Correlation between copy number variations of arm-level result and molecular subtypes
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1XG9PRT
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/C1XG9PRT
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 511 patients, 108 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', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 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'.

  • 6q 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'.

  • 8q 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'.

  • 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' 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',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 19p gain cnv correlated to 'METHLYATION_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' and 'METHLYATION_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' and 'METHLYATION_CNMF'.

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

  • 6p loss cnv correlated to 'CN_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' and 'METHLYATION_CNMF'.

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

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

  • 14q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF'.

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

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'METHLYATION_CNMF'.

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

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

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

  • 20q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_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, 108 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 Fisher's exact test
1q gain 117 (23%) 394 6.88e-07
(0.000517) 		1.78e-08
(1.36e-05) 		0.289
(1.00) 		0.653
(1.00) 		0.000218
(0.153) 		0.00033
(0.229) 		0.00177
(1.00) 		0.231
(1.00) 		0.00579
(1.00) 		0.0386
(1.00)
18q gain 48 (9%) 463 0.00226
(1.00) 		1.82e-05
(0.0133) 		0.0168
(1.00) 		0.408
(1.00) 		0.000206
(0.145) 		2.09e-05
(0.0152) 		5.04e-05
(0.0362) 		0.273
(1.00) 		0.012
(1.00) 		0.113
(1.00)
4p loss 186 (36%) 325 6.96e-20
(5.54e-17) 		4.85e-14
(3.82e-11) 		0.0392
(1.00) 		0.592
(1.00) 		0.000231
(0.162) 		6.23e-05
(0.0446) 		0.377
(1.00) 		0.568
(1.00) 		0.027
(1.00) 		0.0222
(1.00)
13q loss 162 (32%) 349 3.74e-15
(2.96e-12) 		9.39e-07
(0.000704) 		0.377
(1.00) 		0.802
(1.00) 		0.00316
(1.00) 		0.000282
(0.196) 		0.0372
(1.00) 		0.431
(1.00) 		0.336
(1.00) 		0.057
(1.00)
16q loss 78 (15%) 433 0.00579
(1.00) 		1.55e-09
(1.19e-06) 		0.479
(1.00) 		0.078
(1.00) 		1.92e-10
(1.5e-07) 		1.93e-09
(1.49e-06) 		0.00225
(1.00) 		0.0147
(1.00) 		0.000568
(0.39) 		0.000365
(0.253)
18q loss 208 (41%) 303 1.66e-17
(1.32e-14) 		1.43e-14
(1.13e-11) 		0.314
(1.00) 		0.0151
(1.00) 		0.00188
(1.00) 		0.000688
(0.468) 		0.00163
(1.00) 		0.000264
(0.184) 		0.147
(1.00) 		0.0228
(1.00)
2p gain 90 (18%) 421 1.6e-07
(0.000122) 		7.36e-11
(5.72e-08) 		0.0452
(1.00) 		0.695
(1.00) 		0.0494
(1.00) 		0.0347
(1.00) 		0.125
(1.00) 		0.47
(1.00) 		0.0998
(1.00) 		0.813
(1.00)
2q gain 69 (14%) 442 2.04e-06
(0.00151) 		2.68e-10
(2.08e-07) 		0.534
(1.00) 		0.812
(1.00) 		0.0619
(1.00) 		0.0303
(1.00) 		0.243
(1.00) 		1
(1.00) 		0.142
(1.00) 		0.457
(1.00)
3q gain 249 (49%) 262 1.15e-05
(0.00842) 		4.43e-07
(0.000334) 		0.683
(1.00) 		0.73
(1.00) 		0.000661
(0.452) 		0.00182
(1.00) 		0.00121
(0.808) 		0.272
(1.00) 		0.0796
(1.00) 		0.247
(1.00)
7p gain 180 (35%) 331 1.44e-09
(1.11e-06) 		7.57e-10
(5.86e-07) 		0.624
(1.00) 		0.52
(1.00) 		0.269
(1.00) 		0.145
(1.00) 		0.686
(1.00) 		0.923
(1.00) 		0.452
(1.00) 		0.856
(1.00)
7q gain 123 (24%) 388 9.41e-09
(7.23e-06) 		2.99e-11
(2.33e-08) 		0.176
(1.00) 		0.913
(1.00) 		0.484
(1.00) 		0.903
(1.00) 		0.0076
(1.00) 		0.454
(1.00) 		0.486
(1.00) 		0.295
(1.00)
8q gain 304 (59%) 207 3.56e-07
(0.00027) 		2.03e-05
(0.0148) 		0.0816
(1.00) 		0.426
(1.00) 		0.115
(1.00) 		0.0112
(1.00) 		0.084
(1.00) 		0.00665
(1.00) 		0.00755
(1.00) 		0.0155
(1.00)
9p gain 102 (20%) 409 3.17e-18
