Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Chromophobe (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1X63KPN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1X63KPN
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 61 arm-level events and 8 molecular subtypes across 66 patients, 62 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 4p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 1p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 8p loss cnv correlated to 'CN_CNMF'.

  • 8q loss cnv correlated to 'CN_CNMF'.

  • 10p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 17p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 61 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, 62 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
1q loss 52 (79%) 14 0.474
(1.00) 		1e-05
(0.00488) 		7e-05
(0.0313) 		5e-05
(0.0225) 		0.233
(1.00) 		0.00047
(0.201) 		0.0761
(1.00) 		4e-05
(0.0181)
2p loss 46 (70%) 20 0.0881
(1.00) 		1e-05
(0.00488) 		1e-05
(0.00488) 		1e-05
(0.00488) 		0.083
(1.00) 		1e-05
(0.00488) 		0.0231
(1.00) 		1e-05
(0.00488)
2q loss 46 (70%) 20 0.0883
(1.00) 		1e-05
(0.00488) 		1e-05
(0.00488) 		1e-05
(0.00488) 		0.0838
(1.00) 		1e-05
(0.00488) 		0.0225
(1.00) 		1e-05
(0.00488)
10p loss 48 (73%) 18 0.341
(1.00) 		0.00032
(0.138) 		7e-05
(0.0313) 		1e-05
(0.00488) 		0.274
(1.00) 		0.00017
(0.0739) 		0.00639
(1.00) 		1e-05
(0.00488)
10q loss 49 (74%) 17 0.25
(1.00) 		0.00018
(0.0781) 		2e-05
(0.0092) 		1e-05
(0.00488) 		0.226
(1.00) 		0.00025
(0.108) 		0.0132
(1.00) 		9e-05
(0.0395)
17p loss 50 (76%) 16 0.3
(1.00) 		1e-05
(0.00488) 		1e-05
(0.00488) 		1e-05
(0.00488) 		0.0509
(1.00) 		7e-05
(0.0313) 		0.0251
(1.00) 		2e-05
(0.0092)
17q loss 50 (76%) 16 0.3
(1.00) 		1e-05
(0.00488) 		1e-05
(0.00488) 		1e-05
(0.00488) 		0.0512
(1.00) 		6e-05
(0.0269) 		0.0262
(1.00) 		1e-05
(0.00488)
6p loss 51 (77%) 15 0.33
(1.00) 		8e-05
(0.0354) 		9e-05
(0.0395) 		1e-05
(0.00488) 		0.353
(1.00) 		0.0012
(0.504) 		0.304
(1.00) 		0.00012
(0.0524)
6q loss 51 (77%) 15 0.329
(1.00) 		0.00012
(0.0524) 		7e-05
(0.0313) 		1e-05
(0.00488) 		0.352
(1.00) 		0.00111
(0.468) 		0.302
(1.00) 		4e-05
(0.0181)
1p loss 53 (80%) 13 0.674
(1.00) 		3e-05
(0.0137) 		0.0004
(0.172) 		0.00029
(0.125) 		0.164
(1.00) 		0.00129
(0.538) 		0.0991
(1.00) 		0.00143
(0.595)
4p gain 24 (36%) 42 0.0553
(1.00) 		1
(1.00) 		3e-05
(0.0137) 		6e-05
(0.0269) 		0.77
