Correlation between copy number variations of arm-level result and molecular subtypes
Colorectal Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1FF3R7Z
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/C1FF3R7Z
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 80 arm-level events and 12 molecular subtypes across 615 patients, 113 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 3p gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

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

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 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',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 1q loss cnv correlated to 'MRNASEQ_CNMF'.

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

  • 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',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'MRNASEQ_CNMF'.

  • 9q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 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'.

  • 20p loss cnv correlated to 'CN_CNMF'.

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

  • 22q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 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, 113 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
18p loss 379 (62%) 236 1e-05
(0.00935) 		1e-05
(0.00935) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.03
(1.00) 		0.048
(1.00) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.0074
(1.00) 		0.00924
(1.00) 		0.00021
(0.174) 		0.00115
(0.899)
18q loss 408 (66%) 207 1e-05
(0.00935) 		1e-05
(0.00935) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.0507
(1.00) 		0.103
(1.00) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.00074
(0.588) 		0.00462
(1.00) 		0.00015
(0.125) 		0.00035
(0.288)
7q gain 312 (51%) 303 0.00014
(0.117) 		1e-05
(0.00935) 		1e-05
(0.00935) 		7e-05
(0.0591) 		0.132
(1.00) 		0.0276
(1.00) 		5e-05
(0.0424) 		1e-05
(0.00935) 		0.0133
(1.00) 		0.238
(1.00) 		0.077
(1.00) 		0.438
(1.00)
13q gain 368 (60%) 247 1e-05
(0.00935) 		1e-05
(0.00935) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.24
(1.00) 		0.38
(1.00) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.00054
(0.434) 		0.441
(1.00) 		0.0146
(1.00) 		0.07
(1.00)
20q gain 465 (76%) 150 1e-05
(0.00935) 		1e-05
(0.00935) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.00317
(1.00) 		0.00535
(1.00) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.016
(1.00) 		0.00036
(0.295) 		0.00067
(0.535) 		0.0192
(1.00)
14q loss 207 (34%) 408 0.00027
(0.222) 		7e-05
(0.0591) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.00257
(1.00) 		0.182
(1.00) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.134
(1.00) 		0.119
(1.00) 		0.0366
(1.00) 		0.0451
(1.00)
17p loss 341 (55%) 274 2e-05
(0.0172) 		4e-05
(0.034) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.123
(1.00) 		0.00841
(1.00) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.0352
(1.00) 		0.0233
(1.00) 		0.0281
(1.00) 		0.38
(1.00)
7p gain 349 (57%) 266 0.0004
(0.326) 		1e-05
(0.00935) 		1e-05
(0.00935) 		2e-05
(0.0172) 		0.00918
(1.00) 		0.00783
(1.00) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.00577
(1.00) 		0.178
(1.00) 		0.0277
(1.00) 		0.0877
(1.00)
11q gain 77 (13%) 538 0.0169
(1.00) 		0.00101
(0.795) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.194
(1.00) 		0.372
(1.00) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.299
(1.00) 		0.0608
(1.00) 		0.301
(1.00) 		0.18
(1.00)
15q loss 229 (37%) 386 0.0001
(0.0841) 		0.00163
(1.00) 		1e-05
(0.00935) 		0.00041
