Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1D50K10
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/C1D50K10
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, 137 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'.

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

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

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

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

  • 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', 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',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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_MATURE_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',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p loss cnv correlated to 'CN_CNMF'.

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

  • 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, 137 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
3p loss 0 (0%) 193 0.0106
(1.00) 		0.00929
(1.00) 		9.35e-35
(7.36e-32) 		5.49e-06
(0.0039) 		0.000105
(0.0705) 		1.54e-05
(0.0107) 		2.09e-11
(1.61e-08) 		7.09e-10
(5.41e-07) 		4.23e-05
(0.0288) 		1.49e-14
(1.17e-11) 		0.0209
(1.00) 		3.64e-05
(0.0249)
17p loss 0 (0%) 478 0.000117
(0.0781) 		0.000197
(0.13) 		6.44e-07
(0.000473) 		0.608
(1.00) 		2.92e-05
(0.02) 		5.18e-06
(0.0037) 		1.9e-06
(0.00138) 		1.5e-08
(1.13e-05) 		4.9e-07
(0.000361) 		8.54e-09
(6.45e-06) 		0.0796
(1.00) 		0.0065
(1.00)
2q loss 0 (0%) 493 0.000249
(0.163) 		0.000389
(0.253) 		2.38e-06
(0.00172) 		1
(1.00) 		0.000129
(0.0859) 		4.42e-05
(0.03) 		8.96e-08
(6.68e-05) 		7.91e-08
(5.92e-05) 		0.000199
(0.131) 		4.81e-12
(3.72e-09) 		1
(1.00) 		0.0184
(1.00)
12q gain 0 (0%) 423 0.194
(1.00) 		0.201
(1.00) 		6.42e-09
(4.86e-06) 		0.00273
(1.00) 		1.46e-07
(0.000109) 		0.0104
(1.00) 		6.06e-06
(0.00429) 		9.22e-06
(0.00648) 		3.21e-06
(0.00231) 		0.621
(1.00) 		1.15e-06
(0.000841) 		0.000333
(0.217)
20q gain 0 (0%) 435 0.0753
(1.00) 		0.106
(1.00) 		1.37e-15
(1.08e-12) 		0.00198
(1.00) 		3.54e-05
(0.0242) 		0.000855
(0.537) 		3.3e-07
(0.000244) 		1.47e-06
(0.00107) 		1.83e-07
(0.000136) 		0.035
(1.00) 		2.6e-09
(1.98e-06) 		5.31e-06
(0.00378)
2p loss 0 (0%) 494 0.000249
(0.163) 		0.000389
(0.253) 		6.13e-07
(0.00045) 		0.47
(1.00) 		1.37e-05
(0.00955) 		0.000189
(0.125) 		4.72e-07
(0.000349) 		1.87e-08
(1.41e-05) 		0.000598
(0.382) 		1.25e-12
(9.75e-10) 		1
(1.00) 		0.0184
(1.00)
9p loss 0 (0%) 415 0.378
(1.00) 		0.124
(1.00) 		6.57e-33
(5.16e-30) 		2.97e-12
(2.3e-09) 		0.00463
(1.00) 		0.00726
(1.00) 		1.39e-11
(1.07e-08) 		2.71e-12
(2.1e-09) 		8.73e-09
(6.59e-06) 		0.201
(1.00) 		9.03e-07
(0.000661) 		1.17e-05
