Correlation between copy number variations of arm-level result and molecular subtypes
Stomach Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1NK3C49
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1NK3C49
Overview
Introduction

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

Summary

Testing the association between copy number variation 78 arm-level results and 8 molecular subtypes across 306 patients, 112 significant findings detected with Q value < 0.25.

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

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 7q gain cnv correlated to 'CN_CNMF'.

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

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'CN_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF'.

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

  • 18p gain cnv correlated to 'METHLYATION_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'CN_CNMF'.

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

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'CN_CNMF'.

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

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

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'METHLYATION_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

  • 12p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q loss cnv correlated to 'CN_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • 19p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'MRNASEQ_CNMF'.

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 78 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 112 significant findings detected.

Molecular
subtypes 		CN
CNMF 		METHLYATION
CNMF 		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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
20q gain 0 (0%) 149 1.47e-24
(8.98e-22) 		7.34e-14
(4.44e-11) 		1.98e-08
(1.16e-05) 		1.23e-06
(0.000706) 		2.11e-09
(1.25e-06) 		2.63e-11
(1.56e-08) 		6.8e-05
(0.0364) 		1.39e-11
(8.32e-09)
4q loss 0 (0%) 253 3.37e-14
(2.04e-11) 		4.26e-05
(0.0231) 		0.00341
(1.00) 		0.000371
(0.188) 		1.87e-06
(0.00107) 		0.000246
(0.127) 		9.24e-05
(0.0491) 		0.000452
(0.226)
19p loss 0 (0%) 273 1.37e-11
(8.22e-09) 		4.4e-06
(0.00248) 		4.05e-06
(0.00229) 		0.000158
(0.0826) 		4.86e-08
(2.85e-05) 		4.21e-06
(0.00237) 		0.0188
(1.00) 		5e-05
(0.027)
20p gain 0 (0%) 178 1.86e-17
(1.13e-14) 		5.66e-09
(3.33e-06) 		2.44e-07
(0.000142) 		0.000895
(0.434) 		2.71e-06
(0.00154) 		1.61e-06
(0.000924) 		0.00126
(0.595) 		9.62e-07
(0.000555)
4p loss 0 (0%) 251 4.58e-12
(2.75e-09) 		0.000389
(0.197) 		0.00464
(1.00) 		0.000778
(0.381) 		3.22e-05
(0.0177) 		0.000232
(0.12) 		0.000193
(0.1) 		0.000418
(0.211)
5q loss 0 (0%) 271 1.59e-12
(9.54e-10) 		2.47e-06
(0.00141) 		3.87e-05
(0.0211) 		0.00182
(0.842) 		7.98e-05
(0.0427) 		0.000173
(0.0901) 		0.000612
(0.301) 		7.43e-07
(0.00043)
8q gain 0 (0%) 184 4.29e-10
(2.54e-07) 		3.99e-07
(0.000232) 		0.00634
(1.00) 		0.00132
(0.625) 		0.000314
(0.161) 		0.0289
(1.00) 		0.0003
(0.154) 		5.46e-05
(0.0295)
16p loss 0 (0%) 277 2.1e-11
(1.25e-08) 		1.89e-05
(0.0105) 		0.000186
(0.0971) 		0.00104
(0.498) 		0.0055
(1.00) 		0.0261
(1.00) 		8.48e-06
(0.00474) 		8.07e-05
(0.043)
19q loss 0 (0%) 283 2.73e-07
(0.000159) 		1.26e-05
(0.00702) 		0.000109
(0.0575) 		0.0135
(1.00) 		3.91e-06
(0.00221) 		8.88e-05
(0.0473) 		0.0559
(1.00) 		0.00222
(1.00)
17p loss 0 (0%) 242 6.31e-12
(3.78e-09) 		8.72e-07
(0.000504) 		0.000595
(0.294) 		0.0021
(0.962) 		0.000245
(0.126) 		0.0034
(1.00) 		0.00109
(0.519) 		0.000205
(0.106)
1q gain 0 (0%) 263 1.99e-07
(0.000116) 		0.000395
(0.2) 		0.00139
(0.652) 		0.0688
(1.00) 		0.00163
(0.759) 		0.00137
(0.643) 		0.000467
(0.233) 		0.00376
(1.00)
6p gain 0 (0%) 279 3.37e-05
(0.0185) 		5.54e-05
(0.0298) 		0.00808
(1.00) 		0.0195
(1.00) 		0.00972
(1.00) 		0.0221
(1.00) 		9.29e-05
(0.0492) 		0.00128
(0.605)
6q gain 0 (0%) 284 9.53e-05
(0.0504) 		0.000353
(0.179) 		0.0399
(1.00) 		0.0415
(1.00) 		0.057
(1.00) 		0.0722
(1.00) 		8.06e-05
(0.043) 		0.00524
(1.00)
12p loss 0 (0%) 285 4.38e-05
(0.0237) 		0.000447
(0.225) 		0.00234
(1.00) 		0.00436
(1.00) 		0.00286
(1.00) 		0.0117
(1.00) 		0.141
(1.00) 		0.000323
(0.165)
15q loss 0 (0%) 281 1.45e-07
(8.49e-05) 		2.34e-05
(0.013) 		0.0183
(1.00) 		0.0178
(1.00) 		0.0014
(0.656) 		0.00423
(1.00) 		0.00234
(1.00) 		6.2e-05
(0.0333)
22q loss 0 (0%) 266 7.2e-15
(4.37e-12) 		1.9e-06
(0.00109) 		0.00199
(0.919) 		0.0207
(1.00) 		3.76e-05
