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 70 peak regions and 8 molecular subtypes across 352 patients, 113 significant findings detected with Q value < 0.25.

Amp Peak 1(1q21.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Amp Peak 2(2q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 3(2q31.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 4(3q26.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 5(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(5p12) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(6p12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(6q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(7p11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 10(7q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 12(8q11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(8q24.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 14(9p23) cnvs correlated to 'CN_CNMF'.
Amp Peak 15(9p13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 16(11p13) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(11q13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 18(12p13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 19(12q15) cnvs correlated to 'CN_CNMF'.
Amp Peak 20(13q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 21(15q26.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(17q12) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 23(18p11.31) cnvs correlated to 'CN_CNMF'.
Amp Peak 25(20q11.22) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
Del Peak 4(2q21.2) cnvs correlated to 'MIRSEQ_CNMF'.
Del Peak 6(2q36.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 7(3p25.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 8(3p14.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 9(3p14.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 10(3p12.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 11(4p15.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 12(4q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 13(4q35.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 14(5q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 15(5q35.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 16(6p25.3) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 18(7q36.1) cnvs correlated to 'CN_CNMF'.
Del Peak 19(8p23.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 20(9p23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 21(9p21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 22(9q21.11) cnvs correlated to 'CN_CNMF'.
Del Peak 23(9q34.3) cnvs correlated to 'CN_CNMF'.
Del Peak 24(10p15.3) cnvs correlated to 'CN_CNMF'.
Del Peak 25(10p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 26(10q23.31) cnvs correlated to 'CN_CNMF'.
Del Peak 27(11p15.4) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
Del Peak 28(11q14.1) cnvs correlated to 'CN_CNMF'.
Del Peak 29(11q23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 31(13q12.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 32(13q14.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 34(14q32.32) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 36(16q12.1) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Del Peak 37(16q23.3) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
Del Peak 39(18q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 40(18q23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 41(19p13.3) cnvs correlated to 'CN_CNMF'.
Del Peak 42(19q13.43) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 43(Xp21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 44(Xp11.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 45(Xq21.33) cnvs correlated to 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 70 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 113 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	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 13(8q24 21)	0 (0%)	98	3.31e-10 (1.76e-07)	0.000106 (0.0496)	0.19 (1.00)	0.917 (1.00)	0.000102 (0.0482)	0.000135 (0.0632)	0.0159 (1.00)	0.000223 (0.103)
Amp Peak 1(1q21 2)	0 (0%)	270	8.51e-11 (4.55e-08)	2.63e-08 (1.36e-05)	0.473 (1.00)	0.718 (1.00)	0.000509 (0.229)	0.00316 (1.00)	0.000167 (0.0775)	0.698 (1.00)
Del Peak 1(1p36 13)	0 (0%)	283	1.44e-11 (7.71e-09)	5.38e-15 (2.94e-12)	0.0225 (1.00)	0.739 (1.00)	3.03e-05 (0.0148)	0.000716 (0.317)	0.000136 (0.0632)	0.137 (1.00)
Del Peak 32(13q14 2)	0 (0%)	203	2.86e-06 (0.00142)	5.88e-07 (0.000298)	0.151 (1.00)	0.275 (1.00)	5.7e-05 (0.0274)	6.46e-05 (0.0309)	0.00618 (1.00)	0.979 (1.00)
Del Peak 36(16q12 1)	0 (0%)	290	0.00922 (1.00)	1.13e-07 (5.74e-05)	0.746 (1.00)	0.0896 (1.00)	7.1e-08 (3.64e-05)	3.91e-07 (0.000199)	0.000104 (0.0488)	0.0137 (1.00)
Amp Peak 4(3q26 33)	0 (0%)	88	2.94e-13 (1.6e-10)	8.71e-05 (0.0413)	0.244 (1.00)	0.193 (1.00)	0.00128 (0.55)	0.000468 (0.212)	0.000917 (0.402)	0.165 (1.00)
Del Peak 2(1p13 2)	0 (0%)	267	3.1e-10 (1.65e-07)	8.62e-10 (4.56e-07)	0.0124 (1.00)	0.118 (1.00)	0.00546 (1.00)	0.0927 (1.00)	4.41e-05 (0.0213)	0.614 (1.00)
Del Peak 15(5q35 3)	0 (0%)	218	7.2e-18 (3.98e-15)	4.25e-14 (2.32e-11)	0.419 (1.00)	0.0645 (1.00)	0.0146 (1.00)	0.000477 (0.216)	0.204 (1.00)	0.649 (1.00)
Del Peak 27(11p15 4)	0 (0%)	242	1.6e-08 (8.32e-06)	0.000523 (0.234)	0.471 (1.00)	0.458 (1.00)	0.00228 (0.954)	0.0071 (1.00)	0.000501 (0.226)	0.54 (1.00)
Del Peak 29(11q23 1)	0 (0%)	183	7.7e-18 (4.25e-15)	8.45e-07 (0.000423)	0.169 (1.00)	0.254 (1.00)	0.000815 (0.359)	0.00023 (0.106)	0.103 (1.00)	0.35 (1.00)
Del Peak 34(14q32 32)	0 (0%)	299	0.0267 (1.00)	1.42e-07 (7.23e-05)	0.0984 (1.00)	0.413 (1.00)	0.000242 (0.111)	9.8e-05 (0.0462)	0.00137 (0.584)	0.0924 (1.00)
Amp Peak 2(2q11 2)	0 (0%)	278	2.5e-08 (1.29e-05)	1.71e-08 (8.87e-06)	0.991 (1.00)	0.295 (1.00)	0.0119 (1.00)	0.0807 (1.00)	0.00172 (0.727)	0.296 (1.00)
Amp Peak 3(2q31 2)	0 (0%)	280	1.26e-10 (6.74e-08)	9.37e-09 (4.89e-06)	0.803 (1.00)	0.509 (1.00)	0.318 (1.00)	0.11 (1.00)	0.206 (1.00)	0.391 (1.00)
Amp Peak 9(7p11 2)	0 (0%)	205	1.12e-08 (5.84e-06)	6.87e-07 (0.000346)	0.26 (1.00)	0.832 (1.00)	0.5 (1.00)	0.923 (1.00)	0.934 (1.00)	0.0261 (1.00)
Amp Peak 10(7q22 1)	0 (0%)	231	6.99e-15 (3.81e-12)	5.46e-08 (2.8e-05)	0.599 (1.00)	0.567 (1.00)	0.235 (1.00)	0.335 (1.00)	0.011 (1.00)	0.67 (1.00)
Amp Peak 18(12p13 33)	0 (0%)	234	2.85e-10 (1.52e-07)	1.28e-05 (0.00628)	0.276 (1.00)	0.352 (1.00)	0.00912 (1.00)	0.00101 (0.44)	0.00117 (0.507)	0.323 (1.00)
Amp Peak 20(13q22 1)	0 (0%)	280	0.000262 (0.12)	8.43e-05 (0.04)	0.0181 (1.00)	0.205 (1.00)	0.233 (1.00)	0.0924 (1.00)	0.0822 (1.00)	0.135 (1.00)
Amp Peak 22(17q12)	0 (0%)	289	8.2e-08 (4.2e-05)	0.000112 (0.0522)	0.623 (1.00)	0.73 (1.00)	0.0168 (1.00)	0.0308 (1.00)	0.0161 (1.00)	0.167 (1.00)
Del Peak 6(2q36 2)	0 (0%)	248	5.4e-08 (2.78e-05)	5.69e-06 (0.0028)	0.114 (1.00)	0.531 (1.00)	0.000636 (0.283)	0.00125 (0.539)	0.00452 (1.00)	0.232 (1.00)
Del Peak 7(3p25 3)	0 (0%)	105	7.67e-25 (4.25e-22)	2.92e-10 (1.55e-07)	0.213 (1.00)	0.39 (1.00)	0.0134 (1.00)	0.0632 (1.00)	0.146 (1.00)	0.00212 (0.892)
Del Peak 8(3p14 2)	0 (0%)	89	2.49e-29 (1.4e-26)	8.81e-08 (4.5e-05)	0.259 (1.00)	0.5 (1.00)	0.115 (1.00)	0.161 (1.00)	0.534 (1.00)	0.0592 (1.00)
