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 75 peak regions and 6 molecular subtypes across 306 patients, 190 significant findings detected with Q value < 0.25.

Amp Peak 1(1p36.22) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(1q21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 3(1q42.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 4(3q27.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(5p13.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 6(6p21.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 7(6q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 8(6q21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 9(7p22.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 10(7p11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(7q21.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 12(8p23.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(8q24.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 15(9q34.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 16(10q22.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 17(10q26.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 18(11p13) cnvs correlated to 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 19(11q13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 20(12p12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 21(12q15) cnvs correlated to 'METHLYATION_CNMF'.
Amp Peak 22(13q12.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 23(13q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 24(15q26.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 25(17q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 26(18q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 27(19q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 28(20q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 29(Xq27.3) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 5(2q37.2) cnvs correlated to 'CN_CNMF'.
Del Peak 6(3p26.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 7(3p14.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 8(3q26.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 9(4p16.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 10(4q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 11(4q34.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 13(5q23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 14(6p25.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 15(6q26) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 16(7q31.1) cnvs correlated to 'CN_CNMF'.
Del Peak 17(7q36.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 18(8p23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 19(9p23) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 20(9p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 21(9q21.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 22(10p15.1) cnvs correlated to 'CN_CNMF'.
Del Peak 23(10q22.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 24(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 25(11p15.4) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 26(11q23.2) cnvs correlated to 'CN_CNMF'.
Del Peak 27(12p13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 28(13q12.11) cnvs correlated to 'CN_CNMF'.
Del Peak 29(14q21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 30(14q32.33) cnvs correlated to 'CN_CNMF'.
Del Peak 31(15q15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 32(16p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 33(16q23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 34(17p12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 35(17q24.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 36(18q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 37(19p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 38(19q13.11) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 39(20p12.1) cnvs correlated to 'CN_CNMF'.
Del Peak 40(20p12.1) cnvs correlated to 'CN_CNMF'.
Del Peak 41(21q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 42(21q22.13) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 43(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 44(Xp22.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 45(Xp21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 46(Xq21.33) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 75 regions and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 190 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 2(1q21 3)	0 (0%)	198	4.55e-20 (2.02e-17)	5.04e-11 (2.08e-08)	3.28e-08 (1.26e-05)	3.6e-05 (0.0114)	1.31e-05 (0.0044)	1.78e-05 (0.00588)
Amp Peak 3(1q42 3)	0 (0%)	201	5.52e-14 (2.38e-11)	1.11e-07 (4.21e-05)	4.49e-07 (0.000166)	0.000462 (0.13)	1.58e-06 (0.000569)	1.77e-06 (0.000637)
Amp Peak 27(19q12)	0 (0%)	216	1.67e-15 (7.32e-13)	4.66e-10 (1.88e-07)	8.37e-11 (3.43e-08)	4.59e-06 (0.00161)	0.000305 (0.088)	1.71e-10 (6.94e-08)
Del Peak 12(5q11 2)	0 (0%)	203	6.54e-28 (2.94e-25)	1.27e-13 (5.44e-11)	9.48e-07 (0.000343)	3.06e-07 (0.000114)	2.92e-07 (0.000109)	2.53e-09 (1.01e-06)
Del Peak 13(5q23 2)	0 (0%)	213	2.48e-23 (1.11e-20)	2.5e-12 (1.05e-09)	2.02e-07 (7.62e-05)	2.07e-06 (0.000738)	2.65e-07 (9.94e-05)	1.11e-08 (4.35e-06)
Del Peak 37(19p13 3)	0 (0%)	207	2.35e-27 (1.06e-24)	2.38e-16 (1.05e-13)	3.62e-11 (1.5e-08)	1.34e-12 (5.64e-10)	2.21e-07 (8.32e-05)	1.06e-19 (4.7e-17)
Del Peak 9(4p16 3)	0 (0%)	194	2.89e-10 (1.17e-07)	0.000377 (0.107)	0.000266 (0.078)	0.007 (1.00)	0.000848 (0.225)	3.07e-05 (0.00983)
Del Peak 31(15q15 1)	0 (0%)	227	6.44e-13 (2.74e-10)	5.71e-07 (0.00021)	1.79e-05 (0.00592)	7.38e-06 (0.00254)	0.00132 (0.33)	8.73e-07 (0.000317)
Del Peak 34(17p12)	0 (0%)	191	1.81e-23 (8.11e-21)	4.44e-11 (1.84e-08)	9.95e-06 (0.00338)	1.96e-05 (0.00644)	0.00284 (0.633)	6.36e-06 (0.00221)
Del Peak 43(22q13 31)	0 (0%)	205	9.68e-15 (4.22e-12)	0.000142 (0.0431)	0.000528 (0.146)	0.000471 (0.131)	0.00655 (1.00)	6.56e-06 (0.00227)
Amp Peak 6(6p21 1)	0 (0%)	226	3.1e-17 (1.37e-14)	5.99e-10 (2.41e-07)	0.000807 (0.216)	0.00341 (0.747)	0.00998 (1.00)	2.45e-05 (0.00799)
Amp Peak 7(6q12)	0 (0%)	246	2.98e-09 (1.18e-06)	1.69e-08 (6.53e-06)	0.000245 (0.0726)	0.0112 (1.00)	0.046 (1.00)	0.000263 (0.0776)
Amp Peak 24(15q26 1)	0 (0%)	237	1.03e-13 (4.43e-11)	0.00041 (0.116)	0.000136 (0.0416)	7.53e-06 (0.00258)	0.21 (1.00)	0.196 (1.00)
Amp Peak 28(20q13 2)	0 (0%)	105	5.63e-21 (2.51e-18)	2.06e-11 (8.57e-09)	6.87e-07 (0.000252)	0.00828 (1.00)	0.0141 (1.00)	8.89e-09 (3.5e-06)
Del Peak 11(4q34 3)	0 (0%)	179	1.07e-14 (4.66e-12)	7.57e-07 (0.000276)	0.000746 (0.202)	0.0177 (1.00)	0.0116 (1.00)	9.16e-06 (0.00312)
Del Peak 17(7q36 3)	0 (0%)	248	1.82e-14 (7.88e-12)	1.93e-05 (0.00636)	0.000791 (0.213)	0.00554 (1.00)	0.123 (1.00)	0.000113 (0.0349)
Del Peak 18(8p23 2)	0 (0%)	229	4.3e-14 (1.86e-11)	5.78e-06 (0.00201)	0.000543 (0.149)	0.00156 (0.381)	0.134 (1.00)	0.00016 (0.0483)
Del Peak 20(9p21 3)	0 (0%)	188	6.29e-16 (2.77e-13)	5.35e-11 (2.2e-08)	3e-06 (0.00106)	0.00205 (0.478)	0.0263 (1.00)	0.00026 (0.0769)
