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 46 peak regions and 10 molecular subtypes across 197 patients, 61 significant findings detected with Q value < 0.25.

Amp Peak 1(1q21.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 2(3q26.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(7p15.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(7q34) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 5(8p11.22) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(8q24.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(9q34.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(11q13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(20q13.33) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 1(1p31.3) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 3(2q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 6(4q28.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 7(5q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 8(5q21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 9(6q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 11(8p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 12(8p11.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 13(9p22.3) cnvs correlated to 'CN_CNMF'.
Del Peak 14(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 17(13q14.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 18(16q22.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 19(16q24.1) cnvs correlated to 'CN_CNMF'.
Del Peak 20(17p13.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 21(17q21.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 22(18q23) cnvs correlated to 'CN_CNMF'.
Del Peak 25(21q22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 46 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 61 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test
Del Peak 11(8p21 3)	0 (0%)	85	2.84e-06 (0.00124)	5.31e-08 (2.36e-05)	0.00364 (1.00)	0.014 (1.00)	1.79e-05 (0.00761)	5.65e-06 (0.00243)	3.79e-06 (0.00165)	0.0246 (1.00)	2.67e-06 (0.00116)	0.00106 (0.416)
Del Peak 9(6q15)	0 (0%)	134	7.92e-13 (3.61e-10)	3.43e-12 (1.56e-09)	0.000189 (0.0775)	0.0155 (1.00)	1.11e-06 (0.000485)	7.99e-07 (0.000352)	0.000661 (0.262)	0.00123 (0.477)	0.00146 (0.56)	0.504 (1.00)
Del Peak 25(21q22 3)	0 (0%)	133	1.11e-05 (0.00477)	1.2e-11 (5.42e-09)	0.105 (1.00)	0.206 (1.00)	3.79e-14 (1.73e-11)	2.89e-10 (1.29e-07)	0.307 (1.00)	0.000581 (0.233)	0.0469 (1.00)	0.0516 (1.00)
Del Peak 14(10q23 31)	0 (0%)	128	3.88e-06 (0.00168)	1.03e-06 (0.000451)	0.0971 (1.00)	0.222 (1.00)	1.68e-10 (7.55e-08)	6.28e-06 (0.0027)	0.143 (1.00)	0.0922 (1.00)	0.00339 (1.00)	0.193 (1.00)
Del Peak 17(13q14 13)	0 (0%)	108	0.000107 (0.0443)	1.23e-05 (0.00525)	0.0975 (1.00)	0.133 (1.00)	6.55e-05 (0.0274)	4.43e-05 (0.0186)	0.122 (1.00)	0.156 (1.00)	0.28 (1.00)	0.357 (1.00)
Amp Peak 4(7q34)	0 (0%)	162	8.59e-08 (3.8e-05)	4.98e-05 (0.0209)	0.655 (1.00)	0.636 (1.00)	0.000377 (0.151)	0.00783 (1.00)	0.0836 (1.00)	0.00369 (1.00)	0.0197 (1.00)	0.385 (1.00)
Del Peak 3(2q22 1)	0 (0%)	173	5.22e-06 (0.00226)	0.000289 (0.117)	0.00293 (1.00)	0.00946 (1.00)	0.0533 (1.00)	0.00705 (1.00)	0.142 (1.00)	0.000193 (0.0788)	0.00697 (1.00)	0.00487 (1.00)