Del Peak 9(3p14 2)	0 (0%)	89	2.49e-29 (1.4e-26)	5.71e-07 (0.000289)	0.216 (1.00)	0.386 (1.00)	0.115 (1.00)	0.161 (1.00)	0.534 (1.00)	0.0592 (1.00)
Del Peak 10(3p12 2)	0 (0%)	103	6.77e-29 (3.78e-26)	4.04e-09 (2.13e-06)	0.853 (1.00)	0.684 (1.00)	0.241 (1.00)	0.463 (1.00)	0.287 (1.00)	0.273 (1.00)
Del Peak 11(4p15 2)	0 (0%)	202	3.05e-12 (1.65e-09)	5.98e-07 (0.000302)	0.0483 (1.00)	0.13 (1.00)	0.0406 (1.00)	0.0129 (1.00)	0.00483 (1.00)	0.678 (1.00)
Del Peak 12(4q22 1)	0 (0%)	235	8.67e-09 (4.54e-06)	6.5e-07 (0.000327)	0.13 (1.00)	0.651 (1.00)	0.371 (1.00)	0.205 (1.00)	0.334 (1.00)	0.578 (1.00)
Del Peak 13(4q35 2)	0 (0%)	207	7.51e-09 (3.94e-06)	2.97e-05 (0.0145)	0.0962 (1.00)	0.534 (1.00)	0.275 (1.00)	0.353 (1.00)	0.218 (1.00)	0.482 (1.00)
Del Peak 14(5q11 2)	0 (0%)	210	5.27e-17 (2.91e-14)	1.35e-12 (7.3e-10)	0.0186 (1.00)	0.615 (1.00)	0.0401 (1.00)	0.000767 (0.339)	0.0647 (1.00)	0.457 (1.00)
Del Peak 19(8p23 2)	0 (0%)	151	2.17e-15 (1.19e-12)	3.84e-05 (0.0186)	0.134 (1.00)	0.188 (1.00)	0.0166 (1.00)	0.00353 (1.00)	0.143 (1.00)	0.0273 (1.00)
Del Peak 20(9p23)	0 (0%)	191	1.16e-16 (6.36e-14)	5.42e-09 (2.85e-06)	0.538 (1.00)	0.851 (1.00)	0.74 (1.00)	0.493 (1.00)	0.834 (1.00)	0.845 (1.00)
Del Peak 21(9p21 3)	0 (0%)	148	2.71e-13 (1.47e-10)	2.83e-09 (1.49e-06)	0.707 (1.00)	0.423 (1.00)	0.39 (1.00)	0.462 (1.00)	0.746 (1.00)	0.432 (1.00)
Del Peak 31(13q12 11)	0 (0%)	193	2.63e-11 (1.41e-08)	7.28e-07 (0.000366)	0.272 (1.00)	0.371 (1.00)	0.053 (1.00)	0.0289 (1.00)	0.456 (1.00)	0.758 (1.00)
Del Peak 39(18q21 2)	0 (0%)	170	7.27e-17 (4e-14)	1.69e-09 (8.92e-07)	0.603 (1.00)	0.642 (1.00)	0.00268 (1.00)	0.0073 (1.00)	0.00342 (1.00)	0.00548 (1.00)
Del Peak 40(18q23)	0 (0%)	154	8.57e-20 (4.75e-17)	1.38e-11 (7.41e-09)	0.183 (1.00)	0.385 (1.00)	0.00216 (0.908)	0.00333 (1.00)	0.0125 (1.00)	0.0184 (1.00)
Del Peak 42(19q13 43)	0 (0%)	284	1.03e-05 (0.00506)	6.93e-05 (0.033)	0.256 (1.00)	0.0841 (1.00)	0.584 (1.00)	0.262 (1.00)	0.058 (1.00)	0.495 (1.00)
Del Peak 44(Xp11 3)	0 (0%)	238	4.65e-06 (0.0023)	5.8e-05 (0.0278)	0.346 (1.00)	0.00914 (1.00)	0.211 (1.00)	0.0598 (1.00)	0.099 (1.00)	0.931 (1.00)
Amp Peak 5(5p15 33)	0 (0%)	195	1.31e-11 (7.08e-09)	0.0256 (1.00)	0.624 (1.00)	0.282 (1.00)	0.683 (1.00)	0.32 (1.00)	0.687 (1.00)	0.757 (1.00)
Amp Peak 6(5p12)	0 (0%)	221	3.48e-12 (1.88e-09)	0.0182 (1.00)	0.478 (1.00)	1 (1.00)	0.9 (1.00)	0.388 (1.00)	0.784 (1.00)	0.746 (1.00)
Amp Peak 7(6p12 1)	0 (0%)	282	0.000195 (0.0905)	0.0028 (1.00)	0.303 (1.00)	0.47 (1.00)	0.983 (1.00)	0.802 (1.00)	0.928 (1.00)	0.00123 (0.531)
Amp Peak 8(6q12)	0 (0%)	290	0.0004 (0.182)	0.0138 (1.00)	0.811 (1.00)	0.373 (1.00)	1 (1.00)	0.822 (1.00)	0.674 (1.00)	0.00726 (1.00)
Amp Peak 12(8q11 21)	0 (0%)	145	1.8e-06 (0.000895)	0.0111 (1.00)	0.0323 (1.00)	0.518 (1.00)	0.00113 (0.49)	0.000664 (0.295)	0.00334 (1.00)	0.00122 (0.529)
Amp Peak 14(9p23)	0 (0%)	269	3.19e-05 (0.0155)	0.786 (1.00)	0.655 (1.00)	0.888 (1.00)	0.0993 (1.00)	0.227 (1.00)	0.406 (1.00)	0.943 (1.00)
Amp Peak 15(9p13 3)	0 (0%)	257	5.06e-05 (0.0244)	0.222 (1.00)	0.39 (1.00)	0.254 (1.00)	0.00708 (1.00)	0.0379 (1.00)	0.0113 (1.00)	0.085 (1.00)
Amp Peak 16(11p13)	0 (0%)	283	5.66e-05 (0.0272)	0.0971 (1.00)	0.187 (1.00)	0.0539 (1.00)	0.631 (1.00)	0.163 (1.00)	0.384 (1.00)	0.0655 (1.00)
Amp Peak 17(11q13 3)	0 (0%)	188	1.73e-27 (9.63e-25)	0.000897 (0.394)	0.901 (1.00)	0.284 (1.00)	0.361 (1.00)	0.504 (1.00)	0.67 (1.00)	0.0874 (1.00)
Amp Peak 19(12q15)	0 (0%)	280	0.000508 (0.229)	0.00842 (1.00)	0.0609 (1.00)	0.193 (1.00)	0.09 (1.00)	0.0459 (1.00)	0.463 (1.00)	0.726 (1.00)
Amp Peak 21(15q26 3)	0 (0%)	277	0.000327 (0.15)	0.217 (1.00)	0.263 (1.00)	0.624 (1.00)	0.923 (1.00)	0.416 (1.00)	0.918 (1.00)	0.599 (1.00)
Amp Peak 23(18p11 31)	0 (0%)	244	7.58e-07 (0.00038)	0.00315 (1.00)	0.962 (1.00)	0.766 (1.00)	0.262 (1.00)	0.206 (1.00)	0.5 (1.00)	0.927 (1.00)
Amp Peak 25(20q11 22)	0 (0%)	197	4.86e-06 (0.0024)	0.0222 (1.00)	0.845 (1.00)	0.442 (1.00)	0.0128 (1.00)	0.0854 (1.00)	0.308 (1.00)	0.0129 (1.00)
Del Peak 4(2q21 2)	0 (0%)	306	0.717 (1.00)	0.0278 (1.00)	0.91 (1.00)	1 (1.00)	0.0154 (1.00)	0.00564 (1.00)	0.000377 (0.172)	0.155 (1.00)
Del Peak 16(6p25 3)	0 (0%)	284	0.00195 (0.821)	0.00033 (0.151)	0.0727 (1.00)	0.133 (1.00)	0.00752 (1.00)	0.38 (1.00)	0.101 (1.00)	0.667 (1.00)
Del Peak 18(7q36 1)	0 (0%)	266	0.000182 (0.0844)	0.33 (1.00)	0.00511 (1.00)	0.277 (1.00)	0.957 (1.00)	0.674 (1.00)	0.914 (1.00)	0.135 (1.00)
Del Peak 22(9q21 11)	0 (0%)	287	2.86e-08 (1.48e-05)	0.000962 (0.42)	0.96 (1.00)	0.926 (1.00)	0.882 (1.00)	0.673 (1.00)	0.72 (1.00)	0.0485 (1.00)
Del Peak 23(9q34 3)	0 (0%)	296	0.000333 (0.152)	0.0316 (1.00)	0.712 (1.00)	0.108 (1.00)	0.851 (1.00)	0.409 (1.00)	0.29 (1.00)	0.14 (1.00)
Del Peak 24(10p15 3)	0 (0%)	238	5.46e-06 (0.00269)	0.0293 (1.00)	0.504 (1.00)	0.155 (1.00)	0.327 (1.00)	0.307 (1.00)	0.313 (1.00)	0.469 (1.00)
Del Peak 25(10p11 21)	0 (0%)	245	9.79e-06 (0.00481)	0.145 (1.00)	0.225 (1.00)	0.0652 (1.00)	0.702 (1.00)	0.975 (1.00)	0.511 (1.00)	0.705 (1.00)
Del Peak 26(10q23 31)	0 (0%)	263	1.55e-06 (0.000771)	0.00416 (1.00)	0.179 (1.00)	0.548 (1.00)	0.0249 (1.00)	0.0128 (1.00)	0.0224 (1.00)	0.947 (1.00)
Del Peak 28(11q14 1)	0 (0%)	240	4.77e-25 (2.65e-22)	0.0851 (1.00)	0.193 (1.00)	0.769 (1.00)	0.0105 (1.00)	0.0369 (1.00)	0.38 (1.00)	0.821 (1.00)
Del Peak 37(16q23 3)	0 (0%)	280	0.0167 (1.00)	0.000839 (0.369)	0.504 (1.00)	0.0196 (1.00)	0.000601 (0.269)	8.88e-05 (0.042)	0.00604 (1.00)	0.218 (1.00)
Del Peak 41(19p13 3)	0 (0%)	235	3.57e-06 (0.00177)	0.0368 (1.00)	0.31 (1.00)	0.0817 (1.00)	0.0876 (1.00)	0.761 (1.00)	0.487 (1.00)	0.0959 (1.00)
Del Peak 43(Xp21 3)	0 (0%)	236	4.3e-05 (0.0208)	0.00532 (1.00)	0.424 (1.00)	0.0649 (1.00)	0.275 (1.00)	0.0415 (1.00)	0.2 (1.00)	0.564 (1.00)
Del Peak 45(Xq21 33)	0 (0%)	296	0.00168 (0.711)	0.00166 (0.705)	0.0255 (1.00)	0.444 (1.00)	0.00131 (0.56)	0.0123 (1.00)	6.6e-05 (0.0315)	0.00424 (1.00)
Amp Peak 11(8p11 23)	0 (0%)	241	0.0352 (1.00)	0.0369 (1.00)	0.897 (1.00)	0.629 (1.00)	0.15 (1.00)	0.0182 (1.00)	0.0229 (1.00)	0.332 (1.00)
Amp Peak 24(18q11 2)	0 (0%)	278	0.0174 (1.00)	0.033 (1.00)	0.157 (1.00)	0.462 (1.00)	1 (1.00)	0.689 (1.00)	0.182 (1.00)	0.259 (1.00)
Del Peak 3(1q44)	0 (0%)	322	0.139 (1.00)	0.175 (1.00)	0.859 (1.00)	0.931 (1.00)	0.0628 (1.00)	0.0133 (1.00)	0.00447 (1.00)	0.157 (1.00)
Del Peak 5(2q22 1)	0 (0%)	274	0.297 (1.00)	0.00648 (1.00)	0.29 (1.00)	0.522 (1.00)	0.0513 (1.00)	0.0292 (1.00)	0.109 (1.00)	0.139 (1.00)
Del Peak 17(7q31 1)	0 (0%)	298	0.000918 (0.402)	0.0261 (1.00)	0.17 (1.00)	0.581 (1.00)	0.363 (1.00)	0.609 (1.00)	0.635 (1.00)	0.0823 (1.00)
Del Peak 30(12q24 33)	0 (0%)	312	0.0427 (1.00)	0.0646 (1.00)	0.082 (1.00)	0.748 (1.00)	0.859 (1.00)	0.775 (1.00)	0.977 (1.00)	0.387 (1.00)
Del Peak 33(14q11 2)	0 (0%)	301	0.000613 (0.274)	0.00616 (1.00)	0.38 (1.00)	0.515 (1.00)	0.463 (1.00)	0.329 (1.00)	0.0268 (1.00)	0.199 (1.00)
Del Peak 35(15q15 1)	0 (0%)	273	0.0014 (0.598)	0.778 (1.00)	0.293 (1.00)	0.161 (1.00)	0.0226 (1.00)	0.0628 (1.00)	0.2 (1.00)	0.26 (1.00)
Del Peak 38(17q25 3)	0 (0%)	310	0.477 (1.00)	0.123 (1.00)	0.474 (1.00)	1 (1.00)	0.037 (1.00)	0.0612 (1.00)	0.0361 (1.00)	0.073 (1.00)

