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 43 peak regions and 10 molecular subtypes across 220 patients, 72 significant findings detected with Q value < 0.25.

Amp Peak 1(1q32.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 3(7p11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Amp Peak 4(7q32.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 5(8q24.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 6(10p15.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 9(12p13.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 12(19p13.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 13(19q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 15(Xq11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 1(1p36.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 2(1p32.3) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 4(2q37.3) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 7(4q33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
Del Peak 8(4q35.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 9(5q35.2) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 13(9p21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 14(10q26.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 15(11p15.5) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 17(12q24.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 18(13q14.2) cnvs correlated to 'MRNA_CHIERARCHICAL'.
Del Peak 25(19q13.42) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Del Peak 26(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 28(Xq21.1) cnvs correlated to 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 43 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 72 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	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	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test
Del Peak 2(1p32 3)	0 (0%)	143	0.0286 (1.00)	0.000173 (0.0611)	2.88e-37 (1.18e-34)	1e-38 (4.14e-36)	2.7e-18 (1.09e-15)	2.09e-23 (8.51e-21)	4.57e-11 (1.8e-08)	6.29e-05 (0.0226)	0.000248 (0.0876)	9.37e-07 (0.000356)
Del Peak 1(1p36 31)	0 (0%)	137	0.000549 (0.189)	5.86e-05 (0.0211)	3.69e-31 (1.51e-28)	2.03e-35 (8.33e-33)	4.44e-17 (1.78e-14)	7.5e-20 (3.04e-17)	1.39e-07 (5.37e-05)	0.00224 (0.728)	0.00194 (0.636)	6.83e-05 (0.0244)
Del Peak 14(10q26 2)	0 (0%)	150	0.179 (1.00)	0.022 (1.00)	1.05e-17 (4.23e-15)	4.21e-16 (1.68e-13)	1.09e-13 (4.32e-11)	2.8e-08 (1.09e-05)	1.15e-06 (0.000437)	0.000762 (0.258)	9.38e-05 (0.0333)	0.00293 (0.934)
Del Peak 25(19q13 42)	0 (0%)	104	0.0353 (1.00)	0.127 (1.00)	4.4e-29 (1.79e-26)	3.47e-21 (1.41e-18)	4.81e-11 (1.89e-08)	3.35e-12 (1.33e-09)	2.5e-07 (9.57e-05)	0.0523 (1.00)	0.000326 (0.114)	0.00227 (0.736)
Amp Peak 3(7p11 2)	0 (0%)	165	0.864 (1.00)	0.726 (1.00)	1.1e-18 (4.43e-16)	1.07e-12 (4.26e-10)	1.17e-09 (4.59e-07)	0.0172 (1.00)	0.000323 (0.113)	0.00905 (1.00)	0.00547 (1.00)	0.0025 (0.803)
Amp Peak 1(1q32 1)	0 (0%)	197			7.81e-07 (0.000298)	8.13e-05 (0.029)	1.9e-05 (0.00703)	0.378 (1.00)	0.741 (1.00)	0.14 (1.00)	0.578 (1.00)	0.0754 (1.00)
