Correlation between copy number variations of arm-level result and molecular subtypes
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1833QW2
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/C1833QW2
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 522 patients, 135 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 3p gain cnv correlated to 'METHLYATION_CNMF'.

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

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 12q gain cnv correlated to 'CN_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF'.

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

  • 15q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 17q gain cnv correlated to 'CN_CNMF'.

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

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

  • 19p gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 19q gain cnv correlated to 'METHLYATION_CNMF'.

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

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

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

  • xq gain cnv correlated to 'CN_CNMF'.

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

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

  • 4p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_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',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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' and 'METHLYATION_CNMF'.

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

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

  • 14q loss cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF'.

  • 16p 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'.

  • 18p loss cnv correlated to 'METHLYATION_CNMF'.

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

  • 19p loss cnv correlated to 'CN_CNMF' and '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',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'CN_CNMF'.

  • xq loss 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 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, 135 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 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 Fisher's exact test Fisher's exact test
1q gain 121 (23%) 401 1e-05
(0.008) 		1e-05
(0.008) 		0.29
(1.00) 		0.77
(1.00) 		0.0002
(0.135) 		0.00018
(0.122) 		0.00045
(0.297) 		0.00031
(0.208) 		0.0115
(1.00) 		0.0962
(1.00)
5q loss 164 (31%) 358 1e-05
(0.008) 		1e-05
(0.008) 		0.242
(1.00) 		0.773
(1.00) 		0.226
(1.00) 		1e-05
(0.008) 		0.388
(1.00) 		0.00024
(0.162) 		0.00019
(0.129) 		0.0771
(1.00)
9p loss 186 (36%) 336 1e-05
(0.008) 		1e-05
(0.008) 		0.667
(1.00) 		0.114
(1.00) 		0.344
(1.00) 		0.00012
(0.0829) 		0.0569
(1.00) 		3e-05
(0.0215) 		3e-05
(0.0215) 		0.601
(1.00)
18q loss 211 (40%) 311 1e-05
(0.008) 		1e-05
(0.008) 		0.213
(1.00) 		0.332
(1.00) 		0.0016
(1.00) 		1e-05
(0.008) 		0.00075
(0.488) 		2e-05
(0.0145) 		8e-05
(0.0557) 		0.0532
(1.00)
18q gain 53 (10%) 469 0.0016
(1.00) 		2e-05
(0.0145) 		0.00702
(1.00) 		0.0877
(1.00) 		0.00102
(0.654) 		0.00016
(0.109) 		3e-05
(0.0215) 		0.143
(1.00) 		4e-05
(0.0282) 		0.0616
(1.00)
3p loss 297 (57%) 225 1e-05
(0.008) 		1e-05
(0.008) 		0.942
(1.00) 		0.676
(1.00) 		0.0242
(1.00) 		8e-05
(0.0557) 		0.0978
(1.00) 		0.00077
(0.499) 		6e-05
(0.0419) 		0.235
(1.00)
8p loss 187 (36%) 335 1e-05
(0.008) 		1e-05
(0.008) 		0.547
(1.00) 		0.678
(1.00) 		0.0714
(1.00) 		0.0122
(1.00) 		0.14
(1.00) 		0.00273
(1.00) 		0.00015
(0.102) 		5e-05
(0.0351)
16q loss 81 (16%) 441 0.00238
(1.00) 		1e-05
(0.008) 		0.475
(1.00) 		0.243
(1.00) 		1e-05
(0.008) 		1e-05
(0.008) 		0.00807
(1.00) 		0.00825
(1.00) 		1e-05
(0.008) 		0.00245
(1.00)
2q gain 74 (14%) 448 1e-05
(0.008) 		1e-05
(0.008) 		0.387
(1.00) 		0.729
(1.00) 		0.0699
(1.00) 		0.00027
(0.182) 		0.105
(1.00) 		0.102
(1.00) 		0.0172
(1.00) 		0.0396
(1.00)
3q gain 254 (49%) 268 5e-05
(0.0351) 		1e-05
(0.008) 		0.697
(1.00) 		0.279
(1.00) 		0.0003
(0.202) 		0.0251
(1.00) 		0.00845
(1.00) 		0.803
(1.00) 		0.0216
(1.00) 		0.0959
(1.00)