(0.0206) 		0.000558
(0.277) 		0.00731
(1.00) 		0.0101
(1.00)
7p gain 0 (0%) 210 7.19e-14
(4.35e-11) 		3.79e-05
(0.0207) 		0.107
(1.00) 		0.229
(1.00) 		0.0749
(1.00) 		0.0183
(1.00) 		0.00438
(1.00) 		0.000599
(0.296)
8p gain 0 (0%) 216 2.76e-10
(1.64e-07) 		0.00046
(0.23) 		0.276
(1.00) 		0.00862
(1.00) 		0.00249
(1.00) 		0.491
(1.00) 		0.0116
(1.00) 		0.0379
(1.00)
13q gain 0 (0%) 241 1.2e-06
(0.000693) 		0.000325
(0.165) 		0.114
(1.00) 		0.975
(1.00) 		0.0226
(1.00) 		0.0093
(1.00) 		0.0289
(1.00) 		0.0165
(1.00)
3p loss 0 (0%) 281 5.51e-07
(0.000319) 		0.000954
(0.46) 		0.000874
(0.426) 		0.0102
(1.00) 		0.00104
(0.498) 		0.0106
(1.00) 		0.0188
(1.00) 		0.000146
(0.0764)
8p loss 0 (0%) 275 5.9e-06
(0.00332) 		0.0246
(1.00) 		0.0597
(1.00) 		0.281
(1.00) 		0.0248
(1.00) 		0.0564
(1.00) 		2.84e-05
(0.0157) 		0.00487
(1.00)
9p loss 0 (0%) 255 1.45e-11
(8.65e-09) 		2.64e-05
(0.0146) 		0.00233
(1.00) 		0.0106
(1.00) 		0.00156
(0.726) 		0.00117
(0.558) 		0.0553
(1.00) 		0.0351
(1.00)
16q loss 0 (0%) 274 3.96e-11
(2.35e-08) 		3.51e-06
(0.00199) 		0.0062
(1.00) 		0.003
(1.00) 		0.0126
(1.00) 		0.16
(1.00) 		0.00427
(1.00) 		0.00341
(1.00)
21q loss 0 (0%) 244 4.08e-09
(2.4e-06) 		6.83e-06
(0.00383) 		0.0492
(1.00) 		0.00568
(1.00) 		0.178
(1.00) 		0.0489
(1.00) 		0.259
(1.00) 		0.326
(1.00)
2p gain 0 (0%) 282 0.000434
(0.218) 		0.00148
(0.693) 		0.0406
(1.00) 		0.0199
(1.00) 		0.0325
(1.00) 		0.00938
(1.00) 		0.000993
(0.478) 		0.00214
(0.98)
5p gain 0 (0%) 264 1.92e-06
(0.0011) 		0.00442
(1.00) 		0.00536
(1.00) 		0.0207
(1.00) 		0.101
(1.00) 		0.0226
(1.00) 		0.00688
(1.00) 		0.00469
(1.00)
7q gain 0 (0%) 229 2.11e-13
(1.27e-10) 		0.000562
(0.279) 		0.376
(1.00) 		0.494
(1.00) 		0.494
(1.00) 		0.481
(1.00) 		0.133
(1.00) 		0.045
(1.00)
10p gain 0 (0%) 261 3.76e-09
(2.22e-06) 		0.00204
(0.94) 		0.000804
(0.392) 		0.000773
(0.379) 		0.024
(1.00) 		0.00111
(0.529) 		0.173
(1.00) 		0.0281
(1.00)
10q gain 0 (0%) 280 2.63e-05
(0.0145) 		0.0481
(1.00) 		0.224
(1.00) 		0.237
(1.00) 		0.575
(1.00) 		0.141
(1.00) 		0.115
(1.00) 		0.173
(1.00)
18p gain 0 (0%) 281 0.00377
(1.00) 		3.87e-05
(0.0211) 		0.067
(1.00) 		0.577
(1.00) 		0.0404
(1.00) 		0.243
(1.00) 		0.455
(1.00) 		0.175
(1.00)
1p loss 0 (0%) 292 1.5e-05
(0.00833) 		0.0945
(1.00) 		0.0459
(1.00) 		0.0304
(1.00) 		0.122
(1.00) 		0.73
(1.00) 		0.682
(1.00) 		0.832
(1.00)
3q loss 0 (0%) 292 5.76e-05
(0.031) 		0.0197
(1.00) 		0.0392
(1.00) 		0.143
(1.00) 		0.00743
(1.00) 		0.0612
(1.00) 		0.0154
(1.00) 		0.00401
(1.00)
5p loss 0 (0%) 289 2.12e-05
(0.0117) 		0.00392
(1.00) 		0.0182
(1.00) 		0.0363
(1.00) 		0.0107
(1.00) 		0.046
(1.00) 		0.0793
(1.00) 		0.00761
(1.00)
7q loss 0 (0%) 293 0.0002
(0.104) 		0.0414
(1.00) 		0.321
(1.00) 		1
(1.00) 		0.0144
(1.00) 		0.22
(1.00) 		0.00528
(1.00) 		0.212
(1.00)
9q loss 0 (0%) 281 3.06e-05
(0.0168) 		0.00415
(1.00) 		0.0237
(1.00) 		0.0463
(1.00) 		0.032
(1.00) 		0.118
(1.00) 		0.0933
(1.00) 		0.193
(1.00)
10p loss 0 (0%) 289 0.000261
(0.134) 		0.00808
(1.00) 		0.0731
(1.00) 		0.115
(1.00) 		0.016
(1.00) 		0.363
(1.00) 		0.0305
(1.00) 		0.0469
(1.00)
10q loss 0 (0%) 290 0.000133
(0.0702) 		0.00307
(1.00) 		0.106
(1.00) 		0.256
(1.00) 		0.0115
(1.00) 		0.046
(1.00) 		0.0175
(1.00) 		0.00234
(1.00)
11p loss 0 (0%) 288 0.000611
(0.301) 		0.000168
(0.0878) 		0.745
(1.00) 		0.171
(1.00) 		0.0518
(1.00) 		0.0326
(1.00) 		0.0437
(1.00) 		0.0469
(1.00)
11q loss 0 (0%) 290 0.000269
(0.138) 		0.00892
(1.00) 		0.892
(1.00) 		0.892
(1.00) 		0.2
(1.00) 		0.416
(1.00) 		0.0656
(1.00) 		0.386
(1.00)
14q loss 0 (0%) 278 8.18e-06
(0.00458) 		0.000905
(0.438) 		0.00142
(0.667) 		0.0183
(1.00) 		0.0214
(1.00) 		0.0175
(1.00) 		0.0095
(1.00) 		0.00254
(1.00)
17q loss 0 (0%) 286 0.000103
(0.0542) 		0.0245
(1.00) 		0.0808
(1.00) 		0.0906
(1.00) 		0.0729
(1.00) 		0.0599
(1.00) 		0.0549
(1.00) 		0.0529
(1.00)
18q loss 0 (0%) 254 2.74e-06
(0.00155) 		0.0206
(1.00) 		0.0212
(1.00) 		0.00674
(1.00) 		0.00777
(1.00) 		0.0651
(1.00) 		0.0619
(1.00) 		0.0561
(1.00)
20p loss 0 (0%) 297 0.00451
(1.00) 		0.017
(1.00) 		0.000492
(0.245) 		0.00196
(0.903) 		0.0695
(1.00) 		0.812
(1.00) 		0.177
(1.00) 		1
(1.00)
1p gain 0 (0%) 291 0.00429
(1.00) 		0.507
(1.00) 		0.269
(1.00) 		0.588
(1.00) 		0.0806
(1.00) 		0.153
(1.00) 		0.0175
(1.00) 		0.109
(1.00)
2q gain 0 (0%) 283 0.00439
(1.00) 		0.0108
(1.00) 		0.00102
(0.49) 		0.0033
(1.00) 		0.0623
(1.00) 		0.0428
(1.00) 		0.00942
(1.00) 		0.0198
(1.00)
3p gain 0 (0%) 295 0.248
(1.00) 		0.086
(1.00) 		0.629
(1.00) 		0.773
(1.00) 		0.547
