Correlation between copy number variations of arm-level result and molecular subtypes
Thymoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1B8572M
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/C1B8572M
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 50 arm-level events and 8 molecular subtypes across 123 patients, 112 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 15q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

  • 3p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 6p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 12p loss cnv correlated to 'METHLYATION_CNMF'.

  • 12q loss cnv correlated to 'METHLYATION_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • 22q loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 50 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, 112 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
1q gain 22 (18%) 101 1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004)
7p gain 16 (13%) 107 1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		0.00016
(0.0522) 		1e-05
(0.004) 		2e-05
(0.00706)
7q gain 16 (13%) 107 1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		2e-05
(0.00706) 		0.00011
(0.0364) 		1e-05
(0.004) 		4e-05
(0.0136)
14q gain 13 (11%) 110 1e-05
(0.004) 		2e-05
(0.00706) 		1e-05
(0.004) 		4e-05
(0.0136) 		0.00019
(0.0614) 		6e-05
(0.0202) 		1e-05
(0.004) 		2e-05
(0.00706)
6p loss 20 (16%) 103 1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		4e-05
(0.0136) 		1e-05
(0.004) 		1e-05
(0.004)
6q loss 19 (15%) 104 1e-05
(0.004) 		1e-05
(0.004) 		1e-05
(0.004) 		2e-05
(0.00706) 		2e-05
(0.00706) 		0.00028
(0.0885) 		1e-05
(0.004) 		7e-05
(0.0234)
3p loss 12 (10%) 111 1e-05
(0.004) 		1e-05
(0.004) 		0.00058
(0.173) 		0.00038
(0.117) 		0.00073
(0.212) 		0.0044
(1.00) 		1e-05
(0.004) 		0.00045
(0.137)
8p gain 12 (10%) 111 0.00037
(0.115) 		0.0215
(1.00) 		0.00041
(0.126) 		0.0001
(0.0332) 		0.00072
(0.211) 		0.00172
(0.471) 		0.00023
(0.0734) 		0.00037
(0.115)
8q gain 12 (10%) 111 0.00023
(0.0734) 		0.0216
(1.00) 		0.00035
(0.11) 		0.00013
(0.0428) 		0.00077
(0.223) 		0.00169
(0.465) 		0.00019
(0.0614) 		0.00052
(0.156)
9q gain 11 (9%) 112 1e-05
(0.004) 		0.00012
(0.0396) 		0.00035
(0.11) 		0.00044
(0.135) 		0.0106
(1.00) 		0.00595
(1.00) 		0.00491
(1.00) 		0.00079
(0.228)
5p gain 11 (9%) 112 1e-05
(0.004) 		2e-05
(0.00706) 		0.00115
(0.327) 		0.00108
(0.308) 		0.00072
(0.211) 		0.0133
(1.00) 		2e-05
(0.00706) 		0.00184
(0.502)
9p gain 11 (9%) 112 1e-05
(0.004) 		0.00016
(0.0522) 		0.00038
(0.117) 		0.00045
(0.137) 		0.01
(1.00) 		0.0064
(1.00) 		0.00478
(1.00) 		0.00107
(0.306)
16q loss 13 (11%) 110 0.0583
(1.00) 		0.00485
(1.00) 		2e-05
(0.00706) 		1e-05
(0.004) 		0.0595
(1.00) 		2e-05