7p gain 183 (35%) 339 1e-05
(0.008) 		1e-05
(0.008) 		0.631
(1.00) 		0.504
(1.00) 		0.262
(1.00) 		0.115
(1.00) 		0.687
(1.00) 		1e-05
(0.008) 		0.123
(1.00) 		0.533
(1.00)
7q gain 129 (25%) 393 1e-05
(0.008) 		1e-05
(0.008) 		0.175
(1.00) 		0.633
(1.00) 		0.542
(1.00) 		0.876
(1.00) 		0.0124
(1.00) 		7e-05
(0.0488) 		0.326
(1.00) 		0.503
(1.00)
9p gain 102 (20%) 420 1e-05
(0.008) 		2e-05
(0.0145) 		0.39
(1.00) 		0.0944
(1.00) 		0.00187
(1.00) 		0.0157
(1.00) 		0.00724
(1.00) 		0.00966
(1.00) 		8e-05
(0.0557) 		0.157
(1.00)
14q gain 151 (29%) 371 1e-05
(0.008) 		1e-05
(0.008) 		0.217
(1.00) 		0.0971
(1.00) 		0.0192
(1.00) 		0.00065
(0.424) 		0.00704
(1.00) 		0.00038
(0.253) 		5e-05
(0.0351) 		0.00051
(0.336)
16p gain 107 (20%) 415 1e-05
(0.008) 		1e-05
(0.008) 		0.332
(1.00) 		0.176
(1.00) 		0.385
(1.00) 		0.00535
(1.00) 		0.867
(1.00) 		2e-05
(0.0145) 		0.478
(1.00) 		0.54
(1.00)
16q gain 107 (20%) 415 1e-05
(0.008) 		2e-05
(0.0145) 		0.584
(1.00) 		0.817
(1.00) 		0.175
(1.00) 		0.005
(1.00) 		0.289
(1.00) 		3e-05
(0.0215) 		0.0897
(1.00) 		0.194
(1.00)
18p gain 123 (24%) 399 1e-05
(0.008) 		1e-05
(0.008) 		0.331
(1.00) 		0.318
(1.00) 		0.376
(1.00) 		1e-05
(0.008) 		0.248
(1.00) 		0.0153
(1.00) 		0.00087
(0.562) 		0.163
(1.00)
19p gain 56 (11%) 466 0.0132
(1.00) 		3e-05
(0.0215) 		0.0879
(1.00) 		0.767
(1.00) 		0.0117
(1.00) 		0.00022
(0.149) 		0.00036
(0.24) 		0.0528
(1.00) 		0.403
(1.00) 		0.182
(1.00)
22q gain 112 (21%) 410 1e-05
(0.008) 		1e-05
(0.008) 		0.156
(1.00) 		0.517
(1.00) 		0.272
(1.00) 		0.418
(1.00) 		0.00036
(0.24) 		0.0817
(1.00) 		0.0131
(1.00) 		0.529
(1.00)
4p loss 194 (37%) 328 1e-05
(0.008) 		1e-05
(0.008) 		0.0622
(1.00) 		0.55
(1.00) 		0.00054
(0.355) 		0.00012
(0.0829) 		0.183
(1.00) 		0.0272
(1.00) 		0.00062
(0.406) 		0.0656
(1.00)
11q loss 172 (33%) 350 1e-05
(0.008) 		1e-05
(0.008) 		0.176
(1.00) 		0.079
(1.00) 		0.00533
(1.00) 		6e-05
(0.0419) 		0.107
(1.00) 		0.428
(1.00) 		0.152
(1.00) 		0.507
(1.00)
21q loss 184 (35%) 338 1e-05
(0.008) 		1e-05
(0.008) 		0.575
(1.00) 		0.983
(1.00) 		0.0339
(1.00) 		0.034
(1.00) 		0.302
(1.00) 		0.00033
(0.221) 		0.00076
(0.493) 		0.233
(1.00)
2p gain 97 (19%) 425 1e-05
(0.008) 		1e-05
(0.008) 		0.0231
(1.00) 		0.437
(1.00) 		0.0543
(1.00) 		0.00128
(0.817) 		0.0208
(1.00) 		0.0197
(1.00) 		0.0024
(1.00) 		0.0893
(1.00)
8q gain 310 (59%) 212 3e-05
(0.0215) 		3e-05
(0.0215) 		0.0813
(1.00) 		0.889
(1.00) 		0.178
(1.00) 		0.00428
(1.00) 		0.173
(1.00) 		0.0109
(1.00) 		0.0394
(1.00) 		0.0684
(1.00)
10p gain 40 (8%) 482 0.0758
(1.00) 		3e-05
(0.0215) 		0.592
(1.00) 		0.0659
(1.00) 		0.0393
(1.00) 		0.00017
(0.116) 		0.0445
(1.00) 		0.0156
(1.00) 		0.557
(1.00) 		0.365
(1.00)
11p gain 66 (13%) 456 0.00013
(0.0894) 		2e-05
(0.0145) 		0.827
(1.00) 		0.411
(1.00) 		0.134
(1.00) 		0.078
(1.00) 		0.0455
(1.00) 		0.266
(1.00) 		0.003
(1.00) 		0.00824
(1.00)
11q gain 71 (14%) 451 0.00013
(0.0894) 		3e-05
(0.0215) 		0.576
(1.00) 		0.583
(1.00) 		0.154
(1.00) 		0.0302
(1.00) 		0.275
(1.00) 		0.0165
(1.00) 		0.0181
(1.00) 		0.0623
(1.00)
12p gain 148 (28%) 374 1e-05
(0.008) 		1e-05
(0.008) 		0.0164
(1.00) 		0.822
(1.00) 		0.0159
(1.00) 		0.00201
(1.00) 		0.0122
(1.00) 		0.0973
(1.00) 		0.0388
(1.00) 		0.523
(1.00)
17p gain 67 (13%) 455 1e-05
(0.008) 		3e-05
(0.0215) 		0.598
(1.00) 		0.903
(1.00) 		0.00786
(1.00) 		0.013
(1.00) 		0.0569
(1.00) 		0.0473
(1.00) 		0.247
(1.00) 		0.168
(1.00)
20p gain 190 (36%) 332 1e-05
(0.008) 		4e-05
(0.0282) 		0.897
(1.00) 		0.733
(1.00) 		0.104
(1.00) 		0.0252
(1.00) 		0.0931
(1.00) 		0.0132
(1.00) 		0.509
(1.00) 		0.0406
(1.00)
20q gain 201 (39%) 321 1e-05
(0.008) 		1e-05
(0.008) 		0.839
(1.00) 		0.872
(1.00) 		0.0742
(1.00) 		0.00042
(0.278) 		0.0632
(1.00) 		0.00408
(1.00) 		0.0344
(1.00) 		0.0114
(1.00)
1p loss 58 (11%) 464 1e-05
(0.008) 		1e-05
(0.008) 		0.0315
(1.00) 		0.168
(1.00) 		0.00168
(1.00) 		0.00475
(1.00) 		0.403
(1.00) 		0.0875
(1.00) 		0.264
(1.00) 		0.0206
(1.00)
4q loss 151 (29%) 371 1e-05
(0.008) 		1e-05
(0.008) 		0.472
(1.00) 		0.224
(1.00) 		0.0156
(1.00) 		0.00188
(1.00) 		0.258
(1.00) 		0.0912
(1.00) 		0.0301
(1.00) 		0.161
(1.00)
