Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C14J0C28
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Kidney Renal Clear Cell Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C14J0C28
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.

Summary

Testing the association between copy number variation 71 arm-level results and 10 molecular subtypes across 493 patients, 131 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 2p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 6p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 14q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 17p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 71 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 131 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
2q loss 0 (0%) 482 0.000249
(0.138) 		0.000374
(0.204) 		4.75e-06
(0.0029) 		1
(1.00) 		0.000129
(0.0727) 		4.42e-05
(0.0255) 		8.96e-08
(5.69e-05) 		7.91e-08
(5.04e-05) 		0.000199
(0.111) 		4.81e-12
(3.15e-09)
17p loss 0 (0%) 468 0.000117
(0.0662) 		0.000178
(0.0998) 		4.3e-06
(0.00263) 		0.908
(1.00) 		2.92e-05
(0.017) 		5.18e-06
(0.00314) 		1.9e-06
(0.00118) 		1.5e-08
(9.62e-06) 		4.9e-07
(0.000307) 		8.54e-09
(5.48e-06)
2p loss 0 (0%) 483 0.000249
(0.138) 		0.000374
(0.204) 		1.52e-05
(0.00898) 		0.456
(1.00) 		1.37e-05
(0.00812) 		0.000189
(0.106) 		4.72e-07
(0.000297) 		1.87e-08
(1.2e-05) 		0.000598
(0.318) 		1.25e-12
(8.26e-10)
3p loss 0 (0%) 189 0.013
(1.00) 		0.0102
(1.00) 		6.37e-24
(4.24e-21) 		0.000521
(0.278) 		0.00012
(0.0676) 		1.78e-05
(0.0104) 		3.85e-11
(2.51e-08) 		7.09e-10
(4.57e-07) 		4.23e-05
(0.0245) 		5.08e-14
(3.37e-11)
14q loss 0 (0%) 335 0.00179
(0.903) 		0.000956
(0.496) 		2.02e-10
(1.31e-07) 		3.06e-05
(0.0178) 		6.61e-12
(4.32e-09) 		2.08e-07
(0.000131) 		6.97e-11
(4.52e-08) 		2.8e-07
(0.000177) 		4.33e-06
(0.00264) 		0.507
(1.00)
17q loss 0 (0%) 481 0.000668
(0.355) 		0.00077
(0.404) 		0.000224
(0.124) 		0.456
(1.00) 		1.46e-05
(0.00863) 		1.02e-05
(0.00613) 		1.91e-06
(0.00118) 		7.91e-08
(5.04e-05) 		8.98e-05
(0.0511) 		4.05e-11
(2.63e-08)
12p gain 0 (0%) 415 0.194
(1.00) 		0.165
(1.00) 		7.99e-07
(0.000498) 		0.00104
(0.534) 		5.67e-07
(0.000355) 		0.0139
(1.00) 		1.1e-05
(0.00658) 		1.89e-05
(0.0111) 		6.95e-06
(0.00419) 		0.712
(1.00)
12q gain 0 (0%) 415 0.194
(1.00) 		0.165
(1.00) 		7.99e-07
(0.000498) 		0.00104
(0.534) 		5.67e-07
(0.000355) 		0.0141
(1.00) 		1.1e-05
(0.00658) 		1.89e-05
(0.0111) 		6.95e-06
(0.00419) 		0.617
(1.00)
20p gain 0 (0%) 427 0.102
(1.00) 		0.11
(1.00) 		1.05e-12
(6.9e-10) 		0.000674
(0.357) 		0.000453
(0.244) 		0.000979
(0.507) 		3.59e-06
(0.00221) 		5.29e-06
(0.00321) 		2.54e-06
(0.00157) 		0.0344
(1.00)
20q gain 0 (0%) 425 0.0753
(1.00) 		0.092
(1.00) 		6.23e-14
(4.13e-11) 		0.000674
(0.357) 		3.54e-05
(0.0205) 		0.000855
(0.446) 		3.3e-07
(0.000207) 		1.47e-06
(0.00091) 		1.83e-07
(0.000116) 		0.035
(1.00)
1p loss 0 (0%) 461 0.000836
(0.438) 		6.2e-05
(0.0355) 		0.00395
(1.00) 		0.198
(1.00) 		5.05e-08
(3.23e-05) 		0.000435
(0.235) 		0.0123
(1.00) 		4.64e-06
(0.00283) 		0.0187
(1.00) 		1.01e-10
(6.52e-08)
1q loss 0 (0%) 472 0.0217
(1.00) 		0.00286
(1.00) 		2.09e-05
(0.0122) 		0.904
(1.00) 		0.000168
(0.0942) 		0.00191
(0.96) 		6.65e-05
(0.0379) 		6.27e-07
(0.000391) 		0.0493
(1.00) 		2.88e-11
(1.88e-08)
6p loss 0 (0%) 435 0.0139
(1.00) 		0.0029
(1.00) 		4.27e-12
(2.8e-09) 		0.00899
(1.00) 		0.000122
(0.0685) 		7.03e-06
(0.00423) 		0.000722
(0.38) 		0.00105
(0.538) 		2.87e-09
(1.85e-06) 		0.000394
(0.214)
9p loss 0 (0%) 406 0.378
(1.00) 		0.0694
(1.00) 		9.23e-25
(6.15e-22) 		3.57e-12
(2.34e-09) 		0.00463
(1.00) 		0.00726
(1.00) 		1.39e-11
(9.06e-09) 		2.71e-12
(1.78e-09) 		8.73e-09
(5.6e-06) 		0.201
(1.00)
9q loss 0 (0%) 401 0.378
(1.00) 		0.0694
(1.00) 		4.43e-26
(2.96e-23) 		4.3e-13
(2.84e-10) 		0.000999
(0.516) 		0.0104
(1.00) 		1.31e-12
(8.65e-10) 		3.94e-14
(2.62e-11) 		3.82e-10
(2.46e-07) 		0.173
(1.00)
3q gain 0 (0%) 466 0.0823
(1.00) 		0.0851
(1.00) 		6.58e-05
(0.0376) 		0.0804
(1.00) 		0.00718
(1.00) 		0.000107
(0.0609) 		0.000395
(0.214) 		0.00931
(1.00) 		0.000339
(0.186) 		0.00761
(1.00)
8q gain 0 (0%) 459 0.0536
(1.00) 		0.0581
(1.00) 		2.75e-07
(0.000173) 		0.00105
(0.535) 		0.0102
(1.00) 		0.0449
(1.00) 		1.15e-07
(7.27e-05) 		4.88e-05
(0.0282) 		6.77e-06
(0.00409) 		0.0182
(1.00)
18p loss 0 (0%) 447 0.194
(1.00) 		0.433
