Correlation between copy number variations of arm-level result and molecular subtypes
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C15T3J7S
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/C15T3J7S
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, 140 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_MATURE_CHIERARCHICAL'.

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

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

  • 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',  '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' and 'METHLYATION_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',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 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_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_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_MATURE_CHIERARCHICAL'.

  • xq gain cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 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_CHIERARCHICAL'.

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

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

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

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_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 'MRNASEQ_CHIERARCHICAL'.

  • 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',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 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, 140 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 117 (23%) 394 2e-05
(0.0145) 		1e-05
(0.008) 		0.29
(1.00) 		0.769
(1.00) 		0.00017
(0.115) 		0.00017
(0.115) 		0.00164
(1.00) 		0.00414
(1.00) 		0.00562
(1.00) 		0.0001
(0.0694)
3p loss 287 (56%) 224 1e-05
(0.008) 		1e-05
(0.008) 		0.83
(1.00) 		0.678
(1.00) 		0.014
(1.00) 		0.0001
(0.0694) 		0.143
(1.00) 		0.00015
(0.102) 		0.732
(1.00) 		4e-05
(0.0284)
4p loss 186 (36%) 325 1e-05
(0.008) 		1e-05
(0.008) 		0.039
(1.00) 		0.496
(1.00) 		0.00016
(0.109) 		0.00013
(0.0893) 		0.388
(1.00) 		0.0032
(1.00) 		0.0276
(1.00) 		1e-05
(0.008)
5q loss 160 (31%) 351 1e-05
(0.008) 		1e-05
(0.008) 		0.242
(1.00) 		0.773
(1.00) 		0.206
(1.00) 		1e-05
(0.008) 		0.805
(1.00) 		2e-05
(0.0145) 		0.733
(1.00) 		3e-05
(0.0214)
9p loss 176 (34%) 335 1e-05
(0.008) 		1e-05
(0.008) 		0.7
(1.00) 		0.146
(1.00) 		0.303
(1.00) 		0.0001
(0.0694) 		0.406
(1.00) 		9e-05
(0.0626) 		0.335
(1.00) 		1e-05
(0.008)
18q loss 208 (41%) 303 1e-05
(0.008) 		1e-05
(0.008) 		0.315
(1.00) 		0.453
(1.00) 		0.00218
(1.00) 		1e-05
(0.008) 		0.0017
(1.00) 		1e-05
(0.008) 		0.15
(1.00) 		5e-05
(0.0353)
2q gain 69 (14%) 442 1e-05
(0.008) 		1e-05
(0.008) 		0.528
(1.00) 		0.764
(1.00) 		0.0624
(1.00) 		0.00035
(0.232) 		0.243
(1.00) 		0.0148
(1.00) 		0.142
(1.00) 		5e-05
(0.0353)
14q gain 148 (29%) 363 1e-05
(0.008) 		1e-05
(0.008) 		0.218
(1.00) 		0.0967
(1.00) 		0.014
(1.00) 		0.00059
(0.385) 		0.0174
(1.00) 		2e-05
(0.0145) 		0.00768
(1.00) 		0.0001
(0.0694)
18q gain 48 (9%) 463 0.00219
(1.00) 		1e-05
(0.008) 		0.0152
(1.00) 		0.0283
(1.00) 		0.0003
(0.199) 		2e-05
(0.0145) 		6e-05
(0.0421) 		0.211
(1.00) 		0.012