(2.52e-15) 		5.06e-05
(0.0364) 		0.504
(1.00) 		0.0583
(1.00) 		0.00139
(0.928) 		0.00851
(1.00) 		0.00786
(1.00) 		1
(1.00) 		0.0582
(1.00) 		0.558
(1.00)
11p gain 65 (13%) 446 4.27e-06
(0.00314) 		7.54e-06
(0.00553) 		0.93
(1.00) 		0.893
(1.00) 		0.209
(1.00) 		0.0362
(1.00) 		0.0528
(1.00) 		0.0946
(1.00) 		0.188
(1.00) 		0.427
(1.00)
11q gain 70 (14%) 441 0.000168
(0.119) 		7.58e-05
(0.0541) 		0.521
(1.00) 		0.78
(1.00) 		0.229
(1.00) 		0.0331
(1.00) 		0.298
(1.00) 		0.688
(1.00) 		0.892
(1.00) 		0.725
(1.00)
12p gain 143 (28%) 368 7.87e-13
(6.17e-10) 		1.13e-07
(8.6e-05) 		0.0161
(1.00) 		0.318
(1.00) 		0.0155
(1.00) 		0.00962
(1.00) 		0.0662
(1.00) 		0.684
(1.00) 		0.498
(1.00) 		0.533
(1.00)
14q gain 148 (29%) 363 8.85e-13
(6.93e-10) 		1.88e-06
(0.00139) 		0.217
(1.00) 		0.479
(1.00) 		0.0143
(1.00) 		0.148
(1.00) 		0.0174
(1.00) 		0.0033
(1.00) 		0.00767
(1.00) 		0.000895
(0.605)
16p gain 104 (20%) 407 1.29e-06
(0.00096) 		2.34e-06
(0.00174) 		0.332
(1.00) 		0.936
(1.00) 		0.41
(1.00) 		0.577
(1.00) 		0.714
(1.00) 		1
(1.00) 		0.556
(1.00) 		0.921
(1.00)
16q gain 104 (20%) 407 1.23e-08
(9.4e-06) 		5.63e-06
(0.00413) 		0.499
(1.00) 		0.826
(1.00) 		0.151
(1.00) 		0.435
(1.00) 		0.271
(1.00) 		0.0678
(1.00) 		0.0258
(1.00) 		0.123
(1.00)
17p gain 66 (13%) 445 8.67e-07
(0.000651) 		3.04e-06
(0.00224) 		0.597
(1.00) 		0.311
(1.00) 		0.00751
(1.00) 		0.102
(1.00) 		0.0869
(1.00) 		0.00826
(1.00) 		0.265
(1.00) 		0.0829
(1.00)
17q gain 84 (16%) 427 7.57e-06
(0.00554) 		0.000239
(0.167) 		0.578
(1.00) 		0.583
(1.00) 		0.127
(1.00) 		0.272
(1.00) 		0.49
(1.00) 		0.386
(1.00) 		0.958
(1.00) 		0.792
(1.00)
18p gain 119 (23%) 392 7.27e-13
(5.71e-10) 		5.22e-06
(0.00384) 		0.333
(1.00) 		0.769
(1.00) 		0.369
(1.00) 		0.000712
(0.484) 		0.657
(1.00) 		0.914
(1.00) 		0.794
(1.00) 		0.582
(1.00)
20p gain 188 (37%) 323 2.73e-06
(0.00202) 		1.04e-06
(0.000781) 		0.951
(1.00) 		0.12
(1.00) 		0.102
(1.00) 		0.103
(1.00) 		0.204
(1.00) 		0.00232
(1.00) 		0.0191
(1.00) 		0.0233
(1.00)
20q gain 198 (39%) 313 6.26e-09
(4.81e-06) 		6.01e-07
(0.000452) 		0.834
(1.00) 		0.857
(1.00) 		0.108
(1.00) 		0.219
(1.00) 		0.173
(1.00) 		0.00478
(1.00) 		0.0025
(1.00) 		0.00925
(1.00)
22q gain 110 (22%) 401 1.82e-06
(0.00135) 		2.15e-13
(1.7e-10) 		0.153
(1.00) 		0.376
(1.00) 		0.281
(1.00) 		0.633
(1.00) 		0.00113
(0.759) 		0.578
(1.00) 		0.00263
(1.00) 		0.76
(1.00)
1p loss 52 (10%) 459 0.000182
(0.128) 		1.45e-08
(1.11e-05) 		0.02
(1.00) 		0.538
(1.00) 		0.00361
(1.00) 		0.00587
(1.00) 		0.338
(1.00) 		0.539
(1.00) 		0.212
(1.00) 		0.384
(1.00)
3p loss 287 (56%) 224 2.29e-26
(1.83e-23) 		6.52e-21
(5.19e-18) 		0.823
(1.00) 		0.12
(1.00) 		0.0131
(1.00) 		0.0118
(1.00) 		0.142
(1.00) 		0.0127
(1.00) 		0.72
(1.00) 		0.443
(1.00)
4q loss 144 (28%) 367 6.63e-13
(5.21e-10) 		5.02e-07
(0.000378) 		0.469
(1.00) 		0.427
(1.00) 		0.00776
(1.00) 		0.00319
(1.00) 		0.239
(1.00) 		0.184
(1.00) 		0.0797
(1.00) 		0.0332
(1.00)
5p loss 50 (10%) 461 1.55e-05
(0.0113) 		2.51e-05
(0.0181) 		0.407
(1.00) 		0.434
(1.00) 		0.69
(1.00) 		0.578
(1.00) 		0.763
(1.00) 		0.219
(1.00) 		0.124
(1.00) 		0.435
(1.00)
5q loss 160 (31%) 351 2.33e-21
(1.86e-18) 		5.38e-17
(4.26e-14) 		0.243
(1.00) 		0.133
(1.00) 		0.205
(1.00) 		0.00139
(0.928) 		0.799
(1.00) 		0.0923
(1.00) 		0.718
(1.00) 		0.656
(1.00)
8p loss 184 (36%) 327 5.18e-11
(4.03e-08) 		2.02e-06
(0.0015) 		0.55
(1.00) 		0.288
(1.00) 		0.0364
(1.00) 		0.000938
(0.633) 		0.031
(1.00) 		0.000568
(0.39) 		0.000898
(0.606) 		0.000861
(0.584)
9p loss 176 (34%) 335 4.36e-26
(3.48e-23) 		4.9e-17
(3.89e-14) 		0.699
(1.00) 		0.164
(1.00) 		0.299
(1.00) 		0.33
(1.00) 		0.411
(1.00) 		0.847
(1.00) 		0.334
(1.00) 		0.548
(1.00)
9q loss 83 (16%) 428 2.57e-10
(1.99e-07) 		1.02e-06
(0.000764) 		0.984
(1.00) 		1
(1.00) 		0.624
(1.00) 		0.845
(1.00) 		0.806
(1.00) 		0.619
(1.00) 		0.135
(1.00) 		0.251
(1.00)
11p loss 134 (26%) 377 2.21e-08
(1.69e-05) 		0.000353
(0.245) 		0.33
(1.00) 		0.909
(1.00) 		0.0052
(1.00) 		0.0374
(1.00) 		0.00604
(1.00) 		0.678
(1.00) 		0.389
(1.00) 		0.155
(1.00)