(0.333) 		0.233
(1.00) 		0.783
(1.00) 		4e-05
(0.034) 		1e-05
(0.00935) 		0.821
(1.00) 		0.686
(1.00) 		0.0786
(1.00) 		0.208
(1.00)
16p gain 147 (24%) 468 0.006
(1.00) 		0.00424
(1.00) 		1e-05
(0.00935) 		0.00994
(1.00) 		0.142
(1.00) 		0.662
(1.00) 		0.00012
(0.101) 		1e-05
(0.00935) 		0.492
(1.00) 		0.435
(1.00) 		0.223
(1.00) 		0.184
(1.00)
16q gain 145 (24%) 470 0.00877
(1.00) 		0.00374
(1.00) 		1e-05
(0.00935) 		0.0195
(1.00) 		0.231
(1.00) 		0.471
(1.00) 		0.00026
(0.214) 		1e-05
(0.00935) 		0.785
(1.00) 		0.477
(1.00) 		0.107
(1.00) 		0.122
(1.00)
17q gain 113 (18%) 502 0.0112
(1.00) 		0.0034
(1.00) 		1e-05
(0.00935) 		0.00145
(1.00) 		0.275
(1.00) 		0.672
(1.00) 		3e-05
(0.0256) 		0.00015
(0.125) 		0.00227
(1.00) 		0.0436
(1.00) 		0.866
(1.00) 		0.28
(1.00)
20p gain 354 (58%) 261 0.0004
(0.326) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.00129
(1.00) 		0.0278
(1.00) 		0.116
(1.00) 		0.00048
(0.388) 		1e-05
(0.00935) 		0.357
(1.00) 		0.0921
(1.00) 		0.575
(1.00) 		0.11
(1.00)
4p loss 197 (32%) 418 0.0287
(1.00) 		0.0163
(1.00) 		1e-05
(0.00935) 		0.00131
(1.00) 		0.476
(1.00) 		0.296
(1.00) 		0.00019
(0.158) 		0.00014
(0.117) 		0.0825
(1.00) 		0.465
(1.00) 		0.201
(1.00) 		0.919
(1.00)
4q loss 191 (31%) 424 0.0414
(1.00) 		0.0753
(1.00) 		1e-05
(0.00935) 		3e-05
(0.0256) 		0.76
(1.00) 		0.592
(1.00) 		0.00123
(0.961) 		5e-05
(0.0424) 		0.104
(1.00) 		0.137
(1.00) 		0.0384
(1.00) 		0.502
(1.00)
8p loss 218 (35%) 397 0.00899
(1.00) 		0.00562
(1.00) 		1e-05
(0.00935) 		6e-05
(0.0507) 		0.444
(1.00) 		0.0268
(1.00) 		0.00073
(0.58) 		1e-05
(0.00935) 		0.665
(1.00) 		0.24
(1.00) 		0.00251
(1.00) 		0.47
(1.00)
22q loss 203 (33%) 412 0.00496
(1.00) 		0.00021
(0.174) 		1e-05
(0.00935) 		0.0655
(1.00) 		0.779
(1.00) 		0.796
(1.00) 		0.0198
(1.00) 		2e-05
(0.0172) 		0.977
(1.00) 		0.0686
(1.00) 		0.459
(1.00) 		0.417
(1.00)
2p gain 123 (20%) 492 0.0219
(1.00) 		0.00535
(1.00) 		0.0017
(1.00) 		0.00246
(1.00) 		0.621
(1.00) 		0.566
(1.00) 		1e-05
(0.00935) 		3e-05
(0.0256) 		0.0332
(1.00) 		0.00126
(0.983) 		0.988
(1.00) 		0.97
(1.00)
2q gain 121 (20%) 494 0.0131
(1.00) 		0.00142
(1.00) 		0.0002
(0.166) 		0.00087
(0.687) 		0.648
(1.00) 		0.855
(1.00) 		0.00084
(0.664) 		3e-05
(0.0256) 		0.0932
(1.00) 		0.0092
(1.00) 		0.937
(1.00) 		0.813
(1.00)
3q gain 99 (16%) 516 0.034
(1.00) 		0.00211
(1.00) 		1e-05
(0.00935) 		0.0144
(1.00) 		0.125
(1.00) 		0.0196
(1.00) 		0.0521
(1.00) 		0.00022
(0.182) 		0.0427
(1.00) 		0.548
(1.00) 		0.02
(1.00) 		0.0518
(1.00)
5p gain 105 (17%) 510 0.496
(1.00) 		0.129
(1.00) 		0.00027
(0.222) 		0.761
(1.00) 		0.162
(1.00) 		0.132
(1.00) 		0.00558
(1.00) 		0.00013
(0.109) 		0.755
(1.00) 		0.393
(1.00) 		0.46
(1.00) 		0.558
(1.00)
11p gain 85 (14%) 530 0.0124
(1.00) 		0.00523
(1.00) 		1e-05
(0.00935) 		1e-05
(0.00935) 		0.656
(1.00) 		0.631
(1.00) 		0.00107
(0.84) 		0.00061
(0.488) 		0.332
(1.00) 		0.403
(1.00) 		0.787
(1.00) 		0.973
(1.00)
10p loss 102 (17%) 513 0.0104
(1.00) 		0.187
(1.00) 		1e-05
(0.00935) 		0.0109
(1.00) 		0.0177
(1.00) 		0.411
(1.00) 		0.00102
(0.802) 		9e-05
(0.0758) 		0.209
(1.00) 		0.361
(1.00) 		0.0548
(1.00) 		0.251
(1.00)
10q loss 111 (18%) 504 0.023
(1.00) 		0.248
(1.00) 		1e-05
(0.00935) 		0.0095
(1.00) 		0.012
(1.00) 		0.335
(1.00) 		0.00079
(0.626) 		1e-05
(0.00935) 		0.615
(1.00) 		0.416
(1.00) 		0.0479
(1.00) 		0.268
(1.00)
21q loss 194 (32%) 421 0.0172
(1.00) 		0.0216
(1.00) 		1e-05
(0.00935) 		0.021
(1.00) 		0.705
(1.00) 		0.535
(1.00) 		0.00021
(0.174) 		0.00365
(1.00) 		0.138
(1.00) 		0.147
(1.00) 		0.803
(1.00) 		0.185
(1.00)