(1.00) 		0.0081
(1.00)
21q loss 179 (35%) 332 1e-05
(0.008) 		1e-05
(0.008) 		0.572
(1.00) 		0.982
(1.00) 		0.0324
(1.00) 		0.0383
(1.00) 		0.534
(1.00) 		0.0002
(0.134) 		0.733
(1.00) 		0.00019
(0.128)
2p gain 90 (18%) 421 1e-05
(0.008) 		1e-05
(0.008) 		0.0453
(1.00) 		0.423
(1.00) 		0.0512
(1.00) 		0.00209
(1.00) 		0.127
(1.00) 		0.00868
(1.00) 		0.1
(1.00) 		1e-05
(0.008)
7p gain 180 (35%) 331 1e-05
(0.008) 		1e-05
(0.008) 		0.632
(1.00) 		0.504
(1.00) 		0.275
(1.00) 		0.119
(1.00) 		0.679
(1.00) 		1e-05
(0.008) 		0.456
(1.00) 		0.0004
(0.264)
7q gain 123 (24%) 388 1e-05
(0.008) 		1e-05
(0.008) 		0.176
(1.00) 		0.634
(1.00) 		0.475
(1.00) 		0.822
(1.00) 		0.00769
(1.00) 		0.00035
(0.232) 		0.493
(1.00) 		0.00214
(1.00)
16p gain 104 (20%) 407 1e-05
(0.008) 		1e-05
(0.008) 		0.33
(1.00) 		0.177
(1.00) 		0.425
(1.00) 		0.0028
(1.00) 		0.726
(1.00) 		0.00011
(0.0758) 		0.57
(1.00) 		0.0309
(1.00)
16q gain 104 (20%) 407 1e-05
(0.008) 		1e-05
(0.008) 		0.504
(1.00) 		0.893
(1.00) 		0.154
(1.00) 		0.00282
(1.00) 		0.271
(1.00) 		4e-05
(0.0284) 		0.0251
(1.00) 		0.016
(1.00)
18p gain 119 (23%) 392 1e-05
(0.008) 		1e-05
(0.008) 		0.331
(1.00) 		0.319
(1.00) 		0.374
(1.00) 		1e-05
(0.008) 		0.663
(1.00) 		0.0148
(1.00) 		0.804
(1.00) 		0.00101
(0.646)
19p gain 53 (10%) 458 0.0016
(1.00) 		1e-05
(0.008) 		0.0875
(1.00) 		0.77
(1.00) 		0.0119
(1.00) 		0.00017
(0.115) 		0.00028
(0.186) 		0.169
(1.00) 		0.519
(1.00) 		0.315
(1.00)
22q gain 110 (22%) 401 1e-05
(0.008) 		1e-05
(0.008) 		0.153
(1.00) 		0.518
(1.00) 		0.273
(1.00) 		0.418
(1.00) 		0.00117
(0.744) 		0.0401
(1.00) 		0.00246
(1.00) 		4e-05
(0.0284)
4q loss 144 (28%) 367 1e-05
(0.008) 		1e-05
(0.008) 		0.472
(1.00) 		0.222
(1.00) 		0.00795
(1.00) 		0.0006
(0.391) 		0.239
(1.00) 		0.0149
(1.00) 		0.0786
(1.00) 		7e-05
(0.0489)
8p loss 184 (36%) 327 1e-05
(0.008) 		1e-05
(0.008) 		0.551
(1.00) 		0.677
(1.00) 		0.0368
(1.00) 		0.00269
(1.00) 		0.0309
(1.00) 		0.00023
(0.154) 		0.00076
(0.49) 		0.00059
(0.385)
11q loss 164 (32%) 347 0.0001
(0.0694) 		1e-05
(0.008) 		0.257
(1.00) 		0.0332
(1.00) 		0.00491
(1.00) 		4e-05
(0.0284) 		0.265
(1.00) 		0.685
(1.00) 		0.391
(1.00) 		0.0866
(1.00)
16q loss 78 (15%) 433 0.00548
(1.00) 		1e-05
(0.008) 		0.479
(1.00) 		0.242
(1.00) 		1e-05
(0.008) 		1e-05
(0.008) 		0.00258
(1.00) 		0.0174
(1.00) 		0.00057
(0.373) 		0.00095
(0.609)
3q gain 249 (49%) 262 1e-05
(0.008) 		1e-05
(0.008) 		0.686
(1.00) 		0.23
(1.00) 		0.00073
(0.472) 		0.0244
(1.00) 		0.00107
(0.684) 		0.638
(1.00) 		0.0786
(1.00) 		0.00597
(1.00)
8q gain 304 (59%) 207 1e-05
(0.008) 		2e-05
(0.0145) 		0.0796
(1.00) 		0.887
(1.00) 		0.117
(1.00) 		0.00215
(1.00) 		0.0831
(1.00) 		0.00712
(1.00) 		0.00832
(1.00) 		0.00569
(1.00)
9p gain 102 (20%) 409 1e-05
(0.008) 		3e-05
(0.0214) 		0.507
(1.00) 		0.0978
(1.00) 		0.00131
(0.823) 		0.0113
(1.00) 		0.00815
(1.00) 		0.0254
(1.00) 		0.0584
(1.00) 		0.0434
(1.00)
10p gain 40 (8%) 471 0.058
(1.00) 		3e-05
(0.0214) 		0.588
(1.00) 		0.0657
(1.00) 		0.0402
(1.00) 		0.00012
(0.0826) 		0.043
(1.00) 		0.0142
(1.00) 		0.885
(1.00) 		0.0227
(1.00)
11p gain 65 (13%) 446 2e-05
(0.0145) 		2e-05
(0.0145) 		0.942
(1.00) 		0.578
