Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1WH2N9Z
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1WH2N9Z
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 12 molecular subtypes across 504 patients, 133 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF'.

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

  • 5p 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',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 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',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 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 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 133 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 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
17p loss 0 (0%) 478 0.000117
(0.0786) 		0.000197
(0.131) 		6.44e-07
(0.000474) 		0.713
(1.00) 		2.92e-05
(0.0201) 		5.18e-06
(0.0037) 		1.9e-06
(0.00139) 		1.5e-08
(1.14e-05) 		2.83e-06
(0.00204) 		2.73e-11
(2.1e-08) 		0.225
(1.00) 		0.0348
(1.00)
2p loss 0 (0%) 494 0.000249
(0.164) 		0.000389
(0.255) 		6.13e-07
(0.000451) 		0.484
(1.00) 		1.37e-05
(0.00961) 		0.000189
(0.126) 		4.72e-07
(0.000349) 		1.87e-08
(1.42e-05) 		0.000232
(0.154) 		1.38e-12
(1.07e-09) 		1
(1.00) 		0.204
(1.00)
2q loss 0 (0%) 493 0.000249
(0.164) 		0.000389
(0.255) 		2.38e-06
(0.00172) 		1
(1.00) 		0.000129
(0.0866) 		4.42e-05
(0.0301) 		8.96e-08
(6.72e-05) 		7.91e-08
(5.95e-05) 		0.000101
(0.0681) 		1.44e-11
(1.11e-08) 		1
(1.00) 		0.204
(1.00)
3p loss 0 (0%) 193 0.0106
(1.00) 		0.00929
(1.00) 		9.35e-35
(7.38e-32) 		4.94e-06
(0.00353) 		0.000105
(0.071) 		1.54e-05
(0.0108) 		2.09e-11
(1.61e-08) 		7.09e-10
(5.42e-07) 		1.97e-06
(0.00143) 		8.3e-12
(6.44e-09) 		0.00165
(1.00) 		0.000785
(0.502)
9p loss 0 (0%) 415 0.378
(1.00) 		0.124
(1.00) 		6.57e-33
(5.17e-30) 		7.23e-12
(5.61e-09) 		0.00463
(1.00) 		0.00726
(1.00) 		1.39e-11
(1.07e-08) 		2.71e-12
(2.11e-09) 		2.42e-07
(0.00018) 		0.038
(1.00) 		4.42e-06
(0.00317) 		3.42e-05
(0.0234)
14q loss 0 (0%) 342 0.00179
(1.00) 		0.00197
(1.00) 		7.35e-13
(5.76e-10) 		3.84e-05
(0.0262) 		6.61e-12
(5.13e-09) 		2.08e-07
(0.000155) 		6.97e-11
(5.35e-08) 		2.8e-07
(0.000208) 		7.43e-06
(0.00525) 		0.535
(1.00) 		0.0203
(1.00) 		0.622
(1.00)
17q loss 0 (0%) 492 0.000668
(0.431) 		0.000893
(0.564) 		6.84e-06
(0.00485) 		0.484
(1.00) 		1.46e-05
(0.0102) 		1.02e-05
(0.00722) 		1.91e-06
(0.00139) 		7.91e-08
(5.95e-05) 		2.95e-05
(0.0203) 		8.59e-13
(6.71e-10) 		1
(1.00) 		0.204
(1.00)
12p gain 0 (0%) 424 0.194
(1.00) 		0.201
(1.00) 		1.35e-08
(1.02e-05) 		0.00262
(1.00) 		5.67e-07
(0.000418) 		0.0139
(1.00) 		1.1e-05
(0.00775) 		1.89e-05
(0.0131) 		3.26e-06
(0.00235) 		0.237
(1.00) 		2.07e-06
(0.0015) 		0.0455
(1.00)
12q gain 0 (0%) 423 0.194
(1.00) 		0.201
(1.00) 		6.42e-09
(4.89e-06) 		0.00262
(1.00) 		1.46e-07
(0.000109) 		0.0104
(1.00) 		6.06e-06
(0.00431) 		9.22e-06
(0.00651) 		1.72e-06
(0.00125) 		0.206
(1.00) 		8.85e-07
(0.000649) 		0.0299
(1.00)
20q gain 0 (0%) 435 0.0753
(1.00) 		0.106
(1.00) 		1.37e-15
(1.08e-12) 		0.00326
(1.00) 		3.54e-05
(0.0242) 		0.000855
(0.544) 		3.3e-07
(0.000244) 		1.47e-06
(0.00107) 		1.54e-08
(1.17e-05) 		0.00296
(1.00) 		7.31e-08
(5.51e-05) 		0.0081
(1.00)
9q loss 0 (0%) 410 0.378
(1.00) 		0.124
(1.00) 		2.79e-34
(2.2e-31) 		7.61e-13
(5.95e-10) 		0.000999
(0.628) 		0.0104
(1.00) 		1.31e-12
(1.03e-09) 		3.94e-14
(3.09e-11) 		9.59e-09
(7.28e-06) 		0.0159
(1.00) 		2.33e-05
(0.0161) 		0.00122
(0.757)
8q gain 0 (0%) 468 0.0536
(1.00) 		0.0623
(1.00) 		5.94e-11
(4.57e-08) 		0.000901
(0.568) 		0.0102
(1.00) 		0.0449
(1.00) 		1.15e-07
(8.58e-05) 		4.88e-05
(0.0332) 		2.15e-06
(0.00156) 		0.00446
(1.00) 		1.11e-07
(8.29e-05) 		0.0242
(1.00)
20p gain 0 (0%) 437 0.102
(1.00) 		0.149
(1.00) 		1.93e-14
