Correlation between copy number variations of arm-level result and molecular subtypes
Testicular Germ Cell Tumors (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1FB51WH
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/C1FB51WH
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 72 arm-level events and 8 molecular subtypes across 150 patients, 66 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 6q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 19p gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

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

  • 22q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 10p loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • 10q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • 11p loss cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 14q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

  • 22q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • xq 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 72 arm-level events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 66 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
19p loss 50 (33%) 100 1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548)
19q loss 53 (35%) 97 1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548)
17q gain 51 (34%) 99 0.00016
(0.0798) 		7e-05
(0.0353) 		1e-05
(0.00548) 		1e-05
(0.00548) 		0.00034
(0.167) 		0.00041
(0.2) 		8e-05
(0.0402) 		0.00299
(1.00)
22q loss 45 (30%) 105 0.00268
(1.00) 		1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		0.00249
(1.00) 		2e-05
(0.0103) 		5e-05
(0.0254) 		0.00055
(0.264)
17p gain 40 (27%) 110 1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		1e-05
(0.00548) 		0.00147
(0.684) 		0.00053
(0.255) 		0.00063
(0.3) 		0.00209
(0.961)
11q loss 115 (77%) 35 1e-05
(0.00548) 		0.123
(1.00) 		0.0001
(0.0502) 		2e-05
(0.0103) 		0.00019
(0.0944) 		0.00673
(1.00) 		0.00803
(1.00) 		0.0168
(1.00)
22q gain 38 (25%) 112 1e-05
(0.00548) 		0.00138
(0.644) 		2e-05
(0.0103) 		1e-05
(0.00548) 		0.052
(1.00) 		0.00276
(1.00) 		0.0208
(1.00) 		0.00137
(0.641)
11p loss 98 (65%) 52 0.00865
(1.00) 		0.183
(1.00) 		0.00048
(0.232) 		0.00052
(0.251) 		0.00047
(0.227) 		0.00046
(0.223) 		0.00501
(1.00) 		0.017
(1.00)
15q loss 29 (19%) 121 0.0063
(1.00) 		3e-05
(0.0154) 		1e-05
(0.00548) 		1e-05
(0.00548) 		0.0107
(1.00) 		0.00273
(1.00) 		0.00067
(0.318) 		0.0011
(0.516)
8p gain 110 (73%) 40 0.0637
(1.00) 		0.00548
(1.00) 		3e-05
(0.0154) 		0.00023
(0.114) 		0.062
(1.00) 		0.0266
(1.00) 		0.0153
(1.00) 		0.0658
(1.00)
8q gain 111 (74%) 39 0.0203
(1.00) 		0.00322
(1.00) 		0.00013
(0.0651) 		0.00025
(0.123) 		0.00464
(1.00) 		0.00328
(1.00) 		0.00813
(1.00) 		0.00665
(1.00)
15q gain 51 (34%) 99 0.0499
(1.00) 		0.00215
