Correlation between copy number variations of arm-level result and molecular subtypes
Uveal Melanoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C13F4NRQ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13F4NRQ
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 51 arm-level events and 8 molecular subtypes across 80 patients, 91 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 2q gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4p 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 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'METHLYATION_CNMF'.

  • 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'.

  • 9q gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 12p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'CN_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF'.

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

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

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 1q loss cnv correlated to 'CN_CNMF',  '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'.

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

  • 8p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'METHLYATION_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 15q loss cnv correlated to 'METHLYATION_CNMF'.

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

  • xp loss cnv correlated to 'METHLYATION_CNMF'.

  • 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 51 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, 91 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 39 (49%) 41 0.00025
(0.00319) 		0.00433
(0.0376) 		0.00019
(0.00258) 		0.00023
(0.00303) 		2e-05
(0.000355) 		3e-05
(0.00051) 		0.0104
(0.077) 		2e-05
(0.000355)
6q gain 16 (20%) 64 0.0058
(0.0473) 		0.00238
(0.0237) 		0.00035
(0.00408) 		0.00112
(0.0124) 		0.00026
(0.00321) 		0.00034
(0.00408) 		0.00352
(0.0326) 		0.0001
(0.00146)
8p gain 33 (41%) 47 0.00135
(0.0145) 		0.001
(0.0113) 		0.00259
(0.0252) 		0.00412
(0.0367) 		0.0196
(0.123) 		0.0152
(0.105) 		0.0378
(0.191) 		0.0137
(0.0965)
8q gain 53 (66%) 27 1e-05
(0.000204) 		1e-05
(0.000204) 		6e-05
(0.000979) 		1e-05
(0.000204) 		9e-05
(0.00136) 		1e-05
(0.000204) 		2e-05
(0.000355) 		0.00011
(0.00155)
3p loss 43 (54%) 37 1e-05
(0.000204) 		1e-05
(0.000204) 		1e-05
(0.000204) 		1e-05
(0.000204) 		1e-05
(0.000204) 		1e-05
(0.000204) 		1e-05
(0.000204) 		1e-05
(0.000204)
3q loss 43 (54%) 37 1e-05
(0.000204) 		1e-05
(0.000204) 		1e-05
(0.000204) 		1e-05
(0.000204) 		1e-05
(0.000204) 		1e-05
(0.000204) 		1e-05
(0.000204) 		1e-05
(0.000204)
6q loss 17 (21%) 63 8e-05
(0.00126) 		0.00414
(0.0367) 		0.0495
(0.222) 		0.00503
(0.0419) 		0.0988
(0.363) 		0.23
(0.507) 		0.0388
(0.191) 		0.00152
(0.0159)
8p loss 9 (11%) 71 0.0296
(0.17) 		0.345
(0.616) 		0.0357
(0.191) 		0.0244
(0.146) 		0.227
(0.507) 		0.28
(0.541) 		0.165
(0.433) 		0.0178
(0.121)
1q loss 3 (4%) 77 0.0376
(0.191) 		0.167
(0.435) 		0.218
(0.506) 		0.324
(0.601) 		0.429
(0.698) 		0.046