(1.51e-11) 		0.00326
(1.00) 		0.000453
(0.295) 		0.000979
(0.616) 		3.59e-06
(0.00258) 		5.29e-06
(0.00377) 		3.18e-07
(0.000236) 		0.00242
(1.00) 		6.47e-07
(0.000475) 		0.0211
(1.00)
1p loss 0 (0%) 472 0.000836
(0.532) 		5.38e-05
(0.0365) 		2.77e-05
(0.0191) 		0.483
(1.00) 		5.05e-08
(3.81e-05) 		0.000435
(0.284) 		0.0123
(1.00) 		4.64e-06
(0.00332) 		0.112
(1.00) 		9.78e-12
(7.57e-09) 		0.493
(1.00) 		0.0348
(1.00)
6p loss 0 (0%) 445 0.0139
(1.00) 		0.00408
(1.00) 		7.13e-11
(5.47e-08) 		0.00369
(1.00) 		0.000122
(0.0815) 		7.03e-06
(0.00498) 		0.000722
(0.463) 		0.00105
(0.658) 		1.42e-07
(0.000106) 		0.000119
(0.0795) 		0.011
(1.00) 		0.0427
(1.00)
1q loss 0 (0%) 484 0.0107
(1.00) 		0.0133
(1.00) 		6.85e-07
(0.000503) 		1
(1.00) 		0.000863
(0.548) 		0.00112
(0.695) 		1.9e-05
(0.0131) 		3.17e-06
(0.00229) 		0.128
(1.00) 		2.88e-10
(2.2e-07) 		0.488
(1.00) 		0.0896
(1.00)
18p loss 0 (0%) 458 0.194
(1.00) 		0.486
(1.00) 		4.41e-05
(0.0301) 		0.0457
(1.00) 		0.0183
(1.00) 		0.00473
(1.00) 		6.06e-06
(0.00431) 		0.000196
(0.13) 		0.000231
(0.153) 		0.00146
(0.901) 		0.00259
(1.00) 		0.00109
(0.68)
3q gain 0 (0%) 475 0.0249
(1.00) 		0.0289
(1.00) 		4.38e-07
(0.000324) 		0.0593
(1.00) 		0.00718
(1.00) 		0.000107
(0.0722) 		0.000705
(0.453) 		0.00522
(1.00) 		1.06e-05
(0.00744) 		0.00177
(1.00) 		0.0268
(1.00) 		0.329
(1.00)
8p gain 0 (0%) 488 1.74e-05
(0.0121) 		0.089
(1.00) 		0.0868
(1.00) 		0.146
(1.00) 		0.000978
(0.616) 		0.000683
(0.44) 		0.000136
(0.0909) 		0.0286
(1.00) 		0.000293
(0.193) 		0.26
(1.00)
21q loss 0 (0%) 470 0.0145
(1.00) 		0.0238
(1.00) 		0.000106
(0.0715) 		0.236
(1.00) 		0.00501
(1.00) 		0.0399
(1.00) 		0.00192
(1.00) 		1.72e-05
(0.012) 		0.195
(1.00) 		1.65e-05
(0.0115) 		0.749
(1.00) 		0.937
(1.00)
7p gain 0 (0%) 376 0.877
(1.00) 		1
(1.00) 		1.75e-09
(1.33e-06) 		0.0604
(1.00) 		0.000268
(0.177) 		0.00565
(1.00) 		0.068
(1.00) 		0.0824
(1.00) 		0.0165
(1.00) 		0.667
(1.00) 		0.0334
(1.00) 		0.715
(1.00)
7q gain 0 (0%) 374 0.877
(1.00) 		1
(1.00) 		1.84e-09
(1.4e-06) 		0.0441
(1.00) 		0.000118
(0.0791) 		0.000718
(0.461) 		0.0581
(1.00) 		0.131
(1.00) 		0.00739
(1.00) 		0.466
(1.00) 		0.0485
(1.00) 		0.253
(1.00)
6q loss 0 (0%) 419 0.0393
(1.00) 		0.0205
(1.00) 		2.46e-09
(1.87e-06) 		0.147
(1.00) 		0.0014
(0.866) 		0.00103
(0.647) 		0.204
(1.00) 		0.478
(1.00) 		1.78e-05
(0.0124) 		0.000884
(0.561) 		0.0911
(1.00) 		0.18
(1.00)
13q loss 0 (0%) 473 0.0253
(1.00) 		0.0381
(1.00) 		5.97e-06
(0.00425) 		0.148
(1.00) 		0.00137
(0.852) 		0.00139
(0.859) 		0.0025
(1.00) 		0.00046
(0.299) 		0.000157
(0.105) 		0.000796
(0.508) 		0.155
(1.00) 		0.00467
(1.00)
18q loss 0 (0%) 456 0.259
(1.00) 		0.302
(1.00) 		6.3e-05
(0.0427) 		0.0627
(1.00) 		0.0551
(1.00) 		0.0128
(1.00) 		2.87e-05
(0.0197) 		0.000574
(0.371) 		0.000536
(0.348) 		0.000642
(0.414) 		0.00238
(1.00) 		0.00293
(1.00)
1q gain 0 (0%) 472 0.611
(1.00) 		0.617
(1.00) 		2.09e-08
(1.57e-05) 		0.518
(1.00) 		0.434
(1.00) 		0.19
(1.00) 		0.00972
(1.00) 		0.15
(1.00) 		0.0387
(1.00) 		0.473
(1.00) 		0.288
(1.00) 		0.811
(1.00)
2p gain 0 (0%) 455 0.561
(1.00) 		0.4
(1.00) 		1.96e-05
(0.0136) 		0.6
(1.00) 		0.0462
(1.00) 		0.783
(1.00) 		0.144
(1.00) 		0.0785
(1.00) 		0.303
(1.00) 		0.335
(1.00) 		0.388
(1.00) 		0.508
(1.00)
5p gain 0 (0%) 361 0.593
(1.00) 		0.516
(1.00) 		0.000273
(0.18) 		0.228
(1.00) 		0.0817
(1.00) 		0.0546
(1.00) 		0.0458
(1.00) 		0.00844
(1.00) 		0.0185
(1.00) 		0.141
(1.00) 		0.0355
(1.00) 		0.561
(1.00)
19p gain 0 (0%) 479 0.189
(1.00) 		0.207
(1.00) 		1.47e-05
(0.0103) 		0.326
(1.00) 		0.0448
(1.00) 		0.397
(1.00) 		0.0428
(1.00) 		0.0115
(1.00) 		0.0567
(1.00) 		0.0142
(1.00) 		0.124
(1.00) 		1
(1.00)
19q gain 0 (0%) 476 0.0536
(1.00) 		0.0623
(1.00) 		1.53e-06
(0.00112) 		0.221
(1.00) 		0.056
(1.00) 		0.154
(1.00) 		0.0185