(1.00) 		0.205
(1.00) 		0.0153
(1.00) 		0.0542
(1.00) 		0.198
(1.00) 		0.191
(1.00) 		0.00654
(1.00)
11q gain 70 (14%) 441 0.00019
(0.128) 		5e-05
(0.0353) 		0.53
(1.00) 		0.581
(1.00) 		0.234
(1.00) 		0.0129
(1.00) 		0.298
(1.00) 		0.0715
(1.00) 		0.915
(1.00) 		0.0842
(1.00)
12p gain 143 (28%) 368 1e-05
(0.008) 		1e-05
(0.008) 		0.0158
(1.00) 		0.823
(1.00) 		0.0163
(1.00) 		0.00184
(1.00) 		0.0661
(1.00) 		0.0344
(1.00) 		0.502
(1.00) 		0.0112
(1.00)
17p gain 66 (13%) 445 1e-05
(0.008) 		4e-05
(0.0284) 		0.603
(1.00) 		0.902
(1.00) 		0.00795
(1.00) 		0.0132
(1.00) 		0.09
(1.00) 		0.00953
(1.00) 		0.271
(1.00) 		0.0209
(1.00)
20p gain 188 (37%) 323 1e-05
(0.008) 		1e-05
(0.008) 		0.96
(1.00) 		0.813
(1.00) 		0.104
(1.00) 		0.0253
(1.00) 		0.203
(1.00) 		0.00791
(1.00) 		0.0189
(1.00) 		0.0473
(1.00)
20q gain 198 (39%) 313 1e-05
(0.008) 		1e-05
(0.008) 		0.842
(1.00) 		0.873
(1.00) 		0.111
(1.00) 		0.00069
(0.446) 		0.169
(1.00) 		0.00343
(1.00) 		0.0024
(1.00) 		0.00672
(1.00)
1p loss 52 (10%) 459 0.00013
(0.0893) 		1e-05
(0.008) 		0.0189
(1.00) 		0.203
(1.00) 		0.00345
(1.00) 		0.00619
(1.00) 		0.337
(1.00) 		0.136
(1.00) 		0.213
(1.00) 		0.0025
(1.00)
5p loss 50 (10%) 461 2e-05
(0.0145) 		1e-05
(0.008) 		0.415
(1.00) 		0.385
(1.00) 		0.69
(1.00) 		0.106
(1.00) 		0.783
(1.00) 		0.136
(1.00) 		0.128
(1.00) 		0.217
(1.00)
9q loss 83 (16%) 428 1e-05
(0.008) 		1e-05
(0.008) 		0.994
(1.00) 		1
(1.00) 		0.635
(1.00) 		0.349
(1.00) 		0.814
(1.00) 		0.0103
(1.00) 		0.134
(1.00) 		0.00129
(0.813)
10q loss 109 (21%) 402 0.00014
(0.0958) 		0.00025
(0.167) 		0.205
(1.00) 		0.302
(1.00) 		0.0155
(1.00) 		0.0104
(1.00) 		0.0207
(1.00) 		0.106
(1.00) 		0.249
(1.00) 		0.0182
(1.00)
11p loss 134 (26%) 377 1e-05
(0.008) 		0.0002
(0.134) 		0.335
(1.00) 		0.281
(1.00) 		0.00505
(1.00) 		0.072
(1.00) 		0.0059
(1.00) 		0.361
(1.00) 		0.397
(1.00) 		0.0133
(1.00)
13q loss 162 (32%) 349 1e-05
(0.008) 		1e-05
(0.008) 		0.383
(1.00) 		0.827
(1.00) 		0.00307
(1.00) 		0.00117
(0.744) 		0.0377
(1.00) 		0.344
(1.00) 		0.333
(1.00) 		0.00063
(0.409)
14q loss 54 (11%) 457 0.00561
(1.00) 		0.00119
(0.753) 		0.0353
(1.00) 		0.529
(1.00) 		5e-05
(0.0353) 		0.00016
(0.109) 		0.00412
(1.00) 		0.213
(1.00) 		0.238
(1.00) 		0.0093
(1.00)
19p loss 93 (18%) 418 0.00022
(0.147) 		8e-05
(0.0558) 		0.712
(1.00) 		0.713
(1.00) 		0.0227
(1.00) 		0.00701
(1.00) 		0.0409
(1.00) 		0.00303
(1.00) 		0.658
(1.00) 		0.266
(1.00)
19q loss 82 (16%) 429 0.00015
(0.102) 		5e-05
(0.0353) 		0.128
(1.00) 		0.519
(1.00) 		0.205
(1.00) 		0.0878
(1.00) 		0.351
(1.00) 		0.0116
(1.00) 		0.798
(1.00) 		0.61
(1.00)
xq loss 82 (16%) 429 0.00016
(0.109) 		2e-05
(0.0145) 		0.0871
(1.00) 		0.00215
(1.00) 		0.0304
(1.00) 		0.00532
(1.00) 		0.0148
(1.00) 		0.196
(1.00) 		0.169
(1.00) 		0.0972
(1.00)
1p gain 68 (13%) 443 9e-05
(0.0626) 		0.0063
(1.00) 		0.969
(1.00) 		0.757
(1.00) 		0.861
(1.00) 		0.872
(1.00) 		0.699
(1.00) 		0.00797
(1.00) 		0.852
(1.00) 		0.634
(1.00)
3p gain 79 (15%) 432 0.00868
(1.00) 		0.00017
(0.115) 		0.0653
(1.00) 		0.756
(1.00) 		0.00116
(0.74) 		0.0467
(1.00) 		0.00915
(1.00) 		0.178
(1.00) 		0.0434
(1.00) 		0.213
(1.00)
