Correlation between copy number variations of arm-level result and molecular subtypes
Colorectal Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1833QDS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1833QDS
Overview
Introduction

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

Summary

Testing the association between copy number variation 79 arm-level events and 12 molecular subtypes across 589 patients, 122 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 2p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 7q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF'.

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

  • 11p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 13q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 17q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 18p gain cnv correlated to 'METHLYATION_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 4p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 10p loss cnv correlated to 'CN_CNMF'.

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

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 12q loss cnv correlated to 'CN_CNMF'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 15q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 17p loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 18p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 18q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 19p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 122 significant findings detected.

Clinical
Features 		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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
13q gain 354 (60%) 235 4.11e-07
(0.000363) 		5.38e-05
(0.0456) 		2.98e-35
(2.8e-32) 		1.78e-07
(0.000158) 		0.243
(1.00) 		0.422
(1.00) 		1.26e-07
(0.000112) 		5.81e-07
(0.000512) 		0.000631
(0.506) 		0.35
(1.00) 		3.19e-07
(0.000282) 		0.0477
(1.00)
20q gain 446 (76%) 143 1.25e-13
(1.15e-10) 		5.16e-13
(4.71e-10) 		1.04e-33
(9.77e-31) 		1.05e-17
(9.67e-15) 		0.00527
(1.00) 		0.0128
(1.00) 		1.45e-18
(1.34e-15) 		3.41e-14
(3.13e-11) 		0.0203
(1.00) 		0.151
(1.00) 		4.8e-12
(4.37e-09) 		0.000476
(0.386)
14q loss 193 (33%) 396 0.000264
(0.218) 		4.45e-05
(0.0379) 		6.8e-27
(6.35e-24) 		1.88e-06
(0.00164) 		0.00258
(1.00) 		0.0986
(1.00) 		7.26e-11
(6.59e-08) 		3.6e-05
(0.0308) 		0.133
(1.00) 		0.963
(1.00) 		1.2e-07
(0.000107) 		0.118
(1.00)
18p loss 362 (61%) 227 1.91e-12
(1.74e-09) 		3.54e-10
(3.21e-07) 		1.71e-39
(1.6e-36) 		2.24e-22
(2.08e-19) 		0.0286
(1.00) 		0.018
(1.00) 		9.48e-22
(8.82e-19) 		7.19e-17
(6.63e-14) 		0.00979
(1.00) 		0.485
(1.00) 		3.39e-16
(3.12e-13) 		0.000307
(0.251)
18q loss 388 (66%) 201 1.39e-11
(1.26e-08) 		3.68e-10
(3.33e-07) 		1.09e-40
(1.02e-37) 		9.38e-20
(8.69e-17) 		0.0493
(1.00) 		0.0838
(1.00) 		3.96e-18
(3.66e-15) 		1.66e-15
(1.53e-12) 		0.000834
(0.664) 		0.128
(1.00) 		6.09e-14
(5.59e-11) 		0.00137
(1.00)
7q gain 298 (51%) 291 0.000158
(0.132) 		0.00167
(1.00) 		2.03e-13
(1.86e-10) 		0.00025
(0.207) 		0.134
(1.00) 		0.106
(1.00) 		1.62e-07
(0.000145) 		3.47e-07
(0.000307) 		0.0132
(1.00) 		0.043
(1.00) 		4.69e-05
(0.0399) 		0.227
(1.00)
17p loss 323 (55%) 266 2.78e-05
(0.0238) 		0.000448
(0.364) 		3.13e-26
(2.92e-23) 		2.37e-08
(2.13e-05) 		0.122
(1.00) 		0.111
(1.00) 		1.02e-06
(0.000897) 		2.72e-07
(0.000241) 		0.0353
(1.00) 		0.0366
(1.00) 		1.06e-06
(0.000929) 		0.276
(1.00)
7p gain 334 (57%) 255 0.000461
(0.374) 		0.000339
(0.277) 		3.28e-21
(3.05e-18) 		4.75e-06
(0.00414) 		0.00902
(1.00) 		0.0301
(1.00) 		1.63e-08
(1.46e-05) 		3.36e-09
(3.01e-06) 		0.00584
(1.00) 		0.0044
(1.00) 		7.29e-06
(0.00631) 		0.532
(1.00)
11q gain 73 (12%) 516 0.0173
(1.00) 		0.0108
(1.00) 		1.66e-07
(0.000148) 		8.01e-05
(0.0676) 		0.194
(1.00) 		0.596
(1.00) 		1.02e-06
(0.000896) 		3.26e-06
(0.00284) 		0.297
(1.00) 		0.0676
(1.00) 		0.000128
(0.107) 		0.237
(1.00)
20p gain 338 (57%) 251 0.000241
(0.199) 		1.74e-06
(0.00153) 		5.11e-10
(4.62e-07) 		0.000272
(0.224) 		0.0187
(1.00) 		0.163
(1.00) 		0.000108
(0.0905) 		0.000597
(0.48) 		0.343
(1.00) 		0.609
(1.00) 		0.000656
(0.526) 		0.759
(1.00)
15q loss 217 (37%) 372 0.000102
(0.086) 		0.00117
(0.922) 		1.75e-21
(1.63e-18) 		0.00122
(0.964) 		0.237
(1.00) 		0.379
(1.00) 		1.08e-05
(0.00936) 		4.21e-07
(0.000371) 		0.825
(1.00) 		0.618
(1.00) 		6.48e-06
(0.00562) 		0.233
(1.00)
4p loss 185 (31%) 404 0.0291
(1.00) 		0.137
(1.00) 		4.23e-12
(3.85e-09) 		0.000933
(0.741) 		0.475
(1.00) 		0.819
(1.00) 		0.000289
(0.237) 		2.71e-05
(0.0233) 		0.081
(1.00) 		0.0823
(1.00) 		6.28e-05
(0.0531) 		0.151