11q loss 164 (32%) 347 8.53e-05
(0.0608) 		2.85e-07
(0.000216) 		0.254
(1.00) 		0.409
(1.00) 		0.00499
(1.00) 		0.00469
(1.00) 		0.262
(1.00) 		0.696
(1.00) 		0.388
(1.00) 		0.866
(1.00)
19p loss 93 (18%) 418 0.000229
(0.16) 		2.38e-05
(0.0173) 		0.703
(1.00) 		0.204
(1.00) 		0.0227
(1.00) 		0.102
(1.00) 		0.042
(1.00) 		0.0027
(1.00) 		0.657
(1.00) 		0.329
(1.00)
19q loss 82 (16%) 429 9.78e-05
(0.0695) 		4.96e-05
(0.0358) 		0.129
(1.00) 		0.554
(1.00) 		0.209
(1.00) 		0.672
(1.00) 		0.353
(1.00) 		0.0319
(1.00) 		0.783
(1.00) 		0.626
(1.00)
21q loss 179 (35%) 332 2.63e-11
(2.06e-08) 		1.96e-09
(1.51e-06) 		0.571
(1.00) 		0.512
(1.00) 		0.033
(1.00) 		0.12
(1.00) 		0.528
(1.00) 		0.0837
(1.00) 		0.725
(1.00) 		0.207
(1.00)
xq loss 82 (16%) 429 9.79e-05
(0.0695) 		3.67e-05
(0.0265) 		0.0882
(1.00) 		0.0336
(1.00) 		0.0305
(1.00) 		0.0207
(1.00) 		0.0148
(1.00) 		0.379
(1.00) 		0.168
(1.00) 		0.228
(1.00)
1p gain 68 (13%) 443 0.000101
(0.0715) 		0.0119
(1.00) 		0.957
(1.00) 		0.848
(1.00) 		0.866
(1.00) 		0.594
(1.00) 		0.697
(1.00) 		0.349
(1.00) 		0.864
(1.00) 		0.703
(1.00)
3p gain 79 (15%) 432 0.00815
(1.00) 		0.000248
(0.173) 		0.0677
(1.00) 		0.0531
(1.00) 		0.00141
(0.938) 		0.00411
(1.00) 		0.00951
(1.00) 		0.166
(1.00) 		0.0444
(1.00) 		0.111
(1.00)
4p gain 39 (8%) 472 0.00258
(1.00) 		7.04e-05
(0.0504) 		0.576
(1.00) 		0.824
(1.00) 		0.0518
(1.00) 		0.0579
(1.00) 		0.117
(1.00) 		0.168
(1.00) 		0.473
(1.00) 		0.274
(1.00)
5p gain 195 (38%) 316 9.21e-12
(7.2e-09) 		0.00364
(1.00) 		0.958
(1.00) 		0.602
(1.00) 		0.0839
(1.00) 		0.226
(1.00) 		0.605
(1.00) 		1
(1.00) 		0.932
(1.00) 		0.978
(1.00)
6p gain 80 (16%) 431 1.79e-06
(0.00133) 		0.00343
(1.00) 		0.492
(1.00) 		0.563
(1.00) 		0.666
(1.00) 		0.712
(1.00) 		0.567
(1.00) 		0.448
(1.00) 		0.247
(1.00) 		0.46
(1.00)
6q gain 61 (12%) 450 2.24e-05
(0.0163) 		0.0414
(1.00) 		0.197
(1.00) 		0.127
(1.00) 		0.0745
(1.00) 		0.0224
(1.00) 		0.125
(1.00) 		0.672
(1.00) 		0.0569
(1.00) 		0.254
(1.00)
9q gain 136 (27%) 375 4.17e-14
(3.29e-11) 		0.0178
(1.00) 		0.129
(1.00) 		0.207
(1.00) 		0.251
(1.00) 		0.113
(1.00) 		0.652
(1.00) 		0.918
(1.00) 		0.286
(1.00) 		0.676
(1.00)
10p gain 40 (8%) 471 0.0587
(1.00) 		2.49e-06
(0.00184) 		0.579
(1.00) 		0.529
(1.00) 		0.0383
(1.00) 		0.0042
(1.00) 		0.0461
(1.00) 		0.0589
(1.00) 		0.875
(1.00) 		0.195
(1.00)
12q gain 87 (17%) 424 3.81e-07
(0.000288) 		0.000851
(0.578) 		0.119
(1.00) 		0.124
(1.00) 		0.0845
(1.00) 		0.00525
(1.00) 		0.573
(1.00) 		0.717
(1.00) 		0.749
(1.00) 		0.484
(1.00)
13q gain 56 (11%) 455 2.31e-08
(1.76e-05) 		0.000886
(0.6) 		0.588
(1.00) 		0.502
(1.00) 		0.0144
(1.00) 		0.0116
(1.00) 		0.242
(1.00) 		0.053
(1.00) 		0.277
(1.00) 		0.0285
(1.00)
19p gain 53 (10%) 458 0.00169
(1.00) 		3.04e-07
(0.000231) 		0.0892
(1.00) 		0.0684
(1.00) 		0.0122
(1.00) 		0.00138
(0.919) 		0.000442
(0.306) 		0.0504
(1.00) 		0.504
(1.00) 		0.342
(1.00)
19q gain 74 (14%) 437 0.0398
(1.00) 		5.52e-05
(0.0396) 		0.956
(1.00) 		0.393
(1.00) 		0.0176
(1.00) 		0.00202
(1.00) 		0.000557
(0.383) 		0.0914
(1.00) 		0.83
(1.00) 		0.264
(1.00)
xq gain 87 (17%) 424 1.41e-06
(0.00105) 		0.00333
(1.00) 		0.251
(1.00) 		0.751
(1.00) 		0.415
(1.00) 		0.428
(1.00) 		0.0619
(1.00) 		0.221
(1.00) 		0.654
(1.00) 		0.316
(1.00)
6p loss 67 (13%) 444 0.000301
(0.209) 		0.00339
(1.00) 		0.0295
(1.00) 		0.555
(1.00) 		0.0294
(1.00) 		0.0521
(1.00) 		0.327
(1.00) 		0.42
(1.00) 		0.26
(1.00) 		0.468
(1.00)
10p loss 151 (30%) 360 3.54e-05
(0.0256) 		0.000618
(0.423) 		0.316
(1.00) 		0.098
(1.00) 		0.051
(1.00) 		0.132
(1.00) 		0.0974
(1.00) 		0.108
(1.00) 		0.25
(1.00) 		0.301
(1.00)
10q loss 109 (21%) 402 0.000113
(0.0802) 		0.0012
(0.802) 		0.208
(1.00) 		0.33
(1.00) 		0.0149
(1.00) 		0.107
(1.00) 		0.0209
(1.00) 		0.822
(1.00) 		0.254
(1.00) 		0.793
(1.00)
14q loss 54 (11%) 457 0.00625
(1.00) 		0.00218
(1.00) 		0.0372
(1.00) 		0.415
(1.00) 		5.03e-05
(0.0362) 		0.0011
(0.74) 		0.00455
(1.00) 		0.0504
(1.00) 		0.235
(1.00) 		0.0438
(1.00)
15q loss 98 (19%) 413 8.51e-08
(6.49e-05) 		0.23
(1.00) 		0.625
(1.00) 		0.413
(1.00) 		0.121
(1.00) 		0.067