Del Peak 27(12p13 31)	0 (0%)	256	1.49e-10 (6.06e-08)	1.13e-05 (0.00382)	2.66e-05 (0.00862)	0.000281 (0.0817)	0.0679 (1.00)	0.0287 (1.00)
Del Peak 32(16p13 3)	0 (0%)	248	7.42e-11 (3.05e-08)	7.03e-05 (0.0219)	2.03e-05 (0.00665)	0.000382 (0.108)	0.00489 (1.00)	0.0185 (1.00)
Amp Peak 5(5p13 1)	0 (0%)	219	1.64e-14 (7.14e-12)	5.68e-07 (0.000209)	2.72e-05 (0.00879)	0.0175 (1.00)	0.0226 (1.00)	0.00407 (0.864)
Amp Peak 17(10q26 13)	0 (0%)	245	1.18e-05 (0.004)	0.000754 (0.204)	0.000929 (0.244)	0.0573 (1.00)	0.624 (1.00)	0.0183 (1.00)
Amp Peak 23(13q22 1)	0 (0%)	185	1.54e-08 (5.99e-06)	3.74e-05 (0.0118)	0.0133 (1.00)	0.13 (1.00)	0.532 (1.00)	2e-06 (0.000715)
Amp Peak 25(17q12)	0 (0%)	214	9.54e-13 (4.04e-10)	8.07e-06 (0.00276)	6.85e-06 (0.00236)	0.00179 (0.428)	0.0233 (1.00)	0.000996 (0.258)
Del Peak 6(3p26 1)	0 (0%)	222	2.64e-10 (1.07e-07)	0.0003 (0.0869)	0.107 (1.00)	0.166 (1.00)	0.239 (1.00)	0.000517 (0.143)
Del Peak 7(3p14 2)	0 (0%)	204	9.33e-13 (3.95e-10)	1.38e-06 (0.000498)	0.00367 (0.797)	0.00187 (0.441)	0.0981 (1.00)	3.65e-05 (0.0115)
Del Peak 8(3q26 31)	0 (0%)	272	4.23e-06 (0.00148)	8.44e-05 (0.0262)	0.000956 (0.25)	0.00675 (1.00)	0.0163 (1.00)	0.00183 (0.434)
Del Peak 10(4q22 1)	0 (0%)	171	6.72e-19 (2.98e-16)	1.23e-07 (4.66e-05)	0.0213 (1.00)	0.0319 (1.00)	0.00325 (0.716)	0.000102 (0.0314)
Del Peak 14(6p25 3)	0 (0%)	237	5.01e-07 (0.000185)	0.000932 (0.244)	0.0174 (1.00)	0.0023 (0.527)	0.0976 (1.00)	0.000915 (0.242)
Del Peak 19(9p23)	0 (0%)	186	2.66e-15 (1.17e-12)	2.88e-05 (0.00923)	0.00032 (0.0918)	0.0347 (1.00)	0.0801 (1.00)	0.00209 (0.482)
Del Peak 24(10q23 31)	0 (0%)	233	2.72e-12 (1.14e-09)	1.2e-05 (0.00404)	0.144 (1.00)	0.139 (1.00)	0.00287 (0.635)	2.51e-05 (0.00817)
Del Peak 35(17q24 3)	0 (0%)	251	1.32e-10 (5.38e-08)	0.000237 (0.0707)	0.000463 (0.13)	0.00182 (0.434)	0.0246 (1.00)	0.0144 (1.00)
Del Peak 38(19q13 11)	0 (0%)	263	2.69e-09 (1.07e-06)	6.16e-05 (0.0193)	0.0142 (1.00)	0.00155 (0.38)	0.0165 (1.00)	2.44e-06 (0.000866)
Del Peak 41(21q11 2)	0 (0%)	198	1.39e-10 (5.66e-08)	5.41e-05 (0.017)	0.00538 (1.00)	0.000341 (0.0976)	0.0197 (1.00)	0.00116 (0.29)
Amp Peak 8(6q21)	0 (0%)	250	4.38e-09 (1.73e-06)	2.74e-05 (0.00883)	0.0068 (1.00)	0.022 (1.00)	0.247 (1.00)	0.00427 (0.901)
Amp Peak 9(7p22 3)	0 (0%)	149	8.25e-14 (3.55e-11)	3.2e-05 (0.0102)	0.0217 (1.00)	0.118 (1.00)	0.083 (1.00)	0.0057 (1.00)
Amp Peak 13(8q24 21)	0 (0%)	101	2.63e-06 (0.000932)	0.000101 (0.0313)	0.155 (1.00)	0.211 (1.00)	0.273 (1.00)	0.00158 (0.384)
Amp Peak 16(10q22 2)	0 (0%)	250	9.41e-08 (3.6e-05)	0.0748 (1.00)	0.000796 (0.213)	0.00252 (0.57)	0.174 (1.00)	0.0283 (1.00)
Amp Peak 22(13q12 3)	0 (0%)	190	7.07e-10 (2.83e-07)	1.45e-05 (0.00485)	0.148 (1.00)	0.18 (1.00)	0.281 (1.00)	0.00227 (0.522)
Amp Peak 26(18q11 2)	0 (0%)	216	3.31e-06 (0.00117)	0.00023 (0.0687)	0.0413 (1.00)	0.0733 (1.00)	0.291 (1.00)	0.0974 (1.00)
Del Peak 1(1p36 11)	0 (0%)	223	4.2e-15 (1.84e-12)	0.000366 (0.104)	0.00149 (0.367)	0.00241 (0.549)	0.00195 (0.458)	0.00576 (1.00)
Del Peak 15(6q26)	0 (0%)	244	0.000128 (0.039)	0.0591 (1.00)	1.51e-05 (0.00502)	0.00895 (1.00)	0.389 (1.00)	0.0772 (1.00)
Del Peak 21(9q21 11)	0 (0%)	233	2.97e-08 (1.15e-05)	0.000163 (0.049)	0.084 (1.00)	0.243 (1.00)	0.0427 (1.00)	0.00367 (0.797)
Del Peak 23(10q22 3)	0 (0%)	257	2.43e-09 (9.68e-07)	0.00113 (0.285)	0.0829 (1.00)	0.0669 (1.00)	0.0525 (1.00)	0.000641 (0.176)
Del Peak 25(11p15 4)	0 (0%)	247	2.96e-08 (1.14e-05)	1.55e-05 (0.00515)	0.0772 (1.00)	0.0262 (1.00)	0.707 (1.00)	0.0303 (1.00)
Del Peak 36(18q21 2)	0 (0%)	173	4.49e-13 (1.91e-10)	0.000846 (0.225)	0.0141 (1.00)	0.152 (1.00)	0.134 (1.00)	0.00632 (1.00)
Del Peak 42(21q22 13)	0 (0%)	191	1.56e-09 (6.23e-07)	0.000509 (0.142)	0.00507 (1.00)	0.00104 (0.268)	0.34 (1.00)	0.0017 (0.409)
Del Peak 44(Xp22 2)	0 (0%)	245	1.44e-09 (5.77e-07)	0.000642 (0.176)	0.00396 (0.848)	0.0128 (1.00)	0.173 (1.00)	0.0306 (1.00)
Amp Peak 1(1p36 22)	0 (0%)	270	1.19e-07 (4.53e-05)	0.00396 (0.848)	0.0211 (1.00)	0.00567 (1.00)	0.718 (1.00)	0.0894 (1.00)
Amp Peak 4(3q27 1)	0 (0%)	203	1.21e-05 (0.00405)	0.00742 (1.00)	0.215 (1.00)	0.865 (1.00)	0.607 (1.00)	0.0457 (1.00)
Amp Peak 10(7p11 2)	0 (0%)	163	4.23e-12 (1.77e-09)	0.0145 (1.00)	0.0807 (1.00)	0.473 (1.00)	0.267 (1.00)	0.0274 (1.00)
Amp Peak 11(7q21 2)	0 (0%)	169	2.36e-11 (9.81e-09)	0.0249 (1.00)	0.384 (1.00)	0.267 (1.00)	0.466 (1.00)	0.308 (1.00)
Amp Peak 12(8p23 1)	0 (0%)	185	3.39e-13 (1.45e-10)	0.00174 (0.417)	0.456 (1.00)	0.0124 (1.00)	0.753 (1.00)	0.196 (1.00)
Amp Peak 15(9q34 3)	0 (0%)	232	2.86e-07 (0.000107)	0.00775 (1.00)	0.00975 (1.00)	0.014 (1.00)	0.139 (1.00)	0.214 (1.00)
Amp Peak 18(11p13)	0 (0%)	252	0.00658 (1.00)	0.109 (1.00)	0.00516 (1.00)	0.00537 (1.00)	0.187 (1.00)	0.000655 (0.178)
Amp Peak 19(11q13 3)	0 (0%)	238	3.27e-05 (0.0104)	0.188 (1.00)	0.21 (1.00)	0.663 (1.00)	0.00198 (0.464)	0.0216 (1.00)
Amp Peak 20(12p12 1)	0 (0%)	220	0.000304 (0.0877)	0.0184 (1.00)	0.343 (1.00)	0.976 (1.00)	0.759 (1.00)	0.397 (1.00)
Amp Peak 21(12q15)	0 (0%)	229	0.00803 (1.00)	0.000278 (0.0812)	0.171 (1.00)	0.429 (1.00)	0.596 (1.00)	0.282 (1.00)
Amp Peak 29(Xq27 3)	0 (0%)	246	0.000155 (0.047)	0.223 (1.00)	0.0519 (1.00)	0.346 (1.00)	0.259 (1.00)	0.803 (1.00)
Del Peak 2(1p13 2)	0 (0%)	247	5.4e-12 (2.26e-09)	0.00106 (0.274)	0.0127 (1.00)	0.022 (1.00)	0.0255 (1.00)	0.0159 (1.00)
Del Peak 5(2q37 2)	0 (0%)	259	0.000191 (0.0572)	0.00393 (0.846)	0.0612 (1.00)	0.163 (1.00)	0.00285 (0.633)	0.000991 (0.258)
Del Peak 16(7q31 1)	0 (0%)	262	3.11e-07 (0.000115)	0.00141 (0.351)	0.141 (1.00)	0.52 (1.00)	0.00634 (1.00)	0.152 (1.00)
Del Peak 22(10p15 1)	0 (0%)	268	0.000124 (0.0381)	0.18 (1.00)	0.349 (1.00)	0.497 (1.00)	0.265 (1.00)	0.103 (1.00)
Del Peak 26(11q23 2)	0 (0%)	244	0.000264 (0.0777)	0.00248 (0.564)	0.00154 (0.38)	0.701 (1.00)	0.488 (1.00)	0.779 (1.00)
Del Peak 28(13q12 11)	0 (0%)	262	2.32e-06 (0.000827)	0.0715 (1.00)	0.0695 (1.00)	0.118 (1.00)	0.746 (1.00)	0.14 (1.00)
Del Peak 29(14q21 1)	0 (0%)	235	7.69e-07 (0.00028)	0.00456 (0.949)	0.00433 (0.909)	0.00206 (0.478)	0.0198 (1.00)	0.00158 (0.384)
Del Peak 30(14q32 33)	0 (0%)	217	9.24e-09 (3.62e-06)	0.015 (1.00)	0.0362 (1.00)	0.00132 (0.33)	0.023 (1.00)	0.117 (1.00)
Del Peak 33(16q23 1)	0 (0%)	188	2.22e-07 (8.34e-05)	0.00471 (0.974)	0.0226 (1.00)	0.00433 (0.909)	0.667 (1.00)	0.132 (1.00)
Del Peak 39(20p12 1)	0 (0%)	254	1.21e-08 (4.71e-06)	0.00112 (0.284)	0.00107 (0.274)	0.0182 (1.00)	0.197 (1.00)	0.00269 (0.606)
Del Peak 40(20p12 1)	0 (0%)	254	1.21e-08 (4.71e-06)	0.00112 (0.284)	0.00107 (0.274)	0.0182 (1.00)	0.197 (1.00)	0.00269 (0.606)
Del Peak 45(Xp21 1)	0 (0%)	254	6.22e-08 (2.38e-05)	0.00471 (0.974)	0.243 (1.00)	0.094 (1.00)	0.538 (1.00)	0.807 (1.00)
Del Peak 46(Xq21 33)	0 (0%)	264	5.77e-06 (0.00201)	0.0421 (1.00)	0.162 (1.00)	0.174 (1.00)	0.00365 (0.796)	0.0377 (1.00)
Amp Peak 14(9p24 1)	0 (0%)	257	0.364 (1.00)	0.102 (1.00)	0.65 (1.00)	0.269 (1.00)	0.792 (1.00)	0.273 (1.00)
Del Peak 3(1q44)	0 (0%)	283	0.0185 (1.00)	0.01 (1.00)	0.55 (1.00)	0.732 (1.00)	0.42 (1.00)	0.317 (1.00)
Del Peak 4(2q32 1)	0 (0%)	264	0.00895 (1.00)	0.12 (1.00)	0.365 (1.00)	0.929 (1.00)	0.0849 (1.00)	0.227 (1.00)