(1.00) 		0.00414
(1.00) 		0.0166
(1.00) 		0.00276
(1.00) 		0.0641
(1.00) 		0.913
(1.00)
3q loss 0 (0%) 430 0.701
(1.00) 		0.7
(1.00) 		2.72e-06
(0.00197) 		0.132
(1.00) 		0.0955
(1.00) 		0.00661
(1.00) 		0.518
(1.00) 		0.804
(1.00) 		0.649
(1.00) 		0.0751
(1.00) 		0.074
(1.00) 		0.462
(1.00)
4q loss 0 (0%) 476 1
(1.00) 		1
(1.00) 		2.66e-05
(0.0183) 		0.104
(1.00) 		0.251
(1.00) 		0.313
(1.00) 		0.0631
(1.00) 		0.0573
(1.00) 		0.969
(1.00) 		0.745
(1.00) 		0.453
(1.00) 		0.15
(1.00)
10p loss 0 (0%) 472 0.026
(1.00) 		0.0306
(1.00) 		3.88e-06
(0.00279) 		0.151
(1.00) 		0.195
(1.00) 		0.037
(1.00) 		0.0123
(1.00) 		0.0197
(1.00) 		0.161
(1.00) 		0.000543
(0.352) 		0.354
(1.00) 		0.181
(1.00)
1p gain 0 (0%) 499 0.105
(1.00) 		0.439
(1.00) 		0.0359
(1.00) 		0.846
(1.00) 		0.85
(1.00) 		0.62
(1.00) 		1
(1.00)
2q gain 0 (0%) 454 0.561
(1.00) 		0.4
(1.00) 		0.000406
(0.266) 		0.579
(1.00) 		0.0528
(1.00) 		0.862
(1.00) 		0.0519
(1.00) 		0.0498
(1.00) 		0.135
(1.00) 		0.335
(1.00) 		0.699
(1.00) 		0.508
(1.00)
3p gain 0 (0%) 497 0.204
(1.00) 		1
(1.00) 		0.102
(1.00) 		0.00329
(1.00) 		0.294
(1.00) 		0.161
(1.00) 		0.00488
(1.00) 		0.0529
(1.00) 		0.606
(1.00) 		0.694
(1.00)
4p gain 0 (0%) 496 0.121
(1.00) 		0.625
(1.00) 		0.428
(1.00) 		0.0803
(1.00) 		0.0257
(1.00) 		0.378
(1.00) 		0.00158
(0.974) 		0.147
(1.00)
4q gain 0 (0%) 496 0.486
(1.00) 		0.785
(1.00) 		0.878
(1.00) 		0.338
(1.00) 		0.0112
(1.00) 		0.509
(1.00) 		0.00158
(0.974) 		0.179
(1.00)
5q gain 0 (0%) 345 0.105
(1.00) 		0.0689
(1.00) 		0.00308
(1.00) 		0.197
(1.00) 		0.158
(1.00) 		0.175
(1.00) 		0.0381
(1.00) 		0.00512
(1.00) 		0.0596
(1.00) 		0.0184
(1.00) 		0.0563
(1.00) 		0.23
(1.00)
6p gain 0 (0%) 498 0.876
(1.00) 		0.569
(1.00) 		0.819
(1.00) 		0.877
(1.00) 		0.215
(1.00) 		0.449
(1.00) 		0.33
(1.00) 		0.101
(1.00)
6q gain 0 (0%) 499 0.536
(1.00) 		0.625
(1.00) 		0.571
(1.00) 		0.626
(1.00) 		0.442
(1.00) 		0.571
(1.00) 		0.725
(1.00) 		0.055
(1.00)
9p gain 0 (0%) 496 0.385
(1.00) 		0.785
(1.00) 		0.17
(1.00) 		0.17
(1.00) 		0.103
(1.00) 		0.0571
(1.00) 		0.907
(1.00) 		0.0309
(1.00) 		0.356
(1.00) 		0.0195
(1.00)
9q gain 0 (0%) 496 0.068
(1.00) 		0.534
(1.00) 		0.104
(1.00) 		0.338
(1.00) 		0.523
(1.00) 		0.636
(1.00) 		0.533
(1.00) 		0.179
(1.00) 		0.685
(1.00) 		1
(1.00)
10p gain 0 (0%) 498 0.446
(1.00) 		1
(1.00) 		0.981
(1.00) 		1
(1.00) 		0.267
(1.00) 		0.311
(1.00) 		0.769
(1.00) 		0.39
(1.00) 		1
(1.00) 		0.694
(1.00)
10q gain 0 (0%) 500 0.164
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.615
(1.00) 		0.688
(1.00) 		0.508
(1.00) 		0.822
(1.00) 		0.367
(1.00)
11p gain 0 (0%) 487 0.769
(1.00) 		0.783
(1.00) 		0.0169
(1.00) 		0.559
(1.00) 		0.437
(1.00) 		0.395
(1.00) 		0.491
(1.00) 		0.265
(1.00) 		0.701
(1.00) 		0.411
(1.00) 		0.188
(1.00) 		0.325
(1.00)
11q gain 0 (0%) 489 0.769
(1.00) 		0.783
(1.00) 		0.0471
(1.00) 		0.578
(1.00) 		0.541
(1.00) 		0.48
(1.00) 		0.586
(1.00) 		0.505
(1.00) 		0.842
(1.00) 		0.356
(1.00) 		0.528
(1.00) 		0.787
(1.00)
13q gain 0 (0%) 490 0.832
(1.00) 		0.0277
(1.00) 		0.467
(1.00) 		0.771
(1.00) 		0.0685
(1.00) 		0.636
(1.00) 		0.474
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.867
(1.00)
14q gain 0 (0%) 499 0.061
(1.00) 		0.625
(1.00) 		0.869
(1.00) 		0.0596
(1.00) 		0.00354
(1.00) 		0.0477
(1.00) 		0.0297
(1.00) 		0.0249
(1.00)
15q gain 0 (0%) 490 0.0652
(1.00) 		0.513
(1.00) 		0.644
(1.00) 		0.237
(1.00) 		0.116
(1.00) 		0.379
(1.00) 		0.885
(1.00) 		0.504
(1.00) 		0.33
(1.00) 		0.127
(1.00)
16p gain 0 (0%) 436 0.1
(1.00) 		0.302
(1.00) 		0.105
(1.00) 		0.715
(1.00) 		0.0115
(1.00) 		0.0663
(1.00) 		0.635
(1.00) 		0.113
(1.00) 		0.175
(1.00) 		0.56
(1.00) 		0.34
(1.00) 		0.651
(1.00)
16q gain 0 (0%) 443 0.0706
(1.00) 		0.174
(1.00) 		0.101
(1.00) 		0.945
(1.00) 		0.0443
(1.00) 		0.122
(1.00) 		0.696