(1.00) 		0.00859
(1.00) 		0.775
(1.00) 		0.129
(1.00)
4q gain 24 (36%) 42 0.0566
(1.00) 		1
(1.00) 		2e-05
(0.0092) 		4e-05
(0.0181) 		0.769
(1.00) 		0.00908
(1.00) 		0.775
(1.00) 		0.127
(1.00)
11p gain 15 (23%) 51 0.284
(1.00) 		0.677
(1.00) 		3e-05
(0.0137) 		0.00043
(0.184) 		0.87
(1.00) 		0.0271
(1.00) 		0.718
(1.00) 		0.153
(1.00)
11q gain 15 (23%) 51 0.281
(1.00) 		0.681
(1.00) 		1e-05
(0.00488) 		1e-05
(0.00488) 		0.622
(1.00) 		0.0206
(1.00) 		0.387
(1.00) 		0.0558
(1.00)
16p gain 21 (32%) 45 0.108
(1.00) 		1
(1.00) 		1e-05
(0.00488) 		7e-05
(0.0313) 		0.158
(1.00) 		0.00501
(1.00) 		0.8
(1.00) 		0.0844
(1.00)
16q gain 21 (32%) 45 0.106
(1.00) 		1
(1.00) 		2e-05
(0.0092) 		8e-05
(0.0354) 		0.16
(1.00) 		0.00536
(1.00) 		0.801
(1.00) 		0.0843
(1.00)
13q loss 43 (65%) 23 0.26
(1.00) 		0.00053
(0.226) 		0.00353
(1.00) 		8e-05
(0.0354) 		0.852
(1.00) 		0.197
(1.00) 		0.935
(1.00) 		0.0987
(1.00)
8p loss 9 (14%) 57 1e-05
(0.00488) 		0.0844
(1.00) 		0.0532
(1.00) 		0.0391
(1.00) 		0.147
(1.00) 		0.466
(1.00) 		0.073
(1.00) 		0.0088
(1.00)
8q loss 8 (12%) 58 1e-05
(0.00488) 		0.042
(1.00) 		0.134
(1.00) 		0.0715
(1.00) 		0.287
(1.00) 		0.527
(1.00) 		0.171
(1.00) 		0.0497
(1.00)
3p gain 8 (12%) 58 0.271
(1.00) 		0.532
(1.00) 		0.952
(1.00) 		0.648
(1.00) 		0.517
(1.00) 		0.692
(1.00) 		0.0133
(1.00) 		0.795
(1.00)
3q gain 8 (12%) 58 0.271
(1.00) 		0.528
(1.00) 		0.952
(1.00) 		0.651
(1.00) 		0.514
(1.00) 		0.691
(1.00) 		0.0134
(1.00) 		0.795
(1.00)
5p gain 8 (12%) 58 0.427
(1.00) 		0.682
(1.00) 		0.448
(1.00) 		0.448
(1.00) 		0.363
(1.00) 		0.0596
(1.00) 		0.683
(1.00) 		0.314
(1.00)
5q gain 8 (12%) 58 0.425
(1.00) 		0.679
(1.00) 		0.45
(1.00) 		0.449
(1.00) 		0.363
(1.00) 		0.0616
(1.00) 		0.682
(1.00) 		0.312
(1.00)
7p gain 24 (36%) 42 0.152
(1.00) 		1
(1.00) 		0.0163
(1.00) 		0.0616
(1.00) 		0.9
(1.00) 		0.117
(1.00) 		0.775
(1.00) 		0.415
(1.00)
7q gain 24 (36%) 42 0.151
(1.00) 		1
(1.00) 		0.0157
(1.00) 		0.0613
(1.00) 		0.901
(1.00) 		0.119
(1.00) 		0.776
(1.00) 		0.418
(1.00)
8p gain 17 (26%) 49 0.41
(1.00) 		0.418
(1.00) 		0.0038
(1.00) 		0.0317
(1.00) 		0.464
(1.00) 		0.1
(1.00) 		0.731
(1.00) 		0.301
(1.00)
8q gain 18 (27%) 48 0.341
(1.00) 		0.378
(1.00) 		0.0012
(0.504) 		0.0104
(1.00) 		0.694
(1.00) 		0.0873
(1.00) 		0.938
(1.00) 		0.191
(1.00)
9p gain 10 (15%) 56 1
(1.00) 		1
(1.00) 		0.724
(1.00) 		0.814
(1.00) 		0.831
(1.00) 		0.601