'Amp Peak 1(1p36.22)' versus 'CN_CNMF'

P value = 1.19e-07 (Fisher's exact test), Q value = 4.5e-05

Table S1. Gene #1: 'Amp Peak 1(1p36.22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 1(1P36.22) CNV	2	4	3	27
AMP PEAK 1(1P36.22) WILD-TYPE	135	24	25	86

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p36.22)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 4.55e-20 (Fisher's exact test), Q value = 2e-17

Table S2. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 2(1Q21.3) CNV	12	12	12	72
AMP PEAK 2(1Q21.3) WILD-TYPE	125	16	16	41

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 5.04e-11 (Fisher's exact test), Q value = 2.1e-08

Table S3. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 2(1Q21.3) CNV	4	25	11	51
AMP PEAK 2(1Q21.3) WILD-TYPE	33	54	53	27

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 3.28e-08 (Chi-square test), Q value = 1.3e-05

Table S4. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
AMP PEAK 2(1Q21.3) CNV	6	6	8	8	33
AMP PEAK 2(1Q21.3) WILD-TYPE	33	31	20	24	14

Figure S4. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

P value = 3.6e-05 (Fisher's exact test), Q value = 0.011

Table S5. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
AMP PEAK 2(1Q21.3) CNV	8	25	28
AMP PEAK 2(1Q21.3) WILD-TYPE	50	48	24

Figure S5. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

P value = 1.31e-05 (Fisher's exact test), Q value = 0.0044

Table S6. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	53	101
AMP PEAK 2(1Q21.3) CNV	20	10	52
AMP PEAK 2(1Q21.3) WILD-TYPE	63	43	49

Figure S6. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 1.78e-05 (Fisher's exact test), Q value = 0.0059

Table S7. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
AMP PEAK 2(1Q21.3) CNV	34	14	34
AMP PEAK 2(1Q21.3) WILD-TYPE	22	47	86

Figure S7. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 5.52e-14 (Fisher's exact test), Q value = 2.4e-11

Table S8. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 3(1Q42.3) CNV	16	14	11	64
AMP PEAK 3(1Q42.3) WILD-TYPE	121	14	17	49

Figure S8. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(1q42.3)' versus 'METHLYATION_CNMF'

P value = 1.11e-07 (Fisher's exact test), Q value = 4.2e-05

Table S9. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 3(1Q42.3) CNV	5	23	14	47
AMP PEAK 3(1Q42.3) WILD-TYPE	32	56	50	31

Figure S9. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 3(1q42.3)' versus 'MRNASEQ_CNMF'

P value = 4.49e-07 (Chi-square test), Q value = 0.00017

Table S10. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
AMP PEAK 3(1Q42.3) CNV	6	7	7	7	31
AMP PEAK 3(1Q42.3) WILD-TYPE	33	30	21	25	16

Figure S10. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 3(1q42.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000462 (Fisher's exact test), Q value = 0.13

Table S11. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
AMP PEAK 3(1Q42.3) CNV	10	21	27
AMP PEAK 3(1Q42.3) WILD-TYPE	48	52	25

Figure S11. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 3(1q42.3)' versus 'MIRSEQ_CNMF'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.00057

Table S12. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	53	101
AMP PEAK 3(1Q42.3) CNV	16	13	54
AMP PEAK 3(1Q42.3) WILD-TYPE	67	40	47

Figure S12. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Amp Peak 3(1q42.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.77e-06 (Fisher's exact test), Q value = 0.00064

Table S13. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
AMP PEAK 3(1Q42.3) CNV	36	16	31
AMP PEAK 3(1Q42.3) WILD-TYPE	20	45	89

Figure S13. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 4(3q27.1)' versus 'CN_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0041

Table S14. Gene #4: 'Amp Peak 4(3q27.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 4(3Q27.1) CNV	26	12	14	51
AMP PEAK 4(3Q27.1) WILD-TYPE	111	16	14	62

Figure S14. Get High-res Image Gene #4: 'Amp Peak 4(3q27.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 5(5p13.1)' versus 'CN_CNMF'

P value = 1.64e-14 (Fisher's exact test), Q value = 7.1e-12

Table S15. Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 5(5P13.1) CNV	12	9	5	61
AMP PEAK 5(5P13.1) WILD-TYPE	125	19	23	52

Figure S15. Get High-res Image Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 5(5p13.1)' versus 'METHLYATION_CNMF'

P value = 5.68e-07 (Fisher's exact test), Q value = 0.00021

Table S16. Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 5(5P13.1) CNV	7	20	6	39
AMP PEAK 5(5P13.1) WILD-TYPE	30	59	58	39

Figure S16. Get High-res Image Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 5(5p13.1)' versus 'MRNASEQ_CNMF'

P value = 2.72e-05 (Chi-square test), Q value = 0.0088

Table S17. Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
AMP PEAK 5(5P13.1) CNV	8	8	6	7	29
AMP PEAK 5(5P13.1) WILD-TYPE	31	29	22	25	18

Figure S17. Get High-res Image Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 6(6p21.1)' versus 'CN_CNMF'

P value = 3.1e-17 (Fisher's exact test), Q value = 1.4e-14

Table S18. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 6(6P21.1) CNV	6	7	9	58
AMP PEAK 6(6P21.1) WILD-TYPE	131	21	19	55

Figure S18. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(6p21.1)' versus 'METHLYATION_CNMF'

P value = 5.99e-10 (Fisher's exact test), Q value = 2.4e-07

Table S19. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 6(6P21.1) CNV	1	20	5	38
AMP PEAK 6(6P21.1) WILD-TYPE	36	59	59	40

Figure S19. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 6(6p21.1)' versus 'MRNASEQ_CNMF'

P value = 0.000807 (Chi-square test), Q value = 0.22

Table S20. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
AMP PEAK 6(6P21.1) CNV	5	6	6	7	23
AMP PEAK 6(6P21.1) WILD-TYPE	34	31	22	25	24

Figure S20. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 6(6p21.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.45e-05 (Fisher's exact test), Q value = 0.008

Table S21. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
AMP PEAK 6(6P21.1) CNV	29	11	24
AMP PEAK 6(6P21.1) WILD-TYPE	27	50	96

Figure S21. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 7(6q12)' versus 'CN_CNMF'

P value = 2.98e-09 (Fisher's exact test), Q value = 1.2e-06

Table S22. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 7(6Q12) CNV	7	5	7	41
AMP PEAK 7(6Q12) WILD-TYPE	130	23	21	72

Figure S22. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 7(6q12)' versus 'METHLYATION_CNMF'

P value = 1.69e-08 (Fisher's exact test), Q value = 6.5e-06

Table S23. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 7(6Q12) CNV	1	13	2	30
AMP PEAK 7(6Q12) WILD-TYPE	36	66	62	48

Figure S23. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 7(6q12)' versus 'MRNASEQ_CNMF'

P value = 0.000245 (Chi-square test), Q value = 0.073

Table S24. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
AMP PEAK 7(6Q12) CNV	3	4	6	4	20
AMP PEAK 7(6Q12) WILD-TYPE	36	33	22	28	27

Figure S24. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 7(6q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000263 (Fisher's exact test), Q value = 0.078

Table S25. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
AMP PEAK 7(6Q12) CNV	22	8	16
AMP PEAK 7(6Q12) WILD-TYPE	34	53	104

Figure S25. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

P value = 4.38e-09 (Fisher's exact test), Q value = 1.7e-06

Table S26. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 8(6Q21) CNV	6	4	9	37
AMP PEAK 8(6Q21) WILD-TYPE	131	24	19	76

Figure S26. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.74e-05 (Fisher's exact test), Q value = 0.0088

Table S27. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 8(6Q21) CNV	1	13	4	25
AMP PEAK 8(6Q21) WILD-TYPE	36	66	60	53

Figure S27. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 9(7p22.3)' versus 'CN_CNMF'

P value = 8.25e-14 (Fisher's exact test), Q value = 3.5e-11

Table S28. Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 9(7P22.3) CNV	40	26	14	77
AMP PEAK 9(7P22.3) WILD-TYPE	97	2	14	36

Figure S28. Get High-res Image Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 9(7p22.3)' versus 'METHLYATION_CNMF'

P value = 3.2e-05 (Fisher's exact test), Q value = 0.01

Table S29. Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 9(7P22.3) CNV	17	46	18	52
AMP PEAK 9(7P22.3) WILD-TYPE	20	33	46	26

Figure S29. Get High-res Image Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 10(7p11.2)' versus 'CN_CNMF'

P value = 4.23e-12 (Fisher's exact test), Q value = 1.8e-09

Table S30. Gene #10: 'Amp Peak 10(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 10(7P11.2) CNV	39	27	14	63
AMP PEAK 10(7P11.2) WILD-TYPE	98	1	14	50

Figure S30. Get High-res Image Gene #10: 'Amp Peak 10(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 11(7q21.2)' versus 'CN_CNMF'

P value = 2.36e-11 (Fisher's exact test), Q value = 9.8e-09

Table S31. Gene #11: 'Amp Peak 11(7q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 11(7Q21.2) CNV	39	27	13	58
AMP PEAK 11(7Q21.2) WILD-TYPE	98	1	15	55

Figure S31. Get High-res Image Gene #11: 'Amp Peak 11(7q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 12(8p23.1)' versus 'CN_CNMF'