Amp Peak 4(7q32 3)	0 (0%)	143	0.764 (1.00)	0.755 (1.00)	8.39e-17 (3.36e-14)	2.3e-07 (8.85e-05)	2.53e-05 (0.00929)	0.0286 (1.00)	0.0202 (1.00)	0.13 (1.00)	0.0451 (1.00)	0.0582 (1.00)
Amp Peak 13(19q13 2)	0 (0%)	205	0.369 (1.00)	0.194 (1.00)	1.02e-06 (0.000386)	0.000338 (0.118)	0.000267 (0.0938)	0.0101 (1.00)	0.0129 (1.00)	0.00466 (1.00)	0.752 (1.00)	0.0251 (1.00)
Amp Peak 15(Xq11 2)	0 (0%)	189	0.282 (1.00)	0.653 (1.00)	3.63e-06 (0.00136)	1.23e-06 (0.000465)	0.0118 (1.00)	0.000397 (0.137)	0.0866 (1.00)	0.299 (1.00)	0.13 (1.00)	0.348 (1.00)
Del Peak 7(4q33)	0 (0%)	159	1 (1.00)	0.602 (1.00)	0.000502 (0.173)	0.000358 (0.124)	0.0319 (1.00)	0.0186 (1.00)	0.000573 (0.196)	0.264 (1.00)	0.0331 (1.00)	0.0427 (1.00)
Del Peak 15(11p15 5)	0 (0%)	172	0.642 (1.00)	0.000741 (0.252)	1.98e-07 (7.63e-05)	3.07e-09 (1.2e-06)	0.0248 (1.00)	0.000283 (0.0992)	0.163 (1.00)	0.576 (1.00)	0.389 (1.00)	0.284 (1.00)
Del Peak 26(22q13 31)	0 (0%)	189	0.25 (1.00)	0.0588 (1.00)	2.21e-06 (0.000831)	4.76e-05 (0.0173)	4.5e-05 (0.0164)	0.00189 (0.622)	0.215 (1.00)	0.178 (1.00)	0.0508 (1.00)	0.272 (1.00)
Amp Peak 5(8q24 21)	0 (0%)	176	0.37 (1.00)	0.164 (1.00)	6.87e-06 (0.00256)	7.76e-07 (0.000297)	0.00114 (0.382)	0.00189 (0.622)	0.0638 (1.00)	0.025 (1.00)	0.12 (1.00)	0.024 (1.00)
Amp Peak 6(10p15 1)	0 (0%)	185	0.467 (1.00)	0.473 (1.00)	2.61e-09 (1.02e-06)	6.52e-08 (2.53e-05)	0.00335 (1.00)	0.00473 (1.00)	0.0693 (1.00)	0.474 (1.00)	0.0779 (1.00)	0.34 (1.00)
Amp Peak 9(12p13 32)	0 (0%)	186	0.864 (1.00)	0.0486 (1.00)	1e-05 (0.00371)	3.78e-05 (0.0138)	0.0134 (1.00)	0.000959 (0.324)	0.0191 (1.00)	0.0333 (1.00)	0.00199 (0.649)	0.00378 (1.00)
Amp Peak 12(19p13 3)	0 (0%)	169	0.186 (1.00)	0.41 (1.00)	1.69e-09 (6.64e-07)	6.68e-06 (0.00249)	0.00459 (1.00)	0.00296 (0.942)	0.324 (1.00)	0.417 (1.00)	0.838 (1.00)	0.423 (1.00)
Del Peak 8(4q35 2)	0 (0%)	158	1 (1.00)	0.602 (1.00)	8.18e-05 (0.0291)	5.94e-05 (0.0214)	0.019 (1.00)	0.0166 (1.00)	0.00122 (0.405)	0.197 (1.00)	0.039 (1.00)	0.0252 (1.00)
Del Peak 13(9p21 3)	0 (0%)	142	0.333 (1.00)	0.0153 (1.00)	2.4e-07 (9.21e-05)	1.27e-05 (0.00471)	0.00679 (1.00)	0.0465 (1.00)	0.474 (1.00)	0.159 (1.00)	0.0148 (1.00)	0.278 (1.00)
Del Peak 17(12q24 11)	0 (0%)	190	1 (1.00)	0.0138 (1.00)	4.97e-05 (0.018)	3.98e-05 (0.0145)	0.312 (1.00)	0.00896 (1.00)	0.0298 (1.00)	0.635 (1.00)	0.278 (1.00)	0.615 (1.00)
Del Peak 4(2q37 3)	0 (0%)	188	0.18 (1.00)	0.116 (1.00)	0.00134 (0.443)	5.11e-06 (0.00191)	0.0218 (1.00)	0.0217 (1.00)	0.0819 (1.00)	0.15 (1.00)	0.401 (1.00)	0.16 (1.00)
Del Peak 9(5q35 2)	0 (0%)	192	0.446 (1.00)	0.0182 (1.00)	0.00261 (0.834)	0.00056 (0.192)	0.0301 (1.00)	0.0054 (1.00)	0.0114 (1.00)	0.0963 (1.00)	0.116 (1.00)	0.543 (1.00)
Del Peak 18(13q14 2)	0 (0%)	155	0.18 (1.00)	0.000618 (0.211)	0.054 (1.00)	0.0135 (1.00)	0.482 (1.00)	0.202 (1.00)	0.308 (1.00)	0.718 (1.00)	0.594 (1.00)	0.794 (1.00)
Del Peak 28(Xq21 1)	0 (0%)	190	0.73 (1.00)	0.00107 (0.36)	0.468 (1.00)	0.0258 (1.00)	0.00838 (1.00)	0.0258 (1.00)	2.6e-05 (0.00955)	0.878 (1.00)	0.0556 (1.00)	0.662 (1.00)
