Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Chromophobe (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1J38R5F
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/C1J38R5F
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, 54 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', and 'MRNASEQ_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', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 13q loss cnv correlated to 'METHLYATION_CNMF'.

  • 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, 54 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 Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test
2p loss 46 (70%) 20 0.0875
(1.00) 		3.7e-07
(0.000178) 		8.54e-08
(4.16e-05) 		2.91e-07
(0.000141) 		0.0891
(1.00) 		0.000161
(0.072) 		0.0277
(1.00) 		2.02e-05
(0.00934)
2q loss 46 (70%) 20 0.0875
(1.00) 		3.7e-07
(0.000178) 		8.54e-08
(4.16e-05) 		2.91e-07
(0.000141) 		0.0891
(1.00) 		0.000161
(0.072) 		0.0277
(1.00) 		2.02e-05
(0.00934)
17p loss 50 (76%) 16 0.299
(1.00) 		4.75e-07
(0.000228) 		5.74e-07
(0.000273) 		5.55e-07
(0.000266) 		0.0506
(1.00) 		0.000396
(0.173) 		0.05
(1.00) 		0.000108
(0.0486)
17q loss 50 (76%) 16 0.299
(1.00) 		4.75e-07
(0.000228) 		5.74e-07
(0.000273) 		5.55e-07
(0.000266) 		0.0506
(1.00) 		0.000396
(0.173) 		0.05
(1.00) 		0.000108
(0.0486)
10p loss 48 (73%) 18 0.342
(1.00) 		0.00038
(0.166) 		8.47e-05
(0.0383) 		5.23e-06
(0.00245) 		0.287
(1.00) 		0.0097
(1.00) 		0.0145
(1.00) 		0.000336
(0.148)
1p loss 53 (80%) 13 0.671
(1.00) 		2.22e-05
(0.0102) 		0.000362
(0.159) 		5.73e-05
(0.0259) 		0.16
(1.00) 		0.00115
(0.49) 		0.166
(1.00) 		0.00118
(0.5)
1q loss 52 (79%) 14 0.475
(1.00) 		2.29e-06
(0.00108) 		5.05e-05
(0.0229) 		4.21e-06
(0.00198) 		0.24
(1.00) 		0.00192
(0.801) 		0.133
(1.00) 		0.00184
(0.768)
6p loss 51 (77%) 15 0.33
(1.00) 		0.000107
(0.0482) 		4.76e-05
(0.0217) 		0.00033
(0.146) 		0.355
(1.00) 		0.00305
(1.00) 		0.306
(1.00) 		0.00201
(0.837)
6q loss 51 (77%) 15 0.33
(1.00) 		0.000107
(0.0482) 		4.76e-05
(0.0217) 		0.00033
(0.146) 		0.355
(1.00) 		0.00305
(1.00) 		0.306
(1.00) 		0.00201
(0.837)
10q loss 49 (74%) 17 0.248
(1.00) 		0.000262
(0.116) 		2.53e-05
(0.0116) 		2.88e-06
(0.00136) 		0.243
(1.00) 		0.00681
(1.00) 		0.0296
(1.00) 		0.00108
(0.458)
4p gain 24 (36%) 42 0.0552
(1.00) 		1
(1.00) 		2.78e-05
(0.0127) 		0.000215
(0.0956) 		0.788