Del Peak 12(8p11 21)	0 (0%)	135	0.000318 (0.129)	2.71e-05 (0.0114)	0.82 (1.00)	0.709 (1.00)	0.000359 (0.145)	0.00678 (1.00)	0.00119 (0.461)	0.568 (1.00)	0.000893 (0.351)	0.0518 (1.00)
Del Peak 20(17p13 1)	0 (0%)	143	5.83e-11 (2.63e-08)	0.0408 (1.00)	0.0139 (1.00)	0.0164 (1.00)	0.00218 (0.821)	2.25e-05 (0.00951)	0.0427 (1.00)	0.00109 (0.424)	0.00037 (0.149)	0.88 (1.00)
Del Peak 21(17q21 31)	0 (0%)	158	0.000171 (0.0701)	2.19e-06 (0.000961)	0.514 (1.00)	0.877 (1.00)	1.42e-05 (0.00604)	0.00159 (0.61)	0.029 (1.00)	0.217 (1.00)	0.0354 (1.00)	0.699 (1.00)
Amp Peak 1(1q21 3)	0 (0%)	180	1.87e-05 (0.00792)	0.00184 (0.7)	0.000652 (0.259)	0.00838 (1.00)	0.00458 (1.00)	0.000216 (0.0881)	0.102 (1.00)	0.053 (1.00)	0.00541 (1.00)	0.938 (1.00)
Del Peak 1(1p31 3)	0 (0%)	172	0.0688 (1.00)	0.000156 (0.0643)	0.558 (1.00)	0.823 (1.00)	0.00196 (0.741)	7.24e-05 (0.0302)	0.0707 (1.00)	0.142 (1.00)	0.0819 (1.00)	0.367 (1.00)
Del Peak 6(4q28 2)	0 (0%)	178	4.46e-06 (0.00193)	3.26e-05 (0.0137)	0.0725 (1.00)	0.0645 (1.00)	0.00745 (1.00)	0.0479 (1.00)	0.0933 (1.00)	0.06 (1.00)	0.00192 (0.728)	0.243 (1.00)
Del Peak 7(5q11 2)	0 (0%)	164	0.000606 (0.242)	0.000121 (0.0499)	0.00256 (0.955)	0.0144 (1.00)	0.0289 (1.00)	0.00272 (1.00)	0.0789 (1.00)	0.0213 (1.00)	0.309 (1.00)	0.717 (1.00)
Del Peak 8(5q21 1)	0 (0%)	162	1.08e-11 (4.89e-09)	5.81e-09 (2.59e-06)	0.1 (1.00)	0.123 (1.00)	0.00346 (1.00)	0.00889 (1.00)	0.0293 (1.00)	0.136 (1.00)	0.274 (1.00)	0.527 (1.00)
Del Peak 18(16q22 3)	0 (0%)	133	4.34e-12 (1.97e-09)	0.003 (1.00)	0.728 (1.00)	0.285 (1.00)	0.00203 (0.767)	7.67e-05 (0.0319)	0.0942 (1.00)	0.00492 (1.00)	0.0152 (1.00)	0.382 (1.00)
Amp Peak 2(3q26 2)	0 (0%)	166	0.000195 (0.0794)	0.0744 (1.00)	0.0468 (1.00)	0.158 (1.00)	0.169 (1.00)	0.147 (1.00)	0.29 (1.00)	0.0477 (1.00)	0.00644 (1.00)	0.27 (1.00)
Amp Peak 3(7p15 3)	0 (0%)	159	3.35e-09 (1.5e-06)	0.0014 (0.539)	0.245 (1.00)	0.274 (1.00)	0.0016 (0.611)	0.0309 (1.00)	0.246 (1.00)	0.00724 (1.00)	0.0309 (1.00)	0.393 (1.00)
Amp Peak 5(8p11 22)	0 (0%)	177	7.39e-08 (3.27e-05)	0.0674 (1.00)	0.191 (1.00)	0.186 (1.00)	0.0195 (1.00)	0.0317 (1.00)	0.22 (1.00)	0.0749 (1.00)	0.0152 (1.00)	0.533 (1.00)
Amp Peak 6(8q24 21)	0 (0%)	145	5.34e-12 (2.42e-09)	0.0438 (1.00)	0.0177 (1.00)	0.014 (1.00)	0.00243 (0.907)	0.00132 (0.509)	0.0744 (1.00)	0.0193 (1.00)	0.00265 (0.987)	0.589 (1.00)
Amp Peak 7(9q34 3)	0 (0%)	177	7.37e-06 (0.00316)	0.171 (1.00)	0.0866 (1.00)	0.0639 (1.00)	0.535 (1.00)	0.166 (1.00)	0.183 (1.00)	0.0303 (1.00)	0.132 (1.00)	0.634 (1.00)
Amp Peak 8(11q13 2)	0 (0%)	185	0.000532 (0.214)	0.134 (1.00)	0.476 (1.00)	0.35 (1.00)	0.05 (1.00)	0.222 (1.00)	0.999 (1.00)	0.259 (1.00)	0.504 (1.00)	0.631 (1.00)
Amp Peak 11(20q13 33)	0 (0%)	184	0.013 (1.00)	0.000612 (0.244)	0.561 (1.00)	0.652 (1.00)	0.0263 (1.00)	0.0102 (1.00)	0.992 (1.00)	0.0977 (1.00)	0.656 (1.00)	0.856 (1.00)
Del Peak 13(9p22 3)	0 (0%)	181	9.6e-05 (0.0398)	0.412 (1.00)	0.00509 (1.00)	0.00622 (1.00)	0.131 (1.00)	0.021 (1.00)	0.711 (1.00)	0.615 (1.00)	0.726 (1.00)	0.756 (1.00)
Del Peak 19(16q24 1)	0 (0%)	119	8.31e-16 (3.8e-13)	0.00124 (0.481)	0.855 (1.00)	0.658 (1.00)	0.00957 (1.00)	0.00428 (1.00)	0.107 (1.00)	0.00996 (1.00)	0.0113 (1.00)	0.366 (1.00)
Del Peak 22(18q23)	0 (0%)	142	6.8e-08 (3.02e-05)	0.571 (1.00)	0.974 (1.00)	0.69 (1.00)	0.143 (1.00)	0.142 (1.00)	0.673 (1.00)	0.958 (1.00)	0.582 (1.00)	0.632 (1.00)