P value = 3.39e-13 (Fisher's exact test), Q value = 1.4e-10

Table S32. Gene #12: 'Amp Peak 12(8p23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 12(8P23.1) CNV	52	13	28	28
AMP PEAK 12(8P23.1) WILD-TYPE	85	15	0	85

Figure S32. Get High-res Image Gene #12: 'Amp Peak 12(8p23.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.63e-06 (Fisher's exact test), Q value = 0.00093

Table S33. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 13(8Q24.21) CNV	71	19	24	91
AMP PEAK 13(8Q24.21) WILD-TYPE	66	9	4	22

Figure S33. 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 = 0.000101 (Fisher's exact test), Q value = 0.031

Table S34. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 13(8Q24.21) CNV	18	57	31	62
AMP PEAK 13(8Q24.21) WILD-TYPE	19	22	33	16

Figure S34. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 15(9q34.3)' versus 'CN_CNMF'

P value = 2.86e-07 (Fisher's exact test), Q value = 0.00011

Table S35. Gene #15: 'Amp Peak 15(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 15(9Q34.3) CNV	15	7	5	47
AMP PEAK 15(9Q34.3) WILD-TYPE	122	21	23	66

Figure S35. Get High-res Image Gene #15: 'Amp Peak 15(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 16(10q22.2)' versus 'CN_CNMF'

P value = 9.41e-08 (Fisher's exact test), Q value = 3.6e-05

Table S36. Gene #16: 'Amp Peak 16(10q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 16(10Q22.2) CNV	8	3	10	35
AMP PEAK 16(10Q22.2) WILD-TYPE	129	25	18	78

Figure S36. Get High-res Image Gene #16: 'Amp Peak 16(10q22.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 16(10q22.2)' versus 'MRNASEQ_CNMF'

P value = 0.000796 (Chi-square test), Q value = 0.21

Table S37. Gene #16: 'Amp Peak 16(10q22.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
AMP PEAK 16(10Q22.2) CNV	2	6	4	2	17
AMP PEAK 16(10Q22.2) WILD-TYPE	37	31	24	30	30

Figure S37. Get High-res Image Gene #16: 'Amp Peak 16(10q22.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 17(10q26.13)' versus 'CN_CNMF'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.004

Table S38. Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 17(10Q26.13) CNV	12	4	8	37
AMP PEAK 17(10Q26.13) WILD-TYPE	125	24	20	76

Figure S38. Get High-res Image Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 17(10q26.13)' versus 'METHLYATION_CNMF'

P value = 0.000754 (Fisher's exact test), Q value = 0.2

Table S39. Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 17(10Q26.13) CNV	3	11	8	27
AMP PEAK 17(10Q26.13) WILD-TYPE	34	68	56	51

Figure S39. Get High-res Image Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 17(10q26.13)' versus 'MRNASEQ_CNMF'

P value = 0.000929 (Chi-square test), Q value = 0.24

Table S40. Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
AMP PEAK 17(10Q26.13) CNV	3	10	3	4	19
AMP PEAK 17(10Q26.13) WILD-TYPE	36	27	25	28	28

Figure S40. Get High-res Image Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 18(11p13)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000655 (Fisher's exact test), Q value = 0.18

Table S41. Gene #18: 'Amp Peak 18(11p13)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
AMP PEAK 18(11P13) CNV	20	11	13
AMP PEAK 18(11P13) WILD-TYPE	36	50	107

Figure S41. Get High-res Image Gene #18: 'Amp Peak 18(11p13)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 19(11q13.3)' versus 'CN_CNMF'

P value = 3.27e-05 (Fisher's exact test), Q value = 0.01

Table S42. Gene #19: 'Amp Peak 19(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 19(11Q13.3) CNV	15	5	8	40
AMP PEAK 19(11Q13.3) WILD-TYPE	122	23	20	73

Figure S42. Get High-res Image Gene #19: 'Amp Peak 19(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 20(12p12.1)' versus 'CN_CNMF'

P value = 0.000304 (Fisher's exact test), Q value = 0.088

Table S43. Gene #20: 'Amp Peak 20(12p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 20(12P12.1) CNV	24	6	9	47
AMP PEAK 20(12P12.1) WILD-TYPE	113	22	19	66

Figure S43. Get High-res Image Gene #20: 'Amp Peak 20(12p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 21(12q15)' versus 'METHLYATION_CNMF'

P value = 0.000278 (Fisher's exact test), Q value = 0.081

Table S44. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 21(12Q15) CNV	15	12	9	29
AMP PEAK 21(12Q15) WILD-TYPE	22	67	55	49

Figure S44. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 22(13q12.3)' versus 'CN_CNMF'

P value = 7.07e-10 (Fisher's exact test), Q value = 2.8e-07

Table S45. Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 22(13Q12.3) CNV	31	21	5	59
AMP PEAK 22(13Q12.3) WILD-TYPE	106	7	23	54

Figure S45. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 22(13q12.3)' versus 'METHLYATION_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.0049

Table S46. Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 22(13Q12.3) CNV	8	25	17	47
AMP PEAK 22(13Q12.3) WILD-TYPE	29	54	47	31

Figure S46. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 23(13q22.1)' versus 'CN_CNMF'

P value = 1.54e-08 (Fisher's exact test), Q value = 6e-06

Table S47. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 23(13Q22.1) CNV	35	20	5	61
AMP PEAK 23(13Q22.1) WILD-TYPE	102	8	23	52

Figure S47. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 23(13q22.1)' versus 'METHLYATION_CNMF'

P value = 3.74e-05 (Fisher's exact test), Q value = 0.012

Table S48. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 23(13Q22.1) CNV	11	23	17	47
AMP PEAK 23(13Q22.1) WILD-TYPE	26	56	47	31

Figure S48. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 23(13q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-06 (Fisher's exact test), Q value = 0.00072

Table S49. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
AMP PEAK 23(13Q22.1) CNV	38	18	35
AMP PEAK 23(13Q22.1) WILD-TYPE	18	43	85

Figure S49. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 24(15q26.1)' versus 'CN_CNMF'

P value = 1.03e-13 (Fisher's exact test), Q value = 4.4e-11

Table S50. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 24(15Q26.1) CNV	10	5	1	53
AMP PEAK 24(15Q26.1) WILD-TYPE	127	23	27	60

Figure S50. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 24(15q26.1)' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.12

Table S51. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 24(15Q26.1) CNV	1	20	11	27
AMP PEAK 24(15Q26.1) WILD-TYPE	36	59	53	51

Figure S51. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 24(15q26.1)' versus 'MRNASEQ_CNMF'

P value = 0.000136 (Chi-square test), Q value = 0.042

Table S52. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
AMP PEAK 24(15Q26.1) CNV	6	2	11	6	21
AMP PEAK 24(15Q26.1) WILD-TYPE	33	35	17	26	26

Figure S52. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 24(15q26.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.53e-06 (Fisher's exact test), Q value = 0.0026

Table S53. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
AMP PEAK 24(15Q26.1) CNV	4	18	24
AMP PEAK 24(15Q26.1) WILD-TYPE	54	55	28

Figure S53. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 25(17q12)' versus 'CN_CNMF'

P value = 9.54e-13 (Fisher's exact test), Q value = 4e-10

Table S54. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 25(17Q12) CNV	16	9	5	62
AMP PEAK 25(17Q12) WILD-TYPE	121	19	23	51

Figure S54. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 25(17q12)' versus 'METHLYATION_CNMF'

P value = 8.07e-06 (Fisher's exact test), Q value = 0.0028

Table S55. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 25(17Q12) CNV	11	16	11	41
AMP PEAK 25(17Q12) WILD-TYPE	26	63	53	37

Figure S55. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 25(17q12)' versus 'MRNASEQ_CNMF'

P value = 6.85e-06 (Chi-square test), Q value = 0.0024

Table S56. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
AMP PEAK 25(17Q12) CNV	6	3	12	6	25
AMP PEAK 25(17Q12) WILD-TYPE	33	34	16	26	22

Figure S56. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 26(18q11.2)' versus 'CN_CNMF'

P value = 3.31e-06 (Fisher's exact test), Q value = 0.0012

Table S57. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 26(18Q11.2) CNV	23	8	6	53
AMP PEAK 26(18Q11.2) WILD-TYPE	114	20	22	60

Figure S57. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 26(18q11.2)' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.069

Table S58. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 26(18Q11.2) CNV	4	18	15	36
AMP PEAK 26(18Q11.2) WILD-TYPE	33	61	49	42

Figure S58. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 27(19q12)' versus 'CN_CNMF'

P value = 1.67e-15 (Fisher's exact test), Q value = 7.3e-13

Table S59. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 27(19Q12) CNV	14	9	3	64
AMP PEAK 27(19Q12) WILD-TYPE	123	19	25	49

Figure S59. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 27(19q12)' versus 'METHLYATION_CNMF'

P value = 4.66e-10 (Fisher's exact test), Q value = 1.9e-07

Table S60. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 27(19Q12) CNV	8	13	10	47
AMP PEAK 27(19Q12) WILD-TYPE	29	66	54	31

Figure S60. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 27(19q12)' versus 'MRNASEQ_CNMF'

P value = 8.37e-11 (Chi-square test), Q value = 3.4e-08

Table S61. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
AMP PEAK 27(19Q12) CNV	5	4	5	6	33
AMP PEAK 27(19Q12) WILD-TYPE	34	33	23	26	14

Figure S61. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 27(19q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.59e-06 (Fisher's exact test), Q value = 0.0016

Table S62. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
AMP PEAK 27(19Q12) CNV	9	15	29
AMP PEAK 27(19Q12) WILD-TYPE	49	58	23

