Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C17M068H
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C17M068H
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 64 arm-level results and 8 molecular subtypes across 158 patients, 65 significant findings detected with Q value < 0.25.

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

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q 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',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 1q loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 5q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'METHLYATION_CNMF'.

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

  • 14q loss cnv correlated to 'CN_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'MRNASEQ_CNMF'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 64 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 65 significant findings detected.

Molecular
subtypes 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
3q gain 0 (0%) 114 2.83e-21
(1.35e-18) 		0.000345
(0.145) 		1.02e-07
(4.69e-05) 		0.000906
(0.37) 		0.000508
(0.211) 		0.0356
(1.00) 		0.154
(1.00) 		0.00158
(0.629)
7p gain 0 (0%) 74 6.27e-12
(2.96e-09) 		2.19e-09
(1.02e-06) 		1.73e-13
(8.22e-11) 		8.37e-10
(3.9e-07) 		0.00578
(1.00) 		0.0465
(1.00) 		0.307
(1.00) 		0.0176
(1.00)
7q gain 0 (0%) 73 2.4e-11
(1.13e-08) 		9.18e-09
(4.24e-06) 		8.04e-13
(3.79e-10) 		2.75e-09
(1.28e-06) 		0.00264
(1.00) 		0.0579
(1.00) 		0.194
(1.00) 		0.0225
(1.00)
17p gain 0 (0%) 72 2.43e-11
(1.14e-08) 		3.19e-08
(1.47e-05) 		3.05e-10
(1.42e-07) 		1.5e-10
(7.04e-08) 		0.0191
(1.00) 		0.0221
(1.00) 		0.0278
(1.00) 		0.0087
(1.00)
9q loss 0 (0%) 139 5.58e-05
(0.0242) 		2.47e-06
(0.00112) 		1.57e-06
(0.000711) 		0.000561
(0.233) 		0.159
(1.00) 		0.0197
(1.00) 		0.663
(1.00) 		0.00175
(0.694)
22q loss 0 (0%) 130 1.18e-05
(0.00526) 		1.96e-05
(0.00864) 		2.92e-05
(0.0128) 		8e-05
(0.0344) 		0.137
(1.00) 		0.0987
(1.00) 		0.268
(1.00) 		0.61
(1.00)
1q gain 0 (0%) 147 0.000117
(0.05) 		3.41e-06
(0.00154) 		0.00107
(0.431) 		0.000288
(0.122) 		0.434
(1.00) 		0.0609
(1.00) 		0.688
(1.00) 		0.142
(1.00)
3p gain 0 (0%) 119 8.55e-21
(4.08e-18) 		0.00077
(0.316) 		9.1e-07
(0.000414) 		0.000162
(0.0694) 		0.00469
(1.00) 		0.0746
(1.00) 		0.241
(1.00) 		0.0183
(1.00)
16q gain 0 (0%) 83 3.12e-14
(1.48e-11) 		0.0413
(1.00) 		0.000284
(0.12) 		4.78e-05
(0.0208) 		0.0096
(1.00) 		0.00159
(0.633) 		0.0163