(1.00) 		3.02e-06
(0.00186) 		0.0194
(1.00) 		0.0183
(1.00) 		0.00473
(1.00) 		6.06e-06
(0.00366) 		0.000196
(0.109) 		0.00036
(0.197) 		0.00262
(1.00)
13q loss 0 (0%) 462 0.0253
(1.00) 		0.0281
(1.00) 		6.36e-05
(0.0364) 		0.247
(1.00) 		0.00137
(0.698) 		0.00139
(0.704) 		0.0025
(1.00) 		0.00046
(0.247) 		0.000838
(0.438) 		0.000285
(0.157)
21q loss 0 (0%) 461 0.0145
(1.00) 		0.0219
(1.00) 		0.000367
(0.2) 		0.479
(1.00) 		0.00501
(1.00) 		0.0399
(1.00) 		0.00192
(0.966) 		1.72e-05
(0.0101) 		0.24
(1.00) 		9.51e-06
(0.00571)
7p gain 0 (0%) 366 0.877
(1.00) 		0.939
(1.00) 		5.05e-06
(0.00307) 		0.0543
(1.00) 		0.000268
(0.148) 		0.00565
(1.00) 		0.068
(1.00) 		0.0824
(1.00) 		0.0251
(1.00) 		0.703
(1.00)
7q gain 0 (0%) 364 0.877
(1.00) 		0.939
(1.00) 		1.36e-05
(0.00809) 		0.0417
(1.00) 		0.000118
(0.0665) 		0.000718
(0.378) 		0.0581
(1.00) 		0.131
(1.00) 		0.0129
(1.00) 		0.481
(1.00)
6q loss 0 (0%) 411 0.0393
(1.00) 		0.0125
(1.00) 		6.34e-17
(4.21e-14) 		0.121
(1.00) 		0.0014
(0.71) 		0.00103
(0.532) 		0.204
(1.00) 		0.478
(1.00) 		1.42e-05
(0.00843) 		0.00226
(1.00)
18q loss 0 (0%) 445 0.259
(1.00) 		0.238
(1.00) 		3.61e-06
(0.00221) 		0.0324
(1.00) 		0.0551
(1.00) 		0.0128
(1.00) 		2.87e-05
(0.0167) 		0.000574
(0.306) 		0.000948
(0.493) 		0.00546
(1.00)
1q gain 0 (0%) 461 0.611
(1.00) 		1
(1.00) 		1.05e-05
(0.00625) 		0.452
(1.00) 		0.434
(1.00) 		0.19
(1.00) 		0.00972
(1.00) 		0.15
(1.00) 		0.0134
(1.00) 		0.189
(1.00)
2p gain 0 (0%) 445 0.561
(1.00) 		0.472
(1.00) 		1.08e-06
(0.000674) 		0.653
(1.00) 		0.0462
(1.00) 		0.783
(1.00) 		0.144
(1.00) 		0.0785
(1.00) 		0.228
(1.00) 		0.16
(1.00)
2q gain 0 (0%) 444 0.561
(1.00) 		0.472
(1.00) 		4.9e-05
(0.0282) 		0.824
(1.00) 		0.0528
(1.00) 		0.862
(1.00) 		0.0519
(1.00) 		0.0498
(1.00) 		0.146
(1.00) 		0.16
(1.00)
5p gain 0 (0%) 352 0.593
(1.00) 		0.592
(1.00) 		1.25e-05
(0.00745) 		0.441
(1.00) 		0.0817
(1.00) 		0.0546
(1.00) 		0.0458
(1.00) 		0.00844
(1.00) 		0.0362
(1.00) 		0.00595
(1.00)
5q gain 0 (0%) 337 0.105
(1.00) 		0.121
(1.00) 		5.87e-05
(0.0337) 		0.375
(1.00) 		0.158
(1.00) 		0.175
(1.00) 		0.0381
(1.00) 		0.00512
(1.00) 		0.116
(1.00) 		0.00141
(0.714)
8p gain 0 (0%) 479 5.42e-05
(0.0312) 		0.0796
(1.00) 		0.0868
(1.00) 		0.146
(1.00) 		0.000978
(0.507) 		0.000683
(0.361) 		0.00302
(1.00) 		0.117
(1.00)
17p gain 0 (0%) 477 0.00522
(1.00) 		0.00665
(1.00) 		0.000357
(0.196) 		0.42
(1.00) 		0.321
(1.00) 		0.0336
(1.00) 		0.191
(1.00) 		0.0327
(1.00) 		0.726
(1.00) 		0.0488
(1.00)
19p gain 0 (0%) 468 0.189
(1.00) 		0.197
(1.00) 		3.37e-05
(0.0196) 		0.34
(1.00) 		0.0448
(1.00) 		0.397
(1.00) 		0.0428
(1.00) 		0.0115
(1.00) 		0.0423
(1.00) 		0.066
(1.00)
19q gain 0 (0%) 465 0.0536
(1.00) 		0.0581
(1.00) 		3e-06
(0.00185) 		0.201
(1.00) 		0.056
(1.00) 		0.154
(1.00) 		0.0185
(1.00) 		0.00414
(1.00) 		0.014
(1.00) 		0.066
(1.00)
21q gain 0 (0%) 460 0.82
(1.00) 		0.815
(1.00) 		0.000117
(0.0663) 		0.0986
(1.00) 		0.0368
(1.00) 		0.836
(1.00) 		0.0709
(1.00) 		0.08
(1.00) 		0.295
(1.00) 		0.811
(1.00)
22q gain 0 (0%) 468 0.58
(1.00) 		0.039
(1.00) 		0.000399
(0.216) 		0.0756
(1.00) 		0.452
(1.00) 		0.217
(1.00) 		0.826
(1.00) 		0.846
(1.00) 		0.965
(1.00) 		0.844
(1.00)
4q loss 0 (0%) 465 1
(1.00) 		1
(1.00) 		0.000221
(0.123) 		0.255
(1.00) 		0.251
(1.00) 		0.313
(1.00) 		0.0631
(1.00) 		0.0573
(1.00) 		0.969
(1.00) 		0.371
(1.00)
10p loss 0 (0%) 461 0.026
(1.00) 		0.0287
(1.00) 		0.000201
(0.112) 		0.382
(1.00) 		0.195
(1.00) 		0.037
(1.00) 		0.0123
(1.00) 		0.0197
(1.00) 		0.155
(1.00) 		0.00047
(0.252)
1p gain 0 (0%) 488 0.627
(1.00) 		0.439
(1.00) 		0.0359
(1.00) 		0.846
(1.00) 		0.85
(1.00) 		0.457
(1.00) 		1
(1.00)
3p gain 0 (0%) 486 0.386
(1.00) 		1
(1.00) 		0.102
(1.00) 		0.00329
(1.00) 		0.294
(1.00) 		0.161
(1.00) 		0.0114
(1.00) 		0.0528
(1.00)
4p gain 0 (0%) 485 0.206
(1.00) 		0.608
(1.00) 		0.428
(1.00) 		0.0803
(1.00) 		0.0257
(1.00) 		0.378
(1.00) 		0.0005
(0.268) 		0.0407
(1.00)
4q gain 0 (0%) 485 0.67
(1.00) 		0.795
(1.00) 		0.878
(1.00) 		0.338
(1.00) 		0.0112
(1.00) 		0.509
(1.00) 		0.00394
(1.00) 		0.147
(1.00)
6p gain 0 (0%) 487 0.77
(1.00) 		0.555
(1.00) 		0.819
(1.00) 		0.877
(1.00) 		0.215
(1.00) 		0.449
(1.00) 		0.342
(1.00) 		0.389
(1.00)
6q gain 0 (0%) 488 0.532
(1.00) 		0.795
(1.00) 		0.571
(1.00) 		0.626
(1.00) 		0.442
(1.00) 		0.571
(1.00) 		0.737
(1.00) 		0.431
(1.00)
9p gain 0 (0%) 485 0.741