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

P value = 8.51e-11 (Chi-square test), Q value = 4.6e-08

Table S1. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 1(1Q21.2) CNV	32	5	26	12	4	3
AMP PEAK 1(1Q21.2) WILD-TYPE	50	36	24	80	70	10

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.63e-08 (Chi-square test), Q value = 1.4e-05

Table S2. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 1(1Q21.2) CNV	8	13	4	10	31	1	0	4
AMP PEAK 1(1Q21.2) WILD-TYPE	35	34	35	35	27	50	4	15

Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.000509 (Fisher's exact test), Q value = 0.23

Table S3. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
AMP PEAK 1(1Q21.2) CNV	41	16	12
AMP PEAK 1(1Q21.2) WILD-TYPE	77	75	78

Figure S3. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 0.000167 (Fisher's exact test), Q value = 0.077

Table S4. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	138	100
AMP PEAK 1(1Q21.2) CNV	15	48	19
AMP PEAK 1(1Q21.2) WILD-TYPE	98	90	81

Figure S4. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

P value = 2.5e-08 (Chi-square test), Q value = 1.3e-05

Table S5. Gene #2: 'Amp Peak 2(2q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 2(2Q11.2) CNV	23	10	24	3	11	3
AMP PEAK 2(2Q11.2) WILD-TYPE	59	31	26	89	63	10

Figure S5. Get High-res Image Gene #2: 'Amp Peak 2(2q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.71e-08 (Chi-square test), Q value = 8.9e-06

Table S6. Gene #2: 'Amp Peak 2(2q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 2(2Q11.2) CNV	19	9	4	1	26	5	1	2
AMP PEAK 2(2Q11.2) WILD-TYPE	24	38	35	44	32	46	3	17

Figure S6. Get High-res Image Gene #2: 'Amp Peak 2(2q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 3(2q31.2)' versus 'CN_CNMF'

P value = 1.26e-10 (Chi-square test), Q value = 6.7e-08

Table S7. Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 3(2Q31.2) CNV	26	9	25	4	6	2
AMP PEAK 3(2Q31.2) WILD-TYPE	56	32	25	88	68	11

Figure S7. Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(2q31.2)' versus 'METHLYATION_CNMF'

P value = 9.37e-09 (Chi-square test), Q value = 4.9e-06

Table S8. Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 3(2Q31.2) CNV	13	8	5	2	30	5	1	1
AMP PEAK 3(2Q31.2) WILD-TYPE	30	39	34	43	28	46	3	18

Figure S8. Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 4(3q26.33)' versus 'CN_CNMF'

P value = 2.94e-13 (Chi-square test), Q value = 1.6e-10

Table S9. Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 4(3Q26.33) CNV	70	38	48	42	54	12
AMP PEAK 4(3Q26.33) WILD-TYPE	12	3	2	50	20	1

Figure S9. Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(3q26.33)' versus 'METHLYATION_CNMF'

P value = 8.71e-05 (Chi-square test), Q value = 0.041

Table S10. Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 4(3Q26.33) CNV	34	38	25	36	54	30	2	9
AMP PEAK 4(3Q26.33) WILD-TYPE	9	9	14	9	4	21	2	10

Figure S10. Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 4(3q26.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000468 (Fisher's exact test), Q value = 0.21