(1.00) 		0.336
(1.00) 		0.229
(1.00) 		0.628
(1.00) 		0.2
(1.00) 		0.772
(1.00)
17p gain 0 (0%) 488 0.00522
(1.00) 		0.00665
(1.00) 		0.00405
(1.00) 		0.537
(1.00) 		0.321
(1.00) 		0.0336
(1.00) 		0.191
(1.00) 		0.0327
(1.00) 		0.551
(1.00) 		0.0077
(1.00) 		0.25
(1.00) 		0.694
(1.00)
17q gain 0 (0%) 482 0.00827
(1.00) 		0.0106
(1.00) 		0.00919
(1.00) 		0.169
(1.00) 		0.553
(1.00) 		0.0547
(1.00) 		0.253
(1.00) 		0.00949
(1.00) 		0.281
(1.00) 		0.0017
(1.00) 		0.0768
(1.00) 		0.282
(1.00)
18p gain 0 (0%) 486 0.0764
(1.00) 		0.0436
(1.00) 		0.436
(1.00) 		0.144
(1.00) 		0.319
(1.00) 		0.143
(1.00) 		0.0977
(1.00) 		0.41
(1.00) 		0.827
(1.00) 		0.288
(1.00) 		0.421
(1.00) 		0.152
(1.00)
18q gain 0 (0%) 486 0.0764
(1.00) 		0.0436
(1.00) 		0.436
(1.00) 		0.144
(1.00) 		0.319
(1.00) 		0.143
(1.00) 		0.0977
(1.00) 		0.41
(1.00) 		0.827
(1.00) 		0.288
(1.00) 		0.421
(1.00) 		0.152
(1.00)
21q gain 0 (0%) 469 0.82
(1.00) 		0.818
(1.00) 		0.000757
(0.485) 		0.087
(1.00) 		0.0368
(1.00) 		0.836
(1.00) 		0.0709
(1.00) 		0.08
(1.00) 		0.377
(1.00) 		0.375
(1.00) 		0.05
(1.00) 		0.0476
(1.00)
22q gain 0 (0%) 479 0.58
(1.00) 		0.0436
(1.00) 		0.00243
(1.00) 		0.0394
(1.00) 		0.452
(1.00) 		0.217
(1.00) 		0.826
(1.00) 		0.846
(1.00) 		1
(1.00) 		0.564
(1.00) 		0.528
(1.00) 		0.367
(1.00)
Xq gain 0 (0%) 495 0.472
(1.00) 		0.742
(1.00) 		0.126
(1.00) 		0.338
(1.00) 		0.0651
(1.00) 		0.153
(1.00) 		0.465
(1.00) 		0.163
(1.00) 		1
(1.00) 		0.787
(1.00)
4p loss 0 (0%) 469 0.289
(1.00) 		0.298
(1.00) 		0.00354
(1.00) 		0.136
(1.00) 		0.816
(1.00) 		0.948
(1.00) 		0.0888
(1.00) 		0.366
(1.00) 		0.552
(1.00) 		0.96
(1.00) 		0.729
(1.00) 		0.289
(1.00)
8p loss 0 (0%) 405 0.777
(1.00) 		0.784
(1.00) 		0.00339
(1.00) 		0.767
(1.00) 		0.738
(1.00) 		0.656
(1.00) 		0.141
(1.00) 		0.561
(1.00) 		0.422
(1.00) 		0.891
(1.00) 		0.785
(1.00) 		0.446
(1.00)
8q loss 0 (0%) 464 0.49
(1.00) 		0.591
(1.00) 		0.934
(1.00) 		0.307
(1.00) 		0.476
(1.00) 		0.7
(1.00) 		0.188
(1.00) 		0.0552
(1.00) 		0.812
(1.00) 		0.587
(1.00) 		0.574
(1.00) 		0.754
(1.00)
10q loss 0 (0%) 456 0.0972
(1.00) 		0.121
(1.00) 		0.00107
(0.67) 		0.0115
(1.00) 		0.22
(1.00) 		0.0125
(1.00) 		0.095
(1.00) 		0.126
(1.00) 		0.239
(1.00) 		0.0129
(1.00) 		0.68
(1.00) 		0.147
(1.00)
11p loss 0 (0%) 499 0.0313
(1.00) 		0.625
(1.00) 		0.156
(1.00) 		0.0359
(1.00) 		0.359
(1.00) 		0.462
(1.00) 		0.452
(1.00) 		0.329
(1.00)
11q loss 0 (0%) 497 0.00534
(1.00) 		0.83
(1.00) 		0.0533
(1.00) 		0.215
(1.00) 		0.377
(1.00) 		0.311
(1.00) 		0.226
(1.00) 		0.214
(1.00) 		0.102
(1.00) 		0.204
(1.00)
15q loss 0 (0%) 492 0.58
(1.00) 		0.586
(1.00) 		0.00461
(1.00) 		0.534
(1.00) 		0.451
(1.00) 		0.704
(1.00) 		0.0733
(1.00) 		0.136
(1.00) 		0.341
(1.00) 		0.309
(1.00) 		0.126
(1.00) 		0.787
(1.00)
16q loss 0 (0%) 498 0.244
(1.00) 		0.363
(1.00) 		0.167
(1.00) 		0.456
(1.00) 		1
(1.00) 		0.292
(1.00) 		0.452
(1.00) 		0.125
(1.00) 		0.449
(1.00) 		0.282
(1.00)
19p loss 0 (0%) 500 0.126
(1.00) 		0.363
(1.00) 		0.279
(1.00) 		0.0359
(1.00) 		0.341
(1.00) 		0.379
(1.00) 		0.822
(1.00) 		0.723
(1.00)
20p loss 0 (0%) 498 0.209
(1.00) 		1
(1.00) 		0.0172
(1.00) 		0.877
(1.00) 		0.267
(1.00) 		0.747
(1.00) 		0.0489
(1.00) 		0.233
(1.00)
22q loss 0 (0%) 492 0.00143
(0.881) 		0.0167
(1.00) 		0.0462
(1.00) 		0.393
(1.00) 		0.000888
(0.562) 		0.0191
(1.00) 		0.191
(1.00) 		0.812
(1.00) 		1
(1.00) 		0.867
(1.00)
Xq loss 0 (0%) 494 0.256
(1.00) 		0.272
(1.00) 		0.717
(1.00) 		0.631
(1.00) 		0.31
(1.00) 		0.287
(1.00) 		0.0676
(1.00) 		0.00763
(1.00) 		0.031
(1.00) 		0.000416
(0.272) 		0.795
(1.00) 		0.694
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 2.09e-08 (Fisher's exact test), Q value = 1.6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
1Q GAIN CNV 26 5 1
1Q GAIN WILD-TYPE 138 211 123