(1.00) 		0.00154
(0.617)
17q gain 0 (0%) 59 4.38e-09
(2.03e-06) 		0.000627
(0.259) 		4.11e-06
(0.00185) 		4.34e-06
(0.00195) 		0.0971
(1.00) 		0.168
(1.00) 		0.187
(1.00) 		0.0279
(1.00)
3p loss 0 (0%) 147 0.000117
(0.05) 		3.41e-06
(0.00154) 		0.00915
(1.00) 		0.000296
(0.125) 		0.135
(1.00) 		0.259
(1.00) 		0.433
(1.00) 		0.0361
(1.00)
4p loss 0 (0%) 143 1.91e-05
(0.00841) 		7.17e-07
(0.000328) 		2.94e-05
(0.0128) 		0.00129
(0.521) 		0.242
(1.00) 		0.151
(1.00) 		0.931
(1.00) 		0.0237
(1.00)
4q loss 0 (0%) 142 3.64e-07
(0.000167) 		1.72e-07
(7.9e-05) 		8.16e-06
(0.00365) 		0.00103
(0.419) 		0.109
(1.00) 		0.409
(1.00) 		0.821
(1.00) 		0.0315
(1.00)
9p loss 0 (0%) 140 1.45e-05
(0.00645) 		1.05e-05
(0.00469) 		1.57e-06
(0.000711) 		0.00554
(1.00) 		0.223
(1.00) 		0.338
(1.00) 		0.564
(1.00) 		0.0368
(1.00)
16p gain 0 (0%) 79 2.58e-13
(1.22e-10) 		0.162
(1.00) 		0.00236
(0.931) 		2.09e-05
(0.00917) 		0.0201
(1.00) 		0.00784
(1.00) 		0.00781
(1.00) 		0.00469
(1.00)
13q loss 0 (0%) 143 0.00101
(0.413) 		7.17e-07
(0.000328) 		0.000273
(0.116) 		0.00286
(1.00) 		0.0206
(1.00) 		0.0497
(1.00) 		0.0996
(1.00) 		0.0276
(1.00)
2p gain 0 (0%) 136 6.32e-05
(0.0273) 		0.011
(1.00) 		0.00447
(1.00) 		0.197
(1.00) 		0.0834
(1.00) 		0.581
(1.00) 		0.0225
(1.00) 		0.0907
(1.00)
2q gain 0 (0%) 133 3.25e-05
(0.0142) 		0.0356
(1.00) 		0.0234
(1.00) 		0.345
(1.00) 		0.242
(1.00) 		0.623
(1.00) 		0.112
(1.00) 		0.161
(1.00)
5p gain 0 (0%) 140 1.45e-05
(0.00645) 		0.0113
(1.00) 		0.132
(1.00) 		0.072
(1.00) 		0.336
(1.00) 		0.8
(1.00) 		0.255
(1.00) 		1
(1.00)
5q gain 0 (0%) 140 1.45e-05
(0.00645) 		0.0113
(1.00) 		0.191
(1.00) 		0.072
(1.00) 		0.47
(1.00) 		0.8
(1.00) 		0.255
(1.00) 		0.572
(1.00)
1p loss 0 (0%) 139 0.000426
(0.178) 		0.248
(1.00) 		0.0353
(1.00) 		0.551
(1.00) 		0.391
(1.00) 		0.55
(1.00) 		0.161
(1.00) 		0.626
(1.00)
1q loss 0 (0%) 148 0.000192
(0.0817) 		0.0673
(1.00) 		0.76
(1.00) 		0.133
(1.00) 		0.529
(1.00) 		0.153
(1.00) 		0.257
(1.00) 		0.198
(1.00)
5q loss 0 (0%) 153 0.444
(1.00) 		0.0288
(1.00) 		0.0731
(1.00) 		0.000561
(0.233) 		0.111
(1.00) 		0.189
(1.00) 		0.16
(1.00) 		0.258
(1.00)
10p loss 0 (0%) 149 5.57e-05
(0.0242) 		0.00448
(1.00) 		0.0116
(1.00) 		0.0546
(1.00) 		0.0794
(1.00) 		0.212
(1.00) 		0.873
(1.00) 		0.00391
(1.00)
10q loss 0 (0%) 149 5.57e-05
(0.0242) 		0.00133
(0.534) 		0.0116
(1.00) 		0.0047
(1.00) 		0.00929
(1.00) 		0.0722
(1.00) 		0.56
(1.00) 		0.00692
(1.00)
11q loss 0 (0%) 147 0.00226
(0.894) 		0.000419