(1.00) 		0.219
(1.00) 		0.656
(1.00)
9q gain 10 (15%) 56 1
(1.00) 		1
(1.00) 		0.724
(1.00) 		0.811
(1.00) 		0.833
(1.00) 		0.601
(1.00) 		0.221
(1.00) 		0.66
(1.00)
10p gain 4 (6%) 62 0.44
(1.00) 		0.164
(1.00) 		0.515
(1.00) 		0.205
(1.00) 		1
(1.00) 		0.165
(1.00) 		0.588
(1.00) 		0.11
(1.00)
12p gain 19 (29%) 47 0.482
(1.00) 		0.765
(1.00) 		0.078
(1.00) 		0.157
(1.00) 		1
(1.00) 		0.0672
(1.00) 		0.868
(1.00) 		0.429
(1.00)
12q gain 20 (30%) 46 0.445
(1.00) 		0.593
(1.00) 		0.146
(1.00) 		0.0829
(1.00) 		0.944
(1.00) 		0.033
(1.00) 		0.941
(1.00) 		0.33
(1.00)
14q gain 21 (32%) 45 0.107
(1.00) 		0.829
(1.00) 		0.00067
(0.285) 		0.00459
(1.00) 		0.426
(1.00) 		0.057
(1.00) 		0.881
(1.00) 		0.162
(1.00)
15q gain 21 (32%) 45 0.107
(1.00) 		0.827
(1.00) 		0.00184
(0.76) 		0.0621
(1.00) 		0.755
(1.00) 		0.214
(1.00) 		1
(1.00) 		0.136
(1.00)
18p gain 17 (26%) 49 0.516
(1.00) 		0.806
(1.00) 		0.00195
(0.803) 		0.0128
(1.00) 		0.938
(1.00) 		0.0496
(1.00) 		0.33
(1.00) 		0.0381
(1.00)
18q gain 16 (24%) 50 0.64
(1.00) 		0.927
(1.00) 		0.00107
(0.453) 		0.0191
(1.00) 		0.821
(1.00) 		0.0519
(1.00) 		0.416
(1.00) 		0.026
(1.00)
19p gain 19 (29%) 47 0.484
(1.00) 		0.275
(1.00) 		0.022
(1.00) 		0.00939
(1.00) 		0.661
(1.00) 		0.0386
(1.00) 		0.964
(1.00) 		0.126
(1.00)
19q gain 17 (26%) 49 0.521
(1.00) 		0.307
(1.00) 		0.00124
(0.518) 		0.00155
(0.643) 		0.412
(1.00) 		0.0477
(1.00) 		0.919
(1.00) 		0.024
(1.00)
20p gain 20 (30%) 46 0.213
(1.00) 		0.597
(1.00) 		0.0302
(1.00) 		0.0314
(1.00) 		0.707
(1.00) 		0.0312
(1.00) 		0.647
(1.00) 		0.31
(1.00)
20q gain 21 (32%) 45 0.226
(1.00) 		0.388
(1.00) 		0.0684
(1.00) 		0.0168
(1.00) 		0.676
(1.00) 		0.0371
(1.00) 		0.526
(1.00) 		0.436
(1.00)
21q gain 4 (6%) 62 0.439
(1.00) 		0.161
(1.00) 		0.512
(1.00) 		0.106
(1.00) 		0.677
(1.00) 		0.165
(1.00) 		0.497
(1.00) 		0.131
(1.00)
22q gain 19 (29%) 47 0.901
(1.00) 		0.712
(1.00) 		0.0699
(1.00) 		0.363
(1.00) 		0.551
(1.00) 		0.023
(1.00) 		1
(1.00) 		0.251
(1.00)
xq gain 6 (9%) 60 1
(1.00) 		0.722
(1.00) 		0.0067
(1.00) 		0.122
(1.00) 		0.263
(1.00) 		0.117
(1.00) 		0.51
(1.00) 		0.0247
(1.00)
3p loss 9 (14%) 57 0.0371
(1.00) 		0.895
(1.00) 		0.0657
(1.00) 		0.00331
(1.00) 		0.904
(1.00) 		0.204
(1.00) 		0.0291
(1.00) 		0.0699
(1.00)
3q loss 8 (12%) 58 0.0217
(1.00) 		0.369
(1.00) 		0.0254
(1.00) 		0.0017
(0.704) 		0.575
(1.00) 		0.178
(1.00) 		0.00532
(1.00) 		0.0245