(0.215) 		0.0912
(0.348) 		0.0322
(0.18)
16q loss 16 (20%) 64 0.0213
(0.132) 		0.131
(0.399) 		0.0943
(0.35) 		0.0127
(0.0929) 		0.824
(0.947) 		0.127
(0.392) 		0.145
(0.425) 		0.0469
(0.215)
xq loss 13 (16%) 67 0.153
(0.43) 		0.0191
(0.123) 		0.212
(0.506) 		0.146
(0.425) 		0.222
(0.506) 		0.386
(0.661) 		0.018
(0.121) 		0.0464
(0.215)
2p gain 10 (12%) 70 0.319
(0.597) 		1
(1.00) 		0.0381
(0.191) 		0.115
(0.377) 		0.108
(0.365) 		0.851
(0.959) 		0.552
(0.813) 		0.0327
(0.18)
9q gain 5 (6%) 75 0.514
(0.771) 		0.0372
(0.191) 		0.839
(0.952) 		0.84
(0.952) 		0.35
(0.621) 		0.749
(0.931) 		0.0185
(0.122) 		0.758
(0.931)
21q gain 14 (18%) 66 0.00322
(0.0306) 		0.197
(0.479) 		0.104
(0.365) 		0.0135
(0.0965) 		0.869
(0.976) 		0.298
(0.568) 		0.128
(0.393) 		0.468
(0.723)
xq gain 9 (11%) 71 0.66
(0.89) 		0.281
(0.541) 		0.0242
(0.146) 		0.0195
(0.123) 		0.108
(0.365) 		0.104
(0.365) 		0.434
(0.698) 		0.0885
(0.344)
11p loss 3 (4%) 77 0.0371
(0.191) 		0.234
(0.507) 		0.0429
(0.204) 		0.109
(0.365) 		0.232
(0.507) 		0.152
(0.43) 		0.216
(0.506) 		0.186
(0.459)
1q gain 8 (10%) 72 0.717
(0.928) 		0.716
(0.928) 		0.704
(0.921) 		0.8
(0.931) 		0.212
(0.506) 		0.0587
(0.247) 		1
(1.00) 		0.0383
(0.191)
2q gain 8 (10%) 72 0.395
(0.665) 		0.716
(0.928) 		0.0556
(0.244) 		0.11
(0.365) 		0.277
(0.541) 		0.194
(0.474) 		0.346
(0.616) 		0.00756
(0.0605)
4p gain 7 (9%) 73 0.0267
(0.158) 		0.279
(0.541) 		0.153
(0.43) 		0.12
(0.38) 		0.885
(0.986) 		0.367
(0.637) 		0.873
(0.976) 		0.23
(0.507)
7q gain 8 (10%) 72 0.0563
(0.244) 		0.0309
(0.175) 		0.889
(0.988) 		0.445
(0.699) 		0.315
(0.595) 		0.328
(0.602) 		0.261
(0.541) 		0.673
(0.9)
12p gain 3 (4%) 77 0.159
(0.433) 		0.441
(0.698) 		0.088
(0.344) 		0.00999
(0.0755) 		0.795
(0.931) 		0.274
(0.541) 		1
(1.00) 		0.279
(0.541)
12q gain 3 (4%) 77 0.161
(0.433) 		0.441
(0.698) 		0.0882
(0.344) 		0.00979
(0.0754) 		0.796
(0.931) 		0.275
(0.541) 		1
(1.00) 		0.279
(0.541)
14q gain 3 (4%) 77 0.0377
(0.191) 		0.441
(0.698) 		0.588
(0.832) 		0.327
(0.602) 		0.796
(0.931) 		0.597
(0.832) 		1
(1.00) 		0.765
(0.931)
17q gain 9 (11%) 71 0.217
(0.506) 		1
(1.00) 		0.422
(0.694) 		0.308
(0.584) 		0.254
(0.537) 		0.0286
(0.167) 		0.267
(0.541) 		0.632
(0.866)
20p gain 8 (10%) 72 0.00923
(0.0724) 		0.566
(0.831) 		0.389
(0.661) 		0.219
(0.506) 		0.279
(0.541) 		0.237
(0.508) 		0.793
(0.931) 		0.843
(0.953)
20q gain 9 (11%) 71 0.00175
(0.0178) 		0.541
(0.802) 		0.146
(0.425) 		0.0569
(0.244) 		0.18
(0.449) 		0.157
(0.432) 		0.903
(0.995) 		0.779
(0.931)
1p loss 19 (24%) 61 0.00479
(0.0407) 		0.0508
(0.225) 		0.785
(0.931) 		0.665
(0.892) 		0.366
(0.637) 		0.277
(0.541) 		0.268
(0.541) 		0.0764
(0.312)
9p loss 8 (10%) 72 0.109
(0.365) 		0.0414
(0.199) 		0.345
(0.616) 		0.153
(0.43) 		0.187
(0.46) 		0.353
(0.622) 		0.171
(0.438) 		0.791
(0.931)
15q loss 4 (5%) 76 0.156
(0.432) 		0.0482
(0.219) 		0.831
(0.947) 		0.825
(0.947) 		1
(1.00) 		0.911
(0.999) 		1
(1.00) 		0.7
(0.921)
xp loss 12 (15%) 68 0.342
(0.616) 		0.0393
(0.191) 		0.323
(0.601) 		0.267
(0.541) 		0.48
