Correlation between copy number variations of arm-level result and molecular subtypes
Uveal Melanoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1DR2V1X
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1DR2V1X
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 80 patients, 95 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 2p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4p gain cnv correlated to 'CN_CNMF'.

  • 4q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 11p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 13q gain cnv correlated to 'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 21q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 22q gain cnv correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xp gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • xq gain cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 5q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • xp loss cnv correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq loss cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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, 95 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
6p gain 38 (48%) 42 0.0416
(0.179) 		0.0067
(0.0496) 		0.00034
(0.00389) 		0.00013
(0.00168) 		2e-05
(0.000308) 		1e-05
(0.000174) 		0.00027
(0.00318) 		1e-05
(0.000174)
8p gain 39 (49%) 41 1e-05
(0.000174) 		0.00011
(0.00147) 		0.00108
(0.0105) 		6e-05
(0.000857) 		0.00275
(0.0239) 		0.00052
(0.00562) 		0.0316
(0.154) 		0.00826
(0.056)
8q gain 53 (66%) 27 1e-05
(0.000174) 		2e-05
(0.000308) 		0.00017
(0.00212) 		1e-05
(0.000174) 		2e-05
(0.000308) 		1e-05
(0.000174) 		0.00995
(0.0643) 		6e-05
(0.000857)
3p loss 43 (54%) 37 1e-05
(0.000174) 		1e-05
(0.000174) 		1e-05
(0.000174) 		1e-05
(0.000174) 		1e-05
(0.000174) 		1e-05
(0.000174) 		1e-05
(0.000174) 		1e-05
(0.000174)
3q loss 43 (54%) 37 1e-05
(0.000174) 		1e-05
(0.000174) 		1e-05
(0.000174) 		1e-05
(0.000174) 		1e-05
(0.000174) 		1e-05
(0.000174) 		1e-05
(0.000174) 		1e-05
(0.000174)
6q gain 16 (20%) 64 0.604
(0.781) 		0.0144
(0.0822) 		0.0191
(0.105) 		0.00101
(0.0101) 		0.00089
(0.00913) 		0.0002
(0.00242) 		0.0101
(0.0643) 		0.00089
(0.00913)
6q loss 17 (21%) 63 1e-05
(0.000174) 		0.0105
(0.0658) 		0.19
(0.412) 		0.00465
(0.0365) 		0.12
(0.341) 		0.228
(0.452) 		0.0337
(0.159) 		0.00384
(0.0307)
13q gain 6 (8%) 74 0.0251
(0.132) 		0.683
(0.83) 		0.878
(0.942) 		0.751
(0.88) 		0.914
(0.964) 		0.519
(0.705) 		0.00156
(0.0139) 		0.00777
(0.0553)
17q gain 9 (11%) 71 0.00146
(0.0133) 		0.223
(0.45) 		0.33
(0.531) 		0.306
(0.513) 		0.532
(0.719) 		0.0283
(0.145) 		0.281
(0.496) 		0.0383
(0.169)
16q loss 16 (20%) 64 0.0218
(0.116) 		0.0277
(0.144) 		0.154
(0.377) 		0.0131
(0.0772) 		0.195
(0.415) 		0.126
(0.346) 		0.0692
(0.255) 		0.161
(0.385)
xq loss 13 (16%) 67 0.273
(0.496) 		0.0155
(0.0862) 		0.218
(0.45) 		0.146
(0.366) 		0.649