(1.00) 		0.427
(1.00) 		0.887
(1.00) 		0.431
(1.00)
3q gain 0 (0%) 277 0.000666
(0.327) 		0.174
(1.00) 		0.363
(1.00) 		0.249
(1.00) 		0.643
(1.00) 		0.0588
(1.00) 		0.193
(1.00) 		0.134
(1.00)
4p gain 0 (0%) 301 0.0903
(1.00) 		0.286
(1.00) 		0.332
(1.00) 		0.346
(1.00) 		0.872
(1.00) 		1
(1.00) 		0.789
(1.00) 		0.346
(1.00)
5q gain 0 (0%) 296 0.26
(1.00) 		0.95
(1.00) 		0.826
(1.00) 		0.516
(1.00) 		0.651
(1.00) 		0.464
(1.00) 		0.266
(1.00) 		0.554
(1.00)
9p gain 0 (0%) 284 0.0258
(1.00) 		0.139
(1.00) 		0.243
(1.00) 		0.333
(1.00) 		0.466
(1.00) 		0.204
(1.00) 		0.577
(1.00) 		0.0373
(1.00)
9q gain 0 (0%) 277 0.00579
(1.00) 		0.113
(1.00) 		0.379
(1.00) 		0.7
(1.00) 		0.702
(1.00) 		0.867
(1.00) 		0.218
(1.00) 		0.0741
(1.00)
11p gain 0 (0%) 294 0.845
(1.00) 		0.115
(1.00) 		0.741
(1.00) 		0.161
(1.00) 		0.0561
(1.00) 		0.203
(1.00) 		0.601
(1.00) 		0.199
(1.00)
11q gain 0 (0%) 286 0.137
(1.00) 		0.0338
(1.00) 		0.937
(1.00) 		0.721
(1.00) 		0.0872
(1.00) 		0.446
(1.00) 		0.0871
(1.00) 		0.0274
(1.00)
12p gain 0 (0%) 271 0.00368
(1.00) 		0.178
(1.00) 		0.0645
(1.00) 		0.378
(1.00) 		0.0363
(1.00) 		0.583
(1.00) 		0.00174
(0.807) 		0.0735
(1.00)
12q gain 0 (0%) 278 0.329
(1.00) 		0.168
(1.00) 		0.435
(1.00) 		0.483
(1.00) 		0.0923
(1.00) 		0.381
(1.00) 		0.00956
(1.00) 		0.0725
(1.00)
14q gain 0 (0%) 301 0.0438
(1.00) 		0.283
(1.00) 		0.0569
(1.00) 		0.104
(1.00)
15q gain 0 (0%) 296 0.0326
(1.00) 		0.543
(1.00) 		0.0774
(1.00) 		0.0101
(1.00) 		0.0296
(1.00) 		0.0574
(1.00) 		0.0346
(1.00) 		0.0147
(1.00)
16p gain 0 (0%) 293 0.0238
(1.00) 		0.116
(1.00) 		0.29
(1.00) 		0.319
(1.00) 		0.98
(1.00) 		0.0112
(1.00) 		0.755
(1.00) 		0.695
(1.00)
16q gain 0 (0%) 294 0.117
(1.00) 		0.826
(1.00) 		0.848
(1.00) 		0.493
(1.00) 		0.859
(1.00) 		0.121
(1.00) 		0.601
(1.00) 		0.901
(1.00)
17p gain 0 (0%) 299 0.0216
(1.00) 		0.457
(1.00) 		0.756
(1.00) 		0.868
(1.00) 		0.3
(1.00) 		0.875
(1.00) 		0.181
(1.00) 		0.302
(1.00)
17q gain 0 (0%) 291 0.00983
(1.00) 		0.664
(1.00) 		0.314
(1.00) 		0.185
(1.00) 		0.0404
(1.00) 		0.701
(1.00) 		0.126
(1.00) 		0.301
(1.00)
18q gain 0 (0%) 292 0.221
(1.00) 		0.0615
(1.00) 		0.141
(1.00) 		0.486
(1.00) 		0.00679
(1.00) 		0.119
(1.00) 		0.126
(1.00) 		0.282
(1.00)
19p gain 0 (0%) 293 0.261
(1.00) 		0.0219
(1.00) 		0.917
(1.00) 		0.313
(1.00) 		0.841
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.597
(1.00)
19q gain 0 (0%) 274 0.431
(1.00) 		0.382
(1.00) 		0.727
(1.00) 		0.246
(1.00) 		0.524
(1.00) 		0.534
(1.00) 		0.177
(1.00) 		0.244
(1.00)
21q gain 0 (0%) 303 0.212
(1.00) 		0.86
(1.00) 		0.3
(1.00) 		0.259
(1.00) 		0.26
(1.00) 		0.256
(1.00)
22q gain 0 (0%) 300 0.0244
(1.00) 		0.181
(1.00) 		0.747
(1.00) 		0.146
(1.00) 		0.451
(1.00) 		0.768
(1.00) 		0.177
(1.00) 		0.164
(1.00)
Xq gain 0 (0%) 301 0.345
(1.00) 		0.223
(1.00) 		0.114
(1.00) 		0.104
(1.00)
1q loss 0 (0%) 302 0.154
(1.00) 		1
(1.00) 		0.147
(1.00) 		0.793
(1.00) 		1
(1.00) 		0.789
(1.00)
2p loss 0 (0%) 300 0.0268
(1.00) 		0.4
(1.00) 		0.308
(1.00) 		0.231
(1.00) 		0.451
(1.00) 		0.334
(1.00) 		0.28
(1.00) 		0.256
(1.00)
2q loss 0 (0%) 301 0.0438
(1.00) 		0.68
(1.00) 		0.563
(1.00) 		0.43
(1.00) 		0.472
(1.00) 		0.0785
(1.00) 		0.578
(1.00) 		0.56
(1.00)
6p loss 0 (0%) 291 0.0368
(1.00) 		0.29
(1.00) 		0.157
(1.00) 		0.18
(1.00) 		0.228
(1.00) 		0.482
(1.00) 		0.92
(1.00) 		0.17
(1.00)
6q loss 0 (0%) 287 0.0114
(1.00) 		0.107
(1.00) 		0.00564
(1.00) 		0.0727
(1.00) 		0.553
(1.00) 		0.813
(1.00) 		0.514
(1.00) 		0.318
(1.00)
7p loss 0 (0%) 302 0.118
(1.00) 		0.344
(1.00) 		0.615
(1.00) 		0.403
(1.00) 		0.286
(1.00)
8q loss 0 (0%) 298 0.0115
(1.00) 		0.268
(1.00) 		0.756
(1.00) 		0.392
(1.00) 		0.338
(1.00) 		0.13
(1.00) 		0.28
(1.00) 		0.0876
(1.00)
12q loss 0 (0%) 294 0.00807
(1.00) 		0.00679
(1.00) 		0.0606
(1.00) 		0.294
(1.00) 		0.117
(1.00) 		0.165
(1.00) 		0.832
(1.00) 		0.00813
(1.00)
13q loss 0 (0%) 295 0.000884
(0.43) 		0.106
(1.00) 		0.221
(1.00) 		0.236
(1.00) 		0.386
(1.00) 		0.536
(1.00) 		0.263
(1.00) 		0.475
(1.00)
18p loss 0 (0%) 266 0.000932
(0.45) 		0.013
(1.00) 		0.0366
(1.00) 		0.0768
(1.00) 		0.0247
(1.00) 		0.591
(1.00) 		0.0479
(1.00) 		0.175
(1.00)
Xq loss 0 (0%) 292 0.0116
(1.00) 		0.11
(1.00) 		0.527
(1.00) 		0.298
(1.00) 		0.164
(1.00) 		0.14
(1.00) 		0.00451
(1.00) 		0.0502
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 1.99e-07 (Fisher's exact test), Q value = 0.00012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
1Q GAIN CNV 4 6 3 30
1Q GAIN WILD-TYPE 133 22 25 83