(1.00) 		0.249
(1.00) 		0.17
(1.00) 		0.17
(1.00) 		0.103
(1.00) 		0.0571
(1.00) 		0.902
(1.00) 		0.0306
(1.00)
9q gain 0 (0%) 485 0.283
(1.00) 		1
(1.00) 		0.104
(1.00) 		0.338
(1.00) 		0.523
(1.00) 		0.636
(1.00) 		0.602
(1.00) 		0.178
(1.00)
10p gain 0 (0%) 487 0.39
(1.00) 		1
(1.00) 		0.981
(1.00) 		1
(1.00) 		0.267
(1.00) 		0.311
(1.00) 		0.77
(1.00) 		0.389
(1.00)
10q gain 0 (0%) 489 0.184
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.615
(1.00) 		0.688
(1.00) 		0.508
(1.00) 		0.832
(1.00) 		0.367
(1.00)
11p gain 0 (0%) 476 0.769
(1.00) 		0.778
(1.00) 		0.000529
(0.283) 		0.771
(1.00) 		0.437
(1.00) 		0.395
(1.00) 		0.491
(1.00) 		0.265
(1.00) 		0.95
(1.00) 		0.41
(1.00)
11q gain 0 (0%) 478 0.769
(1.00) 		0.778
(1.00) 		0.00118
(0.601) 		0.698
(1.00) 		0.541
(1.00) 		0.48
(1.00) 		0.586
(1.00) 		0.505
(1.00) 		0.946
(1.00) 		0.355
(1.00)
13q gain 0 (0%) 479 0.742
(1.00) 		0.077
(1.00) 		0.467
(1.00) 		0.771
(1.00) 		0.0685
(1.00) 		0.636
(1.00) 		0.614
(1.00) 		0.914
(1.00)
14q gain 0 (0%) 488 0.0496
(1.00) 		0.608
(1.00) 		0.869
(1.00) 		0.0596
(1.00) 		0.00354
(1.00) 		0.0477
(1.00) 		0.0659
(1.00) 		0.00534
(1.00)
15q gain 0 (0%) 479 0.0947
(1.00) 		0.578
(1.00) 		0.644
(1.00) 		0.237
(1.00) 		0.116
(1.00) 		0.379
(1.00) 		0.835
(1.00) 		0.503
(1.00)
16p gain 0 (0%) 428 0.1
(1.00) 		0.212
(1.00) 		0.153
(1.00) 		0.689
(1.00) 		0.0115
(1.00) 		0.0663
(1.00) 		0.635
(1.00) 		0.113
(1.00) 		0.156
(1.00) 		0.598
(1.00)
16q gain 0 (0%) 435 0.0706
(1.00) 		0.171
(1.00) 		0.175
(1.00) 		0.909
(1.00) 		0.0443
(1.00) 		0.122
(1.00) 		0.696
(1.00) 		0.336
(1.00) 		0.23
(1.00) 		0.903
(1.00)
17q gain 0 (0%) 471 0.00827
(1.00) 		0.0102
(1.00) 		0.00481
(1.00) 		0.119
(1.00) 		0.553
(1.00) 		0.0547
(1.00) 		0.253
(1.00) 		0.00949
(1.00) 		0.417
(1.00) 		0.0225
(1.00)
18p gain 0 (0%) 475 0.0764
(1.00) 		0.039
(1.00) 		0.238
(1.00) 		0.153
(1.00) 		0.319
(1.00) 		0.143
(1.00) 		0.0977
(1.00) 		0.41
(1.00) 		0.909
(1.00) 		0.744
(1.00)
18q gain 0 (0%) 475 0.0764
(1.00) 		0.039
(1.00) 		0.238
(1.00) 		0.153
(1.00) 		0.319
(1.00) 		0.143
(1.00) 		0.0977
(1.00) 		0.41
(1.00) 		0.909
(1.00) 		0.744
(1.00)
Xq gain 0 (0%) 482 0.414
(1.00) 		0.432
(1.00) 		0.639
(1.00) 		0.578
(1.00) 		0.392
(1.00) 		0.483
(1.00) 		0.198
(1.00) 		0.277
(1.00) 		0.363
(1.00) 		0.306
(1.00)
3q loss 0 (0%) 420 0.701
(1.00) 		0.7
(1.00) 		0.00144
(0.725) 		0.192
(1.00) 		0.182
(1.00) 		0.00661
(1.00) 		0.518
(1.00) 		0.804
(1.00) 		0.822
(1.00) 		0.00986
(1.00)
4p loss 0 (0%) 458 0.289
(1.00) 		0.296
(1.00) 		0.0658
(1.00) 		0.274
(1.00) 		0.816
(1.00) 		0.948
(1.00) 		0.0888
(1.00) 		0.366
(1.00) 		0.513
(1.00) 		0.749
(1.00)
8p loss 0 (0%) 399 0.777
(1.00) 		0.781
(1.00) 		0.047
(1.00) 		0.706
(1.00) 		0.724
(1.00) 		0.5
(1.00) 		0.185
(1.00) 		0.633
(1.00) 		0.173
(1.00) 		0.45
(1.00)
8q loss 0 (0%) 456 0.49
(1.00) 		0.586
(1.00) 		0.747
(1.00) 		0.255
(1.00) 		0.54
(1.00) 		0.785
(1.00) 		0.112
(1.00) 		0.0266
(1.00) 		0.709
(1.00) 		0.41
(1.00)
10q loss 0 (0%) 445 0.0972
(1.00) 		0.119
(1.00) 		0.00263
(1.00) 		0.0409
(1.00) 		0.22
(1.00) 		0.0125
(1.00) 		0.095
(1.00) 		0.126
(1.00) 		0.312
(1.00) 		0.0146
(1.00)
11p loss 0 (0%) 488 0.121
(1.00) 		0.608
(1.00) 		0.156
(1.00) 		0.0359
(1.00) 		0.359
(1.00) 		0.462
(1.00) 		0.545
(1.00) 		0.0879
(1.00)
11q loss 0 (0%) 486 0.0527
(1.00) 		0.826
(1.00) 		0.0533
(1.00) 		0.215
(1.00) 		0.377
(1.00) 		0.311
(1.00) 		0.349
(1.00) 		0.0298
(1.00)
15q loss 0 (0%) 481 0.58
(1.00) 		0.584
(1.00) 		0.0213
(1.00) 		0.373
(1.00) 		0.451
(1.00) 		0.704
(1.00) 		0.0733
(1.00) 		0.136
(1.00) 		0.232
(1.00) 		1
(1.00)
16q loss 0 (0%) 488 0.0135
(1.00) 		0.167
(1.00) 		0.456
(1.00) 		1
(1.00) 		0.292
(1.00) 		0.832
(1.00) 		0.262
(1.00)
19p loss 0 (0%) 489 0.184
(1.00) 		0.332
(1.00) 		0.279
(1.00) 		0.0359
(1.00) 		0.341
(1.00) 		0.379
(1.00) 		0.832
(1.00) 		0.262
(1.00)
20p loss 0 (0%) 487 0.0475
(1.00) 		1
(1.00) 		0.0172
(1.00) 		0.877
(1.00) 		0.267
(1.00) 		0.747
(1.00) 		0.0721
(1.00) 		0.232
(1.00)
22q loss 0 (0%) 482 0.00501
(1.00) 		0.161
(1.00) 		0.0462
(1.00) 		0.393
(1.00) 		0.000888
(0.463) 		0.0191
(1.00) 		0.363
(1.00) 		0.531
(1.00)
Xq loss 0 (0%) 486 0.0394
(1.00) 		0.0772
(1.00) 		0.308
(1.00) 		0.826
(1.00) 		0.381
(1.00) 		0.564
(1.00) 		0.0676
(1.00) 		0.00763
(1.00) 		0.0269
(1.00) 		0.00846
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0063