4p gain 39 (8%) 472 0.00215
(1.00) 		0.00025
(0.167) 		0.598
(1.00) 		0.46
(1.00) 		0.0512
(1.00) 		0.149
(1.00) 		0.12
(1.00) 		0.442
(1.00) 		0.468
(1.00) 		0.611
(1.00)
5p gain 195 (38%) 316 1e-05
(0.008) 		0.00081
(0.522) 		0.961
(1.00) 		0.833
(1.00) 		0.0836
(1.00) 		0.445
(1.00) 		0.612
(1.00) 		0.0312
(1.00) 		0.935
(1.00) 		0.631
(1.00)
6p gain 80 (16%) 431 1e-05
(0.008) 		0.00245
(1.00) 		0.5
(1.00) 		0.746
(1.00) 		0.663
(1.00) 		0.0377
(1.00) 		0.574
(1.00) 		0.115
(1.00) 		0.251
(1.00) 		0.553
(1.00)
6q gain 61 (12%) 450 2e-05
(0.0145) 		0.0378
(1.00) 		0.194
(1.00) 		0.073
(1.00) 		0.0774
(1.00) 		0.0318
(1.00) 		0.124
(1.00) 		0.851
(1.00) 		0.0575
(1.00) 		0.425
(1.00)
9q gain 136 (27%) 375 1e-05
(0.008) 		0.0047
(1.00) 		0.128
(1.00) 		0.252
(1.00) 		0.254
(1.00) 		0.0276
(1.00) 		0.655
(1.00) 		0.127
(1.00) 		0.281
(1.00) 		0.377
(1.00)
12q gain 87 (17%) 424 1e-05
(0.008) 		0.00122
(0.771) 		0.114
(1.00) 		0.185
(1.00) 		0.0829
(1.00) 		0.00317
(1.00) 		0.577
(1.00) 		0.355
(1.00) 		0.756
(1.00) 		0.402
(1.00)
13q gain 56 (11%) 455 1e-05
(0.008) 		0.00251
(1.00) 		0.594
(1.00) 		0.735
(1.00) 		0.0137
(1.00) 		0.0191
(1.00) 		0.251
(1.00) 		0.0125
(1.00) 		0.272
(1.00) 		0.0311
(1.00)
17q gain 84 (16%) 427 2e-05
(0.0145) 		0.00053
(0.347) 		0.583
(1.00) 		0.677
(1.00) 		0.128
(1.00) 		0.0321
(1.00) 		0.487
(1.00) 		0.014
(1.00) 		0.974
(1.00) 		0.0416
(1.00)
19q gain 74 (14%) 437 0.0378
(1.00) 		6e-05
(0.0421) 		0.961
(1.00) 		0.787
(1.00) 		0.0169
(1.00) 		0.00088
(0.565) 		0.00061
(0.396) 		0.3
(1.00) 		0.827
(1.00) 		0.201
(1.00)
xq gain 87 (17%) 424 1e-05
(0.008) 		0.00189
(1.00) 		0.252
(1.00) 		0.827
(1.00) 		0.426
(1.00) 		0.303
(1.00) 		0.0614
(1.00) 		0.482
(1.00) 		0.645
(1.00) 		0.0622
(1.00)
10p loss 151 (30%) 360 6e-05
(0.0421) 		0.00336
(1.00) 		0.32
(1.00) 		0.231
(1.00) 		0.0511
(1.00) 		0.0815
(1.00) 		0.0969
(1.00) 		0.102
(1.00) 		0.249
(1.00) 		0.0383
(1.00)
15q loss 98 (19%) 413 1e-05
(0.008) 		0.256
(1.00) 		0.628
(1.00) 		0.347
(1.00) 		0.12
(1.00) 		0.287
(1.00) 		0.725
(1.00) 		0.181
(1.00) 		0.54
(1.00) 		0.109
(1.00)
17p loss 103 (20%) 408 0.00013
(0.0893) 		0.00192
(1.00) 		0.388
(1.00) 		0.76
(1.00) 		0.526
(1.00) 		0.118
(1.00) 		0.544
(1.00) 		0.0145
(1.00) 		0.243
(1.00) 		0.56
(1.00)
18p loss 101 (20%) 410 0.0213
(1.00) 		2e-05
(0.0145) 		0.545
(1.00) 		0.328
(1.00) 		0.271
(1.00) 		0.114
(1.00) 		0.644
(1.00) 		0.00786
(1.00) 		0.848
(1.00) 		0.145
(1.00)
20q loss 28 (5%) 483 0.00906
(1.00) 		0.00642
(1.00) 		0.226
(1.00) 		0.587
(1.00) 		0.023
(1.00) 		0.0181
(1.00) 		0.0264
(1.00) 		0.0203
(1.00) 		0.00025
(0.167) 		0.0272
(1.00)
22q loss 72 (14%) 439 0.00354
(1.00) 		0.00127
(0.801) 		0.666
(1.00) 		0.658
(1.00) 		0.00129
(0.813) 		0.157
(1.00) 		0.00049
(0.321) 		0.18
(1.00) 		0.00339
(1.00) 		0.00015
(0.102)
4q gain 35 (7%) 476 0.109
(1.00) 		0.204
(1.00) 		1
(1.00) 		0.769
(1.00) 		0.622
(1.00) 		0.0676
(1.00) 		0.927
(1.00) 		0.878
(1.00) 		0.945
(1.00) 		0.94
(1.00)
5q gain 65 (13%) 446 0.0324
(1.00) 		0.581
(1.00) 		0.617
(1.00) 		0.888
(1.00) 		0.782
(1.00) 		0.752
(1.00) 		0.728
(1.00) 		0.687
(1.00) 		0.467
(1.00) 		0.634
(1.00)