Amp Peak 2(4q12)	0 (0%)	210			0.503 (1.00)	0.565 (1.00)	0.393 (1.00)	0.543 (1.00)	0.647 (1.00)	0.159 (1.00)	0.445 (1.00)	0.3 (1.00)
Amp Peak 7(10q11 21)	0 (0%)	215			0.2 (1.00)	0.402 (1.00)	0.213 (1.00)	0.176 (1.00)	0.00601 (1.00)	1 (1.00)	0.00103 (0.347)	1 (1.00)
Amp Peak 8(11q23 3)	0 (0%)	182	0.0708 (1.00)	0.019 (1.00)	0.922 (1.00)	0.0504 (1.00)	0.217 (1.00)	0.23 (1.00)	0.625 (1.00)	0.498 (1.00)	0.0683 (1.00)	0.751 (1.00)
Amp Peak 10(12p11 22)	0 (0%)	199	1 (1.00)	0.0138 (1.00)	0.0212 (1.00)	0.0402 (1.00)	0.142 (1.00)	0.00329 (1.00)	0.0539 (1.00)	0.0914 (1.00)	0.00125 (0.416)	0.006 (1.00)
Amp Peak 11(12q14 1)	0 (0%)	206			0.122 (1.00)	0.596 (1.00)	0.029 (1.00)	0.328 (1.00)	0.941 (1.00)	0.499 (1.00)	0.324 (1.00)	1 (1.00)
Amp Peak 14(Xp22 33)	0 (0%)	205			0.00248 (0.798)	0.00629 (1.00)	0.323 (1.00)	0.0905 (1.00)	0.402 (1.00)	0.525 (1.00)	0.694 (1.00)	1 (1.00)
Del Peak 3(1q43)	0 (0%)	207			0.666 (1.00)	0.37 (1.00)	0.202 (1.00)	0.0861 (1.00)	0.65 (1.00)	0.239 (1.00)	0.203 (1.00)	0.152 (1.00)
Del Peak 5(3p21 1)	0 (0%)	200	1 (1.00)	0.00815 (1.00)	0.359 (1.00)	0.0204 (1.00)	0.94 (1.00)	0.0143 (1.00)	0.0297 (1.00)	0.0155 (1.00)	0.153 (1.00)	0.0415 (1.00)
Del Peak 6(3q29)	0 (0%)	199	0.175 (1.00)	0.561 (1.00)	0.00982 (1.00)	0.00542 (1.00)	0.114 (1.00)	0.074 (1.00)	0.464 (1.00)	0.164 (1.00)	0.989 (1.00)	0.553 (1.00)
Del Peak 10(6p24 1)	0 (0%)	199			0.131 (1.00)	0.34 (1.00)	0.436 (1.00)	0.233 (1.00)	0.568 (1.00)	0.515 (1.00)	0.265 (1.00)	0.0797 (1.00)
Del Peak 11(6q24 3)	0 (0%)	187	0.0479 (1.00)	0.194 (1.00)	0.0158 (1.00)	0.00992 (1.00)	0.269 (1.00)	0.0519 (1.00)	0.0309 (1.00)	0.24 (1.00)	0.0331 (1.00)	0.0554 (1.00)
Del Peak 12(8p23 2)	0 (0%)	209	1 (1.00)	0.0138 (1.00)	0.00696 (1.00)	0.00993 (1.00)	0.136 (1.00)	0.36 (1.00)	0.238 (1.00)	0.574 (1.00)	0.138 (1.00)	0.55 (1.00)
Del Peak 16(11q25)	0 (0%)	205			0.00183 (0.605)	0.0171 (1.00)	0.126 (1.00)	0.0905 (1.00)	0.282 (1.00)	0.0942 (1.00)	0.54 (1.00)	0.27 (1.00)
Del Peak 19(13q34)	0 (0%)	170	0.508 (1.00)	0.106 (1.00)	0.244 (1.00)	0.113 (1.00)	0.242 (1.00)	0.156 (1.00)	0.0514 (1.00)	0.471 (1.00)	0.0936 (1.00)	0.345 (1.00)
Del Peak 20(14q24 3)	0 (0%)	169	0.303 (1.00)	0.171 (1.00)	0.00236 (0.761)	0.0405 (1.00)	0.0253 (1.00)	0.118 (1.00)	0.00952 (1.00)	0.0226 (1.00)	0.00119 (0.398)	0.0949 (1.00)
Del Peak 21(15q21 3)	0 (0%)	193	0.839 (1.00)	0.653 (1.00)	0.0596 (1.00)	0.0268 (1.00)	0.00699 (1.00)	0.247 (1.00)	0.468 (1.00)	0.379 (1.00)	0.601 (1.00)	1 (1.00)
Del Peak 22(17q25 3)	0 (0%)	205			0.0206 (1.00)	0.18 (1.00)	0.658 (1.00)	0.367 (1.00)	0.238 (1.00)	0.677 (1.00)	0.899 (1.00)	0.371 (1.00)
Del Peak 23(18p11 32)	0 (0%)	188	0.321 (1.00)	0.316 (1.00)	0.552 (1.00)	0.0606 (1.00)	0.481 (1.00)	0.648 (1.00)	0.653 (1.00)	0.653 (1.00)	0.739 (1.00)	0.822 (1.00)
Del Peak 24(18q23)	0 (0%)	185	0.321 (1.00)	0.316 (1.00)	0.918 (1.00)	0.0429 (1.00)	0.489 (1.00)	0.875 (1.00)	0.701 (1.00)	0.263 (1.00)	0.546 (1.00)	0.419 (1.00)
Del Peak 27(Xp22 31)	0 (0%)	169	0.73 (1.00)	0.0182 (1.00)	0.517 (1.00)	0.263 (1.00)	0.548 (1.00)	0.0926 (1.00)	0.0225 (1.00)	0.154 (1.00)	0.0991 (1.00)	0.522 (1.00)