(0.804) 		0.384
(0.577) 		0.00788
(0.0553) 		0.00313
(0.0256)
2p gain 10 (12%) 70 0.0286
(0.145) 		0.549
(0.737) 		0.0591
(0.228) 		0.117
(0.341) 		0.224
(0.45) 		0.851
(0.92) 		0.706
(0.843) 		0.00312
(0.0256)
2q gain 8 (10%) 72 0.0107
(0.0658) 		0.222
(0.45) 		0.0538
(0.222) 		0.111
(0.332) 		0.0593
(0.228) 		0.194
(0.415) 		0.298
(0.506) 		8e-05
(0.0011)
11p gain 10 (12%) 70 0.00824
(0.056) 		0.163
(0.385) 		0.73
(0.867) 		0.383
(0.577) 		0.646
(0.804) 		0.309
(0.513) 		0.134
(0.358) 		0.00638
(0.0482)
17p gain 8 (10%) 72 0.00035
(0.00389) 		0.26
(0.487) 		0.457
(0.653) 		0.217
(0.45) 		0.602
(0.781) 		0.058
(0.228) 		0.189
(0.412) 		0.0396
(0.172)
21q gain 14 (18%) 66 0.033
(0.157) 		0.168
(0.392) 		0.0695
(0.255) 		0.0135
(0.0785) 		0.373
(0.569) 		0.296
(0.505) 		0.151
(0.374) 		0.106
(0.332)
22q gain 5 (6%) 75 0.134
(0.358) 		0.123
(0.344) 		0.107
(0.332) 		0.0718
(0.261) 		0.128
(0.346) 		0.246
(0.469) 		0.00313
(0.0256) 		0.033
(0.157)
xp gain 10 (12%) 70 0.19
(0.412) 		0.0363
(0.168) 		0.796
(0.886) 		0.14
(0.358) 		0.0533
(0.222) 		0.374
(0.569) 		0.0369
(0.168) 		0.0985
(0.331)
xq gain 9 (11%) 71 0.26
(0.487) 		0.111
(0.332) 		0.629
(0.789) 		0.02
(0.108) 		0.0551
(0.223) 		0.102
(0.332) 		0.0984
(0.331) 		0.0316
(0.154)
1p loss 19 (24%) 61 0.303
(0.512) 		0.262
(0.487) 		0.0785
(0.283) 		0.663
(0.813) 		0.967
(1.00) 		0.279
(0.496) 		0.0149
(0.0837) 		0.0302
(0.151)
1q loss 3 (4%) 77 0.382
(0.577) 		0.179
(0.406) 		0.162
(0.385) 		0.325
(0.531) 		0.192
(0.414) 		0.0457
(0.193) 		0.167
(0.392) 		0.012
(0.0714)
xp loss 12 (15%) 68 0.185
(0.412) 		0.0551
(0.223) 		0.406
(0.603) 		0.265
(0.491) 		0.927
(0.971) 		0.58
(0.769) 		0.0368
(0.168) 		0.0112
(0.0678)
4p gain 7 (9%) 73 0.00143
(0.0133) 		0.245
(0.469) 		0.143
(0.361) 		0.12
(0.341) 		0.329
(0.531) 		0.368
(0.568) 		0.326
(0.531) 		0.433
(0.637)
4q gain 4 (5%) 76 0.00575
(0.0442) 		0.309
(0.513) 		0.0994
(0.331) 		0.345
(0.542) 		0.628
(0.789) 		0.826
(0.901) 		0.789
(0.883) 		0.628
(0.789)
11q gain 10 (12%) 70 0.099
(0.331) 		0.727
(0.865) 		1
(1.00) 		0.829
(0.901) 		0.699
(0.84) 		0.116
(0.341) 		0.0942
(0.328) 		0.0383
(0.169)
12p gain 3 (4%) 77 0.141
(0.358) 		0.18
(0.406) 		0.105
(0.332) 		0.0101
(0.0643) 		0.091
(0.322) 		0.271
(0.496) 		0.11
(0.332) 		0.14
(0.358)
12q gain 3 (4%) 77 0.14
(0.358) 		0.182
(0.406) 		0.105
(0.332) 		0.00919
(0.0613) 		0.0903
(0.322) 		0.274
(0.496) 		0.109
(0.332) 		0.138
(0.358)
20q gain 9 (11%) 71 0.0691
(0.255) 		0.616
(0.788) 		0.0423
(0.18) 		0.0578
(0.228) 		0.685
(0.831) 		0.156
(0.379) 		0.238
(0.466) 		0.427
(0.63)
5q loss 3 (4%) 77 0.788
(0.883) 		0.119
(0.341) 		0.246
(0.469) 		0.17
(0.395) 		0.455
(0.652) 		0.871
(0.939) 		0.0385
(0.169) 		0.582
(0.769)
9p loss 8 (10%) 72 0.00138
(0.0131) 		0.127
(0.346) 		0.338
(0.538) 		0.154
(0.377) 		0.336
(0.538) 		0.355
(0.55) 		0.217
(0.45) 		0.293
(0.505)
9q loss 7 (9%) 73 0.00769
(0.0553) 		0.126
