Correlation between copy number variations of arm-level result and molecular subtypes
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C12Z13ZH
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C12Z13ZH
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 80 arm-level events and 10 molecular subtypes across 452 patients, 98 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 3p gain cnv correlated to 'METHLYATION_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 4p gain cnv correlated to 'METHLYATION_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'METHLYATION_CNMF'.

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

  • 12q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

  • 18q gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 19p gain cnv correlated to 'METHLYATION_CNMF'.

  • 19q gain cnv correlated to 'METHLYATION_CNMF'.

  • 20p gain cnv correlated to 'METHLYATION_CNMF'.

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

  • 22q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 4q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

  • 8p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 9q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF'.

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

  • 13q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 18q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'METHLYATION_CNMF'.

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

  • 20p loss cnv correlated to 'CN_CNMF'.

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

  • 22q loss cnv correlated to 'MRNASEQ_CNMF'.

  • xq loss cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level 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, 98 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
1q gain 101 (22%) 351 2.82e-07
(0.000216) 		1.97e-07
(0.000151) 		0.289
(1.00) 		0.653
(1.00) 		0.000414
(0.29) 		0.00102
(0.697) 		0.000191
(0.137) 		0.265
(1.00) 		0.000321
(0.226) 		0.00215
(1.00)
22q gain 95 (21%) 357 0.000195
(0.14) 		4.63e-11
(3.65e-08) 		0.153
(1.00) 		0.376
(1.00) 		0.0314
(1.00) 		0.0759
(1.00) 		0.0139
(1.00) 		0.501
(1.00) 		2.13e-05
(0.0157) 		7.41e-05
(0.0538)
4p loss 167 (37%) 285 2.21e-14
(1.75e-11) 		3e-12
(2.38e-09) 		0.0392
(1.00) 		0.592
(1.00) 		0.000852
(0.586) 		2.88e-05
(0.0213) 		0.0196
(1.00) 		0.885
(1.00) 		0.0213
(1.00) 		4.29e-06
(0.00323)
16q loss 68 (15%) 384 0.561
(1.00) 		2.51e-09
(1.96e-06) 		0.479
(1.00) 		0.078
(1.00) 		2.69e-08
(2.08e-05) 		2.32e-09
(1.81e-06) 		0.0077
(1.00) 		0.0661
(1.00) 		1.07e-05
(0.008) 		0.0605
(1.00)
2p gain 79 (17%) 373 1.32e-08
(1.02e-05) 		2.1e-10
(1.65e-07) 		0.0817
(1.00) 		0.708
(1.00) 		0.0198
(1.00) 		0.0278
(1.00) 		0.225
(1.00) 		0.0574
(1.00) 		0.131
(1.00) 		3.24e-05
(0.0239)
13q loss 145 (32%) 307 7.6e-06
(0.0057) 		2.68e-07
(0.000205) 		0.454
(1.00) 		0.907
(1.00) 		0.00163
(1.00) 		6.58e-05
(0.0479) 		0.0102
(1.00) 		0.931
(1.00) 		0.0105
(1.00) 		0.0248
(1.00)
18q loss 185 (41%) 267 6.8e-11
(5.36e-08) 		9.22e-12
(7.28e-09) 		0.281
(1.00) 		0.0129
(1.00) 		0.0028
(1.00) 		0.000206
(0.147) 		0.0416
(1.00) 		0.00296
(1.00) 		0.0418
(1.00) 		0.104
(1.00)
xq loss 71 (16%) 381 0.000626
(0.433) 		2.76e-06
(0.00208) 		0.181
(1.00) 		0.0725
(1.00) 		0.00912
(1.00) 		0.0195
(1.00) 		3.09e-05
(0.0228) 		0.23
(1.00) 		0.0232
(1.00) 		6.1e-05
(0.0444)
2q gain 62 (14%) 390 1.13e-07
(8.66e-05) 		2.59e-09
(2.02e-06) 		0.534
(1.00) 		0.898
(1.00) 		0.0841
(1.00) 		0.116
(1.00) 		0.648
(1.00) 		0.0864
(1.00) 		0.156
(1.00) 		0.016
(1.00)
3q gain 218 (48%) 234 0.00028
(0.198) 		4.53e-05
(0.0332) 		0.682
(1.00) 		0.628
(1.00) 		0.000422
(0.295) 		0.00382
(1.00) 		0.00312
(1.00) 		0.146
(1.00) 		0.101
(1.00) 		0.582
(1.00)
7p gain 162 (36%) 290 6.58e-10
(5.16e-07) 		3.86e-08
(2.97e-05) 		0.624
(1.00) 		0.52
(1.00) 		0.701
(1.00) 		0.665
(1.00) 		0.136
(1.00) 		0.138
(1.00) 		0.378
(1.00) 		0.0659
(1.00)
7q gain 111 (25%) 341 4.32e-07
(0.00033) 		8.32e-09
(6.47e-06) 		0.176
(1.00) 		0.913
(1.00) 		0.134
(1.00) 		0.107
(1.00) 		0.00345
(1.00) 		0.739
(1.00) 		0.18