'Amp Peak 1(1q32.1)' versus 'CN_CNMF'

P value = 7.81e-07 (Fisher's exact test), Q value = 3e-04

Table S1. Gene #1: 'Amp Peak 1(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 1(1Q32.1) CNV	5	16	2
AMP PEAK 1(1Q32.1) WILD-TYPE	89	34	74

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 1(1q32.1)' versus 'METHLYATION_CNMF'

P value = 8.13e-05 (Fisher's exact test), Q value = 0.029

Table S2. Gene #1: 'Amp Peak 1(1q32.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
AMP PEAK 1(1Q32.1) CNV	8	12	1	2
AMP PEAK 1(1Q32.1) WILD-TYPE	90	22	27	53

Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1q32.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 1(1q32.1)' versus 'MRNASEQ_CNMF'

P value = 1.9e-05 (Chi-square test), Q value = 0.007

Table S3. Gene #1: 'Amp Peak 1(1q32.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
AMP PEAK 1(1Q32.1) CNV	1	13	1	8	0
AMP PEAK 1(1Q32.1) WILD-TYPE	59	29	34	62	11

Figure S3. Get High-res Image Gene #1: 'Amp Peak 1(1q32.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 3(7p11.2)' versus 'CN_CNMF'

P value = 1.1e-18 (Fisher's exact test), Q value = 4.4e-16

Table S4. Gene #3: 'Amp Peak 3(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 3(7P11.2) CNV	9	38	8
AMP PEAK 3(7P11.2) WILD-TYPE	85	12	68

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 3(7p11.2)' versus 'METHLYATION_CNMF'

P value = 1.07e-12 (Fisher's exact test), Q value = 4.3e-10

Table S5. Gene #3: 'Amp Peak 3(7p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
AMP PEAK 3(7P11.2) CNV	17	27	3	6
AMP PEAK 3(7P11.2) WILD-TYPE	81	7	25	49

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(7p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 3(7p11.2)' versus 'MRNASEQ_CNMF'

P value = 1.17e-09 (Chi-square test), Q value = 4.6e-07

Table S6. Gene #3: 'Amp Peak 3(7p11.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
AMP PEAK 3(7P11.2) CNV	14	27	4	9	0
AMP PEAK 3(7P11.2) WILD-TYPE	46	15	31	61	11

Figure S6. Get High-res Image Gene #3: 'Amp Peak 3(7p11.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 3(7p11.2)' versus 'MIRSEQ_CNMF'

P value = 0.000323 (Fisher's exact test), Q value = 0.11

Table S7. Gene #3: 'Amp Peak 3(7p11.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
AMP PEAK 3(7P11.2) CNV	19	3	12	20
AMP PEAK 3(7P11.2) WILD-TYPE	39	29	70	27

Figure S7. Get High-res Image Gene #3: 'Amp Peak 3(7p11.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Amp Peak 4(7q32.3)' versus 'CN_CNMF'

P value = 8.39e-17 (Fisher's exact test), Q value = 3.4e-14

Table S8. Gene #4: 'Amp Peak 4(7q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 4(7Q32.3) CNV	20	43	14
AMP PEAK 4(7Q32.3) WILD-TYPE	74	7	62

Figure S8. Get High-res Image Gene #4: 'Amp Peak 4(7q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(7q32.3)' versus 'METHLYATION_CNMF'

P value = 2.3e-07 (Fisher's exact test), Q value = 8.8e-05

Table S9. Gene #4: 'Amp Peak 4(7q32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
AMP PEAK 4(7Q32.3) CNV	35	25	3	12
AMP PEAK 4(7Q32.3) WILD-TYPE	63	9	25	43

Figure S9. Get High-res Image Gene #4: 'Amp Peak 4(7q32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 4(7q32.3)' versus 'MRNASEQ_CNMF'

P value = 2.53e-05 (Chi-square test), Q value = 0.0093

Table S10. Gene #4: 'Amp Peak 4(7q32.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
AMP PEAK 4(7Q32.3) CNV	26	26	7	16	1
AMP PEAK 4(7Q32.3) WILD-TYPE	34	16	28	54	10

Figure S10. Get High-res Image Gene #4: 'Amp Peak 4(7q32.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 5(8q24.21)' versus 'CN_CNMF'

P value = 6.87e-06 (Fisher's exact test), Q value = 0.0026

Table S11. Gene #5: 'Amp Peak 5(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 5(8Q24.21) CNV	32	8	4
AMP PEAK 5(8Q24.21) WILD-TYPE	62	42	72

Figure S11. Get High-res Image Gene #5: 'Amp Peak 5(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 5(8q24.21)' versus 'METHLYATION_CNMF'

P value = 7.76e-07 (Fisher's exact test), Q value = 3e-04

Table S12. Gene #5: 'Amp Peak 5(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
AMP PEAK 5(8Q24.21) CNV	36	4	1	3
AMP PEAK 5(8Q24.21) WILD-TYPE	62	30	27	52

Figure S12. Get High-res Image Gene #5: 'Amp Peak 5(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 6(10p15.1)' versus 'CN_CNMF'

P value = 2.61e-09 (Fisher's exact test), Q value = 1e-06

Table S13. Gene #6: 'Amp Peak 6(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 6(10P15.1) CNV	31	3	1
AMP PEAK 6(10P15.1) WILD-TYPE	63	47	75

Figure S13. Get High-res Image Gene #6: 'Amp Peak 6(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(10p15.1)' versus 'METHLYATION_CNMF'

P value = 6.52e-08 (Fisher's exact test), Q value = 2.5e-05

Table S14. Gene #6: 'Amp Peak 6(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
AMP PEAK 6(10P15.1) CNV	31	2	2	0
AMP PEAK 6(10P15.1) WILD-TYPE	67	32	26	55

Figure S14. Get High-res Image Gene #6: 'Amp Peak 6(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 9(12p13.32)' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0037

Table S15. Gene #9: 'Amp Peak 9(12p13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 9(12P13.32) CNV	27	4	3
AMP PEAK 9(12P13.32) WILD-TYPE	67	46	73

Figure S15. Get High-res Image Gene #9: 'Amp Peak 9(12p13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(12p13.32)' versus 'METHLYATION_CNMF'

P value = 3.78e-05 (Fisher's exact test), Q value = 0.014

Table S16. Gene #9: 'Amp Peak 9(12p13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
AMP PEAK 9(12P13.32) CNV	28	3	1	2
AMP PEAK 9(12P13.32) WILD-TYPE	70	31	27	53

Figure S16. Get High-res Image Gene #9: 'Amp Peak 9(12p13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 12(19p13.3)' versus 'CN_CNMF'