(0.987) 		1e-05
(0.00548) 		3e-05
(0.0154) 		0.0189
(1.00) 		0.011
(1.00) 		0.0262
(1.00) 		0.0203
(1.00)
19p gain 36 (24%) 114 0.00983
(1.00) 		4e-05
(0.0204) 		7e-05
(0.0353) 		0.00084
(0.396) 		0.0252
(1.00) 		0.0883
(1.00) 		0.369
(1.00) 		0.252
(1.00)
19q gain 29 (19%) 121 0.0162
(1.00) 		0.00018
(0.0896) 		2e-05
(0.0103) 		0.00059
(0.282) 		0.196
(1.00) 		0.0485
(1.00) 		0.37
(1.00) 		0.22
(1.00)
10p loss 77 (51%) 73 0.0216
(1.00) 		0.00042
(0.204) 		0.00034
(0.167) 		0.00551
(1.00) 		0.963
(1.00) 		0.447
(1.00) 		0.445
(1.00) 		0.443
(1.00)
10q loss 72 (48%) 78 0.00858
(1.00) 		6e-05
(0.0304) 		0.00023
(0.114) 		0.00258
(1.00) 		0.363
(1.00) 		0.0765
(1.00) 		0.114
(1.00) 		0.0765
(1.00)
17p loss 37 (25%) 113 1e-05
(0.00548) 		0.0384
(1.00) 		0.00428
(1.00) 		0.00014
(0.07) 		0.0216
(1.00) 		0.0786
(1.00) 		0.00298
(1.00) 		0.0215
(1.00)
1p gain 37 (25%) 113 0.00302
(1.00) 		0.00064
(0.304) 		0.00037
(0.181) 		0.00245
(1.00) 		0.0552
(1.00) 		0.16
(1.00) 		0.0042
(1.00) 		0.0332
(1.00)
6q gain 23 (15%) 127 0.0234
(1.00) 		0.883
(1.00) 		0.0139
(1.00) 		0.00025
(0.123) 		0.0668
(1.00) 		0.0266
(1.00) 		0.164
(1.00) 		0.0776
(1.00)
9q loss 58 (39%) 92 0.00032
(0.157) 		0.338
(1.00) 		0.308
(1.00) 		0.0173
(1.00) 		0.676
(1.00) 		0.0338
(1.00) 		0.127
(1.00) 		0.309
(1.00)
14q loss 20 (13%) 130 0.121
(1.00) 		0.0006
(0.286) 		0.00482
(1.00) 		5e-05
(0.0254) 		0.0538
(1.00) 		0.00484
(1.00) 		0.0112
(1.00) 		0.059
(1.00)
xq loss 29 (19%) 121 0.00033
(0.162) 		0.00194
(0.894) 		0.162
(1.00) 		0.0966
(1.00) 		0.356
(1.00) 		0.243
(1.00) 		0.0848
(1.00) 		0.157
(1.00)
1q gain 61 (41%) 89 0.438
(1.00) 		0.664
(1.00) 		0.825
(1.00) 		0.0593
(1.00) 		0.125
(1.00) 		1
(1.00) 		0.753
(1.00) 		0.318
(1.00)
2p gain 46 (31%) 104 0.0137
(1.00) 		0.00927
(1.00) 		0.0162
(1.00) 		0.167
(1.00) 		0.0592
(1.00) 		0.0874
(1.00) 		0.0835
(1.00) 		0.18
(1.00)
2q gain 42 (28%) 108 0.116
(1.00) 		0.0331
(1.00) 		0.277
(1.00) 		0.746
(1.00) 		0.501
(1.00) 		0.278
(1.00) 		0.128
(1.00) 		0.759
(1.00)
3p gain 27 (18%) 123 0.0228
(1.00) 		0.4
(1.00) 		0.00724
(1.00) 		0.00662
(1.00) 		0.0624
(1.00) 		0.0189
(1.00) 		0.0378
(1.00) 		0.134
(1.00)
3q gain 36 (24%) 114 0.00735
(1.00) 		0.181
(1.00) 		0.0311
(1.00) 		0.0321
(1.00) 		0.192
(1.00) 		0.166
(1.00) 		0.284
(1.00) 		0.698
(1.00)
4p gain 3 (2%) 147 0.636
(1.00) 		0.197
(1.00) 		1
(1.00) 		0.681
(1.00)
5p gain 6 (4%) 144 0.672
(1.00) 		0.0254
(1.00) 		0.0112
(1.00) 		0.00818
(1.00) 		0.018
(1.00) 		0.351
(1.00) 		0.018
(1.00) 		0.251
(1.00)
5q gain 3 (2%) 147 0.777
(1.00) 		0.0588
(1.00) 		0.0356
(1.00) 		0.0417
(1.00)
6p gain 28 (19%) 122 0.00055
(0.264) 		0.752
(1.00) 		0.0129
(1.00) 		0.00081
(0.383) 		0.00434
(1.00) 		0.00192
(0.887) 		0.0386
(1.00) 		0.0293
(1.00)
