Lung Squamous Cell Carcinoma: Correlation between copy number variations of arm-level result and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 80 arm-level results and 10 molecular subtypes across 397 patients, 58 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

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

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

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF'.

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

  • 9p gain cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'CN_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

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

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

  • 6p loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

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

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

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

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

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

  • 16p loss cnv correlated to 'CN_CNMF'.

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

  • 19p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • Xq loss cnv correlated to 'RPPA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 58 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
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
2p gain 97 (24%) 300 0.00698
(1.00) 		0.0105
(1.00) 		1.01e-11
(7.81e-09) 		6.91e-05
(0.051) 		0.0657
(1.00) 		0.216
(1.00) 		0.00436
(1.00) 		0.000131
(0.096) 		1
(1.00) 		0.146
(1.00)
9q loss 103 (26%) 294 0.00394
(1.00) 		0.00469
(1.00) 		5.6e-14
(4.36e-11) 		1.49e-05
(0.0111) 		1
(1.00) 		0.4
(1.00) 		0.00125
(0.876) 		3.53e-05
(0.0261) 		0.134
(1.00) 		0.0637
(1.00)
10p loss 87 (22%) 310 0.0543
(1.00) 		0.134
(1.00) 		9.56e-10
(7.37e-07) 		4.4e-06
(0.00328) 		1
(1.00) 		0.132
(1.00) 		0.0034
(1.00) 		0.0108
(1.00) 		0.0914
(1.00) 		0.000296
(0.214)
10q loss 91 (23%) 306 0.00913
(1.00) 		0.000153
(0.112) 		6.19e-12
(4.81e-09) 		6.37e-05
(0.047) 		0.266
(1.00) 		0.0118
(1.00) 		0.000503
(0.36) 		0.000886
(0.625) 		0.0645
(1.00) 		0.000378
(0.272)
2q gain 43 (11%) 354 0.126
(1.00) 		0.0181
(1.00) 		5.41e-06
(0.00403) 		0.00399
(1.00) 		0.188
(1.00) 		0.306
(1.00) 		0.000177
(0.129) 		0.000397
(0.285) 		0.857
(1.00) 		0.489
(1.00)
7q gain 101 (25%) 296 0.066
(1.00) 		0.0979
(1.00) 		1.72e-13
(1.34e-10) 		5.65e-07
(0.000428) 		0.825
(1.00) 		0.85
(1.00) 		0.0136
(1.00) 		0.0162
(1.00) 		0.188
(1.00) 		0.00629
(1.00)
18p gain 67 (17%) 330 0.00236
(1.00) 		9.45e-06
(0.00704) 		1.66e-07
(0.000126) 		0.0226
(1.00) 		0.175
(1.00) 		0.0917
(1.00) 		0.0371
(1.00) 		0.00417
(1.00) 		0.561
(1.00) 		0.136
(1.00)
1p loss 59 (15%) 338 0.00248
(1.00) 		0.000419
(0.301) 		6.42e-12
(4.98e-09) 		2.4e-06
(0.0018) 		0.251
(1.00) 		0.0392
(1.00) 		0.000766
(0.542) 		0.00707
(1.00) 		0.212
(1.00) 		0.018
(1.00)
3p loss 161 (41%) 236 0.0501
(1.00) 		0.448
(1.00) 		4.11e-06
(0.00307) 		7.19e-05
(0.0529) 		0.493
(1.00) 		0.275