Table S11. Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
AMP PEAK 4(3Q26.33) CNV	75	50	100
AMP PEAK 4(3Q26.33) WILD-TYPE	20	34	20

Figure S11. Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.31e-11 (Chi-square test), Q value = 7.1e-09

Table S12. Gene #5: 'Amp Peak 5(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 5(5P15.33) CNV	45	37	25	27	18	5
AMP PEAK 5(5P15.33) WILD-TYPE	37	4	25	65	56	8

Figure S12. Get High-res Image Gene #5: 'Amp Peak 5(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(5p12)' versus 'CN_CNMF'

P value = 3.48e-12 (Chi-square test), Q value = 1.9e-09

Table S13. Gene #6: 'Amp Peak 6(5p12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 6(5P12) CNV	33	35	24	18	19	2
AMP PEAK 6(5P12) WILD-TYPE	49	6	26	74	55	11

Figure S13. Get High-res Image Gene #6: 'Amp Peak 6(5p12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 7(6p12.1)' versus 'CN_CNMF'

P value = 0.000195 (Chi-square test), Q value = 0.09

Table S14. Gene #7: 'Amp Peak 7(6p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 7(6P12.1) CNV	23	14	15	6	10	2
AMP PEAK 7(6P12.1) WILD-TYPE	59	27	35	86	64	11

Figure S14. Get High-res Image Gene #7: 'Amp Peak 7(6p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 8(6q12)' versus 'CN_CNMF'

P value = 4e-04 (Chi-square test), Q value = 0.18

Table S15. Gene #8: 'Amp Peak 8(6q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 8(6Q12) CNV	15	16	12	6	11	2
AMP PEAK 8(6Q12) WILD-TYPE	67	25	38	86	63	11

Figure S15. Get High-res Image Gene #8: 'Amp Peak 8(6q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(7p11.2)' versus 'CN_CNMF'

P value = 1.12e-08 (Chi-square test), Q value = 5.8e-06

Table S16. Gene #9: 'Amp Peak 9(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 9(7P11.2) CNV	42	30	27	18	28	2
AMP PEAK 9(7P11.2) WILD-TYPE	40	11	23	74	46	11

Figure S16. Get High-res Image Gene #9: 'Amp Peak 9(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(7p11.2)' versus 'METHLYATION_CNMF'

P value = 6.87e-07 (Chi-square test), Q value = 0.00035

Table S17. Gene #9: 'Amp Peak 9(7p11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 9(7P11.2) CNV	27	24	21	3	31	15	1	9
AMP PEAK 9(7P11.2) WILD-TYPE	16	23	18	42	27	36	3	10

Figure S17. Get High-res Image Gene #9: 'Amp Peak 9(7p11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 10(7q22.1)' versus 'CN_CNMF'

P value = 6.99e-15 (Chi-square test), Q value = 3.8e-12

Table S18. Gene #10: 'Amp Peak 10(7q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 10(7Q22.1) CNV	48	13	33	9	16	2
AMP PEAK 10(7Q22.1) WILD-TYPE	34	28	17	83	58	11

Figure S18. Get High-res Image Gene #10: 'Amp Peak 10(7q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 10(7q22.1)' versus 'METHLYATION_CNMF'

P value = 5.46e-08 (Chi-square test), Q value = 2.8e-05

Table S19. Gene #10: 'Amp Peak 10(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 10(7Q22.1) CNV	16	11	15	6	40	11	2	5
AMP PEAK 10(7Q22.1) WILD-TYPE	27	36	24	39	18	40	2	14

Figure S19. Get High-res Image Gene #10: 'Amp Peak 10(7q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 12(8q11.21)' versus 'CN_CNMF'

P value = 1.8e-06 (Chi-square test), Q value = 0.00089

Table S20. Gene #12: 'Amp Peak 12(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 12(8Q11.21) CNV	53	33	25	34	52	10
AMP PEAK 12(8Q11.21) WILD-TYPE	29	8	25	58	22	3

Figure S20. Get High-res Image Gene #12: 'Amp Peak 12(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 13(8q24.21)' versus 'CN_CNMF'

P value = 3.31e-10 (Chi-square test), Q value = 1.8e-07

Table S21. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 13(8Q24.21) CNV	73	37	32	43	57	12
AMP PEAK 13(8Q24.21) WILD-TYPE	9	4	18	49	17	1

Figure S21. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 13(8q24.21)' versus 'METHLYATION_CNMF'

P value = 0.000106 (Chi-square test), Q value = 0.05

Table S22. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 13(8Q24.21) CNV	30	42	32	20	40	33	4	16
AMP PEAK 13(8Q24.21) WILD-TYPE	13	5	7	25	18	18	0	3

Figure S22. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 13(8q24.21)' versus 'MRNASEQ_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.048

Table S23. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
AMP PEAK 13(8Q24.21) CNV	69	77	68
AMP PEAK 13(8Q24.21) WILD-TYPE	49	14	22

Figure S23. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 13(8q24.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000135 (Fisher's exact test), Q value = 0.063

Table S24. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
AMP PEAK 13(8Q24.21) CNV	79	65	70
AMP PEAK 13(8Q24.21) WILD-TYPE	16	19	50

Figure S24. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(8q24.21)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000223 (Fisher's exact test), Q value = 0.1

Table S25. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	132	11	208
AMP PEAK 13(8Q24.21) CNV	111	8	134
AMP PEAK 13(8Q24.21) WILD-TYPE	21	3	74

Figure S25. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 14(9p23)' versus 'CN_CNMF'

P value = 3.19e-05 (Chi-square test), Q value = 0.015

Table S26. Gene #14: 'Amp Peak 14(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 14(9P23) CNV	17	9	11	21	14	11
AMP PEAK 14(9P23) WILD-TYPE	65	32	39	71	60	2

Figure S26. Get High-res Image Gene #14: 'Amp Peak 14(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 15(9p13.3)' versus 'CN_CNMF'

P value = 5.06e-05 (Chi-square test), Q value = 0.024

Table S27. Gene #15: 'Amp Peak 15(9p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 15(9P13.3) CNV	18	8	16	19	23	11
AMP PEAK 15(9P13.3) WILD-TYPE	64	33	34	73	51	2

Figure S27. Get High-res Image Gene #15: 'Amp Peak 15(9p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 16(11p13)' versus 'CN_CNMF'

P value = 5.66e-05 (Chi-square test), Q value = 0.027

Table S28. Gene #16: 'Amp Peak 16(11p13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 16(11P13) CNV	17	7	6	9	22	8
AMP PEAK 16(11P13) WILD-TYPE	65	34	44	83	52	5

Figure S28. Get High-res Image Gene #16: 'Amp Peak 16(11p13)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 17(11q13.3)' versus 'CN_CNMF'

P value = 1.73e-27 (Chi-square test), Q value = 9.6e-25

Table S29. Gene #17: 'Amp Peak 17(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 17(11Q13.3) CNV	81	18	19	12	30	4
AMP PEAK 17(11Q13.3) WILD-TYPE	1	23	31	80	44	9

Figure S29. Get High-res Image Gene #17: 'Amp Peak 17(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.85e-10 (Chi-square test), Q value = 1.5e-07

Table S30. Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 18(12P13.33) CNV	29	26	30	14	14	5
AMP PEAK 18(12P13.33) WILD-TYPE	53	15	20	78	60	8

Figure S30. Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.28e-05 (Chi-square test), Q value = 0.0063

Table S31. Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 18(12P13.33) CNV	20	20	5	14	34	12	0	3
AMP PEAK 18(12P13.33) WILD-TYPE	23	27	34	31	24	39	4	16

Figure S31. Get High-res Image Gene #18: 'Amp Peak 18(12p13.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 19(12q15)' versus 'CN_CNMF'

P value = 0.000508 (Chi-square test), Q value = 0.23

Table S32. Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 19(12Q15) CNV	22	17	12	11	9	1
AMP PEAK 19(12Q15) WILD-TYPE	60	24	38	81	65	12

Figure S32. Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 20(13q22.1)' versus 'CN_CNMF'

P value = 0.000262 (Chi-square test), Q value = 0.12

Table S33. Gene #20: 'Amp Peak 20(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 20(13Q22.1) CNV	23	11	9	6	23	0
AMP PEAK 20(13Q22.1) WILD-TYPE	59	30	41	86	51	13

