Correlation between copy number variation genes (focal events) and molecular subtypes
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 40 focal events and 10 molecular subtypes across 452 patients, 80 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 1q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 2p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 2q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 3p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 3q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 4p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 5q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 6p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 6q cnv correlated to 'CN_CNMF'.

  • 7p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 7q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 8p cnv correlated to 'CN_CNMF'.

  • 8q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 9p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 9q cnv correlated to 'CN_CNMF'.

  • 10p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 10q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 11p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 11q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 12p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 12q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 13q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 14q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 15q cnv correlated to 'CN_CNMF'.

  • 16p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 16q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 17p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 17q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 18p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 18q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 20p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 20q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 21q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 22q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • xq cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 40 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 80 significant findings detected.

Clinical
Features 		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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test
4p 199 (44%) 253 6.71e-18
(2.66e-15) 		7.47e-15
(2.94e-12) 		0.225
(1.00) 		0.612
(1.00) 		0.0202
(1.00) 		0.00032
(0.103) 		0.15
(1.00) 		0.405
(1.00) 		0.058
(1.00) 		4.5e-06
(0.00154)
3q 275 (61%) 177 3.51e-08
(1.29e-05) 		1.24e-06
(0.00043) 		0.203
(1.00) 		0.585
(1.00) 		0.00109
(0.348) 		0.00174
(0.55) 		0.000331
(0.107) 		0.0725
(1.00) 		0.0484
(1.00) 		0.089
(1.00)
4q 161 (36%) 291 1.93e-11
(7.46e-09) 		4.25e-09
(1.62e-06) 		0.586
(1.00) 		0.416
(1.00) 		0.0852
(1.00) 		0.0201
(1.00) 		0.033
(1.00) 		0.658
(1.00) 		0.236
(1.00) 		0.000357
(0.115)
1p 103 (23%) 349 1.03e-08
(3.88e-06) 		1.15e-07
(4.14e-05) 		0.156
(1.00) 		0.851
(1.00) 		0.0627
(1.00) 		0.192
(1.00) 		0.0827
(1.00) 		0.649
(1.00) 		0.42
(1.00) 		0.0154
(1.00)
1q 134 (30%) 318 4.9e-08
(1.79e-05) 		4.88e-08
(1.79e-05) 		0.222
(1.00) 		0.943