(1.00) 		0.515
(1.00) 		0.0118
(1.00) 		0.87
(1.00) 		0.0366
(1.00)
4p loss 164 (41%) 233 0.171
(1.00) 		0.0319
(1.00) 		7.02e-10
(5.42e-07) 		5.36e-08
(4.08e-05) 		0.0533
(1.00) 		0.327
(1.00) 		0.342
(1.00) 		0.0255
(1.00) 		0.166
(1.00) 		0.257
(1.00)
4q loss 143 (36%) 254 0.00796
(1.00) 		0.000975
(0.685) 		5.59e-11
(4.33e-08) 		1.99e-06
(0.0015) 		0.00876
(1.00) 		0.119
(1.00) 		0.00819
(1.00) 		0.00273
(1.00) 		0.0735
(1.00) 		0.00367
(1.00)
5q loss 146 (37%) 251 0.23
(1.00) 		0.213
(1.00) 		1.3e-09
(1e-06) 		6.65e-09
(5.11e-06) 		0.0543
(1.00) 		0.0892
(1.00) 		0.267
(1.00) 		0.248
(1.00) 		0.432
(1.00) 		0.0986
(1.00)
9p loss 164 (41%) 233 0.114
(1.00) 		0.751
(1.00) 		2.79e-16
(2.17e-13) 		3.04e-08
(2.33e-05) 		0.983
(1.00) 		0.487
(1.00) 		0.936
(1.00) 		0.424
(1.00) 		0.701
(1.00) 		0.87
(1.00)
13q loss 146 (37%) 251 0.229
(1.00) 		0.609
(1.00) 		3.86e-08
(2.95e-05) 		0.000231
(0.167) 		0.149
(1.00) 		0.44
(1.00) 		0.42
(1.00) 		0.571
(1.00) 		0.752
(1.00) 		0.0813
(1.00)
14q loss 70 (18%) 327 0.00058
(0.412) 		0.0217
(1.00) 		0.00225
(1.00) 		0.0148
(1.00) 		0.0458
(1.00) 		0.0422
(1.00) 		0.000101
(0.0741) 		6.4e-09
(4.92e-06) 		0.336
(1.00) 		0.0846
(1.00)
17p loss 145 (37%) 252 0.102
(1.00) 		1
(1.00) 		7.1e-05
(0.0523) 		0.000123
(0.0898) 		0.0107
(1.00) 		0.0694
(1.00) 		0.417
(1.00) 		0.403
(1.00) 		0.188
(1.00) 		0.00374
(1.00)
21q loss 122 (31%) 275 0.0247
(1.00) 		0.0161
(1.00) 		8.71e-10
(6.73e-07) 		9.29e-07
(0.000703) 		0.318
(1.00) 		0.241
(1.00) 		0.0115
(1.00) 		0.0159
(1.00) 		0.00605
(1.00) 		0.527
(1.00)
1q gain 83 (21%) 314 0.133
(1.00) 		0.1
(1.00) 		4.61e-05
(0.0341) 		0.0144
(1.00) 		0.627
(1.00) 		0.472
(1.00) 		0.00195
(1.00) 		0.00112
(0.781) 		0.0407
(1.00) 		0.0673
(1.00)
5p gain 185 (47%) 212 0.85
(1.00) 		0.954
(1.00) 		1.87e-06
(0.00141) 		0.0113
(1.00) 		0.216
(1.00) 		0.25
(1.00) 		0.16
(1.00) 		0.619
(1.00) 		0.658
(1.00) 		0.324
(1.00)
6q gain 24 (6%) 373 0.00289
(1.00) 		0.073
(1.00) 		0.000233
(0.169) 		0.00132
(0.919) 		0.723
(1.00) 		0.594
(1.00) 		0.234
(1.00) 		0.00197
(1.00) 		0.707
(1.00) 		0.689
(1.00)
7p gain 109 (27%) 288 0.173
(1.00) 		0.248
(1.00) 		2.78e-06
(0.00208) 		0.00121
(0.847) 		0.731
(1.00) 		0.988
(1.00) 		0.186
(1.00) 		0.0624
(1.00) 		0.639
(1.00) 		0.0158
(1.00)
9p gain 19 (5%) 378 0.29
(1.00) 		0.139
(1.00) 		0.145
(1.00) 		0.871
(1.00) 		0.172
(1.00) 		0.000216
(0.157) 		0.00967
(1.00) 		0.0172
(1.00) 		0.274
(1.00) 		0.0432
(1.00)
12p gain 111 (28%) 286 0.0146
(1.00) 		0.119
(1.00) 		1.03e-06
(0.000778) 		0.0784
(1.00) 		0.197
(1.00) 		0.593
(1.00) 		0.153
(1.00) 		0.0565
(1.00) 		0.734
(1.00) 		0.593
(1.00)
12q gain 49 (12%) 348 0.0488
(1.00) 		0.258
(1.00) 		1.15e-06
(0.000868) 		0.0339
(1.00) 		0.216
(1.00) 		0.775
(1.00) 		0.583
(1.00) 		0.0159
(1.00) 		0.412
(1.00) 		0.56
(1.00)
16q gain 23 (6%) 374 0.237
(1.00) 		0.844
(1.00) 		3.99e-05
(0.0295) 		0.429
(1.00) 		0.455
(1.00) 		0.154
(1.00) 		0.345
(1.00) 		0.735
(1.00) 		0.19
(1.00) 		0.514
(1.00)
17q gain 44 (11%) 353 0.013
(1.00) 		0.0282
(1.00) 		2.36e-07
(0.000179) 		0.00229