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

'2p gain' versus 'CN_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.014

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
2P GAIN CNV 31 12 6
2P GAIN WILD-TYPE 133 204 118

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

'3q gain' versus 'CN_CNMF'

P value = 4.38e-07 (Fisher's exact test), Q value = 0.00032

Table S3.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
3Q GAIN CNV 23 3 3
3Q GAIN WILD-TYPE 141 213 121

Figure S3.  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 = 0.072

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

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0074

Table S5.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
3Q GAIN CNV 5 3 21
3Q GAIN WILD-TYPE 110 208 139

Figure S5.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 0.000273 (Fisher's exact test), Q value = 0.18

Table S6.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
5P GAIN CNV 64 57 22
5P GAIN WILD-TYPE 100 159 102

Figure S6.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1.75e-09 (Fisher's exact test), Q value = 1.3e-06

Table S7.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
7P GAIN CNV 69 29 30
7P GAIN WILD-TYPE 95 187 94

Figure S7.  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 = 0.18

Table S8.  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 S8.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1.84e-09 (Fisher's exact test), Q value = 1.4e-06

Table S9.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
7Q GAIN CNV 69 29 32
7Q GAIN WILD-TYPE 95 187 92

Figure S9.  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 = 0.079

Table S10.  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 S10.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1.74e-05 (Fisher's exact test), Q value = 0.012

Table S11.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
8P GAIN CNV 13 0 3
8P GAIN WILD-TYPE 151 216 121

Figure S11.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.000136 (Fisher's exact test), Q value = 0.091

Table S12.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
8P GAIN CNV 2 1 13
8P GAIN WILD-TYPE 113 210 147

Figure S12.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000293 (Fisher's exact test), Q value = 0.19

Table S13.  Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 97 75
8P GAIN CNV 0 0 8
8P GAIN WILD-TYPE 52 97 67

Figure S13.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 5.94e-11 (Fisher's exact test), Q value = 4.6e-08

Table S14.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
8Q GAIN CNV 27 0 9
8Q GAIN WILD-TYPE 137 216 115

Figure S14.  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 = 8.6e-05

Table S15.  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 S15.  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 = 0.033

Table S16.  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 S16.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 2.15e-06 (Fisher's exact test), Q value = 0.0016

Table S17.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
8Q GAIN CNV 6 4 25
8Q GAIN WILD-TYPE 109 207 135