(1.00) 		0.139
(1.00) 		0.734
(1.00) 		0.0309
(1.00)
4q gain 24 (36%) 42 0.0552
(1.00) 		1
(1.00) 		2.78e-05
(0.0127) 		0.000215
(0.0956) 		0.788
(1.00) 		0.139
(1.00) 		0.734
(1.00) 		0.0309
(1.00)
11p gain 15 (23%) 51 0.282
(1.00) 		0.679
(1.00) 		2e-05
(0.00928) 		4.44e-06
(0.00208) 		0.835
(1.00) 		0.106
(1.00) 		0.741
(1.00) 		0.071
(1.00)
11q gain 15 (23%) 51 0.282
(1.00) 		0.679
(1.00) 		6.69e-07
(0.000316) 		1.11e-07
(5.41e-05) 		0.63
(1.00) 		0.106
(1.00) 		0.441
(1.00) 		0.0453
(1.00)
16p gain 21 (32%) 45 0.106
(1.00) 		1
(1.00) 		6.22e-06
(0.00291) 		9.49e-06
(0.00441) 		0.158
(1.00) 		0.0481
(1.00) 		0.776
(1.00) 		0.0499
(1.00)
16q gain 21 (32%) 45 0.106
(1.00) 		1
(1.00) 		6.22e-06
(0.00291) 		9.49e-06
(0.00441) 		0.158
(1.00) 		0.0481
(1.00) 		0.776
(1.00) 		0.0499
(1.00)
8p loss 9 (14%) 57 8.11e-08
(3.96e-05) 		0.0857
(1.00) 		0.0531
(1.00) 		0.0036
(1.00) 		0.148
(1.00) 		0.341
(1.00) 		0.0757
(1.00) 		0.12
(1.00)
8q loss 8 (12%) 58 5.86e-07
(0.000278) 		0.0437
(1.00) 		0.134
(1.00) 		0.00434
(1.00) 		0.291
(1.00) 		0.586
(1.00) 		0.165
(1.00) 		0.224
(1.00)
13q loss 43 (65%) 23 0.27
(1.00) 		0.000529
(0.23) 		0.00364
(1.00) 		0.00343
(1.00) 		0.853
(1.00) 		0.0555
(1.00) 		0.93
(1.00) 		0.158
(1.00)
3p gain 8 (12%) 58 0.27
(1.00) 		0.53
(1.00) 		0.952
(1.00) 		0.614
(1.00) 		0.515
(1.00) 		0.298
(1.00) 		0.0206
(1.00) 		0.823
(1.00)
3q gain 8 (12%) 58 0.27
(1.00) 		0.53
(1.00) 		0.952
(1.00) 		0.614
(1.00) 		0.515
(1.00) 		0.298
(1.00) 		0.0206
(1.00) 		0.823
(1.00)
5p gain 8 (12%) 58 0.424
(1.00) 		0.682
(1.00) 		0.448
(1.00) 		0.629
(1.00) 		0.363
(1.00) 		0.0706
(1.00) 		0.633
(1.00) 		0.166
(1.00)
5q gain 8 (12%) 58 0.424
(1.00) 		0.682
(1.00) 		0.448
(1.00) 		0.629
(1.00) 		0.363
(1.00) 		0.0706
(1.00) 		0.633
(1.00) 		0.166
(1.00)
7p gain 24 (36%) 42 0.151
(1.00) 		1
(1.00) 		0.0169
(1.00) 		0.0167
(1.00) 		0.844
(1.00) 		1
(1.00) 		0.741
(1.00) 		0.423
(1.00)
7q gain 24 (36%) 42 0.151
(1.00) 		1
(1.00) 		0.0169
(1.00) 		0.0167
(1.00) 		0.844
(1.00) 		1
(1.00) 		0.741
(1.00) 		0.423
(1.00)
8p gain 17 (26%) 49 0.411
(1.00) 		0.411
(1.00) 		0.00393
(1.00) 		0.00701
(1.00) 		0.442
(1.00) 		1
(1.00) 		0.712
(1.00) 		0.155
(1.00)
8q gain 18 (27%) 48 0.342
(1.00) 		0.399
(1.00) 		0.00128
(0.54) 		0.00181
(0.76) 		0.679
(1.00) 		1
(1.00) 		0.926
(1.00) 		0.0785
(1.00)
9p gain 10 (15%) 56 1
(1.00) 		1
(1.00) 		0.722