(0.00816)
9q loss 0 (0%) 410 0.378
(1.00) 		0.124
(1.00) 		2.79e-34
(2.19e-31) 		2.78e-13
(2.17e-10) 		0.000999
(0.618) 		0.0104
(1.00) 		1.31e-12
(1.02e-09) 		3.94e-14
(3.08e-11) 		3.82e-10
(2.92e-07) 		0.173
(1.00) 		9.45e-07
(0.000691) 		3.28e-05
(0.0224)
14q loss 0 (0%) 342 0.00179
(1.00) 		0.00197
(1.00) 		7.35e-13
(5.73e-10) 		6.25e-05
(0.0422) 		6.61e-12
(5.11e-09) 		2.08e-07
(0.000154) 		6.97e-11
(5.35e-08) 		2.8e-07
(0.000208) 		4.33e-06
(0.0031) 		0.507
(1.00) 		0.0316
(1.00) 		0.013
(1.00)
17q loss 0 (0%) 492 0.000668
(0.426) 		0.000893
(0.558) 		6.84e-06
(0.00483) 		0.47
(1.00) 		1.46e-05
(0.0102) 		1.02e-05
(0.00717) 		1.91e-06
(0.00139) 		7.91e-08
(5.92e-05) 		8.98e-05
(0.0604) 		4.05e-11
(3.12e-08) 		1
(1.00) 		0.0184
(1.00)
8q gain 0 (0%) 468 0.0536
(1.00) 		0.0623
(1.00) 		5.94e-11
(4.57e-08) 		0.000613
(0.391) 		0.0102
(1.00) 		0.0449
(1.00) 		1.15e-07
(8.55e-05) 		4.88e-05
(0.033) 		6.77e-06
(0.00478) 		0.0182
(1.00) 		2.12e-06
(0.00154) 		0.000124
(0.0825)
12p gain 0 (0%) 424 0.194
(1.00) 		0.201
(1.00) 		1.35e-08
(1.02e-05) 		0.00273
(1.00) 		5.67e-07
(0.000417) 		0.0139
(1.00) 		1.1e-05
(0.00772) 		1.89e-05
(0.0131) 		6.95e-06
(0.0049) 		0.712
(1.00) 		3.36e-06
(0.00242) 		0.000958
(0.596)
20p gain 0 (0%) 437 0.102
(1.00) 		0.149
(1.00) 		1.93e-14
(1.51e-11) 		0.00198
(1.00) 		0.000453
(0.292) 		0.000979
(0.607) 		3.59e-06
(0.00258) 		5.29e-06
(0.00377) 		2.54e-06
(0.00184) 		0.0344
(1.00) 		2.98e-08
(2.23e-05) 		4.59e-05
(0.0311)
1p loss 0 (0%) 472 0.000836
(0.527) 		5.38e-05
(0.0363) 		2.77e-05
(0.019) 		0.475
(1.00) 		5.05e-08
(3.79e-05) 		0.000435
(0.281) 		0.0123
(1.00) 		4.64e-06
(0.00332) 		0.0187
(1.00) 		1.01e-10
(7.71e-08) 		0.623
(1.00) 		0.0283
(1.00)
6p loss 0 (0%) 445 0.0139
(1.00) 		0.00408
(1.00) 		7.13e-11
(5.47e-08) 		0.00277
(1.00) 		0.000122
(0.0811) 		7.03e-06
(0.00495) 		0.000722
(0.457) 		0.00105
(0.648) 		2.87e-09
(2.18e-06) 		0.000394
(0.256) 		0.000973
(0.604) 		0.000155
(0.103)
18p loss 0 (0%) 458 0.194
(1.00) 		0.486
(1.00) 		4.41e-05
(0.03) 		0.0278
(1.00) 		0.0183
(1.00) 		0.00473
(1.00) 		6.06e-06
(0.00429) 		0.000196
(0.129) 		0.00036
(0.234) 		0.00262
(1.00) 		0.000736
(0.465) 		0.000194
(0.129)
1q loss 0 (0%) 484 0.0107
(1.00) 		0.0133
(1.00) 		6.85e-07
(0.000502) 		1
(1.00) 		0.000863
(0.541) 		0.00112
(0.685) 		1.9e-05
(0.0131) 		3.17e-06
(0.00229) 		0.0841
(1.00) 		4.22e-10
(3.22e-07) 		0.224
(1.00) 		0.00732
(1.00)
3q gain 0 (0%) 475 0.0249
(1.00) 		0.0289
(1.00) 		4.38e-07
(0.000324) 		0.0525
(1.00) 		0.00718
(1.00) 		0.000107
(0.0718) 		0.000705
(0.447) 		0.00522
(1.00) 		0.000126
(0.0839) 		0.00416
(1.00) 		0.00124
(0.759) 		0.21
(1.00)
21q loss 0 (0%) 470 0.0145
(1.00) 		0.0238
(1.00) 		0.000106