(1.00) 		0.721
(1.00) 		0.246
(1.00) 		0.531
(1.00) 		0.35
(1.00)
17p loss 103 (20%) 408 8.58e-05
(0.0611) 		0.00307
(1.00) 		0.393
(1.00) 		0.278
(1.00) 		0.523
(1.00) 		0.0763
(1.00) 		0.533
(1.00) 		0.91
(1.00) 		0.252
(1.00) 		0.543
(1.00)
18p loss 101 (20%) 410 0.0221
(1.00) 		0.000191
(0.135) 		0.536
(1.00) 		0.203
(1.00) 		0.27
(1.00) 		0.116
(1.00) 		0.644
(1.00) 		0.246
(1.00) 		0.861
(1.00) 		0.32
(1.00)
20q loss 28 (5%) 483 0.0108
(1.00) 		0.0182
(1.00) 		0.225
(1.00) 		0.191
(1.00) 		0.0217
(1.00) 		0.00731
(1.00) 		0.0267
(1.00) 		0.0277
(1.00) 		0.000195
(0.137) 		0.0146
(1.00)
4q gain 35 (7%) 476 0.108
(1.00) 		0.405
(1.00) 		1
(1.00) 		0.847
(1.00) 		0.622
(1.00) 		0.116
(1.00) 		0.919
(1.00) 		0.722
(1.00) 		0.948
(1.00) 		0.468
(1.00)
5q gain 65 (13%) 446 0.0322
(1.00) 		0.52
(1.00) 		0.595
(1.00) 		0.707
(1.00) 		0.769
(1.00) 		0.894
(1.00) 		0.728
(1.00) 		0.334
(1.00) 		0.451
(1.00) 		0.503
(1.00)
8p gain 148 (29%) 363 0.00164
(1.00) 		0.0788
(1.00) 		0.583
(1.00) 		0.542
(1.00) 		0.353
(1.00) 		0.0686
(1.00) 		0.677
(1.00) 		0.314
(1.00) 		0.463
(1.00) 		0.59
(1.00)
10q gain 34 (7%) 477 0.000665
(0.454) 		0.305
(1.00) 		0.0973
(1.00) 		0.341
(1.00) 		0.649
(1.00) 		0.381
(1.00) 		0.587
(1.00) 		0.464
(1.00) 		0.838
(1.00) 		0.331
(1.00)
15q gain 71 (14%) 440 0.0824
(1.00) 		0.0199
(1.00) 		0.381
(1.00) 		0.851
(1.00) 		0.206
(1.00) 		0.0703
(1.00) 		0.98
(1.00) 		0.358
(1.00) 		0.847
(1.00) 		0.344
(1.00)
21q gain 35 (7%) 476 0.0465
(1.00) 		0.0172
(1.00) 		0.0151
(1.00) 		0.768
(1.00) 		0.00665
(1.00) 		0.00677
(1.00) 		0.1
(1.00) 		0.476
(1.00) 		0.695
(1.00) 		0.672
(1.00)
1q loss 35 (7%) 476 0.058
(1.00) 		0.124
(1.00) 		0.78
(1.00) 		0.696
(1.00) 		0.098
(1.00) 		0.224
(1.00) 		0.037
(1.00) 		0.0273
(1.00) 		0.0554
(1.00) 		0.456
(1.00)
2p loss 33 (6%) 478 0.0903
(1.00) 		0.00374
(1.00) 		0.159
(1.00) 		0.153
(1.00) 		0.108
(1.00) 		0.0356
(1.00) 		0.0365
(1.00) 		1
(1.00) 		0.0118
(1.00) 		0.823
(1.00)
2q loss 42 (8%) 469 0.922
(1.00) 		0.0386
(1.00) 		0.836
(1.00) 		0.172
(1.00) 		0.738
(1.00) 		0.703
(1.00) 		0.207
(1.00) 		1
(1.00) 		0.0308
(1.00) 		0.514
(1.00)
3q loss 60 (12%) 451 0.0139
(1.00) 		0.192
(1.00) 		0.263
(1.00) 		0.844
(1.00) 		0.605
(1.00) 		0.834
(1.00) 		0.941
(1.00) 		1
(1.00) 		0.465
(1.00) 		0.796
(1.00)
6q loss 67 (13%) 444 0.0652
(1.00) 		0.00955
(1.00) 		0.128
(1.00) 		0.384
(1.00) 		0.769
(1.00) 		0.152
(1.00) 		0.67
(1.00) 		0.498
(1.00) 		0.335
(1.00) 		0.63
(1.00)
7p loss 28 (5%) 483 0.0222
(1.00) 		0.041
(1.00) 		0.0102
(1.00) 		0.207
(1.00) 		0.472
(1.00) 		0.167
(1.00) 		0.3
(1.00) 		0.843
(1.00) 		0.0816
(1.00) 		0.751
(1.00)
7q loss 42 (8%) 469 0.202
(1.00) 		0.383
(1.00) 		0.525
(1.00) 		0.271
(1.00) 		0.324
(1.00) 		0.723
(1.00) 		0.0423
(1.00) 		0.506
(1.00) 		0.829
(1.00) 		0.785
(1.00)
8q loss 30 (6%) 481 0.0767
(1.00) 		0.134
(1.00) 		0.756
(1.00) 		0.344
(1.00) 		0.698
(1.00) 		0.799
(1.00) 		0.217
(1.00) 		1
(1.00) 		0.741
(1.00) 		0.294
(1.00)
12p loss 36 (7%) 475 0.647
(1.00) 		0.111
(1.00) 		0.646
(1.00) 		0.605
(1.00) 		0.855
(1.00) 		0.923
(1.00) 		1
(1.00) 		0.588
(1.00) 		0.37
(1.00) 		0.649
(1.00)
12q loss 32 (6%) 479 0.0163
(1.00) 		0.0169
(1.00) 		0.871
(1.00) 		0.267
(1.00) 		0.489
(1.00) 		0.407
(1.00) 		0.972
(1.00) 		0.701
(1.00) 		0.187
(1.00) 		0.496
(1.00)
16p loss 60 (12%) 451 0.000481
(0.331) 		0.0132
(1.00) 		0.867
(1.00) 		0.723
(1.00) 		0.00619
(1.00) 		0.0664
(1.00) 		0.953
(1.00) 		0.317
(1.00) 		0.826
(1.00) 		0.627
(1.00)
17q loss 34 (7%) 477 0.00112
(0.755) 		0.326
(1.00) 		0.903
(1.00) 		0.00478
(1.00) 		0.437
(1.00) 		0.807
(1.00) 		0.904
(1.00) 		0.355
(1.00) 		0.966
(1.00) 		0.433
(1.00)
20p loss 46 (9%) 465 0.000461
(0.318) 		0.00627
(1.00) 		0.483
(1.00) 		0.476
(1.00) 		0.0837
(1.00) 		0.0875
(1.00) 		0.336
(1.00) 		0.0349
(1.00) 		0.00144
(0.956) 		0.122
(1.00)
22q loss 72 (14%) 439 0.00364
(1.00) 		0.00333
(1.00) 		0.644
(1.00) 		0.538
(1.00) 		0.00138
(0.919) 		0.26
(1.00) 		0.000582
(0.399) 		0.144
(1.00) 		0.00342
(1.00) 		0.433
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.071