Amp Peak 9(12q24 32)	0 (0%)	190	0.0109 (1.00)	0.233 (1.00)	0.231 (1.00)	0.229 (1.00)	1 (1.00)	0.108 (1.00)	0.498 (1.00)	0.534 (1.00)	0.216 (1.00)	0.116 (1.00)
Amp Peak 10(14q21 1)	0 (0%)	185	0.00112 (0.437)	0.0152 (1.00)	0.139 (1.00)	0.104 (1.00)	0.000723 (0.286)	0.19 (1.00)	0.139 (1.00)	0.00416 (1.00)	0.166 (1.00)	0.64 (1.00)
Amp Peak 12(Xp22 11)	0 (0%)	190	0.0787 (1.00)	1 (1.00)			0.4 (1.00)	0.796 (1.00)	0.159 (1.00)	0.0234 (1.00)	0.0441 (1.00)	0.0328 (1.00)
Amp Peak 13(Xp22 11)	0 (0%)	190	0.0787 (1.00)	0.891 (1.00)	0.126 (1.00)	0.322 (1.00)	0.511 (1.00)	0.796 (1.00)	0.0374 (1.00)	0.193 (1.00)	0.235 (1.00)	0.351 (1.00)
Amp Peak 14(Xp21 1)	0 (0%)	191	0.186 (1.00)	0.188 (1.00)	0.636 (1.00)	0.628 (1.00)	0.874 (1.00)	0.766 (1.00)	0.178 (1.00)	0.254 (1.00)	0.117 (1.00)	0.147 (1.00)
Amp Peak 15(Xq12)	0 (0%)	193	0.187 (1.00)	0.105 (1.00)	0.561 (1.00)	0.46 (1.00)	0.0353 (1.00)	0.178 (1.00)	0.532 (1.00)	0.307 (1.00)	0.00709 (1.00)	0.789 (1.00)
Amp Peak 16(Xq21 1)	0 (0%)	190	0.038 (1.00)	0.138 (1.00)	0.488 (1.00)	0.497 (1.00)	0.181 (1.00)	0.381 (1.00)	0.0822 (1.00)	0.727 (1.00)	0.288 (1.00)	0.248 (1.00)
Amp Peak 17(Xq21 1)	0 (0%)	192	0.171 (1.00)	0.00178 (0.679)	0.452 (1.00)	1 (1.00)	0.624 (1.00)	0.63 (1.00)	0.815 (1.00)	0.847 (1.00)	0.769 (1.00)	1 (1.00)
Amp Peak 18(Xq21 31)	0 (0%)	192	0.0598 (1.00)	0.86 (1.00)	0.636 (1.00)	0.628 (1.00)	0.376 (1.00)	0.118 (1.00)	0.548 (1.00)	0.728 (1.00)	0.553 (1.00)	0.693 (1.00)
Amp Peak 19(Xq25)	0 (0%)	193	0.187 (1.00)	0.254 (1.00)	0.631 (1.00)	1 (1.00)	0.465 (1.00)	1 (1.00)	0.151 (1.00)	0.152 (1.00)	0.285 (1.00)	0.19 (1.00)
Amp Peak 20(Xq25)	0 (0%)	191	0.42 (1.00)	0.586 (1.00)	0.88 (1.00)	0.77 (1.00)	0.169 (1.00)	0.661 (1.00)	0.794 (1.00)	0.436 (1.00)	0.423 (1.00)	0.506 (1.00)
Amp Peak 21(Xq27 1)	0 (0%)	188	0.642 (1.00)	0.292 (1.00)	0.425 (1.00)	0.347 (1.00)	0.912 (1.00)	0.91 (1.00)	0.0178 (1.00)	0.028 (1.00)	0.0367 (1.00)	0.0068 (1.00)
Del Peak 2(1q42 13)	0 (0%)	179	0.421 (1.00)	0.00285 (1.00)	0.875 (1.00)	0.121 (1.00)	0.711 (1.00)	0.706 (1.00)	0.0632 (1.00)	0.471 (1.00)	0.39 (1.00)	0.256 (1.00)
Del Peak 4(3p13)	0 (0%)	168	0.359 (1.00)	0.0162 (1.00)	0.685 (1.00)	0.96 (1.00)	0.105 (1.00)	0.107 (1.00)	0.264 (1.00)	0.883 (1.00)	0.124 (1.00)	0.0244 (1.00)
Del Peak 5(3q29)	0 (0%)	183	0.861 (1.00)	0.0398 (1.00)	0.846 (1.00)	0.6 (1.00)	0.0361 (1.00)	0.315 (1.00)	0.0462 (1.00)	0.445 (1.00)	0.129 (1.00)	0.505 (1.00)
Del Peak 10(7q36 1)	0 (0%)	187	0.434 (1.00)	0.781 (1.00)	0.0761 (1.00)	0.192 (1.00)	0.779 (1.00)	0.708 (1.00)	0.731 (1.00)	0.371 (1.00)	0.945 (1.00)	0.9 (1.00)
Del Peak 15(11q23 2)	0 (0%)	173	0.154 (1.00)	0.0871 (1.00)	0.198 (1.00)	0.137 (1.00)	0.482 (1.00)	0.533 (1.00)	0.423 (1.00)	0.343 (1.00)	0.123 (1.00)	1 (1.00)
Del Peak 16(12p13 2)	0 (0%)	156	0.000725 (0.286)	0.00299 (1.00)	0.0701 (1.00)	0.462 (1.00)	0.274 (1.00)	0.0569 (1.00)	0.023 (1.00)	0.357 (1.00)	0.0507 (1.00)	0.241 (1.00)
Del Peak 23(19q13 2)	0 (0%)	180	0.0305 (1.00)	0.0513 (1.00)	0.349 (1.00)	0.392 (1.00)	0.0658 (1.00)	0.133 (1.00)	0.103 (1.00)	0.0196 (1.00)	0.0152 (1.00)	0.166 (1.00)
Del Peak 24(21q22 2)	0 (0%)	179	0.0662 (1.00)	0.318 (1.00)	0.508 (1.00)	0.895 (1.00)	0.0532 (1.00)	0.00226 (0.847)	0.784 (1.00)	0.351 (1.00)	0.749 (1.00)	0.881 (1.00)