(0.00706) 		0.00126
(0.35) 		0.00067
(0.198)
5q gain 9 (7%) 114 1e-05
(0.004) 		2e-05
(0.00706) 		0.00667
(1.00) 		0.00454
(1.00) 		0.00341
(0.883) 		0.0173
(1.00) 		0.00019
(0.0614) 		0.00296
(0.77)
20p gain 10 (8%) 113 0.00058
(0.173) 		0.0243
(1.00) 		0.00089
(0.256) 		0.0003
(0.0942) 		0.0532
(1.00) 		0.0107
(1.00) 		0.00055
(0.164) 		0.054
(1.00)
20q gain 10 (8%) 113 0.00064
(0.189) 		0.0246
(1.00) 		0.001
(0.287) 		0.00028
(0.0885) 		0.0531
(1.00) 		0.0109
(1.00) 		0.00049
(0.147) 		0.0547
(1.00)
11p loss 9 (7%) 114 1e-05
(0.004) 		1e-05
(0.004) 		0.00702
(1.00) 		0.00475
(1.00) 		0.00841
(1.00) 		0.0514
(1.00) 		0.00014
(0.0458) 		0.00831
(1.00)
21q loss 9 (7%) 114 1e-05
(0.004) 		1e-05
(0.004) 		0.00517
(1.00) 		0.00461
(1.00) 		0.00938
(1.00) 		0.0517
(1.00) 		0.00023
(0.0734) 		0.00838
(1.00)
15q gain 12 (10%) 111 0.00017
(0.0551) 		6e-05
(0.0202) 		0.0258
(1.00) 		0.016
(1.00) 		0.0146
(1.00) 		0.0207
(1.00) 		0.00141
(0.391) 		0.00532
(1.00)
3q loss 7 (6%) 116 0.00068
(0.2) 		0.00022
(0.0704) 		0.0243
(1.00) 		0.0221
(1.00) 		0.0326
(1.00) 		0.0851
(1.00) 		0.00218
(0.582) 		0.00902
(1.00)
11q loss 7 (6%) 116 4e-05
(0.0136) 		4e-05
(0.0136) 		0.0246
(1.00) 		0.00805
(1.00) 		0.0338
(1.00) 		0.111
(1.00) 		0.00222
(0.591) 		0.00852
(1.00)
1p gain 8 (7%) 115 0.00013
(0.0428) 		0.0211
(1.00) 		0.00678
(1.00) 		0.00254
(0.668) 		0.0217
(1.00) 		0.0215
(1.00) 		0.00344
(0.888) 		0.00661
(1.00)
12p loss 8 (7%) 115 0.00394
(1.00) 		9e-05
(0.03) 		0.00683
(1.00) 		0.00834
(1.00) 		0.0211
(1.00) 		0.0529
(1.00) 		0.00357
(0.917) 		0.0193
(1.00)
12q loss 7 (6%) 116 0.00198
(0.535) 		1e-05
(0.004) 		0.00771
(1.00) 		0.00878
(1.00) 		0.0331
(1.00) 		0.122
(1.00) 		0.00197
(0.534) 		0.0357
(1.00)
13q loss 14 (11%) 109 2e-05
(0.00706) 		0.00586
(1.00) 		0.0662
(1.00) 		0.0405
(1.00) 		0.371
(1.00) 		0.577
(1.00) 		0.0598
(1.00) 		0.35
(1.00)
19p loss 3 (2%) 120 0.103
(1.00) 		0.35
(1.00) 		0.00121
(0.341) 		0.00044
(0.135) 		0.199
(1.00) 		0.00962
(1.00) 		0.106
(1.00) 		0.06
(1.00)
19q loss 3 (2%) 120 0.103
(1.00) 		0.347
(1.00) 		0.00123
(0.346) 		0.00045
(0.137) 		0.198
(1.00) 		0.00963
(1.00) 		0.106
(1.00) 		0.0594
(1.00)
22q loss 13 (11%) 110 1e-05
(0.004) 		0.114
(1.00) 		0.086
(1.00) 		0.0375
(1.00) 		0.111
(1.00) 		0.334
(1.00) 		0.0546
(1.00) 		0.333
(1.00)
3q gain 5 (4%) 118 0.26
(1.00) 		0.139
(1.00) 		0.178
(1.00) 		0.0422
(1.00) 		0.726
(1.00) 		0.00538
(1.00) 		0.353
(1.00) 		0.171
(1.00)
12p gain 4 (3%) 119 0.0279
(1.00) 		0.149
(1.00) 		0.00471
(1.00) 		0.00272
(0.71) 		0.172
(1.00) 		0.0273
(1.00) 		0.0449
(1.00) 		0.17
(1.00)
12q gain 4 (3%) 119 0.0287
(1.00) 		0.146
(1.00) 		0.00447
(1.00) 		0.0027
(0.707) 		0.171
(1.00) 		0.0268
(1.00) 		0.0455
(1.00) 		0.171
(1.00)