(1.00)
5p loss 10 (15%) 56 0.0999
(1.00) 		0.252
(1.00) 		0.00067
(0.285) 		0.0187
(1.00) 		0.426
(1.00) 		0.0134
(1.00) 		0.635
(1.00) 		0.0307
(1.00)
5q loss 10 (15%) 56 0.0983
(1.00) 		0.251
(1.00) 		0.00074
(0.314) 		0.0189
(1.00) 		0.428
(1.00) 		0.0153
(1.00) 		0.633
(1.00) 		0.0319
(1.00)
9p loss 10 (15%) 56 1
(1.00) 		0.9
(1.00) 		0.0649
(1.00) 		0.0162
(1.00) 		0.912
(1.00) 		0.598
(1.00) 		0.922
(1.00) 		0.498
(1.00)
9q loss 10 (15%) 56 1
(1.00) 		0.902
(1.00) 		0.0643
(1.00) 		0.0156
(1.00) 		0.913
(1.00) 		0.601
(1.00) 		0.922
(1.00) 		0.5
(1.00)
11p loss 7 (11%) 59 0.627
(1.00) 		0.573
(1.00) 		0.111
(1.00) 		0.317
(1.00) 		0.203
(1.00) 		0.938
(1.00) 		0.401
(1.00) 		0.334
(1.00)
11q loss 7 (11%) 59 0.628
(1.00) 		0.572
(1.00) 		0.11
(1.00) 		0.314
(1.00) 		0.204
(1.00) 		0.939
(1.00) 		0.402
(1.00) 		0.334
(1.00)
16p loss 4 (6%) 62 0.686
(1.00) 		0.517
(1.00) 		0.0231
(1.00) 		0.0373
(1.00) 		0.683
(1.00) 		0.0869
(1.00) 		0.496
(1.00) 		0.807
(1.00)
16q loss 5 (8%) 61 0.72
(1.00) 		0.388
(1.00) 		0.00583
(1.00) 		0.00748
(1.00) 		0.427
(1.00) 		0.0481
(1.00) 		0.195
(1.00) 		0.521
(1.00)
18p loss 8 (12%) 58 0.677
(1.00) 		0.0963
(1.00) 		0.315
(1.00) 		0.211
(1.00) 		0.719
(1.00) 		0.949
(1.00) 		0.884
(1.00) 		0.892
(1.00)
18q loss 10 (15%) 56 0.623
(1.00) 		0.0791
(1.00) 		0.442
(1.00) 		0.278
(1.00) 		0.575
(1.00) 		0.864
(1.00) 		0.495
(1.00) 		0.613
(1.00)
19q loss 3 (5%) 63 0.645
(1.00) 		0.767
(1.00) 		0.765
(1.00) 		0.826
(1.00) 		0.513
(1.00) 		0.866
(1.00) 		0.81
(1.00) 		0.767
(1.00)
20p loss 4 (6%) 62 0.305
(1.00) 		0.807
(1.00) 		0.208
(1.00) 		0.212
(1.00) 		0.453
(1.00) 		0.659
(1.00) 		0.245
(1.00) 		0.272
(1.00)
20q loss 3 (5%) 63 1
(1.00) 		0.416
(1.00) 		0.227
(1.00) 		0.0578
(1.00) 		0.295
(1.00) 		0.828
(1.00) 		0.188
(1.00) 		0.538
(1.00)
21q loss 35 (53%) 31 0.775
(1.00) 		0.0103
(1.00) 		0.25
(1.00) 		0.195
(1.00) 		1
(1.00) 		0.128
(1.00) 		0.78
(1.00) 		0.289
(1.00)
22q loss 8 (12%) 58 0.83
(1.00) 		0.133
(1.00) 		0.249
(1.00) 		0.234
(1.00) 		0.898
(1.00) 		0.217
(1.00) 		0.762
(1.00) 		0.61
(1.00)
xq loss 39 (59%) 27 0.599
(1.00) 		0.0728
(1.00) 		0.00674
(1.00) 		0.00337
(1.00) 		0.328
(1.00) 		0.00116
(0.488) 		0.0751
(1.00) 		0.0221
(1.00)
'4p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S1.  Gene #3: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
4P GAIN MUTATED 4 17 2 1
4P GAIN WILD-TYPE 15 5 13 9