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

P value = 1.87e-05 (Fisher's exact test), Q value = 0.0079

Table S1. Gene #1: 'Amp Peak 1(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
AMP PEAK 1(1Q21.3) CNV	1	2	14
AMP PEAK 1(1Q21.3) WILD-TYPE	27	106	47

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000216 (Fisher's exact test), Q value = 0.088

Table S2. Gene #1: 'Amp Peak 1(1q21.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	68	77
AMP PEAK 1(1Q21.3) CNV	6	11	0
AMP PEAK 1(1Q21.3) WILD-TYPE	43	57	77

Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1q21.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(3q26.2)' versus 'CN_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.079

Table S3. Gene #2: 'Amp Peak 2(3q26.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
AMP PEAK 2(3Q26.2) CNV	6	7	18
AMP PEAK 2(3Q26.2) WILD-TYPE	22	101	43

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(3q26.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(7p15.3)' versus 'CN_CNMF'

P value = 3.35e-09 (Fisher's exact test), Q value = 1.5e-06

Table S4. Gene #3: 'Amp Peak 3(7p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
AMP PEAK 3(7P15.3) CNV	7	5	26
AMP PEAK 3(7P15.3) WILD-TYPE	21	103	35

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(7p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(7q34)' versus 'CN_CNMF'

P value = 8.59e-08 (Fisher's exact test), Q value = 3.8e-05

Table S5. Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
AMP PEAK 4(7Q34) CNV	7	5	23
AMP PEAK 4(7Q34) WILD-TYPE	21	103	38

Figure S5. Get High-res Image Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(7q34)' versus 'METHLYATION_CNMF'

P value = 4.98e-05 (Fisher's exact test), Q value = 0.021

Table S6. Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
AMP PEAK 4(7Q34) CNV	20	3	12
AMP PEAK 4(7Q34) WILD-TYPE	37	62	63

Figure S6. Get High-res Image Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 4(7q34)' versus 'MRNASEQ_CNMF'

P value = 0.000377 (Fisher's exact test), Q value = 0.15

Table S7. Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	60	67
AMP PEAK 4(7Q34) CNV	21	3	11
AMP PEAK 4(7Q34) WILD-TYPE	46	57	56

Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 5(8p11.22)' versus 'CN_CNMF'

P value = 7.39e-08 (Fisher's exact test), Q value = 3.3e-05

Table S8. Gene #5: 'Amp Peak 5(8p11.22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
AMP PEAK 5(8P11.22) CNV	6	0	14
AMP PEAK 5(8P11.22) WILD-TYPE	22	108	47

Figure S8. Get High-res Image Gene #5: 'Amp Peak 5(8p11.22)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(8q24.21)' versus 'CN_CNMF'

P value = 5.34e-12 (Fisher's exact test), Q value = 2.4e-09

Table S9. Gene #6: 'Amp Peak 6(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
AMP PEAK 6(8Q24.21) CNV	7	9	36
AMP PEAK 6(8Q24.21) WILD-TYPE	21	99	25