17q gain 7 (6%) 116 0.394
(1.00) 		0.22
(1.00) 		0.0481
(1.00) 		0.0043
(1.00) 		0.77
(1.00) 		0.0682
(1.00) 		0.439
(1.00) 		0.4
(1.00)
18p gain 3 (2%) 120 0.102
(1.00) 		0.176
(1.00) 		0.0329
(1.00) 		0.0321
(1.00) 		0.197
(1.00) 		0.286
(1.00) 		0.104
(1.00) 		0.503
(1.00)
18q gain 3 (2%) 120 0.104
(1.00) 		0.177
(1.00) 		0.0331
(1.00) 		0.0319
(1.00) 		0.196
(1.00) 		0.288
(1.00) 		0.105
(1.00) 		0.501
(1.00)
19p gain 3 (2%) 120 0.0238
(1.00) 		0.175
(1.00) 		0.303
(1.00) 		0.336
(1.00) 		0.198
(1.00) 		0.611
(1.00) 		0.106
(1.00) 		0.302
(1.00)
19q gain 3 (2%) 120 0.0248
(1.00) 		0.177
(1.00) 		0.304
(1.00) 		0.338
(1.00) 		0.196
(1.00) 		0.609
(1.00) 		0.105
(1.00) 		0.302
(1.00)
21q gain 3 (2%) 120 0.276
(1.00) 		0.349
(1.00) 		0.486
(1.00) 		0.199
(1.00) 		0.649
(1.00) 		0.341
(1.00) 		0.74
(1.00) 		0.62
(1.00)
22q gain 5 (4%) 118 0.0355
(1.00) 		0.0319
(1.00) 		0.322
(1.00) 		0.236
(1.00) 		0.323
(1.00) 		0.61
(1.00) 		0.223
(1.00) 		0.683
(1.00)
xq gain 5 (4%) 118 0.00124
(0.347) 		0.00759
(1.00) 		0.0505
(1.00) 		0.0682
(1.00) 		0.147
(1.00) 		0.271
(1.00) 		0.0117
(1.00) 		0.104
(1.00)
1p loss 4 (3%) 119 0.00532
(1.00) 		0.00243
(0.642) 		0.0555
(1.00) 		0.126
(1.00) 		0.173
(1.00) 		0.526
(1.00) 		0.0449
(1.00) 		0.301
(1.00)
4p loss 5 (4%) 118 0.00737
(1.00) 		0.0116
(1.00) 		0.048
(1.00) 		0.0661
(1.00) 		0.325
(1.00) 		0.383
(1.00) 		0.052
(1.00) 		0.264
(1.00)
4q loss 4 (3%) 119 0.0284
(1.00) 		0.061
(1.00) 		0.136
(1.00) 		0.145
(1.00) 		0.435
(1.00) 		0.114
(1.00) 		0.103
(1.00) 		0.0864
(1.00)
9p loss 4 (3%) 119 0.25
(1.00) 		0.106
(1.00) 		0.0214
(1.00) 		0.00385
(0.986) 		1
(1.00) 		0.0595
(1.00) 		1
(1.00) 		0.332
(1.00)
10p loss 3 (2%) 120 0.6
(1.00) 		0.346
(1.00) 		0.0214
(1.00) 		0.0243
(1.00) 		1
(1.00) 		0.0153
(1.00) 		0.741
(1.00) 		0.619
(1.00)
16p loss 5 (4%) 118 0.128
(1.00) 		0.202
(1.00) 		0.166
(1.00) 		0.12
(1.00) 		0.324
(1.00) 		0.579
(1.00) 		0.224
(1.00) 		0.306
(1.00)
17p loss 14 (11%) 109 0.0235
(1.00) 		0.00119
(0.337) 		0.0157
(1.00) 		0.00125
(0.349) 		0.372
(1.00) 		0.00209
(0.562) 		0.0279
(1.00) 		0.0616
(1.00)
17q loss 6 (5%) 117 0.0102
(1.00) 		0.00861
(1.00) 		0.316
(1.00) 		0.155
(1.00) 		0.27
(1.00) 		0.236
(1.00) 		0.0993
(1.00) 		0.437
(1.00)
18p loss 7 (6%) 116 0.00229
(0.607) 		0.00854
(1.00) 		0.0241
(1.00) 		0.0218
(1.00) 		0.0136
(1.00) 		0.0958
(1.00) 		0.00192
(0.522) 		0.0426
(1.00)
18q loss 7 (6%) 116 0.00168
(0.464) 		0.00814
(1.00) 		0.0254
(1.00) 		0.0216
(1.00) 		0.014
(1.00) 		0.0953
(1.00) 		0.00217
(0.582) 		0.0431
(1.00)
xq loss 4 (3%) 119 0.0273
(1.00) 		0.0364
(1.00) 		0.0564
(1.00) 		0.125
(1.00) 		0.026
(1.00) 		0.253
(1.00) 		0.0458
(1.00) 		0.301
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.043