(1.00)
8q gain 303 (51%) 286 0.347
(1.00) 		0.0114
(1.00) 		4.7e-39
(4.41e-36) 		0.0212
(1.00) 		0.0885
(1.00) 		0.125
(1.00) 		2.42e-05
(0.0208) 		1.11e-05
(0.00953) 		0.357
(1.00) 		0.369
(1.00) 		0.0615
(1.00) 		0.275
(1.00)
11p gain 80 (14%) 509 0.0131
(1.00) 		0.0306
(1.00) 		1.2e-07
(0.000107) 		0.000103
(0.0864) 		0.661
(1.00) 		0.591
(1.00) 		0.000771
(0.615) 		0.000276
(0.227) 		0.283
(1.00) 		0.0922
(1.00) 		0.00827
(1.00) 		0.672
(1.00)
16p gain 141 (24%) 448 0.0118
(1.00) 		0.0373
(1.00) 		8.61e-20
(7.98e-17) 		0.014
(1.00) 		0.165
(1.00) 		0.218
(1.00) 		5.54e-05
(0.0469) 		3.36e-05
(0.0287) 		0.472
(1.00) 		0.958
(1.00) 		0.0157
(1.00) 		0.208
(1.00)
16q gain 138 (23%) 451 0.00855
(1.00) 		0.0139
(1.00) 		6.55e-21
(6.08e-18) 		0.0258
(1.00) 		0.232
(1.00) 		0.203
(1.00) 		0.000186
(0.154) 		1.7e-05
(0.0146) 		0.792
(1.00) 		0.843
(1.00) 		0.00281
(1.00) 		0.0722
(1.00)
4q loss 178 (30%) 411 0.0424
(1.00) 		0.159
(1.00) 		1.21e-14
(1.12e-11) 		5.46e-06
(0.00475) 		0.756
(1.00) 		0.507
(1.00) 		0.00057
(0.46) 		0.000101
(0.0844) 		0.104
(1.00) 		0.0531
(1.00) 		0.00104
(0.82) 		0.0107
(1.00)
9q loss 70 (12%) 519 0.0498
(1.00) 		0.0356
(1.00) 		4.74e-05
(0.0403) 		0.00123
(0.969) 		0.929
(1.00) 		0.0321
(1.00) 		0.000187
(0.155) 		0.0106
(1.00) 		0.467
(1.00) 		0.022
(1.00) 		0.000212
(0.176) 		0.0218
(1.00)
10q loss 104 (18%) 485 0.0235
(1.00) 		0.293
(1.00) 		5.21e-12
(4.74e-09) 		0.0102
(1.00) 		0.0138
(1.00) 		0.367
(1.00) 		0.000119
(0.0993) 		4.93e-05
(0.0418) 		0.684
(1.00) 		0.219
(1.00) 		0.000434
(0.353) 		0.000582
(0.469)
2p gain 114 (19%) 475 0.0414
(1.00) 		0.00516
(1.00) 		0.000271
(0.223) 		0.00609
(1.00) 		0.617
(1.00) 		0.33
(1.00) 		2.17e-06
(0.0019) 		0.00119
(0.944) 		0.0449
(1.00) 		0.0092
(1.00) 		0.243
(1.00) 		0.000786
(0.626)
2q gain 112 (19%) 477 0.0273
(1.00) 		0.00183
(1.00) 		6.32e-06
(0.00548) 		0.00157
(1.00) 		0.645
(1.00) 		0.57
(1.00) 		0.000252
(0.208) 		0.00121
(0.957) 		0.111
(1.00) 		0.0429
(1.00) 		0.419
(1.00) 		0.0421
(1.00)
17q gain 106 (18%) 483 0.012
(1.00) 		0.0121
(1.00) 		9.19e-05
(0.0775) 		0.00604
(1.00) 		0.275
(1.00) 		0.266
(1.00) 		5.69e-06
(0.00494) 		0.00723
(1.00) 		0.00239
(1.00) 		0.0948
(1.00) 		0.393
(1.00) 		0.521
(1.00)
1p loss 130 (22%) 459 0.0667
(1.00) 		0.037
(1.00) 		1.92e-07
(0.000171) 		0.000579
(0.467) 		0.984
(1.00) 		0.609
(1.00) 		0.00374
(1.00) 		2.15e-05
(0.0184) 		0.286
(1.00) 		0.115
(1.00) 		0.0449
(1.00) 		0.0264
(1.00)
1q loss 73 (12%) 516 0.236
(1.00) 		0.0545
(1.00) 		9.69e-06
(0.00837) 		0.312
(1.00) 		0.86
(1.00) 		0.735
(1.00) 		0.000276
(0.227) 		0.0015
(1.00) 		0.746
(1.00) 		0.0296
(1.00) 		0.133
(1.00) 		0.0073
(1.00)
8p loss 206 (35%) 383 0.00923
(1.00) 		0.00744
(1.00) 		6.02e-29
(5.63e-26) 		3.86e-05
(0.0329) 		0.328
(1.00) 		0.0081
(1.00) 		0.00329
(1.00) 		0.00396
(1.00) 		0.543
(1.00) 		0.114
(1.00) 		0.00102
(0.812) 		0.0383
(1.00)
19p loss 61 (10%) 528 0.373
(1.00) 		0.202
(1.00) 		9.68e-05
(0.0814) 		0.354
(1.00) 		0.689
(1.00) 		0.777
(1.00) 		0.0851
(1.00) 		0.012
(1.00) 		0.157
(1.00) 		0.000156
(0.13) 		0.487
(1.00) 		0.0138
(1.00)
21q loss 184 (31%) 405 0.0265
(1.00) 		0.039
(1.00) 		5.94e-06
(0.00516) 		0.0189
(1.00) 		0.704
(1.00) 		0.0904
(1.00) 		9.33e-05
(0.0786) 		0.00146
(1.00) 		0.124
(1.00) 		0.0757
(1.00) 		0.00274
(1.00) 		0.165
(1.00)
3p gain 68 (12%) 521 0.0149
(1.00) 		0.541
(1.00) 		1.91e-05
(0.0164) 		0.149
(1.00) 		0.127
(1.00) 		0.234
(1.00) 		0.395
(1.00) 		0.166
(1.00) 		0.148
(1.00) 		0.231
(1.00) 		0.06
(1.00) 		0.556
(1.00)
3q gain 94 (16%) 495 0.036
(1.00) 		0.0399
(1.00) 		6.1e-10
(5.51e-07) 		0.00772
(1.00) 		0.125
(1.00) 		0.207
(1.00) 		0.0185
(1.00) 		0.0106
(1.00) 		0.0442
(1.00) 		0.424
(1.00) 		0.00486
(1.00) 		0.745
(1.00)
6p gain 119 (20%) 470 0.0151
(1.00) 		0.00337
(1.00) 		3.14e-09
(2.82e-06) 		0.225
(1.00) 		0.851
(1.00) 		0.74
(1.00) 		0.0936
(1.00) 		0.0132
(1.00) 		0.451
(1.00) 		0.892
(1.00) 		0.0135
(1.00) 		0.317
(1.00)
6q gain 106 (18%) 483 0.163
(1.00) 		0.0453
(1.00) 		7.6e-10
(6.85e-07) 		0.243
(1.00) 		0.822
(1.00) 		0.25
(1.00) 		0.146
(1.00) 		0.052
(1.00) 		0.352
(1.00) 		0.445
(1.00) 		0.00267
(1.00) 		0.207
(1.00)
8p gain 163 (28%) 426 0.915
(1.00) 		0.432
(1.00) 		8.58e-08
(7.68e-05) 		0.899
(1.00) 		0.445
(1.00) 		0.0224
(1.00) 		0.00133
(1.00) 		0.00244
(1.00) 		0.231
(1.00) 		0.152
(1.00) 		0.765
(1.00) 		0.177
(1.00)
18p gain 30 (5%) 559 0.309
(1.00) 		0.101
(1.00) 		0.00828
(1.00) 		0.000268
(0.221) 		0.602
(1.00) 		0.684
(1.00) 		0.0819
(1.00) 		0.0195
(1.00) 		0.605
(1.00) 		0.146
(1.00) 		0.12
(1.00) 		0.748
(1.00)
