Correlation between copy number variations of arm-level result and molecular subtypes
Uveal Melanoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1833RB9
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/C1833RB9
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 0.00018
(0.00245) 		0.00425
(0.0364) 		0.0002
(0.00255) 		0.0003
(0.0036) 		3e-05
(0.00049) 		1e-05
(0.000185) 		0.0102
(0.0759) 		3e-05
(0.00049)
6q gain 16 (20%) 64 0.00609
(0.0497) 		0.0024
(0.0239) 		0.00029
(0.00359) 		0.00099
(0.0109) 		0.00019
(0.0025) 		0.00033
(0.00385) 		0.00349
(0.0316) 		0.00011
(0.00155)
8p gain 33 (41%) 47 0.00134
(0.0144) 		0.00085
(0.00963) 		0.00283
(0.0269) 		0.00381
(0.0338) 		0.0198
(0.126) 		0.0144
(0.0997) 		0.038
(0.188) 		0.014
(0.0984)
8q gain 53 (66%) 27 1e-05
(0.000185) 		1e-05
(0.000185) 		3e-05
(0.00049) 		1e-05
(0.000185) 		0.00011
(0.00155) 		1e-05
(0.000185) 		1e-05
(0.000185) 		0.0001
(0.00151)
3p loss 43 (54%) 37 1e-05
(0.000185) 		1e-05
(0.000185) 		1e-05
(0.000185) 		1e-05
(0.000185) 		1e-05
(0.000185) 		1e-05
(0.000185) 		1e-05
(0.000185) 		1e-05
(0.000185)
3q loss 43 (54%) 37 1e-05
(0.000185) 		1e-05
(0.000185) 		1e-05
(0.000185) 		1e-05
(0.000185) 		1e-05
(0.000185) 		1e-05
(0.000185) 		1e-05
(0.000185) 		1e-05
(0.000185)
6q loss 17 (21%) 63 7e-05
(0.0011) 		0.00343
(0.0316) 		0.0485
(0.22) 		0.00457
(0.0381) 		0.1
(0.366) 		0.228
(0.504) 		0.0394
(0.191) 		0.00196
(0.02)
8p loss 9 (11%) 71 0.03
(0.172) 		0.345
(0.619) 		0.0376
(0.188) 		0.0229
(0.139) 		0.228
(0.504) 		0.282
(0.543) 		0.161
(0.431) 		0.0186
(0.123)
1q loss 3 (4%) 77 0.0381
(0.188) 		0.17
(0.434) 		0.218
(0.502) 		0.322
(0.598) 		0.43
(0.695) 		0.0469
(0.217) 		0.0893
(0.343) 		0.0314
(0.173)
16q loss 16 (20%) 64 0.0213
(0.131) 		0.132
(0.403) 		0.0955
(0.354) 		0.0132
(0.0964) 		0.823
(0.948) 		0.125
(0.389) 		0.144
(0.424) 		0.0477
(0.219)
xq loss 13 (16%) 67 0.155
(0.431) 		0.019
(0.123) 		0.211
(0.502) 		0.145
(0.424) 		0.221
(0.504) 		0.385
(0.66) 		0.0187
(0.123) 		0.0466
(0.217)
2p gain 10 (12%) 70 0.317
(0.593) 		1
(1.00) 		0.0377
(0.188) 		0.114
(0.374) 		0.108
(0.366) 		0.85
(0.958) 		0.553
(0.814) 		0.0313
(0.173)
9q gain 5 (6%) 75 0.509
(0.763) 		0.0372
(0.188) 		0.838
(0.951) 		0.839
(0.951) 		0.351
(0.621) 		0.752
(0.933) 		0.0186
(0.123) 		0.758
(0.933)
21q gain 14 (18%) 66 0.00283
(0.0269) 		0.199
(0.483) 		0.104
(0.366) 		0.0137
(0.0982) 		0.867
(0.975) 		0.296
(0.567) 		0.126
(0.389) 		0.464
(0.717)
xq gain 9 (11%) 71 0.66
(0.889) 		0.282
(0.543) 		0.0239
(0.143) 		0.0203
(0.127) 		0.106
(0.366) 		0.103
(0.366) 		0.434
(0.695) 		0.0876
(0.343)
11p loss 3 (4%) 77 0.0382