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
1P GAIN MUTATED 0 7 1
1P GAIN WILD-TYPE 65 24 26

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
1Q GAIN MUTATED 3 18 1
1Q GAIN WILD-TYPE 62 13 26

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
1Q GAIN MUTATED 2 6 14 0
1Q GAIN WILD-TYPE 37 30 10 24

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 30 13 29
1Q GAIN MUTATED 15 0 7 0
1Q GAIN WILD-TYPE 28 30 6 29

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
1Q GAIN MUTATED 15 0 0 7
1Q GAIN WILD-TYPE 29 41 20 3

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

'1q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
1Q GAIN MUTATED 21 0 0 1 0
1Q GAIN WILD-TYPE 37 61 1 1 1

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
1Q GAIN MUTATED 7 0 10 5 0 0
1Q GAIN WILD-TYPE 20 18 18 2 16 27

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
1Q GAIN MUTATED 1 0 21
1Q GAIN WILD-TYPE 17 59 25

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
1Q GAIN MUTATED 7 0 15 0
1Q GAIN WILD-TYPE 22 33 18 28

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S10.  Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
5P GAIN MUTATED 0 11 0
5P GAIN WILD-TYPE 65 20 27

Figure S10.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S11.  Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
5P GAIN MUTATED 0 2 9 0
5P GAIN WILD-TYPE 39 34 15 24

Figure S11.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.21

Table S12.  Gene #4: '5p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
5P GAIN MUTATED 10 0 0 1 0
5P GAIN WILD-TYPE 48 61 1 1 1

Figure S12.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S13.  Gene #4: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
5P GAIN MUTATED 0 0 11
5P GAIN WILD-TYPE 18 59 35

Figure S13.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
5Q GAIN MUTATED 0 9 0
5Q GAIN WILD-TYPE 65 22 27

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

'5q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S15.  Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
5Q GAIN MUTATED 0 1 8 0
5Q GAIN WILD-TYPE 39 35 16 24

Figure S15.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.061

Table S16.  Gene #5: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
5Q GAIN MUTATED 0 0 9
5Q GAIN WILD-TYPE 18 59 37

Figure S16.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S17.  Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
7P GAIN MUTATED 0 16 0
7P GAIN WILD-TYPE 65 15 27

Figure S17.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S18.  Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
7P GAIN MUTATED 1 1 14 0
7P GAIN WILD-TYPE 38 35 10 24

Figure S18.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S19.  Gene #6: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 30 13 29
7P GAIN MUTATED 16 0 0 0
7P GAIN WILD-TYPE 27 30 13 29