(0.346) 		0.706
(0.843) 		0.239
(0.466) 		0.422
(0.626) 		0.584
(0.769) 		0.151
(0.374) 		0.449
(0.649)
1q gain 8 (10%) 72 0.814
(0.895) 		0.494
(0.684) 		0.803
(0.887) 		0.803
(0.887) 		0.374
(0.569) 		0.0588
(0.228) 		0.838
(0.908) 		0.952
(0.991)
5p gain 3 (4%) 77 0.188
(0.412) 		0.179
(0.406) 		0.29
(0.505) 		0.109
(0.332) 		0.281
(0.496) 		0.278
(0.496) 		0.487
(0.679) 		0.77
(0.88)
5q gain 3 (4%) 77 0.187
(0.412) 		0.18
(0.406) 		0.292
(0.505) 		0.108
(0.332) 		0.281
(0.496) 		0.277
(0.496) 		0.488
(0.679) 		0.772
(0.88)
7p gain 9 (11%) 71 0.245
(0.469) 		0.403
(0.602) 		1
(1.00) 		0.741
(0.877) 		0.34
(0.539) 		0.181
(0.406) 		0.899
(0.958) 		0.465
(0.662)
7q gain 8 (10%) 72 0.103
(0.332) 		0.12
(0.341) 		0.957
(0.994) 		0.448
(0.649) 		0.373
(0.569) 		0.33
(0.531) 		0.974
(1.00) 		0.778
(0.883)
9p gain 5 (6%) 75 0.482
(0.679) 		0.0926
(0.325) 		0.295
(0.505) 		0.225
(0.45) 		0.288
(0.503) 		1
(1.00) 		0.298
(0.506) 		0.566
(0.757)
9q gain 4 (5%) 76 0.804
(0.887) 		0.162
(0.385) 		0.678
(0.827) 		0.537
(0.723) 		0.33
(0.531) 		0.755
(0.88) 		0.286
(0.502) 		0.473
(0.669)
14q gain 3 (4%) 77 0.141
(0.358) 		1
(1.00) 		0.104
(0.332) 		0.326
(0.531) 		0.916
(0.964) 		0.592
(0.776) 		0.689
(0.832) 		0.583
(0.769)
16p gain 4 (5%) 76 1
(1.00) 		0.455
(0.652) 		0.828
(0.901) 		0.438
(0.642) 		0.788
(0.883) 		0.474
(0.669) 		0.387
(0.579) 		0.748
(0.88)
20p gain 8 (10%) 72 0.0968
(0.331) 		0.28
(0.496) 		0.105
(0.332) 		0.22
(0.45) 		0.927
(0.971) 		0.239
(0.466) 		0.204
(0.432) 		0.119
(0.341)
4q loss 3 (4%) 77 0.789
(0.883) 		0.771
(0.88) 		0.892
(0.954) 		0.605
(0.781) 		0.916
(0.964) 		0.274
(0.496) 		0.642
(0.803) 		0.309
(0.513)
8p loss 4 (5%) 76 0.805
(0.887) 		0.756
(0.88) 		0.623
(0.789) 		0.674
(0.824) 		0.447
(0.649) 		0.629
(0.789) 		0.693
(0.836) 		0.345
(0.542)
8q loss 3 (4%) 77 0.484
(0.679) 		0.66
(0.813) 		1
(1.00) 		0.789
(0.883) 		0.762
(0.88) 		0.772
(0.88) 		0.95
(0.991) 		0.585
(0.769)
12p loss 3 (4%) 77 0.649
(0.804) 		0.662
(0.813) 		0.242
(0.469) 		0.79
(0.883) 		0.61
(0.781) 		0.52
(0.705) 		0.904
(0.961) 		0.77
(0.88)
13q loss 3 (4%) 77 0.875
(0.941) 		0.181
(0.406) 		0.352
(0.549) 		0.602
(0.781) 		0.609
(0.781) 		1
(1.00) 		0.489
(0.679) 		0.315
(0.52)
15q loss 4 (5%) 76 0.343
(0.542) 		0.251
(0.476) 		1
(1.00) 		0.827
(0.901) 		0.448
(0.649) 		0.91
(0.964) 		0.515
(0.703) 		0.629
(0.789)
16p loss 3 (4%) 77 0.26
(0.487) 		0.5
(0.687) 		0.353
(0.55) 		0.6
(0.781) 		0.761
(0.88) 		1
(1.00) 		1
(1.00) 		1
(1.00)
19p loss 3 (4%) 77 0.221
(0.45) 		0.0641
(0.244) 		0.503
(0.689) 		1
(1.00) 		0.761
(0.88) 		0.225
(0.45) 		0.124
(0.344) 		0.14
(0.358)
19q loss 3 (4%) 77 0.224
(0.45) 		0.0649
(0.245) 		0.499
(0.687) 		1
(1.00) 		0.76
(0.88) 		0.228
(0.452) 		0.123
(0.344) 		0.139
(0.358)
'2p gain' versus 'CN_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
2P GAIN MUTATED 2 1 5 2 0 0
2P GAIN WILD-TYPE 20 6 5 29 6 4