(1.00) 		0.00108
(0.736)
9p gain 89 (20%) 363 5.13e-19
(4.1e-16) 		0.000189
(0.136) 		0.354
(1.00) 		0.0214
(1.00) 		0.0374
(1.00) 		0.0111
(1.00) 		0.0232
(1.00) 		0.646
(1.00) 		0.00501
(1.00) 		0.411
(1.00)
12p gain 125 (28%) 327 1.65e-08
(1.28e-05) 		5.49e-07
(0.000417) 		0.0161
(1.00) 		0.318
(1.00) 		0.00279
(1.00) 		0.00247
(1.00) 		0.0256
(1.00) 		0.333
(1.00) 		0.0341
(1.00) 		0.00249
(1.00)
14q gain 131 (29%) 321 5.52e-07
(0.00042) 		5.94e-06
(0.00446) 		0.217
(1.00) 		0.479
(1.00) 		0.0905
(1.00) 		0.406
(1.00) 		0.0899
(1.00) 		0.00169
(1.00) 		0.114
(1.00) 		0.00405
(1.00)
16p gain 93 (21%) 359 2.09e-05
(0.0155) 		4.46e-07
(0.00034) 		0.324
(1.00) 		0.813
(1.00) 		0.472
(1.00) 		0.983
(1.00) 		0.512
(1.00) 		0.418
(1.00) 		0.608
(1.00) 		0.272
(1.00)
16q gain 94 (21%) 358 1.75e-05
(0.013) 		8.69e-05
(0.063) 		0.499
(1.00) 		0.826
(1.00) 		0.19
(1.00) 		0.179
(1.00) 		0.356
(1.00) 		0.0603
(1.00) 		0.495
(1.00) 		0.258
(1.00)
17p gain 59 (13%) 393 4.41e-06
(0.00332) 		5.66e-05
(0.0413) 		0.597
(1.00) 		0.311
(1.00) 		0.00348
(1.00) 		0.0465
(1.00) 		0.0345
(1.00) 		0.0318
(1.00) 		0.701
(1.00) 		0.146
(1.00)
17q gain 76 (17%) 376 2.24e-07
(0.000171) 		0.000194
(0.138) 		0.53
(1.00) 		0.604
(1.00) 		0.069
(1.00) 		0.0743
(1.00) 		0.114
(1.00) 		0.462
(1.00) 		0.249
(1.00) 		0.0163
(1.00)
18p gain 105 (23%) 347 2.81e-08
(2.17e-05) 		2.7e-06
(0.00205) 		0.333
(1.00) 		0.769
(1.00) 		0.0627
(1.00) 		0.00332
(1.00) 		0.678
(1.00) 		0.937
(1.00) 		0.00229
(1.00) 		0.0374
(1.00)
18q gain 43 (10%) 409 0.547
(1.00) 		7.73e-05
(0.0561) 		0.0168
(1.00) 		0.408
(1.00) 		0.000717
(0.495) 		0.00322
(1.00) 		0.00108
(0.739) 		0.353
(1.00) 		0.000107
(0.0775) 		0.194
(1.00)
20q gain 175 (39%) 277 8.75e-05
(0.0634) 		3.19e-06
(0.00241) 		0.874
(1.00) 		0.82
(1.00) 		0.00152
(1.00) 		0.00328
(1.00) 		0.0791
(1.00) 		0.00765
(1.00) 		0.119
(1.00) 		0.0276
(1.00)
1p loss 47 (10%) 405 0.000222
(0.158) 		9.85e-09
(7.65e-06) 		0.065
(1.00) 		0.538
(1.00) 		0.00442
(1.00) 		0.0283
(1.00) 		0.205
(1.00) 		0.685
(1.00) 		0.575
(1.00) 		0.00132
(0.895)
3p loss 262 (58%) 190 5.87e-24
(4.69e-21) 		1.36e-15
(1.08e-12) 		0.884
(1.00) 		0.0886
(1.00) 		0.0335
(1.00) 		0.208
(1.00) 		0.0929
(1.00) 		0.117
(1.00) 		0.345
(1.00) 		0.00291
(1.00)
4q loss 133 (29%) 319 6.94e-11
(5.46e-08) 		3.28e-08
(2.53e-05) 		0.553
(1.00) 		0.434
(1.00) 		0.0174
(1.00) 		0.00508
(1.00) 		0.0124
(1.00) 		0.655
(1.00) 		0.179
(1.00) 		0.00607
(1.00)
5p loss 41 (9%) 411 0.000301
(0.213) 		0.00031
(0.219) 		0.375
(1.00) 		0.591
(1.00) 		0.68
(1.00) 		0.277
(1.00) 		0.579
(1.00) 		0.802
(1.00) 		0.0727
(1.00) 		0.467
(1.00)
5q loss 138 (31%) 314 7.78e-15
(6.18e-12) 		4.15e-15
(3.3e-12) 		0.205
(1.00) 		0.145
(1.00) 		0.222
(1.00) 		0.000761
(0.525) 		0.733
(1.00) 		0.145
(1.00) 		0.334
(1.00) 		0.0666
(1.00)
8p loss 166 (37%) 286 1.84e-05
(0.0137) 		0.00012
(0.0868) 		0.348
(1.00) 		0.311
(1.00) 		0.163
(1.00) 		0.0192
(1.00) 		0.281
(1.00) 		0.0158
(1.00) 		0.107
(1.00) 		0.00311
(1.00)
9p loss 152 (34%) 300 4.88e-29
(3.9e-26) 		3.4e-14
(2.69e-11) 		0.69
(1.00) 		0.136
(1.00) 		0.385
(1.00) 		0.177
(1.00) 		0.0602
(1.00) 		0.507
(1.00) 		0.074
(1.00) 		0.000549
(0.381)
9q loss 70 (15%) 382 1.75e-10
(1.37e-07) 		8.96e-06
(0.0067) 		0.973
(1.00) 		0.851
(1.00) 		0.502
(1.00) 		0.394
(1.00) 		0.877
(1.00) 		0.0045
(1.00) 		0.309
(1.00) 		0.0716
(1.00)
11q loss 139 (31%) 313 0.000147
(0.105) 		5.4e-05
(0.0395) 		0.126
(1.00) 		0.409
(1.00) 		0.00371
(1.00) 		0.0304
(1.00) 		0.561
(1.00) 		0.563
(1.00) 		0.312
(1.00) 		0.906
(1.00)
17p loss 96 (21%) 356 2.05e-05
(0.0152) 		0.000191
(0.137) 		0.393
(1.00) 		0.278
(1.00) 		0.505
(1.00) 		0.136
(1.00) 		0.608
(1.00) 		0.738
(1.00) 		0.169
(1.00) 		0.665
(1.00)
19q loss 77 (17%) 375 5.6e-05
(0.0409) 		4.37e-05
(0.032) 		0.134
(1.00) 		0.442
(1.00) 		0.219
(1.00) 		0.44
(1.00) 		0.294
(1.00) 		0.235
(1.00) 		0.936
(1.00) 		0.589
(1.00)
21q loss 162 (36%) 290 2.67e-09
(2.08e-06) 		1.56e-07
(0.00012) 		0.571
(1.00) 		0.512
(1.00) 		0.304
(1.00) 		0.417
(1.00) 		0.772
(1.00) 		0.401
(1.00) 		0.278