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.000395 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
1Q GAIN CNV 2 14 2 19
1Q GAIN WILD-TYPE 35 66 63 57

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

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000467 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 67 103
1Q GAIN CNV 5 4 26
1Q GAIN WILD-TYPE 62 63 77

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

'2p gain' versus 'CN_CNMF'

P value = 0.000434 (Fisher's exact test), Q value = 0.22

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
2P GAIN CNV 2 4 4 14
2P GAIN WILD-TYPE 135 24 24 99

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1.92e-06 (Fisher's exact test), Q value = 0.0011

Table S5.  Gene #8: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
5P GAIN CNV 6 3 2 31
5P GAIN WILD-TYPE 131 25 26 82

Figure S5.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.018

Table S6.  Gene #10: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
6P GAIN CNV 2 2 3 20
6P GAIN WILD-TYPE 135 26 25 93

Figure S6.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 5.54e-05 (Fisher's exact test), Q value = 0.03

Table S7.  Gene #10: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
6P GAIN CNV 0 8 0 14
6P GAIN WILD-TYPE 37 72 65 62

Figure S7.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.29e-05 (Fisher's exact test), Q value = 0.049

Table S8.  Gene #10: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 67 103
6P GAIN CNV 1 2 19
6P GAIN WILD-TYPE 66 65 84

Figure S8.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 9.53e-05 (Fisher's exact test), Q value = 0.05

