CNMF'

P value = 3.87e-15 (Fisher's exact test), Q value = 2e-12

Table S346. Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 20(11P15.5) CNV	43	85	123
DEL PEAK 20(11P15.5) WILD-TYPE	191	307	132

Figure S346. Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 20(11p15.5)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.42e-16 (Fisher's exact test), Q value = 7.6e-14

Table S347. Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 20(11P15.5) CNV	93	43	115
DEL PEAK 20(11P15.5) WILD-TYPE	269	241	120

Figure S347. Get High-res Image Gene #47: 'Del Peak 20(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 21(11q13.1)' versus 'CN_CNMF'

P value = 3.51e-17 (Chi-square test), Q value = 1.9e-14

Table S348. Gene #48: 'Del Peak 21(11q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 21(11Q13.1) CNV	30	88	23	44	9
DEL PEAK 21(11Q13.1) WILD-TYPE	317	134	49	179	40

Figure S348. Get High-res Image Gene #48: 'Del Peak 21(11q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(11q13.1)' versus 'METHLYATION_CNMF'

P value = 4.39e-06 (Chi-square test), Q value = 0.0013

Table S349. Gene #48: 'Del Peak 21(11q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 21(11Q13.1) CNV	18	19	26	47	7	8
DEL PEAK 21(11Q13.1) WILD-TYPE	83	120	67	90	33	89

Figure S349. Get High-res Image Gene #48: 'Del Peak 21(11q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 22(11q23.2)' versus 'MRNA_CNMF'

P value = 2.08e-08 (Chi-square test), Q value = 7.7e-06

Table S350. Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 22(11Q23.2) CNV	92	21	12	36	37	11	33	22
DEL PEAK 22(11Q23.2) WILD-TYPE	32	15	11	59	35	9	70	18

Figure S350. Get High-res Image Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 22(11q23.2)' versus 'CN_CNMF'

P value = 3.22e-42 (Chi-square test), Q value = 2e-39

Table S351. Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 22(11Q23.2) CNV	93	193	35	111	17
DEL PEAK 22(11Q23.2) WILD-TYPE	254	29	37	112	32

Figure S351. Get High-res Image Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(11q23.2)' versus 'METHLYATION_CNMF'

P value = 7.68e-12 (Chi-square test), Q value = 3.4e-09

Table S352. Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 22(11Q23.2) CNV	41	49	57	98	20	29
DEL PEAK 22(11Q23.2) WILD-TYPE	60	90	36	39	20	68

Figure S352. Get High-res Image Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 22(11q23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000137 (Fisher's exact test), Q value = 0.031

Table S353. Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 22(11Q23.2) CNV	209	125	100
DEL PEAK 22(11Q23.2) WILD-TYPE	153	159	135

Figure S353. Get High-res Image Gene #49: 'Del Peak 22(11q23.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 23(11q25)' versus 'MRNA_CNMF'

P value = 0.000243 (Chi-square test), Q value = 0.052

Table S354. Gene #50: 'Del Peak 23(11q25)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 23(11Q25) CNV	79	20	10	44	37	12	31	20
DEL PEAK 23(11Q25) WILD-TYPE	45	16	13	51	35	8	72	20

Figure S354. Get High-res Image Gene #50: 'Del Peak 23(11q25)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 23(11q25)' versus 'CN_CNMF'

P value = 6.15e-38 (Chi-square test), Q value = 3.8e-35

Table S355. Gene #50: 'Del Peak 23(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 23(11Q25) CNV	81	177	34	114	15
DEL PEAK 23(11Q25) WILD-TYPE	266	45	38	109	34

Figure S355. Get High-res Image Gene #50: 'Del Peak 23(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(11q25)' versus 'METHLYATION_CNMF'

P value = 9.89e-09 (Chi-square test), Q value = 3.8e-06

Table S356. Gene #50: 'Del Peak 23(11q25)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 23(11Q25) CNV	46	42	53	86	16	28
DEL PEAK 23(11Q25) WILD-TYPE	55	97	40	51	24	69

Figure S356. Get High-res Image Gene #50: 'Del Peak 23(11q25)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 24(12p13.1)' versus 'CN_CNMF'

P value = 0.000979 (Chi-square test), Q value = 0.18

Table S357. Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 24(12P13.1) CNV	40	46	11	54	6
DEL PEAK 24(12P13.1) WILD-TYPE	307	176	61	169	43

Figure S357. Get High-res Image Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(12p13.1)' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.046

Table S358. Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 24(12P13.1) CNV	63	19	67
DEL PEAK 24(12P13.1) WILD-TYPE	171	129	379

Figure S358. Get High-res Image Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 24(12p13.1)' versus 'MIRSEQ_CNMF'