(1.00) 		0.0378
(1.00)
3p gain 68 (15%) 384 0.166
(1.00) 		0.000252
(0.179) 		0.112
(1.00) 		0.0505
(1.00) 		0.00267
(1.00) 		0.00593
(1.00) 		0.00278
(1.00) 		0.0973
(1.00) 		0.192
(1.00) 		0.685
(1.00)
4p gain 32 (7%) 420 0.0319
(1.00) 		0.000228
(0.162) 		0.576
(1.00) 		0.824
(1.00) 		0.253
(1.00) 		0.373
(1.00) 		0.0589
(1.00) 		0.123
(1.00) 		0.31
(1.00) 		0.263
(1.00)
5p gain 166 (37%) 286 8.24e-09
(6.42e-06) 		0.00147
(0.995) 		0.936
(1.00) 		0.64
(1.00) 		0.0654
(1.00) 		0.761
(1.00) 		0.281
(1.00) 		1
(1.00) 		0.224
(1.00) 		0.94
(1.00)
6p gain 67 (15%) 385 0.000218
(0.155) 		0.0145
(1.00) 		0.492
(1.00) 		0.563
(1.00) 		0.949
(1.00) 		0.674
(1.00) 		0.88
(1.00) 		0.103
(1.00) 		0.625
(1.00) 		0.466
(1.00)
9q gain 120 (27%) 332 1.97e-16
(1.57e-13) 		0.0449
(1.00) 		0.129
(1.00) 		0.103
(1.00) 		0.52
(1.00) 		0.0889
(1.00) 		0.691
(1.00) 		0.456
(1.00) 		0.172
(1.00) 		0.332
(1.00)
10p gain 34 (8%) 418 0.0356
(1.00) 		7.76e-06
(0.00581) 		0.579
(1.00) 		0.529
(1.00) 		0.144
(1.00) 		0.0309
(1.00) 		0.13
(1.00) 		0.189
(1.00) 		0.279
(1.00) 		0.0493
(1.00)
12q gain 76 (17%) 376 0.000125
(0.0904) 		0.00112
(0.761) 		0.0791
(1.00) 		0.149
(1.00) 		0.0259
(1.00) 		0.078
(1.00) 		0.509
(1.00) 		0.926
(1.00) 		0.0674
(1.00) 		0.0611
(1.00)
19p gain 40 (9%) 412 0.0928
(1.00) 		1.81e-05
(0.0134) 		0.0892
(1.00) 		0.0684
(1.00) 		0.0829
(1.00) 		0.0281
(1.00) 		0.0736
(1.00) 		0.138
(1.00) 		0.315
(1.00) 		0.314
(1.00)
19q gain 57 (13%) 395 0.265
(1.00) 		0.000338
(0.238) 		0.906
(1.00) 		0.338
(1.00) 		0.0606
(1.00) 		0.0129
(1.00) 		0.047
(1.00) 		0.191
(1.00) 		0.377
(1.00) 		0.182
(1.00)
20p gain 165 (37%) 287 0.00679
(1.00) 		3.48e-05
(0.0256) 		0.893
(1.00) 		0.267
(1.00) 		0.00602
(1.00) 		0.0317
(1.00) 		0.0683
(1.00) 		0.0119
(1.00) 		0.528
(1.00) 		0.0247
(1.00)
xq gain 72 (16%) 380 4.04e-05
(0.0297) 		0.00426
(1.00) 		0.251
(1.00) 		0.751
(1.00) 		0.142
(1.00) 		0.0326
(1.00) 		0.242
(1.00) 		0.317
(1.00) 		0.672
(1.00) 		0.905
(1.00)
10p loss 134 (30%) 318 2.28e-06
(0.00173) 		0.00244
(1.00) 		0.316
(1.00) 		0.098
(1.00) 		0.458
(1.00) 		0.293
(1.00) 		0.173
(1.00) 		0.27
(1.00) 		0.63
(1.00) 		0.0938
(1.00)
10q loss 91 (20%) 361 1.64e-05
(0.0122) 		0.000804
(0.554) 		0.208
(1.00) 		0.33
(1.00) 		0.0809
(1.00) 		0.0188
(1.00) 		0.111
(1.00) 		0.779
(1.00) 		0.00579
(1.00) 		0.459
(1.00)
11p loss 116 (26%) 336 7.92e-08
(6.1e-05) 		0.000494
(0.344) 		0.436
(1.00) 		0.917
(1.00) 		0.00223
(1.00) 		0.0137
(1.00) 		0.0138
(1.00) 		0.733
(1.00) 		0.0632
(1.00) 		0.093
(1.00)
15q loss 83 (18%) 369 1.42e-06
(0.00108) 		0.168
(1.00) 		0.625
(1.00) 		0.413
(1.00) 		0.0368
(1.00) 		0.104
(1.00) 		0.223
(1.00) 		0.257
(1.00) 		0.177
(1.00) 		0.324
(1.00)
19p loss 87 (19%) 365 0.00253
(1.00) 		0.000238
(0.169) 		0.703
(1.00) 		0.204
(1.00) 		0.017
(1.00) 		0.0726
(1.00) 		0.36
(1.00) 		0.0383
(1.00) 		0.0465
(1.00) 		0.287
(1.00)
20p loss 44 (10%) 408 5.27e-06
(0.00396) 		0.00112
(0.761) 		0.483
(1.00) 		0.17
(1.00) 		0.201
(1.00) 		0.364
(1.00) 		0.164
(1.00) 		0.125
(1.00) 		0.519
(1.00) 		0.458
(1.00)
22q loss 67 (15%) 385 0.0727
(1.00) 		0.00044
(0.307) 		0.811
(1.00) 		0.459
(1.00) 		0.000139
(0.0999) 		0.0126
(1.00) 		0.00051
(0.354) 		0.172
(1.00) 		0.000523
(0.363) 		0.0945
(1.00)
1p gain 56 (12%) 396 0.000447
(0.311) 		0.106
(1.00) 		1
(1.00) 		0.859
(1.00) 		0.976
(1.00) 		0.973
(1.00) 		0.432
(1.00) 		0.785
(1.00) 		0.645
(1.00) 		0.615
(1.00)
4q gain 28 (6%) 424 0.432
(1.00) 		0.0358
(1.00) 		1
(1.00) 		0.892
(1.00) 		0.615
(1.00) 		0.711
(1.00) 		0.822
(1.00) 		1
(1.00) 		0.765
(1.00) 		0.378
(1.00)
5q gain 59 (13%) 393 0.0104
(1.00) 		0.498
(1.00) 		0.508
(1.00) 		0.673
(1.00) 		0.778
(1.00) 		0.519
(1.00) 		0.492
(1.00) 		0.235
(1.00) 		0.906
(1.00) 		0.52
(1.00)
6q gain 54 (12%) 398 0.00134
(0.906) 		0.0212
(1.00) 		0.197
(1.00) 		0.127
(1.00) 		0.101
(1.00) 		0.107
(1.00) 		0.161
(1.00) 		0.389
(1.00) 		0.251
(1.00) 		0.539
(1.00)
8p gain 129 (29%) 323 0.25
(1.00) 		0.0169
(1.00) 		0.425
(1.00) 		0.628
(1.00) 		0.385
(1.00) 		0.116
(1.00) 		0.404
(1.00) 		0.62
(1.00) 		0.544