Figure S9. Get High-res Image Gene #6: 'Amp Peak 6(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 7(9q34.3)' versus 'CN_CNMF'

P value = 7.37e-06 (Fisher's exact test), Q value = 0.0032

Table S10. Gene #7: 'Amp Peak 7(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
AMP PEAK 7(9Q34.3) CNV	1	3	16
AMP PEAK 7(9Q34.3) WILD-TYPE	27	105	45

Figure S10. Get High-res Image Gene #7: 'Amp Peak 7(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 8(11q13.2)' versus 'CN_CNMF'

P value = 0.000532 (Fisher's exact test), Q value = 0.21

Table S11. Gene #8: 'Amp Peak 8(11q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
AMP PEAK 8(11Q13.2) CNV	0	2	10
AMP PEAK 8(11Q13.2) WILD-TYPE	28	106	51

Figure S11. Get High-res Image Gene #8: 'Amp Peak 8(11q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 11(20q13.33)' versus 'METHLYATION_CNMF'

P value = 0.000612 (Fisher's exact test), Q value = 0.24

Table S12. Gene #11: 'Amp Peak 11(20q13.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
AMP PEAK 11(20Q13.33) CNV	10	1	2
AMP PEAK 11(20Q13.33) WILD-TYPE	47	64	73

Figure S12. Get High-res Image Gene #11: 'Amp Peak 11(20q13.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 1(1p31.3)' versus 'METHLYATION_CNMF'

P value = 0.000156 (Fisher's exact test), Q value = 0.064

Table S13. Gene #22: 'Del Peak 1(1p31.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
DEL PEAK 1(1P31.3) CNV	6	1	18
DEL PEAK 1(1P31.3) WILD-TYPE	51	64	57

Figure S13. Get High-res Image Gene #22: 'Del Peak 1(1p31.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 1(1p31.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.24e-05 (Fisher's exact test), Q value = 0.03

Table S14. Gene #22: 'Del Peak 1(1p31.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	68	77
DEL PEAK 1(1P31.3) CNV	5	18	2
DEL PEAK 1(1P31.3) WILD-TYPE	44	50	75

Figure S14. Get High-res Image Gene #22: 'Del Peak 1(1p31.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q22.1)' versus 'CN_CNMF'

P value = 5.22e-06 (Fisher's exact test), Q value = 0.0023

Table S15. Gene #24: 'Del Peak 3(2q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 3(2Q22.1) CNV	9	3	12
DEL PEAK 3(2Q22.1) WILD-TYPE	19	105	49

Figure S15. Get High-res Image Gene #24: 'Del Peak 3(2q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 3(2q22.1)' versus 'METHLYATION_CNMF'

P value = 0.000289 (Fisher's exact test), Q value = 0.12

Table S16. Gene #24: 'Del Peak 3(2q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
DEL PEAK 3(2Q22.1) CNV	14	1	9
DEL PEAK 3(2Q22.1) WILD-TYPE	43	64	66

Figure S16. Get High-res Image Gene #24: 'Del Peak 3(2q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 3(2q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000193 (Fisher's exact test), Q value = 0.079

Table S17. Gene #24: 'Del Peak 3(2q22.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	21	74	67
DEL PEAK 3(2Q22.1) CNV	2	4	17	1
DEL PEAK 3(2Q22.1) WILD-TYPE	32	17	57	66

Figure S17. Get High-res Image Gene #24: 'Del Peak 3(2q22.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(4q28.2)' versus 'CN_CNMF'

P value = 4.46e-06 (Fisher's exact test), Q value = 0.0019

Table S18. Gene #27: 'Del Peak 6(4q28.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 6(4Q28.2) CNV	5	1	13
DEL PEAK 6(4Q28.2) WILD-TYPE	23	107	48

Figure S18. Get High-res Image Gene #27: 'Del Peak 6(4q28.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(4q28.2)' versus 'METHLYATION_CNMF'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.014

Table S19. Gene #27: 'Del Peak 6(4q28.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
DEL PEAK 6(4Q28.2) CNV	13	0	6
DEL PEAK 6(4Q28.2) WILD-TYPE	44	65	69

Figure S19. Get High-res Image Gene #27: 'Del Peak 6(4q28.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(5q11.2)' versus 'CN_CNMF'

P value = 0.000606 (Fisher's exact test), Q value = 0.24

Table S20. Gene #28: 'Del Peak 7(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 7(5Q11.2) CNV	5	9	19
DEL PEAK 7(5Q11.2) WILD-TYPE	23	99	42

Figure S20. Get High-res Image Gene #28: 'Del Peak 7(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 7(5q11.2)' versus 'METHLYATION_CNMF'