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

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00312 (Fisher's exact test), Q value = 0.026

Table S2.  Gene #2: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
2P GAIN MUTATED 1 2 1 6
2P GAIN WILD-TYPE 17 26 15 6

Figure S2.  Get High-res Image Gene #2: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.066

Table S3.  Gene #3: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
2Q GAIN MUTATED 1 0 5 2 0 0
2Q GAIN WILD-TYPE 21 7 5 29 6 4

Figure S3.  Get High-res Image Gene #3: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.0011

Table S4.  Gene #3: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
2Q GAIN MUTATED 0 2 0 6
2Q GAIN WILD-TYPE 18 26 16 6

Figure S4.  Get High-res Image Gene #3: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
4P GAIN MUTATED 2 4 1 0 0 0
4P GAIN WILD-TYPE 20 3 9 31 6 4

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

'4q gain' versus 'CN_CNMF'

P value = 0.00575 (Fisher's exact test), Q value = 0.044

Table S6.  Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
4Q GAIN MUTATED 1 3 0 0 0 0
4Q GAIN WILD-TYPE 21 4 10 31 6 4

Figure S6.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.18

Table S7.  Gene #8: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
6P GAIN MUTATED 7 3 4 21 3 0
6P GAIN WILD-TYPE 15 4 6 10 3 4

Figure S7.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.0067 (Fisher's exact test), Q value = 0.05

Table S8.  Gene #8: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
6P GAIN MUTATED 8 7 5 18
6P GAIN WILD-TYPE 20 7 9 6

Figure S8.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0039

Table S9.  Gene #8: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
6P GAIN MUTATED 3 5 24 6
6P GAIN WILD-TYPE 15 10 8 9

Figure S9.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0017

Table S10.  Gene #8: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
6P GAIN MUTATED 8 25 5
6P GAIN WILD-TYPE 21 8 13

Figure S10.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S11.  Gene #8: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
6P GAIN MUTATED 1 3 5 22 6 1
6P GAIN WILD-TYPE 7 5 6 3 17 4

Figure S11.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S12.  Gene #8: '6p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
6P GAIN MUTATED 4 6 24 4
6P GAIN WILD-TYPE 13 7 4 18

Figure S12.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0032

Table S13.  Gene #8: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
6P GAIN MUTATED 7 2 15 0 4 4 3
6P GAIN WILD-TYPE 13 5 2 9 4 3 3

Figure S13.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S14.  Gene #8: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
6P GAIN MUTATED 6 23 1 5
6P GAIN WILD-TYPE 12 5 15 7