7p gain 121 (81%) 29 0.00449
(1.00) 		0.0574
(1.00) 		0.00419
(1.00) 		0.00832
(1.00) 		0.128
(1.00) 		0.114
(1.00) 		0.187
(1.00) 		0.583
(1.00)
7q gain 105 (70%) 45 0.547
(1.00) 		0.069
(1.00) 		0.00476
(1.00) 		0.0121
(1.00) 		0.106
(1.00) 		0.038
(1.00) 		0.028
(1.00) 		0.105
(1.00)
9p gain 16 (11%) 134 0.235
(1.00) 		0.335
(1.00) 		0.158
(1.00) 		0.297
(1.00) 		0.614
(1.00) 		0.0994
(1.00) 		0.321
(1.00) 		0.737
(1.00)
9q gain 17 (11%) 133 0.152
(1.00) 		0.5
(1.00) 		1
(1.00) 		0.0792
(1.00) 		1
(1.00) 		1
(1.00) 		0.66
(1.00) 		0.301
(1.00)
10p gain 6 (4%) 144 0.583
(1.00) 		0.0929
(1.00) 		0.322
(1.00) 		0.345
(1.00)
10q gain 8 (5%) 142 0.595
(1.00) 		0.387
(1.00) 		0.369
(1.00) 		0.225
(1.00)
11p gain 10 (7%) 140 0.273
(1.00) 		0.183
(1.00) 		0.165
(1.00) 		0.0514
(1.00) 		0.614
(1.00) 		0.561
(1.00) 		0.229
(1.00) 		0.346
(1.00)
11q gain 4 (3%) 146 0.387
(1.00) 		0.15
(1.00) 		0.0776
(1.00) 		0.013
(1.00)
12p gain 146 (97%) 4 0.193
(1.00) 		0.388
(1.00) 		0.809
(1.00) 		0.368
(1.00) 		0.0695
(1.00) 		1
(1.00) 		0.36
(1.00) 		0.9
(1.00)
12q gain 100 (67%) 50 0.566
(1.00) 		0.841
(1.00) 		0.205
(1.00) 		0.339
(1.00) 		0.348
(1.00) 		0.846
(1.00) 		0.986
(1.00) 		0.754
(1.00)
14q gain 51 (34%) 99 0.253
(1.00) 		0.236
(1.00) 		0.585
(1.00) 		0.396
(1.00) 		0.48
(1.00) 		0.713
(1.00) 		0.71
(1.00) 		0.949
(1.00)
16p gain 16 (11%) 134 0.012
(1.00) 		0.0797
(1.00) 		0.00425
(1.00) 		0.0172
(1.00) 		0.11
(1.00) 		0.0139
(1.00) 		0.0287
(1.00) 		0.0366
(1.00)
16q gain 14 (9%) 136 0.00756
(1.00) 		0.139
(1.00) 		0.0101
(1.00) 		0.0489
(1.00) 		0.109
(1.00) 		0.014
(1.00) 		0.0294
(1.00) 		0.0375
(1.00)
18p gain 4 (3%) 146 0.688
(1.00) 		0.0703
(1.00) 		0.377
(1.00) 		0.783
(1.00)
20p gain 34 (23%) 116 0.00544
(1.00) 		0.113
(1.00) 		0.0412
(1.00) 		0.286
(1.00) 		0.101
(1.00) 		0.0838
(1.00) 		0.11
(1.00) 		0.272
(1.00)
20q gain 40 (27%) 110 0.00668
(1.00) 		0.00584
(1.00) 		0.00685
(1.00) 		0.0532
(1.00) 		0.0624
(1.00) 		0.124
(1.00) 		0.108
(1.00) 		0.15
(1.00)
21q gain 125 (83%) 25 0.402
(1.00) 		0.273
(1.00) 		0.084
(1.00) 		0.238
(1.00) 		0.0909
(1.00) 		0.215
(1.00) 		0.452
(1.00) 		0.254
(1.00)
xq gain 22 (15%) 128 0.00187
(0.866) 		0.0177
(1.00) 		0.00082
(0.387) 		0.00363
(1.00) 		0.0209
(1.00) 		0.0494
(1.00) 		0.155
(1.00) 		0.377
(1.00)
1p loss 18 (12%) 132 0.121
(1.00) 		0.57
(1.00) 		0.649
(1.00) 		0.887
(1.00) 		0.345
(1.00) 		0.352
(1.00) 		0.114
(1.00) 		0.508
(1.00)
1q loss 8 (5%) 142 0.344
(1.00) 		0.243
(1.00) 		0.291
(1.00) 		0.217
(1.00) 		0.0422
(1.00) 		0.0142
(1.00) 		0.00381
(1.00) 		0.0772
(1.00)
2p loss 5 (3%) 145 0.862
(1.00) 		0.377
(1.00) 		1
(1.00) 		1
(1.00) 		0.231
(1.00) 		1
(1.00) 		0.207
(1.00) 		0.679
(1.00)
2q loss 6 (4%) 144 0.444
(1.00) 		0.681
(1.00) 		0.556
(1.00) 		0.901