(1.00) 		0.653
(1.00)
8q gain 272 (60%) 180 0.00443
(1.00) 		0.000409
(0.287) 		0.0935
(1.00) 		0.682
(1.00) 		0.149
(1.00) 		0.105
(1.00) 		0.165
(1.00) 		0.0339
(1.00) 		0.386
(1.00) 		0.0969
(1.00)
10q gain 32 (7%) 420 0.0243
(1.00) 		0.422
(1.00) 		0.0973
(1.00) 		0.341
(1.00) 		0.482
(1.00) 		0.317
(1.00) 		0.529
(1.00) 		0.21
(1.00) 		0.428
(1.00) 		0.0635
(1.00)
11p gain 56 (12%) 396 0.033
(1.00) 		0.000413
(0.289) 		0.839
(1.00) 		0.665
(1.00) 		0.376
(1.00) 		0.0526
(1.00) 		0.452
(1.00) 		0.528
(1.00) 		0.00406
(1.00) 		0.835
(1.00)
11q gain 60 (13%) 392 0.131
(1.00) 		0.00175
(1.00) 		0.428
(1.00) 		0.761
(1.00) 		0.289
(1.00) 		0.0545
(1.00) 		0.717
(1.00) 		0.594
(1.00) 		0.166
(1.00) 		0.619
(1.00)
13q gain 51 (11%) 401 0.000809
(0.557) 		0.00501
(1.00) 		0.588
(1.00) 		0.502
(1.00) 		0.00284
(1.00) 		0.0107
(1.00) 		0.134
(1.00) 		0.0469
(1.00) 		0.0462
(1.00) 		0.613
(1.00)
15q gain 66 (15%) 386 0.00618
(1.00) 		0.0713
(1.00) 		0.381
(1.00) 		0.851
(1.00) 		0.242
(1.00) 		0.512
(1.00) 		0.498
(1.00) 		0.601
(1.00) 		0.197
(1.00) 		0.533
(1.00)
21q gain 29 (6%) 423 0.0738
(1.00) 		0.0274
(1.00) 		0.0151
(1.00) 		0.768
(1.00) 		0.104
(1.00) 		0.121
(1.00) 		0.217
(1.00) 		0.873
(1.00) 		0.00778
(1.00) 		0.304
(1.00)
1q loss 33 (7%) 419 0.324
(1.00) 		0.112
(1.00) 		0.78
(1.00) 		0.696
(1.00) 		0.255
(1.00) 		0.193
(1.00) 		0.118
(1.00) 		0.11
(1.00) 		0.0446
(1.00) 		0.632
(1.00)
2p loss 30 (7%) 422 0.152
(1.00) 		0.0141
(1.00) 		0.159
(1.00) 		0.153
(1.00) 		0.134
(1.00) 		0.41
(1.00) 		0.082
(1.00) 		0.736
(1.00) 		0.284
(1.00) 		0.568
(1.00)
2q loss 40 (9%) 412 0.312
(1.00) 		0.028
(1.00) 		0.836
(1.00) 		0.172
(1.00) 		0.777
(1.00) 		0.529
(1.00) 		0.324
(1.00) 		0.776
(1.00) 		0.439
(1.00) 		0.847
(1.00)
3q loss 57 (13%) 395 0.0124
(1.00) 		0.382
(1.00) 		0.393
(1.00) 		1
(1.00) 		0.611
(1.00) 		0.847
(1.00) 		0.55
(1.00) 		0.715
(1.00) 		0.353
(1.00) 		0.467
(1.00)
6p loss 59 (13%) 393 0.00142
(0.959) 		0.00386
(1.00) 		0.0282
(1.00) 		0.481
(1.00) 		0.171
(1.00) 		0.372
(1.00) 		0.348
(1.00) 		0.957
(1.00) 		0.75
(1.00) 		0.133
(1.00)
6q loss 56 (12%) 396 0.0497
(1.00) 		0.00982
(1.00) 		0.134
(1.00) 		0.273
(1.00) 		0.724
(1.00) 		0.723
(1.00) 		0.622
(1.00) 		0.546
(1.00) 		0.639
(1.00) 		0.742
(1.00)
7p loss 24 (5%) 428 0.0729
(1.00) 		0.119
(1.00) 		0.0102
(1.00) 		0.207
(1.00) 		0.934
(1.00) 		0.29
(1.00) 		0.285
(1.00) 		0.66
(1.00) 		0.0888
(1.00) 		0.298
(1.00)
7q loss 39 (9%) 413 0.398
(1.00) 		0.139
(1.00) 		0.525
(1.00) 		0.271
(1.00) 		0.275
(1.00) 		0.498
(1.00) 		0.123
(1.00) 		0.135
(1.00) 		0.687
(1.00) 		0.202
(1.00)
8q loss 25 (6%) 427 0.0968
(1.00) 		0.588
(1.00) 		0.678
(1.00) 		0.648
(1.00) 		1
(1.00) 		1
(1.00) 		0.749
(1.00) 		0.762
(1.00) 		0.617
(1.00) 		0.302
(1.00)
12p loss 29 (6%) 423 0.589
(1.00) 		0.0364
(1.00) 		0.646
(1.00) 		0.605
(1.00) 		0.749
(1.00) 		1
(1.00) 		0.283
(1.00) 		0.6
(1.00) 		0.3
(1.00) 		0.095
(1.00)
12q loss 25 (6%) 427 0.0674
(1.00) 		0.01
(1.00) 		0.871
(1.00) 		0.267
(1.00) 		0.498
(1.00) 		0.76
(1.00) 		0.546
(1.00) 		0.338
(1.00) 		0.14
(1.00) 		0.232
(1.00)
14q loss 44 (10%) 408 0.133
(1.00) 		0.0149
(1.00) 		0.0372
(1.00) 		0.415
(1.00) 		0.00854
(1.00) 		0.0987
(1.00) 		0.0691
(1.00) 		0.363
(1.00) 		0.00236
(1.00) 		0.00927
(1.00)
16p loss 53 (12%) 399 0.00193
(1.00) 		0.003
(1.00) 		0.987
(1.00) 		0.652
(1.00) 		0.0377
(1.00) 		0.0334
(1.00) 		0.76
(1.00) 		0.212
(1.00) 		0.251
(1.00) 		0.429
(1.00)
17q loss 30 (7%) 422 0.0417
(1.00) 		0.437
(1.00) 		0.903
(1.00) 		0.00478
(1.00) 		0.637
(1.00) 		0.493
(1.00) 		0.782
(1.00) 		0.6
(1.00) 		0.572
(1.00) 		0.83
(1.00)
18p loss 88 (19%) 364 0.00615
(1.00) 		0.000899
(0.616) 		0.647
(1.00) 		0.28
(1.00) 		0.796
(1.00) 		0.648
(1.00) 		0.368
(1.00) 		0.628
(1.00) 		0.24
(1.00) 		0.751
(1.00)
20q loss 28 (6%) 424 0.00421
(1.00) 		0.00523
(1.00) 		0.212
(1.00) 		0.058
(1.00) 		0.0244
(1.00) 		0.00124
(0.842) 		0.0122
(1.00) 		0.144
(1.00) 		0.0148
(1.00) 		0.211
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 2.82e-07 (Fisher's exact test), Q value = 0.00022