Figure S17.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.11e-07 (Fisher's exact test), Q value = 8.3e-05

Table S18.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 97 75
8Q GAIN CNV 0 0 14
8Q GAIN WILD-TYPE 52 97 61

Figure S18.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.35e-08 (Fisher's exact test), Q value = 1e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
12P GAIN CNV 48 14 18
12P GAIN WILD-TYPE 116 202 106

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 = 0.00042

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 = 0.0077

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 = 0.013

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 = 3.26e-06 (Fisher's exact test), Q value = 0.0023

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
12P GAIN CNV 14 20 46
12P GAIN WILD-TYPE 101 191 114

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

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.0015

Table S24.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 97 75
12P GAIN CNV 7 4 24
12P GAIN WILD-TYPE 45 93 51

Figure S24.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 6.42e-09 (Fisher's exact test), Q value = 4.9e-06

Table S25.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
12Q GAIN CNV 49 14 18
12Q GAIN WILD-TYPE 115 202 106

Figure S25.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 1.46e-07 (Chi-square test), Q value = 0.00011

Table S26.  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 22
12Q GAIN WILD-TYPE 96 79 64 66 37 35

Figure S26.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 6.06e-06 (Fisher's exact test), Q value = 0.0043

Table S27.  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 46 12
12Q GAIN WILD-TYPE 182 133 85

Figure S27.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.22e-06 (Fisher's exact test), Q value = 0.0065

Table S28.  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 48
12Q GAIN WILD-TYPE 62 196 142

Figure S28.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1.72e-06 (Fisher's exact test), Q value = 0.0013

Table S29.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
12Q GAIN CNV 14 20 47
12Q GAIN WILD-TYPE 101 191 113

Figure S29.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.85e-07 (Fisher's exact test), Q value = 0.00065

Table S30.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 97 75
12Q GAIN CNV 7 4 25
12Q GAIN WILD-TYPE 45 93 50

Figure S30.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.01

Table S31.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
19P GAIN CNV 16 1 8
19P GAIN WILD-TYPE 148 215 116

Figure S31.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1.53e-06 (Fisher's exact test), Q value = 0.0011

Table S32.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
19Q GAIN CNV 19 1 8
19Q GAIN WILD-TYPE 145 215 116

Figure S32.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.93e-14 (Fisher's exact test), Q value = 1.5e-11

Table S33.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
20P GAIN CNV 44 3 20
20P GAIN WILD-TYPE 120 213 104

Figure S33.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 3.59e-06 (Fisher's exact test), Q value = 0.0026

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 = 0.0038

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 = 3.18e-07 (Fisher's exact test), Q value = 0.00024

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
20P GAIN CNV 11 14 42
20P GAIN WILD-TYPE 104 197 118

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

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.47e-07 (Fisher's exact test), Q value = 0.00048

Table S37.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 97 75
20P GAIN CNV 4 2 21
20P GAIN WILD-TYPE 48 95 54

Figure S37.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.37e-15 (Fisher's exact test), Q value = 1.1e-12

Table S38.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
20Q GAIN CNV 47 3 19
20Q GAIN WILD-TYPE 117 213 105

Figure S38.  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 = 0.024

Table S39.  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 S39.  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 = 0.00024

Table S40.  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 S40.  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 = 0.0011

Table S41.  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 S41.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1.54e-08 (Fisher's exact test), Q value = 1.2e-05

Table S42.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
20Q GAIN CNV 10 14 45
20Q GAIN WILD-TYPE 105 197 115

Figure S42.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.31e-08 (Fisher's exact test), Q value = 5.5e-05

Table S43.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 97 75
20Q GAIN CNV 4 2 23
20Q GAIN WILD-TYPE 48 95 52

Figure S43.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 5.38e-05 (Fisher's exact test), Q value = 0.037

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
1P LOSS CNV 8 2 1
1P LOSS WILD-TYPE 6 30 23

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

'1p loss' versus 'CN_CNMF'

P value = 2.77e-05 (Fisher's exact test), Q value = 0.019

Table S45.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
1P LOSS CNV 10 4 18
1P LOSS WILD-TYPE 154 212 106

Figure S45.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 5.05e-08 (Chi-square test), Q value = 3.8e-05

Table S46.  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 S46.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.64e-06 (Fisher's exact test), Q value = 0.0033

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 = 9.78e-12 (Fisher's exact test), Q value = 7.6e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 36 287
1P LOSS CNV 4 16 12
1P LOSS WILD-TYPE 159 20 275

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

'1q loss' versus 'CN_CNMF'

P value = 6.85e-07 (Fisher's exact test), Q value = 5e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
1Q LOSS CNV 4 1 15
1Q LOSS WILD-TYPE 160 215 109

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

'1q loss' versus 'MRNASEQ_CNMF'

P value = 1.9e-05 (Fisher's exact test), Q value = 0.013

Table S50.  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 2 13
1Q LOSS WILD-TYPE 192 177 84

Figure S50.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.17e-06 (Fisher's exact test), Q value = 0.0023

Table S51.  Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
1Q LOSS CNV 12 5 3
1Q LOSS WILD-TYPE 57 209 187

Figure S51.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.88e-10 (Fisher's exact test), Q value = 2.2e-07

Table S52.  Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 36 287
1Q LOSS CNV 2 12 6
1Q LOSS WILD-TYPE 161 24 281

Figure S52.  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 = 0.16

Table S53.  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 S53.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 6.13e-07 (Fisher's exact test), Q value = 0.00045

Table S54.  Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
2P LOSS CNV 0 0 10
2P LOSS WILD-TYPE 164 216 114

Figure S54.  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 = 0.0096

Table S55.  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 S55.  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 = 0.13