(1.00) 		0.0149
(1.00) 		0.0146
(1.00) 		0.0268
(1.00) 		0.652
(1.00) 		0.0545
(1.00) 		0.00366
(1.00)
2p 109 (24%) 343 2.13e-08
(7.89e-06) 		8.95e-09
(3.37e-06) 		0.19
(1.00) 		0.55
(1.00) 		0.38
(1.00) 		0.221
(1.00) 		0.612
(1.00) 		0.223
(1.00) 		0.737
(1.00) 		0.0138
(1.00)
2q 102 (23%) 350 0.000282
(0.0912) 		8.47e-05
(0.028) 		0.36
(1.00) 		0.896
(1.00) 		0.153
(1.00) 		0.0448
(1.00) 		0.479
(1.00) 		0.095
(1.00) 		0.57
(1.00) 		0.0595
(1.00)
3p 330 (73%) 122 2.61e-32
(1.04e-29) 		4.09e-15
(1.62e-12) 		0.49
(1.00) 		0.171
(1.00) 		0.0436
(1.00) 		0.0527
(1.00) 		0.00102
(0.326) 		0.0497
(1.00) 		0.04
(1.00) 		0.00247
(0.779)
5p 207 (46%) 245 1.12e-14
(4.41e-12) 		1.4e-09
(5.36e-07) 		0.857
(1.00) 		0.466
(1.00) 		0.0652
(1.00) 		0.278
(1.00) 		0.363
(1.00) 		0.869
(1.00) 		0.0873
(1.00) 		0.824
(1.00)
5q 197 (44%) 255 2.25e-19
(8.97e-17) 		1.42e-15
(5.61e-13) 		0.434
(1.00) 		0.0795
(1.00) 		0.149
(1.00) 		0.00303
(0.946) 		0.309
(1.00) 		0.431
(1.00) 		0.2
(1.00) 		0.218
(1.00)
6p 126 (28%) 326 4.46e-07
(0.000156) 		4.31e-05
(0.0144) 		0.284
(1.00) 		0.453
(1.00) 		0.475
(1.00) 		0.249
(1.00) 		0.758
(1.00) 		0.246
(1.00) 		0.674
(1.00) 		0.027
(1.00)
7p 186 (41%) 266 1.27e-11
(4.9e-09) 		1.63e-08
(6.07e-06) 		0.13
(1.00) 		0.831
(1.00) 		0.623
(1.00) 		0.852
(1.00) 		0.204
(1.00) 		0.133
(1.00) 		0.636
(1.00) 		0.0838
(1.00)
7q 150 (33%) 302 2.76e-07
(9.76e-05) 		1.38e-07
(4.93e-05) 		0.0432
(1.00) 		0.925
(1.00) 		0.54
(1.00) 		0.214
(1.00) 		0.132
(1.00) 		0.51
(1.00) 		0.248
(1.00) 		0.0223
(1.00)
8q 297 (66%) 155 8.91e-05
(0.0293) 		0.00019
(0.0618) 		0.0704
(1.00) 		0.575
(1.00) 		0.113
(1.00) 		0.087
(1.00) 		0.19
(1.00) 		0.0191
(1.00) 		0.443
(1.00) 		0.0231
(1.00)
9p 241 (53%) 211 4.08e-18
(1.62e-15) 		5.73e-09
(2.17e-06) 		0.569
(1.00) 		0.881
(1.00) 		0.636
(1.00) 		0.719
(1.00) 		0.464
(1.00) 		0.236
(1.00) 		0.9
(1.00) 		0.0515
(1.00)
10p 168 (37%) 284 8.35e-08
(3.01e-05) 		3.01e-05
(0.0101) 		0.278
(1.00) 		0.296
(1.00) 		0.715
(1.00) 		0.128
(1.00) 		0.163
(1.00) 		0.158
(1.00) 		0.226
(1.00) 		0.0251
(1.00)
10q 123 (27%) 329 4.51e-07
(0.000158) 		6.06e-05
(0.0201) 		0.0501
(1.00) 		0.123
(1.00) 		0.145
(1.00) 		0.00616
(1.00) 		0.451
(1.00) 		0.531
(1.00) 		0.0895
(1.00) 		0.0564
(1.00)
11p 172 (38%) 280 7.31e-08
(2.64e-05) 		8.89e-05
(0.0293) 		0.529
(1.00) 		0.814
(1.00) 		0.101
(1.00) 		0.579
(1.00) 		0.144
(1.00) 		0.964
(1.00) 		0.293
(1.00) 		0.478
(1.00)
11q 199 (44%) 253 7.89e-07
(0.000276) 		1.78e-05
(0.00605) 		0.334
(1.00) 		0.644
(1.00) 		0.116
(1.00) 		0.598
(1.00) 		0.623
(1.00) 		0.863
(1.00) 		0.326
(1.00) 		0.753
(1.00)
12p 154 (34%) 298 1.11e-08
(4.13e-06) 		5.53e-06
(0.00189) 		0.021
(1.00) 		0.207
(1.00) 		0.00934
(1.00) 		0.0052
(1.00) 		0.158
(1.00) 		0.491
(1.00) 		0.062
(1.00) 		0.0379
(1.00)
12q 101 (22%) 351 4.02e-06
(0.00138) 		4.66e-05
(0.0155) 		0.0744
(1.00) 		0.0854
(1.00) 		0.142
(1.00) 		0.0505
(1.00) 		0.362
(1.00) 		0.826
(1.00) 		0.229
(1.00) 		0.341
(1.00)
13q 196 (43%) 256 8.85e-11
(3.41e-08) 		2.62e-09
(9.97e-07) 		0.29
(1.00) 		0.574
(1.00) 		0.0475
(1.00) 		0.00405
(1.00) 		0.196
(1.00) 		0.325
(1.00) 		0.206
(1.00) 		0.0477
(1.00)
14q 175 (39%) 277 1.97e-07
(7e-05) 		5.49e-05
