Colon Adenocarcinoma: 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 76 arm-level results and 10 molecular subtypes across 413 patients, 79 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

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

  • 7q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

  • 13q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 20p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF'.

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

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

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

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

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 12q loss cnv correlated to 'CN_CNMF'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 76 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 79 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
20q gain 267 (65%) 146 1.24e-11
(8.67e-09) 		1.89e-13
(1.34e-10) 		9.42e-47
(6.81e-44) 		1.06e-09
(7.37e-07) 		0.0105
(1.00) 		2.27e-06
(0.00155) 		2.61e-13
(1.84e-10) 		3.58e-11
(2.5e-08) 		0.103
(1.00) 		0.429
(1.00)
18p loss 209 (51%) 204 2.81e-13
(1.99e-10) 		2.92e-10
(2.03e-07) 		2.44e-46
(1.76e-43) 		5.15e-13
(3.63e-10) 		0.00191
(1.00) 		3.18e-05
(0.0211) 		6.98e-15
(4.97e-12) 		5.87e-09
(4.07e-06) 		0.251
(1.00) 		0.497
(1.00)
18q loss 225 (54%) 188 1.92e-12
(1.35e-09) 		3.83e-10
(2.66e-07) 		8.88e-46
(6.4e-43) 		3.62e-15
(2.57e-12) 		0.0238
(1.00) 		0.000181
(0.118) 		4.47e-14
(3.17e-11) 		1.36e-08
(9.43e-06) 		0.0612
(1.00) 		0.499
(1.00)
13q gain 211 (51%) 202 2.95e-06
(0.002) 		3.32e-05
(0.022) 		2.95e-33
(2.13e-30) 		0.000267
(0.173) 		0.246
(1.00) 		0.0146
(1.00) 		1.71e-06
(0.00117) 		7.16e-05
(0.0472) 		0.045
(1.00) 		0.466
(1.00)
14q loss 94 (23%) 319 2.09e-07
(0.000144) 		1.18e-06
(0.000812) 		1.58e-22
(1.13e-19) 		1.2e-06
(0.00082) 		0.000717
(0.457) 		0.00102
(0.646) 		1.5e-06
(0.00102) 		8.78e-05
(0.0576) 		0.532
(1.00) 		0.194
(1.00)
17p loss 164 (40%) 249 1.75e-05
(0.0117) 		3.05e-05
(0.0203) 		4.44e-23
(3.19e-20) 		2.31e-07
(0.000159) 		0.134
(1.00) 		0.0207
(1.00) 		2.65e-06
(0.0018) 		8.2e-06
(0.00552) 		0.147
(1.00) 		0.0464
(1.00)
7p gain 200 (48%) 213 0.00124
(0.775) 		0.00375
(1.00) 		1.92e-15
(1.37e-12) 		9.14e-05
(0.0599) 		0.197
(1.00) 		0.00476
(1.00) 		1.09e-07
(7.5e-05) 		2.85e-05
(0.019) 		0.425
(1.00) 		0.958
(1.00)
20p gain 188 (46%) 225 0.00142
(0.883) 		1.47e-06
(0.00101) 		4.29e-20
(3.07e-17) 		0.0127
(1.00) 		0.114
(1.00) 		0.0168
(1.00) 		3.35e-05
(0.0222) 		0.000197
(0.128) 		0.174
(1.00) 		0.0758
(1.00)
7q gain 175 (42%) 238 0.00476
(1.00) 		0.0236
(1.00) 		7.05e-11
(4.92e-08) 		0.00278
(1.00) 		0.537
(1.00) 		0.0233
(1.00) 		3.01e-06
(0.00204) 		0.000186
(0.121) 		0.474
(1.00) 		0.752
(1.00)
15q loss 99 (24%) 314 0.0193
(1.00) 		0.0122
(1.00) 		9.29e-22
(6.66e-19) 		0.00458
(1.00) 		0.134
(1.00) 		0.314
(1.00) 		4.07e-05
(0.0269) 		7.35e-05
(0.0483) 		0.488
(1.00) 		0.0435
(1.00)
8p loss 93 (23%) 320 0.000317
(0.205) 		0.00156
(0.972) 		7.76e-17
(5.55e-14) 		0.00104
(0.653) 		0.499
(1.00) 		0.0139
(1.00) 		0.141
(1.00) 		0.0665
(1.00) 		0.2
(1.00) 		0.356
(1.00)
11p loss 22 (5%) 391 0.47
(1.00) 		0.0674
(1.00) 		8.34e-05
(0.0548) 		0.000281
(0.182) 		0.806
(1.00) 		0.6
(1.00) 		0.0489
(1.00) 		0.0184
(1.00) 		0.0401
(1.00) 		0.162
(1.00)
11q loss 27 (7%) 386 0.372
(1.00) 		0.0387
(1.00) 		7.92e-06
(0.00534) 		9.61e-06
(0.00645) 		0.917
(1.00) 		0.687
(1.00) 		0.207