Table S56.  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 S56.  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 = 0.00035

Table S57.  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 S57.  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 = 1.4e-05

Table S58.  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 S58.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.000232 (Fisher's exact test), Q value = 0.15

Table S59.  Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
2P LOSS CNV 1 0 9
2P LOSS WILD-TYPE 114 211 151

Figure S59.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.38e-12 (Fisher's exact test), Q value = 1.1e-09

Table S60.  Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 36 287
2P LOSS CNV 0 10 0
2P LOSS WILD-TYPE 163 26 287

Figure S60.  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 = 0.16

Table S61.  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 S61.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 2.38e-06 (Fisher's exact test), Q value = 0.0017

Table S62.  Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
2Q LOSS CNV 1 0 10
2Q LOSS WILD-TYPE 163 216 114

Figure S62.  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 = 0.087

Table S63.  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 S63.  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 = 0.03

Table S64.  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 S64.  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 = 6.7e-05

Table S65.  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 S65.  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 = 6e-05

Table S66.  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 S66.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.068

Table S67.  Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
2Q LOSS CNV 1 0 10
2Q LOSS WILD-TYPE 114 211 150

Figure S67.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.44e-11 (Fisher's exact test), Q value = 1.1e-08

Table S68.  Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 36 287
2Q LOSS CNV 0 10 1
2Q LOSS WILD-TYPE 163 26 286

Figure S68.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 9.35e-35 (Fisher's exact test), Q value = 7.4e-32

Table S69.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
3P LOSS CNV 118 174 19
3P LOSS WILD-TYPE 46 42 105

Figure S69.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 4.94e-06 (Fisher's exact test), Q value = 0.0035

Table S70.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
3P LOSS CNV 66 88 32
3P LOSS WILD-TYPE 34 26 44

Figure S70.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.000105 (Chi-square test), Q value = 0.071

Table S71.  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 55 40 33 26
3P LOSS WILD-TYPE 23 41 29 35 10 31

Figure S71.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.54e-05 (Fisher's exact test), Q value = 0.011

Table S72.  Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
3P LOSS CNV 130 101 47
3P LOSS WILD-TYPE 56 51 62

Figure S72.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 2.09e-11 (Fisher's exact test), Q value = 1.6e-08

Table S73.  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 96 38
3P LOSS WILD-TYPE 43 83 59

Figure S73.  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 = 5.4e-07

Table S74.  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 S74.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1.97e-06 (Fisher's exact test), Q value = 0.0014

Table S75.  Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
3P LOSS CNV 63 156 79
3P LOSS WILD-TYPE 52 55 81

Figure S75.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.3e-12 (Fisher's exact test), Q value = 6.4e-09

Table S76.  Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 36 287
3P LOSS CNV 80 8 210
3P LOSS WILD-TYPE 83 28 77

Figure S76.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 2.72e-06 (Fisher's exact test), Q value = 0.002

Table S77.  Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
3Q LOSS CNV 33 38 3
3Q LOSS WILD-TYPE 131 178 121

Figure S77.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.018

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
4Q LOSS CNV 20 3 5
4Q LOSS WILD-TYPE 144 213 119

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

'6p loss' versus 'CN_CNMF'

P value = 7.13e-11 (Fisher's exact test), Q value = 5.5e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
6P LOSS CNV 40 5 14
6P LOSS WILD-TYPE 124 211 110

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 = 0.082

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 = 0.005

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 = 1.42e-07 (Fisher's exact test), Q value = 0.00011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
6P LOSS CNV 5 14 38
6P LOSS WILD-TYPE 110 197 122

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

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000119 (Fisher's exact test), Q value = 0.08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 36 287
6P LOSS CNV 19 13 25
6P LOSS WILD-TYPE 144 23 262

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

'6q loss' versus 'CN_CNMF'

P value = 2.46e-09 (Fisher's exact test), Q value = 1.9e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
6Q LOSS CNV 53 18 14
6Q LOSS WILD-TYPE 111 198 110

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

'6q loss' versus 'MIRSEQ_CNMF'

P value = 1.78e-05 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
6Q LOSS CNV 9 29 45
6Q LOSS WILD-TYPE 106 182 115

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

'9p loss' versus 'CN_CNMF'

P value = 6.57e-33 (Fisher's exact test), Q value = 5.2e-30

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
9P LOSS CNV 77 3 9
9P LOSS WILD-TYPE 87 213 115

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

'9p loss' versus 'METHLYATION_CNMF'

P value = 7.23e-12 (Fisher's exact test), Q value = 5.6e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
9P LOSS CNV 39 3 11
9P LOSS WILD-TYPE 61 111 65

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 = 1.1e-08

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 = 2.1e-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 = 2.42e-07 (Fisher's exact test), Q value = 0.00018

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
9P LOSS CNV 15 21 51
9P LOSS WILD-TYPE 100 190 109

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

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.42e-06 (Fisher's exact test), Q value = 0.0032

Table S91.  Gene #53: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 97 75
9P LOSS CNV 11 5 25
9P LOSS WILD-TYPE 41 92 50

Figure S91.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.42e-05 (Fisher's exact test), Q value = 0.023

Table S92.  Gene #53: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 19 96
9P LOSS CNV 11 0 30
9P LOSS WILD-TYPE 98 19 66

Figure S92.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 2.79e-34 (Fisher's exact test), Q value = 2.2e-31

Table S93.  Gene #54: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
9Q LOSS CNV 81 4 9
9Q LOSS WILD-TYPE 83 212 115

Figure S93.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 7.61e-13 (Fisher's exact test), Q value = 6e-10

Table S94.  Gene #54: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
9Q LOSS CNV 41 3 11
9Q LOSS WILD-TYPE 59 111 65