5p loss 51 (10%) 471 3e-05
(0.0215) 		1e-05
(0.008) 		0.42
(1.00) 		0.385
(1.00) 		0.585
(1.00) 		0.128
(1.00) 		0.409
(1.00) 		0.257
(1.00) 		0.0936
(1.00) 		0.025
(1.00)
9q loss 87 (17%) 435 1e-05
(0.008) 		1e-05
(0.008) 		0.976
(1.00) 		0.971
(1.00) 		0.388
(1.00) 		0.235
(1.00) 		0.423
(1.00) 		0.00365
(1.00) 		0.0126
(1.00) 		0.309
(1.00)
11p loss 141 (27%) 381 1e-05
(0.008) 		0.00012
(0.0829) 		0.32
(1.00) 		0.333
(1.00) 		0.00573
(1.00) 		0.142
(1.00) 		0.00372
(1.00) 		0.121
(1.00) 		0.0948
(1.00) 		0.232
(1.00)
13q loss 167 (32%) 355 1e-05
(0.008) 		1e-05
(0.008) 		0.386
(1.00) 		0.825
(1.00) 		0.00442
(1.00) 		0.00145
(0.924) 		0.0393
(1.00) 		0.192
(1.00) 		0.107
(1.00) 		0.2
(1.00)
14q loss 58 (11%) 464 0.0629
(1.00) 		0.00329
(1.00) 		0.0346
(1.00) 		0.528
(1.00) 		4e-05
(0.0282) 		0.00038
(0.253) 		0.00044
(0.29) 		0.311
(1.00) 		2e-05
(0.0145) 		0.0129
(1.00)
19p loss 98 (19%) 424 1e-05
(0.008) 		0.00014
(0.0958) 		0.712
(1.00) 		0.716
(1.00) 		0.0227
(1.00) 		0.00707
(1.00) 		0.022
(1.00) 		0.00408
(1.00) 		0.0101
(1.00) 		0.0368
(1.00)
19q loss 86 (16%) 436 1e-05
(0.008) 		2e-05
(0.0145) 		0.128
(1.00) 		0.519
(1.00) 		0.205
(1.00) 		0.0896
(1.00) 		0.154
(1.00) 		0.0324
(1.00) 		0.173
(1.00) 		0.0414
(1.00)
xq loss 86 (16%) 436 1e-05
(0.008) 		1e-05
(0.008) 		0.0847
(1.00) 		0.00184
(1.00) 		0.0303
(1.00) 		0.00504
(1.00) 		0.00348
(1.00) 		0.112
(1.00) 		0.373
(1.00) 		0.754
(1.00)
1p gain 70 (13%) 452 0.00013
(0.0894) 		0.00979
(1.00) 		0.992
(1.00) 		0.625
(1.00) 		0.887
(1.00) 		0.942
(1.00) 		0.687
(1.00) 		0.00521
(1.00) 		0.119
(1.00) 		0.874
(1.00)
3p gain 81 (16%) 441 0.197
(1.00) 		0.00033
(0.221) 		0.131
(1.00) 		0.757
(1.00) 		0.00479
(1.00) 		0.0824
(1.00) 		0.131
(1.00) 		0.154
(1.00) 		0.113
(1.00) 		0.0288
(1.00)
5p gain 201 (39%) 321 1e-05
(0.008) 		0.00224
(1.00) 		0.962
(1.00) 		0.834
(1.00) 		0.112
(1.00) 		0.438
(1.00) 		0.573
(1.00) 		0.0328
(1.00) 		0.837
(1.00) 		0.661
(1.00)
6p gain 83 (16%) 439 0.00036
(0.24) 		0.00225
(1.00) 		0.499
(1.00) 		0.745
(1.00) 		0.659
(1.00) 		0.037
(1.00) 		0.605
(1.00) 		0.0713
(1.00) 		0.32
(1.00) 		0.66
(1.00)
9q gain 139 (27%) 383 1e-05
(0.008) 		0.00323
(1.00) 		0.175
(1.00) 		0.255
(1.00) 		0.285
(1.00) 		0.0183
(1.00) 		0.398
(1.00) 		0.0511
(1.00) 		0.297
(1.00) 		0.441
(1.00)
12q gain 89 (17%) 433 2e-05
(0.0145) 		0.00093
(0.599) 		0.142
(1.00) 		0.183
(1.00) 		0.0738
(1.00) 		0.00291
(1.00) 		0.664
(1.00) 		0.783
(1.00) 		0.45
(1.00) 		0.792
(1.00)
13q gain 57 (11%) 465 1e-05
(0.008) 		0.00266
(1.00) 		0.595
(1.00) 		0.734
(1.00) 		0.0232
(1.00) 		0.0383
(1.00) 		0.123
(1.00) 		0.241
(1.00) 		0.0275
(1.00) 		0.0157
(1.00)
15q gain 72 (14%) 450 8e-05
(0.0557) 		0.0069
(1.00) 		0.385
(1.00) 		0.586
(1.00) 		0.215
(1.00) 		0.568
(1.00) 		0.886
(1.00) 		0.00623
(1.00) 		0.0342
(1.00) 		0.524
(1.00)
17q gain 87 (17%) 435 1e-05
(0.008) 		0.00064
(0.419) 		0.585
(1.00) 		0.677
(1.00) 		0.129
(1.00) 		0.0312
(1.00) 		0.417
(1.00) 		0.00355
(1.00) 		0.0619
(1.00) 		0.0997
(1.00)
19q gain 78 (15%) 444 0.372
(1.00) 		0.00031
(0.208) 		0.962
(1.00) 		0.785
(1.00) 		0.0169
(1.00) 		0.00079
(0.511) 		0.00054
(0.355) 		0.0788
(1.00) 		0.497
(1.00) 		0.0647
(1.00)
xq gain 90 (17%) 432 0.00013
(0.0894) 		0.00095
(0.611) 		0.253
(1.00) 		0.825
(1.00) 		0.428
(1.00) 		0.369
(1.00) 		0.126
(1.00) 		0.505
(1.00) 		0.0303
(1.00) 		0.291
(1.00)
10p loss 156 (30%) 366 1e-05
(0.008) 		0.00337
(1.00) 		0.321
(1.00) 		0.231
(1.00) 		0.0522
(1.00) 		0.0832
(1.00) 		0.0656
(1.00) 		0.0911
(1.00) 		0.0226
(1.00) 		0.24
(1.00)
10q loss 113 (22%) 409 1e-05
(0.008) 		0.00071
(0.463) 		0.208
(1.00) 		0.302
(1.00) 		0.0141
(1.00) 		0.0102
(1.00) 		0.0289
(1.00) 		0.146
(1.00) 		0.121
(1.00) 		0.164
(1.00)
15q loss 103 (20%) 419 1e-05
(0.008) 		0.167
(1.00) 		0.628
(1.00) 		0.346
(1.00) 		0.122
(1.00) 		0.288
(1.00) 		0.606
(1.00) 		0.271
(1.00) 		0.079
(1.00) 		0.94
(1.00)
16p loss 63 (12%) 459 2e-05
(0.0145) 		0.0113
(1.00) 		0.865
(1.00) 		0.0794
(1.00) 		0.00228
(1.00) 		0.0585
(1.00) 		0.66
(1.00) 		0.634
(1.00) 		0.179
(1.00) 		0.896
(1.00)
17p loss 107 (20%) 415 0.00014
(0.0958) 		0.00096
(0.616) 		0.388