(0.736) 		0.581
(0.832) 		0.0691
(0.288) 		0.134
(0.403)
4q gain 4 (5%) 76 0.155
(0.432) 		0.269
(0.541) 		0.399
(0.67) 		0.344
(0.616) 		0.424
(0.694) 		0.824
(0.947) 		1
(1.00) 		0.227
(0.507)
5p gain 3 (4%) 77 0.161
(0.433) 		0.443
(0.698) 		0.781
(0.931) 		0.108
(0.365) 		0.793
(0.931) 		0.276
(0.541) 		1
(1.00) 		0.215
(0.506)
5q gain 3 (4%) 77 0.162
(0.433) 		0.437
(0.698) 		0.784
(0.931) 		0.108
(0.365) 		0.795
(0.931) 		0.274
(0.541) 		1
(1.00) 		0.214
(0.506)
7p gain 9 (11%) 71 0.164
(0.433) 		0.126
(0.392) 		1
(1.00) 		0.74
(0.931) 		0.661
(0.89) 		0.18
(0.449) 		0.643
(0.871) 		0.781
(0.931)
9p gain 6 (8%) 74 0.236
(0.508) 		0.178
(0.449) 		0.405
(0.674) 		0.642
(0.871) 		0.743
(0.931) 		1
(1.00) 		0.126
(0.392) 		0.918
(1.00)
11p gain 9 (11%) 71 0.165
(0.433) 		0.542
(0.802) 		1
(1.00) 		0.739
(0.931) 		0.252
(0.536) 		0.234
(0.507) 		1
(1.00) 		0.702
(0.921)
11q gain 10 (12%) 70 0.317
(0.596) 		0.829
(0.947) 		0.909
(0.999) 		0.829
(0.947) 		0.134
(0.403) 		0.118
(0.378) 		1
(1.00) 		0.701
(0.921)
13q gain 6 (8%) 74 0.106
(0.365) 		1
(1.00) 		0.735
(0.931) 		0.751
(0.931) 		0.488
(0.736) 		0.519
(0.774) 		0.406
(0.674) 		0.118
(0.378)
16p gain 4 (5%) 76 1
(1.00) 		0.436
(0.698) 		1
(1.00) 		0.438
(0.698) 		0.338
(0.615) 		0.474
(0.73) 		0.83
(0.947) 		1
(1.00)
17p gain 8 (10%) 72 0.0806
(0.323) 		0.801
(0.931) 		0.394
(0.665) 		0.22
(0.506) 		0.355
(0.622) 		0.0586
(0.247) 		0.484
(0.736) 		0.703
(0.921)
22q gain 6 (8%) 74 0.108
(0.365) 		0.643
(0.871) 		0.151
(0.43) 		0.222
(0.506) 		0.488
(0.736) 		0.175
(0.443) 		1
(1.00) 		0.118
(0.378)
xp gain 10 (12%) 70 0.389
(0.661) 		0.093
(0.35) 		0.111
(0.367) 		0.141
(0.42) 		0.337
(0.615) 		0.375
(0.649) 		0.377
(0.649) 		0.27
(0.541)
4q loss 3 (4%) 77 1
(1.00) 		0.79
(0.931) 		0.591
(0.832) 		0.604
(0.832) 		0.795
(0.931) 		0.276
(0.541) 		0.406
(0.674) 		0.489
(0.736)
5q loss 3 (4%) 77 0.449
(0.701) 		0.107
(0.365) 		0.0893
(0.344) 		0.169
(0.437) 		0.599
(0.832) 		0.871
(0.976) 		0.298
(0.568) 		0.893
(0.988)
8q loss 3 (4%) 77 0.789
(0.931) 		0.603
(0.832) 		1
(1.00) 		0.792
(0.931) 		1
(1.00) 		0.773
(0.931) 		0.784
(0.931) 		0.893
(0.988)
9q loss 7 (9%) 73 0.165
(0.433) 		0.0754
(0.311) 		0.596
(0.832) 		0.24
(0.514) 		0.0943
(0.35) 		0.581
(0.832) 		0.0805
(0.323) 		0.422
(0.694)
12p loss 3 (4%) 77 0.788
(0.931) 		0.606
(0.832) 		1
(1.00) 		0.792
(0.931) 		1
(1.00) 		0.52
(0.774) 		0.593
(0.832) 		1
(1.00)
13q loss 3 (4%) 77 1
(1.00) 		0.172
(0.438) 		0.592
(0.832) 		0.604
(0.832) 		1
(1.00) 		1
(1.00) 		0.785
(0.931) 		0.488
(0.736)
16p loss 3 (4%) 77 1
(1.00) 		0.443
(0.698) 		0.587
(0.832) 		0.601
(0.832) 		1
(1.00) 		1
(1.00) 		0.784
(0.931) 		0.355
(0.622)
19p loss 3 (4%) 77 0.452
(0.701) 		0.603
(0.832) 		0.784
(0.931) 		1
(1.00) 		0.598
(0.832) 		0.228
(0.507) 		0.785
(0.931) 		0.691
(0.921)
19q loss 3 (4%) 77 0.452
(0.701) 		0.604
(0.832) 		0.781
(0.931) 		1
(1.00) 		0.598
(0.832) 		0.228
(0.507) 		0.789
(0.931) 		0.693
(0.921)
'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.19