19p gain 99 (17%) 490 0.416
(1.00) 		0.329
(1.00) 		3.21e-06
(0.0028) 		0.048
(1.00) 		0.16
(1.00) 		0.192
(1.00) 		0.266
(1.00) 		0.0949
(1.00) 		0.0792
(1.00) 		0.318
(1.00) 		0.0746
(1.00) 		0.123
(1.00)
19q gain 107 (18%) 482 0.0778
(1.00) 		0.0345
(1.00) 		6.66e-05
(0.0562) 		0.0832
(1.00) 		0.032
(1.00) 		0.281
(1.00) 		0.565
(1.00) 		0.237
(1.00) 		0.299
(1.00) 		0.753
(1.00) 		0.1
(1.00) 		0.078
(1.00)
xq gain 101 (17%) 488 0.258
(1.00) 		0.605
(1.00) 		0.000186
(0.154) 		0.197
(1.00) 		0.11
(1.00) 		0.0425
(1.00) 		0.475
(1.00) 		0.169
(1.00) 		0.351
(1.00) 		0.962
(1.00) 		0.696
(1.00) 		0.457
(1.00)
5q loss 113 (19%) 476 0.00934
(1.00) 		0.11
(1.00) 		1.96e-06
(0.00172) 		0.0318
(1.00) 		0.113
(1.00) 		0.608
(1.00) 		0.0244
(1.00) 		0.000711
(0.568) 		0.623
(1.00) 		0.116
(1.00) 		0.000559
(0.452) 		0.021
(1.00)
10p loss 96 (16%) 493 0.0118
(1.00) 		0.108
(1.00) 		3.5e-07
(0.000309) 		0.0309
(1.00) 		0.0181
(1.00) 		0.736
(1.00) 		0.000497
(0.403) 		0.00143
(1.00) 		0.211
(1.00) 		0.12
(1.00) 		0.0203
(1.00) 		0.00368
(1.00)
12p loss 68 (12%) 521 0.0698
(1.00) 		0.097
(1.00) 		7.8e-10
(7.02e-07) 		0.159
(1.00) 		0.864
(1.00) 		0.424
(1.00) 		0.0793
(1.00) 		0.0237
(1.00) 		0.818
(1.00) 		0.918
(1.00) 		0.00624
(1.00) 		0.113
(1.00)
12q loss 68 (12%) 521 0.13
(1.00) 		0.0506
(1.00) 		1.12e-09
(1.01e-06) 		0.109
(1.00) 		0.625
(1.00) 		0.713
(1.00) 		0.0154
(1.00) 		0.00894
(1.00) 		0.268
(1.00) 		0.601
(1.00) 		0.00806
(1.00) 		0.0759
(1.00)
22q loss 193 (33%) 396 0.0052
(1.00) 		0.00549
(1.00) 		4.47e-13
(4.08e-10) 		0.0242
(1.00) 		0.776
(1.00) 		0.908
(1.00) 		0.0314
(1.00) 		0.0102
(1.00) 		0.964
(1.00) 		0.38
(1.00) 		0.000696
(0.557) 		0.17
(1.00)
1p gain 46 (8%) 543 0.24
(1.00) 		0.408
(1.00) 		0.00742
(1.00) 		0.475
(1.00) 		0.00535
(1.00) 		0.0923
(1.00) 		0.989
(1.00) 		0.283
(1.00) 		0.305
(1.00) 		0.552
(1.00) 		0.0367
(1.00) 		0.561
(1.00)
1q gain 113 (19%) 476 0.759
(1.00) 		0.907
(1.00) 		0.00577
(1.00) 		0.336
(1.00) 		0.126
(1.00) 		0.131
(1.00) 		0.796
(1.00) 		0.11
(1.00) 		0.171
(1.00) 		0.067
(1.00) 		0.0152
(1.00) 		0.725
(1.00)
4p gain 17 (3%) 572 0.815
(1.00) 		0.462
(1.00) 		0.0046
(1.00) 		0.269
(1.00) 		0.154
(1.00) 		0.207
(1.00) 		0.0751
(1.00) 		0.456
(1.00) 		0.557
(1.00) 		1
(1.00) 		0.257
(1.00) 		0.0931
(1.00)
4q gain 19 (3%) 570 0.228
(1.00) 		0.26
(1.00) 		0.0521
(1.00) 		0.793
(1.00) 		0.114
(1.00) 		0.439
(1.00) 		0.137
(1.00) 		0.0257
(1.00) 		0.328
(1.00) 		0.0841
(1.00) 		0.0555
(1.00) 		0.771
(1.00)
5p gain 98 (17%) 491 0.494
(1.00) 		0.729
(1.00) 		0.000946
(0.751) 		0.856
(1.00) 		0.198
(1.00) 		0.885
(1.00) 		0.0151
(1.00) 		0.00999
(1.00) 		0.802
(1.00) 		0.89
(1.00) 		0.0153
(1.00) 		0.958
(1.00)
5q gain 62 (11%) 527 0.758
(1.00) 		0.901
(1.00) 		0.00221
(1.00) 		0.755
(1.00) 		0.713
(1.00) 		0.792
(1.00) 		0.234
(1.00) 		0.105
(1.00) 		0.733
(1.00) 		0.288
(1.00) 		0.286
(1.00) 		0.44
(1.00)
9p gain 116 (20%) 473 0.537
(1.00) 		0.793
(1.00) 		0.412
(1.00) 		0.532
(1.00) 		0.128
(1.00) 		0.417
(1.00) 		0.826
(1.00) 		0.216
(1.00) 		0.977
(1.00) 		0.621
(1.00) 		0.0829
(1.00) 		0.683
(1.00)
9q gain 98 (17%) 491 0.642
(1.00) 		0.375
(1.00) 		0.715
(1.00) 		0.803
(1.00) 		0.092
(1.00) 		0.244
(1.00) 		0.935
(1.00) 		0.77
(1.00) 		0.559
(1.00) 		0.941
(1.00) 		0.715
(1.00) 		0.903
(1.00)
10p gain 44 (7%) 545 0.109
(1.00) 		0.569
(1.00) 		0.107
(1.00) 		0.892
(1.00) 		0.109
(1.00) 		0.137
(1.00) 		0.554
(1.00) 		0.263
(1.00) 		0.488
(1.00) 		0.148
(1.00) 		0.0412
(1.00) 		0.422
(1.00)
10q gain 24 (4%) 565 0.911
(1.00) 		0.431
(1.00) 		0.76
(1.00) 		0.123
(1.00) 		0.169
(1.00) 		0.465
(1.00) 		0.99
(1.00) 		0.915
(1.00) 		0.491
(1.00) 		0.684
(1.00) 		0.126
(1.00) 		0.812
(1.00)
12p gain 123 (21%) 466 0.351
(1.00) 		0.717
(1.00) 		0.0353
(1.00) 		0.00518
(1.00) 		0.529
(1.00) 		0.817
(1.00) 		0.835
(1.00) 		0.742
(1.00) 		0.506
(1.00) 		0.548
(1.00) 		0.192
(1.00) 		0.581
(1.00)
12q gain 107 (18%) 482 0.249
(1.00) 		0.776
(1.00) 		0.0243
(1.00) 		0.00309
(1.00) 		0.572
(1.00) 		0.775
(1.00) 		0.492
(1.00) 		0.499
(1.00) 		0.338
(1.00) 		0.279
(1.00) 		0.0736
(1.00) 		0.135
(1.00)
14q gain 42 (7%) 547 0.735
(1.00) 		0.352
(1.00) 		0.318
(1.00) 		0.851
(1.00) 		0.78
(1.00) 		0.885
(1.00) 		0.38
(1.00) 		0.821
(1.00) 		0.867
(1.00) 		0.62
(1.00) 		0.585
(1.00) 		0.8
(1.00)
15q gain 14 (2%) 575 0.297
(1.00) 		0.282
(1.00) 		0.0425
(1.00) 		0.714
(1.00) 		0.173
(1.00) 		0.272
(1.00) 		0.934
(1.00) 		1
(1.00) 		1
(1.00) 		0.762
(1.00) 		0.715
(1.00) 		0.424
(1.00)
17p gain 35 (6%) 554 0.441
(1.00) 		0.0279
(1.00) 		0.639
(1.00) 		1
(1.00) 		0.2
(1.00) 		0.95