(1.00) 		0.759
(1.00) 		0.528
(1.00) 		0.117
(1.00) 		0.395
(1.00) 		0.109
(1.00) 		0.343
(1.00) 		0.857
(1.00)
18p loss 104 (20%) 418 0.00164
(1.00) 		2e-05
(0.0145) 		0.541
(1.00) 		0.331
(1.00) 		0.273
(1.00) 		0.111
(1.00) 		0.618
(1.00) 		0.0126
(1.00) 		0.223
(1.00) 		0.58
(1.00)
20p loss 47 (9%) 475 1e-05
(0.008) 		0.0263
(1.00) 		0.494
(1.00) 		0.774
(1.00) 		0.115
(1.00) 		0.349
(1.00) 		0.325
(1.00) 		0.0219
(1.00) 		0.116
(1.00) 		0.096
(1.00)
22q loss 75 (14%) 447 0.0001
(0.0692) 		0.00311
(1.00) 		0.667
(1.00) 		0.656
(1.00) 		0.00122
(0.78) 		0.159
(1.00) 		0.00157
(0.999) 		0.518
(1.00) 		0.0175
(1.00) 		0.0473
(1.00)
4p gain 41 (8%) 481 0.0225
(1.00) 		0.00197
(1.00) 		0.694
(1.00) 		0.356
(1.00) 		0.105
(1.00) 		0.374
(1.00) 		0.0737
(1.00) 		0.646
(1.00) 		0.733
(1.00) 		0.325
(1.00)
4q gain 37 (7%) 485 0.902
(1.00) 		0.198
(1.00) 		1
(1.00) 		0.766
(1.00) 		0.68
(1.00) 		0.129
(1.00) 		1
(1.00) 		0.909
(1.00) 		0.684
(1.00) 		0.738
(1.00)
5q gain 68 (13%) 454 0.0488
(1.00) 		0.595
(1.00) 		0.618
(1.00) 		0.888
(1.00) 		0.761
(1.00) 		0.758
(1.00) 		0.673
(1.00) 		0.449
(1.00) 		0.86
(1.00) 		0.311
(1.00)
6q gain 63 (12%) 459 0.00261
(1.00) 		0.0304
(1.00) 		0.192
(1.00) 		0.0735
(1.00) 		0.0764
(1.00) 		0.0315
(1.00) 		0.24
(1.00) 		0.913
(1.00) 		0.065
(1.00) 		0.298
(1.00)
8p gain 155 (30%) 367 0.0229
(1.00) 		0.247
(1.00) 		0.586
(1.00) 		0.642
(1.00) 		0.525
(1.00) 		0.225
(1.00) 		0.597
(1.00) 		0.787
(1.00) 		0.451
(1.00) 		0.134
(1.00)
10q gain 34 (7%) 488 0.00452
(1.00) 		0.241
(1.00) 		0.097
(1.00) 		0.402
(1.00) 		0.623
(1.00) 		0.16
(1.00) 		0.876
(1.00) 		0.038
(1.00) 		0.217
(1.00) 		0.614
(1.00)
21q gain 35 (7%) 487 0.0638
(1.00) 		0.0402
(1.00) 		0.0142
(1.00) 		0.127
(1.00) 		0.00732
(1.00) 		0.00936
(1.00) 		0.0953
(1.00) 		0.252
(1.00) 		0.0056
(1.00) 		0.77
(1.00)
1q loss 39 (7%) 483 0.0158
(1.00) 		0.139
(1.00) 		0.78
(1.00) 		0.487
(1.00) 		0.0543
(1.00) 		0.0123
(1.00) 		0.0947
(1.00) 		0.00075
(0.488) 		0.409
(1.00) 		0.512
(1.00)
2p loss 33 (6%) 489 0.0285
(1.00) 		0.00571
(1.00) 		0.16
(1.00) 		0.0442
(1.00) 		0.0829
(1.00) 		0.428
(1.00) 		0.0571
(1.00) 		0.672
(1.00) 		0.199
(1.00) 		0.37
(1.00)
2q loss 46 (9%) 476 0.474
(1.00) 		0.215
(1.00) 		0.871
(1.00) 		0.674
(1.00) 		0.732
(1.00) 		0.548
(1.00) 		0.152
(1.00) 		0.689
(1.00) 		0.403
(1.00) 		0.163
(1.00)
3q loss 61 (12%) 461 0.00932
(1.00) 		0.229
(1.00) 		0.338
(1.00) 		0.759
(1.00) 		0.681
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.00724
(1.00) 		0.363
(1.00) 		0.947
(1.00)
6p loss 68 (13%) 454 0.00043
(0.284) 		0.00089
(0.574) 		0.028
(1.00) 		0.127
(1.00) 		0.0296
(1.00) 		0.0371
(1.00) 		0.307
(1.00) 		0.686
(1.00) 		0.739
(1.00) 		0.0767
(1.00)
6q loss 68 (13%) 454 0.0454
(1.00) 		0.00371
(1.00) 		0.127
(1.00) 		0.122
(1.00) 		0.787
(1.00) 		0.573
(1.00) 		0.759
(1.00) 		0.373
(1.00) 		0.766
(1.00) 		0.0218
(1.00)
7p loss 29 (6%) 493 0.0299
(1.00) 		0.00684
(1.00) 		0.0106
(1.00) 		0.627
(1.00) 		0.299
(1.00) 		0.034
(1.00) 		0.256
(1.00) 		0.761
(1.00) 		0.0214
(1.00) 		0.776
(1.00)
7q loss 40 (8%) 482 0.366
(1.00) 		0.302
(1.00) 		0.529
(1.00) 		1
(1.00) 		0.261
(1.00) 		0.066
(1.00) 		0.101
(1.00) 		0.935
(1.00) 		0.747
(1.00) 		0.287
(1.00)
8q loss 30 (6%) 492 0.0235
(1.00) 		0.288
(1.00) 		0.758
(1.00) 		0.874
(1.00) 		0.639
(1.00) 		0.16
(1.00) 		0.374
(1.00) 		0.415
(1.00) 		0.652
(1.00) 		0.265
(1.00)
12p loss 37 (7%) 485 0.731
(1.00) 		0.0499
(1.00) 		0.629
(1.00) 		0.11
(1.00) 		0.93
(1.00) 		0.816
(1.00) 		0.819
(1.00) 		0.799
(1.00) 		0.341
(1.00) 		0.284
(1.00)
12q loss 33 (6%) 489 0.0463
(1.00) 		0.00113
(0.723) 		0.863
(1.00) 		0.0965
(1.00) 		0.384
(1.00) 		0.923
(1.00) 		1
(1.00) 		0.19
(1.00) 		0.302
(1.00) 		0.216
(1.00)
17q loss 34 (7%) 488 0.0138
(1.00) 		0.113
(1.00) 		0.904
(1.00) 		0.506
(1.00) 		0.443
(1.00) 		0.851
(1.00) 		0.742
(1.00) 		0.947
(1.00) 		0.871
(1.00) 		0.546
(1.00)
20q loss 28 (5%) 494 0.00039
(0.259) 		0.00534
(1.00) 		0.21
(1.00) 		0.756
(1.00) 		0.0156
(1.00) 		0.0131
(1.00) 		0.0697
(1.00) 		0.0477
(1.00) 		0.0179
(1.00) 		0.0304
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.089