(0.176) 		0.039
(1.00) 		0.00949
(1.00) 		0.851
(1.00) 		0.301
(1.00) 		0.727
(1.00) 		0.151
(1.00)
14q loss 0 (0%) 128 1.96e-16
(9.31e-14) 		0.0462
(1.00) 		0.000846
(0.347) 		0.0232
(1.00) 		0.713
(1.00) 		0.633
(1.00) 		0.916
(1.00) 		0.585
(1.00)
15q loss 0 (0%) 143 0.000434
(0.181) 		0.0479
(1.00) 		0.0216
(1.00) 		0.102
(1.00) 		0.887
(1.00) 		0.748
(1.00) 		0.855
(1.00) 		0.48
(1.00)
18q loss 0 (0%) 136 0.0387
(1.00) 		0.00106
(0.429) 		0.000259
(0.11) 		0.00362
(1.00) 		0.706
(1.00) 		0.262
(1.00) 		0.175
(1.00) 		0.441
(1.00)
1p gain 0 (0%) 155 0.0453
(1.00) 		0.043
(1.00) 		0.264
(1.00) 		0.0282
(1.00) 		0.0532
(1.00) 		0.776
(1.00) 		0.0281
(1.00) 		0.678
(1.00)
4p gain 0 (0%) 153 0.614
(1.00) 		0.465
(1.00) 		0.698
(1.00) 		0.706
(1.00) 		0.689
(1.00) 		1
(1.00)
4q gain 0 (0%) 154 0.557
(1.00) 		0.465
(1.00) 		0.915
(1.00) 		0.819
(1.00) 		0.866
(1.00) 		0.639
(1.00)
6p gain 0 (0%) 153 0.372
(1.00) 		0.209
(1.00) 		0.293
(1.00) 		0.24
(1.00) 		0.233
(1.00) 		0.274
(1.00) 		0.465
(1.00) 		1
(1.00)
6q gain 0 (0%) 153 0.119
(1.00) 		0.209
(1.00) 		0.556
(1.00) 		0.484
(1.00) 		0.179
(1.00) 		0.196
(1.00) 		0.4
(1.00) 		1
(1.00)
8p gain 0 (0%) 148 0.234
(1.00) 		0.037
(1.00) 		0.351
(1.00) 		0.141
(1.00) 		0.335
(1.00) 		0.189
(1.00) 		0.345
(1.00) 		0.0533
(1.00)
8q gain 0 (0%) 146 0.929
(1.00) 		0.00265
(1.00) 		0.0454
(1.00) 		0.0121
(1.00) 		0.111
(1.00) 		0.26
(1.00) 		0.188
(1.00) 		0.0297
(1.00)
10p gain 0 (0%) 153 0.52
(1.00) 		0.043
(1.00) 		0.651
(1.00) 		0.706
(1.00) 		0.269
(1.00) 		0.734
(1.00) 		0.293
(1.00) 		0.289
(1.00)
10q gain 0 (0%) 154 0.113
(1.00) 		0.759
(1.00) 		0.819
(1.00) 		0.201
(1.00) 		0.688
(1.00)
11p gain 0 (0%) 155 0.0453
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 0 (0%) 155 0.0453
(1.00) 		1
(1.00) 		1
(1.00)
12p gain 0 (0%) 101 0.00389
(1.00) 		0.217
(1.00) 		0.0401
(1.00) 		0.0169
(1.00) 		0.00711
(1.00) 		0.088
(1.00) 		0.189
(1.00) 		0.0438
(1.00)
12q gain 0 (0%) 101 0.00389
(1.00) 		0.217
(1.00) 		0.0401
(1.00) 		0.0169
(1.00) 		0.00711
(1.00) 		0.088
(1.00) 		0.189
(1.00) 		0.0438
(1.00)
13q gain 0 (0%) 141 0.0858
(1.00) 		0.612
(1.00) 		0.0414
(1.00) 		0.645
(1.00) 		0.566
(1.00) 		0.941
(1.00) 		0.931
(1.00) 		0.814
(1.00)
15q gain 0 (0%) 155 0.0453
(1.00) 		0.465
(1.00)
18p gain 0 (0%) 151 0.376
(1.00) 		0.124
(1.00) 		0.945
(1.00) 		0.763
(1.00) 		0.507
(1.00) 		1
(1.00) 		0.689
(1.00) 		1
(1.00)
18q gain 0 (0%) 154 0.048
(1.00) 		0.257
(1.00) 		0.309
(1.00) 		0.287
(1.00) 		0.83