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
1Q GAIN CNV 21 6 5
1Q GAIN WILD-TYPE 111 191 159

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 1.08e-06 (Fisher's exact test), Q value = 0.00067

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
2P GAIN CNV 29 9 10
2P GAIN WILD-TYPE 103 188 154

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

'2q gain' versus 'CN_CNMF'

P value = 4.9e-05 (Fisher's exact test), Q value = 0.028

Table S3.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
2Q GAIN CNV 27 12 10
2Q GAIN WILD-TYPE 105 185 154

Figure S3.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 6.58e-05 (Fisher's exact test), Q value = 0.038

Table S4.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
3Q GAIN CNV 16 2 9
3Q GAIN WILD-TYPE 116 195 155

Figure S4.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.061

Table S5.  Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
3Q GAIN CNV 3 8 15
3Q GAIN WILD-TYPE 183 144 94

Figure S5.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.000395 (Fisher's exact test), Q value = 0.21

Table S6.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
3Q GAIN CNV 4 20 3
3Q GAIN WILD-TYPE 193 159 94

Figure S6.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.000339 (Fisher's exact test), Q value = 0.19

Table S7.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
3Q GAIN CNV 5 3 19
3Q GAIN WILD-TYPE 110 188 150

Figure S7.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1.25e-05 (Fisher's exact test), Q value = 0.0075

Table S8.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
5P GAIN CNV 58 52 31
5P GAIN WILD-TYPE 74 145 133

Figure S8.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 5.87e-05 (Fisher's exact test), Q value = 0.034

Table S9.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
5Q GAIN CNV 59 63 34
5Q GAIN WILD-TYPE 73 134 130

Figure S9.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 5.05e-06 (Fisher's exact test), Q value = 0.0031

Table S10.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
7P GAIN CNV 55 34 38
7P GAIN WILD-TYPE 77 163 126

Figure S10.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.000268 (Chi-square test), Q value = 0.15

Table S11.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
7P GAIN CNV 18 11 26 31 11 19
7P GAIN WILD-TYPE 82 77 58 44 32 38