(0.0183) 		0.585
(1.00) 		0.944
(1.00) 		0.621
(1.00) 		0.424
(1.00) 		0.36
(1.00) 		0.00691
(1.00) 		0.636
(1.00) 		0.0123
(1.00)
16p 146 (32%) 306 4.45e-09
(1.69e-06) 		9.01e-07
(0.000314) 		0.48
(1.00) 		0.827
(1.00) 		0.832
(1.00) 		0.288
(1.00) 		0.752
(1.00) 		0.126
(1.00) 		0.606
(1.00) 		0.0869
(1.00)
16q 162 (36%) 290 2.72e-05
(0.00919) 		1.08e-06
(0.000375) 		0.326
(1.00) 		0.241
(1.00) 		0.0135
(1.00) 		0.0012
(0.382) 		0.106
(1.00) 		0.661
(1.00) 		0.00409
(1.00) 		0.0585
(1.00)
17p 155 (34%) 297 1.43e-12
(5.59e-10) 		6.95e-08
(2.52e-05) 		0.464
(1.00) 		0.052
(1.00) 		0.00674
(1.00) 		0.00488
(1.00) 		0.0511
(1.00) 		0.155
(1.00) 		0.0558
(1.00) 		0.308
(1.00)
17q 106 (23%) 346 3.58e-08
(1.32e-05) 		0.000119
(0.039) 		0.589
(1.00) 		0.0463
(1.00) 		0.149
(1.00) 		0.147
(1.00) 		0.334
(1.00) 		0.43
(1.00) 		0.311
(1.00) 		0.174
(1.00)
18p 193 (43%) 259 1.2e-11
(4.65e-09) 		4.4e-08
(1.61e-05) 		0.801
(1.00) 		0.331
(1.00) 		0.119
(1.00) 		0.02
(1.00) 		0.221
(1.00) 		0.882
(1.00) 		0.018
(1.00) 		0.0189
(1.00)
18q 228 (50%) 224 2.39e-12
(9.32e-10) 		1.06e-08
(3.97e-06) 		0.751
(1.00) 		0.117
(1.00) 		0.0568
(1.00) 		0.0035
(1.00) 		0.164
(1.00) 		0.0241
(1.00) 		0.463
(1.00) 		0.0451
(1.00)
19p 127 (28%) 325 0.000201
(0.0652) 		3.91e-05
(0.0131) 		0.283
(1.00) 		0.712
(1.00) 		0.0403
(1.00) 		0.31
(1.00) 		0.862
(1.00) 		0.596
(1.00) 		0.295
(1.00) 		0.337
(1.00)
19q 134 (30%) 318 1.89e-05
(0.0064) 		1.97e-07
(7e-05) 		0.138
(1.00) 		0.374
(1.00) 		0.0798
(1.00) 		0.175
(1.00) 		0.0358
(1.00) 		0.965
(1.00) 		0.593
(1.00) 		0.107
(1.00)
20p 209 (46%) 243 1.03e-07
(3.69e-05) 		1.62e-07
(5.79e-05) 		0.572
(1.00) 		0.0268
(1.00) 		0.0343
(1.00) 		0.236
(1.00) 		0.329
(1.00) 		0.0911
(1.00) 		0.757
(1.00) 		0.0796
(1.00)
20q 203 (45%) 249 3.67e-07
(0.000129) 		1.93e-06
(0.000664) 		0.917
(1.00) 		0.407
(1.00) 		0.0281
(1.00) 		0.191
(1.00) 		0.341
(1.00) 		0.0468
(1.00) 		0.617
(1.00) 		0.26
(1.00)
21q 191 (42%) 261 7.74e-12
(3.01e-09) 		9.19e-09
(3.45e-06) 		0.931
(1.00) 		0.728
(1.00) 		0.368
(1.00) 		0.45
(1.00) 		0.774
(1.00) 		0.534
(1.00) 		0.745
(1.00) 		0.052
(1.00)
22q 162 (36%) 290 2.22e-06
(0.000762) 		3.46e-07
(0.000122) 		0.388
(1.00) 		0.876
(1.00) 		0.648
(1.00) 		0.408
(1.00) 		0.739
(1.00) 		0.234
(1.00) 		0.289
(1.00) 		0.00655
(1.00)
xq 143 (32%) 309 2.58e-08
(9.54e-06) 		6.39e-10
(2.45e-07) 		0.175
(1.00) 		0.0434
(1.00) 		0.138
(1.00) 		0.0331
(1.00) 		0.00417
(1.00) 		0.915
(1.00) 		0.375
(1.00) 		0.00863
(1.00)
6q 110 (24%) 342 0.000109
(0.0358) 		0.0234
(1.00) 		0.529
(1.00) 		1
(1.00) 		0.155
(1.00) 		0.563
(1.00) 		0.613
(1.00) 		0.246
(1.00) 		0.933
(1.00) 		0.865
(1.00)
8p 295 (65%) 157 5.32e-08
(1.94e-05) 		0.00254
(0.796) 		0.935
(1.00) 		0.664
(1.00) 		0.736
(1.00) 		0.317
(1.00) 		0.644
(1.00) 		0.0583
(1.00) 		0.701
(1.00) 		0.0429
(1.00)
9q 190 (42%) 262 1.2e-12
(4.69e-10) 		0.00253
(0.793) 		0.305
(1.00) 		0.208
(1.00) 		0.579
(1.00) 		0.246
(1.00) 		0.908
(1.00) 		0.352
(1.00) 		0.414
(1.00) 		0.102
(1.00)
15q 149 (33%) 303 1.08e-09
(4.13e-07) 		0.00127
(0.402) 		0.362
(1.00) 		0.397
(1.00) 		0.158
(1.00) 		0.695
(1.00) 		0.717
(1.00) 		0.548
(1.00) 		0.874
(1.00) 		0.383
(1.00)
'1p' versus 'CN_CNMF'