P value = 8.03e-05 (Fisher's exact test), Q value = 0.019

Table S359. Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 24(12P13.1) CNV	30	56	67
DEL PEAK 24(12P13.1) WILD-TYPE	204	336	188

Figure S359. Get High-res Image Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 24(12p13.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.68e-06 (Fisher's exact test), Q value = 0.0024

Table S360. Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 24(12P13.1) CNV	60	30	63
DEL PEAK 24(12P13.1) WILD-TYPE	302	254	172

Figure S360. Get High-res Image Gene #51: 'Del Peak 24(12p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'MRNA_CNMF'

P value = 9.6e-11 (Chi-square test), Q value = 4.1e-08

Table S361. Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 25(12Q24.21) CNV	17	5	3	41	22	3	4	5
DEL PEAK 25(12Q24.21) WILD-TYPE	107	31	20	54	50	17	99	35

Figure S361. Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 25(12q24.21)' versus 'MRNA_CHIERARCHICAL'

P value = 2.5e-10 (Fisher's exact test), Q value = 1e-07

Table S362. Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 25(12Q24.21) CNV	14	51	35
DEL PEAK 25(12Q24.21) WILD-TYPE	126	74	213

Figure S362. Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'CN_CNMF'

P value = 2.33e-15 (Chi-square test), Q value = 1.2e-12

Table S363. Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 25(12Q24.21) CNV	38	30	16	85	5
DEL PEAK 25(12Q24.21) WILD-TYPE	309	192	56	138	44

Figure S363. Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(12q24.21)' versus 'METHLYATION_CNMF'

P value = 2.68e-14 (Chi-square test), Q value = 1.3e-11

Table S364. Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 25(12Q24.21) CNV	48	13	14	20	2	14
DEL PEAK 25(12Q24.21) WILD-TYPE	53	126	79	117	38	83

Figure S364. Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(12q24.21)' versus 'RPPA_CNMF'

P value = 0.000209 (Fisher's exact test), Q value = 0.046

Table S365. Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
DEL PEAK 25(12Q24.21) CNV	44	14	21
DEL PEAK 25(12Q24.21) WILD-TYPE	103	119	96

Figure S365. Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 25(12q24.21)' versus 'RPPA_CHIERARCHICAL'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00033

Table S366. Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
DEL PEAK 25(12Q24.21) CNV	22	12	45
DEL PEAK 25(12Q24.21) WILD-TYPE	139	98	81

Figure S366. Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'MRNASEQ_CNMF'

P value = 6.55e-16 (Fisher's exact test), Q value = 3.5e-13

Table S367. Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 25(12Q24.21) CNV	86	15	49
DEL PEAK 25(12Q24.21) WILD-TYPE	148	133	397

Figure S367. Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(12q24.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.47e-13 (Fisher's exact test), Q value = 1.6e-10

Table S368. Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 25(12Q24.21) CNV	23	52	75
DEL PEAK 25(12Q24.21) WILD-TYPE	193	356	129

Figure S368. Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(12q24.21)' versus 'MIRSEQ_CNMF'

P value = 1.17e-08 (Fisher's exact test), Q value = 4.5e-06

Table S369. Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 25(12Q24.21) CNV	32	53	81
DEL PEAK 25(12Q24.21) WILD-TYPE	202	339	174

Figure S369. Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(12q24.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.27e-13 (Fisher's exact test), Q value = 1.6e-10

Table S370. Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 25(12Q24.21) CNV	47	34	85
DEL PEAK 25(12Q24.21) WILD-TYPE	315	250	150

Figure S370. Get High-res Image Gene #52: 'Del Peak 25(12q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 26(13q14.2)' versus 'MRNA_CNMF'

P value = 2.15e-05 (Chi-square test), Q value = 0.0057

Table S371. Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 26(13Q14.2) CNV	74	13	7	55	39	9	31	13
DEL PEAK 26(13Q14.2) WILD-TYPE	50	23	16	40	33	11	72	27

Figure S371. Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 26(13q14.2)' versus 'MRNA_CHIERARCHICAL'

P value = 4.23e-05 (Fisher's exact test), Q value = 0.011

Table S372. Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 26(13Q14.2) CNV	46	75	120
DEL PEAK 26(13Q14.2) WILD-TYPE	94	50	128

Figure S372. Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 26(13q14.2)' versus 'CN_CNMF'

P value = 7.07e-28 (Chi-square test), Q value = 4.3e-25

Table S373. Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 26(13Q14.2) CNV	73	138	41	130	31
DEL PEAK 26(13Q14.2) WILD-TYPE	274	84	31	93	18

Figure S373. Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(13q14.2)' versus 'METHLYATION_CNMF'