Figure S62. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 27(19q12)' versus 'MIRSEQ_CNMF'

P value = 0.000305 (Fisher's exact test), Q value = 0.088

Table S63. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	53	101
AMP PEAK 27(19Q12) CNV	18	8	43
AMP PEAK 27(19Q12) WILD-TYPE	65	45	58

Figure S63. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Amp Peak 27(19q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.71e-10 (Fisher's exact test), Q value = 6.9e-08

Table S64. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
AMP PEAK 27(19Q12) CNV	37	11	21
AMP PEAK 27(19Q12) WILD-TYPE	19	50	99

Figure S64. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 28(20q13.2)' versus 'CN_CNMF'

P value = 5.63e-21 (Fisher's exact test), Q value = 2.5e-18

Table S65. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 28(20Q13.2) CNV	52	27	20	102
AMP PEAK 28(20Q13.2) WILD-TYPE	85	1	8	11

Figure S65. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 28(20q13.2)' versus 'METHLYATION_CNMF'

P value = 2.06e-11 (Fisher's exact test), Q value = 8.6e-09

Table S66. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
AMP PEAK 28(20Q13.2) CNV	27	41	29	73
AMP PEAK 28(20Q13.2) WILD-TYPE	10	38	35	5

Figure S66. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 28(20q13.2)' versus 'MRNASEQ_CNMF'

P value = 6.87e-07 (Chi-square test), Q value = 0.00025

Table S67. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
AMP PEAK 28(20Q13.2) CNV	15	19	18	20	45
AMP PEAK 28(20Q13.2) WILD-TYPE	24	18	10	12	2

Figure S67. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Amp Peak 28(20q13.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.89e-09 (Fisher's exact test), Q value = 3.5e-06

Table S68. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
AMP PEAK 28(20Q13.2) CNV	54	34	69
AMP PEAK 28(20Q13.2) WILD-TYPE	2	27	51

Figure S68. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 29(Xq27.3)' versus 'CN_CNMF'

P value = 0.000155 (Fisher's exact test), Q value = 0.047

Table S69. Gene #29: 'Amp Peak 29(Xq27.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
AMP PEAK 29(XQ27.3) CNV	13	10	5	32
AMP PEAK 29(XQ27.3) WILD-TYPE	124	18	23	81

Figure S69. Get High-res Image Gene #29: 'Amp Peak 29(Xq27.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.11)' versus 'CN_CNMF'

P value = 4.2e-15 (Fisher's exact test), Q value = 1.8e-12

Table S70. Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 1(1P36.11) CNV	10	7	6	60
DEL PEAK 1(1P36.11) WILD-TYPE	127	21	22	53

Figure S70. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 1(1p36.11)' versus 'METHLYATION_CNMF'

P value = 0.000366 (Fisher's exact test), Q value = 0.1

Table S71. Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 1(1P36.11) CNV	4	20	9	32
DEL PEAK 1(1P36.11) WILD-TYPE	33	59	55	46

Figure S71. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 5.4e-12 (Fisher's exact test), Q value = 2.3e-09

Table S72. Gene #31: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 2(1P13.2) CNV	6	6	2	45
DEL PEAK 2(1P13.2) WILD-TYPE	131	22	26	68

Figure S72. Get High-res Image Gene #31: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 5(2q37.2)' versus 'CN_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.057

Table S73. Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 5(2Q37.2) CNV	9	3	6	29
DEL PEAK 5(2Q37.2) WILD-TYPE	128	25	22	84

Figure S73. Get High-res Image Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(3p26.1)' versus 'CN_CNMF'

P value = 2.64e-10 (Fisher's exact test), Q value = 1.1e-07

Table S74. Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 6(3P26.1) CNV	13	11	8	52
DEL PEAK 6(3P26.1) WILD-TYPE	124	17	20	61

Figure S74. Get High-res Image Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(3p26.1)' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.087

Table S75. Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 6(3P26.1) CNV	7	21	8	34
DEL PEAK 6(3P26.1) WILD-TYPE	30	58	56	44

Figure S75. Get High-res Image Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 6(3p26.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000517 (Fisher's exact test), Q value = 0.14

Table S76. Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 6(3P26.1) CNV	27	14	24
DEL PEAK 6(3P26.1) WILD-TYPE	29	47	96

Figure S76. Get High-res Image Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(3p14.2)' versus 'CN_CNMF'

P value = 9.33e-13 (Fisher's exact test), Q value = 4e-10

Table S77. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 7(3P14.2) CNV	17	11	10	64
DEL PEAK 7(3P14.2) WILD-TYPE	120	17	18	49

Figure S77. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 7(3p14.2)' versus 'METHLYATION_CNMF'

P value = 1.38e-06 (Fisher's exact test), Q value = 5e-04

Table S78. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 7(3P14.2) CNV	13	25	8	43
DEL PEAK 7(3P14.2) WILD-TYPE	24	54	56	35

Figure S78. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(3p14.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.65e-05 (Fisher's exact test), Q value = 0.012

Table S79. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 7(3P14.2) CNV	32	13	31
DEL PEAK 7(3P14.2) WILD-TYPE	24	48	89

Figure S79. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(3q26.31)' versus 'CN_CNMF'

P value = 4.23e-06 (Fisher's exact test), Q value = 0.0015

Table S80. Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 8(3Q26.31) CNV	4	3	1	26
DEL PEAK 8(3Q26.31) WILD-TYPE	133	25	27	87

Figure S80. Get High-res Image Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 8(3q26.31)' versus 'METHLYATION_CNMF'

P value = 8.44e-05 (Fisher's exact test), Q value = 0.026

Table S81. Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 8(3Q26.31) CNV	2	10	0	17
DEL PEAK 8(3Q26.31) WILD-TYPE	35	69	64	61

Figure S81. Get High-res Image Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 8(3q26.31)' versus 'MRNASEQ_CNMF'

P value = 0.000956 (Chi-square test), Q value = 0.25

Table S82. Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 8(3Q26.31) CNV	1	0	1	5	11
DEL PEAK 8(3Q26.31) WILD-TYPE	38	37	27	27	36

Figure S82. Get High-res Image Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 9(4p16.3)' versus 'CN_CNMF'

P value = 2.89e-10 (Fisher's exact test), Q value = 1.2e-07

Table S83. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 9(4P16.3) CNV	24	12	10	66
DEL PEAK 9(4P16.3) WILD-TYPE	113	16	18	47

Figure S83. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 9(4p16.3)' versus 'METHLYATION_CNMF'

P value = 0.000377 (Fisher's exact test), Q value = 0.11

Table S84. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 9(4P16.3) CNV	6	25	20	42
DEL PEAK 9(4P16.3) WILD-TYPE	31	54	44	36

Figure S84. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 9(4p16.3)' versus 'MRNASEQ_CNMF'

P value = 0.000266 (Chi-square test), Q value = 0.078

Table S85. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 9(4P16.3) CNV	7	14	8	8	29
DEL PEAK 9(4P16.3) WILD-TYPE	32	23	20	24	18

Figure S85. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 9(4p16.3)' versus 'MIRSEQ_CNMF'

P value = 0.000848 (Fisher's exact test), Q value = 0.23

Table S86. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	53	101
DEL PEAK 9(4P16.3) CNV	19	19	50
DEL PEAK 9(4P16.3) WILD-TYPE	64	34	51

Figure S86. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 9(4p16.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.07e-05 (Fisher's exact test), Q value = 0.0098

Table S87. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 9(4P16.3) CNV	35	21	32
DEL PEAK 9(4P16.3) WILD-TYPE	21	40	88

Figure S87. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(4q22.1)' versus 'CN_CNMF'

P value = 6.72e-19 (Fisher's exact test), Q value = 3e-16

Table S88. Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 10(4Q22.1) CNV	24	18	11	82
DEL PEAK 10(4Q22.1) WILD-TYPE	113	10	17	31

Figure S88. Get High-res Image Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 10(4q22.1)' versus 'METHLYATION_CNMF'

P value = 1.23e-07 (Fisher's exact test), Q value = 4.7e-05

Table S89. Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 10(4Q22.1) CNV	6	35	20	53
DEL PEAK 10(4Q22.1) WILD-TYPE	31	44	44	25

Figure S89. Get High-res Image Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 10(4q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000102 (Fisher's exact test), Q value = 0.031

Table S90. Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 10(4Q22.1) CNV	39	23	44
DEL PEAK 10(4Q22.1) WILD-TYPE	17	38	76

Figure S90. Get High-res Image Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 11(4q34.3)' versus 'CN_CNMF'

P value = 1.07e-14 (Fisher's exact test), Q value = 4.7e-12

Table S91. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 11(4Q34.3) CNV	26	15	9	77
DEL PEAK 11(4Q34.3) WILD-TYPE	111	13	19	36

Figure S91. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(4q34.3)' versus 'METHLYATION_CNMF'

P value = 7.57e-07 (Fisher's exact test), Q value = 0.00028

Table S92. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 11(4Q34.3) CNV	4	31	24	49
DEL PEAK 11(4Q34.3) WILD-TYPE	33	48	40	29

Figure S92. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 11(4q34.3)' versus 'MRNASEQ_CNMF'

P value = 0.000746 (Chi-square test), Q value = 0.2

Table S93. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 11(4Q34.3) CNV	8	14	13	12	31
DEL PEAK 11(4Q34.3) WILD-TYPE	31	23	15	20	16

Figure S93. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 11(4q34.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.16e-06 (Fisher's exact test), Q value = 0.0031

Table S94. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 11(4Q34.3) CNV	39	23	38
DEL PEAK 11(4Q34.3) WILD-TYPE	17	38	82

Figure S94. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 12(5q11.2)' versus 'CN_CNMF'