P value = 1.03e-08 (Fisher's exact test), Q value = 3.9e-06

Table S1.  Gene #1: '1p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
1P MUTATED 77 17 9
1P WILD-TYPE 148 160 41

Figure S1.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #1: 'CN_CNMF'

'1p' versus 'METHLYATION_CNMF'

P value = 1.15e-07 (Chi-square test), Q value = 4.1e-05

Table S2.  Gene #1: '1p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
1P MUTATED 14 24 37 7 8 10 3
1P WILD-TYPE 53 53 43 58 64 64 14

Figure S2.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q' versus 'CN_CNMF'

P value = 4.9e-08 (Fisher's exact test), Q value = 1.8e-05

Table S3.  Gene #2: '1q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
1Q MUTATED 93 27 14
1Q WILD-TYPE 132 150 36

Figure S3.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #1: 'CN_CNMF'

'1q' versus 'METHLYATION_CNMF'

P value = 4.88e-08 (Chi-square test), Q value = 1.8e-05

Table S4.  Gene #2: '1q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
1Q MUTATED 24 30 42 12 9 12 5
1Q WILD-TYPE 43 47 38 53 63 62 12

Figure S4.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p' versus 'CN_CNMF'

P value = 2.13e-08 (Fisher's exact test), Q value = 7.9e-06

Table S5.  Gene #3: '2p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
2P MUTATED 78 18 13
2P WILD-TYPE 147 159 37

Figure S5.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #1: 'CN_CNMF'

'2p' versus 'METHLYATION_CNMF'

P value = 8.95e-09 (Chi-square test), Q value = 3.4e-06

Table S6.  Gene #3: '2p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
2P MUTATED 26 27 32 9 9 4 2
2P WILD-TYPE 41 50 48 56 63 70 15

Figure S6.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q' versus 'CN_CNMF'

P value = 0.000282 (Fisher's exact test), Q value = 0.091

Table S7.  Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
2Q MUTATED 68 24 10
2Q WILD-TYPE 157 153 40

Figure S7.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

'2q' versus 'METHLYATION_CNMF'

P value = 8.47e-05 (Chi-square test), Q value = 0.028

Table S8.  Gene #4: '2q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
2Q MUTATED 24 24 25 12 9 6 2
2Q WILD-TYPE 43 53 55 53 63 68 15

Figure S8.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p' versus 'CN_CNMF'

P value = 2.61e-32 (Fisher's exact test), Q value = 1e-29

Table S9.  Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
3P MUTATED 212 75 43
3P WILD-TYPE 13 102 7

Figure S9.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

'3p' versus 'METHLYATION_CNMF'

P value = 4.09e-15 (Chi-square test), Q value = 1.6e-12

Table S10.  Gene #5: '3p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
3P MUTATED 59 69 73 37 31 46 15
3P WILD-TYPE 8 8 7 28 41 28 2

Figure S10.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q' versus 'CN_CNMF'

P value = 3.51e-08 (Fisher's exact test), Q value = 1.3e-05

Table S11.  Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
3Q MUTATED 162 78 35
3Q WILD-TYPE 63 99 15

Figure S11.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

'3q' versus 'METHLYATION_CNMF'

P value = 1.24e-06 (Chi-square test), Q value = 0.00043

Table S12.  Gene #6: '3q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
3Q MUTATED 47 57 58 42 25 38 8
3Q WILD-TYPE 20 20 22 23 47 36 9

Figure S12.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q' versus 'MIRSEQ_CNMF'

P value = 0.000331 (Fisher's exact test), Q value = 0.11

Table S13.  Gene #6: '3q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 182 129
3Q MUTATED 73 131 71
3Q WILD-TYPE 67 51 58