Figure S1.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.027

Table S2.  Gene #3: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
4P GAIN MUTATED 4 14 3 1 1 1 0
4P GAIN WILD-TYPE 15 2 4 5 9 3 4

Figure S2.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0092

Table S3.  Gene #4: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
4Q GAIN MUTATED 4 17 2 1
4Q GAIN WILD-TYPE 15 5 13 9

Figure S3.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S4.  Gene #4: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
4Q GAIN MUTATED 4 14 3 1 1 1 0
4Q GAIN WILD-TYPE 15 2 4 5 9 3 4

Figure S4.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S5.  Gene #14: '11p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
11P GAIN MUTATED 1 13 1 0
11P GAIN WILD-TYPE 18 9 14 10

Figure S5.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.18

Table S6.  Gene #14: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
11P GAIN MUTATED 1 11 1 1 1 0 0
11P GAIN WILD-TYPE 18 5 6 5 9 4 4

Figure S6.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S7.  Gene #15: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
11Q GAIN MUTATED 1 14 0 0
11Q GAIN WILD-TYPE 18 8 15 10

Figure S7.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S8.  Gene #15: '11q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
11Q GAIN MUTATED 1 12 1 1 0 0 0
11Q GAIN WILD-TYPE 18 4 6 5 10 4 4

Figure S8.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S9.  Gene #20: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
16P GAIN MUTATED 4 16 1 0
16P GAIN WILD-TYPE 15 6 14 10

Figure S9.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.031

Table S10.  Gene #20: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
16P GAIN MUTATED 4 13 2 1 0 1 0
16P GAIN WILD-TYPE 15 3 5 5 10 3 4

Figure S10.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0092

Table S11.  Gene #21: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
16Q GAIN MUTATED 4 16 1 0
16Q GAIN WILD-TYPE 15 6 14 10

Figure S11.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.035

Table S12.  Gene #21: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
16Q GAIN MUTATED 4 13 2 1 0 1 0
16Q GAIN WILD-TYPE 15 3 5 5 10 3 4

Figure S12.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.014

Table S13.  Gene #31: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
1P LOSS MUTATED 17 32 4
1P LOSS WILD-TYPE 1 3 9

Figure S13.  Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.17

Table S14.  Gene #31: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
1P LOSS MUTATED 19 16 14 4
1P LOSS WILD-TYPE 0 6 1 6

Figure S14.  Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.13

Table S15.  Gene #31: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
1P LOSS MUTATED 19 11 6 4 9 4 0
1P LOSS WILD-TYPE 0 5 1 2 1 0 4

Figure S15.  Get High-res Image Gene #31: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S16.  Gene #32: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
1Q LOSS MUTATED 17 32 3
1Q LOSS WILD-TYPE 1 3 10

Figure S16.  Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.031

Table S17.  Gene #32: '1q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
1Q LOSS MUTATED 19 16 14 3
1Q LOSS WILD-TYPE 0 6 1 7

Figure S17.  Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.022

Table S18.  Gene #32: '1q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
1Q LOSS MUTATED 19 11 5 3 10 4 0
1Q LOSS WILD-TYPE 0 5 2 3 0 0 4

Figure S18.  Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.2

Table S19.  Gene #32: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
1Q LOSS MUTATED 18 8 11 3 4 5 3
1Q LOSS WILD-TYPE 0 3 1 3 1 0 6

Figure S19.  Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S20.  Gene #32: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 14 8 13 5 9 9 8
1Q LOSS MUTATED 14 5 12 2 9 8 2
1Q LOSS WILD-TYPE 0 3 1 3 0 1 6