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
1P GAIN MUTATED 37 17 11 3
1P GAIN WILD-TYPE 141 85 178 39

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

'1q gain' versus 'CN_CNMF'

P value = 6.88e-07 (Fisher's exact test), Q value = 0.00052

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
1Q GAIN MUTATED 52 37 21 7
1Q GAIN WILD-TYPE 126 65 168 35

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1.78e-08 (Chi-square test), Q value = 1.4e-05

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 73 95 92 79 71 79 22
1Q GAIN MUTATED 24 25 39 15 4 7 3
1Q GAIN WILD-TYPE 49 70 53 64 67 72 19

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

'1q gain' versus 'MRNASEQ_CNMF'

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

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 = 0.00033 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 177 176
1Q GAIN MUTATED 25 30 59
1Q GAIN WILD-TYPE 115 147 117

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

'2p gain' versus 'CN_CNMF'

P value = 1.6e-07 (Fisher's exact test), Q value = 0.00012

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
2P GAIN MUTATED 41 31 12 6
2P GAIN WILD-TYPE 137 71 177 36

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 7.36e-11 (Chi-square test), Q value = 5.7e-08

Table S7.  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 73 95 92 79 71 79 22
2P GAIN MUTATED 25 17 33 3 5 5 2
2P GAIN WILD-TYPE 48 78 59 76 66 74 20

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

'2q gain' versus 'CN_CNMF'

P value = 2.04e-06 (Fisher's exact test), Q value = 0.0015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
2Q GAIN MUTATED 34 23 8 4
2Q GAIN WILD-TYPE 144 79 181 38

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

'2q gain' versus 'METHLYATION_CNMF'

P value = 2.68e-10 (Chi-square test), Q value = 2.1e-07

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 73 95 92 79 71 79 22
2Q GAIN MUTATED 23 13 24 1 2 3 3
2Q GAIN WILD-TYPE 50 82 68 78 69 76 19

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.000248 (Chi-square test), Q value = 0.17

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 73 95 92 79 71 79 22
3P GAIN MUTATED 11 9 15 26 5 11 2
3P GAIN WILD-TYPE 62 86 77 53 66 68 20

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

'3q gain' versus 'CN_CNMF'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0084

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
3Q GAIN MUTATED 95 66 67 21
3Q GAIN WILD-TYPE 83 36 122 21

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 4.43e-07 (Chi-square test), Q value = 0.00033

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 73 95 92 79 71 79 22
3Q GAIN MUTATED 42 53 54 47 14 29 10
3Q GAIN WILD-TYPE 31 42 38 32 57 50 12

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

'4p gain' versus 'METHLYATION_CNMF'

P value = 7.04e-05 (Chi-square test), Q value = 0.05

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 73 95 92 79 71 79 22
4P GAIN MUTATED 6 19 6 4 1 2 1
4P GAIN WILD-TYPE 67 76 86 75 70 77 21

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

'5p gain' versus 'CN_CNMF'

P value = 9.21e-12 (Fisher's exact test), Q value = 7.2e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
5P GAIN MUTATED 90 55 36 14
5P GAIN WILD-TYPE 88 47 153 28

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

'6p gain' versus 'CN_CNMF'

P value = 1.79e-06 (Fisher's exact test), Q value = 0.0013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
6P GAIN MUTATED 43 15 11 11
6P GAIN WILD-TYPE 135 87 178 31

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

'6q gain' versus 'CN_CNMF'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.016

Table S16.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
6Q GAIN MUTATED 32 11 8 10
6Q GAIN WILD-TYPE 146 91 181 32

Figure S16.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1.44e-09 (Fisher's exact test), Q value = 1.1e-06

Table S17.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
7P GAIN MUTATED 87 44 34 15
7P GAIN WILD-TYPE 91 58 155 27

Figure S17.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 7.57e-10 (Chi-square test), Q value = 5.9e-07

Table S18.  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 73 95 92 79 71 79 22
7P GAIN MUTATED 32 41 51 5 24 20 7
7P GAIN WILD-TYPE 41 54 41 74 47 59 15

Figure S18.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 9.41e-09 (Fisher's exact test), Q value = 7.2e-06

Table S19.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
7Q GAIN MUTATED 55 38 18 12
7Q GAIN WILD-TYPE 123 64 171 30

Figure S19.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2.99e-11 (Chi-square test), Q value = 2.3e-08

Table S20.  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 73 95 92 79 71 79 22
7Q GAIN MUTATED 24 24 46 5 12 9 3
7Q GAIN WILD-TYPE 49 71 46 74 59 70 19

Figure S20.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 3.56e-07 (Fisher's exact test), Q value = 0.00027

Table S21.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
8Q GAIN MUTATED 129 56 87 32
8Q GAIN WILD-TYPE 49 46 102 10

Figure S21.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 2.03e-05 (Chi-square test), Q value = 0.015

Table S22.  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 73 95 92 79 71 79 22
8Q GAIN MUTATED 42 74 51 31 38 52 16
8Q GAIN WILD-TYPE 31 21 41 48 33 27 6

Figure S22.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 3.17e-18 (Fisher's exact test), Q value = 2.5e-15

Table S23.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
9P GAIN MUTATED 22 12 34 34
9P GAIN WILD-TYPE 156 90 155 8

Figure S23.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 5.06e-05 (Chi-square test), Q value = 0.036

Table S24.  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 73 95 92 79 71 79 22
9P GAIN MUTATED 6 16 18 13 29 13 7
9P GAIN WILD-TYPE 67 79 74 66 42 66 15

Figure S24.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 4.17e-14 (Fisher's exact test), Q value = 3.3e-11

Table S25.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
9Q GAIN MUTATED 35 31 36 34
9Q GAIN WILD-TYPE 143 71 153 8

Figure S25.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 2.49e-06 (Chi-square test), Q value = 0.0018