Figure S13.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p' versus 'CN_CNMF'

P value = 6.71e-18 (Fisher's exact test), Q value = 2.7e-15

Table S14.  Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
4P MUTATED 143 36 20
4P WILD-TYPE 82 141 30

Figure S14.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 7.47e-15 (Chi-square test), Q value = 2.9e-12

Table S15.  Gene #7: '4p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
4P MUTATED 39 40 59 22 13 15 11
4P WILD-TYPE 28 37 21 43 59 59 6

Figure S15.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.1

Table S16.  Gene #7: '4p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 101 158
4P MUTATED 84 28 74
4P WILD-TYPE 77 73 84

Figure S16.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.5e-06 (Chi-square test), Q value = 0.0015

Table S17.  Gene #7: '4p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 40 91 46 155 79
4P MUTATED 2 10 24 21 67 52
4P WILD-TYPE 2 30 67 25 88 27

Figure S17.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q' versus 'CN_CNMF'

P value = 1.93e-11 (Fisher's exact test), Q value = 7.5e-09

Table S18.  Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
4Q MUTATED 112 30 19
4Q WILD-TYPE 113 147 31

Figure S18.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

'4q' versus 'METHLYATION_CNMF'

P value = 4.25e-09 (Chi-square test), Q value = 1.6e-06

Table S19.  Gene #8: '4q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
4Q MUTATED 32 35 47 16 12 14 5
4Q WILD-TYPE 35 42 33 49 60 60 12

Figure S19.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000357 (Chi-square test), Q value = 0.11

Table S20.  Gene #8: '4q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 4 40 91 46 155 79
4Q MUTATED 3 9 20 19 56 41
4Q WILD-TYPE 1 31 71 27 99 38

Figure S20.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p' versus 'CN_CNMF'

P value = 1.12e-14 (Fisher's exact test), Q value = 4.4e-12

Table S21.  Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
5P MUTATED 140 41 26
5P WILD-TYPE 85 136 24

Figure S21.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

'5p' versus 'METHLYATION_CNMF'

P value = 1.4e-09 (Chi-square test), Q value = 5.4e-07

Table S22.  Gene #9: '5p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
5P MUTATED 40 51 47 24 16 20 9
5P WILD-TYPE 27 26 33 41 56 54 8

Figure S22.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q' versus 'CN_CNMF'

P value = 2.25e-19 (Fisher's exact test), Q value = 9e-17

Table S23.  Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
5Q MUTATED 143 33 21
5Q WILD-TYPE 82 144 29

Figure S23.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

'5q' versus 'METHLYATION_CNMF'

P value = 1.42e-15 (Chi-square test), Q value = 5.6e-13

Table S24.  Gene #10: '5q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
5Q MUTATED 45 48 50 19 10 17 8
5Q WILD-TYPE 22 29 30 46 62 57 9

Figure S24.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p' versus 'CN_CNMF'

P value = 4.46e-07 (Fisher's exact test), Q value = 0.00016

Table S25.  Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
6P MUTATED 82 25 19
6P WILD-TYPE 143 152 31

Figure S25.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

'6p' versus 'METHLYATION_CNMF'

P value = 4.31e-05 (Chi-square test), Q value = 0.014

Table S26.  Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
6P MUTATED 22 31 34 11 11 12 5
6P WILD-TYPE 45 46 46 54 61 62 12

Figure S26.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q' versus 'CN_CNMF'

P value = 0.000109 (Fisher's exact test), Q value = 0.036

Table S27.  Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
6Q MUTATED 67 25 18
6Q WILD-TYPE 158 152 32

Figure S27.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'CN_CNMF'

P value = 1.27e-11 (Fisher's exact test), Q value = 4.9e-09

Table S28.  Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
7P MUTATED 125 38 23
7P WILD-TYPE 100 139 27

Figure S28.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 1.63e-08 (Chi-square test), Q value = 6.1e-06

Table S29.  Gene #13: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
7P MUTATED 36 38 51 11 24 20 6
7P WILD-TYPE 31 39 29 54 48 54 11

Figure S29.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q' versus 'CN_CNMF'

P value = 2.76e-07 (Fisher's exact test), Q value = 9.8e-05

Table S30.  Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
7Q MUTATED 99 33 18
7Q WILD-TYPE 126 144 32

Figure S30.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 1.38e-07 (Chi-square test), Q value = 4.9e-05

Table S31.  Gene #14: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
7Q MUTATED 32 26 45 11 17 15 4
7Q WILD-TYPE 35 51 35 54 55 59 13