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
1Q GAIN MUTATED 73 18 10
1Q GAIN WILD-TYPE 152 159 40

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1.97e-07 (Chi-square test), Q value = 0.00015

Table S2.  Gene #2: '1q gain' 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 GAIN MUTATED 19 19 36 11 6 7 3
1Q GAIN WILD-TYPE 48 58 44 54 66 67 14

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

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.14

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 182 129
1Q GAIN MUTATED 21 59 21
1Q GAIN WILD-TYPE 119 123 108

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000321 (Fisher's exact test), Q value = 0.23

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 102 108 83
1Q GAIN MUTATED 14 36 24 21
1Q GAIN WILD-TYPE 108 66 84 62

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1.32e-08 (Fisher's exact test), Q value = 1e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
2P GAIN MUTATED 62 10 7
2P GAIN WILD-TYPE 163 167 43

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 2.1e-10 (Chi-square test), Q value = 1.7e-07

Table S6.  Gene #3: '2p gain' 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 GAIN MUTATED 24 15 28 3 5 3 1
2P GAIN WILD-TYPE 43 62 52 62 67 71 16

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

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.24e-05 (Chi-square test), Q value = 0.024

Table S7.  Gene #3: '2p gain' 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
2P GAIN MUTATED 1 6 6 6 26 29
2P GAIN WILD-TYPE 3 34 85 40 129 50

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1.13e-07 (Fisher's exact test), Q value = 8.7e-05

Table S8.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
2Q GAIN MUTATED 51 8 3
2Q GAIN WILD-TYPE 174 169 47

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 2.59e-09 (Chi-square test), Q value = 2e-06

Table S9.  Gene #4: '2q gain' 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 GAIN MUTATED 20 13 22 1 2 2 2
2Q GAIN WILD-TYPE 47 64 58 64 70 72 15

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.000252 (Chi-square test), Q value = 0.18

Table S10.  Gene #5: '3p gain' 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 GAIN MUTATED 11 8 12 22 4 10 1
3P GAIN WILD-TYPE 56 69 68 43 68 64 16

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

'3q gain' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
3Q GAIN MUTATED 128 65 25
3Q GAIN WILD-TYPE 97 112 25

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 4.53e-05 (Chi-square test), Q value = 0.033

Table S12.  Gene #6: '3q gain' 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 GAIN MUTATED 38 44 45 37 16 30 8
3Q GAIN WILD-TYPE 29 33 35 28 56 44 9

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

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.000228 (Chi-square test), Q value = 0.16

Table S13.  Gene #7: '4p gain' 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 GAIN MUTATED 5 15 5 2 1 2 2
4P GAIN WILD-TYPE 62 62 75 63 71 72 15

Figure S13.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 8.24e-09 (Fisher's exact test), Q value = 6.4e-06

Table S14.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
5P GAIN MUTATED 111 36 19
5P GAIN WILD-TYPE 114 141 31

Figure S14.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 0.000218 (Fisher's exact test), Q value = 0.15

Table S15.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
6P GAIN MUTATED 40 13 14
6P GAIN WILD-TYPE 185 164 36

Figure S15.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 6.58e-10 (Fisher's exact test), Q value = 5.2e-07

Table S16.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
7P GAIN MUTATED 111 33 18
7P GAIN WILD-TYPE 114 144 32

Figure S16.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 3.86e-08 (Chi-square test), Q value = 3e-05

Table S17.  Gene #13: '7p gain' 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 GAIN MUTATED 32 33 44 5 24 18 6
7P GAIN WILD-TYPE 35 44 36 60 48 56 11

Figure S17.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 4.32e-07 (Fisher's exact test), Q value = 0.00033

Table S18.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
7Q GAIN MUTATED 78 21 12
7Q GAIN WILD-TYPE 147 156 38