Figure S94.  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 = 1e-09

Table S95.  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 S95.  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 = 3.1e-11

Table S96.  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 S96.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 9.59e-09 (Fisher's exact test), Q value = 7.3e-06

Table S97.  Gene #54: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
9Q LOSS CNV 15 21 55
9Q LOSS WILD-TYPE 100 190 105

Figure S97.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.33e-05 (Fisher's exact test), Q value = 0.016

Table S98.  Gene #54: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 97 75
9Q LOSS CNV 12 7 26
9Q LOSS WILD-TYPE 40 90 49

Figure S98.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 3.88e-06 (Fisher's exact test), Q value = 0.0028

Table S99.  Gene #55: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
10P LOSS CNV 14 2 16
10P LOSS WILD-TYPE 150 214 108

Figure S99.  Get High-res Image Gene #55: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 5.97e-06 (Fisher's exact test), Q value = 0.0043

Table S100.  Gene #59: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
13Q LOSS CNV 20 2 9
13Q LOSS WILD-TYPE 144 214 115

Figure S100.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.000157 (Fisher's exact test), Q value = 0.1

Table S101.  Gene #59: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
13Q LOSS CNV 7 4 20
13Q LOSS WILD-TYPE 108 207 140

Figure S101.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 7.35e-13 (Fisher's exact test), Q value = 5.8e-10

Table S102.  Gene #60: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
14Q LOSS CNV 90 46 26
14Q LOSS WILD-TYPE 74 170 98

Figure S102.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 3.84e-05 (Fisher's exact test), Q value = 0.026

Table S103.  Gene #60: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
14Q LOSS CNV 44 19 27
14Q LOSS WILD-TYPE 56 95 49

Figure S103.  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 = 5.1e-09

Table S104.  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 S104.  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 = 0.00015

Table S105.  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 S105.  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 = 5.4e-08

Table S106.  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 S106.  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 = 0.00021

Table S107.  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 S107.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 7.43e-06 (Fisher's exact test), Q value = 0.0053

Table S108.  Gene #60: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
14Q LOSS CNV 24 59 75
14Q LOSS WILD-TYPE 91 152 85

Figure S108.  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 = 0.079

Table S109.  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 S109.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000197 (Fisher's exact test), Q value = 0.13

Table S110.  Gene #63: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
17P LOSS CNV 6 0 3
17P LOSS WILD-TYPE 8 32 21

Figure S110.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 6.44e-07 (Fisher's exact test), Q value = 0.00047

Table S111.  Gene #63: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
17P LOSS CNV 15 0 11
17P LOSS WILD-TYPE 149 216 113

Figure S111.  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 = 0.02

Table S112.  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 S112.  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 = 0.0037

Table S113.  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 S113.  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 = 0.0014

Table S114.  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 S114.  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 = 1.1e-05

Table S115.  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 S115.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 2.83e-06 (Fisher's exact test), Q value = 0.002

Table S116.  Gene #63: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
17P LOSS CNV 4 2 20
17P LOSS WILD-TYPE 111 209 140

Figure S116.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.73e-11 (Fisher's exact test), Q value = 2.1e-08

Table S117.  Gene #63: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 36 287
17P LOSS CNV 7 14 5
17P LOSS WILD-TYPE 156 22 282

Figure S117.  Get High-res Image Gene #63: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 6.84e-06 (Fisher's exact test), Q value = 0.0049

Table S118.  Gene #64: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
17Q LOSS CNV 2 0 10
17Q LOSS WILD-TYPE 162 216 114

Figure S118.  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 = 0.01

Table S119.  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 S119.  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 = 0.0072

Table S120.  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 S120.  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 = 0.0014

Table S121.  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 S121.  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 = 6e-05

Table S122.  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 S122.  Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 2.95e-05 (Fisher's exact test), Q value = 0.02

Table S123.  Gene #64: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
17Q LOSS CNV 1 0 11
17Q LOSS WILD-TYPE 114 211 149

Figure S123.  Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.59e-13 (Fisher's exact test), Q value = 6.7e-10

Table S124.  Gene #64: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 36 287
17Q LOSS CNV 0 11 1
17Q LOSS WILD-TYPE 163 25 286

Figure S124.  Get High-res Image Gene #64: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 4.41e-05 (Fisher's exact test), Q value = 0.03

Table S125.  Gene #65: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
18P LOSS CNV 28 8 10
18P LOSS WILD-TYPE 136 208 114

Figure S125.  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 = 0.0043

Table S126.  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 S126.  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 = 0.13

Table S127.  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 S127.  Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.000231 (Fisher's exact test), Q value = 0.15

Table S128.  Gene #65: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 115 211 160
18P LOSS CNV 10 9 27
18P LOSS WILD-TYPE 105 202 133

Figure S128.  Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 6.3e-05 (Fisher's exact test), Q value = 0.043

Table S129.  Gene #66: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
18Q LOSS CNV 29 9 10
18Q LOSS WILD-TYPE 135 207 114

Figure S129.  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 = 0.02

Table S130.  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 S130.  Get High-res Image Gene #66: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000106 (Fisher's exact test), Q value = 0.072

Table S131.  Gene #69: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 164 216 124
21Q LOSS CNV 11 5 18
21Q LOSS WILD-TYPE 153 211 106

Figure S131.  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 = 0.012

Table S132.  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 S132.  Get High-res Image Gene #69: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.65e-05 (Fisher's exact test), Q value = 0.012

Table S133.  Gene #69: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 36 287
21Q LOSS CNV 9 11 14
21Q LOSS WILD-TYPE 154 25 273

Figure S133.  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 = 504

  • Number of significantly arm-level cnvs = 71

  • Number of molecular subtypes = 12

  • 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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