(1.00) 		0.231
(1.00) 		0.205
(1.00) 		0.702
(1.00) 		0.601
(1.00)
3p loss 30 (20%) 120 0.935
(1.00) 		0.0303
(1.00) 		0.00151
(0.701) 		0.00342
(1.00) 		0.0195
(1.00) 		0.0364
(1.00) 		0.116
(1.00) 		0.187
(1.00)
3q loss 22 (15%) 128 0.741
(1.00) 		0.739
(1.00) 		0.0854
(1.00) 		0.0572
(1.00) 		0.0548
(1.00) 		0.184
(1.00) 		0.0867
(1.00) 		0.539
(1.00)
4p loss 92 (61%) 58 0.63
(1.00) 		0.0455
(1.00) 		0.0312
(1.00) 		0.163
(1.00) 		0.14
(1.00) 		0.139
(1.00) 		0.481
(1.00) 		0.319
(1.00)
4q loss 108 (72%) 42 0.0669
(1.00) 		0.0108
(1.00) 		0.0108
(1.00) 		0.0122
(1.00) 		0.12
(1.00) 		0.107
(1.00) 		0.626
(1.00) 		0.508
(1.00)
5p loss 103 (69%) 47 0.113
(1.00) 		0.208
(1.00) 		0.115
(1.00) 		0.132
(1.00) 		0.53
(1.00) 		0.125
(1.00) 		0.237
(1.00) 		0.308
(1.00)
5q loss 101 (67%) 49 0.059
(1.00) 		0.0627
(1.00) 		0.014
(1.00) 		0.00338
(1.00) 		0.501
(1.00) 		0.0486
(1.00) 		0.103
(1.00) 		0.154
(1.00)
6p loss 13 (9%) 137 0.265
(1.00) 		0.037
(1.00) 		0.161
(1.00) 		0.0142
(1.00) 		0.925
(1.00) 		0.563
(1.00) 		0.546
(1.00) 		0.705
(1.00)
6q loss 16 (11%) 134 0.121
(1.00) 		0.0094
(1.00) 		0.0449
(1.00) 		0.00103
(0.484) 		0.95
(1.00) 		0.626
(1.00) 		0.763
(1.00) 		0.788
(1.00)
8p loss 12 (8%) 138 0.356
(1.00) 		0.0507
(1.00) 		0.0105
(1.00) 		0.0474
(1.00) 		0.422
(1.00) 		0.281
(1.00) 		0.0553
(1.00) 		0.327
(1.00)
8q loss 5 (3%) 145 0.188
(1.00) 		0.0239
(1.00) 		0.0022
(1.00) 		0.0125
(1.00)
9p loss 63 (42%) 87 0.0328
(1.00) 		1
(1.00) 		0.868
(1.00) 		0.437
(1.00) 		0.436
(1.00) 		0.548
(1.00) 		0.285
(1.00) 		0.594
(1.00)
13q loss 113 (75%) 37 0.0441
(1.00) 		0.289
(1.00) 		0.0323
(1.00) 		0.0014
(0.652) 		0.132
(1.00) 		0.134
(1.00) 		0.00608
(1.00) 		0.0413
(1.00)
16p loss 44 (29%) 106 0.149
(1.00) 		0.0068
(1.00) 		0.0808
(1.00) 		0.262
(1.00) 		0.107
(1.00) 		0.287
(1.00) 		0.396
(1.00) 		0.179
(1.00)
16q loss 51 (34%) 99 0.0785
(1.00) 		0.0662
(1.00) 		0.232
(1.00) 		0.484
(1.00) 		0.0772
(1.00) 		0.286
(1.00) 		0.397
(1.00) 		0.352
(1.00)
17q loss 16 (11%) 134 0.00567
(1.00) 		0.129
(1.00) 		0.0197
(1.00) 		0.028
(1.00) 		0.0773
(1.00) 		0.0483
(1.00) 		0.0157
(1.00) 		0.0752
(1.00)
18p loss 116 (77%) 34 0.692
(1.00) 		0.0753
(1.00) 		0.0443
(1.00) 		0.243
(1.00) 		0.124
(1.00) 		0.0989
(1.00) 		0.0844
(1.00) 		0.108
(1.00)
18q loss 122 (81%) 28 0.0855
(1.00) 		0.317
(1.00) 		0.0663
(1.00) 		0.124
(1.00) 		0.0556
(1.00) 		0.0677
(1.00) 		0.0114
(1.00) 		0.0105
(1.00)
20p loss 30 (20%) 120 0.235
(1.00) 		0.188
(1.00) 		0.199
(1.00) 		0.171
(1.00) 		0.702
(1.00) 		0.136
(1.00) 		0.268
(1.00) 		0.159
(1.00)
20q loss 15 (10%) 135 0.586
(1.00) 		0.49
(1.00) 		0.199
(1.00) 		0.27
(1.00) 		0.295
(1.00) 		0.12
(1.00) 		0.101
(1.00) 		0.393
(1.00)
'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.18