P value = 0.000121 (Fisher's exact test), Q value = 0.05

Table S21. Gene #28: 'Del Peak 7(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
DEL PEAK 7(5Q11.2) CNV	17	2	14
DEL PEAK 7(5Q11.2) WILD-TYPE	40	63	61

Figure S21. Get High-res Image Gene #28: 'Del Peak 7(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 8(5q21.1)' versus 'CN_CNMF'

P value = 1.08e-11 (Fisher's exact test), Q value = 4.9e-09

Table S22. Gene #29: 'Del Peak 8(5q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 8(5Q21.1) CNV	14	2	19
DEL PEAK 8(5Q21.1) WILD-TYPE	14	106	42

Figure S22. Get High-res Image Gene #29: 'Del Peak 8(5q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 8(5q21.1)' versus 'METHLYATION_CNMF'

P value = 5.81e-09 (Fisher's exact test), Q value = 2.6e-06

Table S23. Gene #29: 'Del Peak 8(5q21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
DEL PEAK 8(5Q21.1) CNV	25	2	8
DEL PEAK 8(5Q21.1) WILD-TYPE	32	63	67

Figure S23. Get High-res Image Gene #29: 'Del Peak 8(5q21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 9(6q15)' versus 'CN_CNMF'

P value = 7.92e-13 (Fisher's exact test), Q value = 3.6e-10

Table S24. Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 9(6Q15) CNV	21	12	30
DEL PEAK 9(6Q15) WILD-TYPE	7	96	31

Figure S24. Get High-res Image Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 9(6q15)' versus 'METHLYATION_CNMF'

P value = 3.43e-12 (Fisher's exact test), Q value = 1.6e-09

Table S25. Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
DEL PEAK 9(6Q15) CNV	36	3	24
DEL PEAK 9(6Q15) WILD-TYPE	21	62	51

Figure S25. Get High-res Image Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 9(6q15)' versus 'RPPA_CNMF'

P value = 0.000189 (Fisher's exact test), Q value = 0.077

Table S26. Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	41	56	57
DEL PEAK 9(6Q15) CNV	14	7	27
DEL PEAK 9(6Q15) WILD-TYPE	27	49	30

Figure S26. Get High-res Image Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #3: 'RPPA_CNMF'

'Del Peak 9(6q15)' versus 'MRNASEQ_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00049

Table S27. Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	60	67
DEL PEAK 9(6Q15) CNV	35	6	22
DEL PEAK 9(6Q15) WILD-TYPE	32	54	45

Figure S27. Get High-res Image Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 9(6q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.99e-07 (Fisher's exact test), Q value = 0.00035

Table S28. Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	68	77
DEL PEAK 9(6Q15) CNV	25	29	9
DEL PEAK 9(6Q15) WILD-TYPE	24	39	68

Figure S28. Get High-res Image Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(8p21.3)' versus 'CN_CNMF'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0012

Table S29. Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 11(8P21.3) CNV	10	52	50
DEL PEAK 11(8P21.3) WILD-TYPE	18	56	11

Figure S29. Get High-res Image Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(8p21.3)' versus 'METHLYATION_CNMF'

P value = 5.31e-08 (Fisher's exact test), Q value = 2.4e-05

Table S30. Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
DEL PEAK 11(8P21.3) CNV	31	21	60
DEL PEAK 11(8P21.3) WILD-TYPE	26	44	15

Figure S30. Get High-res Image Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 11(8p21.3)' versus 'MRNASEQ_CNMF'

P value = 1.79e-05 (Fisher's exact test), Q value = 0.0076

Table S31. Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	60	67
DEL PEAK 11(8P21.3) CNV	35	24	53
DEL PEAK 11(8P21.3) WILD-TYPE	32	36	14

Figure S31. Get High-res Image Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 11(8p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.65e-06 (Fisher's exact test), Q value = 0.0024

Table S32. Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	68	77
DEL PEAK 11(8P21.3) CNV	23	55	34
DEL PEAK 11(8P21.3) WILD-TYPE	26	13	43

Figure S32. Get High-res Image Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(8p21.3)' versus 'MIRSEQ_CNMF'

P value = 3.79e-06 (Chi-square test), Q value = 0.0016

Table S33. Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	52	39	17	14	74
DEL PEAK 11(8P21.3) CNV	42	14	8	2	45
DEL PEAK 11(8P21.3) WILD-TYPE	10	25	9	12	29

Figure S33. Get High-res Image Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 11(8p21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.67e-06 (Chi-square test), Q value = 0.0012

Table S34. Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	73	18	12	15	78
DEL PEAK 11(8P21.3) CNV	50	2	2	6	51
DEL PEAK 11(8P21.3) WILD-TYPE	23	16	10	9	27

Figure S34. Get High-res Image Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(8p11.21)' versus 'CN_CNMF'