Figure S31.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p' versus 'CN_CNMF'

P value = 5.32e-08 (Fisher's exact test), Q value = 1.9e-05

Table S32.  Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
8P MUTATED 172 87 36
8P WILD-TYPE 53 90 14

Figure S32.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

'8q' versus 'CN_CNMF'

P value = 8.91e-05 (Fisher's exact test), Q value = 0.029

Table S33.  Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
8Q MUTATED 164 95 38
8Q WILD-TYPE 61 82 12

Figure S33.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

'8q' versus 'METHLYATION_CNMF'

P value = 0.00019 (Chi-square test), Q value = 0.062

Table S34.  Gene #16: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
8Q MUTATED 43 66 51 32 41 50 14
8Q WILD-TYPE 24 11 29 33 31 24 3

Figure S34.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p' versus 'CN_CNMF'

P value = 4.08e-18 (Fisher's exact test), Q value = 1.6e-15

Table S35.  Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
9P MUTATED 154 49 38
9P WILD-TYPE 71 128 12

Figure S35.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

'9p' versus 'METHLYATION_CNMF'

P value = 5.73e-09 (Chi-square test), Q value = 2.2e-06

Table S36.  Gene #17: '9p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
9P MUTATED 45 44 59 18 38 25 12
9P WILD-TYPE 22 33 21 47 34 49 5

Figure S36.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q' versus 'CN_CNMF'

P value = 1.2e-12 (Fisher's exact test), Q value = 4.7e-10

Table S37.  Gene #18: '9q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
9Q MUTATED 106 44 40
9Q WILD-TYPE 119 133 10

Figure S37.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'CN_CNMF'

P value = 8.35e-08 (Fisher's exact test), Q value = 3e-05

Table S38.  Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
10P MUTATED 109 38 21
10P WILD-TYPE 116 139 29

Figure S38.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'METHLYATION_CNMF'

P value = 3.01e-05 (Chi-square test), Q value = 0.01

Table S39.  Gene #19: '10p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
10P MUTATED 36 36 36 17 22 13 8
10P WILD-TYPE 31 41 44 48 50 61 9

Figure S39.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q' versus 'CN_CNMF'

P value = 4.51e-07 (Fisher's exact test), Q value = 0.00016

Table S40.  Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
10Q MUTATED 85 25 13
10Q WILD-TYPE 140 152 37

Figure S40.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 6.06e-05 (Chi-square test), Q value = 0.02

Table S41.  Gene #20: '10q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
10Q MUTATED 23 27 33 15 12 7 6
10Q WILD-TYPE 44 50 47 50 60 67 11

Figure S41.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p' versus 'CN_CNMF'

P value = 7.31e-08 (Fisher's exact test), Q value = 2.6e-05

Table S42.  Gene #21: '11p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
11P MUTATED 114 41 17
11P WILD-TYPE 111 136 33

Figure S42.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #1: 'CN_CNMF'

'11p' versus 'METHLYATION_CNMF'

P value = 8.89e-05 (Chi-square test), Q value = 0.029

Table S43.  Gene #21: '11p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
11P MUTATED 22 35 45 24 17 19 10
11P WILD-TYPE 45 42 35 41 55 55 7

Figure S43.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q' versus 'CN_CNMF'

P value = 7.89e-07 (Fisher's exact test), Q value = 0.00028

Table S44.  Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
11Q MUTATED 126 53 20
11Q WILD-TYPE 99 124 30

Figure S44.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

'11q' versus 'METHLYATION_CNMF'

P value = 1.78e-05 (Chi-square test), Q value = 0.006

Table S45.  Gene #22: '11q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
11Q MUTATED 24 41 45 37 21 20 11
11Q WILD-TYPE 43 36 35 28 51 54 6

Figure S45.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p' versus 'CN_CNMF'

P value = 1.11e-08 (Fisher's exact test), Q value = 4.1e-06

Table S46.  Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
12P MUTATED 104 32 18
12P WILD-TYPE 121 145 32

Figure S46.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

'12p' versus 'METHLYATION_CNMF'

P value = 5.53e-06 (Chi-square test), Q value = 0.0019

Table S47.  Gene #23: '12p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
12P MUTATED 32 30 39 23 11 13 6
12P WILD-TYPE 35 47 41 42 61 61 11

Figure S47.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q' versus 'CN_CNMF'

P value = 4.02e-06 (Fisher's exact test), Q value = 0.0014

Table S48.  Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
12Q MUTATED 69 19 13
12Q WILD-TYPE 156 158 37