(1.00) 		0.688
(1.00) 		1
(1.00) 		1
(1.00)
20p gain 0 (0%) 111 0.0356
(1.00) 		0.022
(1.00) 		0.00139
(0.556) 		0.0124
(1.00) 		0.108
(1.00) 		0.624
(1.00) 		0.392
(1.00) 		0.2
(1.00)
20q gain 0 (0%) 110 0.048
(1.00) 		0.0556
(1.00) 		0.00417
(1.00) 		0.0433
(1.00) 		0.0838
(1.00) 		0.701
(1.00) 		0.178
(1.00) 		0.33
(1.00)
21q gain 0 (0%) 150 0.369
(1.00) 		0.416
(1.00) 		0.00626
(1.00) 		0.179
(1.00) 		0.721
(1.00) 		0.772
(1.00) 		0.0248
(1.00) 		1
(1.00)
Xq gain 0 (0%) 153 0.072
(1.00) 		0.209
(1.00) 		0.651
(1.00) 		0.706
(1.00) 		0.288
(1.00) 		0.734
(1.00) 		0.832
(1.00) 		0.0314
(1.00)
3q loss 0 (0%) 155 0.602
(1.00) 		0.043
(1.00) 		0.264
(1.00) 		0.0282
(1.00) 		0.0754
(1.00) 		0.507
(1.00) 		0.775
(1.00) 		0.0571
(1.00)
5p loss 0 (0%) 154 0.819
(1.00) 		0.0604
(1.00) 		0.264
(1.00) 		0.00387
(1.00) 		0.315
(1.00) 		0.386
(1.00) 		0.385
(1.00) 		0.516
(1.00)
6p loss 0 (0%) 148 0.0567
(1.00) 		0.243
(1.00) 		0.245
(1.00) 		0.779
(1.00) 		0.722
(1.00) 		0.832
(1.00) 		0.905
(1.00) 		0.617
(1.00)
6q loss 0 (0%) 146 0.047
(1.00) 		0.056
(1.00) 		0.0147
(1.00) 		0.163
(1.00) 		0.528
(1.00) 		0.522
(1.00) 		0.727
(1.00) 		0.151
(1.00)
8p loss 0 (0%) 154 0.273
(1.00) 		0.789
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
8q loss 0 (0%) 155 0.0453
(1.00)
11p loss 0 (0%) 149 0.0119
(1.00) 		0.017
(1.00) 		0.0299
(1.00) 		0.00859
(1.00) 		0.7
(1.00) 		0.107
(1.00) 		0.813
(1.00) 		0.0361
(1.00)
16q loss 0 (0%) 154 0.0132
(1.00) 		0.0117
(1.00) 		0.0731
(1.00) 		0.0055
(1.00) 		0.866
(1.00) 		0.11
(1.00) 		0.642
(1.00) 		0.187
(1.00)
17p loss 0 (0%) 153 0.119
(1.00) 		0.0117
(1.00) 		0.044
(1.00) 		0.000979
(0.399) 		0.201
(1.00) 		0.189
(1.00) 		0.32
(1.00) 		0.0805
(1.00)
18p loss 0 (0%) 137 0.0534
(1.00) 		0.0027
(1.00) 		0.000669
(0.276) 		0.00739
(1.00) 		0.322
(1.00) 		0.226
(1.00) 		0.175
(1.00) 		0.686
(1.00)
19p loss 0 (0%) 151 0.00378
(1.00) 		0.364
(1.00) 		1
(1.00) 		0.646
(1.00) 		0.415
(1.00) 		0.196
(1.00) 		0.549
(1.00) 		0.375
(1.00)
19q loss 0 (0%) 152 0.0122
(1.00) 		0.573
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.415
(1.00) 		0.553
(1.00) 		0.549
(1.00) 		1
(1.00)
21q loss 0 (0%) 138 0.159
(1.00) 		0.54
(1.00) 		0.858
(1.00) 		0.331
(1.00) 		0.208
(1.00) 		0.568
(1.00) 		0.695
(1.00) 		0.322
(1.00)
Xq loss 0 (0%) 153 0.717
(1.00) 		0.473
(1.00) 		0.539
(1.00) 		0.57
(1.00) 		0.403
(1.00) 		0.197
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
1Q GAIN CNV 0 10 1
1Q GAIN WILD-TYPE 36 42 69