P value = 1.81e-08 (Chi-square test), Q value = 6.8e-06

Table S374. Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 26(13Q14.2) CNV	61	39	50	75	11	32
DEL PEAK 26(13Q14.2) WILD-TYPE	40	100	43	62	29	65

Figure S374. Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(13q14.2)' versus 'MRNASEQ_CNMF'

P value = 1.55e-07 (Fisher's exact test), Q value = 5.4e-05

Table S375. Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 26(13Q14.2) CNV	136	43	207
DEL PEAK 26(13Q14.2) WILD-TYPE	98	105	239

Figure S375. Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 26(13q14.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.39e-06 (Fisher's exact test), Q value = 0.0018

Table S376. Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 26(13Q14.2) CNV	74	194	118
DEL PEAK 26(13Q14.2) WILD-TYPE	142	214	86

Figure S376. Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 26(13q14.2)' versus 'MIRSEQ_CNMF'

P value = 3.86e-10 (Fisher's exact test), Q value = 1.6e-07

Table S377. Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 26(13Q14.2) CNV	69	182	150
DEL PEAK 26(13Q14.2) WILD-TYPE	165	210	105

Figure S377. Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 26(13q14.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-07 (Fisher's exact test), Q value = 3.9e-05

Table S378. Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 26(13Q14.2) CNV	172	94	135
DEL PEAK 26(13Q14.2) WILD-TYPE	190	190	100

Figure S378. Get High-res Image Gene #53: 'Del Peak 26(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'MRNA_CNMF'

P value = 4e-13 (Chi-square test), Q value = 1.9e-10

Table S379. Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 27(14Q24.3) CNV	51	8	4	57	22	10	9	8
DEL PEAK 27(14Q24.3) WILD-TYPE	73	28	19	38	50	10	94	32

Figure S379. Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 27(14q24.3)' versus 'MRNA_CHIERARCHICAL'

P value = 1.56e-08 (Fisher's exact test), Q value = 5.9e-06

Table S380. Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 27(14Q24.3) CNV	33	69	67
DEL PEAK 27(14Q24.3) WILD-TYPE	107	56	181

Figure S380. Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'CN_CNMF'

P value = 8.6e-37 (Chi-square test), Q value = 5.3e-34

Table S381. Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 27(14Q24.3) CNV	42	76	14	143	19
DEL PEAK 27(14Q24.3) WILD-TYPE	305	146	58	80	30

Figure S381. Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(14q24.3)' versus 'METHLYATION_CNMF'

P value = 3.5e-14 (Chi-square test), Q value = 1.7e-11

Table S382. Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 27(14Q24.3) CNV	60	16	28	53	8	22
DEL PEAK 27(14Q24.3) WILD-TYPE	41	123	65	84	32	75

Figure S382. Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 27(14q24.3)' versus 'RPPA_CNMF'

P value = 5.29e-07 (Fisher's exact test), Q value = 0.00017

Table S383. Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
DEL PEAK 27(14Q24.3) CNV	74	29	31
DEL PEAK 27(14Q24.3) WILD-TYPE	73	104	86

Figure S383. Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 27(14q24.3)' versus 'RPPA_CHIERARCHICAL'

P value = 5.53e-06 (Fisher's exact test), Q value = 0.0016

Table S384. Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
DEL PEAK 27(14Q24.3) CNV	45	25	64
DEL PEAK 27(14Q24.3) WILD-TYPE	116	85	62

Figure S384. Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'MRNASEQ_CNMF'

P value = 3.86e-15 (Fisher's exact test), Q value = 2e-12

Table S385. Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 27(14Q24.3) CNV	124	25	120
DEL PEAK 27(14Q24.3) WILD-TYPE	110	123	326

Figure S385. Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 27(14q24.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.04e-13 (Fisher's exact test), Q value = 1.5e-10

Table S386. Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 27(14Q24.3) CNV	41	120	108
DEL PEAK 27(14Q24.3) WILD-TYPE	175	288	96

Figure S386. Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(14q24.3)' versus 'MIRSEQ_CNMF'

P value = 5.44e-18 (Fisher's exact test), Q value = 3e-15

Table S387. Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 27(14Q24.3) CNV	51	91	138
DEL PEAK 27(14Q24.3) WILD-TYPE	183	301	117

Figure S387. Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 27(14q24.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.52e-16 (Fisher's exact test), Q value = 8.1e-14

Table S388. Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 27(14Q24.3) CNV	102	53	125
DEL PEAK 27(14Q24.3) WILD-TYPE	260	231	110

Figure S388. Get High-res Image Gene #54: 'Del Peak 27(14q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'MRNA_CNMF'

P value = 3.46e-07 (Chi-square test), Q value = 0.00012

Table S389. Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 28(15Q13.1) CNV	41	11	7	56	33	10	22	7
DEL PEAK 28(15Q13.1) WILD-TYPE	83	25	16	39	39	10	81	33