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
1P GAIN MUTATED 25 30 11 4
1P GAIN WILD-TYPE 130 105 178 39

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
1Q GAIN MUTATED 36 57 21 7
1Q GAIN WILD-TYPE 119 78 168 36

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S3.  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 84 79 96 92 78 75 18
1Q GAIN MUTATED 7 27 25 38 15 5 4
1Q GAIN WILD-TYPE 77 52 71 54 63 70 14

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.14

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 134 152
1Q GAIN MUTATED 67 23 24
1Q GAIN WILD-TYPE 140 111 128

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.12

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
1Q GAIN MUTATED 16 28 24 46
1Q GAIN WILD-TYPE 35 129 131 84

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
1Q GAIN MUTATED 36 51 34
1Q GAIN WILD-TYPE 154 91 152

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
2P GAIN MUTATED 34 51 9 3
2P GAIN WILD-TYPE 121 84 180 40

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S8.  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 84 79 96 92 78 75 18
2P GAIN MUTATED 5 30 18 35 3 5 1
2P GAIN WILD-TYPE 79 49 78 57 75 70 17

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S9.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
2Q GAIN MUTATED 22 43 7 2
2Q GAIN WILD-TYPE 133 92 182 41

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S10.  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 84 79 96 92 78 75 18
2Q GAIN MUTATED 3 25 15 26 1 2 2
2Q GAIN WILD-TYPE 81 54 81 66 77 73 16

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.18

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
2Q GAIN MUTATED 17 26 12 16
2Q GAIN WILD-TYPE 34 131 143 114

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.22

Table S12.  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 84 79 96 92 78 75 18
3P GAIN MUTATED 13 11 11 15 26 4 1
3P GAIN WILD-TYPE 71 68 85 77 52 71 17

Figure S12.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S13.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
3Q GAIN MUTATED 82 82 67 23
3Q GAIN WILD-TYPE 73 53 122 20

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S14.  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 84 79 96 92 78 75 18
3Q GAIN MUTATED 32 46 51 54 46 15 10
3Q GAIN WILD-TYPE 52 33 45 38 32 60 8

Figure S14.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.2

Table S15.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 134 152
3Q GAIN MUTATED 118 70 55
3Q GAIN WILD-TYPE 89 64 97

Figure S15.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S16.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
5P GAIN MUTATED 80 67 39 15
5P GAIN WILD-TYPE 75 68 150 28

Figure S16.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.24

Table S17.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
6P GAIN MUTATED 35 24 14 10
6P GAIN WILD-TYPE 120 111 175 33

Figure S17.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S18.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
7P GAIN MUTATED 69 64 34 16
7P GAIN WILD-TYPE 86 71 155 27

Figure S18.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S19.  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 84 79 96 92 78 75 18
7P GAIN MUTATED 22 34 42 51 5 22 7
7P GAIN WILD-TYPE 62 45 54 41 73 53 11

Figure S19.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S20.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
7P GAIN MUTATED 67 70 43
7P GAIN WILD-TYPE 123 72 143

Figure S20.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S21.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
7Q GAIN MUTATED 36 58 21 14
7Q GAIN WILD-TYPE 119 77 168 29

Figure S21.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S22.  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 84 79 96 92 78 75 18
7Q GAIN MUTATED 10 27 25 46 5 12 4
7Q GAIN WILD-TYPE 74 52 71 46 73 63 14

Figure S22.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S23.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
7Q GAIN MUTATED 46 52 30
7Q GAIN WILD-TYPE 144 90 156

Figure S23.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S24.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
8Q GAIN MUTATED 108 82 88 32
8Q GAIN WILD-TYPE 47 53 101 11

Figure S24.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S25.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
8Q GAIN MUTATED 57 42 73 55 30 39 14
8Q GAIN WILD-TYPE 27 37 23 37 48 36 4