3p gain 73 (12%) 542 0.0132
(1.00) 		0.0786
(1.00) 		1e-05
(0.00935) 		0.118
(1.00) 		0.122
(1.00) 		0.0242
(1.00) 		0.737
(1.00) 		0.0132
(1.00) 		0.107
(1.00) 		0.436
(1.00) 		0.1
(1.00) 		0.272
(1.00)
6p gain 124 (20%) 491 0.0143
(1.00) 		0.00045
(0.364) 		1e-05
(0.00935) 		0.282
(1.00) 		0.854
(1.00) 		0.967
(1.00) 		0.189
(1.00) 		0.0156
(1.00) 		0.458
(1.00) 		0.711
(1.00) 		0.0263
(1.00) 		0.0338
(1.00)
6q gain 111 (18%) 504 0.155
(1.00) 		0.00109
(0.855) 		1e-05
(0.00935) 		0.327
(1.00) 		0.827
(1.00) 		0.737
(1.00) 		0.163
(1.00) 		0.0232
(1.00) 		0.358
(1.00) 		0.892
(1.00) 		0.0093
(1.00) 		0.0469
(1.00)
8p gain 170 (28%) 445 0.924
(1.00) 		0.531
(1.00) 		2e-05
(0.0172) 		0.81
(1.00) 		0.235
(1.00) 		0.426
(1.00) 		0.00545
(1.00) 		0.0168
(1.00) 		0.204
(1.00) 		0.268
(1.00) 		0.394
(1.00) 		0.12
(1.00)
8q gain 315 (51%) 300 0.329
(1.00) 		0.109
(1.00) 		1e-05
(0.00935) 		0.0569
(1.00) 		0.0594
(1.00) 		0.0772
(1.00) 		0.00045
(0.364) 		0.00052
(0.419) 		0.292
(1.00) 		0.00986
(1.00) 		0.107
(1.00) 		0.0435
(1.00)
18q gain 20 (3%) 595 0.0448
(1.00) 		0.437
(1.00) 		0.00898
(1.00) 		0.00807
(1.00) 		0.613
(1.00) 		0.0141
(1.00) 		0.0085
(1.00) 		1e-05
(0.00935) 		0.13
(1.00) 		0.0223
(1.00) 		0.671
(1.00) 		0.829
(1.00)
19p gain 104 (17%) 511 0.327
(1.00) 		0.0189
(1.00) 		1e-05
(0.00935) 		0.0415
(1.00) 		0.16
(1.00) 		0.772
(1.00) 		0.317
(1.00) 		0.00054
(0.434) 		0.0423
(1.00) 		0.729
(1.00) 		0.517
(1.00) 		0.0898
(1.00)
19q gain 114 (19%) 501 0.0511
(1.00) 		0.00348
(1.00) 		0.00025
(0.206) 		0.0777
(1.00) 		0.0315
(1.00) 		0.493
(1.00) 		0.701
(1.00) 		0.00051
(0.411) 		0.216
(1.00) 		1
(1.00) 		0.165
(1.00) 		0.084
(1.00)
1p loss 138 (22%) 477 0.066
(1.00) 		0.0302
(1.00) 		1e-05
(0.00935) 		0.00238
(1.00) 		0.968
(1.00) 		0.909
(1.00) 		0.0004
(0.326) 		0.00089
(0.702) 		0.348
(1.00) 		0.0669
(1.00) 		0.766
(1.00) 		0.313
(1.00)
1q loss 80 (13%) 535 0.235
(1.00) 		0.212
(1.00) 		0.00035
(0.288) 		0.193
(1.00) 		0.866
(1.00) 		0.813
(1.00) 		4e-05
(0.034) 		0.00723
(1.00) 		0.768
(1.00) 		0.00934
(1.00) 		0.166
(1.00) 		0.153
(1.00)
5q loss 119 (19%) 496 0.0122
(1.00) 		0.0373
(1.00) 		1e-05
(0.00935) 		0.0274
(1.00) 		0.205
(1.00) 		0.0853
(1.00) 		0.0113
(1.00) 		0.0328
(1.00) 		0.479
(1.00) 		0.629
(1.00) 		0.691
(1.00) 		0.674
(1.00)
9p loss 77 (13%) 538 0.492
(1.00) 		0.202
(1.00) 		0.00089
(0.702) 		0.0086
(1.00) 		0.844
(1.00) 		0.473
(1.00) 		0.00018
(0.15) 		0.00753
(1.00) 		0.208
(1.00) 		0.114
(1.00) 		0.677
(1.00) 		0.711
(1.00)
9q loss 77 (13%) 538 0.0477
(1.00) 		0.0143
(1.00) 		0.00076
(0.603) 		0.00162
(1.00) 		0.858
(1.00) 		0.304
(1.00) 		0.0001
(0.0841) 		0.00111
(0.869) 		0.392
(1.00) 		0.0174
(1.00) 		0.801
(1.00) 		0.325
(1.00)
12p loss 71 (12%) 544 0.0665
(1.00) 		0.0145
(1.00) 		1e-05
(0.00935) 		0.0591
(1.00) 		0.875
(1.00) 		0.585
(1.00) 		0.0262
(1.00) 		0.00068
(0.542) 		0.818
(1.00) 		0.822
(1.00) 		0.283
(1.00) 		0.262
(1.00)
12q loss 70 (11%) 545 0.126
(1.00) 		0.0259
(1.00) 		1e-05
(0.00935) 		0.0688
(1.00) 		0.644
(1.00) 		0.974
(1.00) 		0.00396
(1.00) 		0.00038
(0.311) 		0.262
(1.00) 		0.885
(1.00) 		0.427
(1.00) 		0.366
(1.00)
20p loss 66 (11%) 549 0.0614
(1.00) 		0.0127
(1.00) 		5e-05
(0.0424) 		0.00193
(1.00) 		0.777
(1.00) 		0.849
(1.00) 		0.269
(1.00) 		0.00341
(1.00) 		0.816
(1.00) 		0.479
(1.00) 		0.0148
(1.00) 		0.00158
(1.00)
1p gain 50 (8%) 565 0.24
(1.00) 		0.372
(1.00) 		0.0151
(1.00) 		0.748
(1.00) 		0.0146
(1.00) 		0.0162
(1.00) 		0.751
(1.00) 		0.518
(1.00) 		0.384
(1.00) 		0.313
(1.00) 		0.193
(1.00) 		0.59
(1.00)
1q gain 117 (19%) 498 0.775
(1.00) 		0.551