Table S1.  Gene #1: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
1Q GAIN MUTATED 2 1 0 4 1 0
1Q GAIN WILD-TYPE 3 11 16 12 14 10

Figure S1.  Get High-res Image Gene #1: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.19

Table S2.  Gene #2: '2p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
2P GAIN MUTATED 2 5 3
2P GAIN WILD-TYPE 28 10 32

Figure S2.  Get High-res Image Gene #2: '2p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.18

Table S3.  Gene #2: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
2P GAIN MUTATED 0 5 0 2 1 2
2P GAIN WILD-TYPE 5 7 16 14 14 8

Figure S3.  Get High-res Image Gene #2: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00756 (Fisher's exact test), Q value = 0.06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
2Q GAIN MUTATED 0 5 0 2 0 1
2Q GAIN WILD-TYPE 5 7 16 14 15 9

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

'4p gain' versus 'CN_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.16

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
4P GAIN MUTATED 5 2 0
4P GAIN WILD-TYPE 17 34 22

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

'6p gain' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0032

Table S6.  Gene #8: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
6P GAIN MUTATED 9 26 4
6P GAIN WILD-TYPE 13 10 18

Figure S6.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00433 (Fisher's exact test), Q value = 0.038

Table S7.  Gene #8: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
6P GAIN MUTATED 10 8 21
6P GAIN WILD-TYPE 23 10 8

Figure S7.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0026

Table S8.  Gene #8: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
6P GAIN MUTATED 8 5 26
6P GAIN WILD-TYPE 22 10 9

Figure S8.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.003

Table S9.  Gene #8: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
6P GAIN MUTATED 9 25 5
6P GAIN WILD-TYPE 20 8 13

Figure S9.  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 = 0.00035

Table S10.  Gene #8: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
6P GAIN MUTATED 11 4 24
6P GAIN WILD-TYPE 23 13 5

Figure S10.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00051

Table S11.  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 5
6P GAIN WILD-TYPE 13 7 4 17

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

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.077

Table S12.  Gene #8: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
6P GAIN MUTATED 11 20 5
6P GAIN WILD-TYPE 21 8 9

Figure S12.  Get High-res Image Gene #8: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
6P GAIN MUTATED 1 5 8 15 1 6
6P GAIN WILD-TYPE 4 7 8 1 14 4

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

'6q gain' versus 'CN_CNMF'

P value = 0.0058 (Fisher's exact test), Q value = 0.047

Table S14.  Gene #9: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
6Q GAIN MUTATED 1 13 2
6Q GAIN WILD-TYPE 21 23 20

Figure S14.  Get High-res Image Gene #9: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.024