Table S26.  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 73 95 92 79 71 79 22
10P GAIN MUTATED 18 4 7 5 2 2 2
10P GAIN WILD-TYPE 55 91 85 74 69 77 20

Figure S26.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 4.27e-06 (Fisher's exact test), Q value = 0.0031

Table S27.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
11P GAIN MUTATED 35 3 16 11
11P GAIN WILD-TYPE 143 99 173 31

Figure S27.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 7.54e-06 (Chi-square test), Q value = 0.0055

Table S28.  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 73 95 92 79 71 79 22
11P GAIN MUTATED 3 25 13 5 10 3 6
11P GAIN WILD-TYPE 70 70 79 74 61 76 16

Figure S28.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.12

Table S29.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
11Q GAIN MUTATED 40 9 14 7
11Q GAIN WILD-TYPE 138 93 175 35

Figure S29.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 7.58e-05 (Chi-square test), Q value = 0.054

Table S30.  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 73 95 92 79 71 79 22
11Q GAIN MUTATED 10 23 14 2 10 4 7
11Q GAIN WILD-TYPE 63 72 78 77 61 75 15

Figure S30.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 7.87e-13 (Fisher's exact test), Q value = 6.2e-10

Table S31.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
12P GAIN MUTATED 64 46 18 15
12P GAIN WILD-TYPE 114 56 171 27

Figure S31.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Chi-square test), Q value = 8.6e-05

Table S32.  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 73 95 92 79 71 79 22
12P GAIN MUTATED 31 28 43 18 9 11 3
12P GAIN WILD-TYPE 42 67 49 61 62 68 19

Figure S32.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 3.81e-07 (Fisher's exact test), Q value = 0.00029

Table S33.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
12Q GAIN MUTATED 37 27 11 12
12Q GAIN WILD-TYPE 141 75 178 30

Figure S33.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 2.31e-08 (Fisher's exact test), Q value = 1.8e-05

Table S34.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
13Q GAIN MUTATED 41 3 10 2
13Q GAIN WILD-TYPE 137 99 179 40

Figure S34.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 8.85e-13 (Fisher's exact test), Q value = 6.9e-10

Table S35.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
14Q GAIN MUTATED 79 29 21 19
14Q GAIN WILD-TYPE 99 73 168 23

Figure S35.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 1.88e-06 (Chi-square test), Q value = 0.0014

Table S36.  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 73 95 92 79 71 79 22
14Q GAIN MUTATED 26 40 34 4 16 20 8
14Q GAIN WILD-TYPE 47 55 58 75 55 59 14

Figure S36.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1.29e-06 (Fisher's exact test), Q value = 0.00096

Table S37.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
16P GAIN MUTATED 49 30 16 9
16P GAIN WILD-TYPE 129 72 173 33

Figure S37.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 2.34e-06 (Chi-square test), Q value = 0.0017

Table S38.  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 73 95 92 79 71 79 22
16P GAIN MUTATED 29 26 21 6 6 11 5
16P GAIN WILD-TYPE 44 69 71 73 65 68 17

Figure S38.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 1.23e-08 (Fisher's exact test), Q value = 9.4e-06

Table S39.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
16Q GAIN MUTATED 54 28 13 9
16Q GAIN WILD-TYPE 124 74 176 33

Figure S39.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 5.63e-06 (Chi-square test), Q value = 0.0041

Table S40.  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 73 95 92 79 71 79 22
16Q GAIN MUTATED 24 31 22 6 5 11 5
16Q GAIN WILD-TYPE 49 64 70 73 66 68 17

Figure S40.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 8.67e-07 (Fisher's exact test), Q value = 0.00065

Table S41.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
17P GAIN MUTATED 31 21 6 8
17P GAIN WILD-TYPE 147 81 183 34

Figure S41.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 3.04e-06 (Chi-square test), Q value = 0.0022

Table S42.  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 73 95 92 79 71 79 22
17P GAIN MUTATED 10 12 28 3 4 7 2
17P GAIN WILD-TYPE 63 83 64 76 67 72 20

Figure S42.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 7.57e-06 (Fisher's exact test), Q value = 0.0055

Table S43.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
17Q GAIN MUTATED 36 26 12 10
17Q GAIN WILD-TYPE 142 76 177 32

Figure S43.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.000239 (Chi-square test), Q value = 0.17

Table S44.  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 73 95 92 79 71 79 22
17Q GAIN MUTATED 17 16 28 6 6 8 3
17Q GAIN WILD-TYPE 56 79 64 73 65 71 19

Figure S44.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 7.27e-13 (Fisher's exact test), Q value = 5.7e-10

Table S45.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
18P GAIN MUTATED 56 43 14 6
18P GAIN WILD-TYPE 122 59 175 36

Figure S45.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 5.22e-06 (Chi-square test), Q value = 0.0038

Table S46.  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 73 95 92 79 71 79 22
18P GAIN MUTATED 31 24 28 18 7 7 4
18P GAIN WILD-TYPE 42 71 64 61 64 72 18

Figure S46.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1.82e-05 (Chi-square test), Q value = 0.013

Table S47.  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 73 95 92 79 71 79 22
18Q GAIN MUTATED 9 5 12 18 3 0 1
18Q GAIN WILD-TYPE 64 90 80 61 68 79 21

Figure S47.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.000206 (Fisher's exact test), Q value = 0.14

Table S48.  Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 134 152
18Q GAIN MUTATED 31 12 4
18Q GAIN WILD-TYPE 176 122 148

Figure S48.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.09e-05 (Fisher's exact test), Q value = 0.015

Table S49.  Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 177 176
18Q GAIN MUTATED 10 6 31
18Q GAIN WILD-TYPE 130 171 145

Figure S49.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 5.04e-05 (Fisher's exact test), Q value = 0.036

Table S50.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 216 146
18Q GAIN MUTATED 3 33 12
18Q GAIN WILD-TYPE 142 183 134

Figure S50.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 3.04e-07 (Chi-square test), Q value = 0.00023

Table S51.  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 73 95 92 79 71 79 22
19P GAIN MUTATED 6 4 21 17 3 1 1
19P GAIN WILD-TYPE 67 91 71 62 68 78 21

Figure S51.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 5.52e-05 (Chi-square test), Q value = 0.04

Table S52.  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 73 95 92 79 71 79 22
19Q GAIN MUTATED 11 10 23 20 5 2 3
19Q GAIN WILD-TYPE 62 85 69 59 66 77 19

Figure S52.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 2.73e-06 (Fisher's exact test), Q value = 0.002