Figure S33. Get High-res Image Gene #20: 'Amp Peak 20(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 20(13q22.1)' versus 'METHLYATION_CNMF'

P value = 8.43e-05 (Chi-square test), Q value = 0.04

Table S34. Gene #20: 'Amp Peak 20(13q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 20(13Q22.1) CNV	7	23	7	10	12	3	0	5
AMP PEAK 20(13Q22.1) WILD-TYPE	36	24	32	35	46	48	4	14

Figure S34. Get High-res Image Gene #20: 'Amp Peak 20(13q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 21(15q26.3)' versus 'CN_CNMF'

P value = 0.000327 (Chi-square test), Q value = 0.15

Table S35. Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 21(15Q26.3) CNV	26	13	15	6	13	2
AMP PEAK 21(15Q26.3) WILD-TYPE	56	28	35	86	61	11

Figure S35. Get High-res Image Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 22(17q12)' versus 'CN_CNMF'

P value = 8.2e-08 (Chi-square test), Q value = 4.2e-05

Table S36. Gene #22: 'Amp Peak 22(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 22(17Q12) CNV	25	5	19	4	6	4
AMP PEAK 22(17Q12) WILD-TYPE	57	36	31	88	68	9

Figure S36. Get High-res Image Gene #22: 'Amp Peak 22(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 22(17q12)' versus 'METHLYATION_CNMF'

P value = 0.000112 (Chi-square test), Q value = 0.052

Table S37. Gene #22: 'Amp Peak 22(17q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
AMP PEAK 22(17Q12) CNV	10	8	2	4	22	4	0	2
AMP PEAK 22(17Q12) WILD-TYPE	33	39	37	41	36	47	4	17

Figure S37. Get High-res Image Gene #22: 'Amp Peak 22(17q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 23(18p11.31)' versus 'CN_CNMF'

P value = 7.58e-07 (Chi-square test), Q value = 0.00038

Table S38. Gene #23: 'Amp Peak 23(18p11.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 23(18P11.31) CNV	30	21	26	14	13	4
AMP PEAK 23(18P11.31) WILD-TYPE	52	20	24	78	61	9

Figure S38. Get High-res Image Gene #23: 'Amp Peak 23(18p11.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 25(20q11.22)' versus 'CN_CNMF'

P value = 4.86e-06 (Chi-square test), Q value = 0.0024

Table S39. Gene #25: 'Amp Peak 25(20q11.22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
AMP PEAK 25(20Q11.22) CNV	34	33	23	27	30	8
AMP PEAK 25(20Q11.22) WILD-TYPE	48	8	27	65	44	5

Figure S39. Get High-res Image Gene #25: 'Amp Peak 25(20q11.22)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.13)' versus 'CN_CNMF'

P value = 1.44e-11 (Chi-square test), Q value = 7.7e-09

Table S40. Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 1(1P36.13) CNV	17	4	29	7	10	2
DEL PEAK 1(1P36.13) WILD-TYPE	65	37	21	85	64	11

Figure S40. Get High-res Image Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.13)' versus 'METHLYATION_CNMF'

P value = 5.38e-15 (Chi-square test), Q value = 2.9e-12

Table S41. Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 1(1P36.13) CNV	6	4	8	5	36	1	2	2
DEL PEAK 1(1P36.13) WILD-TYPE	37	43	31	40	22	50	2	17

Figure S41. Get High-res Image Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 1(1p36.13)' versus 'MRNASEQ_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.015

Table S42. Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
DEL PEAK 1(1P36.13) CNV	39	17	7
DEL PEAK 1(1P36.13) WILD-TYPE	79	74	83

Figure S42. Get High-res Image Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.13)' versus 'MIRSEQ_CNMF'

P value = 0.000136 (Fisher's exact test), Q value = 0.063

Table S43. Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	138	100
DEL PEAK 1(1P36.13) CNV	16	42	10
DEL PEAK 1(1P36.13) WILD-TYPE	97	96	90

Figure S43. Get High-res Image Gene #26: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 2(1p13.2)' versus 'CN_CNMF'

P value = 3.1e-10 (Chi-square test), Q value = 1.6e-07

Table S44. Gene #27: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 2(1P13.2) CNV	20	14	29	5	13	4
DEL PEAK 2(1P13.2) WILD-TYPE	62	27	21	87	61	9

Figure S44. Get High-res Image Gene #27: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 2(1p13.2)' versus 'METHLYATION_CNMF'

P value = 8.62e-10 (Chi-square test), Q value = 4.6e-07

Table S45. Gene #27: 'Del Peak 2(1p13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 2(1P13.2) CNV	10	9	6	4	35	5	2	4
DEL PEAK 2(1P13.2) WILD-TYPE	33	38	33	41	23	46	2	15

Figure S45. Get High-res Image Gene #27: 'Del Peak 2(1p13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 2(1p13.2)' versus 'MIRSEQ_CNMF'

P value = 4.41e-05 (Fisher's exact test), Q value = 0.021

Table S46. Gene #27: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	138	100
DEL PEAK 2(1P13.2) CNV	16	51	18
DEL PEAK 2(1P13.2) WILD-TYPE	97	87	82

Figure S46. Get High-res Image Gene #27: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 4(2q21.2)' versus 'MIRSEQ_CNMF'

P value = 0.000377 (Fisher's exact test), Q value = 0.17

Table S47. Gene #29: 'Del Peak 4(2q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	138	100
DEL PEAK 4(2Q21.2) CNV	26	15	5
DEL PEAK 4(2Q21.2) WILD-TYPE	87	123	95

Figure S47. Get High-res Image Gene #29: 'Del Peak 4(2q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 6(2q36.2)' versus 'CN_CNMF'

P value = 5.4e-08 (Chi-square test), Q value = 2.8e-05

Table S48. Gene #31: 'Del Peak 6(2q36.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 6(2Q36.2) CNV	24	9	32	12	22	5
DEL PEAK 6(2Q36.2) WILD-TYPE	58	32	18	80	52	8

Figure S48. Get High-res Image Gene #31: 'Del Peak 6(2q36.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(2q36.2)' versus 'METHLYATION_CNMF'

P value = 5.69e-06 (Chi-square test), Q value = 0.0028

Table S49. Gene #31: 'Del Peak 6(2q36.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 6(2Q36.2) CNV	14	11	16	15	29	2	3	3
DEL PEAK 6(2Q36.2) WILD-TYPE	29	36	23	30	29	49	1	16

Figure S49. Get High-res Image Gene #31: 'Del Peak 6(2q36.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(3p25.3)' versus 'CN_CNMF'

P value = 7.67e-25 (Chi-square test), Q value = 4.3e-22

Table S50. Gene #32: 'Del Peak 7(3p25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 7(3P25.3) CNV	73	36	44	23	61	10
DEL PEAK 7(3P25.3) WILD-TYPE	9	5	6	69	13	3

Figure S50. Get High-res Image Gene #32: 'Del Peak 7(3p25.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 7(3p25.3)' versus 'METHLYATION_CNMF'

P value = 2.92e-10 (Chi-square test), Q value = 1.6e-07

Table S51. Gene #32: 'Del Peak 7(3p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 7(3P25.3) CNV	36	42	27	14	50	29	4	14
DEL PEAK 7(3P25.3) WILD-TYPE	7	5	12	31	8	22	0	5

Figure S51. Get High-res Image Gene #32: 'Del Peak 7(3p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 8(3p14.2)' versus 'CN_CNMF'

P value = 2.49e-29 (Chi-square test), Q value = 1.4e-26

Table S52. Gene #33: 'Del Peak 8(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 8(3P14.2) CNV	77	38	47	26	64	11
DEL PEAK 8(3P14.2) WILD-TYPE	5	3	3	66	10	2

Figure S52. Get High-res Image Gene #33: 'Del Peak 8(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 8(3p14.2)' versus 'METHLYATION_CNMF'

P value = 8.81e-08 (Chi-square test), Q value = 4.5e-05

Table S53. Gene #33: 'Del Peak 8(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 8(3P14.2) CNV	41	41	27	22	52	30	4	14
DEL PEAK 8(3P14.2) WILD-TYPE	2	6	12	23	6	21	0	5

Figure S53. Get High-res Image Gene #33: 'Del Peak 8(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 9(3p14.2)' versus 'CN_CNMF'