Figure S20.  Get High-res Image Gene #32: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S21.  Gene #33: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
2P LOSS MUTATED 17 28 1
2P LOSS WILD-TYPE 1 7 12

Figure S21.  Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S22.  Gene #33: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
2P LOSS MUTATED 19 14 13 0
2P LOSS WILD-TYPE 0 8 2 10

Figure S22.  Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S23.  Gene #33: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
2P LOSS MUTATED 19 10 4 0 10 3 0
2P LOSS WILD-TYPE 0 6 3 6 0 1 4

Figure S23.  Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S24.  Gene #33: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
2P LOSS MUTATED 18 7 10 2 3 5 1
2P LOSS WILD-TYPE 0 4 2 4 2 0 8

Figure S24.  Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S25.  Gene #33: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 14 8 13 5 9 9 8
2P LOSS MUTATED 14 4 11 1 9 7 0
2P LOSS WILD-TYPE 0 4 2 4 0 2 8

Figure S25.  Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S26.  Gene #34: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
2Q LOSS MUTATED 17 28 1
2Q LOSS WILD-TYPE 1 7 12

Figure S26.  Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S27.  Gene #34: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
2Q LOSS MUTATED 19 14 13 0
2Q LOSS WILD-TYPE 0 8 2 10

Figure S27.  Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S28.  Gene #34: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
2Q LOSS MUTATED 19 10 4 0 10 3 0
2Q LOSS WILD-TYPE 0 6 3 6 0 1 4

Figure S28.  Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S29.  Gene #34: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
2Q LOSS MUTATED 18 7 10 2 3 5 1
2Q LOSS WILD-TYPE 0 4 2 4 2 0 8

Figure S29.  Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S30.  Gene #34: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 14 8 13 5 9 9 8
2Q LOSS MUTATED 14 4 11 1 9 7 0
2Q LOSS WILD-TYPE 0 4 2 4 0 2 8

Figure S30.  Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.035

Table S31.  Gene #39: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
6P LOSS MUTATED 17 30 4
6P LOSS WILD-TYPE 1 5 9

Figure S31.  Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.04

Table S32.  Gene #39: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
6P LOSS MUTATED 19 15 14 3
6P LOSS WILD-TYPE 0 7 1 7

Figure S32.  Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S33.  Gene #39: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
6P LOSS MUTATED 19 11 6 1 10 4 0
6P LOSS WILD-TYPE 0 5 1 5 0 0 4

Figure S33.  Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.052

Table S34.  Gene #39: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 14 8 13 5 9 9 8
6P LOSS MUTATED 14 5 11 2 9 8 2
6P LOSS WILD-TYPE 0 3 2 3 0 1 6

Figure S34.  Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.052

Table S35.  Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
6Q LOSS MUTATED 17 30 4
6Q LOSS WILD-TYPE 1 5 9

Figure S35.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.031

Table S36.  Gene #40: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
6Q LOSS MUTATED 19 15 14 3
6Q LOSS WILD-TYPE 0 7 1 7

Figure S36.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S37.  Gene #40: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
6Q LOSS MUTATED 19 11 6 1 10 4 0
6Q LOSS WILD-TYPE 0 5 1 5 0 0 4

Figure S37.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.018

Table S38.  Gene #40: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 14 8 13 5 9 9 8
6Q LOSS MUTATED 14 5 11 2 9 8 2
6Q LOSS WILD-TYPE 0 3 2 3 0 1 6

Figure S38.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S39.  Gene #41: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
8P LOSS MUTATED 0 0 9
8P LOSS WILD-TYPE 5 47 5

Figure S39.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S40.  Gene #42: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
8Q LOSS MUTATED 0 0 8
8Q LOSS WILD-TYPE 5 47 6

Figure S40.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.14

Table S41.  Gene #45: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
10P LOSS MUTATED 17 27 4
10P LOSS WILD-TYPE 1 8 9

Figure S41.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.031

Table S42.  Gene #45: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
10P LOSS MUTATED 19 13 13 3
10P LOSS WILD-TYPE 0 9 2 7