Table S53.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
20P GAIN MUTATED 84 40 43 21
20P GAIN WILD-TYPE 94 62 146 21

Figure S53.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1.04e-06 (Chi-square test), Q value = 0.00078

Table S54.  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 73 95 92 79 71 79 22
20P GAIN MUTATED 24 57 40 19 15 25 8
20P GAIN WILD-TYPE 49 38 52 60 56 54 14

Figure S54.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 6.26e-09 (Fisher's exact test), Q value = 4.8e-06

Table S55.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
20Q GAIN MUTATED 93 43 41 21
20Q GAIN WILD-TYPE 85 59 148 21

Figure S55.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 6.01e-07 (Chi-square test), Q value = 0.00045

Table S56.  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 73 95 92 79 71 79 22
20Q GAIN MUTATED 33 56 41 15 18 25 10
20Q GAIN WILD-TYPE 40 39 51 64 53 54 12

Figure S56.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 1.82e-06 (Fisher's exact test), Q value = 0.0014

Table S57.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
22Q GAIN MUTATED 48 35 19 8
22Q GAIN WILD-TYPE 130 67 170 34

Figure S57.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 2.15e-13 (Chi-square test), Q value = 1.7e-10

Table S58.  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 73 95 92 79 71 79 22
22Q GAIN MUTATED 18 24 45 5 1 14 3
22Q GAIN WILD-TYPE 55 71 47 74 70 65 19

Figure S58.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1.41e-06 (Fisher's exact test), Q value = 0.0011

Table S59.  Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
XQ GAIN MUTATED 50 14 14 9
XQ GAIN WILD-TYPE 128 88 175 33

Figure S59.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.000182 (Fisher's exact test), Q value = 0.13

Table S60.  Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
1P LOSS MUTATED 20 20 7 5
1P LOSS WILD-TYPE 158 82 182 37

Figure S60.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1.45e-08 (Chi-square test), Q value = 1.1e-05

Table S61.  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 73 95 92 79 71 79 22
1P LOSS MUTATED 5 8 27 2 5 3 2
1P LOSS WILD-TYPE 68 87 65 77 66 76 20

Figure S61.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 2.29e-26 (Fisher's exact test), Q value = 1.8e-23

Table S62.  Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
3P LOSS MUTATED 142 70 49 26
3P LOSS WILD-TYPE 36 32 140 16

Figure S62.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 6.52e-21 (Chi-square test), Q value = 5.2e-18

Table S63.  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 73 95 92 79 71 79 22
3P LOSS MUTATED 54 75 69 16 24 33 16
3P LOSS WILD-TYPE 19 20 23 63 47 46 6

Figure S63.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 6.96e-20 (Fisher's exact test), Q value = 5.5e-17

Table S64.  Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
4P LOSS MUTATED 79 68 26 13
4P LOSS WILD-TYPE 99 34 163 29

Figure S64.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 4.85e-14 (Chi-square test), Q value = 3.8e-11

Table S65.  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 73 95 92 79 71 79 22
4P LOSS MUTATED 37 26 63 22 12 16 10
4P LOSS WILD-TYPE 36 69 29 57 59 63 12

Figure S65.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.000231 (Fisher's exact test), Q value = 0.16

Table S66.  Gene #47: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 134 152
4P LOSS MUTATED 90 55 36
4P LOSS WILD-TYPE 117 79 116

Figure S66.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.23e-05 (Fisher's exact test), Q value = 0.045

Table S67.  Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 177 176
4P LOSS MUTATED 58 43 80
4P LOSS WILD-TYPE 82 134 96

Figure S67.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 6.63e-13 (Fisher's exact test), Q value = 5.2e-10

Table S68.  Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
4Q LOSS MUTATED 58 53 21 12
4Q LOSS WILD-TYPE 120 49 168 30

Figure S68.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 5.02e-07 (Chi-square test), Q value = 0.00038

Table S69.  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 73 95 92 79 71 79 22
4Q LOSS MUTATED 29 27 45 15 12 12 4
4Q LOSS WILD-TYPE 44 68 47 64 59 67 18

Figure S69.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 1.55e-05 (Fisher's exact test), Q value = 0.011

Table S70.  Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
5P LOSS MUTATED 24 15 4 7
5P LOSS WILD-TYPE 154 87 185 35

Figure S70.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 2.51e-05 (Chi-square test), Q value = 0.018

Table S71.  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 73 95 92 79 71 79 22
5P LOSS MUTATED 13 15 16 2 2 1 1
5P LOSS WILD-TYPE 60 80 76 77 69 78 21

Figure S71.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 2.33e-21 (Fisher's exact test), Q value = 1.9e-18

Table S72.  Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
5Q LOSS MUTATED 79 56 15 10
5Q LOSS WILD-TYPE 99 46 174 32

Figure S72.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 5.38e-17 (Chi-square test), Q value = 4.3e-14

Table S73.  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 73 95 92 79 71 79 22
5Q LOSS MUTATED 41 40 46 8 3 14 8
5Q LOSS WILD-TYPE 32 55 46 71 68 65 14

Figure S73.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'CN_CNMF'

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

Table S74.  Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
6P LOSS MUTATED 28 23 11 5
6P LOSS WILD-TYPE 150 79 178 37

Figure S74.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 5.18e-11 (Fisher's exact test), Q value = 4e-08

Table S75.  Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
8P LOSS MUTATED 100 27 42 15
8P LOSS WILD-TYPE 78 75 147 27

Figure S75.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 2.02e-06 (Chi-square test), Q value = 0.0015

Table S76.  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 73 95 92 79 71 79 22
8P LOSS MUTATED 23 53 39 11 21 30 7
8P LOSS WILD-TYPE 50 42 53 68 50 49 15

Figure S76.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 4.36e-26 (Fisher's exact test), Q value = 3.5e-23

Table S77.  Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
9P LOSS MUTATED 99 53 23 1
9P LOSS WILD-TYPE 79 49 166 41

Figure S77.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 4.9e-17 (Chi-square test), Q value = 3.9e-14

Table S78.  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 73 95 92 79 71 79 22
9P LOSS MUTATED 45 38 51 9 7 16 10
9P LOSS WILD-TYPE 28 57 41 70 64 63 12

Figure S78.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 2.57e-10 (Fisher's exact test), Q value = 2e-07

Table S79.  Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
9Q LOSS MUTATED 52 19 12 0
9Q LOSS WILD-TYPE 126 83 177 42

Figure S79.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.02e-06 (Chi-square test), Q value = 0.00076