(1.00) 		0.285
(1.00) 		0.457
(1.00) 		0.161
(1.00) 		0.8
(1.00) 		0.586
(1.00) 		0.519
(1.00)
18q gain 19 (3%) 570 0.0449
(1.00) 		0.0231
(1.00) 		0.0698
(1.00) 		0.000609
(0.489) 		0.673
(1.00) 		0.364
(1.00) 		0.0195
(1.00) 		0.0694
(1.00) 		0.239
(1.00) 		0.154
(1.00) 		0.0422
(1.00) 		0.904
(1.00)
21q gain 31 (5%) 558 0.312
(1.00) 		0.58
(1.00) 		0.0426
(1.00) 		0.627
(1.00) 		0.487
(1.00) 		0.318
(1.00) 		0.814
(1.00) 		0.351
(1.00) 		0.417
(1.00) 		0.513
(1.00) 		0.253
(1.00) 		0.861
(1.00)
22q gain 22 (4%) 567 0.117
(1.00) 		0.323
(1.00) 		0.0513
(1.00) 		0.419
(1.00) 		0.843
(1.00) 		0.459
(1.00) 		0.171
(1.00) 		0.198
(1.00) 		0.669
(1.00) 		0.302
(1.00) 		0.13
(1.00) 		0.956
(1.00)
2p loss 17 (3%) 572 1
(1.00) 		0.858
(1.00) 		0.0016
(1.00) 		0.0452
(1.00) 		0.347
(1.00) 		1
(1.00) 		0.213
(1.00) 		0.0642
(1.00) 		0.0961
(1.00) 		0.113
(1.00) 		0.741
(1.00) 		0.705
(1.00)
2q loss 13 (2%) 576 0.805
(1.00) 		0.411
(1.00) 		0.0305
(1.00) 		0.263
(1.00) 		0.535
(1.00) 		0.666
(1.00) 		0.413
(1.00) 		0.0429
(1.00) 		0.16
(1.00) 		0.0496
(1.00) 		0.197
(1.00) 		0.686
(1.00)
3p loss 65 (11%) 524 0.349
(1.00) 		0.623
(1.00) 		0.536
(1.00) 		0.393
(1.00) 		0.534
(1.00) 		0.757
(1.00) 		0.77
(1.00) 		0.31
(1.00) 		0.761
(1.00) 		0.107
(1.00) 		0.0609
(1.00) 		0.167
(1.00)
3q loss 42 (7%) 547 0.246
(1.00) 		0.0292
(1.00) 		0.457
(1.00) 		0.191
(1.00) 		0.324
(1.00) 		0.836
(1.00) 		0.712
(1.00) 		0.509
(1.00) 		0.581
(1.00) 		0.117
(1.00) 		0.337
(1.00) 		0.38
(1.00)
5p loss 80 (14%) 509 0.371
(1.00) 		0.912
(1.00) 		0.000541
(0.438) 		0.0185
(1.00) 		0.685
(1.00) 		0.108
(1.00) 		0.788
(1.00) 		0.0704
(1.00) 		1
(1.00) 		0.445
(1.00) 		0.109
(1.00) 		0.014
(1.00)
6p loss 45 (8%) 544 0.549
(1.00) 		0.37
(1.00) 		0.161
(1.00) 		0.854
(1.00) 		0.0727
(1.00) 		0.205
(1.00) 		0.903
(1.00) 		0.279
(1.00) 		0.467
(1.00) 		0.552
(1.00) 		0.0683
(1.00) 		0.0716
(1.00)
6q loss 67 (11%) 522 0.433
(1.00) 		0.239
(1.00) 		0.101
(1.00) 		0.511
(1.00) 		0.23
(1.00) 		0.208
(1.00) 		0.282
(1.00) 		0.255
(1.00) 		0.512
(1.00) 		0.252
(1.00) 		0.785
(1.00) 		0.556
(1.00)
7q loss 4 (1%) 585 0.098
(1.00) 		1
(1.00) 		1
(1.00) 		0.626
(1.00) 		0.574
(1.00) 		1
(1.00) 		1
(1.00) 		0.526
(1.00)
8q loss 31 (5%) 558 0.683
(1.00) 		0.888
(1.00) 		0.0427
(1.00) 		0.637
(1.00) 		0.853
(1.00) 		0.895
(1.00) 		0.378
(1.00) 		0.13
(1.00) 		0.617
(1.00) 		0.686
(1.00) 		0.541
(1.00) 		0.273
(1.00)
9p loss 71 (12%) 518 0.476
(1.00) 		0.261
(1.00) 		0.000344
(0.28) 		0.00448
(1.00) 		0.837
(1.00) 		0.0362
(1.00) 		0.000377
(0.307) 		0.0066
(1.00) 		0.203
(1.00) 		0.0411
(1.00) 		0.00153
(1.00) 		0.0749
(1.00)
11p loss 73 (12%) 516 0.943
(1.00) 		0.605
(1.00) 		0.0574
(1.00) 		0.0975
(1.00) 		0.509
(1.00) 		0.871
(1.00) 		0.904
(1.00) 		0.192
(1.00) 		0.965
(1.00) 		0.339
(1.00) 		0.0878
(1.00) 		0.26
(1.00)
11q loss 89 (15%) 500 0.829
(1.00) 		0.903
(1.00) 		0.016
(1.00) 		0.0156
(1.00) 		0.95
(1.00) 		0.758
(1.00) 		0.989
(1.00) 		0.655
(1.00) 		0.796
(1.00) 		0.0894
(1.00) 		0.149
(1.00) 		0.418
(1.00)
13q loss 20 (3%) 569 0.297
(1.00) 		0.132
(1.00) 		0.0391
(1.00) 		0.39
(1.00) 		0.292
(1.00) 		0.0706
(1.00) 		0.74
(1.00) 		0.229
(1.00) 		0.742
(1.00) 		0.661
(1.00) 		0.0189
(1.00) 		0.204
(1.00)
16p loss 36 (6%) 553 0.107
(1.00) 		0.0763
(1.00) 		0.575
(1.00) 		1
(1.00) 		0.228
(1.00) 		0.184
(1.00) 		0.706
(1.00) 		0.178
(1.00) 		0.632
(1.00) 		0.281
(1.00) 		0.825
(1.00) 		0.489
(1.00)
16q loss 39 (7%) 550 0.0267
(1.00) 		0.242
(1.00) 		0.0391
(1.00) 		0.637
(1.00) 		0.249
(1.00) 		0.27
(1.00) 		0.918
(1.00) 		0.763
(1.00) 		0.563
(1.00) 		0.675
(1.00) 		1
(1.00) 		0.955
(1.00)
17q loss 85 (14%) 504 0.959
(1.00) 		0.485
(1.00) 		0.0243
(1.00) 		0.308
(1.00) 		0.803
(1.00) 		0.81
(1.00) 		0.8
(1.00) 		0.0343
(1.00) 		0.835
(1.00) 		0.468
(1.00) 		0.117
(1.00) 		0.19
(1.00)
19q loss 53 (9%) 536 0.652
(1.00) 		0.018
(1.00) 		0.0012
(0.947) 		0.71
(1.00) 		0.12
(1.00) 		0.881
(1.00) 		0.135
(1.00) 		0.0318
(1.00) 		0.216
(1.00) 		0.0015
(1.00) 		0.236
(1.00) 		0.0772
(1.00)
20p loss 61 (10%) 528 0.116
(1.00) 		0.355
(1.00) 		0.00505
(1.00) 		0.0295
(1.00) 		0.777
(1.00) 		0.713
(1.00) 		0.158
(1.00) 		0.0433
(1.00) 		0.739
(1.00) 		0.967
(1.00) 		0.106
(1.00) 		0.0396
(1.00)
20q loss 5 (1%) 584 0.878
(1.00) 		0.184
(1.00) 		0.0939
(1.00) 		0.649
(1.00) 		0.396
(1.00) 		0.732
(1.00) 		0.828
(1.00) 		1
(1.00)
xq loss 71 (12%) 518 0.985
(1.00) 		0.956
(1.00) 		0.0539
(1.00) 		0.0354
(1.00) 		0.0548
(1.00) 		0.245
(1.00) 		0.653
(1.00) 		0.28
(1.00) 		0.0557
(1.00) 		0.173
(1.00) 		0.538
(1.00) 		0.167
(1.00)
'2p gain' versus 'CN_CNMF'