Figure S11.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1.36e-05 (Fisher's exact test), Q value = 0.0081

Table S12.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
7Q GAIN CNV 54 34 41
7Q GAIN WILD-TYPE 78 163 123

Figure S12.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.000118 (Chi-square test), Q value = 0.067

Table S13.  Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
7Q GAIN CNV 17 12 27 31 10 21
7Q GAIN WILD-TYPE 83 76 57 44 33 36

Figure S13.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 5.42e-05 (Fisher's exact test), Q value = 0.031

Table S14.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
8P GAIN CNV 10 0 4
8P GAIN WILD-TYPE 122 197 160

Figure S14.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 2.75e-07 (Fisher's exact test), Q value = 0.00017

Table S15.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
8Q GAIN CNV 19 1 14
8Q GAIN WILD-TYPE 113 196 150

Figure S15.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1.15e-07 (Fisher's exact test), Q value = 7.3e-05

Table S16.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
8Q GAIN CNV 1 25 5
8Q GAIN WILD-TYPE 196 154 92

Figure S16.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.88e-05 (Fisher's exact test), Q value = 0.028

Table S17.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
8Q GAIN CNV 3 4 24
8Q GAIN WILD-TYPE 66 210 166

Figure S17.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 6.77e-06 (Fisher's exact test), Q value = 0.0041

Table S18.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
8Q GAIN CNV 6 3 24
8Q GAIN WILD-TYPE 109 188 145

Figure S18.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 7.99e-07 (Fisher's exact test), Q value = 5e-04

Table S19.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
12P GAIN CNV 37 13 28
12P GAIN WILD-TYPE 95 184 136

Figure S19.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 5.67e-07 (Chi-square test), Q value = 0.00035

Table S20.  Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
12P GAIN CNV 4 9 20 9 6 21
12P GAIN WILD-TYPE 96 79 64 66 37 36

Figure S20.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0066

Table S21.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
12P GAIN CNV 15 45 12
12P GAIN WILD-TYPE 182 134 85

Figure S21.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.011

Table S22.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
12P GAIN CNV 7 18 47
12P GAIN WILD-TYPE 62 196 143

Figure S22.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 6.95e-06 (Fisher's exact test), Q value = 0.0042

Table S23.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
12P GAIN CNV 13 18 47
12P GAIN WILD-TYPE 102 173 122

Figure S23.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 7.99e-07 (Fisher's exact test), Q value = 5e-04

Table S24.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
12Q GAIN CNV 37 13 28
12Q GAIN WILD-TYPE 95 184 136

Figure S24.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 5.67e-07 (Chi-square test), Q value = 0.00035

Table S25.  Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
12Q GAIN CNV 4 9 20 9 6 21
12Q GAIN WILD-TYPE 96 79 64 66 37 36

Figure S25.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0066

Table S26.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
12Q GAIN CNV 15 45 12
12Q GAIN WILD-TYPE 182 134 85

Figure S26.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.011

Table S27.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
12Q GAIN CNV 7 18 47
12Q GAIN WILD-TYPE 62 196 143

Figure S27.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 6.95e-06 (Fisher's exact test), Q value = 0.0042

Table S28.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
12Q GAIN CNV 13 18 47
12Q GAIN WILD-TYPE 102 173 122

Figure S28.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.000357 (Fisher's exact test), Q value = 0.2

Table S29.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
17P GAIN CNV 6 0 10
17P GAIN WILD-TYPE 126 197 154

Figure S29.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.02

Table S30.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
19P GAIN CNV 14 1 10
19P GAIN WILD-TYPE 118 196 154

Figure S30.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 3e-06 (Fisher's exact test), Q value = 0.0019

Table S31.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
19Q GAIN CNV 17 1 10
19Q GAIN WILD-TYPE 115 196 154

Figure S31.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.05e-12 (Fisher's exact test), Q value = 6.9e-10

Table S32.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
20P GAIN CNV 36 3 27
20P GAIN WILD-TYPE 96 194 137

Figure S32.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.000453 (Chi-square test), Q value = 0.24

Table S33.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
20P GAIN CNV 4 9 13 15 4 16
20P GAIN WILD-TYPE 96 79 71 60 39 41

Figure S33.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 3.59e-06 (Fisher's exact test), Q value = 0.0022

Table S34.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
20P GAIN CNV 12 42 10
20P GAIN WILD-TYPE 185 137 87

Figure S34.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.29e-06 (Fisher's exact test), Q value = 0.0032

Table S35.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
20P GAIN CNV 8 13 43
20P GAIN WILD-TYPE 61 201 147

Figure S35.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 2.54e-06 (Fisher's exact test), Q value = 0.0016

Table S36.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
20P GAIN CNV 11 13 42
20P GAIN WILD-TYPE 104 178 127

Figure S36.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 6.23e-14 (Fisher's exact test), Q value = 4.1e-11

Table S37.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
20Q GAIN CNV 39 3 26
20Q GAIN WILD-TYPE 93 194 138

Figure S37.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 3.54e-05 (Chi-square test), Q value = 0.021

Table S38.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
20Q GAIN CNV 4 8 14 15 4 18
20Q GAIN WILD-TYPE 96 80 70 60 39 39

Figure S38.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 3.3e-07 (Fisher's exact test), Q value = 0.00021

Table S39.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
20Q GAIN CNV 12 45 9
20Q GAIN WILD-TYPE 185 134 88

Figure S39.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.00091

Table S40.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
20Q GAIN CNV 8 13 45
20Q GAIN WILD-TYPE 61 201 145

Figure S40.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1.83e-07 (Fisher's exact test), Q value = 0.00012

Table S41.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
20Q GAIN CNV 10 13 45
20Q GAIN WILD-TYPE 105 178 124

Figure S41.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.066

Table S42.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
21Q GAIN CNV 20 6 7
21Q GAIN WILD-TYPE 112 191 157

Figure S42.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.000399 (Fisher's exact test), Q value = 0.22

Table S43.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
22Q GAIN CNV 15 3 7
22Q GAIN WILD-TYPE 117 194 157

Figure S43.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.2e-05 (Fisher's exact test), Q value = 0.036