Table S9.  Gene #11: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
6Q GAIN CNV 2 0 3 17
6Q GAIN WILD-TYPE 135 28 25 96

Figure S9.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.000353 (Fisher's exact test), Q value = 0.18

Table S10.  Gene #11: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
6Q GAIN CNV 0 6 0 12
6Q GAIN WILD-TYPE 37 74 65 64

Figure S10.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.06e-05 (Fisher's exact test), Q value = 0.043

Table S11.  Gene #11: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 67 103
6Q GAIN CNV 0 2 16
6Q GAIN WILD-TYPE 67 65 87

Figure S11.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 7.19e-14 (Fisher's exact test), Q value = 4.4e-11

Table S12.  Gene #12: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
7P GAIN CNV 21 25 6 44
7P GAIN WILD-TYPE 116 3 22 69

Figure S12.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 3.79e-05 (Fisher's exact test), Q value = 0.021

Table S13.  Gene #12: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
7P GAIN CNV 12 30 6 32
7P GAIN WILD-TYPE 25 50 59 44

Figure S13.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2.11e-13 (Fisher's exact test), Q value = 1.3e-10

Table S14.  Gene #13: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
7Q GAIN CNV 20 25 5 27
7Q GAIN WILD-TYPE 117 3 23 86

Figure S14.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 2.76e-10 (Fisher's exact test), Q value = 1.6e-07

Table S15.  Gene #14: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
8P GAIN CNV 29 11 24 26
8P GAIN WILD-TYPE 108 17 4 87

Figure S15.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.23

Table S16.  Gene #14: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
8P GAIN CNV 13 30 6 21
8P GAIN WILD-TYPE 24 50 59 55

Figure S16.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 4.29e-10 (Fisher's exact test), Q value = 2.5e-07

Table S17.  Gene #15: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
8Q GAIN CNV 36 12 26 48
8Q GAIN WILD-TYPE 101 16 2 65

Figure S17.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 3.99e-07 (Fisher's exact test), Q value = 0.00023

Table S18.  Gene #15: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
8Q GAIN CNV 13 39 7 38
8Q GAIN WILD-TYPE 24 41 58 38

Figure S18.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.16

Table S19.  Gene #15: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 69 97 57
8Q GAIN CNV 31 14 40 30
8Q GAIN WILD-TYPE 30 55 57 27

Figure S19.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.15

Table S20.  Gene #15: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 67 103
8Q GAIN CNV 26 13 51
8Q GAIN WILD-TYPE 41 54 52

Figure S20.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.46e-05 (Fisher's exact test), Q value = 0.029

Table S21.  Gene #15: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 83 96
8Q GAIN CNV 32 17 41
8Q GAIN WILD-TYPE 26 66 55

Figure S21.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 3.76e-09 (Fisher's exact test), Q value = 2.2e-06

Table S22.  Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
10P GAIN CNV 3 7 3 32
10P GAIN WILD-TYPE 134 21 25 81

Figure S22.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.015

Table S23.  Gene #19: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
10Q GAIN CNV 2 1 3 20
10Q GAIN WILD-TYPE 135 27 25 93

Figure S23.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1.2e-06 (Fisher's exact test), Q value = 0.00069

Table S24.  Gene #24: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
13Q GAIN CNV 16 15 2 32
13Q GAIN WILD-TYPE 121 13 26 81

Figure S24.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.000325 (Fisher's exact test), Q value = 0.17

Table S25.  Gene #24: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
13Q GAIN CNV 7 15 5 28
13Q GAIN WILD-TYPE 30 65 60 48

Figure S25.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 3.87e-05 (Fisher's exact test), Q value = 0.021

Table S26.  Gene #31: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
18P GAIN CNV 0 5 0 14
18P GAIN WILD-TYPE 37 75 65 62

Figure S26.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.86e-17 (Fisher's exact test), Q value = 1.1e-14

Table S27.  Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
20P GAIN CNV 23 25 15 65
20P GAIN WILD-TYPE 114 3 13 48

Figure S27.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 5.66e-09 (Fisher's exact test), Q value = 3.3e-06

Table S28.  Gene #35: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
20P GAIN CNV 21 30 8 46
20P GAIN WILD-TYPE 16 50 57 30

Figure S28.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 2.44e-07 (Chi-square test), Q value = 0.00014

Table S29.  Gene #35: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 41 35 37 50
20P GAIN CNV 13 7 6 20 33
20P GAIN WILD-TYPE 32 34 29 17 17

Figure S29.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 2.71e-06 (Fisher's exact test), Q value = 0.0015

Table S30.  Gene #35: '20p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 69 97 57
20P GAIN CNV 22 17 37 40
20P GAIN WILD-TYPE 39 52 60 17

Figure S30.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.61e-06 (Fisher's exact test), Q value = 0.00092

Table S31.  Gene #35: '20p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 89 124
20P GAIN CNV 46 22 48
20P GAIN WILD-TYPE 25 67 76

Figure S31.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.62e-07 (Fisher's exact test), Q value = 0.00056

Table S32.  Gene #35: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 83 96
20P GAIN CNV 38 18 37
20P GAIN WILD-TYPE 20 65 59

Figure S32.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1.47e-24 (Fisher's exact test), Q value = 9e-22

Table S33.  Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
20Q GAIN CNV 27 26 18 86
20Q GAIN WILD-TYPE 110 2 10 27

Figure S33.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 7.34e-14 (Fisher's exact test), Q value = 4.4e-11

Table S34.  Gene #36: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
20Q GAIN CNV 21 37 12 63
20Q GAIN WILD-TYPE 16 43 53 13

Figure S34.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1.98e-08 (Chi-square test), Q value = 1.2e-05

Table S35.  Gene #36: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 41 35 37 50
20Q GAIN CNV 15 11 12 22 42
20Q GAIN WILD-TYPE 30 30 23 15 8