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
1P GAIN MUTATED 9 19 9
1P GAIN WILD-TYPE 61 21 31

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.12

Table S2.  Gene #11: '6q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
6Q GAIN MUTATED 8 0 0 11 0 3 1
6Q GAIN WILD-TYPE 35 27 12 13 8 20 12

Figure S2.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S3.  Gene #14: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
8P GAIN MUTATED 63 26 21
8P GAIN WILD-TYPE 7 14 19

Figure S3.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.11

Table S4.  Gene #14: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
8P GAIN MUTATED 37 26 8 14 5 15 5
8P GAIN WILD-TYPE 6 1 4 10 3 8 8

Figure S4.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.065

Table S5.  Gene #15: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
8Q GAIN MUTATED 62 28 21
8Q GAIN WILD-TYPE 8 12 19

Figure S5.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.12

Table S6.  Gene #15: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
8Q GAIN MUTATED 40 22 8 15 5 17 4
8Q GAIN WILD-TYPE 3 5 4 9 3 6 9

Figure S6.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S7.  Gene #25: '15q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
15Q GAIN MUTATED 38 8 5
15Q GAIN WILD-TYPE 32 32 35

Figure S7.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S8.  Gene #25: '15q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
15Q GAIN MUTATED 26 12 1 4 0 7 1
15Q GAIN WILD-TYPE 17 15 11 20 8 16 12

Figure S8.  Get High-res Image Gene #25: '15q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S9.  Gene #28: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
17P GAIN MUTATED 9 2 29
17P GAIN WILD-TYPE 39 42 29

Figure S9.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S10.  Gene #28: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
17P GAIN MUTATED 3 23 14
17P GAIN WILD-TYPE 53 26 31

Figure S10.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S11.  Gene #28: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
17P GAIN MUTATED 3 19 18
17P GAIN WILD-TYPE 67 21 22

Figure S11.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S12.  Gene #28: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
17P GAIN MUTATED 2 1 5 11 4 12 5
17P GAIN WILD-TYPE 41 26 7 13 4 11 8

Figure S12.  Get High-res Image Gene #28: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.08

Table S13.  Gene #29: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
17Q GAIN MUTATED 13 7 31
17Q GAIN WILD-TYPE 35 37 27

Figure S13.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S14.  Gene #29: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
17Q GAIN MUTATED 8 27 16
17Q GAIN WILD-TYPE 48 22 29

Figure S14.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S15.  Gene #29: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
17Q GAIN MUTATED 7 23 21
17Q GAIN WILD-TYPE 63 17 19

Figure S15.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S16.  Gene #29: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
17Q GAIN MUTATED 4 3 6 13 4 15 6
17Q GAIN WILD-TYPE 39 24 6 11 4 8 7

Figure S16.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.17

Table S17.  Gene #29: '17q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 21 16 25
17Q GAIN MUTATED 1 11 10 3
17Q GAIN WILD-TYPE 11 10 6 22

Figure S17.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.2

Table S18.  Gene #29: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 15 15
17Q GAIN MUTATED 7 9 9
17Q GAIN WILD-TYPE 37 6 6

Figure S18.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.04

Table S19.  Gene #29: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 13 20 19
17Q GAIN MUTATED 2 9 3 11
17Q GAIN WILD-TYPE 20 4 17 8

Figure S19.  Get High-res Image Gene #29: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S20.  Gene #31: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
19P GAIN MUTATED 23 3 10
19P GAIN WILD-TYPE 33 46 35

Figure S20.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S21.  Gene #31: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
19P GAIN MUTATED 28 3 5
19P GAIN WILD-TYPE 42 37 35

Figure S21.  Get High-res Image Gene #31: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.09