Figure S18.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 8.32e-09 (Chi-square test), Q value = 6.5e-06

Table S19.  Gene #14: '7q gain' 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 GAIN MUTATED 22 17 40 5 15 8 4
7Q GAIN WILD-TYPE 45 60 40 60 57 66 13

Figure S19.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 5.13e-19 (Fisher's exact test), Q value = 4.1e-16

Table S20.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
9P GAIN MUTATED 24 28 37
9P GAIN WILD-TYPE 201 149 13

Figure S20.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.000189 (Chi-square test), Q value = 0.14

Table S21.  Gene #17: '9p gain' 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 GAIN MUTATED 6 14 16 11 29 11 2
9P GAIN WILD-TYPE 61 63 64 54 43 63 15

Figure S21.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 1.97e-16 (Fisher's exact test), Q value = 1.6e-13

Table S22.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
9Q GAIN MUTATED 47 33 40
9Q GAIN WILD-TYPE 178 144 10

Figure S22.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 7.76e-06 (Chi-square test), Q value = 0.0058

Table S23.  Gene #19: '10p gain' 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 GAIN MUTATED 16 3 6 5 2 1 1
10P GAIN WILD-TYPE 51 74 74 60 70 73 16

Figure S23.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.65e-08 (Fisher's exact test), Q value = 1.3e-05

Table S24.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
12P GAIN MUTATED 88 23 14
12P GAIN WILD-TYPE 137 154 36

Figure S24.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 5.49e-07 (Chi-square test), Q value = 0.00042

Table S25.  Gene #23: '12p gain' 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 GAIN MUTATED 30 25 34 16 7 11 2
12P GAIN WILD-TYPE 37 52 46 49 65 63 15

Figure S25.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.000125 (Fisher's exact test), Q value = 0.09

Table S26.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
12Q GAIN MUTATED 51 14 11
12Q GAIN WILD-TYPE 174 163 39

Figure S26.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 5.52e-07 (Fisher's exact test), Q value = 0.00042

Table S27.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
14Q GAIN MUTATED 83 27 21
14Q GAIN WILD-TYPE 142 150 29

Figure S27.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 5.94e-06 (Chi-square test), Q value = 0.0045

Table S28.  Gene #26: '14q gain' 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 GAIN MUTATED 22 33 33 3 16 19 5
14Q GAIN WILD-TYPE 45 44 47 62 56 55 12

Figure S28.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 2.09e-05 (Fisher's exact test), Q value = 0.016

Table S29.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
16P GAIN MUTATED 64 18 11
16P GAIN WILD-TYPE 161 159 39

Figure S29.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 4.46e-07 (Chi-square test), Q value = 0.00034

Table S30.  Gene #28: '16p gain' 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 GAIN MUTATED 28 23 15 7 3 12 5
16P GAIN WILD-TYPE 39 54 65 58 69 62 12

Figure S30.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.013

Table S31.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
16Q GAIN MUTATED 64 18 12
16Q GAIN WILD-TYPE 161 159 38

Figure S31.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 8.69e-05 (Chi-square test), Q value = 0.063

Table S32.  Gene #29: '16q gain' 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 GAIN MUTATED 20 28 18 7 5 12 4
16Q GAIN WILD-TYPE 47 49 62 58 67 62 13

Figure S32.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 4.41e-06 (Fisher's exact test), Q value = 0.0033

Table S33.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
17P GAIN MUTATED 43 7 9
17P GAIN WILD-TYPE 182 170 41

Figure S33.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 5.66e-05 (Chi-square test), Q value = 0.041

Table S34.  Gene #30: '17p gain' 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 GAIN MUTATED 9 11 24 3 5 6 1
17P GAIN WILD-TYPE 58 66 56 62 67 68 16

Figure S34.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 2.24e-07 (Fisher's exact test), Q value = 0.00017

Table S35.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
17Q GAIN MUTATED 57 10 9
17Q GAIN WILD-TYPE 168 167 41

Figure S35.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.000194 (Chi-square test), Q value = 0.14

Table S36.  Gene #31: '17q gain' 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 GAIN MUTATED 17 16 24 6 5 6 2
17Q GAIN WILD-TYPE 50 61 56 59 67 68 15

Figure S36.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 2.81e-08 (Fisher's exact test), Q value = 2.2e-05

Table S37.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
18P GAIN MUTATED 78 19 8
18P GAIN WILD-TYPE 147 158 42

Figure S37.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 2.7e-06 (Chi-square test), Q value = 0.002

Table S38.  Gene #32: '18p gain' 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 GAIN MUTATED 29 21 24 16 7 7 1
18P GAIN WILD-TYPE 38 56 56 49 65 67 16

Figure S38.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 7.73e-05 (Chi-square test), Q value = 0.056

Table S39.  Gene #33: '18q gain' 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 GAIN MUTATED 10 4 10 15 2 1 1
18Q GAIN WILD-TYPE 57 73 70 50 70 73 16

Figure S39.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.077

Table S40.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 102 108 83
18Q GAIN MUTATED 2 19 8 9
18Q GAIN WILD-TYPE 120 83 100 74

Figure S40.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1.81e-05 (Chi-square test), Q value = 0.013

Table S41.  Gene #34: '19p gain' 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 GAIN MUTATED 5 3 17 11 3 1 0
19P GAIN WILD-TYPE 62 74 63 54 69 73 17

Figure S41.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.000338 (Chi-square test), Q value = 0.24

Table S42.  Gene #35: '19q gain' 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 GAIN MUTATED 9 7 19 14 6 1 1
19Q GAIN WILD-TYPE 58 70 61 51 66 73 16

Figure S42.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 3.48e-05 (Chi-square test), Q value = 0.026

Table S43.  Gene #36: '20p gain' 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 GAIN MUTATED 22 47 33 17 17 23 6
20P GAIN WILD-TYPE 45 30 47 48 55 51 11

Figure S43.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 8.75e-05 (Fisher's exact test), Q value = 0.063

Table S44.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
20Q GAIN MUTATED 106 47 22
20Q GAIN WILD-TYPE 119 130 28

Figure S44.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 3.19e-06 (Chi-square test), Q value = 0.0024