P value = 2.49e-29 (Chi-square test), Q value = 1.4e-26

Table S54. Gene #34: 'Del Peak 9(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 9(3P14.2) CNV	77	38	47	26	64	11
DEL PEAK 9(3P14.2) WILD-TYPE	5	3	3	66	10	2

Figure S54. Get High-res Image Gene #34: 'Del Peak 9(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 9(3p14.2)' versus 'METHLYATION_CNMF'

P value = 5.71e-07 (Chi-square test), Q value = 0.00029

Table S55. Gene #34: 'Del Peak 9(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 9(3P14.2) CNV	41	41	27	23	51	30	4	14
DEL PEAK 9(3P14.2) WILD-TYPE	2	6	12	22	7	21	0	5

Figure S55. Get High-res Image Gene #34: 'Del Peak 9(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 10(3p12.2)' versus 'CN_CNMF'

P value = 6.77e-29 (Chi-square test), Q value = 3.8e-26

Table S56. Gene #35: 'Del Peak 10(3p12.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 10(3P12.2) CNV	75	36	47	21	59	11
DEL PEAK 10(3P12.2) WILD-TYPE	7	5	3	71	15	2

Figure S56. Get High-res Image Gene #35: 'Del Peak 10(3p12.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 10(3p12.2)' versus 'METHLYATION_CNMF'

P value = 4.04e-09 (Chi-square test), Q value = 2.1e-06

Table S57. Gene #35: 'Del Peak 10(3p12.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 10(3P12.2) CNV	38	38	27	18	53	26	4	13
DEL PEAK 10(3P12.2) WILD-TYPE	5	9	12	27	5	25	0	6

Figure S57. Get High-res Image Gene #35: 'Del Peak 10(3p12.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 11(4p15.2)' versus 'CN_CNMF'

P value = 3.05e-12 (Chi-square test), Q value = 1.7e-09

Table S58. Gene #36: 'Del Peak 11(4p15.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 11(4P15.2) CNV	48	13	39	15	31	4
DEL PEAK 11(4P15.2) WILD-TYPE	34	28	11	77	43	9

Figure S58. Get High-res Image Gene #36: 'Del Peak 11(4p15.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(4p15.2)' versus 'METHLYATION_CNMF'

P value = 5.98e-07 (Chi-square test), Q value = 3e-04

Table S59. Gene #36: 'Del Peak 11(4p15.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 11(4P15.2) CNV	20	15	17	13	44	12	3	7
DEL PEAK 11(4P15.2) WILD-TYPE	23	32	22	32	14	39	1	12

Figure S59. Get High-res Image Gene #36: 'Del Peak 11(4p15.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 12(4q22.1)' versus 'CN_CNMF'

P value = 8.67e-09 (Chi-square test), Q value = 4.5e-06

Table S60. Gene #37: 'Del Peak 12(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 12(4Q22.1) CNV	30	19	32	10	22	4
DEL PEAK 12(4Q22.1) WILD-TYPE	52	22	18	82	52	9

Figure S60. Get High-res Image Gene #37: 'Del Peak 12(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(4q22.1)' versus 'METHLYATION_CNMF'

P value = 6.5e-07 (Chi-square test), Q value = 0.00033

Table S61. Gene #37: 'Del Peak 12(4q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 12(4Q22.1) CNV	17	16	11	7	36	8	1	2
DEL PEAK 12(4Q22.1) WILD-TYPE	26	31	28	38	22	43	3	17

Figure S61. Get High-res Image Gene #37: 'Del Peak 12(4q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 13(4q35.2)' versus 'CN_CNMF'

P value = 7.51e-09 (Chi-square test), Q value = 3.9e-06

Table S62. Gene #38: 'Del Peak 13(4q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 13(4Q35.2) CNV	29	27	31	15	37	6
DEL PEAK 13(4Q35.2) WILD-TYPE	53	14	19	77	37	7

Figure S62. Get High-res Image Gene #38: 'Del Peak 13(4q35.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 13(4q35.2)' versus 'METHLYATION_CNMF'

P value = 2.97e-05 (Chi-square test), Q value = 0.014

Table S63. Gene #38: 'Del Peak 13(4q35.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 13(4Q35.2) CNV	17	25	19	9	36	12	0	6
DEL PEAK 13(4Q35.2) WILD-TYPE	26	22	20	36	22	39	4	13

Figure S63. Get High-res Image Gene #38: 'Del Peak 13(4q35.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 14(5q11.2)' versus 'CN_CNMF'

P value = 5.27e-17 (Chi-square test), Q value = 2.9e-14

Table S64. Gene #39: 'Del Peak 14(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 14(5Q11.2) CNV	40	30	37	8	23	4
DEL PEAK 14(5Q11.2) WILD-TYPE	42	11	13	84	51	9

Figure S64. Get High-res Image Gene #39: 'Del Peak 14(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(5q11.2)' versus 'METHLYATION_CNMF'

P value = 1.35e-12 (Chi-square test), Q value = 7.3e-10

Table S65. Gene #39: 'Del Peak 14(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 14(5Q11.2) CNV	30	27	8	6	41	11	1	6
DEL PEAK 14(5Q11.2) WILD-TYPE	13	20	31	39	17	40	3	13

Figure S65. Get High-res Image Gene #39: 'Del Peak 14(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 7.2e-18 (Chi-square test), Q value = 4e-15

Table S66. Gene #40: 'Del Peak 15(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 15(5Q35.3) CNV	32	29	40	10	19	4
DEL PEAK 15(5Q35.3) WILD-TYPE	50	12	10	82	55	9

Figure S66. Get High-res Image Gene #40: 'Del Peak 15(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 4.25e-14 (Chi-square test), Q value = 2.3e-11

Table S67. Gene #40: 'Del Peak 15(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 15(5Q35.3) CNV	33	24	5	8	37	8	0	6
DEL PEAK 15(5Q35.3) WILD-TYPE	10	23	34	37	21	43	4	13

Figure S67. Get High-res Image Gene #40: 'Del Peak 15(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.000477 (Fisher's exact test), Q value = 0.22

Table S68. Gene #40: 'Del Peak 15(5q35.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 15(5Q35.3) CNV	39	20	61
DEL PEAK 15(5Q35.3) WILD-TYPE	56	64	59

Figure S68. Get High-res Image Gene #40: 'Del Peak 15(5q35.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(6p25.3)' versus 'METHLYATION_CNMF'

P value = 0.00033 (Chi-square test), Q value = 0.15

Table S69. Gene #41: 'Del Peak 16(6p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 16(6P25.3) CNV	7	9	5	6	26	6	1	3
DEL PEAK 16(6P25.3) WILD-TYPE	36	38	34	39	32	45	3	16

Figure S69. Get High-res Image Gene #41: 'Del Peak 16(6p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 18(7q36.1)' versus 'CN_CNMF'

P value = 0.000182 (Chi-square test), Q value = 0.084

Table S70. Gene #43: 'Del Peak 18(7q36.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 18(7Q36.1) CNV	33	13	6	12	17	5
DEL PEAK 18(7Q36.1) WILD-TYPE	49	28	44	80	57	8

Figure S70. Get High-res Image Gene #43: 'Del Peak 18(7q36.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 19(8p23.2)' versus 'CN_CNMF'

P value = 2.17e-15 (Chi-square test), Q value = 1.2e-12

Table S71. Gene #44: 'Del Peak 19(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 19(8P23.2) CNV	67	28	25	20	54	7
DEL PEAK 19(8P23.2) WILD-TYPE	15	13	25	72	20	6

Figure S71. Get High-res Image Gene #44: 'Del Peak 19(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 19(8p23.2)' versus 'METHLYATION_CNMF'

P value = 3.84e-05 (Chi-square test), Q value = 0.019

Table S72. Gene #44: 'Del Peak 19(8p23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 19(8P23.2) CNV	21	34	30	11	36	28	2	11
DEL PEAK 19(8P23.2) WILD-TYPE	22	13	9	34	22	23	2	8

Figure S72. Get High-res Image Gene #44: 'Del Peak 19(8p23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 20(9p23)' versus 'CN_CNMF'

P value = 1.16e-16 (Chi-square test), Q value = 6.4e-14

Table S73. Gene #45: 'Del Peak 20(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 20(9P23) CNV	50	27	30	9	45	0
DEL PEAK 20(9P23) WILD-TYPE	32	14	20	83	29	13