(1.00) 		0.129
(1.00) 		0.358
(1.00) 		0.202
(1.00)
2p gain 40 (10%) 373 0.156
(1.00) 		0.0378
(1.00) 		0.00409
(1.00) 		0.046
(1.00) 		0.182
(1.00) 		0.373
(1.00) 		0.000386
(0.249) 		0.0199
(1.00) 		0.508
(1.00) 		0.355
(1.00)
2q gain 39 (9%) 374 0.0985
(1.00) 		0.0352
(1.00) 		0.000173
(0.113) 		0.00235
(1.00) 		0.122
(1.00) 		0.466
(1.00) 		0.00109
(0.686) 		0.0384
(1.00) 		0.529
(1.00) 		0.405
(1.00)
8p gain 80 (19%) 333 0.925
(1.00) 		0.785
(1.00) 		9.22e-06
(0.00619) 		0.0562
(1.00) 		0.184
(1.00) 		0.223
(1.00) 		0.175
(1.00) 		0.0327
(1.00) 		0.615
(1.00) 		0.571
(1.00)
8q gain 162 (39%) 251 0.751
(1.00) 		0.612
(1.00) 		9.39e-12
(6.6e-09) 		0.000666
(0.425) 		0.648
(1.00) 		0.215
(1.00) 		0.0072
(1.00) 		0.127
(1.00) 		0.0986
(1.00) 		0.154
(1.00)
11p gain 18 (4%) 395 0.151
(1.00) 		0.00135
(0.847) 		0.000314
(0.203) 		0.000575
(0.369) 		0.496
(1.00) 		0.596
(1.00) 		0.871
(1.00) 		0.889
(1.00) 		0.634
(1.00) 		0.882
(1.00)
11q gain 22 (5%) 391 0.0301
(1.00) 		0.00227
(1.00) 		3.72e-06
(0.00251) 		0.00141
(0.881) 		0.121
(1.00) 		0.517
(1.00) 		0.151
(1.00) 		0.22
(1.00) 		0.386
(1.00) 		0.693
(1.00)
16p gain 67 (16%) 346 0.013
(1.00) 		0.0038
(1.00) 		1.08e-14
(7.69e-12) 		0.138
(1.00) 		0.163
(1.00) 		0.0256
(1.00) 		0.051
(1.00) 		0.18
(1.00) 		0.126
(1.00) 		0.0474
(1.00)
16q gain 66 (16%) 347 0.0139
(1.00) 		0.00644
(1.00) 		1.44e-16
(1.03e-13) 		0.136
(1.00) 		0.132
(1.00) 		0.0256
(1.00) 		0.051
(1.00) 		0.18
(1.00) 		0.314
(1.00) 		0.232
(1.00)
17q gain 48 (12%) 365 0.0929
(1.00) 		0.0202
(1.00) 		0.000913
(0.578) 		0.00739
(1.00) 		0.233
(1.00) 		0.13
(1.00) 		1.16e-05
(0.00777) 		0.015
(1.00) 		0.0581
(1.00) 		0.753
(1.00)
1p loss 51 (12%) 362 0.00489
(1.00) 		0.000765
(0.487) 		7.09e-08
(4.9e-05) 		0.00329
(1.00) 		0.518
(1.00) 		0.611
(1.00) 		0.0984
(1.00) 		0.286
(1.00) 		0.18
(1.00) 		0.274
(1.00)
4p loss 84 (20%) 329 0.00469
(1.00) 		0.0521
(1.00) 		1.05e-11
(7.38e-09) 		0.00299
(1.00) 		0.24
(1.00) 		0.309
(1.00) 		0.000754
(0.481) 		0.000599
(0.384) 		0.083
(1.00) 		0.29
(1.00)
4q loss 68 (16%) 345 0.00736
(1.00) 		0.0381
(1.00) 		2.26e-10
(1.57e-07) 		0.00223
(1.00) 		0.372
(1.00) 		0.334
(1.00) 		0.00348
(1.00) 		0.0158
(1.00) 		0.00266
(1.00) 		0.0359
(1.00)
5q loss 38 (9%) 375 0.126
(1.00) 		0.0563
(1.00) 		1.11e-05
(0.00746) 		0.293
(1.00) 		0.537
(1.00) 		0.234
(1.00) 		0.00763
(1.00) 		0.105
(1.00) 		0.551
(1.00) 		0.48
(1.00)
9p loss 27 (7%) 386 0.875
(1.00) 		0.11
(1.00) 		4.4e-05
(0.0291) 		0.0746
(1.00) 		0.429
(1.00) 		0.134
(1.00) 		0.0424
(1.00) 		0.105
(1.00) 		0.53
(1.00) 		0.744
(1.00)
9q loss 26 (6%) 387 0.348
(1.00) 		0.124
(1.00) 		2.55e-06
(0.00173) 		0.000619
(0.396) 		0.429
(1.00) 		0.134
(1.00) 		0.000898
(0.57) 		0.036
(1.00) 		0.114
(1.00) 		0.675
(1.00)
12p loss 21 (5%) 392 0.0909
(1.00) 		0.11
(1.00) 		7.1e-05
(0.0469) 		0.207
(1.00) 		0.672
(1.00) 		0.947
(1.00) 		0.0802
(1.00) 		0.0817
(1.00) 		0.72
(1.00) 		0.208
(1.00)
12q loss 20 (5%) 393 0.17
(1.00) 		0.124
(1.00) 		0.000101
(0.0663) 		0.153
(1.00) 		0.685
(1.00) 		0.913
(1.00) 		0.0161
(1.00) 		0.04
(1.00) 		0.411
(1.00) 		0.362
(1.00)
20p loss 33 (8%) 380 0.0132
(1.00) 		0.00713
(1.00) 		8.88e-08
(6.13e-05) 		0.0514
(1.00) 		0.839
(1.00) 		0.63
(1.00) 		0.353
(1.00) 		0.308
(1.00) 		0.906
(1.00) 		0.53
(1.00)
21q loss 71 (17%) 342 0.00266
(1.00) 		0.00486
(1.00) 		2.6e-06
(0.00176) 		0.258
(1.00) 		0.848
(1.00) 		0.646
(1.00) 		0.122
(1.00) 		0.342
(1.00) 		0.0731
(1.00) 		0.608
(1.00)