Figure S389. Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 28(15q13.1)' versus 'MRNA_CHIERARCHICAL'

P value = 7.57e-08 (Fisher's exact test), Q value = 2.7e-05

Table S390. Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 28(15Q13.1) CNV	29	68	90
DEL PEAK 28(15Q13.1) WILD-TYPE	111	57	158

Figure S390. Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'CN_CNMF'

P value = 6.74e-31 (Chi-square test), Q value = 4.1e-28

Table S391. Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 28(15Q13.1) CNV	56	68	35	143	13
DEL PEAK 28(15Q13.1) WILD-TYPE	291	154	37	80	36

Figure S391. Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(15q13.1)' versus 'METHLYATION_CNMF'

P value = 1.2e-11 (Chi-square test), Q value = 5.3e-09

Table S392. Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 28(15Q13.1) CNV	63	25	30	52	8	25
DEL PEAK 28(15Q13.1) WILD-TYPE	38	114	63	85	32	72

Figure S392. Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 28(15q13.1)' versus 'RPPA_CNMF'

P value = 0.000193 (Fisher's exact test), Q value = 0.043

Table S393. Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
DEL PEAK 28(15Q13.1) CNV	76	39	38
DEL PEAK 28(15Q13.1) WILD-TYPE	71	94	79

Figure S393. Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 28(15q13.1)' versus 'RPPA_CHIERARCHICAL'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.0061

Table S394. Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
DEL PEAK 28(15Q13.1) CNV	54	30	69
DEL PEAK 28(15Q13.1) WILD-TYPE	107	80	57

Figure S394. Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'MRNASEQ_CNMF'

P value = 6.07e-15 (Fisher's exact test), Q value = 3.1e-12

Table S395. Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 28(15Q13.1) CNV	127	24	137
DEL PEAK 28(15Q13.1) WILD-TYPE	107	124	309

Figure S395. Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 28(15q13.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.32e-14 (Fisher's exact test), Q value = 1.2e-11

Table S396. Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 28(15Q13.1) CNV	44	129	115
DEL PEAK 28(15Q13.1) WILD-TYPE	172	279	89

Figure S396. Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(15q13.1)' versus 'MIRSEQ_CNMF'

P value = 6.32e-19 (Fisher's exact test), Q value = 3.6e-16

Table S397. Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 28(15Q13.1) CNV	47	110	145
DEL PEAK 28(15Q13.1) WILD-TYPE	187	282	110

Figure S397. Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 28(15q13.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.96e-18 (Fisher's exact test), Q value = 1.1e-15

Table S398. Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 28(15Q13.1) CNV	112	56	134
DEL PEAK 28(15Q13.1) WILD-TYPE	250	228	101

Figure S398. Get High-res Image Gene #55: 'Del Peak 28(15q13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'MRNA_CNMF'

P value = 1.6e-16 (Chi-square test), Q value = 8.6e-14

Table S399. Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 29(16Q24.3) CNV	86	26	18	26	45	13	88	34
DEL PEAK 29(16Q24.3) WILD-TYPE	38	10	5	69	27	7	15	6

Figure S399. Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 29(16q24.3)' versus 'MRNA_CHIERARCHICAL'

P value = 2.51e-14 (Fisher's exact test), Q value = 1.3e-11

Table S400. Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 29(16Q24.3) CNV	110	45	181
DEL PEAK 29(16Q24.3) WILD-TYPE	30	80	67

Figure S400. Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'CN_CNMF'

P value = 1.66e-14 (Chi-square test), Q value = 8.3e-12

Table S401. Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 29(16Q24.3) CNV	244	153	59	93	38
DEL PEAK 29(16Q24.3) WILD-TYPE	103	69	13	130	11

Figure S401. Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(16q24.3)' versus 'METHLYATION_CNMF'

P value = 4.47e-13 (Chi-square test), Q value = 2.1e-10

Table S402. Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 29(16Q24.3) CNV	37	115	72	83	19	57
DEL PEAK 29(16Q24.3) WILD-TYPE	64	24	21	54	21	40

Figure S402. Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 29(16q24.3)' versus 'RPPA_CNMF'

P value = 1.14e-09 (Fisher's exact test), Q value = 4.6e-07

Table S403. Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
DEL PEAK 29(16Q24.3) CNV	63	103	84
DEL PEAK 29(16Q24.3) WILD-TYPE	84	30	33

Figure S403. Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 29(16q24.3)' versus 'RPPA_CHIERARCHICAL'

P value = 3.45e-11 (Fisher's exact test), Q value = 1.5e-08

Table S404. Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
DEL PEAK 29(16Q24.3) CNV	119	83	48
DEL PEAK 29(16Q24.3) WILD-TYPE	42	27	78