P value = 1.69e-09 (Fisher's exact test), Q value = 6.6e-07

Table S17. Gene #12: 'Amp Peak 12(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 12(19P13.3) CNV	4	15	32
AMP PEAK 12(19P13.3) WILD-TYPE	90	35	44

Figure S17. Get High-res Image Gene #12: 'Amp Peak 12(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(19p13.3)' versus 'METHLYATION_CNMF'

P value = 6.68e-06 (Fisher's exact test), Q value = 0.0025

Table S18. Gene #12: 'Amp Peak 12(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
AMP PEAK 12(19P13.3) CNV	9	10	4	24
AMP PEAK 12(19P13.3) WILD-TYPE	89	24	24	31

Figure S18. Get High-res Image Gene #12: 'Amp Peak 12(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 13(19q13.2)' versus 'CN_CNMF'

P value = 1.02e-06 (Fisher's exact test), Q value = 0.00039

Table S19. Gene #13: 'Amp Peak 13(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 13(19Q13.2) CNV	1	12	2
AMP PEAK 13(19Q13.2) WILD-TYPE	93	38	74

Figure S19. Get High-res Image Gene #13: 'Amp Peak 13(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(19q13.2)' versus 'METHLYATION_CNMF'

P value = 0.000338 (Fisher's exact test), Q value = 0.12

Table S20. Gene #13: 'Amp Peak 13(19q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
AMP PEAK 13(19Q13.2) CNV	4	8	2	0
AMP PEAK 13(19Q13.2) WILD-TYPE	94	26	26	55

Figure S20. Get High-res Image Gene #13: 'Amp Peak 13(19q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 13(19q13.2)' versus 'MRNASEQ_CNMF'

P value = 0.000267 (Chi-square test), Q value = 0.094

Table S21. Gene #13: 'Amp Peak 13(19q13.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
AMP PEAK 13(19Q13.2) CNV	3	9	0	1	1
AMP PEAK 13(19Q13.2) WILD-TYPE	57	33	35	69	10

Figure S21. Get High-res Image Gene #13: 'Amp Peak 13(19q13.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 15(Xq11.2)' versus 'CN_CNMF'

P value = 3.63e-06 (Fisher's exact test), Q value = 0.0014

Table S22. Gene #15: 'Amp Peak 15(Xq11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
AMP PEAK 15(XQ11.2) CNV	26	2	3
AMP PEAK 15(XQ11.2) WILD-TYPE	68	48	73

Figure S22. Get High-res Image Gene #15: 'Amp Peak 15(Xq11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(Xq11.2)' versus 'METHLYATION_CNMF'

P value = 1.23e-06 (Fisher's exact test), Q value = 0.00046

Table S23. Gene #15: 'Amp Peak 15(Xq11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
AMP PEAK 15(XQ11.2) CNV	27	3	1	0
AMP PEAK 15(XQ11.2) WILD-TYPE	71	31	27	55

Figure S23. Get High-res Image Gene #15: 'Amp Peak 15(Xq11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 15(Xq11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000397 (Fisher's exact test), Q value = 0.14

Table S24. Gene #15: 'Amp Peak 15(Xq11.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
AMP PEAK 15(XQ11.2) CNV	0	26	5
AMP PEAK 15(XQ11.2) WILD-TYPE	32	91	64

Figure S24. Get High-res Image Gene #15: 'Amp Peak 15(Xq11.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'MRNA_CNMF'

P value = 0.000549 (Fisher's exact test), Q value = 0.19

Table S25. Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	8
DEL PEAK 1(1P36.31) CNV	0	8	2
DEL PEAK 1(1P36.31) WILD-TYPE	9	2	6

Figure S25. Get High-res Image Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNA_CHIERARCHICAL'

P value = 5.86e-05 (Fisher's exact test), Q value = 0.021

Table S26. Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	6	10	4
DEL PEAK 1(1P36.31) CNV	7	2	0	1
DEL PEAK 1(1P36.31) WILD-TYPE	0	4	10	3

Figure S26. Get High-res Image Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'CN_CNMF'

P value = 3.69e-31 (Fisher's exact test), Q value = 1.5e-28

Table S27. Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 1(1P36.31) CNV	7	9	67
DEL PEAK 1(1P36.31) WILD-TYPE	87	41	9

Figure S27. Get High-res Image Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.31)' versus 'METHLYATION_CNMF'

P value = 2.03e-35 (Fisher's exact test), Q value = 8.3e-33

Table S28. Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
DEL PEAK 1(1P36.31) CNV	6	8	10	55
DEL PEAK 1(1P36.31) WILD-TYPE	92	26	18	0

Figure S28. Get High-res Image Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNASEQ_CNMF'

P value = 4.44e-17 (Chi-square test), Q value = 1.8e-14

Table S29. Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
DEL PEAK 1(1P36.31) CNV	4	10	34	32	3
DEL PEAK 1(1P36.31) WILD-TYPE	56	32	1	38	8

Figure S29. Get High-res Image Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.5e-20 (Fisher's exact test), Q value = 3e-17

Table S30. Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
DEL PEAK 1(1P36.31) CNV	32	19	32
DEL PEAK 1(1P36.31) WILD-TYPE	0	98	37

Figure S30. Get High-res Image Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_CNMF'

P value = 1.39e-07 (Fisher's exact test), Q value = 5.4e-05

Table S31. Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
DEL PEAK 1(1P36.31) CNV	12	22	41	8
DEL PEAK 1(1P36.31) WILD-TYPE	46	10	41	39