(1.00) 		0.42
(1.00) 		0.42
(1.00) 		0.00328
(1.00) 		0.00619
(1.00) 		0.499
(1.00) 		0.196
(1.00)
19p gain 40 (10%) 357 0.0516
(1.00) 		0.163
(1.00) 		1.86e-06
(0.00141) 		0.00415
(1.00) 		0.000468
(0.335) 		0.00166
(1.00) 		0.0695
(1.00) 		0.00866
(1.00) 		0.0581
(1.00) 		0.339
(1.00)
20p gain 109 (27%) 288 0.132
(1.00) 		0.0379
(1.00) 		5.05e-08
(3.85e-05) 		0.0159
(1.00) 		0.684
(1.00) 		0.194
(1.00) 		0.322
(1.00) 		0.322
(1.00) 		0.265
(1.00) 		0.0142
(1.00)
20q gain 95 (24%) 302 0.672
(1.00) 		0.599
(1.00) 		1.6e-08
(1.23e-05) 		0.184
(1.00) 		0.885
(1.00) 		0.331
(1.00) 		0.2
(1.00) 		0.0107
(1.00) 		0.95
(1.00) 		0.104
(1.00)
22q gain 97 (24%) 300 0.00362
(1.00) 		0.00858
(1.00) 		7.95e-09
(6.1e-06) 		0.00207
(1.00) 		0.227
(1.00) 		0.0167
(1.00) 		0.0705
(1.00) 		0.0563
(1.00) 		1
(1.00) 		0.0146
(1.00)
6p loss 35 (9%) 362 0.0798
(1.00) 		0.0164
(1.00) 		0.000112
(0.0824) 		0.00847
(1.00) 		0.0753
(1.00) 		0.0297
(1.00) 		0.00371
(1.00) 		0.00924
(1.00) 		0.516
(1.00) 		0.309
(1.00)
8p loss 117 (29%) 280 0.367
(1.00) 		0.554
(1.00) 		6.3e-08
(4.79e-05) 		0.000785
(0.555) 		0.115
(1.00) 		0.83
(1.00) 		0.514
(1.00) 		0.873
(1.00) 		0.889
(1.00) 		0.517
(1.00)
11p loss 59 (15%) 338 0.0129
(1.00) 		0.184
(1.00) 		0.000175
(0.128) 		0.00332
(1.00) 		0.0905
(1.00) 		0.0415
(1.00) 		0.147
(1.00) 		0.0992
(1.00) 		0.934
(1.00) 		0.644
(1.00)
11q loss 42 (11%) 355 0.42
(1.00) 		0.483
(1.00) 		3.81e-06
(0.00286) 		0.00879
(1.00) 		0.119
(1.00) 		0.315
(1.00) 		0.00583
(1.00) 		0.035
(1.00) 		0.121
(1.00) 		0.0626
(1.00)
16p loss 60 (15%) 337 0.329
(1.00) 		0.388
(1.00) 		1.96e-05
(0.0146) 		0.0247
(1.00) 		0.388
(1.00) 		0.305
(1.00) 		0.398
(1.00) 		0.0202
(1.00) 		0.278
(1.00) 		0.0067
(1.00)
19p loss 65 (16%) 332 0.0166
(1.00) 		0.0152
(1.00) 		0.000572
(0.408) 		0.0984
(1.00) 		0.708
(1.00) 		0.867
(1.00) 		0.000601
(0.426) 		3.22e-05
(0.0239) 		0.0214
(1.00) 		0.00445
(1.00)
Xq loss 15 (4%) 382 0.634
(1.00) 		1
(1.00) 		0.431
(1.00) 		0.914
(1.00) 		0.277
(1.00) 		0.000261
(0.189) 		0.674
(1.00) 		0.853
(1.00) 		0.333
(1.00) 		0.274
(1.00)
1p gain 24 (6%) 373 0.816
(1.00) 		0.642
(1.00) 		0.486
(1.00) 		0.607
(1.00) 		0.867
(1.00) 		0.247
(1.00) 		0.551
(1.00) 		0.27
(1.00) 		0.284
(1.00) 		1
(1.00)
3p gain 47 (12%) 350 0.539
(1.00) 		0.215
(1.00) 		0.0123
(1.00) 		0.000375
(0.27) 		0.741
(1.00) 		0.486
(1.00) 		0.218
(1.00) 		0.102
(1.00) 		0.638
(1.00) 		0.272
(1.00)
3q gain 180 (45%) 217 0.072
(1.00) 		0.653
(1.00) 		0.0114
(1.00) 		0.0373
(1.00) 		0.301
(1.00) 		0.402
(1.00) 		0.647
(1.00) 		0.644
(1.00) 		0.772
(1.00) 		0.382
(1.00)
4p gain 14 (4%) 383 0.148
(1.00) 		0.15
(1.00) 		0.0062
(1.00) 		0.156
(1.00) 		0.132
(1.00) 		0.464
(1.00) 		0.0124
(1.00) 		0.163
(1.00) 		1
(1.00) 		0.924
(1.00)
4q gain 7 (2%) 390 1
(1.00) 		0.715
(1.00) 		0.0634
(1.00) 		0.767
(1.00) 		0.0247
(1.00) 		0.593
(1.00) 		1
(1.00)
5q gain 43 (11%) 354 0.0754
(1.00) 		0.279
(1.00) 		0.0985
(1.00) 		0.148
(1.00) 		0.687
(1.00) 		0.656
(1.00) 		0.187
(1.00) 		0.474
(1.00) 		0.581
(1.00) 		0.0727
(1.00)