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 3.41e-06 (Fisher's exact test), Q value = 0.0015

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
1Q GAIN CNV 0 10 0
1Q GAIN WILD-TYPE 37 33 62

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000288 (Fisher's exact test), Q value = 0.12

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
1Q GAIN CNV 4 0 7
1Q GAIN WILD-TYPE 19 74 37

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 6.32e-05 (Fisher's exact test), Q value = 0.027

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
2P GAIN CNV 12 8 2
2P GAIN WILD-TYPE 24 44 68

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

'2q gain' versus 'CN_CNMF'

P value = 3.25e-05 (Fisher's exact test), Q value = 0.014

Table S5.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
2Q GAIN CNV 12 11 2
2Q GAIN WILD-TYPE 24 41 68

Figure S5.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 8.55e-21 (Fisher's exact test), Q value = 4.1e-18

Table S6.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
3P GAIN CNV 31 5 3
3P GAIN WILD-TYPE 5 47 67

Figure S6.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 9.1e-07 (Fisher's exact test), Q value = 0.00041

Table S7.  Gene #5: '3p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
3P GAIN CNV 1 17 11 7
3P GAIN WILD-TYPE 50 25 14 16

Figure S7.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000162 (Fisher's exact test), Q value = 0.069

Table S8.  Gene #5: '3p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
3P GAIN CNV 0 28 8
3P GAIN WILD-TYPE 23 46 36

Figure S8.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 2.83e-21 (Fisher's exact test), Q value = 1.4e-18

Table S9.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
3Q GAIN CNV 33 6 5
3Q GAIN WILD-TYPE 3 46 65

Figure S9.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.000345 (Fisher's exact test), Q value = 0.14

Table S10.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
3Q GAIN CNV 10 3 25
3Q GAIN WILD-TYPE 27 40 37

Figure S10.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1.02e-07 (Fisher's exact test), Q value = 4.7e-05

Table S11.  Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
3Q GAIN CNV 1 17 12 10
3Q GAIN WILD-TYPE 50 25 13 13

Figure S11.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.000508 (Fisher's exact test), Q value = 0.21

Table S12.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 45 41 22
3Q GAIN CNV 14 6 16 1
3Q GAIN WILD-TYPE 20 39 25 21

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.0065

Table S13.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
5P GAIN CNV 1 15 2
5P GAIN WILD-TYPE 35 37 68

Figure S13.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.0065

Table S14.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
5Q GAIN CNV 1 15 2
5Q GAIN WILD-TYPE 35 37 68

Figure S14.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 6.27e-12 (Fisher's exact test), Q value = 3e-09

Table S15.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
7P GAIN CNV 34 11 39
7P GAIN WILD-TYPE 2 41 31

Figure S15.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 2.19e-09 (Fisher's exact test), Q value = 1e-06

Table S16.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
7P GAIN CNV 17 8 49
7P GAIN WILD-TYPE 20 35 13

Figure S16.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1.73e-13 (Fisher's exact test), Q value = 8.2e-11