Figure S35.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.23e-06 (Fisher's exact test), Q value = 0.00071

Table S36.  Gene #36: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 42 55 69
20Q GAIN CNV 10 22 42 28
20Q GAIN WILD-TYPE 32 20 13 41

Figure S36.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 2.11e-09 (Fisher's exact test), Q value = 1.2e-06

Table S37.  Gene #36: '20q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 69 97 57
20Q GAIN CNV 25 22 49 49
20Q GAIN WILD-TYPE 36 47 48 8

Figure S37.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.63e-11 (Fisher's exact test), Q value = 1.6e-08

Table S38.  Gene #36: '20q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 89 124
20Q GAIN CNV 60 29 56
20Q GAIN WILD-TYPE 11 60 68

Figure S38.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.8e-05 (Fisher's exact test), Q value = 0.036

Table S39.  Gene #36: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 67 103
20Q GAIN CNV 28 24 69
20Q GAIN WILD-TYPE 39 43 34

Figure S39.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.39e-11 (Fisher's exact test), Q value = 8.3e-09

Table S40.  Gene #36: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 83 96
20Q GAIN CNV 50 23 48
20Q GAIN WILD-TYPE 8 60 48

Figure S40.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1.5e-05 (Fisher's exact test), Q value = 0.0083

Table S41.  Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
1P LOSS CNV 0 0 0 14
1P LOSS WILD-TYPE 137 28 28 99

Figure S41.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 5.51e-07 (Fisher's exact test), Q value = 0.00032

Table S42.  Gene #44: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
3P LOSS CNV 1 1 1 22
3P LOSS WILD-TYPE 136 27 27 91

Figure S42.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000146 (Fisher's exact test), Q value = 0.076

Table S43.  Gene #44: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 83 96
3P LOSS CNV 10 0 8
3P LOSS WILD-TYPE 48 83 88

Figure S43.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 5.76e-05 (Fisher's exact test), Q value = 0.031

Table S44.  Gene #45: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
3Q LOSS CNV 0 1 0 13
3Q LOSS WILD-TYPE 137 27 28 100

Figure S44.  Get High-res Image Gene #45: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 4.58e-12 (Fisher's exact test), Q value = 2.8e-09

Table S45.  Gene #46: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
4P LOSS CNV 6 4 1 44
4P LOSS WILD-TYPE 131 24 27 69

Figure S45.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.000389 (Fisher's exact test), Q value = 0.2

Table S46.  Gene #46: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
4P LOSS CNV 1 16 6 23
4P LOSS WILD-TYPE 36 64 59 53

Figure S46.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 3.22e-05 (Fisher's exact test), Q value = 0.018

Table S47.  Gene #46: '4p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 69 97 57
4P LOSS CNV 6 4 20 21
4P LOSS WILD-TYPE 55 65 77 36

Figure S47.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000232 (Fisher's exact test), Q value = 0.12

Table S48.  Gene #46: '4p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 89 124
4P LOSS CNV 24 8 19
4P LOSS WILD-TYPE 47 81 105

Figure S48.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000193 (Fisher's exact test), Q value = 0.1

Table S49.  Gene #46: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 67 103
4P LOSS CNV 5 7 31
4P LOSS WILD-TYPE 62 60 72

Figure S49.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000418 (Fisher's exact test), Q value = 0.21

Table S50.  Gene #46: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 83 96
4P LOSS CNV 21 9 13
4P LOSS WILD-TYPE 37 74 83

Figure S50.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 3.37e-14 (Fisher's exact test), Q value = 2e-11

Table S51.  Gene #47: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
4Q LOSS CNV 4 3 1 45
4Q LOSS WILD-TYPE 133 25 27 68

Figure S51.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 4.26e-05 (Fisher's exact test), Q value = 0.023

Table S52.  Gene #47: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
4Q LOSS CNV 1 18 4 23
4Q LOSS WILD-TYPE 36 62 61 53

Figure S52.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000371 (Fisher's exact test), Q value = 0.19

Table S53.  Gene #47: '4q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 42 55 69
4Q LOSS CNV 1 6 18 8
4Q LOSS WILD-TYPE 41 36 37 61

Figure S53.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1.87e-06 (Fisher's exact test), Q value = 0.0011

Table S54.  Gene #47: '4q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 69 97 57
4Q LOSS CNV 5 3 18 22
4Q LOSS WILD-TYPE 56 66 79 35

Figure S54.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000246 (Fisher's exact test), Q value = 0.13

Table S55.  Gene #47: '4q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 89 124
4Q LOSS CNV 23 7 18
4Q LOSS WILD-TYPE 48 82 106

Figure S55.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.24e-05 (Fisher's exact test), Q value = 0.049

Table S56.  Gene #47: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 67 103
4Q LOSS CNV 5 6 31
4Q LOSS WILD-TYPE 62 61 72

Figure S56.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000452 (Fisher's exact test), Q value = 0.23

Table S57.  Gene #47: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 83 96
4Q LOSS CNV 20 7 15
4Q LOSS WILD-TYPE 38 76 81

Figure S57.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.012

Table S58.  Gene #48: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
5P LOSS CNV 0 1 1 15
5P LOSS WILD-TYPE 137 27 27 98

Figure S58.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1.59e-12 (Fisher's exact test), Q value = 9.5e-10

Table S59.  Gene #49: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
5Q LOSS CNV 0 2 1 32
5Q LOSS WILD-TYPE 137 26 27 81

Figure S59.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 2.47e-06 (Fisher's exact test), Q value = 0.0014

Table S60.  Gene #49: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
5Q LOSS CNV 0 11 1 20
5Q LOSS WILD-TYPE 37 69 64 56

Figure S60.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 3.87e-05 (Chi-square test), Q value = 0.021