6p gain 36 (9%) 361 0.00213
(1.00) 		0.0106
(1.00) 		0.000574
(0.408) 		0.544
(1.00) 		0.643
(1.00) 		0.279
(1.00) 		0.098
(1.00) 		0.00199
(1.00) 		0.804
(1.00) 		0.968
(1.00)
8p gain 48 (12%) 349 0.129
(1.00) 		0.143
(1.00) 		0.0316
(1.00) 		0.0875
(1.00) 		0.756
(1.00) 		0.441
(1.00) 		0.0705
(1.00) 		0.00455
(1.00) 		0.342
(1.00) 		0.194
(1.00)
8q gain 114 (29%) 283 0.0326
(1.00) 		0.0311
(1.00) 		0.0135
(1.00) 		0.00439
(1.00) 		0.708
(1.00) 		0.618
(1.00) 		0.015
(1.00) 		0.00243
(1.00) 		0.0382
(1.00) 		0.282
(1.00)
9q gain 32 (8%) 365 0.186
(1.00) 		0.075
(1.00) 		0.00432
(1.00) 		0.047
(1.00) 		0.0746
(1.00) 		0.00212
(1.00) 		0.00143
(0.995) 		0.00495
(1.00) 		0.141
(1.00) 		0.0795
(1.00)
10p gain 22 (6%) 375 0.208
(1.00) 		1
(1.00) 		0.422
(1.00) 		0.372
(1.00) 		0.53
(1.00) 		0.389
(1.00) 		0.276
(1.00) 		1
(1.00) 		0.536
(1.00) 		0.799
(1.00)
10q gain 8 (2%) 389 0.327
(1.00) 		1
(1.00) 		0.162
(1.00) 		0.684
(1.00) 		0.534
(1.00) 		0.865
(1.00) 		0.753
(1.00) 		0.875
(1.00)
11p gain 23 (6%) 374 1
(1.00) 		0.929
(1.00) 		0.136
(1.00) 		0.12
(1.00) 		0.398
(1.00) 		0.272
(1.00) 		0.662
(1.00) 		0.761
(1.00) 		0.437
(1.00) 		0.87
(1.00)
11q gain 26 (7%) 371 0.096
(1.00) 		0.491
(1.00) 		0.0171
(1.00) 		0.0342
(1.00) 		0.773
(1.00) 		0.379
(1.00) 		0.63
(1.00) 		0.0629
(1.00) 		0.751
(1.00) 		1
(1.00)
13q gain 10 (3%) 387 0.769
(1.00) 		1
(1.00) 		0.00306
(1.00) 		0.582
(1.00) 		0.289
(1.00) 		0.349
(1.00) 		0.132
(1.00) 		0.0835
(1.00) 		0.753
(1.00) 		0.763
(1.00)
14q gain 41 (10%) 356 0.103
(1.00) 		0.82
(1.00) 		0.549
(1.00) 		0.296
(1.00) 		1
(1.00) 		0.676
(1.00) 		0.342
(1.00) 		0.522
(1.00) 		0.042
(1.00) 		0.144
(1.00)
15q gain 39 (10%) 358 0.206
(1.00) 		0.0334
(1.00) 		0.00173
(1.00) 		0.0176
(1.00) 		0.193
(1.00) 		0.112
(1.00) 		0.00936
(1.00) 		0.0457
(1.00) 		0.0581
(1.00) 		0.005
(1.00)
16p gain 17 (4%) 380 0.589
(1.00) 		1
(1.00) 		0.000993
(0.697) 		0.364
(1.00) 		0.723
(1.00) 		0.341
(1.00) 		0.521
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.876
(1.00)
17p gain 11 (3%) 386 0.298
(1.00) 		0.0881
(1.00) 		0.000891
(0.627) 		0.123
(1.00) 		0.0669
(1.00) 		0.343
(1.00) 		0.354
(1.00) 		0.026
(1.00) 		0.277
(1.00) 		0.0297
(1.00)
18q gain 44 (11%) 353 0.00783
(1.00) 		0.000419
(0.301) 		0.00285
(1.00) 		0.165
(1.00) 		0.136
(1.00) 		0.0285
(1.00) 		0.00941
(1.00) 		0.0101
(1.00) 		0.0706
(1.00) 		0.0271
(1.00)
19q gain 58 (15%) 339 0.0577
(1.00) 		0.773
(1.00) 		0.000368
(0.266) 		0.381
(1.00) 		0.0595
(1.00) 		0.019
(1.00) 		0.27
(1.00) 		0.0775
(1.00) 		0.716
(1.00) 		0.911
(1.00)
21q gain 19 (5%) 378 0.968
(1.00) 		0.425
(1.00) 		0.839
(1.00) 		0.00187
(1.00) 		0.524
(1.00) 		0.937
(1.00) 		0.697
(1.00) 		0.354
(1.00) 		0.659
(1.00) 		0.204
(1.00)
Xq gain 11 (3%) 386 0.769
(1.00) 		1
(1.00) 		0.0567
(1.00) 		0.0729
(1.00) 		0.451
(1.00) 		0.582
(1.00) 		0.773
(1.00) 		0.154
(1.00) 		0.682
(1.00) 		0.247
(1.00)
1q loss 9 (2%) 388 0.183
(1.00) 		0.25
(1.00) 		0.799
(1.00) 		0.32
(1.00) 		0.461
(1.00) 		0.58
(1.00) 		1
(1.00) 		0.709
(1.00)
2p loss 4 (1%) 393 0.0769
(1.00) 		0.477