Figure S404. Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'MRNASEQ_CNMF'

P value = 2.82e-16 (Fisher's exact test), Q value = 1.5e-13

Table S405. Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 29(16Q24.3) CNV	99	115	322
DEL PEAK 29(16Q24.3) WILD-TYPE	135	33	124

Figure S405. Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 29(16q24.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.62e-21 (Fisher's exact test), Q value = 2.6e-18

Table S406. Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 29(16Q24.3) CNV	173	287	76
DEL PEAK 29(16Q24.3) WILD-TYPE	43	121	128

Figure S406. Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 29(16q24.3)' versus 'MIRSEQ_CNMF'

P value = 9.22e-15 (Fisher's exact test), Q value = 4.7e-12

Table S407. Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 29(16Q24.3) CNV	168	288	112
DEL PEAK 29(16Q24.3) WILD-TYPE	66	104	143

Figure S407. Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 29(16q24.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.49e-22 (Fisher's exact test), Q value = 4.9e-19

Table S408. Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 29(16Q24.3) CNV	239	233	96
DEL PEAK 29(16Q24.3) WILD-TYPE	123	51	139

Figure S408. Get High-res Image Gene #56: 'Del Peak 29(16q24.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 30(17p12)' versus 'MRNA_CNMF'

P value = 2.14e-10 (Chi-square test), Q value = 9e-08

Table S409. Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 30(17P12) CNV	80	27	14	60	60	15	32	24
DEL PEAK 30(17P12) WILD-TYPE	44	9	9	35	12	5	71	16

Figure S409. Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 30(17p12)' versus 'CN_CNMF'

P value = 9.33e-23 (Chi-square test), Q value = 5.5e-20

Table S410. Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 30(17P12) CNV	142	170	35	172	27
DEL PEAK 30(17P12) WILD-TYPE	205	52	37	51	22

Figure S410. Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(17p12)' versus 'METHLYATION_CNMF'

P value = 7.4e-07 (Chi-square test), Q value = 0.00024

Table S411. Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 30(17P12) CNV	61	62	64	103	21	46
DEL PEAK 30(17P12) WILD-TYPE	40	77	29	34	19	51

Figure S411. Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 30(17p12)' versus 'RPPA_CNMF'

P value = 8.07e-05 (Fisher's exact test), Q value = 0.019

Table S412. Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
DEL PEAK 30(17P12) CNV	109	67	65
DEL PEAK 30(17P12) WILD-TYPE	38	66	52

Figure S412. Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 30(17p12)' versus 'MRNASEQ_CNMF'

P value = 0.000586 (Fisher's exact test), Q value = 0.11

Table S413. Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 30(17P12) CNV	166	83	253
DEL PEAK 30(17P12) WILD-TYPE	68	65	193

Figure S413. Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(17p12)' versus 'MIRSEQ_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.054

Table S414. Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 30(17P12) CNV	133	220	181
DEL PEAK 30(17P12) WILD-TYPE	101	172	74

Figure S414. Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 30(17p12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000127 (Fisher's exact test), Q value = 0.029

Table S415. Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 30(17P12) CNV	219	149	166
DEL PEAK 30(17P12) WILD-TYPE	143	135	69

Figure S415. Get High-res Image Gene #57: 'Del Peak 30(17p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'MRNA_CNMF'

P value = 1.07e-14 (Chi-square test), Q value = 5.4e-12

Table S416. Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 31(17Q21.31) CNV	29	16	7	50	50	9	13	16
DEL PEAK 31(17Q21.31) WILD-TYPE	95	20	16	45	22	11	90	24

Figure S416. Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 31(17q21.31)' versus 'MRNA_CHIERARCHICAL'

P value = 3.91e-07 (Fisher's exact test), Q value = 0.00013

Table S417. Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 31(17Q21.31) CNV	45	72	73
DEL PEAK 31(17Q21.31) WILD-TYPE	95	53	175

Figure S417. Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'CN_CNMF'

P value = 5.42e-22 (Chi-square test), Q value = 3.2e-19

Table S418. Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 31(17Q21.31) CNV	79	69	18	139	10
DEL PEAK 31(17Q21.31) WILD-TYPE	268	153	54	84	39

Figure S418. Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(17q21.31)' versus 'METHLYATION_CNMF'

P value = 1.19e-11 (Chi-square test), Q value = 5.3e-09

Table S419. Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 31(17Q21.31) CNV	60	19	36	39	11	28
DEL PEAK 31(17Q21.31) WILD-TYPE	41	120	57	98	29	69

Figure S419. Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 31(17q21.31)' versus 'RPPA_CNMF'

P value = 1.86e-11 (Fisher's exact test), Q value = 8.2e-09

Table S420. Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
DEL PEAK 31(17Q21.31) CNV	87	25	44
DEL PEAK 31(17Q21.31) WILD-TYPE	60	108	73