(0.0711) 		0.151
(1.00) 		0.00501
(1.00) 		0.0399
(1.00) 		0.00192
(1.00) 		1.72e-05
(0.0119) 		0.24
(1.00) 		9.51e-06
(0.00668) 		0.587
(1.00) 		0.116
(1.00)
7p gain 0 (0%) 376 0.877
(1.00) 		1
(1.00) 		1.75e-09
(1.33e-06) 		0.04
(1.00) 		0.000268
(0.176) 		0.00565
(1.00) 		0.068
(1.00) 		0.0824
(1.00) 		0.0251
(1.00) 		0.703
(1.00) 		0.0171
(1.00) 		0.282
(1.00)
7q gain 0 (0%) 374 0.877
(1.00) 		1
(1.00) 		1.84e-09
(1.4e-06) 		0.0297
(1.00) 		0.000118
(0.0787) 		0.000718
(0.455) 		0.0581
(1.00) 		0.131
(1.00) 		0.0129
(1.00) 		0.481
(1.00) 		0.00518
(1.00) 		0.0994
(1.00)
6q loss 0 (0%) 419 0.0393
(1.00) 		0.0205
(1.00) 		2.46e-09
(1.87e-06) 		0.133
(1.00) 		0.0014
(0.852) 		0.00103
(0.637) 		0.204
(1.00) 		0.478
(1.00) 		1.42e-05
(0.00993) 		0.00226
(1.00) 		0.0312
(1.00) 		0.00118
(0.721)
13q loss 0 (0%) 473 0.0253
(1.00) 		0.0381
(1.00) 		5.97e-06
(0.00424) 		0.0888
(1.00) 		0.00137
(0.838) 		0.00139
(0.845) 		0.0025
(1.00) 		0.00046
(0.296) 		0.000838
(0.527) 		0.000285
(0.186) 		0.0343
(1.00) 		0.00149
(0.901)
18q loss 0 (0%) 456 0.259
(1.00) 		0.302
(1.00) 		6.3e-05
(0.0425) 		0.0468
(1.00) 		0.0551
(1.00) 		0.0128
(1.00) 		2.87e-05
(0.0197) 		0.000574
(0.367) 		0.000948
(0.591) 		0.00546
(1.00) 		0.000516
(0.331) 		0.000923
(0.576)
1q gain 0 (0%) 472 0.611
(1.00) 		0.617
(1.00) 		2.09e-08
(1.57e-05) 		0.61
(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) 		0.322
(1.00) 		0.387
(1.00)
2p gain 0 (0%) 455 0.561
(1.00) 		0.4
(1.00) 		1.96e-05
(0.0135) 		0.579
(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) 		0.232
(1.00) 		0.605
(1.00)
5p gain 0 (0%) 361 0.593
(1.00) 		0.516
(1.00) 		0.000273
(0.179) 		0.196
(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) 		0.118
(1.00) 		0.0296
(1.00)
8p gain 0 (0%) 488 1.74e-05
(0.012) 		0.0635
(1.00) 		0.0868
(1.00) 		0.146
(1.00) 		0.000978
(0.607) 		0.000683
(0.434) 		0.00302
(1.00) 		0.117
(1.00) 		0.00296
(1.00) 		0.0467
(1.00)
19p gain 0 (0%) 479 0.189
(1.00) 		0.207
(1.00) 		1.47e-05
(0.0102) 		0.288
(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) 		0.0165
(1.00) 		0.309
(1.00)
19q gain 0 (0%) 476 0.0536
(1.00) 		0.0623
(1.00) 		1.53e-06
(0.00112) 		0.207
(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) 		0.00758
(1.00) 		0.184
(1.00)
3q loss 0 (0%) 430 0.701
(1.00) 		0.7
(1.00) 		2.72e-06
(0.00196) 		0.194
(1.00) 		0.0955
(1.00) 		0.00661
(1.00) 		0.518
(1.00) 		0.804
(1.00) 		0.822
(1.00) 		0.00747
(1.00) 		0.162
(1.00) 		0.221
(1.00)
4q loss 0 (0%) 476 1
(1.00) 		1
(1.00) 		2.66e-05
(0.0183) 		0.112
(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) 		0.227
(1.00) 		0.196
(1.00)
10p loss 0 (0%) 472 0.026
(1.00) 		0.0306
(1.00) 		3.88e-06
(0.00278) 		0.157
(1.00) 		0.195