Table S45.  Gene #37: '20q gain' 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 GAIN MUTATED 29 47 36 12 19 24 8
20Q GAIN WILD-TYPE 38 30 44 53 53 50 9

Figure S45.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.14

Table S46.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
22Q GAIN MUTATED 64 21 10
22Q GAIN WILD-TYPE 161 156 40

Figure S46.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 4.63e-11 (Chi-square test), Q value = 3.6e-08

Table S47.  Gene #39: '22q gain' 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 GAIN MUTATED 18 18 37 4 2 16 0
22Q GAIN WILD-TYPE 49 59 43 61 70 58 17

Figure S47.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.13e-05 (Fisher's exact test), Q value = 0.016

Table S48.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 102 108 83
22Q GAIN MUTATED 10 31 22 26
22Q GAIN WILD-TYPE 112 71 86 57

Figure S48.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.41e-05 (Chi-square test), Q value = 0.054

Table S49.  Gene #39: '22q gain' 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
22Q GAIN MUTATED 1 15 5 11 31 26
22Q GAIN WILD-TYPE 3 25 86 35 124 53

Figure S49.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 4.04e-05 (Fisher's exact test), Q value = 0.03

Table S50.  Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
XQ GAIN MUTATED 49 12 11
XQ GAIN WILD-TYPE 176 165 39

Figure S50.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.000222 (Fisher's exact test), Q value = 0.16

Table S51.  Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
1P LOSS MUTATED 36 7 4
1P LOSS WILD-TYPE 189 170 46

Figure S51.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 9.85e-09 (Chi-square test), Q value = 7.7e-06

Table S52.  Gene #41: '1p loss' 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 LOSS MUTATED 4 8 25 2 2 5 1
1P LOSS WILD-TYPE 63 69 55 63 70 69 16

Figure S52.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 5.87e-24 (Fisher's exact test), Q value = 4.7e-21

Table S53.  Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
3P LOSS MUTATED 179 52 31
3P LOSS WILD-TYPE 46 125 19

Figure S53.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1.36e-15 (Chi-square test), Q value = 1.1e-12

Table S54.  Gene #45: '3p loss' 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 LOSS MUTATED 48 61 61 15 27 36 14
3P LOSS WILD-TYPE 19 16 19 50 45 38 3

Figure S54.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 2.21e-14 (Fisher's exact test), Q value = 1.8e-11

Table S55.  Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
4P LOSS MUTATED 122 30 15
4P LOSS WILD-TYPE 103 147 35

Figure S55.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 3e-12 (Chi-square test), Q value = 2.4e-09

Table S56.  Gene #47: '4p loss' 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 LOSS MUTATED 34 25 54 20 12 13 9
4P LOSS WILD-TYPE 33 52 26 45 60 61 8

Figure S56.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.88e-05 (Fisher's exact test), Q value = 0.021

Table S57.  Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 101 158
4P LOSS MUTATED 76 20 60
4P LOSS WILD-TYPE 85 81 98

Figure S57.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.29e-06 (Chi-square test), Q value = 0.0032

Table S58.  Gene #47: '4p loss' 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 LOSS MUTATED 1 6 22 18 54 47
4P LOSS WILD-TYPE 3 34 69 28 101 32

Figure S58.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 6.94e-11 (Fisher's exact test), Q value = 5.5e-08

Table S59.  Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
4Q LOSS MUTATED 96 22 15
4Q LOSS WILD-TYPE 129 155 35

Figure S59.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 3.28e-08 (Chi-square test), Q value = 2.5e-05

Table S60.  Gene #48: '4q loss' 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 LOSS MUTATED 26 26 43 14 9 13 2
4Q LOSS WILD-TYPE 41 51 37 51 63 61 15

Figure S60.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 0.000301 (Fisher's exact test), Q value = 0.21

Table S61.  Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
5P LOSS MUTATED 29 5 7
5P LOSS WILD-TYPE 196 172 43

Figure S61.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.00031 (Chi-square test), Q value = 0.22

Table S62.  Gene #49: '5p loss' 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 LOSS MUTATED 10 12 13 2 1 1 2
5P LOSS WILD-TYPE 57 65 67 63 71 73 15

Figure S62.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 7.78e-15 (Fisher's exact test), Q value = 6.2e-12

Table S63.  Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
5Q LOSS MUTATED 106 20 12
5Q LOSS WILD-TYPE 119 157 38

Figure S63.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 4.15e-15 (Chi-square test), Q value = 3.3e-12

Table S64.  Gene #50: '5q loss' 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 LOSS MUTATED 35 36 38 8 2 12 7
5Q LOSS WILD-TYPE 32 41 42 57 70 62 10

Figure S64.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.84e-05 (Fisher's exact test), Q value = 0.014

Table S65.  Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
8P LOSS MUTATED 105 43 18
8P LOSS WILD-TYPE 120 134 32

Figure S65.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Chi-square test), Q value = 0.087

Table S66.  Gene #55: '8p loss' 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
8P LOSS MUTATED 21 43 33 11 28 27 3
8P LOSS WILD-TYPE 46 34 47 54 44 47 14

Figure S66.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 4.88e-29 (Fisher's exact test), Q value = 3.9e-26

Table S67.  Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
9P LOSS MUTATED 130 21 1
9P LOSS WILD-TYPE 95 156 49

Figure S67.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 3.4e-14 (Chi-square test), Q value = 2.7e-11

Table S68.  Gene #57: '9p loss' 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 LOSS MUTATED 39 30 43 7 9 14 10
9P LOSS WILD-TYPE 28 47 37 58 63 60 7

Figure S68.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.75e-10 (Fisher's exact test), Q value = 1.4e-07

Table S69.  Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
9Q LOSS MUTATED 59 11 0
9Q LOSS WILD-TYPE 166 166 50

Figure S69.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 8.96e-06 (Chi-square test), Q value = 0.0067

Table S70.  Gene #58: '9q loss' 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
9Q LOSS MUTATED 17 16 22 3 4 4 4
9Q LOSS WILD-TYPE 50 61 58 62 68 70 13

Figure S70.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 2.28e-06 (Fisher's exact test), Q value = 0.0017

Table S71.  Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
10P LOSS MUTATED 85 29 20
10P LOSS WILD-TYPE 140 148 30