22q loss 81 (20%) 332 0.000916
(0.579) 		0.000455
(0.293) 		1.06e-11
(7.44e-09) 		0.0894
(1.00) 		0.07
(1.00) 		0.0205
(1.00) 		0.00972
(1.00) 		0.0011
(0.691) 		0.624
(1.00) 		0.123
(1.00)
1p gain 11 (3%) 402 0.576
(1.00) 		0.909
(1.00) 		0.0656
(1.00) 		0.209
(1.00) 		0.425
(1.00) 		0.683
(1.00) 		0.46
(1.00) 		1
(1.00)
1q gain 47 (11%) 366 0.0531
(1.00) 		0.732
(1.00) 		0.0788
(1.00) 		0.307
(1.00) 		0.612
(1.00) 		0.125
(1.00) 		0.12
(1.00) 		0.299
(1.00) 		0.437
(1.00) 		0.837
(1.00)
3p gain 20 (5%) 393 0.397
(1.00) 		0.382
(1.00) 		0.071
(1.00) 		0.367
(1.00) 		0.701
(1.00) 		0.137
(1.00) 		0.974
(1.00) 		0.676
(1.00) 		0.626
(1.00) 		0.184
(1.00)
3q gain 30 (7%) 383 0.482
(1.00) 		0.0458
(1.00) 		0.000969
(0.611) 		0.22
(1.00) 		0.463
(1.00) 		0.354
(1.00) 		0.415
(1.00) 		0.635
(1.00) 		0.357
(1.00) 		0.824
(1.00)
4p gain 3 (1%) 410 0.746
(1.00) 		0.473
(1.00) 		0.271
(1.00) 		0.341
(1.00) 		0.208
(1.00) 		0.0334
(1.00)
4q gain 5 (1%) 408 0.842
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.579
(1.00) 		0.335
(1.00)
5p gain 39 (9%) 374 0.29
(1.00) 		0.0418
(1.00) 		0.00223
(1.00) 		0.0236
(1.00) 		0.529
(1.00) 		0.922
(1.00) 		0.618
(1.00) 		1
(1.00) 		0.685
(1.00) 		0.53
(1.00)
5q gain 21 (5%) 392 0.657
(1.00) 		0.564
(1.00) 		0.0391
(1.00) 		0.188
(1.00) 		0.566
(1.00) 		0.65
(1.00) 		0.749
(1.00) 		0.578
(1.00) 		1
(1.00) 		0.948
(1.00)
6p gain 50 (12%) 363 0.17
(1.00) 		0.0116
(1.00) 		0.0267
(1.00) 		0.675
(1.00) 		0.559
(1.00) 		0.684
(1.00) 		0.0367
(1.00) 		0.268
(1.00) 		0.513
(1.00) 		0.246
(1.00)
6q gain 45 (11%) 368 0.312
(1.00) 		0.0248
(1.00) 		0.0317
(1.00) 		0.352
(1.00) 		0.717
(1.00) 		0.623
(1.00) 		0.156
(1.00) 		0.621
(1.00) 		0.441
(1.00) 		0.309
(1.00)
9p gain 46 (11%) 367 0.0335
(1.00) 		0.213
(1.00) 		0.28
(1.00) 		0.433
(1.00) 		0.232
(1.00) 		0.186
(1.00) 		0.879
(1.00) 		0.76
(1.00) 		0.767
(1.00) 		0.763
(1.00)
9q gain 39 (9%) 374 0.0915
(1.00) 		0.0775
(1.00) 		0.0641
(1.00) 		0.113
(1.00) 		0.0184
(1.00) 		0.027
(1.00) 		0.362
(1.00) 		0.659
(1.00) 		0.0589
(1.00) 		0.635
(1.00)
10p gain 18 (4%) 395 0.65
(1.00) 		0.625
(1.00) 		0.104
(1.00) 		0.0477
(1.00) 		0.845
(1.00) 		0.705
(1.00) 		0.904
(1.00) 		0.466
(1.00) 		0.761
(1.00) 		0.941
(1.00)
10q gain 7 (2%) 406 0.114
(1.00) 		0.042
(1.00) 		0.679
(1.00) 		0.746
(1.00) 		0.933
(1.00) 		0.219
(1.00) 		0.202
(1.00) 		0.151
(1.00)
12p gain 66 (16%) 347 0.248
(1.00) 		0.71
(1.00) 		0.00442
(1.00) 		0.0146
(1.00) 		0.205
(1.00) 		0.801
(1.00) 		0.361
(1.00) 		0.682
(1.00) 		0.069
(1.00) 		0.21
(1.00)
12q gain 60 (15%) 353 0.248
(1.00) 		0.542
(1.00) 		0.00181
(1.00) 		0.00291
(1.00) 		0.142
(1.00) 		0.751
(1.00) 		0.27
(1.00) 		0.691
(1.00) 		0.0121
(1.00) 		0.268
(1.00)
14q gain 15 (4%) 398 0.485
(1.00) 		0.443
(1.00) 		0.0566
(1.00) 		0.276
(1.00) 		0.189
(1.00) 		0.438
(1.00) 		0.145
(1.00) 		0.127
(1.00) 		1
(1.00) 		0.805
(1.00)
15q gain 5 (1%) 408 0.0732
(1.00) 		0.683
(1.00) 		0.121
(1.00) 		0.0592
(1.00) 		0.783
(1.00) 		0.481
(1.00) 		0.473
(1.00) 		0.427
(1.00)
17p gain 9 (2%) 404 0.618
(1.00) 		0.893
(1.00) 		0.202
(1.00) 		0.086
(1.00) 		0.0316
(1.00) 		0.225
(1.00) 		0.737
(1.00) 		0.891
(1.00)
18p gain 15 (4%) 398 0.118
(1.00) 		0.637
(1.00) 		0.00548
(1.00) 		0.0139
(1.00) 		0.476
(1.00) 		0.618
(1.00) 		0.171
(1.00) 		0.0581
(1.00) 		0.144
(1.00) 		0.388
(1.00)
18q gain 9 (2%) 404 0.0232
(1.00) 		0.0303
(1.00) 		0.128
(1.00) 		0.0697
(1.00) 		0.142
(1.00) 		0.267
(1.00) 		0.274
(1.00) 		0.327
(1.00)
19p gain 34 (8%) 379 0.142