Figure S31. Get High-res Image Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.83e-05 (Fisher's exact test), Q value = 0.024

Table S32. Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	116	96
DEL PEAK 1(1P36.31) CNV	3	29	51
DEL PEAK 1(1P36.31) WILD-TYPE	4	87	45

Figure S32. Get High-res Image Gene #16: 'Del Peak 1(1p36.31)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000173 (Fisher's exact test), Q value = 0.061

Table S33. Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	6	10	4
DEL PEAK 2(1P32.3) CNV	7	2	1	0
DEL PEAK 2(1P32.3) WILD-TYPE	0	4	9	4

Figure S33. Get High-res Image Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'CN_CNMF'

P value = 2.88e-37 (Fisher's exact test), Q value = 1.2e-34

Table S34. Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 2(1P32.3) CNV	5	4	68
DEL PEAK 2(1P32.3) WILD-TYPE	89	46	8

Figure S34. Get High-res Image Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p32.3)' versus 'METHLYATION_CNMF'

P value = 1e-38 (Fisher's exact test), Q value = 4.1e-36

Table S35. Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
DEL PEAK 2(1P32.3) CNV	4	5	10	55
DEL PEAK 2(1P32.3) WILD-TYPE	94	29	18	0

Figure S35. Get High-res Image Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 2(1p32.3)' versus 'MRNASEQ_CNMF'

P value = 2.7e-18 (Chi-square test), Q value = 1.1e-15

Table S36. Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
DEL PEAK 2(1P32.3) CNV	4	5	33	32	3
DEL PEAK 2(1P32.3) WILD-TYPE	56	37	2	38	8

Figure S36. Get High-res Image Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 2(1p32.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.09e-23 (Fisher's exact test), Q value = 8.5e-21

Table S37. Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
DEL PEAK 2(1P32.3) CNV	32	13	32
DEL PEAK 2(1P32.3) WILD-TYPE	0	104	37

Figure S37. Get High-res Image Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_CNMF'

P value = 4.57e-11 (Fisher's exact test), Q value = 1.8e-08

Table S38. Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
DEL PEAK 2(1P32.3) CNV	11	22	41	3
DEL PEAK 2(1P32.3) WILD-TYPE	47	10	41	44

Figure S38. Get High-res Image Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.29e-05 (Fisher's exact test), Q value = 0.023

Table S39. Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	95	116
DEL PEAK 2(1P32.3) CNV	3	48	26
DEL PEAK 2(1P32.3) WILD-TYPE	5	47	90

Figure S39. Get High-res Image Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000248 (Chi-square test), Q value = 0.088

Table S40. Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	27	70	33	30	20
DEL PEAK 2(1P32.3) CNV	8	15	32	14	2	6
DEL PEAK 2(1P32.3) WILD-TYPE	31	12	38	19	28	14

Figure S40. Get High-res Image Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.37e-07 (Fisher's exact test), Q value = 0.00036

Table S41. Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	116	96
DEL PEAK 2(1P32.3) CNV	3	23	51
DEL PEAK 2(1P32.3) WILD-TYPE	4	93	45

Figure S41. Get High-res Image Gene #17: 'Del Peak 2(1p32.3)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 4(2q37.3)' versus 'METHLYATION_CNMF'

P value = 5.11e-06 (Fisher's exact test), Q value = 0.0019

Table S42. Gene #19: 'Del Peak 4(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
DEL PEAK 4(2Q37.3) CNV	28	1	1	2
DEL PEAK 4(2Q37.3) WILD-TYPE	70	33	27	53

Figure S42. Get High-res Image Gene #19: 'Del Peak 4(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 7(4q33)' versus 'CN_CNMF'

P value = 0.000502 (Fisher's exact test), Q value = 0.17

Table S43. Gene #22: 'Del Peak 7(4q33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 7(4Q33) CNV	25	5	31
DEL PEAK 7(4Q33) WILD-TYPE	69	45	45

Figure S43. Get High-res Image Gene #22: 'Del Peak 7(4q33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(4q33)' versus 'METHLYATION_CNMF'

P value = 0.000358 (Fisher's exact test), Q value = 0.12

Table S44. Gene #22: 'Del Peak 7(4q33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
DEL PEAK 7(4Q33) CNV	31	3	3	24
DEL PEAK 7(4Q33) WILD-TYPE	67	31	25	31

Figure S44. Get High-res Image Gene #22: 'Del Peak 7(4q33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 7(4q33)' versus 'MIRSEQ_CNMF'

P value = 0.000573 (Fisher's exact test), Q value = 0.2

Table S45. Gene #22: 'Del Peak 7(4q33)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
DEL PEAK 7(4Q33) CNV	7	17	24	13
DEL PEAK 7(4Q33) WILD-TYPE	51	15	58	34

Figure S45. Get High-res Image Gene #22: 'Del Peak 7(4q33)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 8(4q35.2)' versus 'CN_CNMF'

P value = 8.18e-05 (Fisher's exact test), Q value = 0.029

Table S46. Gene #23: 'Del Peak 8(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 8(4Q35.2) CNV	26	4	32
DEL PEAK 8(4Q35.2) WILD-TYPE	68	46	44

Figure S46. Get High-res Image Gene #23: 'Del Peak 8(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(4q35.2)' versus 'METHLYATION_CNMF'