P value = 0.000271 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
2P GAIN MUTATED 44 32 31 7
2P GAIN WILD-TYPE 130 213 126 6

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 2.17e-06 (Fisher's exact test), Q value = 0.0019

Table S2.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
2P GAIN MUTATED 22 11 45 30
2P GAIN WILD-TYPE 98 114 84 159

Figure S2.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 6.32e-06 (Fisher's exact test), Q value = 0.0055

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
2Q GAIN MUTATED 44 28 32 8
2Q GAIN WILD-TYPE 130 217 125 5

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.000252 (Fisher's exact test), Q value = 0.21

Table S4.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
2Q GAIN MUTATED 23 13 41 32
2Q GAIN WILD-TYPE 97 112 88 157

Figure S4.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.016

Table S5.  Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
3P GAIN MUTATED 37 14 17 0
3P GAIN WILD-TYPE 137 231 140 13

Figure S5.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 6.1e-10 (Fisher's exact test), Q value = 5.5e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
3Q GAIN MUTATED 52 15 27 0
3Q GAIN WILD-TYPE 122 230 130 13

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

'6p gain' versus 'CN_CNMF'

P value = 3.14e-09 (Fisher's exact test), Q value = 2.8e-06

Table S7.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
6P GAIN MUTATED 59 22 34 4
6P GAIN WILD-TYPE 115 223 123 9

Figure S7.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 7.6e-10 (Fisher's exact test), Q value = 6.9e-07

Table S8.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
6Q GAIN MUTATED 56 18 28 4
6Q GAIN WILD-TYPE 118 227 129 9

Figure S8.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 3.28e-21 (Fisher's exact test), Q value = 3.1e-18

Table S9.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
7P GAIN MUTATED 138 84 101 11
7P GAIN WILD-TYPE 36 161 56 2

Figure S9.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 4.75e-06 (Fisher's exact test), Q value = 0.0041

Table S10.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
7P GAIN MUTATED 118 56 49
7P GAIN WILD-TYPE 38 60 42

Figure S10.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1.63e-08 (Fisher's exact test), Q value = 1.5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
7P GAIN MUTATED 69 52 101 99
7P GAIN WILD-TYPE 51 73 28 90

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

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.36e-09 (Fisher's exact test), Q value = 3e-06

Table S12.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
7P GAIN MUTATED 121 61 139
7P GAIN WILD-TYPE 115 80 47

Figure S12.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.29e-06 (Fisher's exact test), Q value = 0.0063

Table S13.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
7P GAIN MUTATED 71 47 62
7P GAIN WILD-TYPE 29 62 23

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MRNA_CNMF'

P value = 0.000158 (Fisher's exact test), Q value = 0.13

Table S14.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
7Q GAIN MUTATED 9 36 36 12
7Q GAIN WILD-TYPE 34 26 33 29

Figure S14.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2.03e-13 (Fisher's exact test), Q value = 1.9e-10

Table S15.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
7Q GAIN MUTATED 121 81 86 10
7Q GAIN WILD-TYPE 53 164 71 3

Figure S15.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.21

Table S16.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
7Q GAIN MUTATED 104 51 43
7Q GAIN WILD-TYPE 52 65 48

Figure S16.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1.62e-07 (Fisher's exact test), Q value = 0.00014

Table S17.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
7Q GAIN MUTATED 57 47 93 89
7Q GAIN WILD-TYPE 63 78 36 100

Figure S17.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.47e-07 (Fisher's exact test), Q value = 0.00031

Table S18.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
7Q GAIN MUTATED 107 55 124
7Q GAIN WILD-TYPE 129 86 62

Figure S18.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.69e-05 (Fisher's exact test), Q value = 0.04

Table S19.  Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
7Q GAIN MUTATED 62 42 58
7Q GAIN WILD-TYPE 38 67 27

Figure S19.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 8.58e-08 (Fisher's exact test), Q value = 7.7e-05

Table S20.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
8P GAIN MUTATED 38 51 64 10
8P GAIN WILD-TYPE 136 194 93 3

Figure S20.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 4.7e-39 (Fisher's exact test), Q value = 4.4e-36