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
6Q GAIN MUTATED 1 5 10
6Q GAIN WILD-TYPE 32 13 19

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

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0041

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
6Q GAIN MUTATED 1 1 14
6Q GAIN WILD-TYPE 29 14 21

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

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.012

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 = 0.00026 (Fisher's exact test), Q value = 0.0032

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
6Q GAIN MUTATED 2 1 13
6Q GAIN WILD-TYPE 32 16 16

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

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0041

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 = 0.00352 (Fisher's exact test), Q value = 0.033

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
6Q GAIN MUTATED 1 8 5
6Q GAIN WILD-TYPE 31 20 9

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 = 1e-04 (Fisher's exact test), Q value = 0.0015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
6Q GAIN MUTATED 0 1 2 10 0 1
6Q GAIN WILD-TYPE 5 11 14 6 15 9

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

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.18

Table S22.  Gene #11: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
7Q GAIN MUTATED 4 4 0
7Q GAIN WILD-TYPE 29 14 29

Figure S22.  Get High-res Image Gene #11: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.014

Table S23.  Gene #12: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
8P GAIN MUTATED 14 7 12
8P GAIN WILD-TYPE 8 29 10

Figure S23.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.011

Table S24.  Gene #12: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
8P GAIN MUTATED 21 7 5
8P GAIN WILD-TYPE 12 11 24

Figure S24.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00259 (Fisher's exact test), Q value = 0.025

Table S25.  Gene #12: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
8P GAIN MUTATED 17 9 7
8P GAIN WILD-TYPE 13 6 28

Figure S25.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00412 (Fisher's exact test), Q value = 0.037

Table S26.  Gene #12: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
8P GAIN MUTATED 18 7 8
8P GAIN WILD-TYPE 11 26 10

Figure S26.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.12

Table S27.  Gene #12: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
8P GAIN MUTATED 20 6 7
8P GAIN WILD-TYPE 14 11 22

Figure S27.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.11

Table S28.  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 10 2 8 13
8P GAIN WILD-TYPE 7 11 20 9

Figure S28.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.19

Table S29.  Gene #12: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
8P GAIN MUTATED 18 7 7
8P GAIN WILD-TYPE 14 21 7

Figure S29.  Get High-res Image Gene #12: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.097

Table S30.  Gene #12: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
8P GAIN MUTATED 1 8 2 6 8 7
8P GAIN WILD-TYPE 4 4 14 10 7 3

Figure S30.  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 = 2e-04

Table S31.  Gene #13: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
8Q GAIN MUTATED 21 12 20
8Q GAIN WILD-TYPE 1 24 2

Figure S31.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S32.  Gene #13: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
8Q GAIN MUTATED 31 12 10
8Q GAIN WILD-TYPE 2 6 19

Figure S32.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00098

Table S33.  Gene #13: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
8Q GAIN MUTATED 27 12 14
8Q GAIN WILD-TYPE 3 3 21

Figure S33.  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 = 2e-04

Table S34.  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 S34.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0014

Table S35.  Gene #13: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
8Q GAIN MUTATED 31 9 13
8Q GAIN WILD-TYPE 3 8 16

Figure S35.  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 = 2e-04

Table S36.  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 S36.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

Table S37.  Gene #13: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
8Q GAIN MUTATED 30 10 11
8Q GAIN WILD-TYPE 2 18 3

Figure S37.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S38.  Gene #13: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
8Q GAIN MUTATED 5 10 4 9 13 10
8Q GAIN WILD-TYPE 0 2 12 7 2 0

Figure S38.  Get High-res Image Gene #13: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.19

Table S39.  Gene #15: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
9Q GAIN MUTATED 0 3 2
9Q GAIN WILD-TYPE 33 15 27

Figure S39.  Get High-res Image Gene #15: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.12

Table S40.  Gene #15: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
9Q GAIN MUTATED 0 2 3
9Q GAIN WILD-TYPE 32 26 11

Figure S40.  Get High-res Image Gene #15: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00999 (Fisher's exact test), Q value = 0.075

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 = 0.00979 (Fisher's exact test), Q value = 0.075

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'