Figure S25.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S26.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
9P GAIN MUTATED 19 17 31 35
9P GAIN WILD-TYPE 136 118 158 8

Figure S26.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S27.  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 84 79 96 92 78 75 18
9P GAIN MUTATED 12 6 16 18 13 34 3
9P GAIN WILD-TYPE 72 73 80 74 65 41 15

Figure S27.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S28.  Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
9P GAIN MUTATED 8 43 9 29 8
9P GAIN WILD-TYPE 64 97 89 87 39

Figure S28.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S29.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
9Q GAIN MUTATED 30 36 37 36
9Q GAIN WILD-TYPE 125 99 152 7

Figure S29.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S30.  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 84 79 96 92 78 75 18
10P GAIN MUTATED 2 18 3 7 5 2 3
10P GAIN WILD-TYPE 82 61 93 85 73 73 15

Figure S30.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.12

Table S31.  Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
10P GAIN MUTATED 13 6 10 9
10P GAIN WILD-TYPE 38 151 145 121

Figure S31.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.089

Table S32.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
11P GAIN MUTATED 34 10 14 8
11P GAIN WILD-TYPE 121 125 175 35

Figure S32.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S33.  Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
11P GAIN MUTATED 3 4 26 13 5 11 4
11P GAIN WILD-TYPE 81 75 70 79 73 64 14

Figure S33.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.089

Table S34.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
11Q GAIN MUTATED 37 16 13 5
11Q GAIN WILD-TYPE 118 119 176 38

Figure S34.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S35.  Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
11Q GAIN MUTATED 4 12 24 14 2 10 5
11Q GAIN WILD-TYPE 80 67 72 78 76 65 13

Figure S35.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S36.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
12P GAIN MUTATED 53 61 20 14
12P GAIN WILD-TYPE 102 74 169 29

Figure S36.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S37.  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 84 79 96 92 78 75 18
12P GAIN MUTATED 12 34 28 43 18 10 3
12P GAIN WILD-TYPE 72 45 68 49 60 65 15

Figure S37.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S38.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
12Q GAIN MUTATED 29 35 13 12
12Q GAIN WILD-TYPE 126 100 176 31

Figure S38.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S39.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
13Q GAIN MUTATED 35 12 8 2
13Q GAIN WILD-TYPE 120 123 181 41

Figure S39.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S40.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
14Q GAIN MUTATED 73 42 19 17
14Q GAIN WILD-TYPE 82 93 170 26

Figure S40.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S41.  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 84 79 96 92 78 75 18
14Q GAIN MUTATED 21 26 40 35 4 19 6
14Q GAIN WILD-TYPE 63 53 56 57 74 56 12

Figure S41.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S42.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
14Q GAIN MUTATED 22 52 18 45 4
14Q GAIN WILD-TYPE 50 88 80 71 43

Figure S42.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S43.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
15Q GAIN MUTATED 29 28 11 4
15Q GAIN WILD-TYPE 126 107 178 39

Figure S43.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S44.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
16P GAIN MUTATED 52 34 14 7
16P GAIN WILD-TYPE 103 101 175 36

Figure S44.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S45.  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 84 79 96 92 78 75 18
16P GAIN MUTATED 13 32 29 18 7 3 5
16P GAIN WILD-TYPE 71 47 67 74 71 72 13

Figure S45.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S46.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
16P GAIN MUTATED 42 44 20
16P GAIN WILD-TYPE 148 98 166

Figure S46.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S47.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
16Q GAIN MUTATED 56 32 14 5
16Q GAIN WILD-TYPE 99 103 175 38

Figure S47.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S48.  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 84 79 96 92 78 75 18
16Q GAIN MUTATED 13 26 32 20 7 5 4
16Q GAIN WILD-TYPE 71 53 64 72 71 70 14

Figure S48.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S49.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
16Q GAIN MUTATED 48 39 19
16Q GAIN WILD-TYPE 142 103 167

Figure S49.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S50.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
17P GAIN MUTATED 21 33 7 6
17P GAIN WILD-TYPE 134 102 182 37

Figure S50.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S51.  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 84 79 96 92 78 75 18
17P GAIN MUTATED 7 13 13 26 3 4 1
17P GAIN WILD-TYPE 77 66 83 66 75 71 17

Figure S51.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S52.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
17Q GAIN MUTATED 24 41 13 9
17Q GAIN WILD-TYPE 131 94 176 34

Figure S52.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S53.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
18P GAIN MUTATED 49 48 18 8
18P GAIN WILD-TYPE 106 87 171 35

Figure S53.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S54.  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 84 79 96 92 78 75 18
18P GAIN MUTATED 7 35 25 27 18 8 3
18P GAIN WILD-TYPE 77 44 71 65 60 67 15

Figure S54.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S55.  Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
18P GAIN MUTATED 26 37 21 32
18P GAIN WILD-TYPE 25 120 134 98

Figure S55.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S56.  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 84 79 96 92 78 75 18
18Q GAIN MUTATED 1 14 5 11 18 3 1
18Q GAIN WILD-TYPE 83 65 91 81 60 72 17

Figure S56.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S57.  Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
18Q GAIN MUTATED 9 10 7 24
18Q GAIN WILD-TYPE 42 147 148 106

Figure S57.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S58.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
18Q GAIN MUTATED 37 4 12
18Q GAIN WILD-TYPE 184 148 133

Figure S58.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S59.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
18Q GAIN MUTATED 8 4 21 7 6
18Q GAIN WILD-TYPE 64 136 77 109 41

Figure S59.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S60.  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 84 79 96 92 78 75 18
19P GAIN MUTATED 2 7 5 21 17 3 1
19P GAIN WILD-TYPE 82 72 91 71 61 72 17

Figure S60.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.15

Table S61.  Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
19P GAIN MUTATED 4 8 10 26
19P GAIN WILD-TYPE 47 149 145 104

Figure S61.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.24

Table S62.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
19P GAIN MUTATED 38 10 8
19P GAIN WILD-TYPE 183 142 137

Figure S62.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S63.  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 84 79 96 92 78 75 18
19Q GAIN MUTATED 4 12 11 23 20 6 2
19Q GAIN WILD-TYPE 80 67 85 69 58 69 16