Figure S19.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S20.  Gene #6: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
7P GAIN MUTATED 16 0 0 0
7P GAIN WILD-TYPE 28 41 20 10

Figure S20.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S21.  Gene #6: '7p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
7P GAIN MUTATED 15 0 0 1 0
7P GAIN WILD-TYPE 43 61 1 1 1

Figure S21.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.052

Table S22.  Gene #6: '7p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
7P GAIN MUTATED 9 0 7 0 0 0
7P GAIN WILD-TYPE 18 18 21 7 16 27

Figure S22.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S23.  Gene #6: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
7P GAIN MUTATED 0 0 16
7P GAIN WILD-TYPE 18 59 30

Figure S23.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S24.  Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
7P GAIN MUTATED 10 0 6 0
7P GAIN WILD-TYPE 19 33 27 28

Figure S24.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S25.  Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
7Q GAIN MUTATED 0 16 0
7Q GAIN WILD-TYPE 65 15 27

Figure S25.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S26.  Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
7Q GAIN MUTATED 1 1 14 0
7Q GAIN WILD-TYPE 38 35 10 24

Figure S26.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S27.  Gene #7: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 30 13 29
7Q GAIN MUTATED 16 0 0 0
7Q GAIN WILD-TYPE 27 30 13 29

Figure S27.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S28.  Gene #7: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
7Q GAIN MUTATED 16 0 0 0
7Q GAIN WILD-TYPE 28 41 20 10

Figure S28.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S29.  Gene #7: '7q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
7Q GAIN MUTATED 15 0 0 1 0
7Q GAIN WILD-TYPE 43 61 1 1 1

Figure S29.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.036

Table S30.  Gene #7: '7q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
7Q GAIN MUTATED 9 0 7 0 0 0
7Q GAIN WILD-TYPE 18 18 21 7 16 27

Figure S30.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S31.  Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
7Q GAIN MUTATED 0 0 16
7Q GAIN WILD-TYPE 18 59 30

Figure S31.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S32.  Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
7Q GAIN MUTATED 10 0 6 0
7Q GAIN WILD-TYPE 19 33 27 28

Figure S32.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.12

Table S33.  Gene #8: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
8P GAIN MUTATED 2 9 1
8P GAIN WILD-TYPE 63 22 26

Figure S33.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.13

Table S34.  Gene #8: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 30 13 29
8P GAIN MUTATED 8 0 4 0
8P GAIN WILD-TYPE 35 30 9 29

Figure S34.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.033

Table S35.  Gene #8: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
8P GAIN MUTATED 8 0 0 4
8P GAIN WILD-TYPE 36 41 20 6

Figure S35.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.21

Table S36.  Gene #8: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
8P GAIN MUTATED 12 0 0 0 0
8P GAIN WILD-TYPE 46 61 1 2 1

Figure S36.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.073

Table S37.  Gene #8: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
8P GAIN MUTATED 2 0 10
8P GAIN WILD-TYPE 16 59 36

Figure S37.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.12

Table S38.  Gene #8: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
8P GAIN MUTATED 4 0 8 0
8P GAIN WILD-TYPE 25 33 25 28

Figure S38.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.073

Table S39.  Gene #9: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
8Q GAIN MUTATED 2 9 1
8Q GAIN WILD-TYPE 63 22 26

Figure S39.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.11

Table S40.  Gene #9: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 30 13 29
8Q GAIN MUTATED 8 0 4 0
8Q GAIN WILD-TYPE 35 30 9 29

Figure S40.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.043

Table S41.  Gene #9: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
8Q GAIN MUTATED 8 0 0 4
8Q GAIN WILD-TYPE 36 41 20 6

Figure S41.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.22

Table S42.  Gene #9: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
8Q GAIN MUTATED 12 0 0 0 0
8Q GAIN WILD-TYPE 46 61 1 2 1

Figure S42.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.061

Table S43.  Gene #9: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
8Q GAIN MUTATED 2 0 10
8Q GAIN WILD-TYPE 16 59 36