Table S17.  Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
7P GAIN CNV 10 38 10 19
7P GAIN WILD-TYPE 41 4 15 4

Figure S17.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.37e-10 (Fisher's exact test), Q value = 3.9e-07

Table S18.  Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
7P GAIN CNV 6 59 12
7P GAIN WILD-TYPE 17 15 32

Figure S18.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 2.4e-11 (Fisher's exact test), Q value = 1.1e-08

Table S19.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
7Q GAIN CNV 34 12 39
7Q GAIN WILD-TYPE 2 40 31

Figure S19.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 9.18e-09 (Fisher's exact test), Q value = 4.2e-06

Table S20.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
7Q GAIN CNV 17 9 49
7Q GAIN WILD-TYPE 20 34 13

Figure S20.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 8.04e-13 (Fisher's exact test), Q value = 3.8e-10

Table S21.  Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
7Q GAIN CNV 11 38 10 19
7Q GAIN WILD-TYPE 40 4 15 4

Figure S21.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.75e-09 (Fisher's exact test), Q value = 1.3e-06

Table S22.  Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
7Q GAIN CNV 7 59 12
7Q GAIN WILD-TYPE 16 15 32

Figure S22.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 2.58e-13 (Fisher's exact test), Q value = 1.2e-10

Table S23.  Gene #25: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
16P GAIN CNV 36 21 22
16P GAIN WILD-TYPE 0 31 48

Figure S23.  Get High-res Image Gene #25: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.09e-05 (Fisher's exact test), Q value = 0.0092

Table S24.  Gene #25: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
16P GAIN CNV 2 45 25
16P GAIN WILD-TYPE 21 29 19

Figure S24.  Get High-res Image Gene #25: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 3.12e-14 (Fisher's exact test), Q value = 1.5e-11

Table S25.  Gene #26: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
16Q GAIN CNV 36 18 21
16Q GAIN WILD-TYPE 0 34 49

Figure S25.  Get High-res Image Gene #26: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.000284 (Fisher's exact test), Q value = 0.12

Table S26.  Gene #26: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
16Q GAIN CNV 13 25 18 12
16Q GAIN WILD-TYPE 38 17 7 11

Figure S26.  Get High-res Image Gene #26: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.78e-05 (Fisher's exact test), Q value = 0.021

Table S27.  Gene #26: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
16Q GAIN CNV 2 44 22
16Q GAIN WILD-TYPE 21 30 22

Figure S27.  Get High-res Image Gene #26: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 2.43e-11 (Fisher's exact test), Q value = 1.1e-08

Table S28.  Gene #27: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
17P GAIN CNV 34 12 40
17P GAIN WILD-TYPE 2 40 30

Figure S28.  Get High-res Image Gene #27: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 3.19e-08 (Fisher's exact test), Q value = 1.5e-05

Table S29.  Gene #27: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
17P GAIN CNV 17 10 49
17P GAIN WILD-TYPE 20 33 13

Figure S29.  Get High-res Image Gene #27: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 3.05e-10 (Fisher's exact test), Q value = 1.4e-07

Table S30.  Gene #27: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
17P GAIN CNV 10 36 15 16
17P GAIN WILD-TYPE 41 6 10 7

Figure S30.  Get High-res Image Gene #27: '17p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.5e-10 (Fisher's exact test), Q value = 7e-08

Table S31.  Gene #27: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
17P GAIN CNV 3 59 15
17P GAIN WILD-TYPE 20 15 29

Figure S31.  Get High-res Image Gene #27: '17p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 4.38e-09 (Fisher's exact test), Q value = 2e-06

Table S32.  Gene #28: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
17Q GAIN CNV 35 19 45
17Q GAIN WILD-TYPE 1 33 25

Figure S32.  Get High-res Image Gene #28: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 4.11e-06 (Fisher's exact test), Q value = 0.0018