(1.00) 		0.24
(1.00) 		0.00554
(1.00) 		0.0512
(1.00) 		0.747
(1.00) 		0.165
(1.00) 		0.321
(1.00) 		0.481
(1.00) 		0.588
(1.00) 		0.573
(1.00)
19q gain 41 (10%) 372 0.0718
(1.00) 		0.104
(1.00) 		0.437
(1.00) 		0.0666
(1.00) 		0.146
(1.00) 		0.0493
(1.00) 		0.145
(1.00) 		0.297
(1.00) 		0.924
(1.00) 		0.942
(1.00)
21q gain 11 (3%) 402 0.194
(1.00) 		0.195
(1.00) 		0.0858
(1.00) 		0.339
(1.00) 		0.0717
(1.00) 		0.523
(1.00) 		0.282
(1.00) 		0.73
(1.00) 		0.704
(1.00) 		0.684
(1.00)
Xq gain 12 (3%) 401 0.487
(1.00) 		0.777
(1.00) 		0.0331
(1.00) 		0.631
(1.00) 		0.111
(1.00) 		0.232
(1.00) 		0.446
(1.00) 		0.765
(1.00) 		0.352
(1.00) 		0.41
(1.00)
1q loss 18 (4%) 395 0.452
(1.00) 		0.135
(1.00) 		0.0103
(1.00) 		0.269
(1.00) 		0.472
(1.00) 		0.687
(1.00) 		0.151
(1.00) 		0.196
(1.00) 		0.941
(1.00) 		0.44
(1.00)
2p loss 4 (1%) 409 0.572
(1.00) 		0.111
(1.00) 		0.433
(1.00) 		0.662
(1.00) 		0.132
(1.00)
2q loss 6 (1%) 407 1
(1.00) 		0.156
(1.00) 		0.601
(1.00) 		0.0966
(1.00) 		0.224
(1.00) 		0.175
(1.00) 		0.0588
(1.00)
3p loss 27 (7%) 386 0.253
(1.00) 		0.104
(1.00) 		0.00251
(1.00) 		0.252
(1.00) 		0.551
(1.00) 		1
(1.00) 		0.458
(1.00) 		0.556
(1.00) 		0.212
(1.00) 		0.143
(1.00)
3q loss 12 (3%) 401 0.415
(1.00) 		0.564
(1.00) 		0.224
(1.00) 		1
(1.00) 		0.172
(1.00) 		0.323
(1.00) 		0.267
(1.00) 		0.683
(1.00) 		0.423
(1.00) 		0.822
(1.00)
5p loss 25 (6%) 388 0.875
(1.00) 		0.172
(1.00) 		0.00176
(1.00) 		0.102
(1.00) 		0.642
(1.00) 		0.625
(1.00) 		0.126
(1.00) 		0.416
(1.00) 		0.841
(1.00) 		0.907
(1.00)
6p loss 12 (3%) 401 0.54
(1.00) 		0.251
(1.00) 		0.00285
(1.00) 		1
(1.00) 		0.719
(1.00) 		1
(1.00) 		0.666
(1.00) 		0.45
(1.00) 		0.642
(1.00) 		0.624
(1.00)
6q loss 21 (5%) 392 0.943
(1.00) 		0.732
(1.00) 		0.0743
(1.00) 		0.697
(1.00) 		0.235
(1.00) 		0.617
(1.00) 		1
(1.00) 		0.845
(1.00) 		0.864
(1.00) 		1
(1.00)
8q loss 8 (2%) 405 0.403
(1.00) 		0.777
(1.00) 		0.00966
(1.00) 		0.852
(1.00) 		0.213
(1.00) 		0.686
(1.00) 		1
(1.00) 		1
(1.00) 		0.197
(1.00) 		0.436
(1.00)
10p loss 22 (5%) 391 0.67
(1.00) 		0.672
(1.00) 		0.000828
(0.526) 		0.285
(1.00) 		0.279
(1.00) 		0.975
(1.00) 		0.518
(1.00) 		0.352
(1.00) 		0.24
(1.00) 		0.681
(1.00)
10q loss 24 (6%) 389 0.606
(1.00) 		0.71
(1.00) 		0.000526
(0.338) 		0.152
(1.00) 		0.279
(1.00) 		1
(1.00) 		0.295
(1.00) 		0.04
(1.00) 		0.697
(1.00) 		0.393
(1.00)
13q loss 6 (1%) 407 0.0209
(1.00) 		0.232
(1.00) 		0.0359
(1.00) 		0.0163
(1.00) 		0.425
(1.00) 		0.464
(1.00) 		0.869
(1.00) 		0.723
(1.00)
16p loss 9 (2%) 404 0.251
(1.00) 		0.554
(1.00) 		0.305
(1.00) 		0.0298
(1.00) 		0.734
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.711
(1.00) 		1
(1.00)
16q loss 7 (2%) 406 0.464
(1.00) 		1
(1.00) 		0.228
(1.00) 		0.175
(1.00) 		0.17
(1.00)
17q loss 32 (8%) 381 0.113
(1.00) 		0.225
(1.00) 		0.00216
(1.00) 		0.22
(1.00) 		0.731
(1.00) 		0.366
(1.00) 		0.0813
(1.00) 		0.109
(1.00) 		0.322
(1.00) 		0.291
(1.00)
19p loss 14 (3%) 399 1
(1.00) 		0.319
(1.00) 		0.00275
(1.00) 		0.0957
(1.00) 		0.195
(1.00) 		0.134
(1.00) 		0.00708
(1.00) 		0.0789
(1.00) 		0.693
(1.00) 		0.0876
(1.00)
19q loss 13 (3%) 400 0.922
(1.00) 		0.38
(1.00) 		0.0115
(1.00) 		0.0957
(1.00) 		0.679
(1.00) 		0.188
(1.00) 		0.00708
(1.00) 		0.0789
(1.00) 		0.57
(1.00) 		0.0611
(1.00)
Xq loss 5 (1%) 408 0.842
(1.00) 		1
(1.00) 		0.0726
(1.00) 		0.682
(1.00) 		0.851
(1.00) 		0.14
(1.00)
'2p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000386 (Fisher's exact test), Q value = 0.25