Figure S14.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.082

Table S15.  Gene #9: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
6Q GAIN MUTATED 1 3 3 9
6Q GAIN WILD-TYPE 27 11 11 15

Figure S15.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.1

Table S16.  Gene #9: '6q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
6Q GAIN MUTATED 1 1 12 2
6Q GAIN WILD-TYPE 17 14 20 13

Figure S16.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.01

Table S17.  Gene #9: '6q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
6Q GAIN MUTATED 1 13 2
6Q GAIN WILD-TYPE 28 20 16

Figure S17.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0091

Table S18.  Gene #9: '6q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
6Q GAIN MUTATED 0 0 3 12 1 0
6Q GAIN WILD-TYPE 8 8 8 13 22 5

Figure S18.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0024

Table S19.  Gene #9: '6q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
6Q GAIN MUTATED 1 3 12 0
6Q GAIN WILD-TYPE 16 10 16 22

Figure S19.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.064

Table S20.  Gene #9: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
6Q GAIN MUTATED 1 0 7 0 2 1 3
6Q GAIN WILD-TYPE 19 7 10 9 6 6 3

Figure S20.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0091

Table S21.  Gene #9: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
6Q GAIN MUTATED 1 12 0 1
6Q GAIN WILD-TYPE 17 16 16 11

Figure S21.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S22.  Gene #12: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
8P GAIN MUTATED 12 6 9 5 5 2
8P GAIN WILD-TYPE 10 1 1 26 1 2

Figure S22.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0015

Table S23.  Gene #12: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
8P GAIN MUTATED 23 3 6 7
8P GAIN WILD-TYPE 5 11 8 17

Figure S23.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.011

Table S24.  Gene #12: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
8P GAIN MUTATED 12 9 7 11
8P GAIN WILD-TYPE 6 6 25 4

Figure S24.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00086

Table S25.  Gene #12: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
8P GAIN MUTATED 23 8 8
8P GAIN WILD-TYPE 6 25 10

Figure S25.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.024

Table S26.  Gene #12: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
8P GAIN MUTATED 5 5 3 7 18 1
8P GAIN WILD-TYPE 3 3 8 18 5 4

Figure S26.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0056

Table S27.  Gene #12: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
8P GAIN MUTATED 13 2 9 15
8P GAIN WILD-TYPE 4 11 19 7

Figure S27.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.15

Table S28.  Gene #12: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
8P GAIN MUTATED 15 5 6 1 4 4 3
8P GAIN WILD-TYPE 5 2 11 8 4 3 3

Figure S28.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00826 (Fisher's exact test), Q value = 0.056

Table S29.  Gene #12: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
8P GAIN MUTATED 14 8 10 6
8P GAIN WILD-TYPE 4 20 6 6

Figure S29.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S30.  Gene #13: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
8Q GAIN MUTATED 18 6 10 9 6 4
8Q GAIN WILD-TYPE 4 1 0 22 0 0

Figure S30.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S31.  Gene #13: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
8Q GAIN MUTATED 27 5 10 11
8Q GAIN WILD-TYPE 1 9 4 13

Figure S31.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0021

Table S32.  Gene #13: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
8Q GAIN MUTATED 15 12 12 14
8Q GAIN WILD-TYPE 3 3 20 1

Figure S32.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S33.  Gene #13: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
8Q GAIN MUTATED 27 12 14
8Q GAIN WILD-TYPE 2 21 4

Figure S33.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S34.  Gene #13: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
8Q GAIN MUTATED 7 7 3 12 22 2
8Q GAIN WILD-TYPE 1 1 8 13 1 3

Figure S34.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S35.  Gene #13: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
8Q GAIN MUTATED 16 3 14 20
8Q GAIN WILD-TYPE 1 10 14 2

Figure S35.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00995 (Fisher's exact test), Q value = 0.064

Table S36.  Gene #13: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
8Q GAIN MUTATED 19 6 8 4 5 4 5
8Q GAIN WILD-TYPE 1 1 9 5 3 3 1