Table S33.  Gene #28: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
17Q GAIN CNV 19 37 17 16
17Q GAIN WILD-TYPE 32 5 8 7

Figure S33.  Get High-res Image Gene #28: '17q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.34e-06 (Fisher's exact test), Q value = 0.0019

Table S34.  Gene #28: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
17Q GAIN CNV 7 60 22
17Q GAIN WILD-TYPE 16 14 22

Figure S34.  Get High-res Image Gene #28: '17q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.000426 (Fisher's exact test), Q value = 0.18

Table S35.  Gene #35: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
1P LOSS CNV 1 14 4
1P LOSS WILD-TYPE 35 38 66

Figure S35.  Get High-res Image Gene #35: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.082

Table S36.  Gene #36: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
1Q LOSS CNV 1 9 0
1Q LOSS WILD-TYPE 35 43 70

Figure S36.  Get High-res Image Gene #36: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.05

Table S37.  Gene #37: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
3P LOSS CNV 0 10 1
3P LOSS WILD-TYPE 36 42 69

Figure S37.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 3.41e-06 (Fisher's exact test), Q value = 0.0015

Table S38.  Gene #37: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
3P LOSS CNV 0 10 0
3P LOSS WILD-TYPE 37 33 62

Figure S38.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000296 (Fisher's exact test), Q value = 0.12

Table S39.  Gene #37: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
3P LOSS CNV 2 0 8
3P LOSS WILD-TYPE 21 74 36

Figure S39.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.0084

Table S40.  Gene #39: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
4P LOSS CNV 0 13 2
4P LOSS WILD-TYPE 36 39 68

Figure S40.  Get High-res Image Gene #39: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 7.17e-07 (Fisher's exact test), Q value = 0.00033

Table S41.  Gene #39: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
4P LOSS CNV 0 13 1
4P LOSS WILD-TYPE 37 30 61

Figure S41.  Get High-res Image Gene #39: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 2.94e-05 (Fisher's exact test), Q value = 0.013

Table S42.  Gene #39: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
4P LOSS CNV 12 0 0 0
4P LOSS WILD-TYPE 39 42 25 23

Figure S42.  Get High-res Image Gene #39: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 3.64e-07 (Fisher's exact test), Q value = 0.00017

Table S43.  Gene #40: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
4Q LOSS CNV 0 15 1
4Q LOSS WILD-TYPE 36 37 69

Figure S43.  Get High-res Image Gene #40: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1.72e-07 (Fisher's exact test), Q value = 7.9e-05

Table S44.  Gene #40: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
4Q LOSS CNV 0 14 1
4Q LOSS WILD-TYPE 37 29 61

Figure S44.  Get High-res Image Gene #40: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 8.16e-06 (Fisher's exact test), Q value = 0.0036

Table S45.  Gene #40: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
4Q LOSS CNV 13 0 0 0
4Q LOSS WILD-TYPE 38 42 25 23

Figure S45.  Get High-res Image Gene #40: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000561 (Fisher's exact test), Q value = 0.23

Table S46.  Gene #42: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
5Q LOSS CNV 4 0 0
5Q LOSS WILD-TYPE 19 74 44

Figure S46.  Get High-res Image Gene #42: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.0065

Table S47.  Gene #47: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
9P LOSS CNV 1 15 2
9P LOSS WILD-TYPE 35 37 68

Figure S47.  Get High-res Image Gene #47: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0047

Table S48.  Gene #47: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
9P LOSS CNV 3 12 0
9P LOSS WILD-TYPE 34 31 62

Figure S48.  Get High-res Image Gene #47: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1.57e-06 (Fisher's exact test), Q value = 0.00071

Table S49.  Gene #47: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
9P LOSS CNV 16 0 1 0
9P LOSS WILD-TYPE 35 42 24 23

Figure S49.  Get High-res Image Gene #47: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 5.58e-05 (Fisher's exact test), Q value = 0.024