Table S44.  Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
1P LOSS CNV 8 1 2
1P LOSS WILD-TYPE 6 22 31

Figure S44.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'RPPA_CNMF'

P value = 5.05e-08 (Chi-square test), Q value = 3.2e-05

Table S45.  Gene #41: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
1P LOSS CNV 3 1 3 16 3 0
1P LOSS WILD-TYPE 97 87 81 59 40 57

Figure S45.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.000435 (Fisher's exact test), Q value = 0.24

Table S46.  Gene #41: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
1P LOSS CNV 10 2 14
1P LOSS WILD-TYPE 176 150 95

Figure S46.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.64e-06 (Fisher's exact test), Q value = 0.0028

Table S47.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
1P LOSS CNV 15 9 6
1P LOSS WILD-TYPE 54 205 184

Figure S47.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.01e-10 (Fisher's exact test), Q value = 6.5e-08

Table S48.  Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
1P LOSS CNV 15 4 13
1P LOSS WILD-TYPE 20 156 267

Figure S48.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 2.09e-05 (Fisher's exact test), Q value = 0.012

Table S49.  Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
1Q LOSS CNV 2 2 17
1Q LOSS WILD-TYPE 130 195 147

Figure S49.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'RPPA_CNMF'

P value = 0.000168 (Chi-square test), Q value = 0.094

Table S50.  Gene #42: '1q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
1Q LOSS CNV 3 0 1 10 2 1
1Q LOSS WILD-TYPE 97 88 83 65 41 56

Figure S50.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 6.65e-05 (Fisher's exact test), Q value = 0.038

Table S51.  Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
1Q LOSS CNV 5 3 13
1Q LOSS WILD-TYPE 192 176 84

Figure S51.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.27e-07 (Fisher's exact test), Q value = 0.00039

Table S52.  Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
1Q LOSS CNV 13 5 3
1Q LOSS WILD-TYPE 56 209 187

Figure S52.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.88e-11 (Fisher's exact test), Q value = 1.9e-08

Table S53.  Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
1Q LOSS CNV 13 3 5
1Q LOSS WILD-TYPE 22 157 275

Figure S53.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.14

Table S54.  Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
2P LOSS CNV 0 1 5
2P LOSS WILD-TYPE 33 23 8

Figure S54.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000374 (Fisher's exact test), Q value = 0.2

Table S55.  Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
2P LOSS CNV 5 1 0
2P LOSS WILD-TYPE 9 22 33

Figure S55.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.009

Table S56.  Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
2P LOSS CNV 0 0 10
2P LOSS WILD-TYPE 132 197 154

Figure S56.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 1.37e-05 (Chi-square test), Q value = 0.0081

Table S57.  Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
2P LOSS CNV 0 0 0 6 0 0
2P LOSS WILD-TYPE 100 88 84 69 43 57

Figure S57.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.000189 (Fisher's exact test), Q value = 0.11

Table S58.  Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
2P LOSS CNV 0 0 6
2P LOSS WILD-TYPE 186 152 103

Figure S58.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 4.72e-07 (Fisher's exact test), Q value = 3e-04

Table S59.  Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
2P LOSS CNV 0 0 9
2P LOSS WILD-TYPE 197 179 88

Figure S59.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.87e-08 (Fisher's exact test), Q value = 1.2e-05

Table S60.  Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
2P LOSS CNV 9 0 0
2P LOSS WILD-TYPE 60 214 190

Figure S60.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-12 (Fisher's exact test), Q value = 8.3e-10

Table S61.  Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
2P LOSS CNV 10 0 0
2P LOSS WILD-TYPE 25 160 280

Figure S61.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.14

Table S62.  Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
2Q LOSS CNV 0 1 5
2Q LOSS WILD-TYPE 33 23 8

Figure S62.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000374 (Fisher's exact test), Q value = 0.2

Table S63.  Gene #44: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
2Q LOSS CNV 5 1 0
2Q LOSS WILD-TYPE 9 22 33

Figure S63.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 4.75e-06 (Fisher's exact test), Q value = 0.0029

Table S64.  Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
2Q LOSS CNV 0 0 11
2Q LOSS WILD-TYPE 132 197 153

Figure S64.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.000129 (Chi-square test), Q value = 0.073

Table S65.  Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
2Q LOSS CNV 0 0 0 6 0 1
2Q LOSS WILD-TYPE 100 88 84 69 43 56

Figure S65.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 4.42e-05 (Fisher's exact test), Q value = 0.026

Table S66.  Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
2Q LOSS CNV 0 0 7
2Q LOSS WILD-TYPE 186 152 102

Figure S66.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 8.96e-08 (Fisher's exact test), Q value = 5.7e-05

Table S67.  Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
2Q LOSS CNV 0 0 10
2Q LOSS WILD-TYPE 197 179 87

Figure S67.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.91e-08 (Fisher's exact test), Q value = 5e-05

Table S68.  Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
2Q LOSS CNV 9 0 1
2Q LOSS WILD-TYPE 60 214 189

Figure S68.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.000199 (Fisher's exact test), Q value = 0.11

Table S69.  Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
2Q LOSS CNV 1 0 10
2Q LOSS WILD-TYPE 114 191 159

Figure S69.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.81e-12 (Fisher's exact test), Q value = 3.1e-09

Table S70.  Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
2Q LOSS CNV 10 1 0
2Q LOSS WILD-TYPE 25 159 280

Figure S70.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 6.37e-24 (Fisher's exact test), Q value = 4.2e-21

Table S71.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
3P LOSS CNV 107 148 49
3P LOSS WILD-TYPE 25 49 115

Figure S71.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.00012 (Chi-square test), Q value = 0.068

Table S72.  Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
3P LOSS CNV 77 47 54 40 33 26
3P LOSS WILD-TYPE 23 41 30 35 10 31

Figure S72.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.78e-05 (Fisher's exact test), Q value = 0.01

Table S73.  Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
3P LOSS CNV 130 100 47
3P LOSS WILD-TYPE 56 52 62

Figure S73.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 3.85e-11 (Fisher's exact test), Q value = 2.5e-08

Table S74.  Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
3P LOSS CNV 154 95 39
3P LOSS WILD-TYPE 43 84 58

Figure S74.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.09e-10 (Fisher's exact test), Q value = 4.6e-07