Table S80.  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 73 95 92 79 71 79 22
9Q LOSS MUTATED 21 18 26 4 4 5 5
9Q LOSS WILD-TYPE 52 77 66 75 67 74 17

Figure S80.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 3.54e-05 (Fisher's exact test), Q value = 0.026

Table S81.  Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
10P LOSS MUTATED 72 31 34 14
10P LOSS WILD-TYPE 106 71 155 28

Figure S81.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.08

Table S82.  Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
10Q LOSS MUTATED 50 30 22 7
10Q LOSS WILD-TYPE 128 72 167 35

Figure S82.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 2.21e-08 (Fisher's exact test), Q value = 1.7e-05

Table S83.  Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
11P LOSS MUTATED 62 41 27 4
11P LOSS WILD-TYPE 116 61 162 38

Figure S83.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.000353 (Chi-square test), Q value = 0.24

Table S84.  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 73 95 92 79 71 79 22
11P LOSS MUTATED 23 20 38 21 6 21 5
11P LOSS WILD-TYPE 50 75 54 58 65 58 17

Figure S84.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 8.53e-05 (Fisher's exact test), Q value = 0.061

Table S85.  Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
11Q LOSS MUTATED 73 41 41 9
11Q LOSS WILD-TYPE 105 61 148 33

Figure S85.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 2.85e-07 (Chi-square test), Q value = 0.00022

Table S86.  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 73 95 92 79 71 79 22
11Q LOSS MUTATED 19 28 39 44 9 20 5
11Q LOSS WILD-TYPE 54 67 53 35 62 59 17

Figure S86.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 3.74e-15 (Fisher's exact test), Q value = 3e-12

Table S87.  Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
13Q LOSS MUTATED 52 66 31 13
13Q LOSS WILD-TYPE 126 36 158 29

Figure S87.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 9.39e-07 (Chi-square test), Q value = 7e-04

Table S88.  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 73 95 92 79 71 79 22
13Q LOSS MUTATED 34 30 44 25 11 17 1
13Q LOSS WILD-TYPE 39 65 48 54 60 62 21

Figure S88.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000282 (Fisher's exact test), Q value = 0.2

Table S89.  Gene #65: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 177 176
13Q LOSS MUTATED 44 39 74
13Q LOSS WILD-TYPE 96 138 102

Figure S89.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 5.03e-05 (Fisher's exact test), Q value = 0.036

Table S90.  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 10 6
14Q LOSS WILD-TYPE 170 124 146

Figure S90.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 8.51e-08 (Fisher's exact test), Q value = 6.5e-05

Table S91.  Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
15Q LOSS MUTATED 48 20 14 16
15Q LOSS WILD-TYPE 130 82 175 26

Figure S91.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1.55e-09 (Chi-square test), Q value = 1.2e-06

Table S92.  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 73 95 92 79 71 79 22
16Q LOSS MUTATED 11 4 25 27 4 4 3
16Q LOSS WILD-TYPE 62 91 67 52 67 75 19

Figure S92.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1.92e-10 (Fisher's exact test), Q value = 1.5e-07

Table S93.  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 S93.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-09 (Fisher's exact test), Q value = 1.5e-06

Table S94.  Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 177 176
16Q LOSS MUTATED 17 9 51
16Q LOSS WILD-TYPE 123 168 125

Figure S94.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 8.58e-05 (Fisher's exact test), Q value = 0.061

Table S95.  Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
17P LOSS MUTATED 43 32 20 8
17P LOSS WILD-TYPE 135 70 169 34

Figure S95.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.000191 (Chi-square test), Q value = 0.13

Table S96.  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 73 95 92 79 71 79 22
18P LOSS MUTATED 14 24 29 2 10 17 5
18P LOSS WILD-TYPE 59 71 63 77 61 62 17

Figure S96.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1.66e-17 (Fisher's exact test), Q value = 1.3e-14

Table S97.  Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
18Q LOSS MUTATED 113 37 36 22
18Q LOSS WILD-TYPE 65 65 153 20

Figure S97.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1.43e-14 (Chi-square test), Q value = 1.1e-11

Table S98.  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 73 95 92 79 71 79 22
18Q LOSS MUTATED 39 57 48 2 20 32 10
18Q LOSS WILD-TYPE 34 38 44 77 51 47 12

Figure S98.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000264 (Fisher's exact test), Q value = 0.18

Table S99.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 190 317
18Q LOSS MUTATED 97 109
18Q LOSS WILD-TYPE 93 208

Figure S99.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.000229 (Fisher's exact test), Q value = 0.16

Table S100.  Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
19P LOSS MUTATED 48 16 19 10
19P LOSS WILD-TYPE 130 86 170 32

Figure S100.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 2.38e-05 (Chi-square test), Q value = 0.017

Table S101.  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 73 95 92 79 71 79 22
19P LOSS MUTATED 12 33 20 7 8 7 6
19P LOSS WILD-TYPE 61 62 72 72 63 72 16

Figure S101.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 9.78e-05 (Fisher's exact test), Q value = 0.07

Table S102.  Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
19Q LOSS MUTATED 39 21 13 9
19Q LOSS WILD-TYPE 139 81 176 33

Figure S102.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 4.96e-05 (Chi-square test), Q value = 0.036

Table S103.  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 73 95 92 79 71 79 22
19Q LOSS MUTATED 12 27 23 5 7 5 3
19Q LOSS WILD-TYPE 61 68 69 74 64 74 19

Figure S103.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S104.  Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 159 138
20Q LOSS MUTATED 2 18 6
20Q LOSS WILD-TYPE 172 141 132

Figure S104.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 2.63e-11 (Fisher's exact test), Q value = 2.1e-08

Table S105.  Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
21Q LOSS MUTATED 81 47 30 21
21Q LOSS WILD-TYPE 97 55 159 21

Figure S105.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1.96e-09 (Chi-square test), Q value = 1.5e-06

Table S106.  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 73 95 92 79 71 79 22
21Q LOSS MUTATED 26 50 49 10 18 18 8
21Q LOSS WILD-TYPE 47 45 43 69 53 61 14

Figure S106.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 9.79e-05 (Fisher's exact test), Q value = 0.07

Table S107.  Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 178 102 189 42
XQ LOSS MUTATED 36 26 19 1
XQ LOSS WILD-TYPE 142 76 170 41

Figure S107.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 3.67e-05 (Chi-square test), Q value = 0.026

Table S108.  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 73 95 92 79 71 79 22
XQ LOSS MUTATED 12 20 28 12 2 6 2
XQ LOSS WILD-TYPE 61 75 64 67 69 73 20

Figure S108.  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 = 511

  • 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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