(1.00) 		0.00516
(1.00) 		0.528
(1.00) 		0.126
(1.00) 		0.0174
(1.00) 		0.914
(1.00) 		0.548
(1.00) 		0.17
(1.00) 		0.141
(1.00) 		0.558
(1.00) 		0.408
(1.00)
4p gain 20 (3%) 595 0.815
(1.00) 		0.569
(1.00) 		0.00685
(1.00) 		0.21
(1.00) 		0.156
(1.00) 		0.175
(1.00) 		0.0185
(1.00) 		0.123
(1.00) 		0.583
(1.00) 		0.504
(1.00) 		0.674
(1.00) 		0.134
(1.00)
4q gain 21 (3%) 594 0.227
(1.00) 		0.216
(1.00) 		0.0234
(1.00) 		0.604
(1.00) 		0.114
(1.00) 		0.516
(1.00) 		0.0873
(1.00) 		0.275
(1.00) 		0.33
(1.00) 		0.366
(1.00) 		0.88
(1.00) 		1
(1.00)
5q gain 67 (11%) 548 0.906
(1.00) 		0.552
(1.00) 		0.0004
(0.326) 		0.818
(1.00) 		0.65
(1.00) 		0.767
(1.00) 		0.0576
(1.00) 		0.00457
(1.00) 		0.549
(1.00) 		0.0018
(1.00) 		0.997
(1.00) 		1
(1.00)
9p gain 123 (20%) 492 0.539
(1.00) 		0.586
(1.00) 		0.00241
(1.00) 		0.583
(1.00) 		0.128
(1.00) 		0.255
(1.00) 		0.915
(1.00) 		0.182
(1.00) 		0.979
(1.00) 		0.921
(1.00) 		0.629
(1.00) 		0.791
(1.00)
9q gain 102 (17%) 513 0.656
(1.00) 		0.832
(1.00) 		0.0371
(1.00) 		0.953
(1.00) 		0.102
(1.00) 		0.317
(1.00) 		0.951
(1.00) 		0.59
(1.00) 		0.642
(1.00) 		0.417
(1.00) 		0.933
(1.00) 		0.836
(1.00)
10p gain 49 (8%) 566 0.11
(1.00) 		0.114
(1.00) 		0.00378
(1.00) 		0.837
(1.00) 		0.107
(1.00) 		0.0489
(1.00) 		0.473
(1.00) 		0.98
(1.00) 		0.505
(1.00) 		0.303
(1.00) 		0.543
(1.00) 		0.463
(1.00)
10q gain 29 (5%) 586 0.911
(1.00) 		0.259
(1.00) 		0.0576
(1.00) 		0.149
(1.00) 		0.167
(1.00) 		0.707
(1.00) 		0.965
(1.00) 		0.858
(1.00) 		0.519
(1.00) 		0.661
(1.00) 		0.18
(1.00) 		0.953
(1.00)
12p gain 127 (21%) 488 0.358
(1.00) 		0.359
(1.00) 		0.00466
(1.00) 		0.00337
(1.00) 		0.46
(1.00) 		0.242
(1.00) 		0.774
(1.00) 		0.126
(1.00) 		0.414
(1.00) 		0.784
(1.00) 		0.565
(1.00) 		0.485
(1.00)
12q gain 112 (18%) 503 0.251
(1.00) 		0.346
(1.00) 		0.00258
(1.00) 		0.00149
(1.00) 		0.494
(1.00) 		0.349
(1.00) 		0.539
(1.00) 		0.0571
(1.00) 		0.255
(1.00) 		0.525
(1.00) 		0.552
(1.00) 		0.421
(1.00)
14q gain 43 (7%) 572 0.736
(1.00) 		0.403
(1.00) 		0.0154
(1.00) 		0.878
(1.00) 		0.789
(1.00) 		0.828
(1.00) 		0.541
(1.00) 		0.805
(1.00) 		0.884
(1.00) 		0.89
(1.00) 		0.784
(1.00) 		0.341
(1.00)
15q gain 15 (2%) 600 0.298
(1.00) 		0.153
(1.00) 		0.0625
(1.00) 		0.542
(1.00) 		0.173
(1.00) 		0.209
(1.00) 		0.925
(1.00) 		0.694
(1.00) 		1
(1.00) 		0.726
(1.00)
17p gain 38 (6%) 577 0.441
(1.00) 		0.163
(1.00) 		0.754
(1.00) 		0.9
(1.00) 		0.199
(1.00) 		1
(1.00) 		0.11
(1.00) 		0.252
(1.00) 		0.169
(1.00) 		0.722
(1.00) 		0.074
(1.00) 		0.939
(1.00)
18p gain 33 (5%) 582 0.308
(1.00) 		0.372
(1.00) 		0.00172
(1.00) 		0.00061
(0.488) 		0.604
(1.00) 		0.0607
(1.00) 		0.00942
(1.00) 		0.00056
(0.449) 		0.394
(1.00) 		0.0782
(1.00) 		0.758
(1.00) 		0.977
(1.00)
21q gain 34 (6%) 581 0.313
(1.00) 		0.264
(1.00) 		0.0004
(0.326) 		0.764
(1.00) 		0.486
(1.00) 		0.256
(1.00) 		0.801
(1.00) 		0.337
(1.00) 		0.407
(1.00) 		0.968
(1.00) 		0.46
(1.00) 		0.743
(1.00)
22q gain 23 (4%) 592 0.118
(1.00) 		0.137
(1.00) 		0.0101
(1.00) 		0.33
(1.00) 		0.86
(1.00) 		0.694
(1.00) 		0.116
(1.00) 		0.322
(1.00) 		0.692
(1.00) 		0.917
(1.00) 		0.842
(1.00) 		1
(1.00)
xq gain 105 (17%) 510 0.14
(1.00) 		0.269
(1.00) 		0.00053
(0.426) 		0.119
(1.00) 		0.11
(1.00) 		0.0666
(1.00) 		0.663
(1.00) 		0.958
(1.00) 		0.377
(1.00) 		0.978
(1.00) 		0.769
(1.00) 		0.944
(1.00)
2p loss 17 (3%) 598 1
(1.00) 		0.62
(1.00) 		0.0005
(0.403) 		0.0328
(1.00) 		0.349
(1.00) 		0.809
(1.00) 		0.167
(1.00) 		0.0282
(1.00) 		0.0939
(1.00) 		0.23
(1.00)
2q loss 14 (2%) 601 0.674
(1.00) 		0.246
(1.00) 		0.0147
(1.00) 		0.187