'14q gain' versus 'CN_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.19

Table S43.  Gene #21: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
14Q GAIN MUTATED 0 0 3
14Q GAIN WILD-TYPE 22 36 19

Figure S43.  Get High-res Image Gene #21: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.17

Table S44.  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 S44.  Get High-res Image Gene #24: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.072

Table S45.  Gene #25: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
20P GAIN MUTATED 0 2 6
20P GAIN WILD-TYPE 22 34 16

Figure S45.  Get High-res Image Gene #25: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.018

Table S46.  Gene #26: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
20Q GAIN MUTATED 0 2 7
20Q GAIN WILD-TYPE 22 34 15

Figure S46.  Get High-res Image Gene #26: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.00322 (Fisher's exact test), Q value = 0.031

Table S47.  Gene #27: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
21Q GAIN MUTATED 3 2 9
21Q GAIN WILD-TYPE 19 34 13

Figure S47.  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 = 0.097

Table S48.  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 S48.  Get High-res Image Gene #27: '21q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.15

Table S49.  Gene #30: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
XQ GAIN MUTATED 0 3 6
XQ GAIN WILD-TYPE 30 12 29

Figure S49.  Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.12

Table S50.  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 S50.  Get High-res Image Gene #30: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.00479 (Fisher's exact test), Q value = 0.041

Table S51.  Gene #31: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
1P LOSS MUTATED 2 6 11
1P LOSS WILD-TYPE 20 30 11

Figure S51.  Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.19

Table S52.  Gene #32: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
1Q LOSS MUTATED 0 0 3
1Q LOSS WILD-TYPE 22 36 19

Figure S52.  Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.21

Table S53.  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 S53.  Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.18

Table S54.  Gene #32: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
1Q LOSS MUTATED 0 0 0 0 3 0
1Q LOSS WILD-TYPE 5 12 16 16 12 10

Figure S54.  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 = 2e-04

Table S55.  Gene #33: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
3P LOSS MUTATED 22 2 19
3P LOSS WILD-TYPE 0 34 3

Figure S55.  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 = 2e-04

Table S56.  Gene #33: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
3P LOSS MUTATED 33 9 1
3P LOSS WILD-TYPE 0 9 28

Figure S56.  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 = 2e-04

Table S57.  Gene #33: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
3P LOSS MUTATED 30 10 3
3P LOSS WILD-TYPE 0 5 32

Figure S57.  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 = 2e-04

Table S58.  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 S58.  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 = 2e-04

Table S59.  Gene #33: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
3P LOSS MUTATED 29 12 2
3P LOSS WILD-TYPE 5 5 27

Figure S59.  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 = 2e-04

Table S60.  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 S60.  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 = 2e-04

Table S61.  Gene #33: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
3P LOSS MUTATED 29 4 9
3P LOSS WILD-TYPE 3 24 5

Figure S61.  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 = 2e-04

Table S62.  Gene #33: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
3P LOSS MUTATED 5 7 4 1 15 10
3P LOSS WILD-TYPE 0 5 12 15 0 0

Figure S62.  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 = 2e-04

Table S63.  Gene #34: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
3Q LOSS MUTATED 22 2 19
3Q LOSS WILD-TYPE 0 34 3

Figure S63.  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 = 2e-04

Table S64.  Gene #34: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
3Q LOSS MUTATED 33 9 1
3Q LOSS WILD-TYPE 0 9 28

Figure S64.  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 = 2e-04

Table S65.  Gene #34: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
3Q LOSS MUTATED 30 10 3
3Q LOSS WILD-TYPE 0 5 32

Figure S65.  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 = 2e-04

Table S66.  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 S66.  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 = 2e-04

Table S67.  Gene #34: '3q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
3Q LOSS MUTATED 29 12 2
3Q LOSS WILD-TYPE 5 5 27

Figure S67.  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 = 2e-04

Table S68.  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 S68.  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 = 2e-04

Table S69.  Gene #34: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
3Q LOSS MUTATED 29 4 9
3Q LOSS WILD-TYPE 3 24 5

Figure S69.  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 = 2e-04

Table S70.  Gene #34: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
3Q LOSS MUTATED 5 7 4 1 15 10
3Q LOSS WILD-TYPE 0 5 12 15 0 0