(1.00) 		0.037
(1.00) 		0.0123
(1.00) 		0.0197
(1.00) 		0.155
(1.00) 		0.00047
(0.302) 		0.19
(1.00) 		0.0504
(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) 		0.457
(1.00) 		1
(1.00)
2q gain 0 (0%) 454 0.561
(1.00) 		0.4
(1.00) 		0.000406
(0.263) 		0.479
(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) 		0.497
(1.00) 		0.397
(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) 		0.0114
(1.00) 		0.0528
(1.00) 		0.335
(1.00) 		0.47
(1.00)
4p gain 0 (0%) 496 0.121
(1.00) 		0.615
(1.00) 		0.428
(1.00) 		0.0803
(1.00) 		0.0257
(1.00) 		0.378
(1.00) 		0.0005
(0.321) 		0.0407
(1.00)
4q gain 0 (0%) 496 0.486
(1.00) 		0.79
(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)
5q gain 0 (0%) 345 0.105
(1.00) 		0.0689
(1.00) 		0.00308
(1.00) 		0.186
(1.00) 		0.158
(1.00) 		0.175
(1.00) 		0.0381
(1.00) 		0.00512
(1.00) 		0.116
(1.00) 		0.00141
(0.857) 		0.357
(1.00) 		0.0413
(1.00)
6p gain 0 (0%) 498 0.876
(1.00) 		0.683
(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%) 499 0.536
(1.00) 		0.615
(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%) 496 0.385
(1.00) 		0.79
(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) 		0.0549
(1.00) 		0.577
(1.00)
9q gain 0 (0%) 496 0.068
(1.00) 		0.456
(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) 		0.163
(1.00) 		0.817
(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) 		0.77
(1.00) 		0.389
(1.00) 		1
(1.00) 		1
(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) 		0.832
(1.00) 		0.367
(1.00)
11p gain 0 (0%) 487 0.769
(1.00) 		0.783
(1.00) 		0.0169
(1.00) 		0.659
(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) 		0.259
(1.00) 		0.634
(1.00)
11q gain 0 (0%) 489 0.769
(1.00) 		0.783
(1.00) 		0.0471
(1.00) 		0.572
(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) 		0.538
(1.00) 		1
(1.00)
13q gain 0 (0%) 490 0.832
(1.00) 		0.0545
(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) 		0.902
(1.00) 		0.731
(1.00)
14q gain 0 (0%) 499 0.061
(1.00) 		0.615
(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%) 490 0.0652
(1.00) 		0.577
(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) 		0.459
(1.00) 		0.62
(1.00)
16p gain 0 (0%) 436 0.1
(1.00) 		0.302
(1.00) 		0.105
(1.00) 		0.642
(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) 		0.0657
(1.00) 		0.17
(1.00)
16q gain 0 (0%) 443 0.0706
(1.00) 		0.174
(1.00) 		0.101
(1.00) 		0.892
(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) 		0.0542
(1.00) 		0.353
(1.00)
17p gain 0 (0%) 488 0.00522
(1.00) 		0.00665
(1.00) 		0.00405
(1.00) 		0.425
(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) 		0.335
(1.00) 		0.109
(1.00)
17q gain 0 (0%) 482 0.00827
(1.00) 		0.0106
(1.00) 		0.00919
(1.00) 		0.162