Figure S48.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

'12q' versus 'METHLYATION_CNMF'

P value = 4.66e-05 (Chi-square test), Q value = 0.016

Table S49.  Gene #24: '12q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
12Q MUTATED 23 22 25 16 5 6 4
12Q WILD-TYPE 44 55 55 49 67 68 13

Figure S49.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q' versus 'CN_CNMF'

P value = 8.85e-11 (Fisher's exact test), Q value = 3.4e-08

Table S50.  Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
13Q MUTATED 131 44 21
13Q WILD-TYPE 94 133 29

Figure S50.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 2.62e-09 (Chi-square test), Q value = 1e-06

Table S51.  Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
13Q MUTATED 44 42 46 23 13 21 7
13Q WILD-TYPE 23 35 34 42 59 53 10

Figure S51.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q' versus 'CN_CNMF'

P value = 1.97e-07 (Fisher's exact test), Q value = 7e-05

Table S52.  Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
14Q MUTATED 111 41 23
14Q WILD-TYPE 114 136 27

Figure S52.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

'14q' versus 'METHLYATION_CNMF'

P value = 5.49e-05 (Chi-square test), Q value = 0.018

Table S53.  Gene #26: '14q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
14Q MUTATED 32 37 44 14 21 20 7
14Q WILD-TYPE 35 40 36 51 51 54 10

Figure S53.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q' versus 'CN_CNMF'

P value = 1.08e-09 (Fisher's exact test), Q value = 4.1e-07

Table S54.  Gene #27: '15q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
15Q MUTATED 99 28 22
15Q WILD-TYPE 126 149 28

Figure S54.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #1: 'CN_CNMF'

'16p' versus 'CN_CNMF'

P value = 4.45e-09 (Fisher's exact test), Q value = 1.7e-06

Table S55.  Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
16P MUTATED 97 28 21
16P WILD-TYPE 128 149 29

Figure S55.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

'16p' versus 'METHLYATION_CNMF'

P value = 9.01e-07 (Chi-square test), Q value = 0.00031

Table S56.  Gene #28: '16p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
16P MUTATED 33 31 34 15 9 15 9
16P WILD-TYPE 34 46 46 50 63 59 8

Figure S56.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q' versus 'CN_CNMF'

P value = 2.72e-05 (Fisher's exact test), Q value = 0.0092

Table S57.  Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
16Q MUTATED 100 41 21
16Q WILD-TYPE 125 136 29

Figure S57.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

'16q' versus 'METHLYATION_CNMF'

P value = 1.08e-06 (Chi-square test), Q value = 0.00037

Table S58.  Gene #29: '16q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
16Q MUTATED 31 30 39 30 9 15 8
16Q WILD-TYPE 36 47 41 35 63 59 9

Figure S58.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p' versus 'CN_CNMF'

P value = 1.43e-12 (Fisher's exact test), Q value = 5.6e-10

Table S59.  Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
17P MUTATED 109 26 20
17P WILD-TYPE 116 151 30

Figure S59.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 6.95e-08 (Chi-square test), Q value = 2.5e-05

Table S60.  Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
17P MUTATED 33 33 42 19 11 12 5
17P WILD-TYPE 34 44 38 46 61 62 12

Figure S60.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q' versus 'CN_CNMF'

P value = 3.58e-08 (Fisher's exact test), Q value = 1.3e-05

Table S61.  Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
17Q MUTATED 73 17 16
17Q WILD-TYPE 152 160 34

Figure S61.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

'17q' versus 'METHLYATION_CNMF'

P value = 0.000119 (Chi-square test), Q value = 0.039

Table S62.  Gene #31: '17q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
17Q MUTATED 19 23 32 12 8 9 3
17Q WILD-TYPE 48 54 48 53 64 65 14

Figure S62.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p' versus 'CN_CNMF'

P value = 1.2e-11 (Fisher's exact test), Q value = 4.6e-09

Table S63.  Gene #32: '18p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
18P MUTATED 130 41 22
18P WILD-TYPE 95 136 28

Figure S63.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #1: 'CN_CNMF'

'18p' versus 'METHLYATION_CNMF'

P value = 4.4e-08 (Chi-square test), Q value = 1.6e-05

Table S64.  Gene #32: '18p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
18P MUTATED 42 39 48 18 16 23 7
18P WILD-TYPE 25 38 32 47 56 51 10

Figure S64.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q' versus 'CN_CNMF'