P value = 0.000318 (Fisher's exact test), Q value = 0.13

Table S35. Gene #33: 'Del Peak 12(8p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 12(8P11.21) CNV	1	35	26
DEL PEAK 12(8P11.21) WILD-TYPE	27	73	35

Figure S35. Get High-res Image Gene #33: 'Del Peak 12(8p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(8p11.21)' versus 'METHLYATION_CNMF'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.011

Table S36. Gene #33: 'Del Peak 12(8p11.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
DEL PEAK 12(8P11.21) CNV	16	9	37
DEL PEAK 12(8P11.21) WILD-TYPE	41	56	38

Figure S36. Get High-res Image Gene #33: 'Del Peak 12(8p11.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 12(8p11.21)' versus 'MRNASEQ_CNMF'

P value = 0.000359 (Fisher's exact test), Q value = 0.15

Table S37. Gene #33: 'Del Peak 12(8p11.21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	60	67
DEL PEAK 12(8P11.21) CNV	19	10	33
DEL PEAK 12(8P11.21) WILD-TYPE	48	50	34

Figure S37. Get High-res Image Gene #33: 'Del Peak 12(8p11.21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 13(9p22.3)' versus 'CN_CNMF'

P value = 9.6e-05 (Fisher's exact test), Q value = 0.04

Table S38. Gene #34: 'Del Peak 13(9p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 13(9P22.3) CNV	0	3	13
DEL PEAK 13(9P22.3) WILD-TYPE	28	105	48

Figure S38. Get High-res Image Gene #34: 'Del Peak 13(9p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(10q23.31)' versus 'CN_CNMF'

P value = 3.88e-06 (Fisher's exact test), Q value = 0.0017

Table S39. Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 14(10Q23.31) CNV	6	26	37
DEL PEAK 14(10Q23.31) WILD-TYPE	22	82	24

Figure S39. Get High-res Image Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(10q23.31)' versus 'METHLYATION_CNMF'

P value = 1.03e-06 (Fisher's exact test), Q value = 0.00045

Table S40. Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
DEL PEAK 14(10Q23.31) CNV	15	11	43
DEL PEAK 14(10Q23.31) WILD-TYPE	42	54	32

Figure S40. Get High-res Image Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 14(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 1.68e-10 (Fisher's exact test), Q value = 7.5e-08

Table S41. Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	60	67
DEL PEAK 14(10Q23.31) CNV	15	9	45
DEL PEAK 14(10Q23.31) WILD-TYPE	52	51	22

Figure S41. Get High-res Image Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 14(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.28e-06 (Fisher's exact test), Q value = 0.0027

Table S42. Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	68	77
DEL PEAK 14(10Q23.31) CNV	11	40	18
DEL PEAK 14(10Q23.31) WILD-TYPE	38	28	59

Figure S42. Get High-res Image Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(13q14.13)' versus 'CN_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.044

Table S43. Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 17(13Q14.13) CNV	17	34	38
DEL PEAK 17(13Q14.13) WILD-TYPE	11	74	23

Figure S43. Get High-res Image Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(13q14.13)' versus 'METHLYATION_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0053

Table S44. Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
DEL PEAK 17(13Q14.13) CNV	33	14	42
DEL PEAK 17(13Q14.13) WILD-TYPE	24	51	33

Figure S44. Get High-res Image Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 17(13q14.13)' versus 'MRNASEQ_CNMF'

P value = 6.55e-05 (Fisher's exact test), Q value = 0.027

Table S45. Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	60	67
DEL PEAK 17(13Q14.13) CNV	33	14	41
DEL PEAK 17(13Q14.13) WILD-TYPE	34	46	26

Figure S45. Get High-res Image Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 17(13q14.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.43e-05 (Fisher's exact test), Q value = 0.019

Table S46. Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	68	77
DEL PEAK 17(13Q14.13) CNV	27	41	20
DEL PEAK 17(13Q14.13) WILD-TYPE	22	27	57

Figure S46. Get High-res Image Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(16q22.3)' versus 'CN_CNMF'

P value = 4.34e-12 (Fisher's exact test), Q value = 2e-09

Table S47. Gene #39: 'Del Peak 18(16q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 18(16Q22.3) CNV	4	18	42
DEL PEAK 18(16Q22.3) WILD-TYPE	24	90	19

Figure S47. Get High-res Image Gene #39: 'Del Peak 18(16q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 18(16q22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.67e-05 (Fisher's exact test), Q value = 0.032

Table S48. Gene #39: 'Del Peak 18(16q22.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	68	77
DEL PEAK 18(16Q22.3) CNV	9	36	19
DEL PEAK 18(16Q22.3) WILD-TYPE	40	32	58

Figure S48. Get High-res Image Gene #39: 'Del Peak 18(16q22.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(16q24.1)' versus 'CN_CNMF'