Figure S420. Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 31(17q21.31)' versus 'RPPA_CHIERARCHICAL'

P value = 3.12e-11 (Fisher's exact test), Q value = 1.4e-08

Table S421. Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
DEL PEAK 31(17Q21.31) CNV	42	33	81
DEL PEAK 31(17Q21.31) WILD-TYPE	119	77	45

Figure S421. Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'MRNASEQ_CNMF'

P value = 2.86e-21 (Fisher's exact test), Q value = 1.6e-18

Table S422. Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 31(17Q21.31) CNV	144	41	109
DEL PEAK 31(17Q21.31) WILD-TYPE	90	107	337

Figure S422. Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(17q21.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.32e-17 (Fisher's exact test), Q value = 4.5e-14

Table S423. Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 31(17Q21.31) CNV	64	106	124
DEL PEAK 31(17Q21.31) WILD-TYPE	152	302	80

Figure S423. Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(17q21.31)' versus 'MIRSEQ_CNMF'

P value = 1.14e-12 (Fisher's exact test), Q value = 5.3e-10

Table S424. Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 31(17Q21.31) CNV	69	102	137
DEL PEAK 31(17Q21.31) WILD-TYPE	165	290	118

Figure S424. Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 31(17q21.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.76e-11 (Fisher's exact test), Q value = 7.8e-09

Table S425. Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 31(17Q21.31) CNV	110	72	126
DEL PEAK 31(17Q21.31) WILD-TYPE	252	212	109

Figure S425. Get High-res Image Gene #58: 'Del Peak 31(17q21.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(18q23)' versus 'MRNA_CNMF'

P value = 0.000347 (Chi-square test), Q value = 0.071

Table S426. Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 32(18Q23) CNV	40	13	4	36	37	6	19	9
DEL PEAK 32(18Q23) WILD-TYPE	84	23	19	59	35	14	84	31

Figure S426. Get High-res Image Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 32(18q23)' versus 'CN_CNMF'

P value = 1.32e-15 (Chi-square test), Q value = 7e-13

Table S427. Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 32(18Q23) CNV	58	84	28	111	12
DEL PEAK 32(18Q23) WILD-TYPE	289	138	44	112	37

Figure S427. Get High-res Image Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(18q23)' versus 'METHLYATION_CNMF'

P value = 1.2e-08 (Chi-square test), Q value = 4.6e-06

Table S428. Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 32(18Q23) CNV	40	25	47	59	9	19
DEL PEAK 32(18Q23) WILD-TYPE	61	114	46	78	31	78

Figure S428. Get High-res Image Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 32(18q23)' versus 'MRNASEQ_CNMF'

P value = 2.54e-05 (Fisher's exact test), Q value = 0.0066

Table S429. Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 32(18Q23) CNV	102	33	134
DEL PEAK 32(18Q23) WILD-TYPE	132	115	312

Figure S429. Get High-res Image Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(18q23)' versus 'MIRSEQ_CNMF'

P value = 0.000375 (Fisher's exact test), Q value = 0.076

Table S430. Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 32(18Q23) CNV	60	120	107
DEL PEAK 32(18Q23) WILD-TYPE	174	272	148

Figure S430. Get High-res Image Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 32(18q23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000143 (Fisher's exact test), Q value = 0.032

Table S431. Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 32(18Q23) CNV	113	73	101
DEL PEAK 32(18Q23) WILD-TYPE	249	211	134

Figure S431. Get High-res Image Gene #59: 'Del Peak 32(18q23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 33(19p13.3)' versus 'MRNA_CNMF'

P value = 5.99e-11 (Chi-square test), Q value = 2.6e-08

Table S432. Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 33(19P13.3) CNV	53	11	6	53	37	6	12	6
DEL PEAK 33(19P13.3) WILD-TYPE	71	25	17	42	35	14	91	34

Figure S432. Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 33(19p13.3)' versus 'MRNA_CHIERARCHICAL'

P value = 4.57e-08 (Fisher's exact test), Q value = 1.7e-05

Table S433. Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 33(19P13.3) CNV	26	65	93
DEL PEAK 33(19P13.3) WILD-TYPE	114	60	155

Figure S433. Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 33(19p13.3)' versus 'CN_CNMF'

P value = 1.25e-44 (Chi-square test), Q value = 7.9e-42

Table S434. Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 33(19P13.3) CNV	30	112	11	136	16
DEL PEAK 33(19P13.3) WILD-TYPE	317	110	61	87	33

Figure S434. Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 33(19p13.3)' versus 'METHLYATION_CNMF'