Table S1.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
2P GAIN MUTATED 1 15 5 1
2P GAIN WILD-TYPE 30 44 42 53

Figure S1.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'2q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000173 (Fisher's exact test), Q value = 0.11

Table S2.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
2Q GAIN MUTATED 28 6 3 2
2Q GAIN WILD-TYPE 142 181 29 22

Figure S2.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 1.92e-15 (Fisher's exact test), Q value = 1.4e-12

Table S3.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
7P GAIN MUTATED 112 49 23 16
7P GAIN WILD-TYPE 58 138 9 8

Figure S3.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.14e-05 (Fisher's exact test), Q value = 0.06

Table S4.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
7P GAIN MUTATED 71 38 23
7P GAIN WILD-TYPE 34 48 40

Figure S4.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.09e-07 (Fisher's exact test), Q value = 7.5e-05

Table S5.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
7P GAIN MUTATED 19 43 20 11
7P GAIN WILD-TYPE 12 16 27 43

Figure S5.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.85e-05 (Fisher's exact test), Q value = 0.019

Table S6.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
7P GAIN MUTATED 13 43 37
7P GAIN WILD-TYPE 36 19 43

Figure S6.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 7.05e-11 (Fisher's exact test), Q value = 4.9e-08

Table S7.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
7Q GAIN MUTATED 96 45 21 13
7Q GAIN WILD-TYPE 74 142 11 11

Figure S7.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.01e-06 (Fisher's exact test), Q value = 0.002

Table S8.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
7Q GAIN MUTATED 16 39 18 10
7Q GAIN WILD-TYPE 15 20 29 44

Figure S8.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000186 (Fisher's exact test), Q value = 0.12

Table S9.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
7Q GAIN MUTATED 12 39 32
7Q GAIN WILD-TYPE 37 23 48

Figure S9.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain mutation analysis' versus 'CN_CNMF'

P value = 9.22e-06 (Fisher's exact test), Q value = 0.0062

Table S10.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
8P GAIN MUTATED 23 32 12 13
8P GAIN WILD-TYPE 147 155 20 11

Figure S10.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8q gain mutation analysis' versus 'CN_CNMF'

P value = 9.39e-12 (Fisher's exact test), Q value = 6.6e-09

Table S11.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
8Q GAIN MUTATED 78 45 17 22
8Q GAIN WILD-TYPE 92 142 15 2

Figure S11.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.2

Table S12.  Gene #21: '11p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
11P GAIN MUTATED 16 1 1 0
11P GAIN WILD-TYPE 154 186 31 24

Figure S12.  Get High-res Image Gene #21: '11p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11q gain mutation analysis' versus 'CN_CNMF'

P value = 3.72e-06 (Fisher's exact test), Q value = 0.0025

Table S13.  Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
11Q GAIN MUTATED 19 0 2 1
11Q GAIN WILD-TYPE 151 187 30 23

Figure S13.  Get High-res Image Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q gain mutation analysis' versus 'MRNA_CNMF'

P value = 2.95e-06 (Fisher's exact test), Q value = 0.002

Table S14.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
13Q GAIN MUTATED 10 46 7 14
13Q GAIN WILD-TYPE 21 16 23 9

Figure S14.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'13q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.32e-05 (Fisher's exact test), Q value = 0.022

Table S15.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
13Q GAIN MUTATED 34 11 32
13Q GAIN WILD-TYPE 22 33 14

Figure S15.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'13q gain mutation analysis' versus 'CN_CNMF'

P value = 2.95e-33 (Fisher's exact test), Q value = 2.1e-30

Table S16.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
13Q GAIN MUTATED 143 42 11 15
13Q GAIN WILD-TYPE 27 145 21 9

Figure S16.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.17

Table S17.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
13Q GAIN MUTATED 70 35 26
13Q GAIN WILD-TYPE 35 51 37

Figure S17.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'13q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.71e-06 (Fisher's exact test), Q value = 0.0012

Table S18.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
13Q GAIN MUTATED 19 40 20 11
13Q GAIN WILD-TYPE 12 19 27 43

Figure S18.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'13q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.16e-05 (Fisher's exact test), Q value = 0.047

Table S19.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
13Q GAIN MUTATED 11 39 40
13Q GAIN WILD-TYPE 38 23 40

Figure S19.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain mutation analysis' versus 'CN_CNMF'

P value = 1.08e-14 (Fisher's exact test), Q value = 7.7e-12

Table S20.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
16P GAIN MUTATED 56 5 5 1
16P GAIN WILD-TYPE 114 182 27 23

Figure S20.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'16q gain mutation analysis' versus 'CN_CNMF'

P value = 1.44e-16 (Fisher's exact test), Q value = 1e-13

Table S21.  Gene #29: '16q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
16Q GAIN MUTATED 58 4 3 1
16Q GAIN WILD-TYPE 112 183 29 23

Figure S21.  Get High-res Image Gene #29: '16q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0078

Table S22.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
17Q GAIN MUTATED 4 16 0 2
17Q GAIN WILD-TYPE 27 43 47 52

Figure S22.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.001

Table S23.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
20P GAIN MUTATED 37 8 28
20P GAIN WILD-TYPE 19 36 18

Figure S23.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 4.29e-20 (Fisher's exact test), Q value = 3.1e-17

Table S24.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
20P GAIN MUTATED 98 44 31 15
20P GAIN WILD-TYPE 72 143 1 9

Figure S24.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.35e-05 (Fisher's exact test), Q value = 0.022

Table S25.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
20P GAIN MUTATED 15 31 20 7
20P GAIN WILD-TYPE 16 28 27 47

Figure S25.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000197 (Fisher's exact test), Q value = 0.13

Table S26.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
20P GAIN MUTATED 7 29 37
20P GAIN WILD-TYPE 42 33 43

Figure S26.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.24e-11 (Fisher's exact test), Q value = 8.7e-09

Table S27.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
20Q GAIN MUTATED 10 58 12 19
20Q GAIN WILD-TYPE 21 4 18 4

Figure S27.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'20q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.89e-13 (Fisher's exact test), Q value = 1.3e-10

Table S28.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
20Q GAIN MUTATED 48 10 41
20Q GAIN WILD-TYPE 8 34 5

Figure S28.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 9.42e-47 (Fisher's exact test), Q value = 6.8e-44

Table S29.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
20Q GAIN MUTATED 160 54 32 21
20Q GAIN WILD-TYPE 10 133 0 3

Figure S29.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.06e-09 (Fisher's exact test), Q value = 7.4e-07

Table S30.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
20Q GAIN MUTATED 89 37 33
20Q GAIN WILD-TYPE 16 49 30

Figure S30.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.27e-06 (Fisher's exact test), Q value = 0.0015

Table S31.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 25 140 48
20Q GAIN MUTATED 19 11 96 40
20Q GAIN WILD-TYPE 32 14 44 8

Figure S31.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.61e-13 (Fisher's exact test), Q value = 1.8e-10

Table S32.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
20Q GAIN MUTATED 19 53 30 11
20Q GAIN WILD-TYPE 12 6 17 43

Figure S32.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.58e-11 (Fisher's exact test), Q value = 2.5e-08

Table S33.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
20Q GAIN MUTATED 9 49 55
20Q GAIN WILD-TYPE 40 13 25

Figure S33.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 7.09e-08 (Fisher's exact test), Q value = 4.9e-05

Table S34.  Gene #40: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
1P LOSS MUTATED 36 6 8 1
1P LOSS WILD-TYPE 134 181 24 23

Figure S34.  Get High-res Image Gene #40: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4p loss mutation analysis' versus 'CN_CNMF'

P value = 1.05e-11 (Fisher's exact test), Q value = 7.4e-09

Table S35.  Gene #46: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
4P LOSS MUTATED 56 11 13 4
4P LOSS WILD-TYPE 114 176 19 20

Figure S35.  Get High-res Image Gene #46: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4q loss mutation analysis' versus 'CN_CNMF'

P value = 2.26e-10 (Fisher's exact test), Q value = 1.6e-07

Table S36.  Gene #47: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
4Q LOSS MUTATED 49 8 9 2
4Q LOSS WILD-TYPE 121 179 23 22

Figure S36.  Get High-res Image Gene #47: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5q loss mutation analysis' versus 'CN_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0075

Table S37.  Gene #49: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
5Q LOSS MUTATED 27 4 3 4
5Q LOSS WILD-TYPE 143 183 29 20