Table S22.  Gene #32: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
19Q GAIN MUTATED 20 2 7
19Q GAIN WILD-TYPE 36 47 38

Figure S22.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S23.  Gene #32: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
19Q GAIN MUTATED 24 1 4
19Q GAIN WILD-TYPE 46 39 36

Figure S23.  Get High-res Image Gene #32: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S24.  Gene #36: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
22Q GAIN MUTATED 9 23 6
22Q GAIN WILD-TYPE 39 21 52

Figure S24.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S25.  Gene #36: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
22Q GAIN MUTATED 30 3 5
22Q GAIN WILD-TYPE 40 37 35

Figure S25.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S26.  Gene #36: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
22Q GAIN MUTATED 11 19 1 4 1 1 1
22Q GAIN WILD-TYPE 32 8 11 20 7 22 12

Figure S26.  Get High-res Image Gene #36: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.16

Table S27.  Gene #53: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
9Q LOSS MUTATED 11 13 34
9Q LOSS WILD-TYPE 37 31 24

Figure S27.  Get High-res Image Gene #53: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.2

Table S28.  Gene #54: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
10P LOSS MUTATED 20 36 21
10P LOSS WILD-TYPE 36 13 24

Figure S28.  Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.17

Table S29.  Gene #54: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
10P LOSS MUTATED 27 31 19
10P LOSS WILD-TYPE 43 9 21

Figure S29.  Get High-res Image Gene #54: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.03

Table S30.  Gene #55: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
10Q LOSS MUTATED 16 36 20
10Q LOSS WILD-TYPE 40 13 25

Figure S30.  Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.11

Table S31.  Gene #55: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
10Q LOSS MUTATED 24 30 18
10Q LOSS WILD-TYPE 46 10 22

Figure S31.  Get High-res Image Gene #55: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.23

Table S32.  Gene #56: '11p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
11P LOSS MUTATED 54 28 16
11P LOSS WILD-TYPE 16 12 24

Figure S32.  Get High-res Image Gene #56: '11p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.23

Table S33.  Gene #56: '11p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 21 16 25
11P LOSS MUTATED 10 16 4 21
11P LOSS WILD-TYPE 2 5 12 4

Figure S33.  Get High-res Image Gene #56: '11p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.22

Table S34.  Gene #56: '11p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 15 15
11P LOSS MUTATED 36 11 4
11P LOSS WILD-TYPE 8 4 11

Figure S34.  Get High-res Image Gene #56: '11p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S35.  Gene #57: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
11Q LOSS MUTATED 30 44 41
11Q LOSS WILD-TYPE 18 0 17

Figure S35.  Get High-res Image Gene #57: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.05

Table S36.  Gene #57: '11q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
11Q LOSS MUTATED 62 32 21
11Q LOSS WILD-TYPE 8 8 19

Figure S36.  Get High-res Image Gene #57: '11q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S37.  Gene #57: '11q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
11Q LOSS MUTATED 35 27 11 15 6 18 3
11Q LOSS WILD-TYPE 8 0 1 9 2 5 10

Figure S37.  Get High-res Image Gene #57: '11q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.094

Table S38.  Gene #57: '11q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 21 16 25
11Q LOSS MUTATED 9 19 8 25
11Q LOSS WILD-TYPE 3 2 8 0

Figure S38.  Get High-res Image Gene #57: '11q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S39.  Gene #59: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
14Q LOSS MUTATED 0 3 0 5 0 10 2
14Q LOSS WILD-TYPE 43 24 12 19 8 13 11

Figure S39.  Get High-res Image Gene #59: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S40.  Gene #60: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
15Q LOSS MUTATED 1 17 11
15Q LOSS WILD-TYPE 55 32 34

Figure S40.  Get High-res Image Gene #60: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S41.  Gene #60: '15q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
15Q LOSS MUTATED 1 13 15
15Q LOSS WILD-TYPE 69 27 25

Figure S41.  Get High-res Image Gene #60: '15q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S42.  Gene #60: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
15Q LOSS MUTATED 0 1 3 7 4 8 6
15Q LOSS WILD-TYPE 43 26 9 17 4 15 7

Figure S42.  Get High-res Image Gene #60: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S43.  Gene #63: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
17P LOSS MUTATED 5 23 9
17P LOSS WILD-TYPE 43 21 49