(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) 		0.0596
(1.00) 		0.0793
(1.00)
18p gain 0 (0%) 486 0.0764
(1.00) 		0.0436
(1.00) 		0.436
(1.00) 		0.156
(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) 		0.417
(1.00) 		0.264
(1.00)
18q gain 0 (0%) 486 0.0764
(1.00) 		0.0436
(1.00) 		0.436
(1.00) 		0.156
(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) 		0.417
(1.00) 		0.264
(1.00)
21q gain 0 (0%) 469 0.82
(1.00) 		0.818
(1.00) 		0.000757
(0.478) 		0.0946
(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) 		0.042
(1.00) 		0.00389
(1.00)
22q gain 0 (0%) 479 0.58
(1.00) 		0.0436
(1.00) 		0.00243
(1.00) 		0.0475
(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) 		0.453
(1.00) 		0.862
(1.00)
Xq gain 0 (0%) 495 0.472
(1.00) 		0.851
(1.00) 		0.126
(1.00) 		0.338
(1.00) 		0.0651
(1.00) 		0.153
(1.00) 		0.198
(1.00) 		0.163
(1.00) 		1
(1.00) 		0.731
(1.00)
4p loss 0 (0%) 469 0.289
(1.00) 		0.298
(1.00) 		0.00354
(1.00) 		0.132
(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) 		0.436
(1.00) 		0.499
(1.00)
8p loss 0 (0%) 405 0.777
(1.00) 		0.784
(1.00) 		0.00339
(1.00) 		0.654
(1.00) 		0.738
(1.00) 		0.656
(1.00) 		0.141
(1.00) 		0.561
(1.00) 		0.158
(1.00) 		0.423
(1.00) 		0.446
(1.00) 		0.521
(1.00)
8q loss 0 (0%) 464 0.49
(1.00) 		0.591
(1.00) 		0.934
(1.00) 		0.151
(1.00) 		0.476
(1.00) 		0.7
(1.00) 		0.188
(1.00) 		0.0552
(1.00) 		0.91
(1.00) 		0.272
(1.00) 		0.501
(1.00) 		0.258
(1.00)
10q loss 0 (0%) 456 0.0972
(1.00) 		0.121
(1.00) 		0.00107
(0.659) 		0.015
(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) 		0.506
(1.00) 		0.0151
(1.00)
11p loss 0 (0%) 499 0.0313
(1.00) 		0.615
(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%) 497 0.00534
(1.00) 		0.827
(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) 		0.335
(1.00) 		0.109
(1.00)
15q loss 0 (0%) 492 0.58
(1.00) 		0.586
(1.00) 		0.00461
(1.00) 		0.456
(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) 		0.0596
(1.00) 		0.0793
(1.00)
16q loss 0 (0%) 498 0.244
(1.00) 		0.345
(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) 		0.826
(1.00) 		0.0348
(1.00)
19p loss 0 (0%) 500 0.126
(1.00) 		0.345
(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%) 498 0.209
(1.00) 		1
(1.00) 		0.0172
(1.00) 		0.877
(1.00) 		0.267
(1.00) 		0.747
(1.00) 		0.0721
(1.00) 		0.232
(1.00)
22q loss 0 (0%) 492 0.00143
(0.865) 		0.0112
(1.00) 		0.0462
(1.00) 		0.393
(1.00) 		0.000888
(0.556) 		0.0191
(1.00) 		0.363
(1.00) 		0.531
(1.00) 		0.612
(1.00) 		0.113
(1.00)
Xq loss 0 (0%) 494 0.256
(1.00) 		0.272
(1.00) 		0.717
(1.00) 		0.626
(1.00) 		0.31
(1.00) 		0.287
(1.00) 		0.0676
(1.00) 		0.00763
(1.00) 		0.0308
(1.00) 		0.0428
(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 = 0.013