P value = 6.54e-28 (Fisher's exact test), Q value = 2.9e-25

Table S95. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 12(5Q11.2) CNV	6	11	9	77
DEL PEAK 12(5Q11.2) WILD-TYPE	131	17	19	36

Figure S95. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(5q11.2)' versus 'METHLYATION_CNMF'

P value = 1.27e-13 (Fisher's exact test), Q value = 5.4e-11

Table S96. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 12(5Q11.2) CNV	3	28	7	51
DEL PEAK 12(5Q11.2) WILD-TYPE	34	51	57	27

Figure S96. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 12(5q11.2)' versus 'MRNASEQ_CNMF'

P value = 9.48e-07 (Chi-square test), Q value = 0.00034

Table S97. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 12(5Q11.2) CNV	10	2	6	11	29
DEL PEAK 12(5Q11.2) WILD-TYPE	29	35	22	21	18

Figure S97. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 12(5q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.06e-07 (Fisher's exact test), Q value = 0.00011

Table S98. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
DEL PEAK 12(5Q11.2) CNV	5	24	29
DEL PEAK 12(5Q11.2) WILD-TYPE	53	49	23

Figure S98. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(5q11.2)' versus 'MIRSEQ_CNMF'

P value = 2.92e-07 (Fisher's exact test), Q value = 0.00011

Table S99. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	53	101
DEL PEAK 12(5Q11.2) CNV	23	5	51
DEL PEAK 12(5Q11.2) WILD-TYPE	60	48	50

Figure S99. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 12(5q11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.53e-09 (Fisher's exact test), Q value = 1e-06

Table S100. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 12(5Q11.2) CNV	38	10	31
DEL PEAK 12(5Q11.2) WILD-TYPE	18	51	89

Figure S100. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(5q23.2)' versus 'CN_CNMF'

P value = 2.48e-23 (Fisher's exact test), Q value = 1.1e-20

Table S101. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 13(5Q23.2) CNV	5	12	9	67
DEL PEAK 13(5Q23.2) WILD-TYPE	132	16	19	46

Figure S101. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 13(5q23.2)' versus 'METHLYATION_CNMF'

P value = 2.5e-12 (Fisher's exact test), Q value = 1.1e-09

Table S102. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 13(5Q23.2) CNV	5	22	5	48
DEL PEAK 13(5Q23.2) WILD-TYPE	32	57	59	30

Figure S102. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 13(5q23.2)' versus 'MRNASEQ_CNMF'

P value = 2.02e-07 (Chi-square test), Q value = 7.6e-05

Table S103. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 13(5Q23.2) CNV	11	1	4	9	28
DEL PEAK 13(5Q23.2) WILD-TYPE	28	36	24	23	19

Figure S103. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 13(5q23.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.00074

Table S104. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
DEL PEAK 13(5Q23.2) CNV	5	21	27
DEL PEAK 13(5Q23.2) WILD-TYPE	53	52	25

Figure S104. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(5q23.2)' versus 'MIRSEQ_CNMF'

P value = 2.65e-07 (Fisher's exact test), Q value = 9.9e-05

Table S105. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	53	101
DEL PEAK 13(5Q23.2) CNV	18	4	47
DEL PEAK 13(5Q23.2) WILD-TYPE	65	49	54

Figure S105. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 13(5q23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.11e-08 (Fisher's exact test), Q value = 4.3e-06

Table S106. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 13(5Q23.2) CNV	34	7	28
DEL PEAK 13(5Q23.2) WILD-TYPE	22	54	92

Figure S106. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(6p25.3)' versus 'CN_CNMF'

P value = 5.01e-07 (Fisher's exact test), Q value = 0.00018

Table S107. Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 14(6P25.3) CNV	15	6	3	45
DEL PEAK 14(6P25.3) WILD-TYPE	122	22	25	68

Figure S107. Get High-res Image Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(6p25.3)' versus 'METHLYATION_CNMF'

P value = 0.000932 (Fisher's exact test), Q value = 0.24

Table S108. Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 14(6P25.3) CNV	3	20	9	29
DEL PEAK 14(6P25.3) WILD-TYPE	34	59	55	49

Figure S108. Get High-res Image Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 14(6p25.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000915 (Fisher's exact test), Q value = 0.24

Table S109. Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 14(6P25.3) CNV	22	7	22
DEL PEAK 14(6P25.3) WILD-TYPE	34	54	98

Figure S109. Get High-res Image Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(6q26)' versus 'CN_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.039

Table S110. Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 15(6Q26) CNV	14	9	4	35
DEL PEAK 15(6Q26) WILD-TYPE	123	19	24	78

Figure S110. Get High-res Image Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(6q26)' versus 'MRNASEQ_CNMF'

P value = 1.51e-05 (Chi-square test), Q value = 0.005

Table S111. Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 15(6Q26) CNV	8	3	16	3	16
DEL PEAK 15(6Q26) WILD-TYPE	31	34	12	29	31

Figure S111. Get High-res Image Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 16(7q31.1)' versus 'CN_CNMF'

P value = 3.11e-07 (Fisher's exact test), Q value = 0.00012

Table S112. Gene #45: 'Del Peak 16(7q31.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 16(7Q31.1) CNV	6	1	5	32
DEL PEAK 16(7Q31.1) WILD-TYPE	131	27	23	81

Figure S112. Get High-res Image Gene #45: 'Del Peak 16(7q31.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(7q36.3)' versus 'CN_CNMF'

P value = 1.82e-14 (Fisher's exact test), Q value = 7.9e-12

Table S113. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 17(7Q36.3) CNV	4	2	5	47
DEL PEAK 17(7Q36.3) WILD-TYPE	133	26	23	66

Figure S113. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(7q36.3)' versus 'METHLYATION_CNMF'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.0064

Table S114. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 17(7Q36.3) CNV	0	19	6	24
DEL PEAK 17(7Q36.3) WILD-TYPE	37	60	58	54

Figure S114. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 17(7q36.3)' versus 'MRNASEQ_CNMF'

P value = 0.000791 (Chi-square test), Q value = 0.21

Table S115. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 17(7Q36.3) CNV	4	6	5	2	19
DEL PEAK 17(7Q36.3) WILD-TYPE	35	31	23	30	28

Figure S115. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 17(7q36.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000113 (Fisher's exact test), Q value = 0.035

Table S116. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 17(7Q36.3) CNV	22	6	17
DEL PEAK 17(7Q36.3) WILD-TYPE	34	55	103

Figure S116. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(8p23.2)' versus 'CN_CNMF'

P value = 4.3e-14 (Fisher's exact test), Q value = 1.9e-11

Table S117. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 18(8P23.2) CNV	13	9	0	55
DEL PEAK 18(8P23.2) WILD-TYPE	124	19	28	58

Figure S117. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 18(8p23.2)' versus 'METHLYATION_CNMF'

P value = 5.78e-06 (Fisher's exact test), Q value = 0.002

Table S118. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 18(8P23.2) CNV	3	16	10	36
DEL PEAK 18(8P23.2) WILD-TYPE	34	63	54	42

Figure S118. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 18(8p23.2)' versus 'MRNASEQ_CNMF'

P value = 0.000543 (Chi-square test), Q value = 0.15

Table S119. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 18(8P23.2) CNV	5	5	7	7	23
DEL PEAK 18(8P23.2) WILD-TYPE	34	32	21	25	24

Figure S119. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 18(8p23.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.048

Table S120. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 18(8P23.2) CNV	27	13	22
DEL PEAK 18(8P23.2) WILD-TYPE	29	48	98

Figure S120. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 19(9p23)' versus 'CN_CNMF'

P value = 2.66e-15 (Fisher's exact test), Q value = 1.2e-12

Table S121. Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 19(9P23) CNV	22	10	13	75
DEL PEAK 19(9P23) WILD-TYPE	115	18	15	38

Figure S121. Get High-res Image Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 19(9p23)' versus 'METHLYATION_CNMF'

P value = 2.88e-05 (Fisher's exact test), Q value = 0.0092

Table S122. Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 19(9P23) CNV	7	28	19	47
DEL PEAK 19(9P23) WILD-TYPE	30	51	45	31

Figure S122. Get High-res Image Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 19(9p23)' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Chi-square test), Q value = 0.092

Table S123. Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 19(9P23) CNV	12	13	17	8	31
DEL PEAK 19(9P23) WILD-TYPE	27	24	11	24	16

Figure S123. Get High-res Image Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 20(9p21.3)' versus 'CN_CNMF'

P value = 6.29e-16 (Fisher's exact test), Q value = 2.8e-13

Table S124. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 20(9P21.3) CNV	22	8	12	76
DEL PEAK 20(9P21.3) WILD-TYPE	115	20	16	37

Figure S124. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(9p21.3)' versus 'METHLYATION_CNMF'

P value = 5.35e-11 (Fisher's exact test), Q value = 2.2e-08

Table S125. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 20(9P21.3) CNV	1	28	20	51
DEL PEAK 20(9P21.3) WILD-TYPE	36	51	44	27

Figure S125. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 20(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 3e-06 (Chi-square test), Q value = 0.0011

Table S126. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 20(9P21.3) CNV	7	11	16	10	33
DEL PEAK 20(9P21.3) WILD-TYPE	32	26	12	22	14

Figure S126. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 20(9p21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.077

Table S127. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 20(9P21.3) CNV	36	22	39
DEL PEAK 20(9P21.3) WILD-TYPE	20	39	81

Figure S127. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 21(9q21.11)' versus 'CN_CNMF'

P value = 2.97e-08 (Fisher's exact test), Q value = 1.1e-05

Table S128. Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 21(9Q21.11) CNV	12	7	8	46
DEL PEAK 21(9Q21.11) WILD-TYPE	125	21	20	67

Figure S128. Get High-res Image Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 21(9q21.11)' versus 'METHLYATION_CNMF'