Table S21.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
8Q GAIN MUTATED 81 68 143 11
8Q GAIN WILD-TYPE 93 177 14 2

Figure S21.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 2.42e-05 (Fisher's exact test), Q value = 0.021

Table S22.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
8Q GAIN MUTATED 66 45 85 92
8Q GAIN WILD-TYPE 54 80 44 97

Figure S22.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0095

Table S23.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
8Q GAIN MUTATED 113 55 120
8Q GAIN WILD-TYPE 123 86 66

Figure S23.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1.2e-07 (Fisher's exact test), Q value = 0.00011

Table S24.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
11P GAIN MUTATED 39 11 28 2
11P GAIN WILD-TYPE 135 234 129 11

Figure S24.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.000103 (Fisher's exact test), Q value = 0.086

Table S25.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
11P GAIN MUTATED 36 6 11
11P GAIN WILD-TYPE 120 110 80

Figure S25.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000276 (Fisher's exact test), Q value = 0.23

Table S26.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
11P GAIN MUTATED 32 8 39
11P GAIN WILD-TYPE 204 133 147

Figure S26.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1.66e-07 (Fisher's exact test), Q value = 0.00015

Table S27.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
11Q GAIN MUTATED 34 9 28 2
11Q GAIN WILD-TYPE 140 236 129 11

Figure S27.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 8.01e-05 (Fisher's exact test), Q value = 0.068

Table S28.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
11Q GAIN MUTATED 33 5 8
11Q GAIN WILD-TYPE 123 111 83

Figure S28.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 1.02e-06 (Fisher's exact test), Q value = 9e-04

Table S29.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
11Q GAIN MUTATED 13 3 32 23
11Q GAIN WILD-TYPE 107 122 97 166

Figure S29.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.26e-06 (Fisher's exact test), Q value = 0.0028

Table S30.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
11Q GAIN MUTATED 29 4 38
11Q GAIN WILD-TYPE 207 137 148

Figure S30.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.11

Table S31.  Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
11Q GAIN MUTATED 18 3 16
11Q GAIN WILD-TYPE 82 106 69

Figure S31.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MRNA_CNMF'

P value = 4.11e-07 (Fisher's exact test), Q value = 0.00036

Table S32.  Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
13Q GAIN MUTATED 16 46 52 14
13Q GAIN WILD-TYPE 27 16 17 27

Figure S32.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 5.38e-05 (Fisher's exact test), Q value = 0.046

Table S33.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
13Q GAIN MUTATED 31 34 22 41
13Q GAIN WILD-TYPE 11 16 41 19

Figure S33.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 2.98e-35 (Fisher's exact test), Q value = 2.8e-32

Table S34.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
13Q GAIN MUTATED 163 88 94 9
13Q GAIN WILD-TYPE 11 157 63 4

Figure S34.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1.78e-07 (Fisher's exact test), Q value = 0.00016

Table S35.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
13Q GAIN MUTATED 121 54 49
13Q GAIN WILD-TYPE 35 62 42

Figure S35.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1.26e-07 (Fisher's exact test), Q value = 0.00011

Table S36.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
13Q GAIN MUTATED 65 52 98 122
13Q GAIN WILD-TYPE 55 73 31 67

Figure S36.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.81e-07 (Fisher's exact test), Q value = 0.00051

Table S37.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
13Q GAIN MUTATED 139 62 136
13Q GAIN WILD-TYPE 97 79 50

Figure S37.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.19e-07 (Fisher's exact test), Q value = 0.00028

Table S38.  Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
13Q GAIN MUTATED 78 48 62
13Q GAIN WILD-TYPE 22 61 23

Figure S38.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 8.61e-20 (Fisher's exact test), Q value = 8e-17

Table S39.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
16P GAIN MUTATED 83 19 37 2
16P GAIN WILD-TYPE 91 226 120 11

Figure S39.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 5.54e-05 (Fisher's exact test), Q value = 0.047

Table S40.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
16P GAIN MUTATED 24 15 45 55
16P GAIN WILD-TYPE 96 110 84 134

Figure S40.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.36e-05 (Fisher's exact test), Q value = 0.029

Table S41.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
16P GAIN MUTATED 65 16 58
16P GAIN WILD-TYPE 171 125 128

Figure S41.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 6.55e-21 (Fisher's exact test), Q value = 6.1e-18

Table S42.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
16Q GAIN MUTATED 84 18 34 2
16Q GAIN WILD-TYPE 90 227 123 11

Figure S42.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.000186 (Fisher's exact test), Q value = 0.15

Table S43.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
16Q GAIN MUTATED 24 15 44 51
16Q GAIN WILD-TYPE 96 110 85 138

Figure S43.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.015

Table S44.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
16Q GAIN MUTATED 60 15 59
16Q GAIN WILD-TYPE 176 126 127

Figure S44.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 9.19e-05 (Fisher's exact test), Q value = 0.078

Table S45.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
17Q GAIN MUTATED 42 24 38 2
17Q GAIN WILD-TYPE 132 221 119 11

Figure S45.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 5.69e-06 (Fisher's exact test), Q value = 0.0049

Table S46.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
17Q GAIN MUTATED 14 14 44 31
17Q GAIN WILD-TYPE 106 111 85 158

Figure S46.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.000268 (Fisher's exact test), Q value = 0.22

Table S47.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
18P GAIN MUTATED 1 12 8
18P GAIN WILD-TYPE 155 104 83

Figure S47.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 3.21e-06 (Fisher's exact test), Q value = 0.0028

Table S48.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
19P GAIN MUTATED 47 20 29 3
19P GAIN WILD-TYPE 127 225 128 10

Figure S48.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 6.66e-05 (Fisher's exact test), Q value = 0.056

Table S49.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
19Q GAIN MUTATED 50 27 27 3
19Q GAIN WILD-TYPE 124 218 130 10

Figure S49.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.2

Table S50.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
20P GAIN MUTATED 16 40 51 18
20P GAIN WILD-TYPE 27 22 18 23

Figure S50.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1.74e-06 (Fisher's exact test), Q value = 0.0015

Table S51.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
20P GAIN MUTATED 32 34 19 40
20P GAIN WILD-TYPE 10 16 44 20

Figure S51.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 5.11e-10 (Fisher's exact test), Q value = 4.6e-07

Table S52.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
20P GAIN MUTATED 121 105 99 13
20P GAIN WILD-TYPE 53 140 58 0

Figure S52.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.000272 (Fisher's exact test), Q value = 0.22

Table S53.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
20P GAIN MUTATED 108 53 48
20P GAIN WILD-TYPE 48 63 43

Figure S53.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.091

Table S54.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
20P GAIN MUTATED 64 53 89 117
20P GAIN WILD-TYPE 56 72 40 72

Figure S54.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNA_CNMF'

P value = 1.25e-13 (Fisher's exact test), Q value = 1.1e-10

Table S55.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
20Q GAIN MUTATED 18 60 63 22
20Q GAIN WILD-TYPE 25 2 6 19

Figure S55.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 5.16e-13 (Fisher's exact test), Q value = 4.7e-10