8p gain 148 (29%) 363 0.00169
(1.00) 		0.217
(1.00) 		0.589
(1.00) 		0.638
(1.00) 		0.355
(1.00) 		0.17
(1.00) 		0.677
(1.00) 		0.479
(1.00) 		0.466
(1.00) 		0.686
(1.00)
10q gain 34 (7%) 477 0.00065
(0.421) 		0.216
(1.00) 		0.0992
(1.00) 		0.399
(1.00) 		0.622
(1.00) 		0.161
(1.00) 		0.591
(1.00) 		0.105
(1.00) 		0.848
(1.00) 		0.0362
(1.00)
15q gain 71 (14%) 440 0.0817
(1.00) 		0.00843
(1.00) 		0.386
(1.00) 		0.587
(1.00) 		0.216
(1.00) 		0.565
(1.00) 		0.973
(1.00) 		0.00331
(1.00) 		0.838
(1.00) 		0.291
(1.00)
21q gain 35 (7%) 476 0.0456
(1.00) 		0.0327
(1.00) 		0.0143
(1.00) 		0.129
(1.00) 		0.00719
(1.00) 		0.00893
(1.00) 		0.104
(1.00) 		0.214
(1.00) 		0.729
(1.00) 		0.33
(1.00)
1q loss 35 (7%) 476 0.0555
(1.00) 		0.135
(1.00) 		0.78
(1.00) 		0.488
(1.00) 		0.0991
(1.00) 		0.018
(1.00) 		0.036
(1.00) 		0.00082
(0.527) 		0.0533
(1.00) 		0.779
(1.00)
2p loss 33 (6%) 478 0.0878
(1.00) 		0.00736
(1.00) 		0.157
(1.00) 		0.045
(1.00) 		0.106
(1.00) 		0.671
(1.00) 		0.0338
(1.00) 		0.849
(1.00) 		0.0114
(1.00) 		0.965
(1.00)
2q loss 42 (8%) 469 0.93
(1.00) 		0.0567
(1.00) 		0.839
(1.00) 		0.624
(1.00) 		0.745
(1.00) 		0.579
(1.00) 		0.197
(1.00) 		0.916
(1.00) 		0.028
(1.00) 		0.507
(1.00)
3q loss 60 (12%) 451 0.0133
(1.00) 		0.238
(1.00) 		0.259
(1.00) 		0.767
(1.00) 		0.602
(1.00) 		0.169
(1.00) 		0.953
(1.00) 		0.0259
(1.00) 		0.472
(1.00) 		0.385
(1.00)
6p loss 67 (13%) 444 0.00038
(0.251) 		0.00118
(0.748) 		0.0281
(1.00) 		0.128
(1.00) 		0.0298
(1.00) 		0.0366
(1.00) 		0.334
(1.00) 		0.489
(1.00) 		0.261
(1.00) 		0.0605
(1.00)
6q loss 67 (13%) 444 0.0642
(1.00) 		0.0043
(1.00) 		0.128
(1.00) 		0.124
(1.00) 		0.782
(1.00) 		0.572
(1.00) 		0.665
(1.00) 		0.12
(1.00) 		0.346
(1.00) 		0.559
(1.00)
7p loss 28 (5%) 483 0.0199
(1.00) 		0.0253
(1.00) 		0.00971
(1.00) 		0.63
(1.00) 		0.506
(1.00) 		0.0465
(1.00) 		0.306
(1.00) 		0.969
(1.00) 		0.0811
(1.00) 		0.754
(1.00)
7q loss 42 (8%) 469 0.198
(1.00) 		0.309
(1.00) 		0.531
(1.00) 		1
(1.00) 		0.326
(1.00) 		0.128
(1.00) 		0.0434
(1.00) 		0.677
(1.00) 		0.857
(1.00) 		0.471
(1.00)
8q loss 30 (6%) 481 0.0757
(1.00) 		0.282
(1.00) 		0.757
(1.00) 		0.874
(1.00) 		0.695
(1.00) 		0.0845
(1.00) 		0.209
(1.00) 		0.0939
(1.00) 		0.767
(1.00) 		0.603
(1.00)
12p loss 36 (7%) 475 0.656
(1.00) 		0.0568
(1.00) 		0.642
(1.00) 		0.125
(1.00) 		0.861
(1.00) 		0.875
(1.00) 		1
(1.00) 		0.627
(1.00) 		0.371
(1.00) 		0.726
(1.00)
12q loss 32 (6%) 479 0.0151
(1.00) 		0.00179
(1.00) 		0.871
(1.00) 		0.148
(1.00) 		0.512
(1.00) 		0.93
(1.00) 		0.972
(1.00) 		0.434
(1.00) 		0.195
(1.00) 		0.475
(1.00)
16p loss 60 (12%) 451 0.00042
(0.276) 		0.0135
(1.00) 		0.864
(1.00) 		0.0805
(1.00) 		0.00625
(1.00) 		0.0555
(1.00) 		0.967
(1.00) 		0.42
(1.00) 		0.842
(1.00) 		0.588
(1.00)
17q loss 34 (7%) 477 0.00116
(0.74) 		0.112
(1.00) 		0.902
(1.00) 		0.504
(1.00) 		0.444
(1.00) 		0.853
(1.00) 		0.922
(1.00) 		0.685
(1.00) 		0.972
(1.00) 		0.237
(1.00)
20p loss 46 (9%) 465 0.0004
(0.264) 		0.0156
(1.00) 		0.473
(1.00) 		0.765
(1.00) 		0.0818
(1.00) 		0.315
(1.00) 		0.328
(1.00) 		0.0085
(1.00) 		0.0017
(1.00) 		0.0911
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.063