(1.00) 		0.561
(1.00)
2q loss 11 (3%) 386 0.532
(1.00) 		1
(1.00) 		0.0131
(1.00) 		0.131
(1.00) 		0.737
(1.00) 		0.582
(1.00) 		0.619
(1.00) 		0.765
(1.00) 		0.63
(1.00) 		0.654
(1.00)
3q loss 26 (7%) 371 0.261
(1.00) 		0.701
(1.00) 		0.0411
(1.00) 		0.12
(1.00) 		0.703
(1.00) 		1
(1.00) 		0.496
(1.00) 		0.135
(1.00) 		0.614
(1.00) 		0.876
(1.00)
5p loss 24 (6%) 373 0.122
(1.00) 		0.252
(1.00) 		0.0331
(1.00) 		0.14
(1.00) 		0.255
(1.00) 		0.207
(1.00) 		0.694
(1.00) 		0.26
(1.00) 		1
(1.00) 		0.748
(1.00)
6q loss 40 (10%) 357 0.166
(1.00) 		0.0264
(1.00) 		0.0141
(1.00) 		0.0667
(1.00) 		0.0883
(1.00) 		0.159
(1.00) 		0.0785
(1.00) 		0.165
(1.00) 		0.933
(1.00) 		0.699
(1.00)
7p loss 23 (6%) 374 0.408
(1.00) 		0.834
(1.00) 		0.00207
(1.00) 		0.0131
(1.00) 		0.504
(1.00) 		0.114
(1.00) 		0.462
(1.00) 		0.187
(1.00) 		0.0887
(1.00) 		0.0847
(1.00)
7q loss 13 (3%) 384 0.472
(1.00) 		0.848
(1.00) 		0.078
(1.00) 		0.34
(1.00) 		1
(1.00) 		0.696
(1.00) 		0.0825
(1.00) 		0.045
(1.00) 		0.474
(1.00) 		0.458
(1.00)
8q loss 12 (3%) 385 0.254
(1.00) 		0.0397
(1.00) 		0.0303
(1.00) 		0.0254
(1.00) 		0.0801
(1.00) 		0.288
(1.00) 		0.28
(1.00) 		0.00649
(1.00) 		0.162
(1.00) 		0.843
(1.00)
12p loss 7 (2%) 390 0.131
(1.00) 		0.684
(1.00) 		0.225
(1.00) 		0.431
(1.00) 		0.769
(1.00) 		0.214
(1.00)
12q loss 9 (2%) 388 0.34
(1.00) 		0.383
(1.00) 		0.292
(1.00) 		0.381
(1.00) 		0.775
(1.00) 		0.0917
(1.00) 		0.849
(1.00) 		0.859
(1.00)
15q loss 44 (11%) 353 0.764
(1.00) 		0.115
(1.00) 		0.152
(1.00) 		0.00246
(1.00) 		0.00801
(1.00) 		0.00172
(1.00) 		0.169
(1.00) 		0.0119
(1.00) 		0.133
(1.00) 		0.325
(1.00)
16q loss 80 (20%) 317 0.0651
(1.00) 		0.237
(1.00) 		0.000639
(0.453) 		0.00453
(1.00) 		0.172
(1.00) 		0.132
(1.00) 		0.154
(1.00) 		0.00052
(0.371) 		0.855
(1.00) 		0.00079
(0.558)
17q loss 25 (6%) 372 0.275
(1.00) 		0.282
(1.00) 		0.0524
(1.00) 		0.00497
(1.00) 		0.304
(1.00) 		0.943
(1.00) 		0.00352
(1.00) 		0.0641
(1.00) 		0.558
(1.00) 		0.956
(1.00)
18p loss 43 (11%) 354 0.49
(1.00) 		0.653
(1.00) 		0.00527
(1.00) 		0.0637
(1.00) 		0.213
(1.00) 		0.86
(1.00) 		0.0464
(1.00) 		0.28
(1.00) 		0.686
(1.00) 		0.918
(1.00)
18q loss 76 (19%) 321 0.363
(1.00) 		0.932
(1.00) 		0.00107
(0.751) 		0.341
(1.00) 		0.253
(1.00) 		0.79
(1.00) 		0.209
(1.00) 		0.658
(1.00) 		0.244
(1.00) 		0.948
(1.00)
19q loss 43 (11%) 354 0.541
(1.00) 		0.243
(1.00) 		0.307
(1.00) 		0.0513
(1.00) 		0.0346
(1.00) 		0.103
(1.00) 		0.811
(1.00) 		0.138
(1.00) 		0.292
(1.00) 		0.415
(1.00)
20p loss 17 (4%) 380 0.268
(1.00) 		0.0237
(1.00) 		0.0868
(1.00) 		0.212
(1.00) 		0.0412
(1.00) 		0.555
(1.00) 		0.802
(1.00) 		0.597
(1.00) 		0.27
(1.00) 		0.336
(1.00)
20q loss 22 (6%) 375 0.0376
(1.00) 		0.0203
(1.00) 		0.0349
(1.00) 		0.084
(1.00) 		0.0774
(1.00) 		0.429
(1.00) 		0.0126
(1.00) 		0.0108
(1.00) 		0.586
(1.00) 		0.182
(1.00)
22q loss 38 (10%) 359 0.057
(1.00) 		0.157
(1.00) 		0.466
(1.00) 		0.479
(1.00) 		0.485
(1.00) 		0.202
(1.00) 		0.46
(1.00) 		0.0524
(1.00) 		0.0907
(1.00) 		0.383
(1.00)
'1q gain mutation analysis' versus 'CN_CNMF'