(0.188) 		0.235
(0.508) 		0.0441
(0.209) 		0.108
(0.366) 		0.23
(0.504) 		0.152
(0.431) 		0.214
(0.502) 		0.184
(0.456)
1q gain 8 (10%) 72 0.715
(0.926) 		0.714
(0.926) 		0.701
(0.922) 		0.802
(0.933) 		0.211
(0.502) 		0.0575
(0.245) 		1
(1.00) 		0.0378
(0.188)
2q gain 8 (10%) 72 0.394
(0.664) 		0.715
(0.926) 		0.0549
(0.24) 		0.112
(0.369) 		0.278
(0.543) 		0.195
(0.476) 		0.346
(0.619) 		0.007
(0.056)
4p gain 7 (9%) 73 0.0278
(0.164) 		0.282
(0.543) 		0.154
(0.431) 		0.121
(0.384) 		0.884
(0.985) 		0.368
(0.639) 		0.873
(0.976) 		0.23
(0.504)
7q gain 8 (10%) 72 0.0552
(0.24) 		0.0313
(0.173) 		0.89
(0.989) 		0.448
(0.699) 		0.315
(0.593) 		0.328
(0.604) 		0.261
(0.543) 		0.672
(0.899)
12p gain 3 (4%) 77 0.162
(0.431) 		0.441
(0.695) 		0.0899
(0.343) 		0.0101
(0.0759) 		0.798
(0.933) 		0.278
(0.543) 		1
(1.00) 		0.279
(0.543)
12q gain 3 (4%) 77 0.161
(0.431) 		0.441
(0.695) 		0.0879
(0.343) 		0.00955
(0.0735) 		0.794
(0.933) 		0.272
(0.543) 		1
(1.00) 		0.282
(0.543)
14q gain 3 (4%) 77 0.0373
(0.188) 		0.438
(0.695) 		0.592
(0.833) 		0.327
(0.603) 		0.797
(0.933) 		0.596
(0.833) 		1
(1.00) 		0.765
(0.933)
17q gain 9 (11%) 71 0.218
(0.502) 		1
(1.00) 		0.42
(0.692) 		0.314
(0.593) 		0.253
(0.535) 		0.0292
(0.17) 		0.264
(0.543) 		0.632
(0.866)
20p gain 8 (10%) 72 0.0092
(0.0722) 		0.567
(0.832) 		0.39
(0.663) 		0.219
(0.502) 		0.278
(0.543) 		0.239
(0.514) 		0.791
(0.933) 		0.844
(0.954)
20q gain 9 (11%) 71 0.00172
(0.018) 		0.54
(0.798) 		0.144
(0.424) 		0.0581
(0.245) 		0.182
(0.454) 		0.159
(0.431) 		0.905
(0.997) 		0.78
(0.933)
1p loss 19 (24%) 61 0.00428
(0.0364) 		0.0518
(0.23) 		0.783
(0.933) 		0.662
(0.889) 		0.366
(0.639) 		0.278
(0.543) 		0.265
(0.543) 		0.0762
(0.311)
9p loss 8 (10%) 72 0.109
(0.366) 		0.0405
(0.194) 		0.348
(0.62) 		0.154
(0.431) 		0.186
(0.457) 		0.353
(0.621) 		0.17
(0.434) 		0.792
(0.933)
15q loss 4 (5%) 76 0.158
(0.431) 		0.05
(0.224) 		0.832
(0.948) 		0.824
(0.948) 		1
(1.00) 		0.911
(0.999) 		1
(1.00) 		0.696
(0.922)
xp loss 12 (15%) 68 0.34
(0.617) 		0.0376
(0.188) 		0.323
(0.598) 		0.264
(0.543) 		0.481
(0.736) 		0.579
(0.833) 		0.07
(0.291) 		0.135
(0.406)
4q gain 4 (5%) 76 0.157
(0.431) 		0.267
(0.543) 		0.397
(0.667) 		0.345
(0.619) 		0.425
(0.695) 		0.824
(0.948) 		1
(1.00) 		0.226
(0.504)
5p gain 3 (4%) 77 0.161
(0.431) 		0.441
(0.695) 		0.784
(0.933) 		0.107
(0.366) 		0.793
(0.933) 		0.279
(0.543) 		1
(1.00) 		0.216
(0.502)
5q gain 3 (4%) 77 0.16
(0.431) 		0.439
(0.695) 		0.784
(0.933) 		0.107
(0.366) 		0.797
(0.933) 		0.275
(0.543) 		1
(1.00) 		0.215
(0.502)
7p gain 9 (11%) 71 0.165
(0.431) 		0.131
(0.401) 		1
(1.00) 		0.74
(0.933) 		0.661