Table S56.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
20Q GAIN MUTATED 39 43 25 56
20Q GAIN WILD-TYPE 3 7 38 4

Figure S56.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1.04e-33 (Fisher's exact test), Q value = 9.8e-31

Table S57.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
20Q GAIN MUTATED 171 126 136 13
20Q GAIN WILD-TYPE 3 119 21 0

Figure S57.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1.05e-17 (Fisher's exact test), Q value = 9.7e-15

Table S58.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
20Q GAIN MUTATED 151 65 61
20Q GAIN WILD-TYPE 5 51 30

Figure S58.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1.45e-18 (Fisher's exact test), Q value = 1.3e-15

Table S59.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
20Q GAIN MUTATED 85 64 126 149
20Q GAIN WILD-TYPE 35 61 3 40

Figure S59.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.41e-14 (Fisher's exact test), Q value = 3.1e-11

Table S60.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
20Q GAIN MUTATED 178 76 170
20Q GAIN WILD-TYPE 58 65 16

Figure S60.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.8e-12 (Fisher's exact test), Q value = 4.4e-09

Table S61.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
20Q GAIN MUTATED 93 59 75
20Q GAIN WILD-TYPE 7 50 10

Figure S61.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.000186 (Fisher's exact test), Q value = 0.15

Table S62.  Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
XQ GAIN MUTATED 41 23 35 2
XQ GAIN WILD-TYPE 133 222 122 11

Figure S62.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1.92e-07 (Fisher's exact test), Q value = 0.00017

Table S63.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
1P LOSS MUTATED 58 33 31 8
1P LOSS WILD-TYPE 116 212 126 5

Figure S63.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.15e-05 (Fisher's exact test), Q value = 0.018

Table S64.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
1P LOSS MUTATED 52 15 59
1P LOSS WILD-TYPE 184 126 127

Figure S64.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 9.69e-06 (Fisher's exact test), Q value = 0.0084

Table S65.  Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
1Q LOSS MUTATED 29 16 21 7
1Q LOSS WILD-TYPE 145 229 136 6

Figure S65.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.000276 (Fisher's exact test), Q value = 0.23

Table S66.  Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
1Q LOSS MUTATED 16 4 26 24
1Q LOSS WILD-TYPE 104 121 103 165

Figure S66.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 4.23e-12 (Fisher's exact test), Q value = 3.9e-09

Table S67.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
4P LOSS MUTATED 85 43 48 9
4P LOSS WILD-TYPE 89 202 109 4

Figure S67.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.000289 (Fisher's exact test), Q value = 0.24

Table S68.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
4P LOSS MUTATED 39 22 54 64
4P LOSS WILD-TYPE 81 103 75 125

Figure S68.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.023

Table S69.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
4P LOSS MUTATED 78 25 76
4P LOSS WILD-TYPE 158 116 110

Figure S69.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.28e-05 (Fisher's exact test), Q value = 0.053

Table S70.  Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
4P LOSS MUTATED 43 18 31
4P LOSS WILD-TYPE 57 91 54

Figure S70.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1.21e-14 (Fisher's exact test), Q value = 1.1e-11

Table S71.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
4Q LOSS MUTATED 85 36 48 9
4Q LOSS WILD-TYPE 89 209 109 4

Figure S71.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 5.46e-06 (Fisher's exact test), Q value = 0.0047

Table S72.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
4Q LOSS MUTATED 65 17 26
4Q LOSS WILD-TYPE 91 99 65

Figure S72.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000101 (Fisher's exact test), Q value = 0.084

Table S73.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
4Q LOSS MUTATED 75 25 73
4Q LOSS WILD-TYPE 161 116 113

Figure S73.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1.96e-06 (Fisher's exact test), Q value = 0.0017

Table S74.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
5Q LOSS MUTATED 38 24 47 4
5Q LOSS WILD-TYPE 136 221 110 9

Figure S74.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 6.02e-29 (Fisher's exact test), Q value = 5.6e-26

Table S75.  Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
8P LOSS MUTATED 93 27 86 0
8P LOSS WILD-TYPE 81 218 71 13

Figure S75.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 3.86e-05 (Fisher's exact test), Q value = 0.033

Table S76.  Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
8P LOSS MUTATED 72 24 27
8P LOSS WILD-TYPE 84 92 64

Figure S76.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 4.74e-05 (Fisher's exact test), Q value = 0.04

Table S77.  Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
9Q LOSS MUTATED 35 13 21 1
9Q LOSS WILD-TYPE 139 232 136 12

Figure S77.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.16

Table S78.  Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
9Q LOSS MUTATED 18 5 27 18
9Q LOSS WILD-TYPE 102 120 102 171

Figure S78.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000212 (Fisher's exact test), Q value = 0.18

Table S79.  Gene #57: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
9Q LOSS MUTATED 20 4 16
9Q LOSS WILD-TYPE 80 105 69

Figure S79.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 3.5e-07 (Fisher's exact test), Q value = 0.00031

Table S80.  Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
10P LOSS MUTATED 34 20 34 8
10P LOSS WILD-TYPE 140 225 123 5

Figure S80.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 5.21e-12 (Fisher's exact test), Q value = 4.7e-09

Table S81.  Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
10Q LOSS MUTATED 39 15 41 9
10Q LOSS WILD-TYPE 135 230 116 4

Figure S81.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.000119 (Fisher's exact test), Q value = 0.099

Table S82.  Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
10Q LOSS MUTATED 20 9 37 34
10Q LOSS WILD-TYPE 100 116 92 155

Figure S82.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.93e-05 (Fisher's exact test), Q value = 0.042

Table S83.  Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
10Q LOSS MUTATED 40 11 49
10Q LOSS WILD-TYPE 196 130 137

Figure S83.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 7.8e-10 (Fisher's exact test), Q value = 7e-07

Table S84.  Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
12P LOSS MUTATED 37 7 19 5
12P LOSS WILD-TYPE 137 238 138 8

Figure S84.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 1.12e-09 (Fisher's exact test), Q value = 1e-06

Table S85.  Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
12Q LOSS MUTATED 36 8 18 6
12Q LOSS WILD-TYPE 138 237 139 7

Figure S85.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 0.000264 (Fisher's exact test), Q value = 0.22

Table S86.  Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
14Q LOSS MUTATED 10 29 33 6
14Q LOSS WILD-TYPE 33 33 36 35

Figure S86.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.45e-05 (Fisher's exact test), Q value = 0.038

Table S87.  Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
14Q LOSS MUTATED 23 19 9 27
14Q LOSS WILD-TYPE 19 31 54 33

Figure S87.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 6.8e-27 (Fisher's exact test), Q value = 6.3e-24

Table S88.  Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
14Q LOSS MUTATED 113 36 38 6
14Q LOSS WILD-TYPE 61 209 119 7

Figure S88.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1.88e-06 (Fisher's exact test), Q value = 0.0016

Table S89.  Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
14Q LOSS MUTATED 70 19 25
14Q LOSS WILD-TYPE 86 97 66