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 = 0.000126 (Fisher's exact test), Q value = 0.084

Table S5.  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 20
3Q GAIN WILD-TYPE 110 188 149

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'

'8q gain' versus 'CN_CNMF'

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

Table S12.  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 S12.  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 = 8.5e-05

Table S13.  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 S13.  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 S14.  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 S14.  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 = 0.0048

Table S15.  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 S15.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.0015

Table S16.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
8Q GAIN CNV 0 0 12
8Q GAIN WILD-TYPE 50 89 62

Figure S16.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000124 (Fisher's exact test), Q value = 0.083

Table S17.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
8Q GAIN CNV 9 0 3
8Q GAIN WILD-TYPE 48 92 61

Figure S17.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

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

Table S18.  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 S18.  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 S19.  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 S19.  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 S20.  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 S20.  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 S21.  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 S21.  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 = 0.0049

Table S22.  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 S22.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.36e-06 (Fisher's exact test), Q value = 0.0024

Table S23.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
12P GAIN CNV 5 4 24
12P GAIN WILD-TYPE 45 85 50

Figure S23.  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 S24.  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 S24.  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 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 22
12Q GAIN WILD-TYPE 96 79 64 66 37 35

Figure S25.  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 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 46 12
12Q GAIN WILD-TYPE 182 133 85

Figure S26.  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 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 48
12Q GAIN WILD-TYPE 62 196 142

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

'12q gain' versus 'MIRSEQ_CNMF'

P value = 3.21e-06 (Fisher's exact test), Q value = 0.0023

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 48
12Q GAIN WILD-TYPE 102 173 121

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

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00084

Table S29.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
12Q GAIN CNV 5 4 25
12Q GAIN WILD-TYPE 45 85 49

Figure S29.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000333 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
12Q GAIN CNV 19 8 7
12Q GAIN WILD-TYPE 38 84 57

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

'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 = 2.54e-06 (Fisher's exact test), Q value = 0.0018

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'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.98e-08 (Fisher's exact test), Q value = 2.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
20P GAIN CNV 3 1 22
20P GAIN WILD-TYPE 47 88 52

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

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.59e-05 (Fisher's exact test), Q value = 0.031

Table S38.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
20P GAIN CNV 16 3 7
20P GAIN WILD-TYPE 41 89 57

Figure S38.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

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

Table S39.  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 S39.  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 S40.  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 S40.  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 S41.  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 S41.  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 S42.  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 S42.  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 = 0.00014

Table S43.  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 S43.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.6e-09 (Fisher's exact test), Q value = 2e-06

Table S44.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
20Q GAIN CNV 3 1 24
20Q GAIN WILD-TYPE 47 88 50

Figure S44.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.31e-06 (Fisher's exact test), Q value = 0.0038

Table S45.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
20Q GAIN CNV 18 3 7
20Q GAIN WILD-TYPE 39 89 57

Figure S45.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 5.38e-05 (Fisher's exact test), Q value = 0.036

Table S46.  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 S46.  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 S47.  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 S47.  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 S48.  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 S48.  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 S49.  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 S49.  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 = 7.7e-08

Table S50.  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 S50.  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 S51.  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 S51.  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 S52.  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 S52.  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 S53.  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 S53.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.22e-10 (Fisher's exact test), Q value = 3.2e-07

Table S54.  Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 160 280
1Q LOSS CNV 12 3 5
1Q LOSS WILD-TYPE 23 157 275

Figure S54.  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 S55.  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 S55.  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 S56.  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 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 = 0.0096

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 = 0.13

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 = 0.00035

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 = 1.4e-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 = 9.8e-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 = 0.16

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 'CN_CNMF'

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

Table S63.  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 S63.  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 = 0.086

Table S64.  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 S64.  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 S65.  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 S65.  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 S66.  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 S66.  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 = 5.9e-05

Table S67.  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 S67.  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 = 0.13

Table S68.  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 S68.  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 = 3.7e-09

Table S69.  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 S69.  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 S70.  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 S70.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0039

Table S71.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
3P LOSS CNV 65 91 29
3P LOSS WILD-TYPE 34 28 42

Figure S71.  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 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 55 40 33 26
3P LOSS WILD-TYPE 23 41 29 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 = 1.54e-05 (Fisher's exact test), Q value = 0.011

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 130 101 47
3P LOSS WILD-TYPE 56 51 62

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

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 = 5.4e-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 = 0.029

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 = 1.49e-14 (Fisher's exact test), Q value = 1.2e-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 74 210
3P LOSS WILD-TYPE 28 86 70

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

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.64e-05 (Fisher's exact test), Q value = 0.025

Table S78.  Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
3P LOSS CNV 35 69 25
3P LOSS WILD-TYPE 22 23 39

Figure S78.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

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

Table S79.  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 S79.  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 S80.  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 S80.  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 S81.  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 S81.  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 = 0.081