P value = 0.000163 (Fisher's exact test), Q value = 0.049

Table S129. Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 21(9Q21.11) CNV	2	17	13	32
DEL PEAK 21(9Q21.11) WILD-TYPE	35	62	51	46

Figure S129. Get High-res Image Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 22(10p15.1)' versus 'CN_CNMF'

P value = 0.000124 (Fisher's exact test), Q value = 0.038

Table S130. Gene #51: 'Del Peak 22(10p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 22(10P15.1) CNV	6	3	3	26
DEL PEAK 22(10P15.1) WILD-TYPE	131	25	25	87

Figure S130. Get High-res Image Gene #51: 'Del Peak 22(10p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(10q22.3)' versus 'CN_CNMF'

P value = 2.43e-09 (Fisher's exact test), Q value = 9.7e-07

Table S131. Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 23(10Q22.3) CNV	4	9	3	33
DEL PEAK 23(10Q22.3) WILD-TYPE	133	19	25	80

Figure S131. Get High-res Image Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(10q22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000641 (Fisher's exact test), Q value = 0.18

Table S132. Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 23(10Q22.3) CNV	17	3	17
DEL PEAK 23(10Q22.3) WILD-TYPE	39	58	103

Figure S132. Get High-res Image Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 24(10q23.31)' versus 'CN_CNMF'

P value = 2.72e-12 (Fisher's exact test), Q value = 1.1e-09

Table S133. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 24(10Q23.31) CNV	7	10	9	47
DEL PEAK 24(10Q23.31) WILD-TYPE	130	18	19	66

Figure S133. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 24(10q23.31)' versus 'METHLYATION_CNMF'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.004

Table S134. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 24(10Q23.31) CNV	4	12	9	34
DEL PEAK 24(10Q23.31) WILD-TYPE	33	67	55	44

Figure S134. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 24(10q23.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.51e-05 (Fisher's exact test), Q value = 0.0082

Table S135. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 24(10Q23.31) CNV	25	5	30
DEL PEAK 24(10Q23.31) WILD-TYPE	31	56	90

Figure S135. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(11p15.4)' versus 'CN_CNMF'

P value = 2.96e-08 (Fisher's exact test), Q value = 1.1e-05

Table S136. Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 25(11P15.4) CNV	9	3	6	41
DEL PEAK 25(11P15.4) WILD-TYPE	128	25	22	72

Figure S136. Get High-res Image Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 25(11p15.4)' versus 'METHLYATION_CNMF'

P value = 1.55e-05 (Fisher's exact test), Q value = 0.0051

Table S137. Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 25(11P15.4) CNV	2	9	6	28
DEL PEAK 25(11P15.4) WILD-TYPE	35	70	58	50

Figure S137. Get High-res Image Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 26(11q23.2)' versus 'CN_CNMF'

P value = 0.000264 (Fisher's exact test), Q value = 0.078

Table S138. Gene #55: 'Del Peak 26(11q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 26(11Q23.2) CNV	15	6	4	37
DEL PEAK 26(11Q23.2) WILD-TYPE	122	22	24	76

Figure S138. Get High-res Image Gene #55: 'Del Peak 26(11q23.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 27(12p13.31)' versus 'CN_CNMF'

P value = 1.49e-10 (Fisher's exact test), Q value = 6.1e-08

Table S139. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 27(12P13.31) CNV	3	5	5	37
DEL PEAK 27(12P13.31) WILD-TYPE	134	23	23	76

Figure S139. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 27(12p13.31)' versus 'METHLYATION_CNMF'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0038

Table S140. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 27(12P13.31) CNV	2	10	4	27
DEL PEAK 27(12P13.31) WILD-TYPE	35	69	60	51

Figure S140. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 27(12p13.31)' versus 'MRNASEQ_CNMF'

P value = 2.66e-05 (Chi-square test), Q value = 0.0086

Table S141. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 27(12P13.31) CNV	1	2	5	2	17
DEL PEAK 27(12P13.31) WILD-TYPE	38	35	23	30	30

Figure S141. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 27(12p13.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000281 (Fisher's exact test), Q value = 0.082

Table S142. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
DEL PEAK 27(12P13.31) CNV	2	9	16
DEL PEAK 27(12P13.31) WILD-TYPE	56	64	36

Figure S142. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 28(13q12.11)' versus 'CN_CNMF'

P value = 2.32e-06 (Fisher's exact test), Q value = 0.00083

Table S143. Gene #57: 'Del Peak 28(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 28(13Q12.11) CNV	6	2	6	30
DEL PEAK 28(13Q12.11) WILD-TYPE	131	26	22	83

Figure S143. Get High-res Image Gene #57: 'Del Peak 28(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(14q21.1)' versus 'CN_CNMF'

P value = 7.69e-07 (Fisher's exact test), Q value = 0.00028

Table S144. Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 29(14Q21.1) CNV	13	8	7	43
DEL PEAK 29(14Q21.1) WILD-TYPE	124	20	21	70

Figure S144. Get High-res Image Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 30(14q32.33)' versus 'CN_CNMF'

P value = 9.24e-09 (Fisher's exact test), Q value = 3.6e-06

Table S145. Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 30(14Q32.33) CNV	17	9	9	54
DEL PEAK 30(14Q32.33) WILD-TYPE	120	19	19	59

Figure S145. Get High-res Image Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 31(15q15.1)' versus 'CN_CNMF'

P value = 6.44e-13 (Fisher's exact test), Q value = 2.7e-10

Table S146. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 31(15Q15.1) CNV	9	10	7	53
DEL PEAK 31(15Q15.1) WILD-TYPE	128	18	21	60

Figure S146. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 31(15q15.1)' versus 'METHLYATION_CNMF'

P value = 5.71e-07 (Fisher's exact test), Q value = 0.00021

Table S147. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 31(15Q15.1) CNV	5	16	7	38
DEL PEAK 31(15Q15.1) WILD-TYPE	32	63	57	40

Figure S147. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 31(15q15.1)' versus 'MRNASEQ_CNMF'

P value = 1.79e-05 (Chi-square test), Q value = 0.0059

Table S148. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 31(15Q15.1) CNV	7	2	11	6	24
DEL PEAK 31(15Q15.1) WILD-TYPE	32	35	17	26	23

Figure S148. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 31(15q15.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.38e-06 (Fisher's exact test), Q value = 0.0025

Table S149. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
DEL PEAK 31(15Q15.1) CNV	4	22	24
DEL PEAK 31(15Q15.1) WILD-TYPE	54	51	28

Figure S149. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q15.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.73e-07 (Fisher's exact test), Q value = 0.00032

Table S150. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 31(15Q15.1) CNV	29	6	26
DEL PEAK 31(15Q15.1) WILD-TYPE	27	55	94

Figure S150. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 32(16p13.3)' versus 'CN_CNMF'

P value = 7.42e-11 (Fisher's exact test), Q value = 3e-08

Table S151. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 32(16P13.3) CNV	7	2	5	44
DEL PEAK 32(16P13.3) WILD-TYPE	130	26	23	69

Figure S151. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 32(16p13.3)' versus 'METHLYATION_CNMF'

P value = 7.03e-05 (Fisher's exact test), Q value = 0.022

Table S152. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 32(16P13.3) CNV	1	14	7	27
DEL PEAK 32(16P13.3) WILD-TYPE	36	65	57	51

Figure S152. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 32(16p13.3)' versus 'MRNASEQ_CNMF'

P value = 2.03e-05 (Chi-square test), Q value = 0.0067

Table S153. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 32(16P13.3) CNV	3	4	2	2	19
DEL PEAK 32(16P13.3) WILD-TYPE	36	33	26	30	28

Figure S153. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 32(16p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000382 (Fisher's exact test), Q value = 0.11

Table S154. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
DEL PEAK 32(16P13.3) CNV	5	7	18
DEL PEAK 32(16P13.3) WILD-TYPE	53	66	34

Figure S154. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 33(16q23.1)' versus 'CN_CNMF'

P value = 2.22e-07 (Fisher's exact test), Q value = 8.3e-05

Table S155. Gene #62: 'Del Peak 33(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 33(16Q23.1) CNV	33	12	7	66
DEL PEAK 33(16Q23.1) WILD-TYPE	104	16	21	47

Figure S155. Get High-res Image Gene #62: 'Del Peak 33(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 34(17p12)' versus 'CN_CNMF'

P value = 1.81e-23 (Fisher's exact test), Q value = 8.1e-21

Table S156. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 34(17P12) CNV	13	14	9	79
DEL PEAK 34(17P12) WILD-TYPE	124	14	19	34

Figure S156. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 34(17p12)' versus 'METHLYATION_CNMF'

P value = 4.44e-11 (Fisher's exact test), Q value = 1.8e-08

Table S157. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 34(17P12) CNV	4	29	13	53
DEL PEAK 34(17P12) WILD-TYPE	33	50	51	25

Figure S157. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 34(17p12)' versus 'MRNASEQ_CNMF'

P value = 9.95e-06 (Chi-square test), Q value = 0.0034

Table S158. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 34(17P12) CNV	10	5	13	11	31
DEL PEAK 34(17P12) WILD-TYPE	29	32	15	21	16

Figure S158. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 34(17p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.0064

Table S159. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
DEL PEAK 34(17P12) CNV	10	29	31
DEL PEAK 34(17P12) WILD-TYPE	48	44	21

Figure S159. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 34(17p12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.36e-06 (Fisher's exact test), Q value = 0.0022

Table S160. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 34(17P12) CNV	36	13	42
DEL PEAK 34(17P12) WILD-TYPE	20	48	78

Figure S160. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 35(17q24.3)' versus 'CN_CNMF'

P value = 1.32e-10 (Fisher's exact test), Q value = 5.4e-08

Table S161. Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 35(17Q24.3) CNV	4	6	6	39
DEL PEAK 35(17Q24.3) WILD-TYPE	133	22	22	74