P value = 6.53e-18 (Chi-square test), Q value = 3.6e-15

Table S435. Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 33(19P13.3) CNV	52	9	22	67	6	24
DEL PEAK 33(19P13.3) WILD-TYPE	49	130	71	70	34	73

Figure S435. Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 33(19p13.3)' versus 'RPPA_CNMF'

P value = 3.03e-06 (Fisher's exact test), Q value = 0.00089

Table S436. Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
DEL PEAK 33(19P13.3) CNV	79	40	31
DEL PEAK 33(19P13.3) WILD-TYPE	68	93	86

Figure S436. Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 33(19p13.3)' versus 'RPPA_CHIERARCHICAL'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.0086

Table S437. Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
DEL PEAK 33(19P13.3) CNV	51	31	68
DEL PEAK 33(19P13.3) WILD-TYPE	110	79	58

Figure S437. Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 33(19p13.3)' versus 'MRNASEQ_CNMF'

P value = 1.19e-12 (Fisher's exact test), Q value = 5.5e-10

Table S438. Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 33(19P13.3) CNV	121	24	142
DEL PEAK 33(19P13.3) WILD-TYPE	113	124	304

Figure S438. Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 33(19p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.4e-10 (Fisher's exact test), Q value = 2.2e-07

Table S439. Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 33(19P13.3) CNV	43	142	102
DEL PEAK 33(19P13.3) WILD-TYPE	173	266	102

Figure S439. Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 9.67e-16 (Fisher's exact test), Q value = 5.1e-13

Table S440. Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 33(19P13.3) CNV	47	111	137
DEL PEAK 33(19P13.3) WILD-TYPE	187	281	118

Figure S440. Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 33(19p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.54e-17 (Fisher's exact test), Q value = 3.5e-14

Table S441. Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 33(19P13.3) CNV	124	48	123
DEL PEAK 33(19P13.3) WILD-TYPE	238	236	112

Figure S441. Get High-res Image Gene #60: 'Del Peak 33(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'MRNA_CNMF'

P value = 1.57e-06 (Chi-square test), Q value = 0.00048

Table S442. Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 34(19Q13.32) CNV	24	7	3	23	29	1	7	3
DEL PEAK 34(19Q13.32) WILD-TYPE	100	29	20	72	43	19	96	37

Figure S442. Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 34(19q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 8.8e-05 (Fisher's exact test), Q value = 0.021

Table S443. Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 34(19Q13.32) CNV	12	36	49
DEL PEAK 34(19Q13.32) WILD-TYPE	128	89	199

Figure S443. Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'CN_CNMF'

P value = 4.48e-20 (Chi-square test), Q value = 2.6e-17

Table S444. Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 34(19Q13.32) CNV	22	68	5	79	9
DEL PEAK 34(19Q13.32) WILD-TYPE	325	154	67	144	40

Figure S444. Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 34(19q13.32)' versus 'METHLYATION_CNMF'

P value = 1.52e-10 (Chi-square test), Q value = 6.4e-08

Table S445. Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 34(19Q13.32) CNV	37	6	19	43	5	12
DEL PEAK 34(19Q13.32) WILD-TYPE	64	133	74	94	35	85

Figure S445. Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 34(19q13.32)' versus 'RPPA_CNMF'

P value = 0.000783 (Fisher's exact test), Q value = 0.14

Table S446. Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	133	117
DEL PEAK 34(19Q13.32) CNV	44	20	15
DEL PEAK 34(19Q13.32) WILD-TYPE	103	113	102

Figure S446. Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 34(19q13.32)' versus 'RPPA_CHIERARCHICAL'

P value = 4.95e-05 (Fisher's exact test), Q value = 0.012

Table S447. Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	110	126
DEL PEAK 34(19Q13.32) CNV	27	11	41
DEL PEAK 34(19Q13.32) WILD-TYPE	134	99	85

Figure S447. Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'MRNASEQ_CNMF'

P value = 5.28e-09 (Fisher's exact test), Q value = 2.1e-06

Table S448. Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 34(19Q13.32) CNV	79	13	82
DEL PEAK 34(19Q13.32) WILD-TYPE	155	135	364

Figure S448. Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 34(19q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.75e-09 (Fisher's exact test), Q value = 2.6e-06

Table S449. Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 34(19Q13.32) CNV	19	89	66
DEL PEAK 34(19Q13.32) WILD-TYPE	197	319	138

Figure S449. Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(19q13.32)' versus 'MIRSEQ_CNMF'

P value = 3.6e-10 (Fisher's exact test), Q value = 1.5e-07

Table S450. Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 34(19Q13.32) CNV	24	66	85
DEL PEAK 34(19Q13.32) WILD-TYPE	210	326	170

Figure S450. Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 34(19q13.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.78e-12 (Fisher's exact test), Q value = 2.6e-09