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

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 = 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 82 76 96 87 78 74 18
1Q GAIN MUTATED 7 25 25 37 15 4 4
1Q GAIN WILD-TYPE 75 51 71 50 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 = 0.00017 (Fisher's exact test), Q value = 0.12

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 = 0.00017 (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_MATURE_CHIERARCHICAL'

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

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
1Q GAIN MUTATED 23 46 10 27 5
1Q GAIN WILD-TYPE 76 82 69 81 52

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_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 178 102 189 42
2P GAIN MUTATED 41 31 12 6
2P GAIN WILD-TYPE 137 71 177 36

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 82 76 96 87 78 74 18
2P GAIN MUTATED 5 27 18 31 3 5 1
2P GAIN WILD-TYPE 77 49 78 56 75 69 17

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

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
2P GAIN MUTATED 19 35 1 19 11
2P GAIN WILD-TYPE 80 93 78 89 46

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

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

Table S10.  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 S10.  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 S11.  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 82 76 96 87 78 74 18
2Q GAIN MUTATED 3 24 15 22 1 2 2
2Q GAIN WILD-TYPE 79 52 81 65 77 72 16

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

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.23

Table S12.  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 16 25 11 16
2Q GAIN WILD-TYPE 35 132 144 114

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S13.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
2Q GAIN MUTATED 12 26 0 17 9
2Q GAIN WILD-TYPE 87 102 79 91 48

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'METHLYATION_CNMF'

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

Table S14.  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 82 76 96 87 78 74 18
3P GAIN MUTATED 12 11 10 15 26 4 1
3P GAIN WILD-TYPE 70 65 86 72 52 70 17

Figure S14.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'CN_CNMF'

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

Table S15.  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 S15.  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 S16.  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 82 76 96 87 78 74 18
3Q GAIN MUTATED 31 45 52 51 46 14 10
3Q GAIN WILD-TYPE 51 31 44 36 32 60 8

Figure S16.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.17

Table S17.  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 82 76 96 87 78 74 18
4P GAIN MUTATED 2 6 19 6 4 1 1
4P GAIN WILD-TYPE 80 70 77 81 74 73 17

Figure S17.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'CN_CNMF'

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

Table S18.  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 S18.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

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

Table S19.  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 S19.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

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

Table S20.  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 S20.  Get High-res Image Gene #12: '6q 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 S21.  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 S21.  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 S22.  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 82 76 96 87 78 74 18
7P GAIN MUTATED 21 33 42 50 5 22 7
7P GAIN WILD-TYPE 61 43 54 37 73 52 11

Figure S22.  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 S23.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 198 124 185
7P GAIN MUTATED 73 63 41
7P GAIN WILD-TYPE 125 61 144

Figure S23.  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 S24.  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 S24.  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 S25.  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 82 76 96 87 78 74 18
7Q GAIN MUTATED 9 25 24 45 5 11 4
7Q GAIN WILD-TYPE 73 51 72 42 73 63 14

Figure S25.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.23

Table S26.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 198 124 185
7Q GAIN MUTATED 49 44 29
7Q GAIN WILD-TYPE 149 80 156

Figure S26.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

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

Table S27.  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 S27.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

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

Table S28.  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 82 76 96 87 78 74 18
8Q GAIN MUTATED 55 42 73 51 30 39 14
8Q GAIN WILD-TYPE 27 34 23 36 48 35 4

Figure S28.  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 S29.  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 S29.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

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

Table S30.  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 82 76 96 87 78 74 18
9P GAIN MUTATED 14 6 16 17 13 33 3
9P GAIN WILD-TYPE 68 70 80 70 65 41 15

Figure S30.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'CN_CNMF'

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

Table S31.  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 S31.  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 S32.  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 82 76 96 87 78 74 18
10P GAIN MUTATED 2 18 3 7 5 2 3
10P GAIN WILD-TYPE 80 58 93 80 73 72 15

Figure S32.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S33.  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 S33.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

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

Table S34.  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 S34.  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 S35.  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 82 76 96 87 78 74 18
11P GAIN MUTATED 3 3 26 13 5 11 4
11P GAIN WILD-TYPE 79 73 70 74 73 63 14

Figure S35.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'CN_CNMF'

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

Table S36.  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 S36.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

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

Table S37.  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 82 76 96 87 78 74 18
11Q GAIN MUTATED 4 11 23 14 2 11 5
11Q GAIN WILD-TYPE 78 65 73 73 76 63 13

Figure S37.  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 S38.  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 S38.  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 S39.  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 82 76 96 87 78 74 18
12P GAIN MUTATED 11 34 28 40 18 9 3
12P GAIN WILD-TYPE 71 42 68 47 60 65 15

Figure S39.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'CN_CNMF'

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

Table S40.  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 S40.  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 S41.  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 S41.  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 S42.  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 S42.  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 S43.  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 82 76 96 87 78 74 18
14Q GAIN MUTATED 20 26 41 33 4 18 6
14Q GAIN WILD-TYPE 62 50 55 54 74 56 12

Figure S43.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S44.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 198 124 185
14Q GAIN MUTATED 74 42 31
14Q GAIN WILD-TYPE 124 82 154

Figure S44.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S45.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
14Q GAIN MUTATED 36 33 9 38 24
14Q GAIN WILD-TYPE 63 95 70 70 33

Figure S45.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

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

Table S46.  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 S46.  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 S47.  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 82 76 96 87 78 74 18
16P GAIN MUTATED 13 31 27 18 6 4 5
16P GAIN WILD-TYPE 69 45 69 69 72 70 13

Figure S47.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.076

Table S48.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 198 124 185
16P GAIN MUTATED 44 38 21
16P GAIN WILD-TYPE 154 86 164

Figure S48.  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 S49.  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 S49.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

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

Table S50.  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 82 76 96 87 78 74 18
16Q GAIN MUTATED 13 25 31 20 6 5 4
16Q GAIN WILD-TYPE 69 51 65 67 72 69 14

Figure S50.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S51.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 198 124 185
16Q GAIN MUTATED 51 33 19
16Q GAIN WILD-TYPE 147 91 166

Figure S51.  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 S52.  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 S52.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

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

Table S53.  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 82 76 96 87 78 74 18
17P GAIN MUTATED 7 12 13 26 3 4 1
17P GAIN WILD-TYPE 75 64 83 61 75 70 17