Table S50.  Gene #48: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
9Q LOSS CNV 1 15 3
9Q LOSS WILD-TYPE 35 37 67

Figure S50.  Get High-res Image Gene #48: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 2.47e-06 (Fisher's exact test), Q value = 0.0011

Table S51.  Gene #48: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
9Q LOSS CNV 4 13 0
9Q LOSS WILD-TYPE 33 30 62

Figure S51.  Get High-res Image Gene #48: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1.57e-06 (Fisher's exact test), Q value = 0.00071

Table S52.  Gene #48: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
9Q LOSS CNV 16 0 1 0
9Q LOSS WILD-TYPE 35 42 24 23

Figure S52.  Get High-res Image Gene #48: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000561 (Fisher's exact test), Q value = 0.23

Table S53.  Gene #48: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
9Q LOSS CNV 6 2 9
9Q LOSS WILD-TYPE 17 72 35

Figure S53.  Get High-res Image Gene #48: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 5.57e-05 (Fisher's exact test), Q value = 0.024

Table S54.  Gene #49: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
10P LOSS CNV 0 9 0
10P LOSS WILD-TYPE 36 43 70

Figure S54.  Get High-res Image Gene #49: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 5.57e-05 (Fisher's exact test), Q value = 0.024

Table S55.  Gene #50: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
10Q LOSS CNV 0 9 0
10Q LOSS WILD-TYPE 36 43 70

Figure S55.  Get High-res Image Gene #50: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.000419 (Fisher's exact test), Q value = 0.18

Table S56.  Gene #52: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
11Q LOSS CNV 0 9 2
11Q LOSS WILD-TYPE 37 34 60

Figure S56.  Get High-res Image Gene #52: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 7.17e-07 (Fisher's exact test), Q value = 0.00033

Table S57.  Gene #53: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
13Q LOSS CNV 0 13 1
13Q LOSS WILD-TYPE 37 30 61

Figure S57.  Get High-res Image Gene #53: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.000273 (Fisher's exact test), Q value = 0.12

Table S58.  Gene #53: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
13Q LOSS CNV 12 1 0 0
13Q LOSS WILD-TYPE 39 41 25 23

Figure S58.  Get High-res Image Gene #53: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 1.96e-16 (Fisher's exact test), Q value = 9.3e-14

Table S59.  Gene #54: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
14Q LOSS CNV 1 29 0
14Q LOSS WILD-TYPE 35 23 70

Figure S59.  Get High-res Image Gene #54: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.000434 (Fisher's exact test), Q value = 0.18

Table S60.  Gene #55: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
15Q LOSS CNV 1 12 2
15Q LOSS WILD-TYPE 35 40 68

Figure S60.  Get High-res Image Gene #55: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.000259 (Fisher's exact test), Q value = 0.11

Table S61.  Gene #59: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
18Q LOSS CNV 14 1 0 2
18Q LOSS WILD-TYPE 37 41 25 21

Figure S61.  Get High-res Image Gene #59: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0053

Table S62.  Gene #63: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 52 70
22Q LOSS CNV 1 20 7
22Q LOSS WILD-TYPE 35 32 63

Figure S62.  Get High-res Image Gene #63: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.0086

Table S63.  Gene #63: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 43 62
22Q LOSS CNV 2 18 6
22Q LOSS WILD-TYPE 35 25 56

Figure S63.  Get High-res Image Gene #63: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 2.92e-05 (Fisher's exact test), Q value = 0.013

Table S64.  Gene #63: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 42 25 23
22Q LOSS CNV 19 3 2 0
22Q LOSS WILD-TYPE 32 39 23 23

Figure S64.  Get High-res Image Gene #63: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.034

Table S65.  Gene #63: '22q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 44
22Q LOSS CNV 4 4 16
22Q LOSS WILD-TYPE 19 70 28

Figure S65.  Get High-res Image Gene #63: '22q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 158

  • Number of significantly arm-level cnvs = 64

  • 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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