(1.00) 		0.25
(1.00) 		0.371
(1.00) 		0.126
(1.00) 		0.0118
(1.00) 		0.0897
(1.00) 		0.0221
(1.00)
3p loss 70 (11%) 545 0.359
(1.00) 		0.836
(1.00) 		0.489
(1.00) 		0.462
(1.00) 		0.536
(1.00) 		0.626
(1.00) 		0.535
(1.00) 		0.665
(1.00) 		0.77
(1.00) 		0.399
(1.00) 		0.384
(1.00) 		0.351
(1.00)
3q loss 45 (7%) 570 0.247
(1.00) 		0.248
(1.00) 		0.903
(1.00) 		0.536
(1.00) 		0.323
(1.00) 		0.958
(1.00) 		0.599
(1.00) 		0.129
(1.00) 		0.576
(1.00) 		0.339
(1.00) 		0.654
(1.00) 		0.788
(1.00)
5p loss 85 (14%) 530 0.377
(1.00) 		0.698
(1.00) 		0.00036
(0.295) 		0.0453
(1.00) 		0.746
(1.00) 		0.643
(1.00) 		0.629
(1.00) 		0.166
(1.00) 		0.956
(1.00) 		0.263
(1.00) 		0.453
(1.00) 		0.944
(1.00)
6p loss 46 (7%) 569 0.561
(1.00) 		0.0225
(1.00) 		0.518
(1.00) 		0.871
(1.00) 		0.0695
(1.00) 		0.0775
(1.00) 		0.659
(1.00) 		0.253
(1.00) 		0.458
(1.00) 		0.936
(1.00) 		0.533
(1.00) 		0.777
(1.00)
6q loss 69 (11%) 546 0.438
(1.00) 		0.31
(1.00) 		0.318
(1.00) 		0.691
(1.00) 		0.231
(1.00) 		0.156
(1.00) 		0.138
(1.00) 		0.158
(1.00) 		0.515
(1.00) 		0.516
(1.00) 		0.134
(1.00) 		0.532
(1.00)
7p loss 3 (0%) 612 0.615
(1.00)
7q loss 5 (1%) 610 0.625
(1.00) 		1
(1.00) 		1
(1.00) 		0.742
(1.00) 		0.576
(1.00) 		0.737
(1.00) 		1
(1.00) 		0.224
(1.00)
8q loss 37 (6%) 578 0.911
(1.00) 		0.781
(1.00) 		0.00439
(1.00) 		0.716
(1.00) 		0.957
(1.00) 		0.226
(1.00) 		0.465
(1.00) 		0.753
(1.00) 		0.272
(1.00) 		0.581
(1.00) 		0.0515
(1.00) 		0.0395
(1.00)
11p loss 75 (12%) 540 0.954
(1.00) 		1
(1.00) 		0.0213
(1.00) 		0.191
(1.00) 		0.5
(1.00) 		0.607
(1.00) 		0.711
(1.00) 		0.213
(1.00) 		0.912
(1.00) 		0.236
(1.00) 		0.659
(1.00) 		0.852
(1.00)
11q loss 93 (15%) 522 0.846
(1.00) 		0.684
(1.00) 		0.027
(1.00) 		0.047
(1.00) 		0.957
(1.00) 		0.7
(1.00) 		0.958
(1.00) 		0.487
(1.00) 		0.805
(1.00) 		0.417
(1.00) 		0.277
(1.00) 		0.285
(1.00)
13q loss 20 (3%) 595 0.298
(1.00) 		0.0165
(1.00) 		0.0143
(1.00) 		0.347
(1.00) 		0.298
(1.00) 		0.00692
(1.00) 		0.451
(1.00) 		0.258
(1.00) 		0.734
(1.00) 		0.789
(1.00) 		0.0141
(1.00) 		0.414
(1.00)
16p loss 41 (7%) 574 0.0726
(1.00) 		0.374
(1.00) 		0.329
(1.00) 		0.941
(1.00) 		0.343
(1.00) 		0.238
(1.00) 		0.462
(1.00) 		0.549
(1.00) 		0.835
(1.00) 		0.238
(1.00) 		0.303
(1.00) 		0.953
(1.00)
16q loss 44 (7%) 571 0.0253
(1.00) 		0.585
(1.00) 		0.00796
(1.00) 		0.909
(1.00) 		0.239
(1.00) 		0.237
(1.00) 		0.614
(1.00) 		0.712
(1.00) 		0.574
(1.00) 		0.558
(1.00) 		0.278
(1.00) 		0.87
(1.00)
17q loss 94 (15%) 521 0.979
(1.00) 		0.619
(1.00) 		0.00069
(0.549) 		0.529
(1.00) 		0.947
(1.00) 		0.037
(1.00) 		0.862
(1.00) 		0.0255
(1.00) 		0.771
(1.00) 		0.443
(1.00) 		0.715
(1.00) 		0.962
(1.00)
19p loss 64 (10%) 551 0.378
(1.00) 		0.477
(1.00) 		0.00039
(0.319) 		0.284
(1.00) 		0.696
(1.00) 		0.246
(1.00) 		0.00383
(1.00) 		0.115
(1.00) 		0.156
(1.00) 		0.00621
(1.00) 		0.291
(1.00) 		0.00963
(1.00)
19q loss 55 (9%) 560 0.665
(1.00) 		0.149
(1.00) 		0.00165
(1.00) 		0.688
(1.00) 		0.117
(1.00) 		0.432
(1.00) 		0.0339
(1.00) 		0.198
(1.00) 		0.227
(1.00) 		0.0755
(1.00) 		0.72
(1.00) 		0.0529
(1.00)
20q loss 6 (1%) 609 0.585
(1.00) 		0.822
(1.00) 		0.0425
(1.00) 		1
(1.00) 		0.205
(1.00) 		0.555
(1.00) 		0.407
(1.00) 		0.532
(1.00)
xq loss 81 (13%) 534 0.987
(1.00) 		0.691
(1.00) 		0.108
(1.00) 		0.344
(1.00) 		0.053
(1.00) 		0.438
(1.00) 		0.508
(1.00) 		0.664
(1.00) 		0.0438
(1.00) 		0.717
(1.00) 		0.461
(1.00) 		0.00718
(1.00)
'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S1.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
2P GAIN MUTATED 47 25 12 31
2P GAIN WILD-TYPE 92 105 123 160