Figure S71.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.012

Table S72.  Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
10Q LOSS MUTATED 65 19 7
10Q LOSS WILD-TYPE 160 158 43

Figure S72.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 7.92e-08 (Fisher's exact test), Q value = 6.1e-05

Table S73.  Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
11P LOSS MUTATED 84 26 6
11P LOSS WILD-TYPE 141 151 44

Figure S73.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.000147 (Fisher's exact test), Q value = 0.11

Table S74.  Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
11Q LOSS MUTATED 89 36 14
11Q LOSS WILD-TYPE 136 141 36

Figure S74.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 5.4e-05 (Chi-square test), Q value = 0.04

Table S75.  Gene #62: '11q loss' 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 LOSS MUTATED 16 23 32 34 11 17 6
11Q LOSS WILD-TYPE 51 54 48 31 61 57 11

Figure S75.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 7.6e-06 (Fisher's exact test), Q value = 0.0057

Table S76.  Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
13Q LOSS MUTATED 93 34 18
13Q LOSS WILD-TYPE 132 143 32

Figure S76.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 2.68e-07 (Chi-square test), Q value = 2e-04

Table S77.  Gene #65: '13q loss' 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 LOSS MUTATED 35 26 38 19 9 16 2
13Q LOSS WILD-TYPE 32 51 42 46 63 58 15

Figure S77.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.58e-05 (Fisher's exact test), Q value = 0.048

Table S78.  Gene #65: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 101 158
13Q LOSS MUTATED 70 18 50
13Q LOSS WILD-TYPE 91 83 108

Figure S78.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1.42e-06 (Fisher's exact test), Q value = 0.0011

Table S79.  Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
15Q LOSS MUTATED 55 13 15
15Q LOSS WILD-TYPE 170 164 35

Figure S79.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 2.51e-09 (Chi-square test), Q value = 2e-06

Table S80.  Gene #69: '16q loss' 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 LOSS MUTATED 11 2 21 23 4 3 4
16Q LOSS WILD-TYPE 56 75 59 42 68 71 13

Figure S80.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 2.69e-08 (Fisher's exact test), Q value = 2.1e-05

Table S81.  Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 122 133
16Q LOSS MUTATED 45 14 5
16Q LOSS WILD-TYPE 120 108 128

Figure S81.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.32e-09 (Fisher's exact test), Q value = 1.8e-06

Table S82.  Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 101 158
16Q LOSS MUTATED 47 4 13
16Q LOSS WILD-TYPE 114 97 145

Figure S82.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.008

Table S83.  Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 122 102 108 83
16Q LOSS MUTATED 7 30 11 11
16Q LOSS WILD-TYPE 115 72 97 72

Figure S83.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.015

Table S84.  Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
17P LOSS MUTATED 66 19 11
17P LOSS WILD-TYPE 159 158 39

Figure S84.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.000191 (Chi-square test), Q value = 0.14

Table S85.  Gene #70: '17p loss' 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 LOSS MUTATED 24 22 18 16 6 6 4
17P LOSS WILD-TYPE 43 55 62 49 66 68 13

Figure S85.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 6.8e-11 (Fisher's exact test), Q value = 5.4e-08

Table S86.  Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
18Q LOSS MUTATED 124 39 22
18Q LOSS WILD-TYPE 101 138 28

Figure S86.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 9.22e-12 (Chi-square test), Q value = 7.3e-09

Table S87.  Gene #73: '18q loss' 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 LOSS MUTATED 36 46 40 2 20 32 9
18Q LOSS WILD-TYPE 31 31 40 63 52 42 8

Figure S87.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000206 (Fisher's exact test), Q value = 0.15

Table S88.  Gene #73: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 161 101 158
18Q LOSS MUTATED 50 37 84
18Q LOSS WILD-TYPE 111 64 74

Figure S88.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.000238 (Chi-square test), Q value = 0.17

Table S89.  Gene #74: '19p loss' 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 LOSS MUTATED 13 28 19 5 9 9 4
19P LOSS WILD-TYPE 54 49 61 60 63 65 13

Figure S89.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 5.6e-05 (Fisher's exact test), Q value = 0.041

Table S90.  Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
19Q LOSS MUTATED 54 14 9
19Q LOSS WILD-TYPE 171 163 41

Figure S90.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 4.37e-05 (Chi-square test), Q value = 0.032

Table S91.  Gene #75: '19q loss' 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 LOSS MUTATED 12 24 22 4 6 7 2
19Q LOSS WILD-TYPE 55 53 58 61 66 67 15

Figure S91.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 5.27e-06 (Fisher's exact test), Q value = 0.004

Table S92.  Gene #76: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
20P LOSS MUTATED 37 5 2
20P LOSS WILD-TYPE 188 172 48

Figure S92.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 2.67e-09 (Fisher's exact test), Q value = 2.1e-06

Table S93.  Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 225 177 50
21Q LOSS MUTATED 106 33 23
21Q LOSS WILD-TYPE 119 144 27

Figure S93.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1.56e-07 (Chi-square test), Q value = 0.00012

Table S94.  Gene #78: '21q loss' 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 LOSS MUTATED 24 43 41 10 18 18 8
21Q LOSS WILD-TYPE 43 34 39 55 54 56 9

Figure S94.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.1

Table S95.  Gene #79: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 122 133
22Q LOSS MUTATED 12 18 33
22Q LOSS WILD-TYPE 153 104 100

Figure S95.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 2.76e-06 (Chi-square test), Q value = 0.0021

Table S96.  Gene #80: 'xq loss' 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 LOSS MUTATED 11 14 28 9 3 5 1
XQ LOSS WILD-TYPE 56 63 52 56 69 69 16

Figure S96.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 3.09e-05 (Fisher's exact test), Q value = 0.023

Table S97.  Gene #80: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 182 129
XQ LOSS MUTATED 15 46 10
XQ LOSS WILD-TYPE 125 136 119

Figure S97.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.1e-05 (Chi-square test), Q value = 0.044

Table S98.  Gene #80: 'xq loss' 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
XQ LOSS MUTATED 0 8 7 4 19 26
XQ LOSS WILD-TYPE 4 32 84 42 136 53

Figure S98.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 452

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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