Figure S73. Get High-res Image Gene #45: 'Del Peak 20(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(9p23)' versus 'METHLYATION_CNMF'

P value = 5.42e-09 (Chi-square test), Q value = 2.8e-06

Table S74. Gene #45: 'Del Peak 20(9p23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 20(9P23) CNV	30	25	20	5	38	13	3	8
DEL PEAK 20(9P23) WILD-TYPE	13	22	19	40	20	38	1	11

Figure S74. Get High-res Image Gene #45: 'Del Peak 20(9p23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 21(9p21.3)' versus 'CN_CNMF'

P value = 2.71e-13 (Chi-square test), Q value = 1.5e-10

Table S75. Gene #46: 'Del Peak 21(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 21(9P21.3) CNV	65	25	36	24	51	3
DEL PEAK 21(9P21.3) WILD-TYPE	17	16	14	68	23	10

Figure S75. Get High-res Image Gene #46: 'Del Peak 21(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 21(9p21.3)' versus 'METHLYATION_CNMF'

P value = 2.83e-09 (Chi-square test), Q value = 1.5e-06

Table S76. Gene #46: 'Del Peak 21(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 21(9P21.3) CNV	35	30	26	7	40	23	3	14
DEL PEAK 21(9P21.3) WILD-TYPE	8	17	13	38	18	28	1	5

Figure S76. Get High-res Image Gene #46: 'Del Peak 21(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 22(9q21.11)' versus 'CN_CNMF'

P value = 2.86e-08 (Chi-square test), Q value = 1.5e-05

Table S77. Gene #47: 'Del Peak 22(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 22(9Q21.11) CNV	30	15	7	4	8	1
DEL PEAK 22(9Q21.11) WILD-TYPE	52	26	43	88	66	12

Figure S77. Get High-res Image Gene #47: 'Del Peak 22(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000333 (Chi-square test), Q value = 0.15

Table S78. Gene #48: 'Del Peak 23(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 23(9Q34.3) CNV	21	12	7	4	12	0
DEL PEAK 23(9Q34.3) WILD-TYPE	61	29	43	88	62	13

Figure S78. Get High-res Image Gene #48: 'Del Peak 23(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 24(10p15.3)' versus 'CN_CNMF'

P value = 5.46e-06 (Chi-square test), Q value = 0.0027

Table S79. Gene #49: 'Del Peak 24(10p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 24(10P15.3) CNV	34	16	20	8	30	6
DEL PEAK 24(10P15.3) WILD-TYPE	48	25	30	84	44	7

Figure S79. Get High-res Image Gene #49: 'Del Peak 24(10p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 25(10p11.21)' versus 'CN_CNMF'

P value = 9.79e-06 (Chi-square test), Q value = 0.0048

Table S80. Gene #50: 'Del Peak 25(10p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 25(10P11.21) CNV	32	17	19	7	27	5
DEL PEAK 25(10P11.21) WILD-TYPE	50	24	31	85	47	8

Figure S80. Get High-res Image Gene #50: 'Del Peak 25(10p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 26(10q23.31)' versus 'CN_CNMF'

P value = 1.55e-06 (Chi-square test), Q value = 0.00077

Table S81. Gene #51: 'Del Peak 26(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 26(10Q23.31) CNV	22	10	28	11	16	2
DEL PEAK 26(10Q23.31) WILD-TYPE	60	31	22	81	58	11

Figure S81. Get High-res Image Gene #51: 'Del Peak 26(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 27(11p15.4)' versus 'CN_CNMF'

P value = 1.6e-08 (Chi-square test), Q value = 8.3e-06

Table S82. Gene #52: 'Del Peak 27(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 27(11P15.4) CNV	43	15	24	16	10	2
DEL PEAK 27(11P15.4) WILD-TYPE	39	26	26	76	64	11

Figure S82. Get High-res Image Gene #52: 'Del Peak 27(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 27(11p15.4)' versus 'METHLYATION_CNMF'

P value = 0.000523 (Chi-square test), Q value = 0.23

Table S83. Gene #52: 'Del Peak 27(11p15.4)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 27(11P15.4) CNV	17	14	9	13	32	8	1	3
DEL PEAK 27(11P15.4) WILD-TYPE	26	33	30	32	26	43	3	16

Figure S83. Get High-res Image Gene #52: 'Del Peak 27(11p15.4)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 27(11p15.4)' versus 'MIRSEQ_CNMF'

P value = 0.000501 (Fisher's exact test), Q value = 0.23

Table S84. Gene #52: 'Del Peak 27(11p15.4)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	138	100
DEL PEAK 27(11P15.4) CNV	27	60	23
DEL PEAK 27(11P15.4) WILD-TYPE	86	78	77

Figure S84. Get High-res Image Gene #52: 'Del Peak 27(11p15.4)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 28(11q14.1)' versus 'CN_CNMF'

P value = 4.77e-25 (Chi-square test), Q value = 2.7e-22

Table S85. Gene #53: 'Del Peak 28(11q14.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 28(11Q14.1) CNV	65	6	11	21	3	6
DEL PEAK 28(11Q14.1) WILD-TYPE	17	35	39	71	71	7

Figure S85. Get High-res Image Gene #53: 'Del Peak 28(11q14.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(11q23.1)' versus 'CN_CNMF'

P value = 7.7e-18 (Chi-square test), Q value = 4.3e-15

Table S86. Gene #54: 'Del Peak 29(11q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 29(11Q23.1) CNV	74	13	23	36	15	8
DEL PEAK 29(11Q23.1) WILD-TYPE	8	28	27	56	59	5

Figure S86. Get High-res Image Gene #54: 'Del Peak 29(11q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(11q23.1)' versus 'METHLYATION_CNMF'

P value = 8.45e-07 (Chi-square test), Q value = 0.00042

Table S87. Gene #54: 'Del Peak 29(11q23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 29(11Q23.1) CNV	18	21	16	40	31	16	1	6
DEL PEAK 29(11Q23.1) WILD-TYPE	25	26	23	5	27	35	3	13

Figure S87. Get High-res Image Gene #54: 'Del Peak 29(11q23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 29(11q23.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.11

Table S88. Gene #54: 'Del Peak 29(11q23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 29(11Q23.1) CNV	37	33	76
DEL PEAK 29(11Q23.1) WILD-TYPE	58	51	44

Figure S88. Get High-res Image Gene #54: 'Del Peak 29(11q23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(13q12.11)' versus 'CN_CNMF'

P value = 2.63e-11 (Chi-square test), Q value = 1.4e-08

Table S89. Gene #56: 'Del Peak 31(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 31(13Q12.11) CNV	44	26	39	17	27	6
DEL PEAK 31(13Q12.11) WILD-TYPE	38	15	11	75	47	7

Figure S89. Get High-res Image Gene #56: 'Del Peak 31(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 31(13q12.11)' versus 'METHLYATION_CNMF'

P value = 7.28e-07 (Chi-square test), Q value = 0.00037

Table S90. Gene #56: 'Del Peak 31(13q12.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 31(13Q12.11) CNV	31	22	15	13	39	12	1	6
DEL PEAK 31(13Q12.11) WILD-TYPE	12	25	24	32	19	39	3	13

Figure S90. Get High-res Image Gene #56: 'Del Peak 31(13q12.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 32(13q14.2)' versus 'CN_CNMF'

P value = 2.86e-06 (Chi-square test), Q value = 0.0014

Table S91. Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 32(13Q14.2) CNV	38	24	35	27	21	4
DEL PEAK 32(13Q14.2) WILD-TYPE	44	17	15	65	53	9

Figure S91. Get High-res Image Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 32(13q14.2)' versus 'METHLYATION_CNMF'

P value = 5.88e-07 (Chi-square test), Q value = 3e-04

Table S92. Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 32(13Q14.2) CNV	32	17	13	23	31	10	0	4
DEL PEAK 32(13Q14.2) WILD-TYPE	11	30	26	22	27	41	4	15

Figure S92. Get High-res Image Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 32(13q14.2)' versus 'MRNASEQ_CNMF'

P value = 5.7e-05 (Fisher's exact test), Q value = 0.027

Table S93. Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
DEL PEAK 32(13Q14.2) CNV	66	39	23
DEL PEAK 32(13Q14.2) WILD-TYPE	52	52	67