Figure S36.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00086

Table S37.  Gene #13: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
8Q GAIN MUTATED 18 12 14 7
8Q GAIN WILD-TYPE 0 16 2 5

Figure S37.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 0.00824 (Fisher's exact test), Q value = 0.056

Table S38.  Gene #16: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
11P GAIN MUTATED 4 0 5 1 0 0
11P GAIN WILD-TYPE 18 7 5 30 6 4

Figure S38.  Get High-res Image Gene #16: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00638 (Fisher's exact test), Q value = 0.048

Table S39.  Gene #16: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
11P GAIN MUTATED 0 3 1 5
11P GAIN WILD-TYPE 18 25 15 7

Figure S39.  Get High-res Image Gene #16: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.17

Table S40.  Gene #17: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
11Q GAIN MUTATED 0 3 1 4
11Q GAIN WILD-TYPE 18 25 15 8

Figure S40.  Get High-res Image Gene #17: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.064

Table S41.  Gene #18: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
12P GAIN MUTATED 0 0 3
12P GAIN WILD-TYPE 29 33 15

Figure S41.  Get High-res Image Gene #18: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00919 (Fisher's exact test), Q value = 0.061

Table S42.  Gene #19: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
12Q GAIN MUTATED 0 0 3
12Q GAIN WILD-TYPE 29 33 15

Figure S42.  Get High-res Image Gene #19: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.13

Table S43.  Gene #20: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
13Q GAIN MUTATED 1 0 4 1 0 0
13Q GAIN WILD-TYPE 21 7 6 30 6 4

Figure S43.  Get High-res Image Gene #20: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.014

Table S44.  Gene #20: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
13Q GAIN MUTATED 1 0 0 0 1 4 0
13Q GAIN WILD-TYPE 19 7 17 9 7 3 6

Figure S44.  Get High-res Image Gene #20: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00777 (Fisher's exact test), Q value = 0.055

Table S45.  Gene #20: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
13Q GAIN MUTATED 0 2 0 4
13Q GAIN WILD-TYPE 18 26 16 8

Figure S45.  Get High-res Image Gene #20: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0039

Table S46.  Gene #23: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
17P GAIN MUTATED 1 0 6 1 0 0
17P GAIN WILD-TYPE 21 7 4 30 6 4

Figure S46.  Get High-res Image Gene #23: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 0.17

Table S47.  Gene #23: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
17P GAIN MUTATED 0 3 1 4
17P GAIN WILD-TYPE 18 25 15 8

Figure S47.  Get High-res Image Gene #23: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.013

Table S48.  Gene #24: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
17Q GAIN MUTATED 1 0 6 2 0 0
17Q GAIN WILD-TYPE 21 7 4 29 6 4

Figure S48.  Get High-res Image Gene #24: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.14

Table S49.  Gene #24: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
17Q GAIN MUTATED 3 0 6 0
17Q GAIN WILD-TYPE 14 13 22 22

Figure S49.  Get High-res Image Gene #24: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.17

Table S50.  Gene #24: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
17Q GAIN MUTATED 0 4 1 4
17Q GAIN WILD-TYPE 18 24 15 8

Figure S50.  Get High-res Image Gene #24: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.18

Table S51.  Gene #26: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
20Q GAIN MUTATED 1 4 1 3
20Q GAIN WILD-TYPE 17 11 31 12

Figure S51.  Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.16

Table S52.  Gene #27: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
21Q GAIN MUTATED 5 1 5 2 0 1
21Q GAIN WILD-TYPE 17 6 5 29 6 3

Figure S52.  Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.078

Table S53.  Gene #27: '21q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
21Q GAIN MUTATED 5 2 7
21Q GAIN WILD-TYPE 24 31 11

Figure S53.  Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.026

Table S54.  Gene #28: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
22Q GAIN MUTATED 0 1 0 0 1 3 0
22Q GAIN WILD-TYPE 20 6 17 9 7 4 6

Figure S54.  Get High-res Image Gene #28: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 0.16