(1.00) 		0.644
(1.00) 		0.832
(1.00) 		0.616
(1.00) 		0.188
(1.00) 		0.47
(1.00)
9q gain 10 (15%) 56 1
(1.00) 		1
(1.00) 		0.722
(1.00) 		0.644
(1.00) 		0.832
(1.00) 		0.616
(1.00) 		0.188
(1.00) 		0.47
(1.00)
10p gain 4 (6%) 62 0.438
(1.00) 		0.162
(1.00) 		0.515
(1.00) 		0.336
(1.00) 		1
(1.00) 		0.452
(1.00) 		0.534
(1.00) 		0.0739
(1.00)
12p gain 19 (29%) 47 0.482
(1.00) 		0.766
(1.00) 		0.0793
(1.00) 		0.13
(1.00) 		1
(1.00) 		0.709
(1.00) 		0.845
(1.00) 		0.0871
(1.00)
12q gain 20 (30%) 46 0.445
(1.00) 		0.591
(1.00) 		0.14
(1.00) 		0.052
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.921
(1.00) 		0.169
(1.00)
14q gain 21 (32%) 45 0.106
(1.00) 		0.796
(1.00) 		0.000833
(0.36) 		0.00261
(1.00) 		0.423
(1.00) 		0.252
(1.00) 		0.878
(1.00) 		0.0499
(1.00)
15q gain 21 (32%) 45 0.106
(1.00) 		0.796
(1.00) 		0.00209
(0.866) 		0.00789
(1.00) 		0.761
(1.00) 		0.252
(1.00) 		0.998
(1.00) 		0.312
(1.00)
18p gain 17 (26%) 49 0.518
(1.00) 		0.806
(1.00) 		0.00215
(0.887) 		0.00497
(1.00) 		0.905
(1.00) 		0.684
(1.00) 		0.315
(1.00) 		0.033
(1.00)
18q gain 16 (24%) 50 0.638
(1.00) 		0.928
(1.00) 		0.00105
(0.448) 		0.00379
(1.00) 		0.785
(1.00) 		1
(1.00) 		0.385
(1.00) 		0.0366
(1.00)
19p gain 19 (29%) 47 0.482
(1.00) 		0.268
(1.00) 		0.0218
(1.00) 		0.0111
(1.00) 		0.642
(1.00) 		1
(1.00) 		0.929
(1.00) 		0.0518
(1.00)
19q gain 17 (26%) 49 0.518
(1.00) 		0.305
(1.00) 		0.00143
(0.602) 		0.00123
(0.52) 		0.4
(1.00) 		0.427
(1.00) 		0.912
(1.00) 		0.00957
(1.00)
20p gain 20 (30%) 46 0.216
(1.00) 		0.591
(1.00) 		0.0316
(1.00) 		0.00987
(1.00) 		0.681
(1.00) 		0.712
(1.00) 		0.637
(1.00) 		0.349
(1.00)
20q gain 21 (32%) 45 0.227
(1.00) 		0.394
(1.00) 		0.067
(1.00) 		0.0217
(1.00) 		0.667
(1.00) 		1
(1.00) 		0.519
(1.00) 		0.368
(1.00)
21q gain 4 (6%) 62 0.438
(1.00) 		0.162
(1.00) 		0.515
(1.00) 		0.336
(1.00) 		0.678
(1.00) 		0.452
(1.00) 		0.461
(1.00) 		0.361
(1.00)
22q gain 19 (29%) 47 0.901
(1.00) 		0.698
(1.00) 		0.0721
(1.00) 		0.16
(1.00) 		0.505
(1.00) 		1
(1.00) 		0.996
(1.00) 		0.169
(1.00)
xq gain 6 (9%) 60 1
(1.00) 		0.722
(1.00) 		0.00689
(1.00) 		0.163
(1.00) 		0.264
(1.00) 		0.585
(1.00) 		0.52
(1.00) 		0.00993
(1.00)
3p loss 9 (14%) 57 0.0367
(1.00) 		0.895
(1.00) 		0.0643
(1.00) 		0.00352
(1.00) 		0.904
(1.00) 		0.341
(1.00) 		0.0267
(1.00) 		0.0345
(1.00)
3q loss 8 (12%) 58 0.0211
(1.00) 		0.367
(1.00) 		0.0251