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S2.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
2P GAIN MUTATED 24 21 27 8 32 1 2
2P GAIN WILD-TYPE 54 103 69 55 118 35 46

Figure S2.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.17

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
2Q GAIN MUTATED 30 56 35
2Q GAIN WILD-TYPE 223 153 118

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

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S4.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
2Q GAIN MUTATED 21 21 29 5 33 1 3
2Q GAIN WILD-TYPE 57 103 67 58 117 35 45

Figure S4.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
3P GAIN MUTATED 13 45 15
3P GAIN WILD-TYPE 240 164 138

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

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
3Q GAIN MUTATED 14 59 26
3Q GAIN WILD-TYPE 239 150 127

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

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.18

Table S7.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
3Q GAIN MUTATED 12 18 27 4 29 0 5
3Q GAIN WILD-TYPE 66 106 69 59 121 36 43

Figure S7.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
5P GAIN MUTATED 26 50 29
5P GAIN WILD-TYPE 227 159 124

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

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.11

Table S9.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
5P GAIN MUTATED 17 6 25 8 33 3 7
5P GAIN WILD-TYPE 61 118 71 55 117 33 41

Figure S9.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S10.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
6P GAIN MUTATED 22 66 36
6P GAIN WILD-TYPE 231 143 117

Figure S10.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S11.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
6Q GAIN MUTATED 18 60 33
6Q GAIN WILD-TYPE 235 149 120

Figure S11.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S12.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
7P GAIN MUTATED 12 27 30 37
7P GAIN WILD-TYPE 37 14 46 12

Figure S12.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S13.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
7P GAIN MUTATED 86 159 104
7P GAIN WILD-TYPE 167 50 49

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S14.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 158 121
7P GAIN MUTATED 53 120 57
7P GAIN WILD-TYPE 45 38 64

Figure S14.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S15.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
7P GAIN MUTATED 102 78 57 100
7P GAIN WILD-TYPE 37 52 78 91

Figure S15.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S16.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
7P GAIN MUTATED 52 72 79 14 95 9 16
7P GAIN WILD-TYPE 26 52 17 49 55 27 32

Figure S16.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MRNA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.12

Table S17.  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 S17.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S18.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
7Q GAIN MUTATED 9 22 26 36
7Q GAIN WILD-TYPE 40 19 50 13

Figure S18.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S19.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
7Q GAIN MUTATED 82 141 89
7Q GAIN WILD-TYPE 171 68 64

Figure S19.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.059

Table S20.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 158 121
7Q GAIN MUTATED 46 106 52
7Q GAIN WILD-TYPE 52 52 69

Figure S20.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.042

Table S21.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
7Q GAIN MUTATED 92 67 52 89
7Q GAIN WILD-TYPE 47 63 83 102

Figure S21.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S22.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
7Q GAIN MUTATED 48 64 69 13 85 5 16
7Q GAIN WILD-TYPE 30 60 27 50 65 31 32

Figure S22.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S23.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
8P GAIN MUTATED 54 48 68
8P GAIN WILD-TYPE 199 161 85

Figure S23.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S24.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
8Q GAIN MUTATED 81 95 139
8Q GAIN WILD-TYPE 172 114 14

Figure S24.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S25.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
11P GAIN MUTATED 13 42 30
11P GAIN WILD-TYPE 240 167 123

Figure S25.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S26.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 158 121
11P GAIN MUTATED 12 38 6
11P GAIN WILD-TYPE 86 120 115

Figure S26.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
11Q GAIN MUTATED 7 39 31
11Q GAIN WILD-TYPE 246 170 122

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

'11q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 158 121
11Q GAIN MUTATED 8 35 5
11Q GAIN WILD-TYPE 90 123 116

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

'11q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
11Q GAIN MUTATED 31 14 4 25
11Q GAIN WILD-TYPE 108 116 131 166

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

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
11Q GAIN MUTATED 18 7 20 0 25 1 3
11Q GAIN WILD-TYPE 60 117 76 63 125 35 45

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

'13q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S31.  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 51 14
13Q GAIN WILD-TYPE 27 16 18 27

Figure S31.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S32.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
13Q GAIN MUTATED 12 29 48 38
13Q GAIN WILD-TYPE 37 12 28 11

Figure S32.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S33.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
13Q GAIN MUTATED 87 184 97
13Q GAIN WILD-TYPE 166 25 56

Figure S33.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S34.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 158 121
13Q GAIN MUTATED 56 122 54
13Q GAIN WILD-TYPE 42 36 67

Figure S34.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S35.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
13Q GAIN MUTATED 106 69 58 122
13Q GAIN WILD-TYPE 33 61 77 69