Figure S43.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.16

Table S44.  Gene #9: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
8Q GAIN MUTATED 4 0 8 0
8Q GAIN WILD-TYPE 25 33 25 28

Figure S44.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S45.  Gene #10: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
9P GAIN MUTATED 0 11 0
9P GAIN WILD-TYPE 65 20 27

Figure S45.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.052

Table S46.  Gene #10: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
9P GAIN MUTATED 2 0 8 1
9P GAIN WILD-TYPE 37 36 16 23

Figure S46.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.12

Table S47.  Gene #10: '9p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 30 13 29
9P GAIN MUTATED 10 0 0 0
9P GAIN WILD-TYPE 33 30 13 29

Figure S47.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.14

Table S48.  Gene #10: '9p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
9P GAIN MUTATED 10 0 0 0
9P GAIN WILD-TYPE 34 41 20 10

Figure S48.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S49.  Gene #11: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
9Q GAIN MUTATED 0 11 0
9Q GAIN WILD-TYPE 65 20 27

Figure S49.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.04

Table S50.  Gene #11: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
9Q GAIN MUTATED 2 0 8 1
9Q GAIN WILD-TYPE 37 36 16 23

Figure S50.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.11

Table S51.  Gene #11: '9q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 30 13 29
9Q GAIN MUTATED 10 0 0 0
9Q GAIN WILD-TYPE 33 30 13 29

Figure S51.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.13

Table S52.  Gene #11: '9q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
9Q GAIN MUTATED 10 0 0 0
9Q GAIN WILD-TYPE 34 41 20 10

Figure S52.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.23

Table S53.  Gene #11: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
9Q GAIN MUTATED 8 0 2 1
9Q GAIN WILD-TYPE 21 33 31 27

Figure S53.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S54.  Gene #14: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
14Q GAIN MUTATED 0 13 0
14Q GAIN WILD-TYPE 65 18 27

Figure S54.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S55.  Gene #14: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
14Q GAIN MUTATED 2 1 10 0
14Q GAIN WILD-TYPE 37 35 14 24

Figure S55.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S56.  Gene #14: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 30 13 29
14Q GAIN MUTATED 13 0 0 0
14Q GAIN WILD-TYPE 30 30 13 29

Figure S56.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S57.  Gene #14: '14q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
14Q GAIN MUTATED 13 0 0 0
14Q GAIN WILD-TYPE 31 41 20 10

Figure S57.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.061

Table S58.  Gene #14: '14q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
14Q GAIN MUTATED 12 0 0 1 0
14Q GAIN WILD-TYPE 46 61 1 1 1

Figure S58.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.02

Table S59.  Gene #14: '14q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
14Q GAIN MUTATED 10 0 3 0 0 0
14Q GAIN WILD-TYPE 17 18 25 7 16 27

Figure S59.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S60.  Gene #14: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
14Q GAIN MUTATED 0 0 13
14Q GAIN WILD-TYPE 18 59 33

Figure S60.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S61.  Gene #14: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
14Q GAIN MUTATED 10 0 3 0
14Q GAIN WILD-TYPE 19 33 30 28

Figure S61.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.055

Table S62.  Gene #15: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
15Q GAIN MUTATED 1 9 2
15Q GAIN WILD-TYPE 64 22 25

Figure S62.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.02

Table S63.  Gene #15: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
15Q GAIN MUTATED 2 1 9 0
15Q GAIN WILD-TYPE 37 35 15 24

Figure S63.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.17

Table S64.  Gene #21: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
20P GAIN MUTATED 1 8 1
20P GAIN WILD-TYPE 64 23 26

Figure S64.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.094

Table S65.  Gene #21: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
20P GAIN MUTATED 6 0 0 4
20P GAIN WILD-TYPE 38 41 20 6

Figure S65.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.16

Table S66.  Gene #21: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
20P GAIN MUTATED 1 0 9
20P GAIN WILD-TYPE 17 59 37