P value = 8.31e-16 (Fisher's exact test), Q value = 3.8e-13

Table S49. Gene #40: 'Del Peak 19(16q24.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 19(16Q24.1) CNV	4	24	50
DEL PEAK 19(16Q24.1) WILD-TYPE	24	84	11

Figure S49. Get High-res Image Gene #40: 'Del Peak 19(16q24.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(17p13.1)' versus 'CN_CNMF'

P value = 5.83e-11 (Fisher's exact test), Q value = 2.6e-08

Table S50. Gene #41: 'Del Peak 20(17p13.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 20(17P13.1) CNV	3	14	37
DEL PEAK 20(17P13.1) WILD-TYPE	25	94	24

Figure S50. Get High-res Image Gene #41: 'Del Peak 20(17p13.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(17p13.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.0095

Table S51. Gene #41: 'Del Peak 20(17p13.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	68	77
DEL PEAK 20(17P13.1) CNV	8	33	13
DEL PEAK 20(17P13.1) WILD-TYPE	41	35	64

Figure S51. Get High-res Image Gene #41: 'Del Peak 20(17p13.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(17p13.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Chi-square test), Q value = 0.15

Table S52. Gene #41: 'Del Peak 20(17p13.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	73	18	12	15	78
DEL PEAK 20(17P13.1) CNV	20	1	0	10	22
DEL PEAK 20(17P13.1) WILD-TYPE	53	17	12	5	56

Figure S52. Get High-res Image Gene #41: 'Del Peak 20(17p13.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 21(17q21.31)' versus 'CN_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.07

Table S53. Gene #42: 'Del Peak 21(17q21.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 21(17Q21.31) CNV	2	14	23
DEL PEAK 21(17Q21.31) WILD-TYPE	26	94	38

Figure S53. Get High-res Image Gene #42: 'Del Peak 21(17q21.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 21(17q21.31)' versus 'METHLYATION_CNMF'

P value = 2.19e-06 (Fisher's exact test), Q value = 0.00096

Table S54. Gene #42: 'Del Peak 21(17q21.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
DEL PEAK 21(17Q21.31) CNV	4	6	29
DEL PEAK 21(17Q21.31) WILD-TYPE	53	59	46

Figure S54. Get High-res Image Gene #42: 'Del Peak 21(17q21.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 21(17q21.31)' versus 'MRNASEQ_CNMF'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.006

Table S55. Gene #42: 'Del Peak 21(17q21.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	60	67
DEL PEAK 21(17Q21.31) CNV	9	4	26
DEL PEAK 21(17Q21.31) WILD-TYPE	58	56	41

Figure S55. Get High-res Image Gene #42: 'Del Peak 21(17q21.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 22(18q23)' versus 'CN_CNMF'

P value = 6.8e-08 (Fisher's exact test), Q value = 3e-05

Table S56. Gene #43: 'Del Peak 22(18q23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 22(18Q23) CNV	3	18	34
DEL PEAK 22(18Q23) WILD-TYPE	25	90	27

Figure S56. Get High-res Image Gene #43: 'Del Peak 22(18q23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 25(21q22.3)' versus 'CN_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0048

Table S57. Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	108	61
DEL PEAK 25(21Q22.3) CNV	1	32	31
DEL PEAK 25(21Q22.3) WILD-TYPE	27	76	30

Figure S57. Get High-res Image Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 25(21q22.3)' versus 'METHLYATION_CNMF'

P value = 1.2e-11 (Fisher's exact test), Q value = 5.4e-09

Table S58. Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	65	75
DEL PEAK 25(21Q22.3) CNV	7	10	47
DEL PEAK 25(21Q22.3) WILD-TYPE	50	55	28

Figure S58. Get High-res Image Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 25(21q22.3)' versus 'MRNASEQ_CNMF'

P value = 3.79e-14 (Fisher's exact test), Q value = 1.7e-11

Table S59. Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	60	67
DEL PEAK 25(21Q22.3) CNV	6	12	46
DEL PEAK 25(21Q22.3) WILD-TYPE	61	48	21

Figure S59. Get High-res Image Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 25(21q22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.89e-10 (Fisher's exact test), Q value = 1.3e-07

Table S60. Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	68	77
DEL PEAK 25(21Q22.3) CNV	2	40	22
DEL PEAK 25(21Q22.3) WILD-TYPE	47	28	55

Figure S60. Get High-res Image Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(21q22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000581 (Fisher's exact test), Q value = 0.23

Table S61. Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	21	74	67
DEL PEAK 25(21Q22.3) CNV	4	13	20	26
DEL PEAK 25(21Q22.3) WILD-TYPE	30	8	54	41

Figure S61. Get High-res Image Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = PRAD-TP.transferedmergedcluster.txt
Number of patients = 197
Number of copy number variation regions = 46
Number of molecular subtypes = 10
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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