Figure S63.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S64.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
20P GAIN MUTATED 80 49 44 17
20P GAIN WILD-TYPE 75 86 145 26

Figure S64.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S65.  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 84 79 96 92 78 75 18
20P GAIN MUTATED 26 27 54 40 19 17 7
20P GAIN WILD-TYPE 58 52 42 52 59 58 11

Figure S65.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S66.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
20Q GAIN MUTATED 88 54 41 18
20Q GAIN WILD-TYPE 67 81 148 25

Figure S66.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S67.  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 84 79 96 92 78 75 18
20Q GAIN MUTATED 27 35 54 41 15 20 9
20Q GAIN WILD-TYPE 57 44 42 51 63 55 9

Figure S67.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S68.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
22Q GAIN MUTATED 34 52 20 6
22Q GAIN WILD-TYPE 121 83 169 37

Figure S68.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S69.  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 84 79 96 92 78 75 18
22Q GAIN MUTATED 15 22 24 43 5 1 2
22Q GAIN WILD-TYPE 69 57 72 49 73 74 16

Figure S69.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.24

Table S70.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 221 152 145
22Q GAIN MUTATED 60 17 35
22Q GAIN WILD-TYPE 161 135 110

Figure S70.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.089

Table S71.  Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
XQ GAIN MUTATED 38 29 15 8
XQ GAIN WILD-TYPE 117 106 174 35

Figure S71.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S72.  Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
1P LOSS MUTATED 18 30 7 3
1P LOSS WILD-TYPE 137 105 182 40

Figure S72.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S73.  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 84 79 96 92 78 75 18
1P LOSS MUTATED 6 7 8 30 2 4 1
1P LOSS WILD-TYPE 78 72 88 62 76 71 17

Figure S73.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S74.  Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
3P LOSS MUTATED 123 102 45 27
3P LOSS WILD-TYPE 32 33 144 16

Figure S74.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S75.  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 84 79 96 92 78 75 18
3P LOSS MUTATED 36 60 73 70 15 27 16
3P LOSS WILD-TYPE 48 19 23 22 63 48 2

Figure S75.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S76.  Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
3P LOSS MUTATED 38 104 78 58
3P LOSS WILD-TYPE 13 53 77 72

Figure S76.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S77.  Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
3P LOSS MUTATED 48 77 61 70 12
3P LOSS WILD-TYPE 24 63 37 46 35

Figure S77.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S78.  Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
4P LOSS MUTATED 67 89 24 14
4P LOSS WILD-TYPE 88 46 165 29

Figure S78.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S79.  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 84 79 96 92 78 75 18
4P LOSS MUTATED 17 43 29 61 21 12 11
4P LOSS WILD-TYPE 67 36 67 31 57 63 7

Figure S79.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.083

Table S80.  Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
4P LOSS MUTATED 26 65 36 54
4P LOSS WILD-TYPE 25 92 119 76

Figure S80.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S81.  Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
4Q LOSS MUTATED 51 70 17 13
4Q LOSS WILD-TYPE 104 65 172 30

Figure S81.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S82.  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 84 79 96 92 78 75 18
4Q LOSS MUTATED 14 32 27 48 15 11 4
4Q LOSS WILD-TYPE 70 47 69 44 63 64 14

Figure S82.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S83.  Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
5P LOSS MUTATED 18 22 4 7
5P LOSS WILD-TYPE 137 113 185 36

Figure S83.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S84.  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 84 79 96 92 78 75 18
5P LOSS MUTATED 1 15 14 16 2 2 1
5P LOSS WILD-TYPE 83 64 82 76 76 73 17

Figure S84.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S85.  Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
5Q LOSS MUTATED 62 76 16 10
5Q LOSS WILD-TYPE 93 59 173 33

Figure S85.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S86.  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 84 79 96 92 78 75 18
5Q LOSS MUTATED 14 46 41 45 6 4 8
5Q LOSS WILD-TYPE 70 33 55 47 72 71 10

Figure S86.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S87.  Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
5Q LOSS MUTATED 29 58 27 42
5Q LOSS WILD-TYPE 22 99 128 88

Figure S87.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.16

Table S88.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
5Q LOSS MUTATED 67 57 38
5Q LOSS WILD-TYPE 123 85 148

Figure S88.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.13

Table S89.  Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
5Q LOSS MUTATED 21 45 44 33 4
5Q LOSS WILD-TYPE 51 95 54 83 43

Figure S89.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S90.  Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
8P LOSS MUTATED 87 46 36 18
8P LOSS WILD-TYPE 68 89 153 25

Figure S90.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S91.  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 84 79 96 92 78 75 18
8P LOSS MUTATED 29 27 52 39 10 25 5
8P LOSS WILD-TYPE 55 52 44 53 68 50 13

Figure S91.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S92.  Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
8P LOSS MUTATED 30 60 28 48 5
8P LOSS WILD-TYPE 42 80 70 68 42

Figure S92.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.035

Table S93.  Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 244 89
8P LOSS MUTATED 63 65 43
8P LOSS WILD-TYPE 77 179 46

Figure S93.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S94.  Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
9P LOSS MUTATED 79 81 25 1
9P LOSS WILD-TYPE 76 54 164 42

Figure S94.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S95.  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 84 79 96 92 78 75 18
9P LOSS MUTATED 20 51 37 52 9 8 9
9P LOSS WILD-TYPE 64 28 59 40 69 67 9

Figure S95.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.083

Table S96.  Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
9P LOSS MUTATED 33 56 48 38
9P LOSS WILD-TYPE 18 101 107 92

Figure S96.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S97.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
9P LOSS MUTATED 64 72 48
9P LOSS WILD-TYPE 126 70 138

Figure S97.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S98.  Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
9P LOSS MUTATED 32 40 53 34 7
9P LOSS WILD-TYPE 40 100 45 82 40

Figure S98.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S99.  Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
9Q LOSS MUTATED 41 32 13 1
9Q LOSS WILD-TYPE 114 103 176 42