Figure S70.  Get High-res Image Gene #34: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0013

Table S71.  Gene #37: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
6Q LOSS MUTATED 12 4 1
6Q LOSS WILD-TYPE 10 32 21

Figure S71.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.037

Table S72.  Gene #37: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
6Q LOSS MUTATED 13 2 2
6Q LOSS WILD-TYPE 20 16 27

Figure S72.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.22

Table S73.  Gene #37: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
6Q LOSS MUTATED 11 2 4
6Q LOSS WILD-TYPE 19 13 31

Figure S73.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00503 (Fisher's exact test), Q value = 0.042

Table S74.  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 S74.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.19

Table S75.  Gene #37: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
6Q LOSS MUTATED 12 4 1
6Q LOSS WILD-TYPE 20 24 13

Figure S75.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00152 (Fisher's exact test), Q value = 0.016

Table S76.  Gene #37: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
6Q LOSS MUTATED 3 1 2 2 2 7
6Q LOSS WILD-TYPE 2 11 14 14 13 3

Figure S76.  Get High-res Image Gene #37: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.17

Table S77.  Gene #38: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
8P LOSS MUTATED 6 2 1
8P LOSS WILD-TYPE 16 34 21

Figure S77.  Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.19

Table S78.  Gene #38: '8p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
8P LOSS MUTATED 7 0 2
8P LOSS WILD-TYPE 23 15 33

Figure S78.  Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.15

Table S79.  Gene #38: '8p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
8P LOSS MUTATED 7 2 0
8P LOSS WILD-TYPE 22 31 18

Figure S79.  Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.12

Table S80.  Gene #38: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
8P LOSS MUTATED 3 1 0 1 3 1
8P LOSS WILD-TYPE 2 11 16 15 12 9

Figure S80.  Get High-res Image Gene #38: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.2

Table S81.  Gene #40: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
9P LOSS MUTATED 6 2 0
9P LOSS WILD-TYPE 27 16 29

Figure S81.  Get High-res Image Gene #40: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.19

Table S82.  Gene #42: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
11P LOSS MUTATED 0 0 3
11P LOSS WILD-TYPE 22 36 19

Figure S82.  Get High-res Image Gene #42: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.2

Table S83.  Gene #42: '11p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
11P LOSS MUTATED 1 2 0
11P LOSS WILD-TYPE 29 13 35

Figure S83.  Get High-res Image Gene #42: '11p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.22

Table S84.  Gene #45: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
15Q LOSS MUTATED 1 3 0
15Q LOSS WILD-TYPE 32 15 29

Figure S84.  Get High-res Image Gene #45: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.13

Table S85.  Gene #47: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
16Q LOSS MUTATED 9 5 2
16Q LOSS WILD-TYPE 13 31 20

Figure S85.  Get High-res Image Gene #47: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.093

Table S86.  Gene #47: '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 S86.  Get High-res Image Gene #47: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.21

Table S87.  Gene #47: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
16Q LOSS MUTATED 3 2 0 4 4 3
16Q LOSS WILD-TYPE 2 10 16 12 11 7

Figure S87.  Get High-res Image Gene #47: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.19

Table S88.  Gene #50: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
XP LOSS MUTATED 6 5 1
XP LOSS WILD-TYPE 27 13 28

Figure S88.  Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.12

Table S89.  Gene #51: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
XQ LOSS MUTATED 6 6 1
XQ LOSS WILD-TYPE 27 12 28

Figure S89.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.12

Table S90.  Gene #51: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
XQ LOSS MUTATED 5 2 6
XQ LOSS WILD-TYPE 27 26 8

Figure S90.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0464 (Fisher's exact test), Q value = 0.21

Table S91.  Gene #51: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
XQ LOSS MUTATED 1 1 2 2 7 0
XQ LOSS WILD-TYPE 4 11 14 14 8 10

Figure S91.  Get High-res Image Gene #51: '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/15908355/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/15952300/UVM-TP.transferedmergedcluster.txt

  • Number of patients = 80

  • Number of significantly arm-level cnvs = 51

  • 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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