Table S75.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
3P LOSS CNV 23 160 105
3P LOSS WILD-TYPE 46 54 85

Figure S75.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 4.23e-05 (Fisher's exact test), Q value = 0.024

Table S76.  Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
3P LOSS CNV 63 140 88
3P LOSS WILD-TYPE 52 51 81

Figure S76.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.08e-14 (Fisher's exact test), Q value = 3.4e-11

Table S77.  Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
3P LOSS CNV 7 75 209
3P LOSS WILD-TYPE 28 85 71

Figure S77.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 0.000221 (Fisher's exact test), Q value = 0.12

Table S78.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
4Q LOSS CNV 16 3 9
4Q LOSS WILD-TYPE 116 194 155

Figure S78.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 4.27e-12 (Fisher's exact test), Q value = 2.8e-09

Table S79.  Gene #49: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
6P LOSS CNV 37 4 17
6P LOSS WILD-TYPE 95 193 147

Figure S79.  Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 0.000122 (Chi-square test), Q value = 0.068

Table S80.  Gene #49: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
6P LOSS CNV 10 3 9 14 1 15
6P LOSS WILD-TYPE 90 85 75 61 42 42

Figure S80.  Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 7.03e-06 (Fisher's exact test), Q value = 0.0042

Table S81.  Gene #49: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
6P LOSS CNV 8 19 25
6P LOSS WILD-TYPE 178 133 84

Figure S81.  Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 2.87e-09 (Fisher's exact test), Q value = 1.8e-06

Table S82.  Gene #49: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
6P LOSS CNV 3 12 41
6P LOSS WILD-TYPE 112 179 128

Figure S82.  Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000394 (Fisher's exact test), Q value = 0.21

Table S83.  Gene #49: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
6P LOSS CNV 12 19 25
6P LOSS WILD-TYPE 23 141 255

Figure S83.  Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 6.34e-17 (Fisher's exact test), Q value = 4.2e-14

Table S84.  Gene #50: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
6Q LOSS CNV 54 9 19
6Q LOSS WILD-TYPE 78 188 145

Figure S84.  Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.0084

Table S85.  Gene #50: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
6Q LOSS CNV 8 26 46
6Q LOSS WILD-TYPE 107 165 123

Figure S85.  Get High-res Image Gene #50: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 9.23e-25 (Fisher's exact test), Q value = 6.2e-22

Table S86.  Gene #53: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
9P LOSS CNV 60 3 24
9P LOSS WILD-TYPE 72 194 140

Figure S86.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 3.57e-12 (Fisher's exact test), Q value = 2.3e-09

Table S87.  Gene #53: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
9P LOSS CNV 38 3 10
9P LOSS WILD-TYPE 58 115 54

Figure S87.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1.39e-11 (Fisher's exact test), Q value = 9.1e-09

Table S88.  Gene #53: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
9P LOSS CNV 14 60 9
9P LOSS WILD-TYPE 183 119 88

Figure S88.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.71e-12 (Fisher's exact test), Q value = 1.8e-09

Table S89.  Gene #53: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
9P LOSS CNV 5 15 63
9P LOSS WILD-TYPE 64 199 127

Figure S89.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 8.73e-09 (Fisher's exact test), Q value = 5.6e-06

Table S90.  Gene #53: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
9P LOSS CNV 13 17 55
9P LOSS WILD-TYPE 102 174 114

Figure S90.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 4.43e-26 (Fisher's exact test), Q value = 3e-23

Table S91.  Gene #54: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
9Q LOSS CNV 64 4 24
9Q LOSS WILD-TYPE 68 193 140

Figure S91.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 4.3e-13 (Fisher's exact test), Q value = 2.8e-10

Table S92.  Gene #54: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
9Q LOSS CNV 40 3 10
9Q LOSS WILD-TYPE 56 115 54

Figure S92.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1.31e-12 (Fisher's exact test), Q value = 8.7e-10

Table S93.  Gene #54: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
9Q LOSS CNV 15 64 9
9Q LOSS WILD-TYPE 182 115 88

Figure S93.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.94e-14 (Fisher's exact test), Q value = 2.6e-11

Table S94.  Gene #54: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
9Q LOSS CNV 5 15 68
9Q LOSS WILD-TYPE 64 199 122

Figure S94.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 3.82e-10 (Fisher's exact test), Q value = 2.5e-07

Table S95.  Gene #54: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
9Q LOSS CNV 13 17 59
9Q LOSS WILD-TYPE 102 174 110

Figure S95.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 0.000201 (Fisher's exact test), Q value = 0.11

Table S96.  Gene #55: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
10P LOSS CNV 10 3 19
10P LOSS WILD-TYPE 122 194 145

Figure S96.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 6.36e-05 (Fisher's exact test), Q value = 0.036

Table S97.  Gene #59: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
13Q LOSS CNV 14 2 15
13Q LOSS WILD-TYPE 118 195 149

Figure S97.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.25

Table S98.  Gene #59: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
13Q LOSS CNV 7 4 19
13Q LOSS WILD-TYPE 62 210 171

Figure S98.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000285 (Fisher's exact test), Q value = 0.16

Table S99.  Gene #59: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
13Q LOSS CNV 7 15 9
13Q LOSS WILD-TYPE 28 145 271

Figure S99.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 2.02e-10 (Fisher's exact test), Q value = 1.3e-07

Table S100.  Gene #60: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
14Q LOSS CNV 73 41 44
14Q LOSS WILD-TYPE 59 156 120

Figure S100.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 3.06e-05 (Fisher's exact test), Q value = 0.018

Table S101.  Gene #60: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
14Q LOSS CNV 43 20 23
14Q LOSS WILD-TYPE 53 98 41

Figure S101.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 6.61e-12 (Chi-square test), Q value = 4.3e-09

Table S102.  Gene #60: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
14Q LOSS CNV 20 18 54 18 11 28
14Q LOSS WILD-TYPE 80 70 30 57 32 29

Figure S102.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2.08e-07 (Fisher's exact test), Q value = 0.00013

Table S103.  Gene #60: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
14Q LOSS CNV 37 73 39
14Q LOSS WILD-TYPE 149 79 70