Figure S66.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.19

Table S67.  Gene #22: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
20Q GAIN MUTATED 1 8 1
20Q GAIN WILD-TYPE 64 23 26

Figure S67.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.088

Table S68.  Gene #22: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
20Q GAIN MUTATED 6 0 0 4
20Q GAIN WILD-TYPE 38 41 20 6

Figure S68.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.15

Table S69.  Gene #22: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
20Q GAIN MUTATED 1 0 9
20Q GAIN WILD-TYPE 17 59 37

Figure S69.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S70.  Gene #27: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
3P LOSS MUTATED 1 10 1
3P LOSS WILD-TYPE 64 21 26

Figure S70.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S71.  Gene #27: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
3P LOSS MUTATED 0 2 10 0
3P LOSS WILD-TYPE 39 34 14 24

Figure S71.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.17

Table S72.  Gene #27: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 30 13 29
3P LOSS MUTATED 9 0 3 0
3P LOSS WILD-TYPE 34 30 10 29

Figure S72.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.12

Table S73.  Gene #27: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
3P LOSS MUTATED 10 0 0 2
3P LOSS WILD-TYPE 34 41 20 8

Figure S73.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.21

Table S74.  Gene #27: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
3P LOSS MUTATED 12 0 0 0 0
3P LOSS WILD-TYPE 46 61 1 2 1

Figure S74.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S75.  Gene #27: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
3P LOSS MUTATED 0 0 12
3P LOSS WILD-TYPE 18 59 34

Figure S75.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.14

Table S76.  Gene #27: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
3P LOSS MUTATED 7 0 5 0
3P LOSS WILD-TYPE 22 33 28 28

Figure S76.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.2

Table S77.  Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
3Q LOSS MUTATED 0 6 1
3Q LOSS WILD-TYPE 65 25 26

Figure S77.  Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.07

Table S78.  Gene #28: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
3Q LOSS MUTATED 0 1 6 0
3Q LOSS WILD-TYPE 39 35 18 24

Figure S78.  Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S79.  Gene #31: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
6P LOSS MUTATED 1 18 1
6P LOSS WILD-TYPE 64 13 26

Figure S79.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S80.  Gene #31: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
6P LOSS MUTATED 2 3 15 0
6P LOSS WILD-TYPE 37 33 9 24

Figure S80.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S81.  Gene #31: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 30 13 29
6P LOSS MUTATED 14 0 6 0
6P LOSS WILD-TYPE 29 30 7 29

Figure S81.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S82.  Gene #31: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
6P LOSS MUTATED 15 0 0 5
6P LOSS WILD-TYPE 29 41 20 5

Figure S82.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S83.  Gene #31: '6p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
6P LOSS MUTATED 19 0 0 1 0
6P LOSS WILD-TYPE 39 61 1 1 1

Figure S83.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S84.  Gene #31: '6p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
6P LOSS MUTATED 9 0 8 3 0 0
6P LOSS WILD-TYPE 18 18 20 4 16 27

Figure S84.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S85.  Gene #31: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
6P LOSS MUTATED 1 0 19
6P LOSS WILD-TYPE 17 59 27

Figure S85.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S86.  Gene #31: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
6P LOSS MUTATED 10 0 10 0
6P LOSS WILD-TYPE 19 33 23 28

Figure S86.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S87.  Gene #32: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
6Q LOSS MUTATED 0 17 2
6Q LOSS WILD-TYPE 65 14 25

Figure S87.  Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S88.  Gene #32: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
6Q LOSS MUTATED 1 3 15 0
6Q LOSS WILD-TYPE 38 33 9 24

Figure S88.  Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S89.  Gene #32: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 30 13 29
6Q LOSS MUTATED 12 0 7 0
6Q LOSS WILD-TYPE 31 30 6 29

Figure S89.  Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S90.  Gene #32: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
6Q LOSS MUTATED 13 0 1 5
6Q LOSS WILD-TYPE 31 41 19 5