Table S82.  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 S82.  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 S83.  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 S83.  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 = 2.2e-06

Table S84.  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 S84.  Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000155 (Fisher's exact test), Q value = 0.1

Table S85.  Gene #49: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
6P LOSS CNV 14 3 4
6P LOSS WILD-TYPE 43 89 60

Figure S85.  Get High-res Image Gene #49: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

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

Table S86.  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 S86.  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 = 0.0099

Table S87.  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 S87.  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 S88.  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 S88.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 2.97e-12 (Fisher's exact test), Q value = 2.3e-09

Table S89.  Gene #53: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
9P LOSS CNV 39 3 11
9P LOSS WILD-TYPE 60 116 60

Figure S89.  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 S90.  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 S90.  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 S91.  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 S91.  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 = 6.6e-06

Table S92.  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 S92.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.03e-07 (Fisher's exact test), Q value = 0.00066

Table S93.  Gene #53: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
9P LOSS CNV 5 6 28
9P LOSS WILD-TYPE 45 83 46

Figure S93.  Get High-res Image Gene #53: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0082

Table S94.  Gene #53: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
9P LOSS CNV 23 9 7
9P LOSS WILD-TYPE 34 83 57

Figure S94.  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 S95.  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 S95.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 2.78e-13 (Fisher's exact test), Q value = 2.2e-10

Table S96.  Gene #54: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
9Q LOSS CNV 41 3 11
9Q LOSS WILD-TYPE 58 116 60

Figure S96.  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 S97.  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 S97.  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 S98.  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 S98.  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 = 2.9e-07

Table S99.  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 S99.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.45e-07 (Fisher's exact test), Q value = 0.00069

Table S100.  Gene #54: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 89 74
9Q LOSS CNV 5 8 30
9Q LOSS WILD-TYPE 45 81 44

Figure S100.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.28e-05 (Fisher's exact test), Q value = 0.022

Table S101.  Gene #54: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
9Q LOSS CNV 24 11 8
9Q LOSS WILD-TYPE 33 81 56

Figure S101.  Get High-res Image Gene #54: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

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

Table S102.  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 S102.  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 = 0.0042

Table S103.  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 S103.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000285 (Fisher's exact test), Q value = 0.19

Table S104.  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 S104.  Get High-res Image Gene #59: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 7.35e-13 (Fisher's exact test), Q value = 5.7e-10

Table S105.  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 S105.  Get High-res Image Gene #60: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 6.25e-05 (Fisher's exact test), Q value = 0.042

Table S106.  Gene #60: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 119 71
14Q LOSS CNV 44 21 25
14Q LOSS WILD-TYPE 55 98 46

Figure S106.  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 S107.  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 S107.  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 S108.  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 S108.  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 S109.  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 S109.  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 S110.  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 S110.  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 = 0.0031

Table S111.  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 S111.  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 = 0.078

Table S112.  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 S112.  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 S113.  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 S113.  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 S114.  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 S114.  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 S115.  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 S115.  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 S116.  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 S116.  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 S117.  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 S117.  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 S118.  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 S118.  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 = 0.00036

Table S119.  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 S119.  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 = 6.5e-06

Table S120.  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 S120.  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 = 0.0048

Table S121.  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 S121.  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 S122.  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 S122.  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 S123.  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 S123.  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 S124.  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 S124.  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 = 5.9e-05

Table S125.  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 S125.  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 = 0.06

Table S126.  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 S126.  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 = 3.1e-08

Table S127.  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 S127.  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 S128.  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 S128.  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 S129.  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 S129.  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 S130.  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 S130.  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 = 0.23

Table S131.  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 S131.  Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000194 (Fisher's exact test), Q value = 0.13

Table S132.  Gene #65: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 92 64
18P LOSS CNV 13 2 8
18P LOSS WILD-TYPE 44 90 56

Figure S132.  Get High-res Image Gene #65: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 6.3e-05 (Fisher's exact test), Q value = 0.042

Table S133.  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 S133.  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 S134.  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 S134.  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 = 0.071

Table S135.  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 S135.  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 S136.  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 S136.  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 = 0.0067

Table S137.  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 S137.  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

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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