Table S61.  Gene #49: '5q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 41 35 37 50
5Q LOSS CNV 3 0 2 3 15
5Q LOSS WILD-TYPE 42 41 33 34 35

Figure S61.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 7.98e-05 (Fisher's exact test), Q value = 0.043

Table S62.  Gene #49: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 69 97 57
5Q LOSS CNV 3 2 11 16
5Q LOSS WILD-TYPE 58 67 86 41

Figure S62.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000173 (Fisher's exact test), Q value = 0.09

Table S63.  Gene #49: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 89 124
5Q LOSS CNV 18 4 10
5Q LOSS WILD-TYPE 53 85 114

Figure S63.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.43e-07 (Fisher's exact test), Q value = 0.00043

Table S64.  Gene #49: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 83 96
5Q LOSS CNV 19 2 9
5Q LOSS WILD-TYPE 39 81 87

Figure S64.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.1

Table S65.  Gene #53: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
7Q LOSS CNV 0 0 1 12
7Q LOSS WILD-TYPE 137 28 27 101

Figure S65.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 5.9e-06 (Fisher's exact test), Q value = 0.0033

Table S66.  Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
8P LOSS CNV 4 3 0 24
8P LOSS WILD-TYPE 133 25 28 89

Figure S66.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.84e-05 (Fisher's exact test), Q value = 0.016

Table S67.  Gene #54: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 67 103
8P LOSS CNV 4 0 20
8P LOSS WILD-TYPE 63 67 83

Figure S67.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1.45e-11 (Fisher's exact test), Q value = 8.6e-09

Table S68.  Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
9P LOSS CNV 4 3 3 41
9P LOSS WILD-TYPE 133 25 25 72

Figure S68.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 2.64e-05 (Fisher's exact test), Q value = 0.015

Table S69.  Gene #56: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
9P LOSS CNV 0 13 6 24
9P LOSS WILD-TYPE 37 67 59 52

Figure S69.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 3.06e-05 (Fisher's exact test), Q value = 0.017

Table S70.  Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
9Q LOSS CNV 2 1 2 20
9Q LOSS WILD-TYPE 135 27 26 93

Figure S70.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 0.000261 (Fisher's exact test), Q value = 0.13

Table S71.  Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
10P LOSS CNV 1 2 0 14
10P LOSS WILD-TYPE 136 26 28 99

Figure S71.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 0.000133 (Fisher's exact test), Q value = 0.07

Table S72.  Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
10Q LOSS CNV 0 3 1 12
10Q LOSS WILD-TYPE 137 25 27 101

Figure S72.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.088

Table S73.  Gene #60: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
11P LOSS CNV 0 2 0 11
11P LOSS WILD-TYPE 37 78 65 65

Figure S73.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.000269 (Fisher's exact test), Q value = 0.14

Table S74.  Gene #61: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
11Q LOSS CNV 1 0 1 14
11Q LOSS WILD-TYPE 136 28 27 99

Figure S74.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 4.38e-05 (Fisher's exact test), Q value = 0.024

Table S75.  Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
12P LOSS CNV 2 1 0 18
12P LOSS WILD-TYPE 135 27 28 95

Figure S75.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.000447 (Fisher's exact test), Q value = 0.22

Table S76.  Gene #62: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
12P LOSS CNV 0 2 2 13
12P LOSS WILD-TYPE 37 78 63 63

Figure S76.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000323 (Fisher's exact test), Q value = 0.16

Table S77.  Gene #62: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 83 96
12P LOSS CNV 11 3 2
12P LOSS WILD-TYPE 47 80 94

Figure S77.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 8.18e-06 (Fisher's exact test), Q value = 0.0046

Table S78.  Gene #65: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
14Q LOSS CNV 3 1 1 23
14Q LOSS WILD-TYPE 134 27 27 90

Figure S78.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1.45e-07 (Fisher's exact test), Q value = 8.5e-05

Table S79.  Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
15Q LOSS CNV 0 2 2 21
15Q LOSS WILD-TYPE 137 26 26 92

Figure S79.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 2.34e-05 (Fisher's exact test), Q value = 0.013

Table S80.  Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
15Q LOSS CNV 0 7 0 15
15Q LOSS WILD-TYPE 37 73 65 61

Figure S80.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.2e-05 (Fisher's exact test), Q value = 0.033

Table S81.  Gene #66: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 83 96
15Q LOSS CNV 11 0 9
15Q LOSS WILD-TYPE 47 83 87

Figure S81.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 2.1e-11 (Fisher's exact test), Q value = 1.3e-08

Table S82.  Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
16P LOSS CNV 0 0 1 28
16P LOSS WILD-TYPE 137 28 27 85

Figure S82.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.011

Table S83.  Gene #67: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
16P LOSS CNV 0 10 0 15
16P LOSS WILD-TYPE 37 70 65 61

Figure S83.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.000186 (Chi-square test), Q value = 0.097

Table S84.  Gene #67: '16p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 41 35 37 50
16P LOSS CNV 2 0 1 1 11
16P LOSS WILD-TYPE 43 41 34 36 39

Figure S84.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.48e-06 (Fisher's exact test), Q value = 0.0047

Table S85.  Gene #67: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 67 103
16P LOSS CNV 1 1 20
16P LOSS WILD-TYPE 66 66 83

Figure S85.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.07e-05 (Fisher's exact test), Q value = 0.043

Table S86.  Gene #67: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 83 96
16P LOSS CNV 13 1 8
16P LOSS WILD-TYPE 45 82 88

Figure S86.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 3.96e-11 (Fisher's exact test), Q value = 2.4e-08

Table S87.  Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
16Q LOSS CNV 1 0 1 30
16Q LOSS WILD-TYPE 136 28 27 83

Figure S87.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 3.51e-06 (Fisher's exact test), Q value = 0.002