Figure S93. Get High-res Image Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 32(13q14.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.46e-05 (Fisher's exact test), Q value = 0.031

Table S94. Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 32(13Q14.2) CNV	38	22	68
DEL PEAK 32(13Q14.2) WILD-TYPE	57	62	52

Figure S94. Get High-res Image Gene #57: 'Del Peak 32(13q14.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(14q32.32)' versus 'METHLYATION_CNMF'

P value = 1.42e-07 (Chi-square test), Q value = 7.2e-05

Table S95. Gene #59: 'Del Peak 34(14q32.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 34(14Q32.32) CNV	5	3	4	20	13	1	0	1
DEL PEAK 34(14Q32.32) WILD-TYPE	38	44	35	25	45	50	4	18

Figure S95. Get High-res Image Gene #59: 'Del Peak 34(14q32.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 34(14q32.32)' versus 'MRNASEQ_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.11

Table S96. Gene #59: 'Del Peak 34(14q32.32)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
DEL PEAK 34(14Q32.32) CNV	30	11	5
DEL PEAK 34(14Q32.32) WILD-TYPE	88	80	85

Figure S96. Get High-res Image Gene #59: 'Del Peak 34(14q32.32)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 34(14q32.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.046

Table S97. Gene #59: 'Del Peak 34(14q32.32)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 34(14Q32.32) CNV	11	4	31
DEL PEAK 34(14Q32.32) WILD-TYPE	84	80	89

Figure S97. Get High-res Image Gene #59: 'Del Peak 34(14q32.32)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(16q12.1)' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Chi-square test), Q value = 5.7e-05

Table S98. Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 36(16Q12.1) CNV	8	1	5	21	13	2	1	1
DEL PEAK 36(16Q12.1) WILD-TYPE	35	46	34	24	45	49	3	18

Figure S98. Get High-res Image Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 36(16q12.1)' versus 'MRNASEQ_CNMF'

P value = 7.1e-08 (Fisher's exact test), Q value = 3.6e-05

Table S99. Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	118	91	90
DEL PEAK 36(16Q12.1) CNV	38	9	4
DEL PEAK 36(16Q12.1) WILD-TYPE	80	82	86

Figure S99. Get High-res Image Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 36(16q12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.91e-07 (Fisher's exact test), Q value = 2e-04

Table S100. Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 36(16Q12.1) CNV	7	6	38
DEL PEAK 36(16Q12.1) WILD-TYPE	88	78	82

Figure S100. Get High-res Image Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 36(16q12.1)' versus 'MIRSEQ_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.049

Table S101. Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	138	100
DEL PEAK 36(16Q12.1) CNV	15	39	8
DEL PEAK 36(16Q12.1) WILD-TYPE	98	99	92

Figure S101. Get High-res Image Gene #61: 'Del Peak 36(16q12.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 37(16q23.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.88e-05 (Fisher's exact test), Q value = 0.042

Table S102. Gene #62: 'Del Peak 37(16q23.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	84	120
DEL PEAK 37(16Q23.3) CNV	11	9	38
DEL PEAK 37(16Q23.3) WILD-TYPE	84	75	82

Figure S102. Get High-res Image Gene #62: 'Del Peak 37(16q23.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(18q21.2)' versus 'CN_CNMF'

P value = 7.27e-17 (Chi-square test), Q value = 4e-14

Table S103. Gene #64: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 39(18Q21.2) CNV	51	28	27	11	56	9
DEL PEAK 39(18Q21.2) WILD-TYPE	31	13	23	81	18	4

Figure S103. Get High-res Image Gene #64: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 39(18q21.2)' versus 'METHLYATION_CNMF'

P value = 1.69e-09 (Chi-square test), Q value = 8.9e-07

Table S104. Gene #64: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 39(18Q21.2) CNV	30	35	22	4	34	24	4	8
DEL PEAK 39(18Q21.2) WILD-TYPE	13	12	17	41	24	27	0	11

Figure S104. Get High-res Image Gene #64: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 40(18q23)' versus 'CN_CNMF'

P value = 8.57e-20 (Chi-square test), Q value = 4.7e-17

Table S105. Gene #65: 'Del Peak 40(18q23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 40(18Q23) CNV	56	31	31	12	59	9
DEL PEAK 40(18Q23) WILD-TYPE	26	10	19	80	15	4

Figure S105. Get High-res Image Gene #65: 'Del Peak 40(18q23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 40(18q23)' versus 'METHLYATION_CNMF'

P value = 1.38e-11 (Chi-square test), Q value = 7.4e-09

Table S106. Gene #65: 'Del Peak 40(18q23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 40(18Q23) CNV	31	40	23	5	39	23	3	8
DEL PEAK 40(18Q23) WILD-TYPE	12	7	16	40	19	28	1	11

Figure S106. Get High-res Image Gene #65: 'Del Peak 40(18q23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 41(19p13.3)' versus 'CN_CNMF'

P value = 3.57e-06 (Chi-square test), Q value = 0.0018

Table S107. Gene #66: 'Del Peak 41(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 41(19P13.3) CNV	38	16	17	10	28	8
DEL PEAK 41(19P13.3) WILD-TYPE	44	25	33	82	46	5

Figure S107. Get High-res Image Gene #66: 'Del Peak 41(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 42(19q13.43)' versus 'CN_CNMF'

P value = 1.03e-05 (Chi-square test), Q value = 0.0051

Table S108. Gene #67: 'Del Peak 42(19q13.43)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 42(19Q13.43) CNV	18	7	20	3	16	4
DEL PEAK 42(19Q13.43) WILD-TYPE	64	34	30	89	58	9

Figure S108. Get High-res Image Gene #67: 'Del Peak 42(19q13.43)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 42(19q13.43)' versus 'METHLYATION_CNMF'

P value = 6.93e-05 (Chi-square test), Q value = 0.033

Table S109. Gene #67: 'Del Peak 42(19q13.43)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 42(19Q13.43) CNV	7	14	9	3	22	3	0	1
DEL PEAK 42(19Q13.43) WILD-TYPE	36	33	30	42	36	48	4	18

Figure S109. Get High-res Image Gene #67: 'Del Peak 42(19q13.43)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 43(Xp21.3)' versus 'CN_CNMF'

P value = 4.3e-05 (Chi-square test), Q value = 0.021

Table S110. Gene #68: 'Del Peak 43(Xp21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 43(XP21.3) CNV	38	18	23	14	19	4
DEL PEAK 43(XP21.3) WILD-TYPE	44	23	27	78	55	9

Figure S110. Get High-res Image Gene #68: 'Del Peak 43(Xp21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 44(Xp11.3)' versus 'CN_CNMF'

P value = 4.65e-06 (Chi-square test), Q value = 0.0023

Table S111. Gene #69: 'Del Peak 44(Xp11.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	82	41	50	92	74	13
DEL PEAK 44(XP11.3) CNV	38	17	24	12	18	5
DEL PEAK 44(XP11.3) WILD-TYPE	44	24	26	80	56	8

Figure S111. Get High-res Image Gene #69: 'Del Peak 44(Xp11.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 44(Xp11.3)' versus 'METHLYATION_CNMF'

P value = 5.8e-05 (Chi-square test), Q value = 0.028

Table S112. Gene #69: 'Del Peak 44(Xp11.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	43	47	39	45	58	51	4	19
DEL PEAK 44(XP11.3) CNV	15	18	13	7	34	8	2	6
DEL PEAK 44(XP11.3) WILD-TYPE	28	29	26	38	24	43	2	13

Figure S112. Get High-res Image Gene #69: 'Del Peak 44(Xp11.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 45(Xq21.33)' versus 'MIRSEQ_CNMF'

P value = 6.6e-05 (Fisher's exact test), Q value = 0.031

Table S113. Gene #70: 'Del Peak 45(Xq21.33)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	113	138	100
DEL PEAK 45(XQ21.33) CNV	11	37	8
DEL PEAK 45(XQ21.33) WILD-TYPE	102	101	92

Figure S113. Get High-res Image Gene #70: 'Del Peak 45(Xq21.33)' versus Molecular Subtype #7: 'MIRSEQ_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 = HNSC-TP.transferedmergedcluster.txt
Number of patients = 352
Number of copy number variation regions = 70
Number of molecular subtypes = 8
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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