Figure S35.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S36.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
13Q GAIN MUTATED 57 75 71 15 111 9 17
13Q GAIN WILD-TYPE 21 49 25 48 39 27 31

Figure S36.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S37.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
16P GAIN MUTATED 17 88 42
16P GAIN WILD-TYPE 236 121 111

Figure S37.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.1

Table S38.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
16P GAIN MUTATED 44 25 16 55
16P GAIN WILD-TYPE 95 105 119 136

Figure S38.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S39.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
16P GAIN MUTATED 16 21 35 4 52 2 10
16P GAIN WILD-TYPE 62 103 61 59 98 34 38

Figure S39.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S40.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
16Q GAIN MUTATED 16 90 39
16Q GAIN WILD-TYPE 237 119 114

Figure S40.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.21

Table S41.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
16Q GAIN MUTATED 44 26 16 52
16Q GAIN WILD-TYPE 95 104 119 139

Figure S41.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S42.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
16Q GAIN MUTATED 16 21 37 4 49 1 10
16Q GAIN WILD-TYPE 62 103 59 59 101 35 38

Figure S42.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S43.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
17Q GAIN MUTATED 23 48 42
17Q GAIN WILD-TYPE 230 161 111

Figure S43.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S44.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
17Q GAIN MUTATED 44 15 14 35
17Q GAIN WILD-TYPE 95 115 121 156

Figure S44.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.13

Table S45.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
17Q GAIN MUTATED 25 19 20 3 34 3 4
17Q GAIN WILD-TYPE 53 105 76 60 116 33 44

Figure S45.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S46.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
18Q GAIN MUTATED 1 2 4 8 0 5 0
18Q GAIN WILD-TYPE 77 122 92 55 150 31 48

Figure S46.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S47.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
19P GAIN MUTATED 19 54 31
19P GAIN WILD-TYPE 234 155 122

Figure S47.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

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

Table S48.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
19Q GAIN MUTATED 29 55 30
19Q GAIN WILD-TYPE 224 154 123

Figure S48.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S49.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
20P GAIN MUTATED 13 27 51 35
20P GAIN WILD-TYPE 36 14 25 14

Figure S49.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S50.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
20P GAIN MUTATED 110 154 90
20P GAIN WILD-TYPE 143 55 63

Figure S50.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S51.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
20P GAIN MUTATED 52 77 62 17 108 5 21
20P GAIN WILD-TYPE 26 47 34 46 42 31 27

Figure S51.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S52.  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 S52.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S53.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
20Q GAIN MUTATED 15 39 61 48
20Q GAIN WILD-TYPE 34 2 15 1

Figure S53.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S54.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
20Q GAIN MUTATED 128 206 131
20Q GAIN WILD-TYPE 125 3 22

Figure S54.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S55.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 158 121
20Q GAIN MUTATED 68 152 67
20Q GAIN WILD-TYPE 30 6 54

Figure S55.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S56.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
20Q GAIN MUTATED 134 93 71 151
20Q GAIN WILD-TYPE 5 37 64 40

Figure S56.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S57.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
20Q GAIN MUTATED 71 93 88 20 143 6 28
20Q GAIN WILD-TYPE 7 31 8 43 7 30 20

Figure S57.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S58.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
1P LOSS MUTATED 33 74 31
1P LOSS WILD-TYPE 220 135 122

Figure S58.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S59.  Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
1Q LOSS MUTATED 29 17 4 25
1Q LOSS WILD-TYPE 110 113 131 166

Figure S59.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S60.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
4P LOSS MUTATED 44 106 47
4P LOSS WILD-TYPE 209 103 106

Figure S60.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.16

Table S61.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
4P LOSS MUTATED 59 41 24 65
4P LOSS WILD-TYPE 80 89 111 126

Figure S61.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.12

Table S62.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
4P LOSS MUTATED 33 33 38 7 57 8 13
4P LOSS WILD-TYPE 45 91 58 56 93 28 35

Figure S62.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S63.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
4Q LOSS MUTATED 38 103 50
4Q LOSS WILD-TYPE 215 106 103

Figure S63.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S64.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 158 121
4Q LOSS MUTATED 29 66 20
4Q LOSS WILD-TYPE 69 92 101

Figure S64.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.042

Table S65.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
4Q LOSS MUTATED 34 32 36 6 55 7 13
4Q LOSS WILD-TYPE 44 92 60 57 95 29 35

Figure S65.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S66.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
5Q LOSS MUTATED 23 47 49
5Q LOSS WILD-TYPE 230 162 104

Figure S66.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S67.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
8P LOSS MUTATED 36 103 79
8P LOSS WILD-TYPE 217 106 74

Figure S67.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.051

Table S68.  Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 158 121
8P LOSS MUTATED 29 74 26
8P LOSS WILD-TYPE 69 84 95

Figure S68.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S69.  Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
8P LOSS MUTATED 29 40 43 8 73 3 16
8P LOSS WILD-TYPE 49 84 53 55 77 33 32

Figure S69.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.15

Table S70.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
9P LOSS MUTATED 30 17 6 20
9P LOSS WILD-TYPE 109 113 129 171

Figure S70.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.084

Table S71.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
9Q LOSS MUTATED 29 19 5 20
9Q LOSS WILD-TYPE 110 111 130 171

Figure S71.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S72.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
10P LOSS MUTATED 20 47 35
10P LOSS WILD-TYPE 233 162 118

Figure S72.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.076

Table S73.  Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
10P LOSS MUTATED 17 15 29 3 25 1 7
10P LOSS WILD-TYPE 61 109 67 60 125 35 41