P value = 4.61e-05 (Fisher's exact test), Q value = 0.034

Table S1.  Gene #2: '1q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
1Q GAIN MUTATED 18 44 21
1Q GAIN WILD-TYPE 125 85 104

Figure S1.  Get High-res Image Gene #2: '1q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2p gain mutation analysis' versus 'CN_CNMF'

P value = 1.01e-11 (Fisher's exact test), Q value = 7.8e-09

Table S2.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
2P GAIN MUTATED 12 58 27
2P GAIN WILD-TYPE 131 71 98

Figure S2.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.91e-05 (Fisher's exact test), Q value = 0.051

Table S3.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
2P GAIN MUTATED 14 35 14
2P GAIN WILD-TYPE 84 48 55

Figure S3.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'2p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000131 (Fisher's exact test), Q value = 0.096

Table S4.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
2P GAIN MUTATED 15 33 15
2P GAIN WILD-TYPE 101 53 40

Figure S4.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain mutation analysis' versus 'CN_CNMF'

P value = 5.41e-06 (Fisher's exact test), Q value = 0.004

Table S5.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
2Q GAIN MUTATED 4 27 12
2Q GAIN WILD-TYPE 139 102 113

Figure S5.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000177 (Fisher's exact test), Q value = 0.13

Table S6.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 80 79 38
2Q GAIN MUTATED 3 19 7 0
2Q GAIN WILD-TYPE 57 61 72 38

Figure S6.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'5p gain mutation analysis' versus 'CN_CNMF'

P value = 1.87e-06 (Fisher's exact test), Q value = 0.0014

Table S7.  Gene #9: '5p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
5P GAIN MUTATED 47 58 80
5P GAIN WILD-TYPE 96 71 45

Figure S7.  Get High-res Image Gene #9: '5p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000233 (Fisher's exact test), Q value = 0.17

Table S8.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
6Q GAIN MUTATED 3 4 17
6Q GAIN WILD-TYPE 140 125 108

Figure S8.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 2.78e-06 (Fisher's exact test), Q value = 0.0021

Table S9.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
7P GAIN MUTATED 22 55 32
7P GAIN WILD-TYPE 121 74 93

Figure S9.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 1.72e-13 (Fisher's exact test), Q value = 1.3e-10

Table S10.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
7Q GAIN MUTATED 13 63 25
7Q GAIN WILD-TYPE 130 66 100

Figure S10.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.65e-07 (Fisher's exact test), Q value = 0.00043

Table S11.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
7Q GAIN MUTATED 9 35 12
7Q GAIN WILD-TYPE 89 48 57

Figure S11.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'9p gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000216 (Fisher's exact test), Q value = 0.16

Table S12.  Gene #17: '9p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 47 49 40
9P GAIN MUTATED 9 0 0 1
9P GAIN WILD-TYPE 49 47 49 39

Figure S12.  Get High-res Image Gene #17: '9p gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'12p gain mutation analysis' versus 'CN_CNMF'

P value = 1.03e-06 (Fisher's exact test), Q value = 0.00078

Table S13.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
12P GAIN MUTATED 19 52 40
12P GAIN WILD-TYPE 124 77 85

Figure S13.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12q gain mutation analysis' versus 'CN_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00087

Table S14.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
12Q GAIN MUTATED 5 31 13
12Q GAIN WILD-TYPE 138 98 112

Figure S14.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'16q gain mutation analysis' versus 'CN_CNMF'

P value = 3.99e-05 (Fisher's exact test), Q value = 0.03

Table S15.  Gene #29: '16q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
16Q GAIN MUTATED 0 10 13
16Q GAIN WILD-TYPE 143 119 112

Figure S15.  Get High-res Image Gene #29: '16q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17q gain mutation analysis' versus 'CN_CNMF'

P value = 2.36e-07 (Fisher's exact test), Q value = 0.00018

Table S16.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
17Q GAIN MUTATED 3 29 12
17Q GAIN WILD-TYPE 140 100 113

Figure S16.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 9.45e-06 (Fisher's exact test), Q value = 0.007

Table S17.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
18P GAIN MUTATED 2 21 5
18P GAIN WILD-TYPE 26 33 67

Figure S17.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'18p gain mutation analysis' versus 'CN_CNMF'

P value = 1.66e-07 (Fisher's exact test), Q value = 0.00013

Table S18.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
18P GAIN MUTATED 14 42 11
18P GAIN WILD-TYPE 129 87 114

Figure S18.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19p gain mutation analysis' versus 'CN_CNMF'