Figure S53.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'CN_CNMF'

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

Table S54.  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 S54.  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 S55.  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 S55.  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 S56.  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 82 76 96 87 78 74 18
18P GAIN MUTATED 7 33 25 25 18 8 3
18P GAIN WILD-TYPE 75 43 71 62 60 66 15

Figure S56.  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 S57.  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 S57.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'METHLYATION_CNMF'

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

Table S58.  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 82 76 96 87 78 74 18
18Q GAIN MUTATED 0 11 5 10 18 3 1
18Q GAIN WILD-TYPE 82 65 91 77 60 71 17

Figure S58.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

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

Table S59.  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 S59.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S60.  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 8 10 5 24
18Q GAIN WILD-TYPE 43 147 150 106

Figure S60.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

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

Table S61.  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 S61.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

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

Table S62.  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 82 76 96 87 78 74 18
19P GAIN MUTATED 1 6 5 20 17 3 1
19P GAIN WILD-TYPE 81 70 91 67 61 71 17

Figure S62.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S63.  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 S63.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.19

Table S64.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 216 146
19P GAIN MUTATED 10 36 7
19P GAIN WILD-TYPE 135 180 139

Figure S64.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

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

Table S65.  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 82 76 96 87 78 74 18
19Q GAIN MUTATED 2 11 11 22 20 6 2
19Q GAIN WILD-TYPE 80 65 85 65 58 68 16

Figure S65.  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 S66.  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 S66.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

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

Table S67.  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 82 76 96 87 78 74 18
20P GAIN MUTATED 26 26 55 39 19 16 7
20P GAIN WILD-TYPE 56 50 41 48 59 58 11

Figure S67.  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 S68.  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 S68.  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 S69.  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 82 76 96 87 78 74 18
20Q GAIN MUTATED 26 34 55 40 15 19 9
20Q GAIN WILD-TYPE 56 42 41 47 63 55 9

Figure S69.  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 S70.  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 S70.  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 S71.  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 82 76 96 87 78 74 18
22Q GAIN MUTATED 15 21 24 42 5 1 2
22Q GAIN WILD-TYPE 67 55 72 45 73 73 16

Figure S71.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S72.  Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
22Q GAIN MUTATED 22 39 4 31 8
22Q GAIN WILD-TYPE 77 89 75 77 49

Figure S72.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

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

Table S73.  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 S73.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

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

Table S74.  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 S74.  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 S75.  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 82 76 96 87 78 74 18
1P LOSS MUTATED 4 6 8 27 2 4 1
1P LOSS WILD-TYPE 78 70 88 60 76 70 17

Figure S75.  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 S76.  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 S76.  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 S77.  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 82 76 96 87 78 74 18
3P LOSS MUTATED 35 57 73 65 15 26 16
3P LOSS WILD-TYPE 47 19 23 22 63 48 2

Figure S77.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S78.  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 37 105 78 58
3P LOSS WILD-TYPE 14 52 77 72

Figure S78.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S79.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 198 124 185
3P LOSS MUTATED 127 76 81
3P LOSS WILD-TYPE 71 48 104

Figure S79.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S80.  Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
3P LOSS MUTATED 53 85 25 65 36
3P LOSS WILD-TYPE 46 43 54 43 21

Figure S80.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

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

Table S81.  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 S81.  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 S82.  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 82 76 96 87 78 74 18
4P LOSS MUTATED 16 41 27 58 21 12 11
4P LOSS WILD-TYPE 66 35 69 29 57 62 7

Figure S82.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

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

Table S83.  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 S83.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S84.  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 64 35 56
4P LOSS WILD-TYPE 25 93 120 74

Figure S84.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S85.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
4P LOSS MUTATED 24 65 16 45 16
4P LOSS WILD-TYPE 75 63 63 63 41

Figure S85.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

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

Table S86.  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 S86.  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 S87.  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 82 76 96 87 78 74 18
4Q LOSS MUTATED 13 31 26 44 15 11 4
4Q LOSS WILD-TYPE 69 45 70 43 63 63 14

Figure S87.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S88.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
4Q LOSS MUTATED 15 53 14 36 16
4Q LOSS WILD-TYPE 84 75 65 72 41

Figure S88.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

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

Table S89.  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 S89.  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 S90.  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 82 76 96 87 78 74 18
5P LOSS MUTATED 1 14 15 15 2 2 1
5P LOSS WILD-TYPE 81 62 81 72 76 72 17

Figure S90.  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 S91.  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 S91.  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 S92.  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 82 76 96 87 78 74 18
5Q LOSS MUTATED 14 44 41 43 7 3 8
5Q LOSS WILD-TYPE 68 32 55 44 71 71 10

Figure S92.  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 S93.  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 43
5Q LOSS WILD-TYPE 22 99 128 87

Figure S93.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S94.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 198 124 185
5Q LOSS MUTATED 71 51 36
5Q LOSS WILD-TYPE 127 73 149

Figure S94.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S95.  Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
5Q LOSS MUTATED 28 54 7 38 19
5Q LOSS WILD-TYPE 71 74 72 70 38

Figure S95.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

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

Table S96.  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 S96.  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 S97.  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 82 76 96 87 78 74 18
8P LOSS MUTATED 31 26 52 35 10 25 5
8P LOSS WILD-TYPE 51 50 44 52 68 49 13