P value = 2.39e-12 (Fisher's exact test), Q value = 9.3e-10

Table S65.  Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
18Q MUTATED 149 53 26
18Q WILD-TYPE 76 124 24

Figure S65.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

'18q' versus 'METHLYATION_CNMF'

P value = 1.06e-08 (Chi-square test), Q value = 4e-06

Table S66.  Gene #33: '18q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
18Q MUTATED 46 50 50 17 22 33 10
18Q WILD-TYPE 21 27 30 48 50 41 7

Figure S66.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p' versus 'CN_CNMF'

P value = 0.000201 (Fisher's exact test), Q value = 0.065

Table S67.  Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
19P MUTATED 80 31 16
19P WILD-TYPE 145 146 34

Figure S67.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

'19p' versus 'METHLYATION_CNMF'

P value = 3.91e-05 (Chi-square test), Q value = 0.013

Table S68.  Gene #34: '19p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
19P MUTATED 18 31 36 16 12 10 4
19P WILD-TYPE 49 46 44 49 60 64 13

Figure S68.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0064

Table S69.  Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
19Q MUTATED 86 31 17
19Q WILD-TYPE 139 146 33

Figure S69.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

'19q' versus 'METHLYATION_CNMF'

P value = 1.97e-07 (Chi-square test), Q value = 7e-05

Table S70.  Gene #35: '19q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
19Q MUTATED 21 31 41 18 12 8 3
19Q WILD-TYPE 46 46 39 47 60 66 14

Figure S70.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p' versus 'CN_CNMF'

P value = 1.03e-07 (Fisher's exact test), Q value = 3.7e-05

Table S71.  Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
20P MUTATED 132 54 23
20P WILD-TYPE 93 123 27

Figure S71.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

'20p' versus 'METHLYATION_CNMF'

P value = 1.62e-07 (Chi-square test), Q value = 5.8e-05

Table S72.  Gene #36: '20p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
20P MUTATED 32 53 50 22 21 25 6
20P WILD-TYPE 35 24 30 43 51 49 11

Figure S72.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q' versus 'CN_CNMF'

P value = 3.67e-07 (Fisher's exact test), Q value = 0.00013

Table S73.  Gene #37: '20q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
20Q MUTATED 128 53 22
20Q WILD-TYPE 97 124 28

Figure S73.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #1: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 1.93e-06 (Chi-square test), Q value = 0.00066

Table S74.  Gene #37: '20q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
20Q MUTATED 34 49 47 19 21 24 9
20Q WILD-TYPE 33 28 33 46 51 50 8

Figure S74.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q' versus 'CN_CNMF'

P value = 7.74e-12 (Fisher's exact test), Q value = 3e-09

Table S75.  Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
21Q MUTATED 126 39 26
21Q WILD-TYPE 99 138 24

Figure S75.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

'21q' versus 'METHLYATION_CNMF'

P value = 9.19e-09 (Chi-square test), Q value = 3.5e-06

Table S76.  Gene #38: '21q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
21Q MUTATED 33 45 50 14 19 21 9
21Q WILD-TYPE 34 32 30 51 53 53 8

Figure S76.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q' versus 'CN_CNMF'

P value = 2.22e-06 (Fisher's exact test), Q value = 0.00076

Table S77.  Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
22Q MUTATED 104 39 19
22Q WILD-TYPE 121 138 31

Figure S77.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'METHLYATION_CNMF'

P value = 3.46e-07 (Chi-square test), Q value = 0.00012

Table S78.  Gene #39: '22q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
22Q MUTATED 25 40 44 14 12 21 6
22Q WILD-TYPE 42 37 36 51 60 53 11

Figure S78.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq' versus 'CN_CNMF'

P value = 2.58e-08 (Fisher's exact test), Q value = 9.5e-06

Table S79.  Gene #40: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
XQ MUTATED 99 30 14
XQ WILD-TYPE 126 147 36

Figure S79.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

'xq' versus 'METHLYATION_CNMF'

P value = 6.39e-10 (Chi-square test), Q value = 2.5e-07

Table S80.  Gene #40: 'xq' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 67 77 80 65 72 74 17
XQ MUTATED 22 36 45 16 10 10 4
XQ WILD-TYPE 45 41 35 49 62 64 13

Figure S80.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = HNSC-TP.transferedmergedcluster.txt

  • Number of patients = 452

  • Number of significantly focal cnvs = 40

  • Number of molecular subtypes = 10

  • Exclude genes 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)
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