P value = 5.94e-05 (Fisher's exact test), Q value = 0.021

Table S47. Gene #23: 'Del Peak 8(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
DEL PEAK 8(4Q35.2) CNV	33	2	3	24
DEL PEAK 8(4Q35.2) WILD-TYPE	65	32	25	31

Figure S47. Get High-res Image Gene #23: 'Del Peak 8(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 9(5q35.2)' versus 'METHLYATION_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.19

Table S48. Gene #24: 'Del Peak 9(5q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
DEL PEAK 9(5Q35.2) CNV	20	5	3	0
DEL PEAK 9(5Q35.2) WILD-TYPE	78	29	25	55

Figure S48. Get High-res Image Gene #24: 'Del Peak 9(5q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 13(9p21.3)' versus 'CN_CNMF'

P value = 2.4e-07 (Fisher's exact test), Q value = 9.2e-05

Table S49. Gene #28: 'Del Peak 13(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 13(9P21.3) CNV	28	34	16
DEL PEAK 13(9P21.3) WILD-TYPE	66	16	60

Figure S49. Get High-res Image Gene #28: 'Del Peak 13(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(9p21.3)' versus 'METHLYATION_CNMF'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.0047

Table S50. Gene #28: 'Del Peak 13(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
DEL PEAK 13(9P21.3) CNV	37	23	4	12
DEL PEAK 13(9P21.3) WILD-TYPE	61	11	24	43

Figure S50. Get High-res Image Gene #28: 'Del Peak 13(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(10q26.2)' versus 'CN_CNMF'

P value = 1.05e-17 (Fisher's exact test), Q value = 4.2e-15

Table S51. Gene #29: 'Del Peak 14(10q26.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 14(10Q26.2) CNV	27	39	4
DEL PEAK 14(10Q26.2) WILD-TYPE	67	11	72

Figure S51. Get High-res Image Gene #29: 'Del Peak 14(10q26.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(10q26.2)' versus 'METHLYATION_CNMF'

P value = 4.21e-16 (Fisher's exact test), Q value = 1.7e-13

Table S52. Gene #29: 'Del Peak 14(10q26.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
DEL PEAK 14(10Q26.2) CNV	32	30	4	3
DEL PEAK 14(10Q26.2) WILD-TYPE	66	4	24	52

Figure S52. Get High-res Image Gene #29: 'Del Peak 14(10q26.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(10q26.2)' versus 'MRNASEQ_CNMF'

P value = 1.09e-13 (Chi-square test), Q value = 4.3e-11

Table S53. Gene #29: 'Del Peak 14(10q26.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
DEL PEAK 14(10Q26.2) CNV	18	34	2	13	1
DEL PEAK 14(10Q26.2) WILD-TYPE	42	8	33	57	10

Figure S53. Get High-res Image Gene #29: 'Del Peak 14(10q26.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 14(10q26.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.8e-08 (Fisher's exact test), Q value = 1.1e-05

Table S54. Gene #29: 'Del Peak 14(10q26.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
DEL PEAK 14(10Q26.2) CNV	1	55	12
DEL PEAK 14(10Q26.2) WILD-TYPE	31	62	57

Figure S54. Get High-res Image Gene #29: 'Del Peak 14(10q26.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 14(10q26.2)' versus 'MIRSEQ_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00044

Table S55. Gene #29: 'Del Peak 14(10q26.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
DEL PEAK 14(10Q26.2) CNV	23	6	13	28
DEL PEAK 14(10Q26.2) WILD-TYPE	35	26	69	19

Figure S55. Get High-res Image Gene #29: 'Del Peak 14(10q26.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 14(10q26.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.38e-05 (Chi-square test), Q value = 0.033

Table S56. Gene #29: 'Del Peak 14(10q26.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	27	70	33	30	20
DEL PEAK 14(10Q26.2) CNV	20	4	13	16	14	3
DEL PEAK 14(10Q26.2) WILD-TYPE	19	23	57	17	16	17

Figure S56. Get High-res Image Gene #29: 'Del Peak 14(10q26.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 15(11p15.5)' versus 'CN_CNMF'

P value = 1.98e-07 (Fisher's exact test), Q value = 7.6e-05

Table S57. Gene #30: 'Del Peak 15(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 15(11P15.5) CNV	35	10	3
DEL PEAK 15(11P15.5) WILD-TYPE	59	40	73

Figure S57. Get High-res Image Gene #30: 'Del Peak 15(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(11p15.5)' versus 'METHLYATION_CNMF'

P value = 3.07e-09 (Fisher's exact test), Q value = 1.2e-06

Table S58. Gene #30: 'Del Peak 15(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
DEL PEAK 15(11P15.5) CNV	39	5	4	0
DEL PEAK 15(11P15.5) WILD-TYPE	59	29	24	55

Figure S58. Get High-res Image Gene #30: 'Del Peak 15(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 15(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000283 (Fisher's exact test), Q value = 0.099

Table S59. Gene #30: 'Del Peak 15(11p15.5)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
DEL PEAK 15(11P15.5) CNV	0	34	13
DEL PEAK 15(11P15.5) WILD-TYPE	32	83	56

Figure S59. Get High-res Image Gene #30: 'Del Peak 15(11p15.5)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(12q24.11)' versus 'CN_CNMF'

P value = 4.97e-05 (Fisher's exact test), Q value = 0.018

Table S60. Gene #32: 'Del Peak 17(12q24.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 17(12Q24.11) CNV	24	3	3
DEL PEAK 17(12Q24.11) WILD-TYPE	70	47	73