Table S55.  Gene #28: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
22Q GAIN MUTATED 0 2 0 3
22Q GAIN WILD-TYPE 18 26 16 9

Figure S55.  Get High-res Image Gene #28: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.17

Table S56.  Gene #29: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
XP GAIN MUTATED 1 1 5 3
XP GAIN WILD-TYPE 27 13 9 21

Figure S56.  Get High-res Image Gene #29: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.17

Table S57.  Gene #29: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
XP GAIN MUTATED 0 1 4 0 3 1 0
XP GAIN WILD-TYPE 20 6 13 9 5 6 6

Figure S57.  Get High-res Image Gene #29: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.11

Table S58.  Gene #30: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
XQ GAIN MUTATED 0 5 4
XQ GAIN WILD-TYPE 29 28 14

Figure S58.  Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.15

Table S59.  Gene #30: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
XQ GAIN MUTATED 0 5 0 3
XQ GAIN WILD-TYPE 18 23 16 9

Figure S59.  Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.084

Table S60.  Gene #31: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
1P LOSS MUTATED 6 1 3 0 5 4 0
1P LOSS WILD-TYPE 14 6 14 9 3 3 6

Figure S60.  Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.15

Table S61.  Gene #31: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
1P LOSS MUTATED 1 7 8 3
1P LOSS WILD-TYPE 17 21 8 9

Figure S61.  Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0457 (Fisher's exact test), Q value = 0.19

Table S62.  Gene #32: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
1Q LOSS MUTATED 0 0 0 3
1Q LOSS WILD-TYPE 17 13 28 19

Figure S62.  Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.071

Table S63.  Gene #32: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
1Q LOSS MUTATED 0 0 3 0
1Q LOSS WILD-TYPE 18 28 13 12

Figure S63.  Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S64.  Gene #33: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
3P LOSS MUTATED 17 7 8 2 6 3
3P LOSS WILD-TYPE 5 0 2 29 0 1

Figure S64.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S65.  Gene #33: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
3P LOSS MUTATED 28 3 10 2
3P LOSS WILD-TYPE 0 11 4 22

Figure S65.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S66.  Gene #33: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
3P LOSS MUTATED 18 10 2 13
3P LOSS WILD-TYPE 0 5 30 2

Figure S66.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S67.  Gene #33: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
3P LOSS MUTATED 29 2 12
3P LOSS WILD-TYPE 0 31 6

Figure S67.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S68.  Gene #33: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
3P LOSS MUTATED 8 5 2 2 23 3
3P LOSS WILD-TYPE 0 3 9 23 0 2

Figure S68.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S69.  Gene #33: '3p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
3P LOSS MUTATED 17 1 3 22
3P LOSS WILD-TYPE 0 12 25 0

Figure S69.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S70.  Gene #33: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
3P LOSS MUTATED 20 6 2 4 5 2 3
3P LOSS WILD-TYPE 0 1 15 5 3 5 3

Figure S70.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S71.  Gene #33: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
3P LOSS MUTATED 17 3 16 6
3P LOSS WILD-TYPE 1 25 0 6

Figure S71.  Get High-res Image Gene #33: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S72.  Gene #34: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
3Q LOSS MUTATED 17 7 8 2 6 3
3Q LOSS WILD-TYPE 5 0 2 29 0 1

Figure S72.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S73.  Gene #34: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
3Q LOSS MUTATED 28 3 10 2
3Q LOSS WILD-TYPE 0 11 4 22

Figure S73.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S74.  Gene #34: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
3Q LOSS MUTATED 18 10 2 13
3Q LOSS WILD-TYPE 0 5 30 2

Figure S74.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S75.  Gene #34: '3q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
3Q LOSS MUTATED 29 2 12
3Q LOSS WILD-TYPE 0 31 6

Figure S75.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S76.  Gene #34: '3q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
3Q LOSS MUTATED 8 5 2 2 23 3
3Q LOSS WILD-TYPE 0 3 9 23 0 2

Figure S76.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S77.  Gene #34: '3q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
3Q LOSS MUTATED 17 1 3 22
3Q LOSS WILD-TYPE 0 12 25 0