P value = 1.86e-06 (Fisher's exact test), Q value = 0.0014

Table S19.  Gene #34: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
19P GAIN MUTATED 6 28 6
19P GAIN WILD-TYPE 137 101 119

Figure S19.  Get High-res Image Gene #34: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 5.05e-08 (Fisher's exact test), Q value = 3.9e-05

Table S20.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
20P GAIN MUTATED 16 51 42
20P GAIN WILD-TYPE 127 78 83

Figure S20.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 1.6e-08 (Fisher's exact test), Q value = 1.2e-05

Table S21.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
20Q GAIN MUTATED 12 36 47
20Q GAIN WILD-TYPE 131 93 78

Figure S21.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q gain mutation analysis' versus 'CN_CNMF'

P value = 7.95e-09 (Fisher's exact test), Q value = 6.1e-06

Table S22.  Gene #39: '22q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
22Q GAIN MUTATED 12 49 36
22Q GAIN WILD-TYPE 131 80 89

Figure S22.  Get High-res Image Gene #39: '22q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 6.42e-12 (Fisher's exact test), Q value = 5e-09

Table S23.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
1P LOSS MUTATED 5 43 11
1P LOSS WILD-TYPE 138 86 114

Figure S23.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0018

Table S24.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
1P LOSS MUTATED 3 24 9
1P LOSS WILD-TYPE 95 59 60

Figure S24.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'3p loss mutation analysis' versus 'CN_CNMF'

P value = 4.11e-06 (Fisher's exact test), Q value = 0.0031

Table S25.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
3P LOSS MUTATED 35 63 63
3P LOSS WILD-TYPE 108 66 62

Figure S25.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'3p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.19e-05 (Fisher's exact test), Q value = 0.053

Table S26.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
3P LOSS MUTATED 23 41 36
3P LOSS WILD-TYPE 75 42 33

Figure S26.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4p loss mutation analysis' versus 'CN_CNMF'

P value = 7.02e-10 (Fisher's exact test), Q value = 5.4e-07

Table S27.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
4P LOSS MUTATED 35 81 48
4P LOSS WILD-TYPE 108 48 77

Figure S27.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.36e-08 (Fisher's exact test), Q value = 4.1e-05

Table S28.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
4P LOSS MUTATED 17 46 34
4P LOSS WILD-TYPE 81 37 35

Figure S28.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4q loss mutation analysis' versus 'CN_CNMF'

P value = 5.59e-11 (Fisher's exact test), Q value = 4.3e-08

Table S29.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
4Q LOSS MUTATED 28 76 39
4Q LOSS WILD-TYPE 115 53 86

Figure S29.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.99e-06 (Fisher's exact test), Q value = 0.0015

Table S30.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
4Q LOSS MUTATED 15 40 29
4Q LOSS WILD-TYPE 83 43 40

Figure S30.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'5q loss mutation analysis' versus 'CN_CNMF'

P value = 1.3e-09 (Fisher's exact test), Q value = 1e-06

Table S31.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
5Q LOSS MUTATED 24 62 60
5Q LOSS WILD-TYPE 119 67 65

Figure S31.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.65e-09 (Fisher's exact test), Q value = 5.1e-06

Table S32.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
5Q LOSS MUTATED 15 35 41
5Q LOSS WILD-TYPE 83 48 28

Figure S32.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'6p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000112 (Fisher's exact test), Q value = 0.082

Table S33.  Gene #51: '6p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
6P LOSS MUTATED 5 23 7
6P LOSS WILD-TYPE 138 106 118

Figure S33.  Get High-res Image Gene #51: '6p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 6.3e-08 (Fisher's exact test), Q value = 4.8e-05

Table S34.  Gene #55: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
8P LOSS MUTATED 23 34 60
8P LOSS WILD-TYPE 120 95 65

Figure S34.  Get High-res Image Gene #55: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 2.79e-16 (Fisher's exact test), Q value = 2.2e-13

Table S35.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
9P LOSS MUTATED 28 49 87
9P LOSS WILD-TYPE 115 80 38

Figure S35.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.04e-08 (Fisher's exact test), Q value = 2.3e-05

Table S36.  Gene #57: '9p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
9P LOSS MUTATED 20 34 45
9P LOSS WILD-TYPE 78 49 24

Figure S36.  Get High-res Image Gene #57: '9p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 5.6e-14 (Fisher's exact test), Q value = 4.4e-11

Table S37.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
9Q LOSS MUTATED 20 18 65
9Q LOSS WILD-TYPE 123 111 60

Figure S37.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.49e-05 (Fisher's exact test), Q value = 0.011

Table S38.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
9Q LOSS MUTATED 17 13 32
9Q LOSS WILD-TYPE 81 70 37

Figure S38.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'9q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.53e-05 (Fisher's exact test), Q value = 0.026

Table S39.  Gene #58: '9q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
9Q LOSS MUTATED 31 11 26
9Q LOSS WILD-TYPE 85 75 29

Figure S39.  Get High-res Image Gene #58: '9q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss mutation analysis' versus 'CN_CNMF'