(1.00) 		0.000866
(0.371) 		0.572
(1.00) 		0.586
(1.00) 		0.00763
(1.00) 		0.0089
(1.00)
5p loss 10 (15%) 56 0.0987
(1.00) 		0.253
(1.00) 		0.000748
(0.324) 		0.000841
(0.361) 		0.427
(1.00) 		0.334
(1.00) 		0.619
(1.00) 		0.154
(1.00)
5q loss 10 (15%) 56 0.0987
(1.00) 		0.253
(1.00) 		0.000748
(0.324) 		0.000841
(0.361) 		0.427
(1.00) 		0.334
(1.00) 		0.619
(1.00) 		0.154
(1.00)
9p loss 10 (15%) 56 1
(1.00) 		0.902
(1.00) 		0.0649
(1.00) 		0.714
(1.00) 		0.912
(1.00) 		0.616
(1.00) 		0.896
(1.00) 		0.371
(1.00)
9q loss 10 (15%) 56 1
(1.00) 		0.902
(1.00) 		0.0649
(1.00) 		0.714
(1.00) 		0.912
(1.00) 		0.616
(1.00) 		0.896
(1.00) 		0.371
(1.00)
11p loss 7 (11%) 59 0.628
(1.00) 		0.574
(1.00) 		0.11
(1.00) 		0.497
(1.00) 		0.203
(1.00) 		1
(1.00) 		0.269
(1.00) 		0.0436
(1.00)
11q loss 7 (11%) 59 0.628
(1.00) 		0.574
(1.00) 		0.11
(1.00) 		0.497
(1.00) 		0.203
(1.00) 		1
(1.00) 		0.269
(1.00) 		0.0436
(1.00)
16p loss 4 (6%) 62 0.685
(1.00) 		0.517
(1.00) 		0.0232
(1.00) 		0.00987
(1.00) 		0.678
(1.00) 		0.452
(1.00) 		0.461
(1.00) 		1
(1.00)
16q loss 5 (8%) 61 0.721
(1.00) 		0.385
(1.00) 		0.00592
(1.00) 		0.000834
(0.36) 		0.428
(1.00) 		0.134
(1.00) 		0.192
(1.00) 		0.616
(1.00)
18p loss 8 (12%) 58 0.677
(1.00) 		0.0965
(1.00) 		0.315
(1.00) 		0.0503
(1.00) 		0.72
(1.00) 		1
(1.00) 		0.877
(1.00) 		1
(1.00)
18q loss 10 (15%) 56 0.62
(1.00) 		0.0796
(1.00) 		0.443
(1.00) 		0.138
(1.00) 		0.575
(1.00) 		0.616
(1.00) 		0.49
(1.00) 		0.958
(1.00)
19q loss 3 (5%) 63 0.646
(1.00) 		0.766
(1.00) 		0.767
(1.00) 		0.823
(1.00) 		0.515
(1.00) 		0.361
(1.00) 		0.69
(1.00) 		0.439
(1.00)
20p loss 4 (6%) 62 0.301
(1.00) 		0.807
(1.00) 		0.209
(1.00) 		0.213
(1.00) 		0.45
(1.00) 		1
(1.00) 		0.37
(1.00) 		0.202
(1.00)
20q loss 3 (5%) 63 1
(1.00) 		0.418
(1.00) 		0.226
(1.00) 		0.132
(1.00) 		0.294
(1.00) 		1
(1.00) 		0.219
(1.00) 		0.439
(1.00)
21q loss 35 (53%) 31 0.742
(1.00) 		0.00886
(1.00) 		0.247
(1.00) 		0.0443
(1.00) 		1
(1.00) 		0.724
(1.00) 		0.754
(1.00) 		0.141
(1.00)
22q loss 8 (12%) 58 0.83
(1.00) 		0.134
(1.00) 		0.247
(1.00) 		0.0645
(1.00) 		0.897
(1.00) 		0.586
(1.00) 		0.731
(1.00) 		0.267
(1.00)
xq loss 39 (59%) 27 0.532
(1.00) 		0.0787
(1.00) 		0.00683
(1.00) 		0.00129
(0.545) 		0.293
(1.00) 		0.026
(1.00) 		0.0691
(1.00) 		0.0281
(1.00)
'4p gain' versus 'MRNASEQ_CNMF'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.013