Figure S73.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S74.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
10Q LOSS MUTATED 16 52 43
10Q LOSS WILD-TYPE 237 157 110

Figure S74.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S75.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
10Q LOSS MUTATED 17 16 32 1 28 3 9
10Q LOSS WILD-TYPE 61 108 64 62 122 33 39

Figure S75.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S76.  Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
12P LOSS MUTATED 6 44 21
12P LOSS WILD-TYPE 247 165 132

Figure S76.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S77.  Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
12Q LOSS MUTATED 8 42 20
12Q LOSS WILD-TYPE 245 167 133

Figure S77.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.22

Table S78.  Gene #66: '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 S78.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.059

Table S79.  Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
14Q LOSS MUTATED 6 20 27 25
14Q LOSS WILD-TYPE 43 21 49 24

Figure S79.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S80.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
14Q LOSS MUTATED 33 141 33
14Q LOSS WILD-TYPE 220 68 120

Figure S80.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S81.  Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 158 121
14Q LOSS MUTATED 28 74 20
14Q LOSS WILD-TYPE 70 84 101

Figure S81.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S82.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
14Q LOSS MUTATED 71 28 21 78
14Q LOSS WILD-TYPE 68 102 114 113

Figure S82.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S83.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
14Q LOSS MUTATED 33 39 39 3 72 4 8
14Q LOSS WILD-TYPE 45 85 57 60 78 32 40

Figure S83.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.084

Table S84.  Gene #67: '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 S84.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S85.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
15Q LOSS MUTATED 38 124 67
15Q LOSS WILD-TYPE 215 85 86

Figure S85.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S86.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
15Q LOSS MUTATED 67 47 28 79
15Q LOSS WILD-TYPE 72 83 107 112

Figure S86.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S87.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
15Q LOSS MUTATED 35 39 50 2 71 7 17
15Q LOSS WILD-TYPE 43 85 46 61 79 29 31

Figure S87.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S88.  Gene #70: '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 S88.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.034

Table S89.  Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
17P LOSS MUTATED 13 27 47 34
17P LOSS WILD-TYPE 36 14 29 15

Figure S89.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S90.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
17P LOSS MUTATED 68 156 117
17P LOSS WILD-TYPE 185 53 36

Figure S90.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S91.  Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 158 121
17P LOSS MUTATED 43 116 50
17P LOSS WILD-TYPE 55 42 71

Figure S91.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S92.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
17P LOSS MUTATED 95 72 50 111
17P LOSS WILD-TYPE 44 58 85 80

Figure S92.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S93.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
17P LOSS MUTATED 49 69 69 8 102 8 23
17P LOSS WILD-TYPE 29 55 27 55 48 28 25

Figure S93.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S94.  Gene #72: '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 S94.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S95.  Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
18P LOSS MUTATED 10 35 44 42
18P LOSS WILD-TYPE 39 6 32 7

Figure S95.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S96.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
18P LOSS MUTATED 75 190 114
18P LOSS WILD-TYPE 178 19 39

Figure S96.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S97.  Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 158 121
18P LOSS MUTATED 50 144 43
18P LOSS WILD-TYPE 48 14 78

Figure S97.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S98.  Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
18P LOSS MUTATED 125 74 43 123
18P LOSS WILD-TYPE 14 56 92 68

Figure S98.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S99.  Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
18P LOSS MUTATED 66 70 77 8 118 6 20
18P LOSS WILD-TYPE 12 54 19 55 32 30 28

Figure S99.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S100.  Gene #72: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
18P LOSS MUTATED 21 10 25 20 12 5
18P LOSS WILD-TYPE 3 10 3 8 6 12

Figure S100.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S101.  Gene #73: '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 S101.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S102.  Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
18Q LOSS MUTATED 13 36 49 42
18Q LOSS WILD-TYPE 36 5 27 7

Figure S102.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S103.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
18Q LOSS MUTATED 84 193 131
18Q LOSS WILD-TYPE 169 16 22

Figure S103.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S104.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 98 158 121
18Q LOSS MUTATED 57 145 54
18Q LOSS WILD-TYPE 41 13 67

Figure S104.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S105.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
18Q LOSS MUTATED 127 84 53 130
18Q LOSS WILD-TYPE 12 46 82 61

Figure S105.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S106.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
18Q LOSS MUTATED 67 80 82 11 123 7 24
18Q LOSS WILD-TYPE 11 44 14 52 27 29 24

Figure S106.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.13

Table S107.  Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
18Q LOSS MUTATED 21 12 26 21 14 5
18Q LOSS WILD-TYPE 3 8 2 7 4 12

Figure S107.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.042

Table S108.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
20P LOSS MUTATED 12 28 26
20P LOSS WILD-TYPE 241 181 127

Figure S108.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S109.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
21Q LOSS MUTATED 54 97 43
21Q LOSS WILD-TYPE 199 112 110

Figure S109.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S110.  Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 139 130 135 191
21Q LOSS MUTATED 62 36 27 61
21Q LOSS WILD-TYPE 77 94 108 130

Figure S110.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.17

Table S111.  Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
22Q LOSS MUTATED 5 16 31 22
22Q LOSS WILD-TYPE 44 25 45 27

Figure S111.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0093

Table S112.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
22Q LOSS MUTATED 49 104 50
22Q LOSS WILD-TYPE 204 105 103

Figure S112.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S113.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 78 124 96 63 150 36 48
22Q LOSS MUTATED 30 41 37 6 63 4 15
22Q LOSS WILD-TYPE 48 83 59 57 87 32 33

Figure S113.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 615

  • Number of significantly arm-level cnvs = 80

  • 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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