Figure S103.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 6.97e-11 (Fisher's exact test), Q value = 4.5e-08

Table S104.  Gene #60: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
14Q LOSS CNV 54 88 11
14Q LOSS WILD-TYPE 143 91 86

Figure S104.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.8e-07 (Fisher's exact test), Q value = 0.00018

Table S105.  Gene #60: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
14Q LOSS CNV 8 60 85
14Q LOSS WILD-TYPE 61 154 105

Figure S105.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 4.33e-06 (Fisher's exact test), Q value = 0.0026

Table S106.  Gene #60: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
14Q LOSS CNV 25 50 79
14Q LOSS WILD-TYPE 90 141 90

Figure S106.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MRNA_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.066

Table S107.  Gene #63: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
17P LOSS CNV 0 3 6
17P LOSS WILD-TYPE 33 21 7

Figure S107.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000178 (Fisher's exact test), Q value = 0.1

Table S108.  Gene #63: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
17P LOSS CNV 6 3 0
17P LOSS WILD-TYPE 8 20 33

Figure S108.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 4.3e-06 (Fisher's exact test), Q value = 0.0026

Table S109.  Gene #63: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
17P LOSS CNV 12 0 13
17P LOSS WILD-TYPE 120 197 151

Figure S109.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 2.92e-05 (Chi-square test), Q value = 0.017

Table S110.  Gene #63: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
17P LOSS CNV 1 1 2 10 0 7
17P LOSS WILD-TYPE 99 87 82 65 43 50

Figure S110.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 5.18e-06 (Fisher's exact test), Q value = 0.0031

Table S111.  Gene #63: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
17P LOSS CNV 2 4 15
17P LOSS WILD-TYPE 184 148 94

Figure S111.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1.9e-06 (Fisher's exact test), Q value = 0.0012

Table S112.  Gene #63: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
17P LOSS CNV 0 12 11
17P LOSS WILD-TYPE 197 167 86

Figure S112.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.5e-08 (Fisher's exact test), Q value = 9.6e-06

Table S113.  Gene #63: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
17P LOSS CNV 12 0 11
17P LOSS WILD-TYPE 57 214 179

Figure S113.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 4.9e-07 (Fisher's exact test), Q value = 0.00031

Table S114.  Gene #63: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
17P LOSS CNV 3 1 21
17P LOSS WILD-TYPE 112 190 148

Figure S114.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.54e-09 (Fisher's exact test), Q value = 5.5e-06

Table S115.  Gene #63: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
17P LOSS CNV 12 7 6
17P LOSS WILD-TYPE 23 153 274

Figure S115.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.12

Table S116.  Gene #64: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
17Q LOSS CNV 2 0 10
17Q LOSS WILD-TYPE 130 197 154

Figure S116.  Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 1.46e-05 (Chi-square test), Q value = 0.0086

Table S117.  Gene #64: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
17Q LOSS CNV 0 0 0 7 0 1
17Q LOSS WILD-TYPE 100 88 84 68 43 56

Figure S117.  Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.0061

Table S118.  Gene #64: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
17Q LOSS CNV 0 0 8
17Q LOSS WILD-TYPE 186 152 101

Figure S118.  Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1.91e-06 (Fisher's exact test), Q value = 0.0012

Table S119.  Gene #64: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
17Q LOSS CNV 0 1 9
17Q LOSS WILD-TYPE 197 178 88

Figure S119.  Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.91e-08 (Fisher's exact test), Q value = 5e-05

Table S120.  Gene #64: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
17Q LOSS CNV 9 0 1
17Q LOSS WILD-TYPE 60 214 189

Figure S120.  Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 8.98e-05 (Fisher's exact test), Q value = 0.051

Table S121.  Gene #64: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
17Q LOSS CNV 1 0 11
17Q LOSS WILD-TYPE 114 191 158

Figure S121.  Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.05e-11 (Fisher's exact test), Q value = 2.6e-08

Table S122.  Gene #64: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
17Q LOSS CNV 10 0 2
17Q LOSS WILD-TYPE 25 160 278

Figure S122.  Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 3.02e-06 (Fisher's exact test), Q value = 0.0019

Table S123.  Gene #65: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
18P LOSS CNV 26 6 14
18P LOSS WILD-TYPE 106 191 150

Figure S123.  Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 6.06e-06 (Fisher's exact test), Q value = 0.0037

Table S124.  Gene #65: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
18P LOSS CNV 8 32 4
18P LOSS WILD-TYPE 189 147 93

Figure S124.  Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000196 (Fisher's exact test), Q value = 0.11

Table S125.  Gene #65: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
18P LOSS CNV 7 8 29
18P LOSS WILD-TYPE 62 206 161

Figure S125.  Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.2

Table S126.  Gene #65: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 191 169
18P LOSS CNV 10 8 28
18P LOSS WILD-TYPE 105 183 141

Figure S126.  Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 3.61e-06 (Fisher's exact test), Q value = 0.0022

Table S127.  Gene #66: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
18Q LOSS CNV 27 7 14
18Q LOSS WILD-TYPE 105 190 150

Figure S127.  Get High-res Image Gene #66: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.017

Table S128.  Gene #66: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
18Q LOSS CNV 9 32 5
18Q LOSS WILD-TYPE 188 147 92

Figure S128.  Get High-res Image Gene #66: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000367 (Fisher's exact test), Q value = 0.2

Table S129.  Gene #69: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
21Q LOSS CNV 6 5 21
21Q LOSS WILD-TYPE 126 192 143

Figure S129.  Get High-res Image Gene #69: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.72e-05 (Fisher's exact test), Q value = 0.01

Table S130.  Gene #69: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
21Q LOSS CNV 14 6 9
21Q LOSS WILD-TYPE 55 208 181

Figure S130.  Get High-res Image Gene #69: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.51e-06 (Fisher's exact test), Q value = 0.0057

Table S131.  Gene #69: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
21Q LOSS CNV 11 8 13
21Q LOSS WILD-TYPE 24 152 267

Figure S131.  Get High-res Image Gene #69: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

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

  • Number of patients = 493

  • Number of significantly arm-level cnvs = 71

  • Number of molecular subtypes = 10

  • 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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