Figure S161. Get High-res Image Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 35(17q24.3)' versus 'METHLYATION_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.071

Table S162. Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 35(17Q24.3) CNV	0	16	6	21
DEL PEAK 35(17Q24.3) WILD-TYPE	37	63	58	57

Figure S162. Get High-res Image Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 35(17q24.3)' versus 'MRNASEQ_CNMF'

P value = 0.000463 (Chi-square test), Q value = 0.13

Table S163. Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 35(17Q24.3) CNV	5	1	1	7	16
DEL PEAK 35(17Q24.3) WILD-TYPE	34	36	27	25	31

Figure S163. Get High-res Image Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 36(18q21.2)' versus 'CN_CNMF'

P value = 4.49e-13 (Fisher's exact test), Q value = 1.9e-10

Table S164. Gene #65: 'Del Peak 36(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 36(18Q21.2) CNV	31	20	8	74
DEL PEAK 36(18Q21.2) WILD-TYPE	106	8	20	39

Figure S164. Get High-res Image Gene #65: 'Del Peak 36(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 36(18q21.2)' versus 'METHLYATION_CNMF'

P value = 0.000846 (Fisher's exact test), Q value = 0.23

Table S165. Gene #65: 'Del Peak 36(18q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 36(18Q21.2) CNV	18	30	17	46
DEL PEAK 36(18Q21.2) WILD-TYPE	19	49	47	32

Figure S165. Get High-res Image Gene #65: 'Del Peak 36(18q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 37(19p13.3)' versus 'CN_CNMF'

P value = 2.35e-27 (Fisher's exact test), Q value = 1.1e-24

Table S166. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 37(19P13.3) CNV	6	10	7	76
DEL PEAK 37(19P13.3) WILD-TYPE	131	18	21	37

Figure S166. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 37(19p13.3)' versus 'METHLYATION_CNMF'

P value = 2.38e-16 (Fisher's exact test), Q value = 1.1e-13

Table S167. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 37(19P13.3) CNV	4	18	6	54
DEL PEAK 37(19P13.3) WILD-TYPE	33	61	58	24

Figure S167. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 37(19p13.3)' versus 'MRNASEQ_CNMF'

P value = 3.62e-11 (Chi-square test), Q value = 1.5e-08

Table S168. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 37(19P13.3) CNV	8	3	8	7	36
DEL PEAK 37(19P13.3) WILD-TYPE	31	34	20	25	11

Figure S168. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 37(19p13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.34e-12 (Fisher's exact test), Q value = 5.6e-10

Table S169. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
DEL PEAK 37(19P13.3) CNV	3	23	36
DEL PEAK 37(19P13.3) WILD-TYPE	55	50	16

Figure S169. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(19p13.3)' versus 'MIRSEQ_CNMF'

P value = 2.21e-07 (Fisher's exact test), Q value = 8.3e-05

Table S170. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	53	101
DEL PEAK 37(19P13.3) CNV	20	6	52
DEL PEAK 37(19P13.3) WILD-TYPE	63	47	49

Figure S170. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'Del Peak 37(19p13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.06e-19 (Fisher's exact test), Q value = 4.7e-17

Table S171. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 37(19P13.3) CNV	47	7	24
DEL PEAK 37(19P13.3) WILD-TYPE	9	54	96

Figure S171. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 38(19q13.11)' versus 'CN_CNMF'

P value = 2.69e-09 (Fisher's exact test), Q value = 1.1e-06

Table S172. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 38(19Q13.11) CNV	2	5	5	31
DEL PEAK 38(19Q13.11) WILD-TYPE	135	23	23	82

Figure S172. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 38(19q13.11)' versus 'METHLYATION_CNMF'

P value = 6.16e-05 (Fisher's exact test), Q value = 0.019

Table S173. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 38(19Q13.11) CNV	1	11	2	21
DEL PEAK 38(19Q13.11) WILD-TYPE	36	68	62	57

Figure S173. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 38(19q13.11)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.44e-06 (Fisher's exact test), Q value = 0.00087

Table S174. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 38(19Q13.11) CNV	20	3	10
DEL PEAK 38(19Q13.11) WILD-TYPE	36	58	110

Figure S174. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 39(20p12.1)' versus 'CN_CNMF'

P value = 1.21e-08 (Fisher's exact test), Q value = 4.7e-06

Table S175. Gene #68: 'Del Peak 39(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 39(20P12.1) CNV	11	0	2	39
DEL PEAK 39(20P12.1) WILD-TYPE	126	28	26	74

Figure S175. Get High-res Image Gene #68: 'Del Peak 39(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 40(20p12.1)' versus 'CN_CNMF'

P value = 1.21e-08 (Fisher's exact test), Q value = 4.7e-06

Table S176. Gene #69: 'Del Peak 40(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 40(20P12.1) CNV	11	0	2	39
DEL PEAK 40(20P12.1) WILD-TYPE	126	28	26	74

Figure S176. Get High-res Image Gene #69: 'Del Peak 40(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 41(21q11.2)' versus 'CN_CNMF'

P value = 1.39e-10 (Fisher's exact test), Q value = 5.7e-08

Table S177. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 41(21Q11.2) CNV	22	9	13	64
DEL PEAK 41(21Q11.2) WILD-TYPE	115	19	15	49

Figure S177. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 41(21q11.2)' versus 'METHLYATION_CNMF'

P value = 5.41e-05 (Fisher's exact test), Q value = 0.017

Table S178. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 41(21Q11.2) CNV	4	30	18	41
DEL PEAK 41(21Q11.2) WILD-TYPE	33	49	46	37

Figure S178. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 41(21q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000341 (Fisher's exact test), Q value = 0.098

Table S179. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
DEL PEAK 41(21Q11.2) CNV	13	19	29
DEL PEAK 41(21Q11.2) WILD-TYPE	45	54	23

Figure S179. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(21q22.13)' versus 'CN_CNMF'

P value = 1.56e-09 (Fisher's exact test), Q value = 6.2e-07

Table S180. Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 42(21Q22.13) CNV	25	12	14	64
DEL PEAK 42(21Q22.13) WILD-TYPE	112	16	14	49

Figure S180. Get High-res Image Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 42(21q22.13)' versus 'METHLYATION_CNMF'

P value = 0.000509 (Fisher's exact test), Q value = 0.14

Table S181. Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 42(21Q22.13) CNV	4	34	21	37
DEL PEAK 42(21Q22.13) WILD-TYPE	33	45	43	41

Figure S181. Get High-res Image Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 43(22q13.31)' versus 'CN_CNMF'

P value = 9.68e-15 (Fisher's exact test), Q value = 4.2e-12

Table S182. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 43(22Q13.31) CNV	15	9	11	66
DEL PEAK 43(22Q13.31) WILD-TYPE	122	19	17	47

Figure S182. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 43(22q13.31)' versus 'METHLYATION_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.043

Table S183. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 43(22Q13.31) CNV	4	27	15	38
DEL PEAK 43(22Q13.31) WILD-TYPE	33	52	49	40

Figure S183. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 43(22q13.31)' versus 'MRNASEQ_CNMF'

P value = 0.000528 (Chi-square test), Q value = 0.15

Table S184. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	39	37	28	32	47
DEL PEAK 43(22Q13.31) CNV	9	7	12	6	26
DEL PEAK 43(22Q13.31) WILD-TYPE	30	30	16	26	21

Figure S184. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Del Peak 43(22q13.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000471 (Fisher's exact test), Q value = 0.13

Table S185. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	58	73	52
DEL PEAK 43(22Q13.31) CNV	9	25	26
DEL PEAK 43(22Q13.31) WILD-TYPE	49	48	26

Figure S185. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 43(22q13.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.56e-06 (Fisher's exact test), Q value = 0.0023

Table S186. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	61	120
DEL PEAK 43(22Q13.31) CNV	34	14	31
DEL PEAK 43(22Q13.31) WILD-TYPE	22	47	89

Figure S186. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 44(Xp22.2)' versus 'CN_CNMF'

P value = 1.44e-09 (Fisher's exact test), Q value = 5.8e-07

Table S187. Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 44(XP22.2) CNV	10	3	3	45
DEL PEAK 44(XP22.2) WILD-TYPE	127	25	25	68

Figure S187. Get High-res Image Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 44(Xp22.2)' versus 'METHLYATION_CNMF'

P value = 0.000642 (Fisher's exact test), Q value = 0.18

Table S188. Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	37	79	64	78
DEL PEAK 44(XP22.2) CNV	1	19	9	25
DEL PEAK 44(XP22.2) WILD-TYPE	36	60	55	53

Figure S188. Get High-res Image Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 45(Xp21.1)' versus 'CN_CNMF'

P value = 6.22e-08 (Fisher's exact test), Q value = 2.4e-05

Table S189. Gene #74: 'Del Peak 45(Xp21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 45(XP21.1) CNV	8	4	2	38
DEL PEAK 45(XP21.1) WILD-TYPE	129	24	26	75

Figure S189. Get High-res Image Gene #74: 'Del Peak 45(Xp21.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 46(Xq21.33)' versus 'CN_CNMF'

P value = 5.77e-06 (Fisher's exact test), Q value = 0.002

Table S190. Gene #75: 'Del Peak 46(Xq21.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	28	28	113
DEL PEAK 46(XQ21.33) CNV	7	4	1	30
DEL PEAK 46(XQ21.33) WILD-TYPE	130	24	27	83

Figure S190. Get High-res Image Gene #75: 'Del Peak 46(Xq21.33)' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = STAD-TP.transferedmergedcluster.txt
Number of patients = 306
Number of copy number variation regions = 75
Number of molecular subtypes = 6
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

[4] GISTIC_version2

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