Table S88.  Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
16Q LOSS CNV 0 9 0 17
16Q LOSS WILD-TYPE 37 71 65 59

Figure S88.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 6.31e-12 (Fisher's exact test), Q value = 3.8e-09

Table S89.  Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
17P LOSS CNV 6 9 4 45
17P LOSS WILD-TYPE 131 19 24 68

Figure S89.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 8.72e-07 (Fisher's exact test), Q value = 5e-04

Table S90.  Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
17P LOSS CNV 2 18 4 30
17P LOSS WILD-TYPE 35 62 61 46

Figure S90.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.000245 (Fisher's exact test), Q value = 0.13

Table S91.  Gene #69: '17p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 69 97 57
17P LOSS CNV 10 6 20 23
17P LOSS WILD-TYPE 51 63 77 34

Figure S91.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000205 (Fisher's exact test), Q value = 0.11

Table S92.  Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 83 96
17P LOSS CNV 23 9 17
17P LOSS WILD-TYPE 35 74 79

Figure S92.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.000103 (Fisher's exact test), Q value = 0.054

Table S93.  Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
17Q LOSS CNV 1 2 1 16
17Q LOSS WILD-TYPE 136 26 27 97

Figure S93.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 2.74e-06 (Fisher's exact test), Q value = 0.0016

Table S94.  Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
18Q LOSS CNV 10 8 1 33
18Q LOSS WILD-TYPE 127 20 27 80

Figure S94.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1.37e-11 (Fisher's exact test), Q value = 8.2e-09

Table S95.  Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
19P LOSS CNV 0 2 1 30
19P LOSS WILD-TYPE 137 26 27 83

Figure S95.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 4.4e-06 (Fisher's exact test), Q value = 0.0025

Table S96.  Gene #73: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
19P LOSS CNV 0 7 1 19
19P LOSS WILD-TYPE 37 73 64 57

Figure S96.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 4.05e-06 (Chi-square test), Q value = 0.0023

Table S97.  Gene #73: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 41 35 37 50
19P LOSS CNV 1 0 2 3 15
19P LOSS WILD-TYPE 44 41 33 34 35

Figure S97.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000158 (Fisher's exact test), Q value = 0.083

Table S98.  Gene #73: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 42 55 69
19P LOSS CNV 0 2 14 5
19P LOSS WILD-TYPE 42 40 41 64

Figure S98.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 4.86e-08 (Fisher's exact test), Q value = 2.8e-05

Table S99.  Gene #73: '19p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 69 97 57
19P LOSS CNV 4 1 7 20
19P LOSS WILD-TYPE 57 68 90 37

Figure S99.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.21e-06 (Fisher's exact test), Q value = 0.0024

Table S100.  Gene #73: '19p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 89 124
19P LOSS CNV 20 3 9
19P LOSS WILD-TYPE 51 86 115

Figure S100.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.027

Table S101.  Gene #73: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 83 96
19P LOSS CNV 16 3 7
19P LOSS WILD-TYPE 42 80 89

Figure S101.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 2.73e-07 (Fisher's exact test), Q value = 0.00016

Table S102.  Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
19Q LOSS CNV 0 2 1 20
19Q LOSS WILD-TYPE 137 26 27 93

Figure S102.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.007

Table S103.  Gene #74: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
19Q LOSS CNV 0 2 1 15
19Q LOSS WILD-TYPE 37 78 64 61

Figure S103.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.000109 (Chi-square test), Q value = 0.058

Table S104.  Gene #74: '19q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 41 35 37 50
19Q LOSS CNV 0 0 2 2 11
19Q LOSS WILD-TYPE 45 41 33 35 39

Figure S104.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 3.91e-06 (Fisher's exact test), Q value = 0.0022

Table S105.  Gene #74: '19q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 69 97 57
19Q LOSS CNV 2 1 5 15
19Q LOSS WILD-TYPE 59 68 92 42

Figure S105.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.88e-05 (Fisher's exact test), Q value = 0.047

Table S106.  Gene #74: '19q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 89 124
19Q LOSS CNV 15 3 5
19Q LOSS WILD-TYPE 56 86 119

Figure S106.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.000492 (Chi-square test), Q value = 0.24

Table S107.  Gene #75: '20p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 45 41 35 37 50
20P LOSS CNV 0 0 5 0 1
20P LOSS WILD-TYPE 45 41 30 37 49

Figure S107.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 4.08e-09 (Fisher's exact test), Q value = 2.4e-06

Table S108.  Gene #76: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
21Q LOSS CNV 8 4 10 40
21Q LOSS WILD-TYPE 129 24 18 73

Figure S108.  Get High-res Image Gene #76: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 6.83e-06 (Fisher's exact test), Q value = 0.0038

Table S109.  Gene #76: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
21Q LOSS CNV 1 28 5 18
21Q LOSS WILD-TYPE 36 52 60 58

Figure S109.  Get High-res Image Gene #76: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 7.2e-15 (Fisher's exact test), Q value = 4.4e-12

Table S110.  Gene #77: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 137 28 28 113
22Q LOSS CNV 0 2 1 37
22Q LOSS WILD-TYPE 137 26 27 76

Figure S110.  Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1.9e-06 (Fisher's exact test), Q value = 0.0011

Table S111.  Gene #77: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
22Q LOSS CNV 0 9 2 22
22Q LOSS WILD-TYPE 37 71 63 54

Figure S111.  Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 3.76e-05 (Fisher's exact test), Q value = 0.021

Table S112.  Gene #77: '22q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 69 97 57
22Q LOSS CNV 6 2 10 18
22Q LOSS WILD-TYPE 55 67 87 39

Figure S112.  Get High-res Image Gene #77: '22q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

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

  • Number of patients = 306

  • Number of significantly arm-level cnvs = 78

  • Number of molecular subtypes = 8

  • 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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