Figure S97.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.15

Table S98.  Gene #55: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 198 124 185
8P LOSS MUTATED 91 45 47
8P LOSS WILD-TYPE 107 79 138

Figure S98.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

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

Table S99.  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 S99.  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 S100.  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 82 76 96 87 78 74 18
9P LOSS MUTATED 17 48 37 48 9 8 9
9P LOSS WILD-TYPE 65 28 59 39 69 66 9

Figure S100.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S101.  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 54 47 38
9P LOSS WILD-TYPE 18 103 108 92

Figure S101.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.063

Table S102.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 198 124 185
9P LOSS MUTATED 66 61 47
9P LOSS WILD-TYPE 132 63 138

Figure S102.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S103.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
9P LOSS MUTATED 32 65 7 38 17
9P LOSS WILD-TYPE 67 63 72 70 40

Figure S103.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

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

Table S104.  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 S104.  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 S105.  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 82 76 96 87 78 74 18
9Q LOSS MUTATED 5 24 17 24 4 4 5
9Q LOSS WILD-TYPE 77 52 79 63 74 70 13

Figure S105.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'CN_CNMF'

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

Table S106.  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 S106.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

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

Table S107.  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 S107.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.17

Table S108.  Gene #60: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 82 76 96 87 78 74 18
10Q LOSS MUTATED 7 19 26 29 13 9 6
10Q LOSS WILD-TYPE 75 57 70 58 65 65 12

Figure S108.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'CN_CNMF'

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

Table S109.  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 S109.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.13

Table S110.  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 82 76 96 87 78 74 18
11P LOSS MUTATED 21 25 21 35 21 6 5
11P LOSS WILD-TYPE 61 51 75 52 57 68 13

Figure S110.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'CN_CNMF'

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

Table S111.  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 S111.  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 S112.  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 82 76 96 87 78 74 18
11Q LOSS MUTATED 20 21 30 35 44 9 5
11Q LOSS WILD-TYPE 62 55 66 52 34 65 13

Figure S112.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S113.  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 44 40 64
11Q LOSS WILD-TYPE 41 113 115 66

Figure S113.  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 S114.  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 S114.  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 S115.  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 82 76 96 87 78 74 18
13Q LOSS MUTATED 17 35 30 42 25 12 1
13Q LOSS WILD-TYPE 65 41 66 45 53 62 17

Figure S115.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

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

Table S116.  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 S116.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S117.  Gene #66: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 157 155 130
14Q LOSS MUTATED 6 12 8 27
14Q LOSS WILD-TYPE 45 145 147 103

Figure S117.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

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

Table S118.  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 S118.  Get High-res Image Gene #67: '15q 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 S119.  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 82 76 96 87 78 74 18
16Q LOSS MUTATED 4 12 4 24 27 4 3
16Q LOSS WILD-TYPE 78 64 92 63 51 70 15

Figure S119.  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 S120.  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 S120.  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 S121.  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 S121.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

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

Table S122.  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 S122.  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 S123.  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 82 76 96 87 78 74 18
18P LOSS MUTATED 18 15 23 28 2 10 5
18P LOSS WILD-TYPE 64 61 73 59 76 64 13

Figure S123.  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 S124.  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 S124.  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 S125.  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 82 76 96 87 78 74 18
18Q LOSS MUTATED 34 41 56 45 2 21 9
18Q LOSS WILD-TYPE 48 35 40 42 76 53 9

Figure S125.  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 S126.  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 28 80 69 26
18Q LOSS WILD-TYPE 23 77 86 104

Figure S126.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S127.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 198 124 185
18Q LOSS MUTATED 100 60 46
18Q LOSS WILD-TYPE 98 64 139

Figure S127.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S128.  Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
18Q LOSS MUTATED 46 54 13 47 29
18Q LOSS WILD-TYPE 53 74 66 61 28

Figure S128.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

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

Table S129.  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 S129.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

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

Table S130.  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 82 76 96 87 78 74 18
19P LOSS MUTATED 8 13 33 19 7 9 4
19P LOSS WILD-TYPE 74 63 63 68 71 65 14

Figure S130.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'CN_CNMF'

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

Table S131.  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 S131.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

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

Table S132.  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 82 76 96 87 78 74 18
19Q LOSS MUTATED 6 13 27 22 5 7 2
19Q LOSS WILD-TYPE 76 63 69 65 73 67 16

Figure S132.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.17

Table S133.  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 S133.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'CN_CNMF'

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

Table S134.  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 S134.  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 S135.  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 82 76 96 87 78 74 18
21Q LOSS MUTATED 20 27 50 47 9 18 8
21Q LOSS WILD-TYPE 62 49 46 40 69 56 10

Figure S135.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.13

Table S136.  Gene #78: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 198 124 185
21Q LOSS MUTATED 79 55 44
21Q LOSS WILD-TYPE 119 69 141

Figure S136.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S137.  Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
21Q LOSS MUTATED 32 55 13 43 28
21Q LOSS WILD-TYPE 67 73 66 65 29

Figure S137.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S138.  Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 99 128 79 108 57
22Q LOSS MUTATED 17 9 11 9 18
22Q LOSS WILD-TYPE 82 119 68 99 39

Figure S138.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

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

Table S139.  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 S139.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

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

Table S140.  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 82 76 96 87 78 74 18
XQ LOSS MUTATED 6 12 19 28 12 2 3
XQ LOSS WILD-TYPE 76 64 77 59 66 72 15

Figure S140.  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

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)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle