Correlation between copy number variations of arm-level result and molecular subtypes
Adrenocortical Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C170807D
Overview
Introduction

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

Summary

Testing the association between copy number variation 80 arm-level events and 10 molecular subtypes across 90 patients, 49 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 2p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 4p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 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'.

  • 9p gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

  • xq gain cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 17p loss cnv correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 49 significant findings detected.

Clinical
Features
CN
CNMF
METHLYATION
CNMF
RPPA
CNMF
RPPA
CHIERARCHICAL
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
14q gain 21 (23%) 69 0.0142
(1.00)
0.0561
(1.00)
0.104
(1.00)
0.427
(1.00)
0.00031
(0.214)
0.00105
(0.706)
1e-05
(0.00736)
0.00017
(0.118)
3e-05
(0.0214)
2e-05
(0.0144)
4p gain 37 (41%) 53 1e-05
(0.00736)
0.0444
(1.00)
1
(1.00)
0.464
(1.00)
2e-05
(0.0144)
4e-05
(0.0284)
0.297
(1.00)
0.00236
(1.00)
0.343
(1.00)
0.861
(1.00)
4q gain 33 (37%) 57 2e-05
(0.0144)
0.0367
(1.00)
0.927
(1.00)
0.729
(1.00)
3e-05
(0.0214)
2e-05
(0.0144)
0.557
(1.00)
0.0008
(0.542)
0.361
(1.00)
0.95
(1.00)
7q gain 48 (53%) 42 1e-05
(0.00736)
0.117
(1.00)
0.139
(1.00)
0.247
(1.00)
1e-05
(0.00736)
8e-05
(0.0563)
0.915
(1.00)
0.328
(1.00)
0.277
(1.00)
0.194
(1.00)
12p gain 64 (71%) 26 1e-05
(0.00736)
0.209
(1.00)
0.204
(1.00)
0.0668
(1.00)
0.00011
(0.077)
7e-05
(0.0494)
0.243
(1.00)
0.209
(1.00)
0.13
(1.00)
0.25
(1.00)
16p gain 49 (54%) 41 1e-05
(0.00736)
0.0107
(1.00)
0.894
(1.00)
0.0401
(1.00)
1e-05
(0.00736)
1e-05
(0.00736)
0.0464
(1.00)
0.0261
(1.00)
0.0284
(1.00)
0.276
(1.00)
16q gain 47 (52%) 43 1e-05
(0.00736)
0.00778
(1.00)
0.954
(1.00)
0.327
(1.00)
8e-05
(0.0563)
1e-05
(0.00736)
0.0246
(1.00)
0.0129
(1.00)
0.0139
(1.00)
0.462
(1.00)
20p gain 46 (51%) 44 1e-05
(0.00736)
0.234
(1.00)
0.0228
(1.00)
0.00851
(1.00)
0.00016
(0.111)
0.00011
(0.077)
0.00475
(1.00)
0.0893
(1.00)
0.0095
(1.00)
0.00428
(1.00)
20q gain 49 (54%) 41 1e-05
(0.00736)
0.0668
(1.00)
0.00981
(1.00)
0.078
(1.00)
6e-05
(0.0425)
0.00029
(0.2)
0.0197
(1.00)
0.277
(1.00)
0.0114
(1.00)
0.0146
(1.00)
5p gain 57 (63%) 33 1e-05
(0.00736)
0.0376
(1.00)
0.0459
(1.00)
0.0346
(1.00)
0.00051
(0.349)
2e-05
(0.0144)
0.252
(1.00)
0.228
(1.00)
0.0724
(1.00)
0.357
(1.00)
5q gain 53 (59%) 37 1e-05
(0.00736)
0.00851
(1.00)
0.419
(1.00)
0.148
(1.00)
0.00063
(0.428)
1e-05
(0.00736)
0.336
(1.00)
0.134
(1.00)
0.209
(1.00)
0.169
(1.00)
7p gain 48 (53%) 42 5e-05
(0.0355)
0.119
(1.00)
0.139
(1.00)
0.0929
(1.00)
0.00011
(0.077)
0.00165
(1.00)
0.915
(1.00)
0.551
(1.00)
0.278
(1.00)
0.288
(1.00)
10p gain 25 (28%) 65 0.0019
(1.00)
0.0597
(1.00)
0.0193
(1.00)
0.0137
(1.00)
7e-05
(0.0494)
0.00014
(0.0976)
0.0343
(1.00)
0.505
(1.00)
0.0573
(1.00)
0.454
(1.00)
12q gain 64 (71%) 26 1e-05
(0.00736)
0.308
(1.00)
0.151
(1.00)
0.028
(1.00)
0.00049
(0.336)
0.00021
(0.146)
0.236
(1.00)
0.455
(1.00)
0.22
(1.00)
0.591
(1.00)
19q gain 52 (58%) 38 5e-05
(0.0355)
0.0518
(1.00)
0.295
(1.00)
0.0558
(1.00)
0.00031
(0.214)
0.00097
(0.656)
0.143
(1.00)
0.111
(1.00)
0.517
(1.00)
0.119
(1.00)
2p gain 13 (14%) 77 0.00738
(1.00)
0.00142
(0.949)
0.596
(1.00)
0.34
(1.00)
0.0121
(1.00)
0.00025
(0.173)
0.375
(1.00)
0.0191
(1.00)
0.125
(1.00)
0.0741
(1.00)
8p gain 32 (36%) 58 9e-05
(0.0632)
0.14
(1.00)
0.517
(1.00)
0.441
(1.00)
0.17
(1.00)
0.147
(1.00)
0.112
(1.00)
0.172
(1.00)
0.242
(1.00)
0.517
(1.00)
8q gain 38 (42%) 52 0.00022
(0.152)
0.291
(1.00)
0.723
(1.00)
0.468
(1.00)
0.418
(1.00)
0.229
(1.00)
0.499
(1.00)
0.258
(1.00)
0.52
(1.00)
0.642
(1.00)
9p gain 20 (22%) 70 6e-05
(0.0425)
0.00218
(1.00)
0.0878
(1.00)
0.136
(1.00)
0.00908
(1.00)
0.0118
(1.00)
0.382
(1.00)
0.549
(1.00)
0.461
(1.00)
0.252
(1.00)
10q gain 26 (29%) 64 0.00147
(0.979)
0.0712
(1.00)
0.0172
(1.00)
0.0145
(1.00)
1e-05
(0.00736)
0.00056
(0.381)
0.02
(1.00)
0.343
(1.00)
0.031
(1.00)
0.844
(1.00)
xq gain 40 (44%) 50 2e-05
(0.0144)
0.165
(1.00)
0.283
(1.00)
0.0431
(1.00)
0.00136
(0.91)
0.0087
(1.00)
0.796
(1.00)
0.152
(1.00)
0.343
(1.00)
0.139
(1.00)
9p loss 20 (22%) 70 0.00171
(1.00)
0.048
(1.00)
0.554
(1.00)
0.117
(1.00)
0.0001
(0.0701)
0.001
(0.674)
0.00901
(1.00)
0.139
(1.00)
0.00476
(1.00)
0.938
(1.00)
17p loss 32 (36%) 58 0.00305
(1.00)
0.00016
(0.111)
0.456
(1.00)
0.197
(1.00)
0.0116
(1.00)
0.0134
(1.00)
0.0811
(1.00)
0.00285
(1.00)
0.0142
(1.00)
0.111
(1.00)
1p gain 4 (4%) 86 0.183
(1.00)
1q gain 8 (9%) 82 0.043
(1.00)
0.658
(1.00)
0.202
(1.00)
0.559
(1.00)
0.0459
(1.00)
0.079
(1.00)
0.0646
(1.00)
0.241
(1.00)
0.147
(1.00)
0.85
(1.00)
2q gain 12 (13%) 78 0.0522
(1.00)
0.00249
(1.00)
0.421
(1.00)
0.176
(1.00)
0.019
(1.00)
0.0026
(1.00)
0.0562
(1.00)
0.00489
(1.00)
0.0208
(1.00)
0.0243
(1.00)
3p gain 13 (14%) 77 0.286
(1.00)
0.069
(1.00)
0.45
(1.00)
0.883
(1.00)
0.332
(1.00)
0.365
(1.00)
0.409
(1.00)
0.109
(1.00)
0.634
(1.00)
0.388
(1.00)
3q gain 15 (17%) 75 0.398
(1.00)
0.0508
(1.00)
0.893
(1.00)
0.822
(1.00)
0.053
(1.00)
0.792
(1.00)
0.652
(1.00)
0.246
(1.00)
0.679
(1.00)
0.711
(1.00)
6p gain 18 (20%) 72 0.0171
(1.00)
0.683
(1.00)
1
(1.00)
0.876
(1.00)
0.0667
(1.00)
0.472
(1.00)
0.162
(1.00)
0.055
(1.00)
0.419
(1.00)
0.236
(1.00)
6q gain 16 (18%) 74 0.0732
(1.00)
0.458
(1.00)
0.607
(1.00)
0.685
(1.00)
0.2
(1.00)
0.293
(1.00)
0.298
(1.00)
0.197
(1.00)
0.15
(1.00)
0.436
(1.00)
9q gain 29 (32%) 61 0.00043
(0.295)
0.0011
(0.737)
0.0386
(1.00)
0.0703
(1.00)
0.0236
(1.00)
0.00206
(1.00)
0.0347
(1.00)
0.353
(1.00)
0.0894
(1.00)
0.0831
(1.00)
11p gain 5 (6%) 85 0.0917
(1.00)
11q gain 6 (7%) 84 0.126
(1.00)
0.177
(1.00)
0.201
(1.00)
0.484
(1.00)
0.0444
(1.00)
0.0794
(1.00)
0.186
(1.00)
0.368
(1.00)
0.00544
(1.00)
0.39
(1.00)
13q gain 6 (7%) 84 0.403
(1.00)
0.463
(1.00)
0.497
(1.00)
0.724
(1.00)
0.0391
(1.00)
0.634
(1.00)
0.141
(1.00)
0.916
(1.00)
0.185
(1.00)
0.7
(1.00)
15q gain 11 (12%) 79 0.0941
(1.00)
0.0473
(1.00)
0.445
(1.00)
0.845
(1.00)
0.0108
(1.00)
0.00472
(1.00)
0.36
(1.00)
0.0007
(0.475)
0.506
(1.00)
0.257
(1.00)
17p gain 5 (6%) 85 0.112
(1.00)
0.336
(1.00)
0.686
(1.00)
0.144
(1.00)
0.208
(1.00)
0.795
(1.00)
0.0595
(1.00)
0.062
(1.00)
17q gain 7 (8%) 83 0.0249
(1.00)
0.338
(1.00)
0.688
(1.00)
0.142
(1.00)
0.207
(1.00)
0.794
(1.00)
0.0597
(1.00)
0.0617
(1.00)
18p gain 6 (7%) 84 0.26
(1.00)
18q gain 5 (6%) 85 0.493
(1.00)
19p gain 56 (62%) 34 0.00387
(1.00)
0.0546
(1.00)
0.0617
(1.00)
0.019
(1.00)
0.00103
(0.693)
0.00051
(0.349)
0.466
(1.00)
0.471
(1.00)
0.639
(1.00)
0.221
(1.00)
21q gain 31 (34%) 59 0.0205
(1.00)
0.00909
(1.00)
0.06
(1.00)
0.233
(1.00)
0.0199
(1.00)
0.00098
(0.661)
0.0138
(1.00)
0.02
(1.00)
0.00288
(1.00)
0.0829
(1.00)
22q gain 3 (3%) 87 0.634
(1.00)
1p loss 29 (32%) 61 0.117
(1.00)
0.141
(1.00)
0.949
(1.00)
0.128
(1.00)
0.438
(1.00)
0.0645
(1.00)
0.467
(1.00)
0.41
(1.00)
0.0278
(1.00)
0.948
(1.00)
1q loss 20 (22%) 70 0.204
(1.00)
0.0904
(1.00)
0.518
(1.00)
0.0257
(1.00)
0.961
(1.00)
0.597
(1.00)
0.37
(1.00)
0.841
(1.00)
0.0783
(1.00)
0.49
(1.00)
2p loss 17 (19%) 73 0.00676
(1.00)
0.0276
(1.00)
0.836
(1.00)
0.659
(1.00)
0.615
(1.00)
0.268
(1.00)
0.0385
(1.00)
0.769
(1.00)
0.228
(1.00)
0.699
(1.00)
2q loss 15 (17%) 75 0.00498
(1.00)
0.00109
(0.731)
0.734
(1.00)
0.885
(1.00)
0.114
(1.00)
0.0525
(1.00)
0.0315
(1.00)
0.728
(1.00)
0.0693
(1.00)
0.537
(1.00)
3p loss 20 (22%) 70 0.256
(1.00)
0.142
(1.00)
0.23
(1.00)
0.29
(1.00)
0.111
(1.00)
0.137
(1.00)
0.526
(1.00)
0.388
(1.00)
0.685
(1.00)
0.316
(1.00)
3q loss 20 (22%) 70 0.167
(1.00)
0.165
(1.00)
0.533
(1.00)
0.603
(1.00)
0.0221
(1.00)
0.0299
(1.00)
0.191
(1.00)
0.341
(1.00)
0.314
(1.00)
0.117
(1.00)
4p loss 10 (11%) 80 0.0955
(1.00)
0.233
(1.00)
1
(1.00)
0.989
(1.00)
0.0237
(1.00)
0.0815
(1.00)
0.307
(1.00)
0.93
(1.00)
0.0513
(1.00)
1
(1.00)
4q loss 11 (12%) 79 0.237
(1.00)
0.0935
(1.00)
0.879
(1.00)
0.923
(1.00)
0.0073
(1.00)
0.0275
(1.00)
0.248
(1.00)
0.811
(1.00)
0.013
(1.00)
0.902
(1.00)
5p loss 8 (9%) 82 0.287
(1.00)
0.0524
(1.00)
0.695
(1.00)
0.192
(1.00)
0.231
(1.00)
0.0102
(1.00)
0.774
(1.00)
0.299
(1.00)
0.695
(1.00)
1
(1.00)
5q loss 7 (8%) 83 0.899
(1.00)
0.654
(1.00)
0.276
(1.00)
0.133
(1.00)
0.658
(1.00)
0.125
(1.00)
0.66
(1.00)
0.849
(1.00)
6p loss 19 (21%) 71 0.145
(1.00)
0.853
(1.00)
0.573
(1.00)
0.231
(1.00)
0.62
(1.00)
0.692
(1.00)
0.627
(1.00)
0.099
(1.00)
0.726
(1.00)
0.528
(1.00)
6q loss 22 (24%) 68 0.0615
(1.00)
0.86
(1.00)
0.568
(1.00)
0.274
(1.00)
0.633
(1.00)
0.692
(1.00)
0.731
(1.00)
0.173
(1.00)
0.558
(1.00)
0.323
(1.00)
7p loss 5 (6%) 85 0.391
(1.00)
0.585
(1.00)
0.532
(1.00)
0.204
(1.00)
0.909
(1.00)
0.892
(1.00)
0.816
(1.00)
0.414
(1.00)
0.832
(1.00)
0.114
(1.00)
7q loss 6 (7%) 84 0.316
(1.00)
0.303
(1.00)
0.685
(1.00)
0.779
(1.00)
0.618
(1.00)
0.656
(1.00)
1
(1.00)
0.236
(1.00)
0.733
(1.00)
0.15
(1.00)
8p loss 16 (18%) 74 0.00546
(1.00)
0.223
(1.00)
0.104
(1.00)
0.00064
(0.435)
0.182
(1.00)
0.141
(1.00)
0.181
(1.00)
0.0231
(1.00)
0.254
(1.00)
0.0297
(1.00)
8q loss 12 (13%) 78 0.00444
(1.00)
0.0866
(1.00)
0.409
(1.00)
0.0359
(1.00)
0.034
(1.00)
0.123
(1.00)
0.0769
(1.00)
0.0357
(1.00)
0.18
(1.00)
0.0378
(1.00)
9q loss 11 (12%) 79 0.323
(1.00)
0.936
(1.00)
1
(1.00)
0.037
(1.00)
0.0812
(1.00)
0.321
(1.00)
0.557
(1.00)
0.497
(1.00)
0.214
(1.00)
0.806
(1.00)
10p loss 12 (13%) 78 0.223
(1.00)
0.427
(1.00)
1
(1.00)
0.0555
(1.00)
0.265
(1.00)
1
(1.00)
0.682
(1.00)
0.707
(1.00)
1
(1.00)
0.326
(1.00)
10q loss 10 (11%) 80 0.535
(1.00)
0.625
(1.00)
1
(1.00)
0.238
(1.00)
0.533
(1.00)
1
(1.00)
1
(1.00)
0.707
(1.00)
1
(1.00)
0.288
(1.00)
11p loss 24 (27%) 66 0.00644
(1.00)
0.0179
(1.00)
0.965
(1.00)
0.799
(1.00)
0.218
(1.00)
0.19
(1.00)
0.281
(1.00)
0.892
(1.00)
0.69
(1.00)
1
(1.00)
11q loss 23 (26%) 67 0.0119
(1.00)
0.0029
(1.00)
0.837
(1.00)
0.396
(1.00)
0.137
(1.00)
0.128
(1.00)
0.106
(1.00)
0.826
(1.00)
0.491
(1.00)
0.781
(1.00)
12p loss 5 (6%) 85 0.0907
(1.00)
0.252
(1.00)
0.254
(1.00)
0.0826
(1.00)
0.621
(1.00)
0.0381
(1.00)
0.103
(1.00)
0.519
(1.00)
0.431
(1.00)
0.149
(1.00)
12q loss 4 (4%) 86 0.183
(1.00)
0.0478
(1.00)
0.257
(1.00)
0.0837
(1.00)
0.443
(1.00)
0.00936
(1.00)
0.332
(1.00)
0.239
(1.00)
0.675
(1.00)
0.114
(1.00)
13q loss 39 (43%) 51 0.0144
(1.00)
0.0826
(1.00)
0.885
(1.00)
0.943
(1.00)
0.626
(1.00)
0.886
(1.00)
0.752
(1.00)
0.306
(1.00)
0.614
(1.00)
0.491
(1.00)
14q loss 18 (20%) 72 0.0275
(1.00)
0.444
(1.00)
0.249
(1.00)
0.0531
(1.00)
0.0182
(1.00)
0.0474
(1.00)
0.408
(1.00)
0.53
(1.00)
0.215
(1.00)
0.147
(1.00)
15q loss 21 (23%) 69 0.0818
(1.00)
0.416
(1.00)
0.554
(1.00)
0.511
(1.00)
0.11
(1.00)
0.225
(1.00)
0.606
(1.00)
0.0411
(1.00)
0.289
(1.00)
0.876
(1.00)
16p loss 6 (7%) 84 0.125
(1.00)
0.0498
(1.00)
0.138
(1.00)
0.0474
(1.00)
0.00215
(1.00)
0.00426
(1.00)
0.0132
(1.00)
0.443
(1.00)
0.0004
(0.275)
0.467
(1.00)
16q loss 5 (6%) 85 0.215
(1.00)
0.0777
(1.00)
0.196
(1.00)
0.178
(1.00)
0.058
(1.00)
0.0848
(1.00)
0.168
(1.00)
0.305
(1.00)
0.00145
(0.967)
0.702
(1.00)
17q loss 24 (27%) 66 0.0148
(1.00)
0.00513
(1.00)
0.639
(1.00)
0.516
(1.00)
0.118
(1.00)
0.034
(1.00)
0.0686
(1.00)
0.0204
(1.00)
0.228
(1.00)
0.108
(1.00)
18p loss 37 (41%) 53 0.0238
(1.00)
0.26
(1.00)
0.976
(1.00)
0.687
(1.00)
0.774
(1.00)
0.645
(1.00)
0.695
(1.00)
0.693
(1.00)
0.353
(1.00)
0.34
(1.00)
18q loss 35 (39%) 55 0.0364
(1.00)
0.424
(1.00)
0.933
(1.00)
0.533
(1.00)
0.825
(1.00)
0.935
(1.00)
0.495
(1.00)
0.915
(1.00)
0.292
(1.00)
0.354
(1.00)
19p loss 5 (6%) 85 0.0923
(1.00)
0.444
(1.00)
0.158
(1.00)
0.0133
(1.00)
0.14
(1.00)
0.718
(1.00)
0.28
(1.00)
0.111
(1.00)
19q loss 4 (4%) 86 0.184
(1.00)
0.706
(1.00)
0.771
(1.00)
0.118
(1.00)
0.784
(1.00)
0.206
(1.00)
1
(1.00)
0.432
(1.00)
20p loss 9 (10%) 81 0.0418
(1.00)
0.303
(1.00)
0.544
(1.00)
0.854
(1.00)
0.214
(1.00)
0.123
(1.00)
0.0674
(1.00)
0.447
(1.00)
0.0203
(1.00)
0.444
(1.00)
20q loss 3 (3%) 87 0.18
(1.00)
21q loss 15 (17%) 75 0.114
(1.00)
0.339
(1.00)
0.0498
(1.00)
0.0521
(1.00)
0.254
(1.00)
0.251
(1.00)
0.226
(1.00)
0.509
(1.00)
0.0836
(1.00)
0.101
(1.00)
22q loss 48 (53%) 42 0.0153
(1.00)
0.0805
(1.00)
0.974
(1.00)
0.483
(1.00)
0.621
(1.00)
0.281
(1.00)
0.876
(1.00)
0.825
(1.00)
0.682
(1.00)
0.229
(1.00)
xq loss 17 (19%) 73 0.00055
(0.375)
0.244
(1.00)
0.267
(1.00)
0.264
(1.00)
0.0329
(1.00)
0.0456
(1.00)
0.654
(1.00)
0.168
(1.00)
0.245
(1.00)
0.798
(1.00)
'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S1.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
2P GAIN MUTATED 8 0 1 0
2P GAIN WILD-TYPE 15 23 6 24

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S2.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
4P GAIN MUTATED 4 13 12 8
4P GAIN WILD-TYPE 32 13 4 4

Figure S2.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S3.  Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
4P GAIN MUTATED 1 8 11 10
4P GAIN WILD-TYPE 23 5 6 13

Figure S3.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S4.  Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
4P GAIN MUTATED 2 15 0 13
4P GAIN WILD-TYPE 21 8 7 11

Figure S4.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S5.  Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
4Q GAIN MUTATED 3 12 11 7
4Q GAIN WILD-TYPE 33 14 5 5

Figure S5.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

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

Table S6.  Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
4Q GAIN MUTATED 0 8 9 10
4Q GAIN WILD-TYPE 24 5 8 13

Figure S6.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S7.  Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
4Q GAIN MUTATED 1 15 0 11
4Q GAIN WILD-TYPE 22 8 7 13

Figure S7.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S8.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
5P GAIN MUTATED 10 24 14 9
5P GAIN WILD-TYPE 26 2 2 3

Figure S8.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S9.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
5P GAIN MUTATED 6 18 3 22
5P GAIN WILD-TYPE 17 5 4 2

Figure S9.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S10.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
5Q GAIN MUTATED 8 21 14 10
5Q GAIN WILD-TYPE 28 5 2 2

Figure S10.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S11.  Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
5Q GAIN MUTATED 5 19 3 20
5Q GAIN WILD-TYPE 18 4 4 4

Figure S11.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

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

Table S12.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
7P GAIN MUTATED 8 20 12 8
7P GAIN WILD-TYPE 28 6 4 4

Figure S12.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.077

Table S13.  Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
7P GAIN MUTATED 6 12 13 11
7P GAIN WILD-TYPE 18 1 4 12

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S14.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
7Q GAIN MUTATED 7 20 13 8
7Q GAIN WILD-TYPE 29 6 3 4

Figure S14.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S15.  Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
7Q GAIN MUTATED 5 13 13 11
7Q GAIN WILD-TYPE 19 0 4 12

Figure S15.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S16.  Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
7Q GAIN MUTATED 6 20 2 14
7Q GAIN WILD-TYPE 17 3 5 10

Figure S16.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
8P GAIN MUTATED 5 18 4 5
8P GAIN WILD-TYPE 31 8 12 7

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

'8q gain' versus 'CN_CNMF'

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

Table S18.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
8Q GAIN MUTATED 9 20 4 5
8Q GAIN WILD-TYPE 27 6 12 7

Figure S18.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'CN_CNMF'

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

Table S19.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
9P GAIN MUTATED 2 4 10 4
9P GAIN WILD-TYPE 34 22 6 8

Figure S19.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

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

Table S20.  Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
10P GAIN MUTATED 6 11 4 2
10P GAIN WILD-TYPE 18 2 13 21

Figure S20.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.098

Table S21.  Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
10P GAIN MUTATED 7 14 1 1
10P GAIN WILD-TYPE 16 9 6 23

Figure S21.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S22.  Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
10Q GAIN MUTATED 7 11 3 2
10Q GAIN WILD-TYPE 17 2 14 21

Figure S22.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S23.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
12P GAIN MUTATED 14 26 15 9
12P GAIN WILD-TYPE 22 0 1 3

Figure S23.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.077

Table S24.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
12P GAIN MUTATED 9 13 14 18
12P GAIN WILD-TYPE 15 0 3 5

Figure S24.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S25.  Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
12P GAIN MUTATED 10 20 2 22
12P GAIN WILD-TYPE 13 3 5 2

Figure S25.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S26.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
12Q GAIN MUTATED 13 26 16 9
12Q GAIN WILD-TYPE 23 0 0 3

Figure S26.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.15

Table S27.  Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
12Q GAIN MUTATED 11 20 2 22
12Q GAIN WILD-TYPE 12 3 5 2

Figure S27.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S28.  Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
14Q GAIN MUTATED 2 6 8 1
14Q GAIN WILD-TYPE 22 7 9 22

Figure S28.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S29.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 16 26
14Q GAIN MUTATED 17 0 1
14Q GAIN WILD-TYPE 19 16 25

Figure S29.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S30.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 27 11 20 4
14Q GAIN MUTATED 7 0 3 5 3
14Q GAIN WILD-TYPE 9 27 8 15 1

Figure S30.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S31.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 22 27
14Q GAIN MUTATED 14 2 1
14Q GAIN WILD-TYPE 14 20 26

Figure S31.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S32.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 24 14
14Q GAIN MUTATED 17 0 0
14Q GAIN WILD-TYPE 22 24 14

Figure S32.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S33.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
16P GAIN MUTATED 6 26 11 6
16P GAIN WILD-TYPE 30 0 5 6

Figure S33.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S34.  Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
16P GAIN MUTATED 3 10 13 16
16P GAIN WILD-TYPE 21 3 4 7

Figure S34.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S35.  Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
16P GAIN MUTATED 4 20 0 18
16P GAIN WILD-TYPE 19 3 7 6

Figure S35.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S36.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
16Q GAIN MUTATED 5 25 11 6
16Q GAIN WILD-TYPE 31 1 5 6

Figure S36.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

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

Table S37.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
16Q GAIN MUTATED 4 9 13 16
16Q GAIN WILD-TYPE 20 4 4 7

Figure S37.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S38.  Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
16Q GAIN MUTATED 4 19 1 18
16Q GAIN WILD-TYPE 19 4 6 6

Figure S38.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

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

Table S39.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
19Q GAIN MUTATED 13 16 16 7
19Q GAIN WILD-TYPE 23 10 0 5

Figure S39.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S40.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
19Q GAIN MUTATED 10 13 12 9
19Q GAIN WILD-TYPE 14 0 5 14

Figure S40.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S41.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
20P GAIN MUTATED 6 22 11 7
20P GAIN WILD-TYPE 30 4 5 5

Figure S41.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

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

Table S42.  Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
20P GAIN MUTATED 4 9 8 18
20P GAIN WILD-TYPE 20 4 9 5

Figure S42.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.077

Table S43.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
20P GAIN MUTATED 6 12 1 20
20P GAIN WILD-TYPE 17 11 6 4

Figure S43.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0074

Table S44.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
20Q GAIN MUTATED 8 22 12 7
20Q GAIN WILD-TYPE 28 4 4 5

Figure S44.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

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

Table S45.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
20Q GAIN MUTATED 5 11 8 18
20Q GAIN WILD-TYPE 19 2 9 5

Figure S45.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.2

Table S46.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 23 7 24
20Q GAIN MUTATED 6 14 2 20
20Q GAIN WILD-TYPE 17 9 5 4

Figure S46.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S47.  Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 26 16 12
XQ GAIN MUTATED 6 21 8 5
XQ GAIN WILD-TYPE 30 5 8 7

Figure S47.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.07

Table S48.  Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 13 17 23
9P LOSS MUTATED 14 1 3 1
9P LOSS WILD-TYPE 10 12 14 22

Figure S48.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

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

Table S49.  Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 11 20 18 11
17P LOSS MUTATED 11 0 12 4 1
17P LOSS WILD-TYPE 7 11 8 14 10

Figure S49.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input
  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 90

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)