Figure S89.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 7.26e-11 (Fisher's exact test), Q value = 6.6e-08

Table S90.  Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
14Q LOSS MUTATED 27 18 66 75
14Q LOSS WILD-TYPE 93 107 63 114

Figure S90.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.6e-05 (Fisher's exact test), Q value = 0.031

Table S91.  Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
14Q LOSS MUTATED 84 26 76
14Q LOSS WILD-TYPE 152 115 110

Figure S91.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.2e-07 (Fisher's exact test), Q value = 0.00011

Table S92.  Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
14Q LOSS MUTATED 49 15 30
14Q LOSS WILD-TYPE 51 94 55

Figure S92.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MRNA_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.086

Table S93.  Gene #66: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
15Q LOSS MUTATED 11 32 36 7
15Q LOSS WILD-TYPE 32 30 33 34

Figure S93.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1.75e-21 (Fisher's exact test), Q value = 1.6e-18

Table S94.  Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
15Q LOSS MUTATED 105 39 64 9
15Q LOSS WILD-TYPE 69 206 93 4

Figure S94.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0094

Table S95.  Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
15Q LOSS MUTATED 46 25 63 78
15Q LOSS WILD-TYPE 74 100 66 111

Figure S95.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.21e-07 (Fisher's exact test), Q value = 0.00037

Table S96.  Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
15Q LOSS MUTATED 95 28 89
15Q LOSS WILD-TYPE 141 113 97

Figure S96.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.48e-06 (Fisher's exact test), Q value = 0.0056

Table S97.  Gene #66: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
15Q LOSS MUTATED 48 21 39
15Q LOSS WILD-TYPE 52 88 46

Figure S97.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MRNA_CNMF'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.024

Table S98.  Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
17P LOSS MUTATED 15 44 47 15
17P LOSS WILD-TYPE 28 18 22 26

Figure S98.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 3.13e-26 (Fisher's exact test), Q value = 2.9e-23

Table S99.  Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
17P LOSS MUTATED 129 70 115 9
17P LOSS WILD-TYPE 45 175 42 4

Figure S99.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 2.37e-08 (Fisher's exact test), Q value = 2.1e-05

Table S100.  Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
17P LOSS MUTATED 113 47 39
17P LOSS WILD-TYPE 43 69 52

Figure S100.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1.02e-06 (Fisher's exact test), Q value = 9e-04

Table S101.  Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
17P LOSS MUTATED 65 45 90 110
17P LOSS WILD-TYPE 55 80 39 79

Figure S101.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.72e-07 (Fisher's exact test), Q value = 0.00024

Table S102.  Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
17P LOSS MUTATED 133 52 125
17P LOSS WILD-TYPE 103 89 61

Figure S102.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00093

Table S103.  Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
17P LOSS MUTATED 72 40 51
17P LOSS WILD-TYPE 28 69 34

Figure S103.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MRNA_CNMF'

P value = 1.91e-12 (Fisher's exact test), Q value = 1.7e-09

Table S104.  Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18P LOSS MUTATED 13 52 54 12
18P LOSS WILD-TYPE 30 10 15 29

Figure S104.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 3.54e-10 (Fisher's exact test), Q value = 3.2e-07

Table S105.  Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
18P LOSS MUTATED 36 30 18 47
18P LOSS WILD-TYPE 6 20 45 13

Figure S105.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1.71e-39 (Fisher's exact test), Q value = 1.6e-36

Table S106.  Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
18P LOSS MUTATED 159 78 113 12
18P LOSS WILD-TYPE 15 167 44 1

Figure S106.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 2.24e-22 (Fisher's exact test), Q value = 2.1e-19

Table S107.  Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
18P LOSS MUTATED 141 43 45
18P LOSS WILD-TYPE 15 73 46

Figure S107.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 9.48e-22 (Fisher's exact test), Q value = 8.8e-19

Table S108.  Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
18P LOSS MUTATED 70 40 117 119
18P LOSS WILD-TYPE 50 85 12 70

Figure S108.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.19e-17 (Fisher's exact test), Q value = 6.6e-14

Table S109.  Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
18P LOSS MUTATED 144 50 152
18P LOSS WILD-TYPE 92 91 34

Figure S109.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.39e-16 (Fisher's exact test), Q value = 3.1e-13

Table S110.  Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
18P LOSS MUTATED 87 36 61
18P LOSS WILD-TYPE 13 73 24

Figure S110.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MRNA_CNMF'

P value = 1.39e-11 (Fisher's exact test), Q value = 1.3e-08

Table S111.  Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18Q LOSS MUTATED 16 54 56 14
18Q LOSS WILD-TYPE 27 8 13 27

Figure S111.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3.68e-10 (Fisher's exact test), Q value = 3.3e-07

Table S112.  Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
18Q LOSS MUTATED 37 32 21 50
18Q LOSS WILD-TYPE 5 18 42 10

Figure S112.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1.09e-40 (Fisher's exact test), Q value = 1e-37

Table S113.  Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
18Q LOSS MUTATED 158 86 131 13
18Q LOSS WILD-TYPE 16 159 26 0

Figure S113.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 9.38e-20 (Fisher's exact test), Q value = 8.7e-17

Table S114.  Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
18Q LOSS MUTATED 144 52 49
18Q LOSS WILD-TYPE 12 64 42

Figure S114.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 3.96e-18 (Fisher's exact test), Q value = 3.7e-15

Table S115.  Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
18Q LOSS MUTATED 75 49 118 129
18Q LOSS WILD-TYPE 45 76 11 60

Figure S115.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.66e-15 (Fisher's exact test), Q value = 1.5e-12

Table S116.  Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
18Q LOSS MUTATED 154 59 158
18Q LOSS WILD-TYPE 82 82 28

Figure S116.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.09e-14 (Fisher's exact test), Q value = 5.6e-11

Table S117.  Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
18Q LOSS MUTATED 89 44 64
18Q LOSS WILD-TYPE 11 65 21

Figure S117.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 9.68e-05 (Fisher's exact test), Q value = 0.081

Table S118.  Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
19P LOSS MUTATED 23 10 26 2
19P LOSS WILD-TYPE 151 235 131 11

Figure S118.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000156 (Fisher's exact test), Q value = 0.13

Table S119.  Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 253 248
19P LOSS MUTATED 12 18 26
19P LOSS WILD-TYPE 25 235 222

Figure S119.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 5.94e-06 (Fisher's exact test), Q value = 0.0052

Table S120.  Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
21Q LOSS MUTATED 77 54 46 7
21Q LOSS WILD-TYPE 97 191 111 6

Figure S120.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 9.33e-05 (Fisher's exact test), Q value = 0.079

Table S121.  Gene #77: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
21Q LOSS MUTATED 35 23 58 59
21Q LOSS WILD-TYPE 85 102 71 130

Figure S121.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 4.47e-13 (Fisher's exact test), Q value = 4.1e-10

Table S122.  Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
22Q LOSS MUTATED 94 47 45 7
22Q LOSS WILD-TYPE 80 198 112 6

Figure S122.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 589

  • Number of significantly arm-level cnvs = 79

  • 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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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