Figure S90.  Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S91.  Gene #32: '6q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
6Q LOSS MUTATED 17 1 0 1 0
6Q LOSS WILD-TYPE 41 60 1 1 1

Figure S91.  Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.088

Table S92.  Gene #32: '6q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
6Q LOSS MUTATED 9 0 6 3 1 0
6Q LOSS WILD-TYPE 18 18 22 4 15 27

Figure S92.  Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S93.  Gene #32: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
6Q LOSS MUTATED 0 0 19
6Q LOSS WILD-TYPE 18 59 27

Figure S93.  Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.023

Table S94.  Gene #32: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
6Q LOSS MUTATED 10 1 8 0
6Q LOSS WILD-TYPE 19 32 25 28

Figure S94.  Get High-res Image Gene #32: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S95.  Gene #35: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
11P LOSS MUTATED 0 9 0
11P LOSS WILD-TYPE 65 22 27

Figure S95.  Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S96.  Gene #35: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
11P LOSS MUTATED 0 1 8 0
11P LOSS WILD-TYPE 39 35 16 24

Figure S96.  Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.046

Table S97.  Gene #35: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
11P LOSS MUTATED 0 0 9
11P LOSS WILD-TYPE 18 59 37

Figure S97.  Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S98.  Gene #36: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
11Q LOSS MUTATED 0 7 0
11Q LOSS WILD-TYPE 65 24 27

Figure S98.  Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S99.  Gene #36: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
11Q LOSS MUTATED 0 0 7 0
11Q LOSS WILD-TYPE 39 36 17 24

Figure S99.  Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.03

Table S100.  Gene #37: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
12P LOSS MUTATED 1 0 7 0
12P LOSS WILD-TYPE 38 36 17 24

Figure S100.  Get High-res Image Gene #37: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S101.  Gene #38: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
12Q LOSS MUTATED 0 0 7 0
12Q LOSS WILD-TYPE 39 36 17 24

Figure S101.  Get High-res Image Gene #38: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S102.  Gene #39: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
13Q LOSS MUTATED 0 9 5
13Q LOSS WILD-TYPE 65 22 22

Figure S102.  Get High-res Image Gene #39: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S103.  Gene #41: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 30 13 29
16Q LOSS MUTATED 3 1 8 1
16Q LOSS WILD-TYPE 40 29 5 28

Figure S103.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S104.  Gene #41: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
16Q LOSS MUTATED 3 1 1 8
16Q LOSS WILD-TYPE 41 40 19 2

Figure S104.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0071

Table S105.  Gene #41: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
16Q LOSS MUTATED 1 0 4 6 1 1
16Q LOSS WILD-TYPE 26 18 24 1 15 26

Figure S105.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.2

Table S106.  Gene #41: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
16Q LOSS MUTATED 1 1 10 1
16Q LOSS WILD-TYPE 28 32 23 27

Figure S106.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.13

Table S107.  Gene #46: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
19P LOSS MUTATED 0 0 0 3
19P LOSS WILD-TYPE 44 41 20 7

Figure S107.  Get High-res Image Gene #46: '19p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.14

Table S108.  Gene #47: '19q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 41 20 10
19Q LOSS MUTATED 0 0 0 3
19Q LOSS WILD-TYPE 44 41 20 7

Figure S108.  Get High-res Image Gene #47: '19q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S109.  Gene #48: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
21Q LOSS MUTATED 0 9 0
21Q LOSS WILD-TYPE 65 22 27

Figure S109.  Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S110.  Gene #48: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
21Q LOSS MUTATED 0 1 8 0
21Q LOSS WILD-TYPE 39 35 16 24

Figure S110.  Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.073

Table S111.  Gene #48: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
21Q LOSS MUTATED 0 0 9
21Q LOSS WILD-TYPE 18 59 37

Figure S111.  Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S112.  Gene #49: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
22Q LOSS MUTATED 0 4 9
22Q LOSS WILD-TYPE 65 27 18

Figure S112.  Get High-res Image Gene #49: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 123

  • Number of significantly arm-level cnvs = 50

  • 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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