P value = 9.56e-10 (Fisher's exact test), Q value = 7.4e-07

Table S40.  Gene #59: '10p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
10P LOSS MUTATED 8 44 35
10P LOSS WILD-TYPE 135 85 90

Figure S40.  Get High-res Image Gene #59: '10p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.4e-06 (Fisher's exact test), Q value = 0.0033

Table S41.  Gene #59: '10p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
10P LOSS MUTATED 8 32 15
10P LOSS WILD-TYPE 90 51 54

Figure S41.  Get High-res Image Gene #59: '10p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'10p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000296 (Fisher's exact test), Q value = 0.21

Table S42.  Gene #59: '10p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 176 118
10P LOSS MUTATED 21 25 30
10P LOSS WILD-TYPE 32 151 88

Figure S42.  Get High-res Image Gene #59: '10p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.11

Table S43.  Gene #60: '10q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 54 72
10Q LOSS MUTATED 5 21 6
10Q LOSS WILD-TYPE 23 33 66

Figure S43.  Get High-res Image Gene #60: '10q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 6.19e-12 (Fisher's exact test), Q value = 4.8e-09

Table S44.  Gene #60: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
10Q LOSS MUTATED 7 49 35
10Q LOSS WILD-TYPE 136 80 90

Figure S44.  Get High-res Image Gene #60: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.37e-05 (Fisher's exact test), Q value = 0.047

Table S45.  Gene #60: '10q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
10Q LOSS MUTATED 10 31 17
10Q LOSS WILD-TYPE 88 52 52

Figure S45.  Get High-res Image Gene #60: '10q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'11p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000175 (Fisher's exact test), Q value = 0.13

Table S46.  Gene #61: '11p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
11P LOSS MUTATED 9 20 30
11P LOSS WILD-TYPE 134 109 95

Figure S46.  Get High-res Image Gene #61: '11p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11q loss mutation analysis' versus 'CN_CNMF'

P value = 3.81e-06 (Fisher's exact test), Q value = 0.0029

Table S47.  Gene #62: '11q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
11Q LOSS MUTATED 2 20 20
11Q LOSS WILD-TYPE 141 109 105

Figure S47.  Get High-res Image Gene #62: '11q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q loss mutation analysis' versus 'CN_CNMF'

P value = 3.86e-08 (Fisher's exact test), Q value = 3e-05

Table S48.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
13Q LOSS MUTATED 31 45 70
13Q LOSS WILD-TYPE 112 84 55

Figure S48.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000231 (Fisher's exact test), Q value = 0.17

Table S49.  Gene #65: '13q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
13Q LOSS MUTATED 21 34 35
13Q LOSS WILD-TYPE 77 49 34

Figure S49.  Get High-res Image Gene #65: '13q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.074

Table S50.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 80 79 38
14Q LOSS MUTATED 2 20 23 4
14Q LOSS WILD-TYPE 58 60 56 34

Figure S50.  Get High-res Image Gene #66: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.4e-09 (Fisher's exact test), Q value = 4.9e-06

Table S51.  Gene #66: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
14Q LOSS MUTATED 5 22 22
14Q LOSS WILD-TYPE 111 64 33

Figure S51.  Get High-res Image Gene #66: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss mutation analysis' versus 'CN_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.015

Table S52.  Gene #68: '16p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
16P LOSS MUTATED 7 24 29
16P LOSS WILD-TYPE 136 105 96

Figure S52.  Get High-res Image Gene #68: '16p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'CN_CNMF'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.052

Table S53.  Gene #70: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
17P LOSS MUTATED 39 41 65
17P LOSS WILD-TYPE 104 88 60

Figure S53.  Get High-res Image Gene #70: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000123 (Fisher's exact test), Q value = 0.09

Table S54.  Gene #70: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
17P LOSS MUTATED 23 26 38
17P LOSS WILD-TYPE 75 57 31

Figure S54.  Get High-res Image Gene #70: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.22e-05 (Fisher's exact test), Q value = 0.024

Table S55.  Gene #74: '19p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 86 55
19P LOSS MUTATED 16 7 21
19P LOSS WILD-TYPE 100 79 34

Figure S55.  Get High-res Image Gene #74: '19p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 8.71e-10 (Fisher's exact test), Q value = 6.7e-07

Table S56.  Gene #78: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 129 125
21Q LOSS MUTATED 17 57 48
21Q LOSS WILD-TYPE 126 72 77

Figure S56.  Get High-res Image Gene #78: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'21q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.29e-07 (Fisher's exact test), Q value = 7e-04

Table S57.  Gene #78: '21q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 83 69
21Q LOSS MUTATED 10 32 28
21Q LOSS WILD-TYPE 88 51 41

Figure S57.  Get High-res Image Gene #78: '21q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'Xq loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000261 (Fisher's exact test), Q value = 0.19

Table S58.  Gene #80: 'Xq loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 47 49 40
XQ LOSS MUTATED 0 7 1 0
XQ LOSS WILD-TYPE 58 40 48 40

Figure S58.  Get High-res Image Gene #80: 'Xq loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 397

  • 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

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] 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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