Figure S37.  Get High-res Image Gene #49: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000317 (Fisher's exact test), Q value = 0.2

Table S38.  Gene #52: '8p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
8P LOSS MUTATED 2 24 3 9
8P LOSS WILD-TYPE 29 38 27 14

Figure S38.  Get High-res Image Gene #52: '8p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 7.76e-17 (Fisher's exact test), Q value = 5.5e-14

Table S39.  Gene #52: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
8P LOSS MUTATED 73 11 3 6
8P LOSS WILD-TYPE 97 176 29 18

Figure S39.  Get High-res Image Gene #52: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 4.4e-05 (Fisher's exact test), Q value = 0.029

Table S40.  Gene #54: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
9P LOSS MUTATED 19 2 5 1
9P LOSS WILD-TYPE 151 185 27 23

Figure S40.  Get High-res Image Gene #54: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 2.55e-06 (Fisher's exact test), Q value = 0.0017

Table S41.  Gene #55: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
9Q LOSS MUTATED 21 1 4 0
9Q LOSS WILD-TYPE 149 186 28 24

Figure S41.  Get High-res Image Gene #55: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p loss mutation analysis' versus 'CN_CNMF'

P value = 8.34e-05 (Fisher's exact test), Q value = 0.055

Table S42.  Gene #58: '11p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
11P LOSS MUTATED 14 2 6 0
11P LOSS WILD-TYPE 156 185 26 24

Figure S42.  Get High-res Image Gene #58: '11p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.18

Table S43.  Gene #58: '11p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
11P LOSS MUTATED 10 0 0
11P LOSS WILD-TYPE 95 86 63

Figure S43.  Get High-res Image Gene #58: '11p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'11q loss mutation analysis' versus 'CN_CNMF'

P value = 7.92e-06 (Fisher's exact test), Q value = 0.0053

Table S44.  Gene #59: '11q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
11Q LOSS MUTATED 19 2 6 0
11Q LOSS WILD-TYPE 151 185 26 24

Figure S44.  Get High-res Image Gene #59: '11q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.61e-06 (Fisher's exact test), Q value = 0.0064

Table S45.  Gene #59: '11q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
11Q LOSS MUTATED 14 0 0
11Q LOSS WILD-TYPE 91 86 63

Figure S45.  Get High-res Image Gene #59: '11q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'12p loss mutation analysis' versus 'CN_CNMF'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.047

Table S46.  Gene #60: '12p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
12P LOSS MUTATED 17 1 3 0
12P LOSS WILD-TYPE 153 186 29 24

Figure S46.  Get High-res Image Gene #60: '12p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.066

Table S47.  Gene #61: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
12Q LOSS MUTATED 15 1 4 0
12Q LOSS WILD-TYPE 155 186 28 24

Figure S47.  Get High-res Image Gene #61: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q loss mutation analysis' versus 'MRNA_CNMF'

P value = 2.09e-07 (Fisher's exact test), Q value = 0.00014

Table S48.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
14Q LOSS MUTATED 2 30 1 9
14Q LOSS WILD-TYPE 29 32 29 14

Figure S48.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'14q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.18e-06 (Fisher's exact test), Q value = 0.00081

Table S49.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
14Q LOSS MUTATED 21 1 20
14Q LOSS WILD-TYPE 35 43 26

Figure S49.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'14q loss mutation analysis' versus 'CN_CNMF'

P value = 1.58e-22 (Fisher's exact test), Q value = 1.1e-19

Table S50.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
14Q LOSS MUTATED 78 8 8 0
14Q LOSS WILD-TYPE 92 179 24 24

Figure S50.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.2e-06 (Fisher's exact test), Q value = 0.00082

Table S51.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
14Q LOSS MUTATED 36 6 6
14Q LOSS WILD-TYPE 69 80 57

Figure S51.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.5e-06 (Fisher's exact test), Q value = 0.001

Table S52.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
14Q LOSS MUTATED 8 23 6 1
14Q LOSS WILD-TYPE 23 36 41 53

Figure S52.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.78e-05 (Fisher's exact test), Q value = 0.058

Table S53.  Gene #63: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
14Q LOSS MUTATED 1 20 17
14Q LOSS WILD-TYPE 48 42 63

Figure S53.  Get High-res Image Gene #63: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 9.29e-22 (Fisher's exact test), Q value = 6.7e-19

Table S54.  Gene #64: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
15Q LOSS MUTATED 70 9 19 1
15Q LOSS WILD-TYPE 100 178 13 23

Figure S54.  Get High-res Image Gene #64: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'15q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.07e-05 (Fisher's exact test), Q value = 0.027

Table S55.  Gene #64: '15q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
15Q LOSS MUTATED 8 20 10 1
15Q LOSS WILD-TYPE 23 39 37 53

Figure S55.  Get High-res Image Gene #64: '15q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'15q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.35e-05 (Fisher's exact test), Q value = 0.048

Table S56.  Gene #64: '15q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
15Q LOSS MUTATED 1 20 18
15Q LOSS WILD-TYPE 48 42 62

Figure S56.  Get High-res Image Gene #64: '15q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss mutation analysis' versus 'MRNA_CNMF'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.012

Table S57.  Gene #67: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
17P LOSS MUTATED 7 38 5 13
17P LOSS WILD-TYPE 24 24 25 10

Figure S57.  Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'17p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.02