Figure S77.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S78.  Gene #34: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
3Q LOSS MUTATED 20 6 2 4 5 2 3
3Q LOSS WILD-TYPE 0 1 15 5 3 5 3

Figure S78.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S79.  Gene #34: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
3Q LOSS MUTATED 17 3 16 6
3Q LOSS WILD-TYPE 1 25 0 6

Figure S79.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.17

Table S80.  Gene #36: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
5Q LOSS MUTATED 0 0 0 0 2 1 0
5Q LOSS WILD-TYPE 20 7 17 9 6 6 6

Figure S80.  Get High-res Image Gene #36: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S81.  Gene #37: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
6Q LOSS MUTATED 0 7 2 4 4 0
6Q LOSS WILD-TYPE 22 0 8 27 2 4

Figure S81.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.066

Table S82.  Gene #37: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
6Q LOSS MUTATED 12 1 1 3
6Q LOSS WILD-TYPE 16 13 13 21

Figure S82.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00465 (Fisher's exact test), Q value = 0.036

Table S83.  Gene #37: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
6Q LOSS MUTATED 12 4 1
6Q LOSS WILD-TYPE 17 29 17

Figure S83.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.16

Table S84.  Gene #37: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
6Q LOSS MUTATED 10 2 2 2 0 1 0
6Q LOSS WILD-TYPE 10 5 15 7 8 6 6

Figure S84.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.031

Table S85.  Gene #37: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
6Q LOSS MUTATED 10 3 2 2
6Q LOSS WILD-TYPE 8 25 14 10

Figure S85.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.013

Table S86.  Gene #40: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
9P LOSS MUTATED 0 2 3 1 0 2
9P LOSS WILD-TYPE 22 5 7 30 6 2

Figure S86.  Get High-res Image Gene #40: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 0.00769 (Fisher's exact test), Q value = 0.055

Table S87.  Gene #41: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
9Q LOSS MUTATED 0 2 3 1 0 1
9Q LOSS WILD-TYPE 22 5 7 30 6 3

Figure S87.  Get High-res Image Gene #41: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.12

Table S88.  Gene #46: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
16Q LOSS MUTATED 4 5 1 4 2 0
16Q LOSS WILD-TYPE 18 2 9 27 4 4

Figure S88.  Get High-res Image Gene #46: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.14

Table S89.  Gene #46: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
16Q LOSS MUTATED 10 0 3 3
16Q LOSS WILD-TYPE 18 14 11 21

Figure S89.  Get High-res Image Gene #46: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.077

Table S90.  Gene #46: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
16Q LOSS MUTATED 11 4 1
16Q LOSS WILD-TYPE 18 29 17

Figure S90.  Get High-res Image Gene #46: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.17

Table S91.  Gene #49: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
XP LOSS MUTATED 4 1 0 1 4 2 0
XP LOSS WILD-TYPE 16 6 17 8 4 5 6

Figure S91.  Get High-res Image Gene #49: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.068

Table S92.  Gene #49: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
XP LOSS MUTATED 2 3 7 0
XP LOSS WILD-TYPE 16 25 9 12

Figure S92.  Get High-res Image Gene #49: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.086

Table S93.  Gene #50: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
XQ LOSS MUTATED 5 1 6 1
XQ LOSS WILD-TYPE 23 13 8 23

Figure S93.  Get High-res Image Gene #50: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00788 (Fisher's exact test), Q value = 0.055

Table S94.  Gene #50: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
XQ LOSS MUTATED 4 1 0 1 5 2 0
XQ LOSS WILD-TYPE 16 6 17 8 3 5 6

Figure S94.  Get High-res Image Gene #50: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00313 (Fisher's exact test), Q value = 0.026

Table S95.  Gene #50: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
XQ LOSS MUTATED 2 3 8 0
XQ LOSS WILD-TYPE 16 25 8 12

Figure S95.  Get High-res Image Gene #50: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UVM-TP/22534465/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/22542449/UVM-TP.transferedmergedcluster.txt

  • Number of patients = 80

  • 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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