(0.889) 		0.179
(0.447) 		0.641
(0.872) 		0.782
(0.933)
9p gain 6 (8%) 74 0.233
(0.507) 		0.179
(0.447) 		0.401
(0.671) 		0.643
(0.872) 		0.748
(0.933) 		1
(1.00) 		0.125
(0.389) 		0.919
(1.00)
11p gain 9 (11%) 71 0.163
(0.431) 		0.54
(0.798) 		1
(1.00) 		0.738
(0.933) 		0.251
(0.534) 		0.235
(0.508) 		1
(1.00) 		0.706
(0.923)
11q gain 10 (12%) 70 0.317
(0.593) 		0.83
(0.948) 		0.909
(0.999) 		0.829
(0.948) 		0.135
(0.406) 		0.117
(0.379) 		1
(1.00) 		0.701
(0.922)
13q gain 6 (8%) 74 0.105
(0.366) 		1
(1.00) 		0.735
(0.933) 		0.752
(0.933) 		0.488
(0.739) 		0.517
(0.77) 		0.408
(0.677) 		0.119
(0.381)
16p gain 4 (5%) 76 1
(1.00) 		0.436
(0.695) 		1
(1.00) 		0.438
(0.695) 		0.339
(0.617) 		0.472
(0.726) 		0.831
(0.948) 		1
(1.00)
17p gain 8 (10%) 72 0.0816
(0.326) 		0.803
(0.933) 		0.393
(0.664) 		0.219
(0.502) 		0.352
(0.621) 		0.0582
(0.245) 		0.481
(0.736) 		0.702
(0.922)
22q gain 6 (8%) 74 0.105
(0.366) 		0.641
(0.872) 		0.15
(0.431) 		0.218
(0.502) 		0.492
(0.741) 		0.175
(0.444) 		1
(1.00) 		0.12
(0.381)
xp gain 10 (12%) 70 0.388
(0.662) 		0.0907
(0.343) 		0.111
(0.367) 		0.14
(0.418) 		0.337
(0.617) 		0.375
(0.647) 		0.376
(0.647) 		0.265
(0.543)
4q loss 3 (4%) 77 1
(1.00) 		0.79
(0.933) 		0.589
(0.833) 		0.6
(0.833) 		0.797
(0.933) 		0.274
(0.543) 		0.407
(0.677) 		0.489
(0.739)
5q loss 3 (4%) 77 0.449
(0.699) 		0.109
(0.366) 		0.0901
(0.343) 		0.169
(0.434) 		0.596
(0.833) 		0.872
(0.976) 		0.298
(0.568) 		0.894
(0.989)
8q loss 3 (4%) 77 0.788
(0.933) 		0.603
(0.833) 		1
(1.00) 		0.791
(0.933) 		1
(1.00) 		0.773
(0.933) 		0.787
(0.933) 		0.893
(0.989)
9q loss 7 (9%) 73 0.164
(0.431) 		0.074
(0.305) 		0.592
(0.833) 		0.243
(0.518) 		0.0952
(0.354) 		0.584
(0.833) 		0.0788
(0.318) 		0.418
(0.691)
12p loss 3 (4%) 77 0.787
(0.933) 		0.607
(0.833) 		1
(1.00) 		0.792
(0.933) 		1
(1.00) 		0.516
(0.77) 		0.592
(0.833) 		1
(1.00)
13q loss 3 (4%) 77 1
(1.00) 		0.169
(0.434) 		0.592
(0.833) 		0.603
(0.833) 		1
(1.00) 		1
(1.00) 		0.786
(0.933) 		0.487
(0.739)
16p loss 3 (4%) 77 1
(1.00) 		0.441
(0.695) 		0.59
(0.833) 		0.602
(0.833) 		1
(1.00) 		1
(1.00) 		0.785
(0.933) 		0.355
(0.621)
19p loss 3 (4%) 77 0.451
(0.7) 		0.605
(0.833) 		0.783
(0.933) 		1
(1.00) 		0.596
(0.833) 		0.229
(0.504) 		0.785
(0.933) 		0.692
(0.919)
19q loss 3 (4%) 77 0.449
(0.699) 		0.604
(0.833) 		0.781
(0.933) 		1
(1.00) 		0.6
(0.833) 		0.228
(0.504) 		0.786
(0.933) 		0.692
(0.919)
'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0378 (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 = 0.0377 (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 = 0.0313 (Fisher's exact test), Q value = 0.17

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 = 0.007 (Fisher's exact test), Q value = 0.056

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 = 0.0278 (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 = 0.00018 (Fisher's exact test), Q value = 0.0024

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 = 0.00425 (Fisher's exact test), Q value = 0.036

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 = 2e-04 (Fisher's exact test), Q value = 0.0025

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 = 3e-04 (Fisher's exact test), Q value = 0.0036

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 = 3e-05 (Fisher's exact test), Q value = 0.00049

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 = 1e-05 (Fisher's exact test), Q value = 0.00019

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 = 0.0102 (Fisher's exact test), Q value = 0.076

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 = 3e-05 (Fisher's exact test), Q value = 0.00049

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 = 0.00609 (Fisher's exact test), Q value = 0.05

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 = 0.0024 (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 = 0.00029 (Fisher's exact test), Q value = 0.0036

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 = 0.00099 (Fisher's exact test), Q value = 0.011

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 = 0.00019 (Fisher's exact test), Q value = 0.0025

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 = 0.00033 (Fisher's exact test), Q value = 0.0038

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 = 0.00349 (Fisher's exact test), Q value = 0.032

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 = 0.00011 (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 = 0.0313 (Fisher's exact test), Q value = 0.17

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 = 0.00134 (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 = 0.00085 (Fisher's exact test), Q value = 0.0096

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 = 0.00283 (Fisher's exact test), Q value = 0.027

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 = 0.00381 (Fisher's exact test), Q value = 0.034

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 = 0.0198 (Fisher's exact test), Q value = 0.13

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 = 0.0144 (Fisher's exact test), Q value = 0.1

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 = 0.038 (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 = 0.014 (Fisher's exact test), Q value = 0.098

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 = 0.00019

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 = 0.00019

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 = 3e-05 (Fisher's exact test), Q value = 0.00049

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 = 0.00019

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

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 = 0.00019

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 = 1e-05 (Fisher's exact test), Q value = 0.00019

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 = 1e-04 (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 = 0.0186 (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 = 0.0101 (Fisher's exact test), Q value = 0.076

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 = 0.00955 (Fisher's exact test), Q value = 0.074

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 = 0.0373 (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 = 0.0292 (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 = 0.0092 (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 = 0.00172 (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 = 0.00283 (Fisher's exact test), Q value = 0.027

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 = 0.0137 (Fisher's exact test), Q value = 0.098

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 = 0.0239 (Fisher's exact test), Q value = 0.14

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 = 0.0203 (Fisher's exact test), Q value = 0.13

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 = 0.00428 (Fisher's exact test), Q value = 0.036

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 = 0.0381 (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 = 0.0469 (Fisher's exact test), Q value = 0.22

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 = 0.0314 (Fisher's exact test), Q value = 0.17

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 0.00019

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 = 7e-05 (Fisher's exact test), Q value = 0.0011

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 = 0.00343 (Fisher's exact test), Q value = 0.032

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 = 0.0485 (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 = 0.00457 (Fisher's exact test), Q value = 0.038

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 = 0.0394 (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 = 0.00196 (Fisher's exact test), Q value = 0.02

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 = 0.03 (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 = 0.0376 (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 = 0.0229 (Fisher's exact test), Q value = 0.14

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 = 0.0186 (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 = 0.0405 (Fisher's exact test), Q value = 0.19

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 = 0.0382 (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 = 0.0441 (Fisher's exact test), Q value = 0.21

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 = 0.05 (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 = 0.0132 (Fisher's exact test), Q value = 0.096

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 = 0.0477 (Fisher's exact test), Q value = 0.22

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 = 0.0376 (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 = 0.019 (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 = 0.0187 (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 = 0.0466 (Fisher's exact test), Q value = 0.22

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/19783310/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/19785804/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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