Table S58.  Gene #67: '17p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
17P LOSS MUTATED 29 7 27
17P LOSS WILD-TYPE 27 37 19

Figure S58.  Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'17p loss mutation analysis' versus 'CN_CNMF'

P value = 4.44e-23 (Fisher's exact test), Q value = 3.2e-20

Table S59.  Gene #67: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
17P LOSS MUTATED 109 26 16 13
17P LOSS WILD-TYPE 61 161 16 11

Figure S59.  Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.31e-07 (Fisher's exact test), Q value = 0.00016

Table S60.  Gene #67: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
17P LOSS MUTATED 61 19 17
17P LOSS WILD-TYPE 44 67 46

Figure S60.  Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'17p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.65e-06 (Fisher's exact test), Q value = 0.0018

Table S61.  Gene #67: '17p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
17P LOSS MUTATED 14 36 14 8
17P LOSS WILD-TYPE 17 23 33 46

Figure S61.  Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'17p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.2e-06 (Fisher's exact test), Q value = 0.0055

Table S62.  Gene #67: '17p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
17P LOSS MUTATED 7 36 29
17P LOSS WILD-TYPE 42 26 51

Figure S62.  Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss mutation analysis' versus 'MRNA_CNMF'

P value = 2.81e-13 (Fisher's exact test), Q value = 2e-10

Table S63.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
18P LOSS MUTATED 5 51 5 16
18P LOSS WILD-TYPE 26 11 25 7

Figure S63.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'18p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.92e-10 (Fisher's exact test), Q value = 2e-07

Table S64.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
18P LOSS MUTATED 35 6 36
18P LOSS WILD-TYPE 21 38 10

Figure S64.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 2.44e-46 (Fisher's exact test), Q value = 1.8e-43

Table S65.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
18P LOSS MUTATED 143 26 27 13
18P LOSS WILD-TYPE 27 161 5 11

Figure S65.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.15e-13 (Fisher's exact test), Q value = 3.6e-10

Table S66.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
18P LOSS MUTATED 81 24 21
18P LOSS WILD-TYPE 24 62 42

Figure S66.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18p loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 3.18e-05 (Fisher's exact test), Q value = 0.021

Table S67.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 25 140 48
18P LOSS MUTATED 13 7 84 26
18P LOSS WILD-TYPE 38 18 56 22

Figure S67.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'18p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.98e-15 (Fisher's exact test), Q value = 5e-12

Table S68.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
18P LOSS MUTATED 14 49 21 5
18P LOSS WILD-TYPE 17 10 26 49

Figure S68.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.87e-09 (Fisher's exact test), Q value = 4.1e-06

Table S69.  Gene #69: '18p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
18P LOSS MUTATED 6 42 41
18P LOSS WILD-TYPE 43 20 39

Figure S69.  Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss mutation analysis' versus 'MRNA_CNMF'

P value = 1.92e-12 (Fisher's exact test), Q value = 1.4e-09

Table S70.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 62 30 23
18Q LOSS MUTATED 6 52 6 16
18Q LOSS WILD-TYPE 25 10 24 7

Figure S70.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'18q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 3.83e-10 (Fisher's exact test), Q value = 2.7e-07

Table S71.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 44 46
18Q LOSS MUTATED 36 7 37
18Q LOSS WILD-TYPE 20 37 9

Figure S71.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 8.88e-46 (Fisher's exact test), Q value = 6.4e-43

Table S72.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
18Q LOSS MUTATED 149 33 27 16
18Q LOSS WILD-TYPE 21 154 5 8

Figure S72.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.62e-15 (Fisher's exact test), Q value = 2.6e-12

Table S73.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 86 63
18Q LOSS MUTATED 88 28 22
18Q LOSS WILD-TYPE 17 58 41

Figure S73.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18q loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000181 (Fisher's exact test), Q value = 0.12

Table S74.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 25 140 48
18Q LOSS MUTATED 16 8 87 29
18Q LOSS WILD-TYPE 35 17 53 19

Figure S74.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'18q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.47e-14 (Fisher's exact test), Q value = 3.2e-11

Table S75.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 59 47 54
18Q LOSS MUTATED 18 51 21 8
18Q LOSS WILD-TYPE 13 8 26 46

Figure S75.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.36e-08 (Fisher's exact test), Q value = 9.4e-06

Table S76.  Gene #70: '18q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 62 80
18Q LOSS MUTATED 9 46 43
18Q LOSS WILD-TYPE 40 16 37

Figure S76.  Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss mutation analysis' versus 'CN_CNMF'

P value = 8.88e-08 (Fisher's exact test), Q value = 6.1e-05

Table S77.  Gene #73: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
20P LOSS MUTATED 27 2 0 4
20P LOSS WILD-TYPE 143 185 32 20

Figure S77.  Get High-res Image Gene #73: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 2.6e-06 (Fisher's exact test), Q value = 0.0018

Table S78.  Gene #74: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
21Q LOSS MUTATED 40 15 13 3
21Q LOSS WILD-TYPE 130 172 19 21

Figure S78.  Get High-res Image Gene #74: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 1.06e-11 (Fisher's exact test), Q value = 7.4e-09

Table S79.  Gene #75: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 170 187 32 24
22Q LOSS MUTATED 56 11 12 2
22Q LOSS WILD-TYPE 114 176 20 22

Figure S79.  Get High-res Image Gene #75: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 413

  • Number of significantly arm-level cnvs = 76

  • 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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