Figure S99.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S100.  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 84 79 96 92 78 75 18
9Q LOSS MUTATED 5 26 17 26 4 4 5
9Q LOSS WILD-TYPE 79 53 79 66 74 71 13

Figure S100.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S101.  Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
10P LOSS MUTATED 68 46 27 15
10P LOSS WILD-TYPE 87 89 162 28

Figure S101.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S102.  Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
10Q LOSS MUTATED 40 47 19 7
10Q LOSS WILD-TYPE 115 88 170 36

Figure S102.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S103.  Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
11P LOSS MUTATED 38 71 26 6
11P LOSS WILD-TYPE 117 64 163 37

Figure S103.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.083

Table S104.  Gene #61: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
11P LOSS MUTATED 22 27 21 38 21 7 5
11P LOSS WILD-TYPE 62 52 75 54 57 68 13

Figure S104.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S105.  Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
11Q LOSS MUTATED 43 71 44 14
11Q LOSS WILD-TYPE 112 64 145 29

Figure S105.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S106.  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 84 79 96 92 78 75 18
11Q LOSS MUTATED 21 23 29 39 44 11 5
11Q LOSS WILD-TYPE 63 56 67 53 34 64 13

Figure S106.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S107.  Gene #62: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
11Q LOSS MUTATED 10 45 41 63
11Q LOSS WILD-TYPE 41 112 114 67

Figure S107.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S108.  Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
13Q LOSS MUTATED 37 79 36 15
13Q LOSS WILD-TYPE 118 56 153 28

Figure S108.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S109.  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 84 79 96 92 78 75 18
13Q LOSS MUTATED 18 37 30 43 25 13 1
13Q LOSS WILD-TYPE 66 42 66 49 53 62 17

Figure S109.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S110.  Gene #66: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 134 152
14Q LOSS MUTATED 37 11 6
14Q LOSS WILD-TYPE 170 123 146

Figure S110.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S111.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
14Q LOSS MUTATED 8 6 24 8 9
14Q LOSS WILD-TYPE 64 134 74 108 38

Figure S111.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S112.  Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
15Q LOSS MUTATED 43 26 17 17
15Q LOSS WILD-TYPE 112 109 172 26

Figure S112.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S113.  Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
16P LOSS MUTATED 17 28 9 9
16P LOSS WILD-TYPE 138 107 180 34

Figure S113.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S114.  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 84 79 96 92 78 75 18
16Q LOSS MUTATED 5 12 4 26 27 4 3
16Q LOSS WILD-TYPE 79 67 92 66 51 71 15

Figure S114.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S115.  Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 134 152
16Q LOSS MUTATED 57 15 5
16Q LOSS WILD-TYPE 150 119 147

Figure S115.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S116.  Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
16Q LOSS MUTATED 9 17 8 43
16Q LOSS WILD-TYPE 42 140 147 87

Figure S116.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S117.  Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
16Q LOSS MUTATED 9 11 32 9 10
16Q LOSS WILD-TYPE 63 129 66 107 37

Figure S117.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.096

Table S118.  Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
17P LOSS MUTATED 41 37 20 9
17P LOSS WILD-TYPE 114 98 169 34

Figure S118.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S119.  Gene #72: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 79 96 92 78 75 18
18P LOSS MUTATED 18 15 23 30 2 11 5
18P LOSS WILD-TYPE 66 64 73 62 76 64 13

Figure S119.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S120.  Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
18Q LOSS MUTATED 106 51 33 21
18Q LOSS WILD-TYPE 49 84 156 22

Figure S120.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S121.  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 84 79 96 92 78 75 18
18Q LOSS MUTATED 35 40 56 47 2 22 9
18Q LOSS WILD-TYPE 49 39 40 45 76 53 9

Figure S121.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S122.  Gene #73: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
18Q LOSS MUTATED 27 80 67 26
18Q LOSS WILD-TYPE 24 77 88 104

Figure S122.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S123.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
18Q LOSS MUTATED 93 65 51
18Q LOSS WILD-TYPE 97 77 135

Figure S123.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S124.  Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 140 98 116 47
18Q LOSS MUTATED 29 65 31 59 7
18Q LOSS WILD-TYPE 43 75 67 57 40

Figure S124.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S125.  Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
19P LOSS MUTATED 48 26 16 8
19P LOSS WILD-TYPE 107 109 173 35

Figure S125.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.096

Table S126.  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 84 79 96 92 78 75 18
19P LOSS MUTATED 8 13 33 23 7 10 4
19P LOSS WILD-TYPE 76 66 63 69 71 65 14

Figure S126.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S127.  Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
19Q LOSS MUTATED 37 32 9 8
19Q LOSS WILD-TYPE 118 103 180 35

Figure S127.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S128.  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 84 79 96 92 78 75 18
19Q LOSS MUTATED 6 13 27 26 5 7 2
19Q LOSS WILD-TYPE 78 66 69 66 73 68 16

Figure S128.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S129.  Gene #76: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
20P LOSS MUTATED 14 27 5 1
20P LOSS WILD-TYPE 141 108 184 42

Figure S129.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S130.  Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
21Q LOSS MUTATED 77 66 23 18
21Q LOSS WILD-TYPE 78 69 166 25

Figure S130.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S131.  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 84 79 96 92 78 75 18
21Q LOSS MUTATED 22 29 50 47 9 19 8
21Q LOSS WILD-TYPE 62 50 46 45 69 56 10

Figure S131.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.22

Table S132.  Gene #78: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 142 186
21Q LOSS MUTATED 79 59 45
21Q LOSS WILD-TYPE 111 83 141

Figure S132.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.069

Table S133.  Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
22Q LOSS MUTATED 34 17 13 11
22Q LOSS WILD-TYPE 121 118 176 32

Figure S133.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S134.  Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 135 189 43
XQ LOSS MUTATED 35 36 14 1
XQ LOSS WILD-TYPE 120 99 175 42

Figure S134.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S135.  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 84 79 96 92 78 75 18
XQ LOSS MUTATED 6 14 19 30 12 2 3
XQ LOSS WILD-TYPE 78 65 77 62 66 73 15

Figure S135.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 522

  • 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

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] 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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