Table S451. Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 34(19Q13.32) CNV	78	22	75
DEL PEAK 34(19Q13.32) WILD-TYPE	284	262	160

Figure S451. Get High-res Image Gene #61: 'Del Peak 34(19q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 35(20p13)' versus 'MRNA_CNMF'

P value = 8.81e-06 (Chi-square test), Q value = 0.0024

Table S452. Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 35(20P13) CNV	28	3	1	24	16	3	3	1
DEL PEAK 35(20P13) WILD-TYPE	96	33	22	71	56	17	100	39

Figure S452. Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(20p13)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000158 (Fisher's exact test), Q value = 0.035

Table S453. Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	140	125	248
DEL PEAK 35(20P13) CNV	10	32	37
DEL PEAK 35(20P13) WILD-TYPE	130	93	211

Figure S453. Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 35(20p13)' versus 'CN_CNMF'

P value = 2.59e-13 (Chi-square test), Q value = 1.2e-10

Table S454. Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 35(20P13) CNV	18	36	5	61	14
DEL PEAK 35(20P13) WILD-TYPE	329	186	67	162	35

Figure S454. Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(20p13)' versus 'METHLYATION_CNMF'

P value = 7.15e-09 (Chi-square test), Q value = 2.8e-06

Table S455. Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 35(20P13) CNV	31	4	11	24	3	7
DEL PEAK 35(20P13) WILD-TYPE	70	135	82	113	37	90

Figure S455. Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 35(20p13)' versus 'MRNASEQ_CNMF'

P value = 2.44e-10 (Fisher's exact test), Q value = 1e-07

Table S456. Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	148	446
DEL PEAK 35(20P13) CNV	64	6	55
DEL PEAK 35(20P13) WILD-TYPE	170	142	391

Figure S456. Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(20p13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.06e-10 (Fisher's exact test), Q value = 2.9e-07

Table S457. Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	408	204
DEL PEAK 35(20P13) CNV	11	58	56
DEL PEAK 35(20P13) WILD-TYPE	205	350	148

Figure S457. Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(20p13)' versus 'MIRSEQ_CNMF'

P value = 2.69e-12 (Fisher's exact test), Q value = 1.2e-09

Table S458. Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	392	255
DEL PEAK 35(20P13) CNV	15	40	72
DEL PEAK 35(20P13) WILD-TYPE	219	352	183

Figure S458. Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 35(20p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.91e-13 (Fisher's exact test), Q value = 9.2e-11

Table S459. Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	362	284	235
DEL PEAK 35(20P13) CNV	48	13	66
DEL PEAK 35(20P13) WILD-TYPE	314	271	169

Figure S459. Get High-res Image Gene #62: 'Del Peak 35(20p13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 36(21q11.2)' versus 'MRNA_CNMF'

P value = 0.000252 (Chi-square test), Q value = 0.054

Table S460. Gene #63: 'Del Peak 36(21q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	124	36	23	95	72	20	103	40
DEL PEAK 36(21Q11.2) CNV	38	11	4	15	22	3	10	3
DEL PEAK 36(21Q11.2) WILD-TYPE	86	25	19	80	50	17	93	37

Figure S460. Get High-res Image Gene #63: 'Del Peak 36(21q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 36(21q11.2)' versus 'CN_CNMF'

P value = 4.31e-11 (Chi-square test), Q value = 1.9e-08

Table S461. Gene #63: 'Del Peak 36(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	347	222	72	223	49
DEL PEAK 36(21Q11.2) CNV	28	66	13	63	12
DEL PEAK 36(21Q11.2) WILD-TYPE	319	156	59	160	37

Figure S461. Get High-res Image Gene #63: 'Del Peak 36(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 36(21q11.2)' versus 'METHLYATION_CNMF'

P value = 2.01e-06 (Chi-square test), Q value = 6e-04

Table S462. Gene #63: 'Del Peak 36(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 36(21Q11.2) CNV	17	16	18	48	7	9
DEL PEAK 36(21Q11.2) WILD-TYPE	84	123	75	89	33	88

Figure S462. Get High-res Image Gene #63: 'Del Peak 36(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(22q13.32)' versus 'METHLYATION_CNMF'

P value = 0.000674 (Chi-square test), Q value = 0.13

Table S463. Gene #64: 'Del Peak 37(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	101	139	93	137	40	97
DEL PEAK 37(22Q13.32) CNV	49	52	42	79	10	36
DEL PEAK 37(22Q13.32) WILD-TYPE	52	87	51	58	30	61

Figure S463. Get High-res Image Gene #64: 'Del Peak 37(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = BRCA-TP.transferedmergedcluster.txt
Number of patients = 913
Number of copy number variation regions = 64
Number of molecular subtypes = 10
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.

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)

[4] GISTIC_version2

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