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 = 0.000215 (Chi-square test), Q value = 0.096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
4P GAIN MUTATED 1 2 14 2 5
4P GAIN WILD-TYPE 9 8 3 4 18

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

'4q gain' versus 'MRNASEQ_CNMF'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.013

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 = 0.000215 (Chi-square test), Q value = 0.096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
4Q GAIN MUTATED 1 2 14 2 5
4Q GAIN WILD-TYPE 9 8 3 4 18

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

'11p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0093

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 = 4.44e-06 (Chi-square test), Q value = 0.0021

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
11P GAIN MUTATED 1 1 12 0 1
11P GAIN WILD-TYPE 9 9 5 6 22

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

'11q gain' versus 'MRNASEQ_CNMF'

P value = 6.69e-07 (Fisher's exact test), Q value = 0.00032

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 = 1.11e-07 (Chi-square test), Q value = 5.4e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
11Q GAIN MUTATED 0 1 13 0 1
11Q GAIN WILD-TYPE 10 9 4 6 22

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

'16p gain' versus 'MRNASEQ_CNMF'

P value = 6.22e-06 (Fisher's exact test), Q value = 0.0029

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 = 9.49e-06 (Chi-square test), Q value = 0.0044

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
16P GAIN MUTATED 0 1 14 1 5
16P GAIN WILD-TYPE 10 9 3 5 18

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

'16q gain' versus 'MRNASEQ_CNMF'

P value = 6.22e-06 (Fisher's exact test), Q value = 0.0029

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 = 9.49e-06 (Chi-square test), Q value = 0.0044

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
16Q GAIN MUTATED 0 1 14 1 5
16Q GAIN WILD-TYPE 10 9 3 5 18

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

'1p loss' versus 'METHLYATION_CNMF'

P value = 2.22e-05 (Fisher's exact test), Q value = 0.01

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 = 0.000362 (Fisher's exact test), Q value = 0.16

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 = 5.73e-05 (Chi-square test), Q value = 0.026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
1P LOSS MUTATED 9 3 12 6 23
1P LOSS WILD-TYPE 1 7 5 0 0

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

'1q loss' versus 'METHLYATION_CNMF'

P value = 2.29e-06 (Fisher's exact test), Q value = 0.0011

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 = 5.05e-05 (Fisher's exact test), Q value = 0.023

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 = 4.21e-06 (Chi-square test), Q value = 0.002

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
1Q LOSS MUTATED 10 2 12 5 23
1Q LOSS WILD-TYPE 0 8 5 1 0

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

'2p loss' versus 'METHLYATION_CNMF'

P value = 3.7e-07 (Fisher's exact test), Q value = 0.00018

Table S19.  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 S19.  Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 8.54e-08 (Fisher's exact test), Q value = 4.2e-05

Table S20.  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 S20.  Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.91e-07 (Chi-square test), Q value = 0.00014

Table S21.  Gene #33: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
2P LOSS MUTATED 10 0 11 3 22
2P LOSS WILD-TYPE 0 10 6 3 1

Figure S21.  Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.072

Table S22.  Gene #33: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 57
2P LOSS MUTATED 1 45
2P LOSS WILD-TYPE 8 12

Figure S22.  Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.0093

Table S23.  Gene #33: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 8 25 21
2P LOSS MUTATED 3 4 18 21
2P LOSS WILD-TYPE 9 4 7 0

Figure S23.  Get High-res Image Gene #33: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'METHLYATION_CNMF'

P value = 3.7e-07 (Fisher's exact test), Q value = 0.00018

Table S24.  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 S24.  Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 8.54e-08 (Fisher's exact test), Q value = 4.2e-05

Table S25.  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 S25.  Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.91e-07 (Chi-square test), Q value = 0.00014

Table S26.  Gene #34: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
2Q LOSS MUTATED 10 0 11 3 22
2Q LOSS WILD-TYPE 0 10 6 3 1

Figure S26.  Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000161 (Fisher's exact test), Q value = 0.072