Figure S60. Get High-res Image Gene #32: 'Del Peak 17(12q24.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(12q24.11)' versus 'METHLYATION_CNMF'

P value = 3.98e-05 (Fisher's exact test), Q value = 0.015

Table S61. Gene #32: 'Del Peak 17(12q24.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
DEL PEAK 17(12Q24.11) CNV	25	1	3	1
DEL PEAK 17(12Q24.11) WILD-TYPE	73	33	25	54

Figure S61. Get High-res Image Gene #32: 'Del Peak 17(12q24.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(13q14.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000618 (Fisher's exact test), Q value = 0.21

Table S62. Gene #33: 'Del Peak 18(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	6	10	4
DEL PEAK 18(13Q14.2) CNV	0	0	5	4
DEL PEAK 18(13Q14.2) WILD-TYPE	7	6	5	0

Figure S62. Get High-res Image Gene #33: 'Del Peak 18(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 25(19q13.42)' versus 'CN_CNMF'

P value = 4.4e-29 (Fisher's exact test), Q value = 1.8e-26

Table S63. Gene #40: 'Del Peak 25(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 25(19Q13.42) CNV	26	14	76
DEL PEAK 25(19Q13.42) WILD-TYPE	68	36	0

Figure S63. Get High-res Image Gene #40: 'Del Peak 25(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(19q13.42)' versus 'METHLYATION_CNMF'

P value = 3.47e-21 (Fisher's exact test), Q value = 1.4e-18

Table S64. Gene #40: 'Del Peak 25(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
DEL PEAK 25(19Q13.42) CNV	42	4	12	55
DEL PEAK 25(19Q13.42) WILD-TYPE	56	30	16	0

Figure S64. Get High-res Image Gene #40: 'Del Peak 25(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(19q13.42)' versus 'MRNASEQ_CNMF'

P value = 4.81e-11 (Chi-square test), Q value = 1.9e-08

Table S65. Gene #40: 'Del Peak 25(19q13.42)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
DEL PEAK 25(19Q13.42) CNV	24	9	35	43	5
DEL PEAK 25(19Q13.42) WILD-TYPE	36	33	0	27	6

Figure S65. Get High-res Image Gene #40: 'Del Peak 25(19q13.42)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 25(19q13.42)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.35e-12 (Fisher's exact test), Q value = 1.3e-09

Table S66. Gene #40: 'Del Peak 25(19q13.42)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	32	117	69
DEL PEAK 25(19Q13.42) CNV	32	42	42
DEL PEAK 25(19Q13.42) WILD-TYPE	0	75	27

Figure S66. Get High-res Image Gene #40: 'Del Peak 25(19q13.42)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_CNMF'

P value = 2.5e-07 (Fisher's exact test), Q value = 9.6e-05

Table S67. Gene #40: 'Del Peak 25(19q13.42)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
DEL PEAK 25(19Q13.42) CNV	25	28	50	13
DEL PEAK 25(19Q13.42) WILD-TYPE	33	4	32	34

Figure S67. Get High-res Image Gene #40: 'Del Peak 25(19q13.42)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000326 (Chi-square test), Q value = 0.11

Table S68. Gene #40: 'Del Peak 25(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	27	70	33	30	20
DEL PEAK 25(19Q13.42) CNV	16	22	42	18	7	11
DEL PEAK 25(19Q13.42) WILD-TYPE	23	5	28	15	23	9

Figure S68. Get High-res Image Gene #40: 'Del Peak 25(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 26(22q13.31)' versus 'CN_CNMF'

P value = 2.21e-06 (Fisher's exact test), Q value = 0.00083

Table S69. Gene #41: 'Del Peak 26(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	50	76
DEL PEAK 26(22Q13.31) CNV	14	16	1
DEL PEAK 26(22Q13.31) WILD-TYPE	80	34	75

Figure S69. Get High-res Image Gene #41: 'Del Peak 26(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(22q13.31)' versus 'METHLYATION_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.017

Table S70. Gene #41: 'Del Peak 26(22q13.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	98	34	28	55
DEL PEAK 26(22Q13.31) CNV	18	10	2	0
DEL PEAK 26(22Q13.31) WILD-TYPE	80	24	26	55

Figure S70. Get High-res Image Gene #41: 'Del Peak 26(22q13.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(22q13.31)' versus 'MRNASEQ_CNMF'

P value = 4.5e-05 (Chi-square test), Q value = 0.016

Table S71. Gene #41: 'Del Peak 26(22q13.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	42	35	70	11
DEL PEAK 26(22Q13.31) CNV	8	15	0	7	0
DEL PEAK 26(22Q13.31) WILD-TYPE	52	27	35	63	11

Figure S71. Get High-res Image Gene #41: 'Del Peak 26(22q13.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 28(Xq21.1)' versus 'MIRSEQ_CNMF'

P value = 2.6e-05 (Fisher's exact test), Q value = 0.0096

Table S72. Gene #43: 'Del Peak 28(Xq21.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	32	82	47
DEL PEAK 28(XQ21.1) CNV	4	12	4	10
DEL PEAK 28(XQ21.1) WILD-TYPE	54	20	78	37

Figure S72. Get High-res Image Gene #43: 'Del Peak 28(Xq21.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = LGG-TP.transferedmergedcluster.txt
Number of patients = 220
Number of copy number variation regions = 43
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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