Figure S43.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.07

Table S44.  Gene #63: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
17P LOSS MUTATED 10 16 2 1 0 4 4
17P LOSS WILD-TYPE 33 11 10 23 8 19 9

Figure S44.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S45.  Gene #67: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
19P LOSS MUTATED 12 5 33
19P LOSS WILD-TYPE 36 39 25

Figure S45.  Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S46.  Gene #67: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
19P LOSS MUTATED 2 31 17
19P LOSS WILD-TYPE 54 18 28

Figure S46.  Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S47.  Gene #67: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
19P LOSS MUTATED 2 27 21
19P LOSS WILD-TYPE 68 13 19

Figure S47.  Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S48.  Gene #67: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
19P LOSS MUTATED 0 2 9 12 5 16 6
19P LOSS WILD-TYPE 43 25 3 12 3 7 7

Figure S48.  Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S49.  Gene #67: '19p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 21 16 25
19P LOSS MUTATED 0 15 7 1
19P LOSS WILD-TYPE 12 6 9 24

Figure S49.  Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S50.  Gene #67: '19p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 15 15
19P LOSS MUTATED 2 14 7
19P LOSS WILD-TYPE 42 1 8

Figure S50.  Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S51.  Gene #67: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 13 20 19
19P LOSS MUTATED 1 11 0 11
19P LOSS WILD-TYPE 21 2 20 8

Figure S51.  Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S52.  Gene #67: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 8 15 11 5 13 11
19P LOSS MUTATED 0 0 14 6 2 1 0
19P LOSS WILD-TYPE 11 8 1 5 3 12 11

Figure S52.  Get High-res Image Gene #67: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S53.  Gene #68: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
19Q LOSS MUTATED 11 7 35
19Q LOSS WILD-TYPE 37 37 23

Figure S53.  Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S54.  Gene #68: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
19Q LOSS MUTATED 1 34 18
19Q LOSS WILD-TYPE 55 15 27

Figure S54.  Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S55.  Gene #68: '19q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
19Q LOSS MUTATED 1 30 22
19Q LOSS WILD-TYPE 69 10 18

Figure S55.  Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S56.  Gene #68: '19q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
19Q LOSS MUTATED 0 1 9 13 5 19 6
19Q LOSS WILD-TYPE 43 26 3 11 3 4 7

Figure S56.  Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S57.  Gene #68: '19q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 21 16 25
19Q LOSS MUTATED 0 15 6 1
19Q LOSS WILD-TYPE 12 6 10 24

Figure S57.  Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S58.  Gene #68: '19q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 15 15
19Q LOSS MUTATED 2 14 6
19Q LOSS WILD-TYPE 42 1 9

Figure S58.  Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S59.  Gene #68: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 13 20 19
19Q LOSS MUTATED 1 11 0 10
19Q LOSS WILD-TYPE 21 2 20 9

Figure S59.  Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S60.  Gene #68: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 8 15 11 5 13 11
19Q LOSS MUTATED 0 0 14 5 2 1 0
19Q LOSS WILD-TYPE 11 8 1 6 3 12 11

Figure S60.  Get High-res Image Gene #68: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S61.  Gene #71: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 49 45
22Q LOSS MUTATED 4 28 13
22Q LOSS WILD-TYPE 52 21 32

Figure S61.  Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S62.  Gene #71: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 40
22Q LOSS MUTATED 6 23 16
22Q LOSS WILD-TYPE 64 17 24

Figure S62.  Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S63.  Gene #71: '22q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 27 12 24 8 23 13
22Q LOSS MUTATED 5 1 7 10 4 13 5
22Q LOSS WILD-TYPE 38 26 5 14 4 10 8

Figure S63.  Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S64.  Gene #71: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 15 15
22Q LOSS MUTATED 3 10 6
22Q LOSS WILD-TYPE 41 5 9

Figure S64.  Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.025

Table S65.  Gene #71: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 13 20 19
22Q LOSS MUTATED 0 7 3 9
22Q LOSS WILD-TYPE 22 6 17 10

Figure S65.  Get High-res Image Gene #71: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.16

Table S66.  Gene #72: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 44 58
XQ LOSS MUTATED 1 11 17
XQ LOSS WILD-TYPE 47 33 41

Figure S66.  Get High-res Image Gene #72: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 150

  • Number of significantly arm-level cnvs = 72

  • Number of molecular subtypes = 8

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

Fisher's exact test

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

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)
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