Table S27.  Gene #34: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 57
2Q LOSS MUTATED 1 45
2Q LOSS WILD-TYPE 8 12

Figure S27.  Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.0093

Table S28.  Gene #34: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 8 25 21
2Q LOSS MUTATED 3 4 18 21
2Q LOSS WILD-TYPE 9 4 7 0

Figure S28.  Get High-res Image Gene #34: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.048

Table S29.  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 S29.  Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.022

Table S30.  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 S30.  Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Chi-square test), Q value = 0.15

Table S31.  Gene #39: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
6P LOSS MUTATED 10 3 12 4 22
6P LOSS WILD-TYPE 0 7 5 2 1

Figure S31.  Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.048

Table S32.  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 S32.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.022

Table S33.  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 S33.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Chi-square test), Q value = 0.15

Table S34.  Gene #40: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
6Q LOSS MUTATED 10 3 12 4 22
6Q LOSS WILD-TYPE 0 7 5 2 1

Figure S34.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 8.11e-08 (Fisher's exact test), Q value = 4e-05

Table S35.  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 S35.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 5.86e-07 (Fisher's exact test), Q value = 0.00028

Table S36.  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 S36.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.17

Table S37.  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 S37.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 8.47e-05 (Fisher's exact test), Q value = 0.038

Table S38.  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 S38.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.23e-06 (Chi-square test), Q value = 0.0024

Table S39.  Gene #45: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
10P LOSS MUTATED 10 2 9 4 23
10P LOSS WILD-TYPE 0 8 8 2 0

Figure S39.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000336 (Fisher's exact test), Q value = 0.15

Table S40.  Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 8 25 21
10P LOSS MUTATED 6 3 18 21
10P LOSS WILD-TYPE 6 5 7 0

Figure S40.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.000262 (Fisher's exact test), Q value = 0.12

Table S41.  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 S41.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 2.53e-05 (Fisher's exact test), Q value = 0.012

Table S42.  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 S42.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.88e-06 (Chi-square test), Q value = 0.0014

Table S43.  Gene #46: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
10Q LOSS MUTATED 10 2 9 5 23
10Q LOSS WILD-TYPE 0 8 8 1 0

Figure S43.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.000529 (Fisher's exact test), Q value = 0.23

Table S44.  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 S44.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 4.75e-07 (Fisher's exact test), Q value = 0.00023

Table S45.  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 S45.  Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 5.74e-07 (Fisher's exact test), Q value = 0.00027

Table S46.  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 S46.  Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.55e-07 (Chi-square test), Q value = 0.00027

Table S47.  Gene #52: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
17P LOSS MUTATED 10 1 12 4 23
17P LOSS WILD-TYPE 0 9 5 2 0

Figure S47.  Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000396 (Fisher's exact test), Q value = 0.17

Table S48.  Gene #52: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 57
17P LOSS MUTATED 2 48
17P LOSS WILD-TYPE 7 9

Figure S48.  Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.049

Table S49.  Gene #52: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 8 25 21
17P LOSS MUTATED 4 5 20 21
17P LOSS WILD-TYPE 8 3 5 0

Figure S49.  Get High-res Image Gene #52: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'METHLYATION_CNMF'

P value = 4.75e-07 (Fisher's exact test), Q value = 0.00023

Table S50.  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 S50.  Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 5.74e-07 (Fisher's exact test), Q value = 0.00027

Table S51.  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 S51.  Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.55e-07 (Chi-square test), Q value = 0.00027

Table S52.  Gene #53: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
17Q LOSS MUTATED 10 1 12 4 23
17Q LOSS WILD-TYPE 0 9 5 2 0

Figure S52.  Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000396 (Fisher's exact test), Q value = 0.17

Table S53.  Gene #53: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 57
17Q LOSS MUTATED 2 48
17Q LOSS WILD-TYPE 7 9

Figure S53.  Get High-res Image Gene #53: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.049

Table S54.  Gene #53: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 8 25 21
17Q LOSS MUTATED 4 5 20 21
17Q LOSS WILD-TYPE 8 3 5 0

Figure S54.  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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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