Figure S42.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S43.  Gene #45: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
10P LOSS MUTATED 19 8 6 2 10 3 0
10P LOSS WILD-TYPE 0 8 1 4 0 1 4

Figure S43.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.074

Table S44.  Gene #45: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
10P LOSS MUTATED 18 6 11 2 4 4 3
10P LOSS WILD-TYPE 0 5 1 4 1 1 6

Figure S44.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S45.  Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 14 8 13 5 9 9 8
10P LOSS MUTATED 14 3 12 2 9 6 2
10P LOSS WILD-TYPE 0 5 1 3 0 3 6

Figure S45.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.078

Table S46.  Gene #46: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
10Q LOSS MUTATED 17 28 4
10Q LOSS WILD-TYPE 1 7 9

Figure S46.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0092

Table S47.  Gene #46: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
10Q LOSS MUTATED 19 13 14 3
10Q LOSS WILD-TYPE 0 9 1 7

Figure S47.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S48.  Gene #46: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
10Q LOSS MUTATED 19 8 6 2 10 4 0
10Q LOSS WILD-TYPE 0 8 1 4 0 0 4

Figure S48.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.11

Table S49.  Gene #46: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
10Q LOSS MUTATED 18 7 11 2 4 4 3
10Q LOSS WILD-TYPE 0 4 1 4 1 1 6

Figure S49.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.04

Table S50.  Gene #46: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 14 8 13 5 9 9 8
10Q LOSS MUTATED 14 4 12 2 9 6 2
10Q LOSS WILD-TYPE 0 4 1 3 0 3 6

Figure S50.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.23

Table S51.  Gene #49: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
13Q LOSS MUTATED 11 29 3
13Q LOSS WILD-TYPE 7 6 10

Figure S51.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.035

Table S52.  Gene #49: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
13Q LOSS MUTATED 15 10 5 0 10 3 0
13Q LOSS WILD-TYPE 4 6 2 6 0 1 4

Figure S52.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S53.  Gene #52: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
17P LOSS MUTATED 17 31 2
17P LOSS WILD-TYPE 1 4 11

Figure S53.  Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S54.  Gene #52: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
17P LOSS MUTATED 19 16 14 1
17P LOSS WILD-TYPE 0 6 1 9

Figure S54.  Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S55.  Gene #52: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
17P LOSS MUTATED 19 11 6 0 10 4 0
17P LOSS WILD-TYPE 0 5 1 6 0 0 4

Figure S55.  Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.031

Table S56.  Gene #52: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
17P LOSS MUTATED 18 8 11 3 3 5 2
17P LOSS WILD-TYPE 0 3 1 3 2 0 7

Figure S56.  Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0092

Table S57.  Gene #52: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 14 8 13 5 9 9 8
17P LOSS MUTATED 14 5 12 2 9 7 1
17P LOSS WILD-TYPE 0 3 1 3 0 2 7

Figure S57.  Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S58.  Gene #53: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
17Q LOSS MUTATED 17 31 2
17Q LOSS WILD-TYPE 1 4 11

Figure S58.  Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S59.  Gene #53: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
17Q LOSS MUTATED 19 16 14 1
17Q LOSS WILD-TYPE 0 6 1 9

Figure S59.  Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S60.  Gene #53: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
17Q LOSS MUTATED 19 11 6 0 10 4 0
17Q LOSS WILD-TYPE 0 5 1 6 0 0 4

Figure S60.  Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.027

Table S61.  Gene #53: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
17Q LOSS MUTATED 18 8 11 3 3 5 2
17Q LOSS WILD-TYPE 0 3 1 3 2 0 7

Figure S61.  Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0049

Table S62.  Gene #53: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 14 8 13 5 9 9 8
17Q LOSS MUTATED 14 5 12 2 9 7 1
17Q LOSS WILD-TYPE 0 3 1 3 0 2 7

Figure S62.  Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 66

  • Number of significantly arm-level cnvs = 61

  • 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)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle