Correlation between copy number variations of arm-level result and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1RR1X58
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/C1RR1X58
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 515 patients, 192 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

  • 1q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 2p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 3p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 4p gain cnv correlated to 'CN_CNMF'.

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

  • 5q gain cnv correlated to 'METHLYATION_CNMF'.

  • 6p gain cnv correlated to 'METHLYATION_CNMF'.

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

  • 7q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 9p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 11q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 15q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 20p gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 21q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • 3p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 12p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 15q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

  • 17p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF'.

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

  • 19p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'CN_CNMF'.

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

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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, 192 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
12p gain 137 (27%) 378 0.22
(1.00) 		0.0478
(1.00) 		1e-05
(0.00946) 		2e-05
(0.0169) 		0.00802
(1.00) 		0.357
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.371
(1.00) 		2e-05
(0.0169)
12q gain 130 (25%) 385 0.22
(1.00) 		0.137
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.0232
(1.00) 		0.199
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.226
(1.00) 		1e-05
(0.00946)
17q gain 191 (37%) 324 0.306
(1.00) 		0.876
(1.00) 		1e-05
(0.00946) 		4e-05
(0.0326) 		0.297
(1.00) 		0.272
(1.00) 		4e-05
(0.0326) 		1e-05
(0.00946) 		0.00012
(0.0935) 		4e-05
(0.0326) 		0.395
(1.00) 		0.00029
(0.22)
20q gain 199 (39%) 316 0.00426
(1.00) 		0.00892
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.109
(1.00) 		0.249
(1.00) 		2e-05
(0.0169) 		1e-05
(0.00946) 		2e-05
(0.0169) 		0.00012
(0.0935) 		0.161
(1.00) 		1e-05
(0.00946)
4p loss 120 (23%) 395 0.184
(1.00) 		0.382
(1.00) 		3e-05
(0.0248) 		1e-05
(0.00946) 		0.523
(1.00) 		0.693
(1.00) 		0.0001
(0.0786) 		2e-05
(0.0169) 		2e-05
(0.0169) 		1e-05
(0.00946) 		0.191
(1.00) 		0.0001
(0.0786)
4q loss 136 (26%) 379 0.00045
(0.335) 		0.00678
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.273
(1.00) 		0.337
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.0579
(1.00) 		2e-05
(0.0169)
5q loss 141 (27%) 374 0.064
(1.00) 		0.035
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.0654
(1.00) 		0.0544
(1.00) 		2e-05
(0.0169) 		0.0001
(0.0786) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.467
(1.00) 		2e-05
(0.0169)
22q loss 220 (43%) 295 0.126
(1.00) 		0.168
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.89
(1.00) 		0.62
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		7e-05
(0.0557) 		3e-05
(0.0248) 		0.112
(1.00) 		0.00016
(0.123)
2p gain 155 (30%) 360 0.301
(1.00) 		0.242
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.819
(1.00) 		0.973
(1.00) 		3e-05
(0.0248) 		4e-05
(0.0326) 		1e-05
(0.00946) 		0.00049
(0.363) 		0.0267
(1.00) 		0.00016
(0.123)
7p gain 264 (51%) 251 0.853
(1.00) 		0.538
(1.00) 		1e-05
(0.00946) 		0.0015
(1.00) 		0.00077
(0.561) 		0.00777
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.00035
(0.264) 		0.00016
(0.123) 		1e-05
(0.00946)
8q gain 246 (48%) 269 0.0236
(1.00) 		0.0474
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.649
(1.00) 		0.793
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.00362
(1.00) 		0.0149
(1.00) 		6e-05
(0.0481)
15q loss 242 (47%) 273 0.101
(1.00) 		0.282
(1.00) 		1e-05
(0.00946) 		0.00013
(0.101) 		0.0532
(1.00) 		0.00547
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		3e-05
(0.0248) 		0.00461
(1.00) 		0.308
(1.00) 		1e-05
(0.00946)
19p loss 244 (47%) 271 0.817
(1.00) 		1
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.877
(1.00) 		0.389
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.0312
(1.00) 		0.00157
(1.00)
19q loss 159 (31%) 356 0.344
(1.00) 		0.461
(1.00) 		1e-05
(0.00946) 		0.00012
(0.0935) 		0.267
(1.00) 		0.6
(1.00) 		0.00015
(0.116) 		5e-05
(0.0403) 		5e-05
(0.0403) 		2e-05
(0.0169) 		0.284
(1.00) 		0.00911
(1.00)
10p gain 112 (22%) 403 0.236
(1.00) 		0.298
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.0314
(1.00) 		0.169
(1.00) 		5e-05
(0.0403) 		1e-05
(0.00946) 		0.00043
(0.321) 		0.00018
(0.137) 		0.306
(1.00) 		0.00094
(0.683)
21q loss 165 (32%) 350 0.185
(1.00) 		0.145
(1.00) 		1e-05
(0.00946) 		0.00048
(0.356) 		0.0146
(1.00) 		0.048
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		2e-05
(0.0169) 		9e-05
(0.0709) 		0.591
(1.00) 		0.00044
(0.328)
3q gain 92 (18%) 423 0.0561
(1.00) 		0.0708
(1.00) 		5e-05
(0.0403) 		0.00013
(0.101) 		0.483
(1.00) 		0.0994
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.0138
(1.00) 		0.0328
(1.00) 		0.143
(1.00) 		0.00107
(0.766)
7q gain 217 (42%) 298 0.481
(1.00) 		0.31
(1.00) 		1e-05
(0.00946) 		0.00975
(1.00) 		0.0644
(1.00) 		0.0538
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.00308
(1.00) 		0.00125
(0.891) 		0.149
(1.00) 		2e-05
(0.0169)
11q gain 118 (23%) 397 0.0106
(1.00) 		0.0172
(1.00) 		1e-05
(0.00946) 		0.0134
(1.00) 		0.00854
(1.00) 		0.773
(1.00) 		0.00273
(1.00) 		0.00032
(0.242) 		0.00013
(0.101) 		3e-05
(0.0248) 		0.465
(1.00) 		0.00311
(1.00)
14q gain 126 (24%) 389 0.804
(1.00) 		0.846
(1.00) 		1e-05
(0.00946) 		0.00315
(1.00) 		0.433
(1.00) 		0.126
(1.00) 		0.00016
(0.123) 		5e-05
(0.0403) 		7e-05
(0.0557) 		0.00171
(1.00) 		0.148
(1.00) 		0.153
(1.00)
16q loss 140 (27%) 375 0.552
(1.00) 		0.626
(1.00) 		1e-05
(0.00946) 		3e-05
(0.0248) 		0.192
(1.00) 		0.038
(1.00) 		1e-05
(0.00946) 		3e-05
(0.0248) 		0.0104
(1.00) 		0.00282
(1.00) 		0.873
(1.00) 		0.00069
(0.505)
18q loss 216 (42%) 299 0.517
(1.00) 		0.425
(1.00) 		1e-05
(0.00946) 		0.23
(1.00) 		0.00409
(1.00) 		3e-05
(0.0248) 		0.00011
(0.086) 		0.00013
(0.101) 		0.0427
(1.00) 		0.635
(1.00) 		0.594
(1.00) 		0.167
(1.00)
5p gain 274 (53%) 241 0.798
(1.00) 		0.361
(1.00) 		1e-05
(0.00946) 		0.0952
(1.00) 		0.0509
(1.00) 		0.00339
(1.00) 		0.0414
(1.00) 		1e-05
(0.00946) 		0.0338
(1.00) 		0.126
(1.00) 		0.654
(1.00) 		0.00016
(0.123)
18p gain 93 (18%) 422 0.877
(1.00) 		0.637
(1.00) 		4e-05
(0.0326) 		1e-05
(0.00946) 		0.183
(1.00) 		0.894
(1.00) 		0.0223
(1.00) 		0.00327
(1.00) 		0.0249
(1.00) 		0.0178
(1.00) 		0.15
(1.00) 		0.00025
(0.189)
18q gain 71 (14%) 444 0.595
(1.00) 		0.147
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.0714
(1.00) 		0.234
(1.00) 		2e-05
(0.0169) 		0.0006
(0.442) 		0.0127
(1.00) 		0.00258
(1.00) 		0.0439
(1.00) 		0.0031
(1.00)
20p gain 173 (34%) 342 0.0701
(1.00) 		0.139
(1.00) 		0.00351
(1.00) 		0.00012
(0.0935) 		0.168
(1.00) 		0.515
(1.00) 		0.00037
(0.278) 		1e-05
(0.00946) 		6e-05
(0.0481) 		0.00051
(0.376) 		0.0632
(1.00) 		0.00039
(0.292)
1p loss 82 (16%) 433 0.0811
(1.00) 		0.126
(1.00) 		1e-05
(0.00946) 		0.00128
(0.911) 		0.133
(1.00) 		0.135
(1.00) 		0.00015
(0.116) 		1e-05
(0.00946) 		0.226
(1.00) 		0.0315
(1.00) 		0.14
(1.00) 		0.263
(1.00)
3p loss 213 (41%) 302 0.342
(1.00) 		0.113
(1.00) 		4e-05
(0.0326) 		6e-05
(0.0481) 		0.517
(1.00) 		0.321
(1.00) 		0.0406
(1.00) 		1e-05
(0.00946) 		0.0122
(1.00) 		0.00985
(1.00) 		0.256
(1.00) 		0.018
(1.00)
8p loss 202 (39%) 313 0.131
(1.00) 		0.0797
(1.00) 		1e-05
(0.00946) 		0.00989
(1.00) 		0.266
(1.00) 		0.00649
(1.00) 		6e-05
(0.0481) 		1e-05
(0.00946) 		0.0056
(1.00) 		0.0151
(1.00) 		0.00763
(1.00) 		0.00305
(1.00)
9q loss 248 (48%) 267 0.5
(1.00) 		0.902
(1.00) 		0.00011
(0.086) 		0.00022
(0.167) 		0.549
(1.00) 		0.0866
(1.00) 		0.135
(1.00) 		0.00037
(0.278) 		0.00237
(1.00) 		2e-05
(0.0169) 		0.174
(1.00) 		0.00457
(1.00)
10p loss 110 (21%) 405 0.815
(1.00) 		0.788
(1.00) 		1e-05
(0.00946) 		0.033
(1.00) 		0.0624
(1.00) 		0.0169
(1.00) 		6e-05
(0.0481) 		1e-05
(0.00946) 		0.00314
(1.00) 		0.277
(1.00) 		0.0243
(1.00) 		0.0324
(1.00)
13q loss 252 (49%) 263 0.106
(1.00) 		0.625
(1.00) 		1e-05
(0.00946) 		0.054
(1.00) 		0.00333
(1.00) 		0.0163
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.00998
(1.00) 		0.0225
(1.00) 		0.234
(1.00) 		0.00335
(1.00)
16p loss 111 (22%) 404 0.452
(1.00) 		0.483
(1.00) 		1e-05
(0.00946) 		7e-05
(0.0557) 		0.744
(1.00) 		0.00301
(1.00) 		8e-05
(0.0634) 		0.00103
(0.742) 		0.00358
(1.00) 		0.00433
(1.00) 		0.504
(1.00) 		0.00225
(1.00)
2q gain 140 (27%) 375 0.126
(1.00) 		0.289
(1.00) 		1e-05
(0.00946) 		2e-05
(0.0169) 		0.915
(1.00) 		0.707
(1.00) 		0.0786
(1.00) 		0.0145
(1.00) 		0.0019
(1.00) 		0.089
(1.00) 		0.0153
(1.00) 		0.00877
(1.00)
3p gain 41 (8%) 474 0.00186
(1.00) 		0.0372
(1.00) 		0.926
(1.00) 		0.743
(1.00) 		3e-05
(0.0248) 		0.00015
(0.116) 		0.111
(1.00) 		0.117
(1.00) 		0.557
(1.00) 		0.0149
(1.00)
8p gain 126 (24%) 389 0.15
(1.00) 		0.254
(1.00) 		1e-05
(0.00946) 		0.0952
(1.00) 		0.59
(1.00) 		0.253
(1.00) 		0.00072
(0.526) 		9e-05
(0.0709) 		0.425
(1.00) 		0.839
(1.00) 		0.395
(1.00) 		0.478
(1.00)
10q gain 78 (15%) 437 0.00229
(1.00) 		2e-05
(0.0169) 		0.36
(1.00) 		0.195
(1.00) 		0.00049
(0.363) 		3e-05
(0.0248) 		0.147
(1.00) 		0.0415
(1.00) 		0.984
(1.00) 		0.064
(1.00)
11p gain 96 (19%) 419 0.0006
(0.442) 		0.00098
(0.71) 		2e-05
(0.0169) 		0.327
(1.00) 		0.00098
(0.71) 		0.678
(1.00) 		0.104
(1.00) 		0.00045
(0.335) 		0.00095
(0.69) 		1e-05
(0.00946) 		0.395
(1.00) 		0.0279
(1.00)
15q gain 39 (8%) 476 0.193
(1.00) 		0.147
(1.00) 		0.798
(1.00) 		0.137
(1.00) 		0.272
(1.00) 		0.349
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.737
(1.00) 		0.661
(1.00) 		0.145
(1.00) 		0.902
(1.00)
6q loss 217 (42%) 298 0.247
(1.00) 		0.542
(1.00) 		0.00832
(1.00) 		0.00011
(0.086) 		0.2
(1.00) 		0.235
(1.00) 		0.131
(1.00) 		0.00022
(0.167) 		0.675
(1.00) 		0.00136
(0.963) 		0.744
(1.00) 		0.173
(1.00)
10q loss 132 (26%) 383 0.816
(1.00) 		0.789
(1.00) 		4e-05
(0.0326) 		0.0307
(1.00) 		0.0295
(1.00) 		0.0302
(1.00) 		0.00136
(0.963) 		1e-05
(0.00946) 		0.00344
(1.00) 		0.00613
(1.00) 		0.0138
(1.00) 		0.00119
(0.85)
12q loss 99 (19%) 416 0.555
(1.00) 		0.425
(1.00) 		4e-05
(0.0326) 		0.0844
(1.00) 		0.201
(1.00) 		0.0822
(1.00) 		0.00129
(0.917) 		8e-05
(0.0634) 		0.0956
(1.00) 		0.227
(1.00) 		0.906
(1.00) 		0.213
(1.00)
17p loss 215 (42%) 300 0.551
(1.00) 		0.362
(1.00) 		1e-05
(0.00946) 		0.0001
(0.0786) 		0.0265
(1.00) 		0.00902
(1.00) 		0.00103
(0.742) 		0.00132
(0.936) 		0.297
(1.00) 		0.128
(1.00) 		0.77
(1.00) 		0.0166
(1.00)
1p gain 141 (27%) 374 0.631
(1.00) 		1
(1.00) 		1e-05
(0.00946) 		0.612
(1.00) 		0.0133
(1.00) 		0.0279
(1.00) 		0.204
(1.00) 		0.0484
(1.00) 		0.0442
(1.00) 		0.2
(1.00) 		0.183
(1.00) 		0.0968
(1.00)
1q gain 311 (60%) 204 0.121
(1.00) 		1
(1.00) 		0.0134
(1.00) 		0.00805
(1.00) 		0.00102
(0.735) 		0.0067
(1.00) 		0.128
(1.00) 		0.00031
(0.234) 		0.618
(1.00) 		0.0594
(1.00) 		0.0227
(1.00) 		0.118
(1.00)
4p gain 83 (16%) 432 0.876
(1.00) 		1
(1.00) 		2e-05
(0.0169) 		0.153
(1.00) 		0.434
(1.00) 		0.111
(1.00) 		0.043
(1.00) 		0.283
(1.00) 		0.136
(1.00) 		0.237
(1.00) 		0.915
(1.00) 		0.18
(1.00)
5q gain 129 (25%) 386 0.196
(1.00) 		0.288
(1.00) 		0.00954
(1.00) 		8e-05
(0.0634) 		0.372
(1.00) 		0.313
(1.00) 		0.00625
(1.00) 		0.0267
(1.00) 		0.158
(1.00) 		0.00994
(1.00) 		0.429
(1.00) 		0.0721
(1.00)
6p gain 142 (28%) 373 0.353
(1.00) 		0.0879
(1.00) 		0.00034
(0.256) 		1e-05
(0.00946) 		0.031
(1.00) 		0.856
(1.00) 		0.0761
(1.00) 		0.00895
(1.00) 		0.0615
(1.00) 		0.00732
(1.00) 		0.642
(1.00) 		0.00985
(1.00)
9p gain 45 (9%) 470 0.00129
(0.917) 		0.137
(1.00) 		0.939
(1.00) 		0.277
(1.00) 		0.00024
(0.182) 		0.00473
(1.00) 		0.15
(1.00) 		0.639
(1.00) 		0.0952
(1.00) 		0.138
(1.00)
17p gain 85 (17%) 430 0.454
(1.00) 		0.687
(1.00) 		3e-05
(0.0248) 		0.0618
(1.00) 		0.96
(1.00) 		0.691
(1.00) 		0.0124
(1.00) 		0.0384
(1.00) 		0.0041
(1.00) 		0.063
(1.00) 		0.661
(1.00) 		0.387
(1.00)
21q gain 97 (19%) 418 0.539
(1.00) 		0.264
(1.00) 		0.00515
(1.00) 		0.673
(1.00) 		0.431
(1.00) 		0.0221
(1.00) 		0.0298
(1.00) 		7e-05
(0.0557) 		0.682
(1.00) 		0.743
(1.00) 		0.456
(1.00) 		0.406
(1.00)
9p loss 264 (51%) 251 0.0516
(1.00) 		0.601
(1.00) 		0.00049
(0.363) 		0.0211
(1.00) 		0.813
(1.00) 		0.0567
(1.00) 		0.00097
(0.703) 		6e-05
(0.0481) 		0.0172
(1.00) 		0.00061
(0.448) 		0.194
(1.00) 		0.0684
(1.00)
11p loss 112 (22%) 403 0.0527
(1.00) 		0.126
(1.00) 		1e-05
(0.00946) 		0.00815
(1.00) 		0.707
(1.00) 		0.755
(1.00) 		0.00276
(1.00) 		0.00705
(1.00) 		0.0251
(1.00) 		0.0418
(1.00) 		0.202
(1.00) 		0.0421
(1.00)
12p loss 113 (22%) 402 0.63
(1.00) 		0.881
(1.00) 		0.00101
(0.729) 		0.244
(1.00) 		0.0321
(1.00) 		0.15
(1.00) 		0.00608
(1.00) 		0.0002
(0.152) 		0.106
(1.00) 		0.347
(1.00) 		0.989
(1.00) 		0.153
(1.00)
18p loss 181 (35%) 334 0.436
(1.00) 		0.454
(1.00) 		1e-05
(0.00946) 		0.608
(1.00) 		0.0229
(1.00) 		0.021
(1.00) 		0.0193
(1.00) 		0.00234
(1.00) 		0.0401
(1.00) 		0.375
(1.00) 		0.973
(1.00) 		0.596
(1.00)
20p loss 117 (23%) 398 0.221
(1.00) 		0.241
(1.00) 		8e-05
(0.0634) 		0.00039
(0.292) 		0.00057
(0.42) 		0.00263
(1.00) 		0.00665
(1.00) 		0.0011
(0.786) 		0.951
(1.00) 		0.959
(1.00) 		0.252
(1.00) 		0.0178
(1.00)
4q gain 47 (9%) 468 0.33
(1.00) 		0.582
(1.00) 		0.00142
(1.00) 		0.84
(1.00) 		0.68
(1.00) 		0.163
(1.00) 		0.00754
(1.00) 		0.0035
(1.00) 		0.071
(1.00) 		0.274
(1.00) 		0.506
(1.00) 		0.198
(1.00)
6q gain 60 (12%) 455 1
(1.00) 		1
(1.00) 		0.0435
(1.00) 		0.00335
(1.00) 		0.431
(1.00) 		0.846
(1.00) 		0.163
(1.00) 		0.0142
(1.00) 		0.00922
(1.00) 		0.00842
(1.00) 		0.981
(1.00) 		0.256
(1.00)
9q gain 34 (7%) 481 0.0306
(1.00) 		0.452
(1.00) 		0.773
(1.00) 		0.705
(1.00) 		0.0772
(1.00) 		0.116
(1.00) 		0.194
(1.00) 		0.805
(1.00) 		0.27
(1.00) 		0.135
(1.00)
13q gain 43 (8%) 472 0.413
(1.00) 		0.543
(1.00) 		0.978
(1.00) 		0.00691
(1.00) 		0.0426
(1.00) 		0.0341
(1.00) 		0.0593
(1.00) 		0.128
(1.00) 		0.83
(1.00) 		0.363
(1.00) 		0.431
(1.00) 		0.537
(1.00)
16p gain 136 (26%) 379 0.531
(1.00) 		0.336
(1.00) 		0.00924
(1.00) 		0.0129
(1.00) 		0.0863
(1.00) 		0.0214
(1.00) 		0.111
(1.00) 		0.00484
(1.00) 		0.00259
(1.00) 		0.721
(1.00) 		0.0265
(1.00) 		0.101
(1.00)
16q gain 102 (20%) 413 0.439
(1.00) 		0.154
(1.00) 		0.00736
(1.00) 		0.0829
(1.00) 		0.0101
(1.00) 		0.0268
(1.00) 		0.45
(1.00) 		0.0219
(1.00) 		0.00147
(1.00) 		0.11
(1.00) 		0.16
(1.00) 		0.13
(1.00)
19p gain 33 (6%) 482 0.192
(1.00) 		0.0418
(1.00) 		0.416
(1.00) 		0.735
(1.00) 		0.702
(1.00) 		0.774
(1.00) 		0.993
(1.00) 		0.746
(1.00) 		0.437
(1.00) 		0.858
(1.00) 		0.905
(1.00) 		0.475
(1.00)
19q gain 76 (15%) 439 0.0497
(1.00) 		0.04
(1.00) 		0.00333
(1.00) 		0.0168
(1.00) 		0.872
(1.00) 		0.927
(1.00) 		0.216
(1.00) 		0.0143
(1.00) 		0.173
(1.00) 		0.478
(1.00) 		0.423
(1.00) 		0.00228
(1.00)
22q gain 62 (12%) 453 0.11
(1.00) 		0.119
(1.00) 		0.00421
(1.00) 		0.925
(1.00) 		0.108
(1.00) 		0.282
(1.00) 		0.177
(1.00) 		0.0964
(1.00) 		0.449
(1.00) 		0.564
(1.00) 		0.278
(1.00) 		0.538
(1.00)
xq gain 77 (15%) 438 0.658
(1.00) 		0.247
(1.00) 		0.00035
(0.264) 		0.1
(1.00) 		0.869
(1.00) 		0.151
(1.00) 		0.0516
(1.00) 		0.0201
(1.00) 		0.0448
(1.00) 		0.158
(1.00) 		0.268
(1.00) 		0.0692
(1.00)
1q loss 27 (5%) 488 0.133
(1.00) 		0.0194
(1.00) 		0.106
(1.00) 		0.026
(1.00) 		0.0725
(1.00) 		0.173
(1.00) 		0.832
(1.00) 		0.498
(1.00) 		0.926
(1.00) 		0.146
(1.00)
2p loss 23 (4%) 492 0.751
(1.00) 		0.58
(1.00) 		0.0645
(1.00) 		0.173
(1.00) 		0.549
(1.00) 		0.989
(1.00) 		0.974
(1.00) 		0.909
(1.00) 		0.0448
(1.00) 		0.491
(1.00) 		0.253
(1.00) 		0.125
(1.00)
2q loss 24 (5%) 491 0.00066
(0.484) 		0.0478
(1.00) 		0.463
(1.00) 		0.442
(1.00) 		0.292
(1.00) 		0.39
(1.00) 		0.14
(1.00) 		0.665
(1.00) 		0.632
(1.00) 		0.223
(1.00)
3q loss 146 (28%) 369 0.553
(1.00) 		0.144
(1.00) 		0.00705
(1.00) 		0.0139
(1.00) 		0.806
(1.00) 		0.491
(1.00) 		0.0741
(1.00) 		0.00103
(0.742) 		0.233
(1.00) 		0.412
(1.00) 		0.389
(1.00) 		0.866
(1.00)
5p loss 44 (9%) 471 0.597
(1.00) 		0.308
(1.00) 		0.198
(1.00) 		0.00922
(1.00) 		0.0874
(1.00) 		0.24
(1.00) 		0.00706
(1.00) 		0.00179
(1.00) 		0.114
(1.00) 		0.00178
(1.00) 		0.624
(1.00) 		0.00164
(1.00)
6p loss 105 (20%) 410 0.0129
(1.00) 		0.00442
(1.00) 		0.0163
(1.00) 		0.219
(1.00) 		0.522
(1.00) 		0.264
(1.00) 		0.154
(1.00) 		0.254
(1.00) 		0.336
(1.00) 		0.0236
(1.00) 		0.734
(1.00) 		0.181
(1.00)
7p loss 35 (7%) 480 1
(1.00) 		1
(1.00) 		0.00212
(1.00) 		0.0112
(1.00) 		0.291
(1.00) 		0.993
(1.00) 		0.00534
(1.00) 		0.00175
(1.00) 		0.0906
(1.00) 		0.141
(1.00) 		0.065
(1.00) 		0.0791
(1.00)
7q loss 42 (8%) 473 0.805
(1.00) 		0.256
(1.00) 		0.0586
(1.00) 		0.0201
(1.00) 		0.889
(1.00) 		0.961
(1.00) 		0.111
(1.00) 		0.0375
(1.00) 		0.388
(1.00) 		0.143
(1.00) 		0.728
(1.00) 		0.825
(1.00)
8q loss 56 (11%) 459 0.031
(1.00) 		0.664
(1.00) 		0.492
(1.00) 		0.249
(1.00) 		0.23
(1.00) 		0.0778
(1.00) 		0.535
(1.00) 		0.599
(1.00) 		0.149
(1.00) 		0.254
(1.00)
11q loss 90 (17%) 425 0.841
(1.00) 		0.482
(1.00) 		0.0007
(0.512) 		0.0143
(1.00) 		0.305
(1.00) 		0.231
(1.00) 		0.00104
(0.746) 		0.00639
(1.00) 		0.0423
(1.00) 		0.0302
(1.00) 		0.0364
(1.00) 		0.213
(1.00)
14q loss 115 (22%) 400 0.929
(1.00) 		0.411
(1.00) 		0.0202
(1.00) 		0.442
(1.00) 		0.331
(1.00) 		0.107
(1.00) 		0.0308
(1.00) 		0.00463
(1.00) 		0.0238
(1.00) 		0.17
(1.00) 		0.191
(1.00) 		0.0477
(1.00)
17q loss 58 (11%) 457 0.293
(1.00) 		0.474
(1.00) 		0.00086
(0.626) 		0.0842
(1.00) 		0.00885
(1.00) 		0.0734
(1.00) 		0.138
(1.00) 		0.506
(1.00) 		0.836
(1.00) 		0.161
(1.00) 		0.98
(1.00) 		0.807
(1.00)
20q loss 69 (13%) 446 0.256
(1.00) 		0.498
(1.00) 		0.456
(1.00) 		0.62
(1.00) 		0.105
(1.00) 		0.216
(1.00) 		0.529
(1.00) 		0.478
(1.00) 		0.497
(1.00) 		0.63
(1.00) 		0.0928
(1.00) 		0.897
(1.00)
xq loss 68 (13%) 447 0.172
(1.00) 		0.254
(1.00) 		0.00046
(0.342) 		0.00477
(1.00) 		0.399
(1.00) 		0.813
(1.00) 		0.324
(1.00) 		0.58
(1.00) 		0.209
(1.00) 		0.13
(1.00) 		0.84
(1.00) 		0.455
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
1P GAIN MUTATED 81 44 16
1P GAIN WILD-TYPE 110 185 79

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.23

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
1Q GAIN MUTATED 54 38 15 46 36 36 30 6 31
1Q GAIN WILD-TYPE 29 19 29 38 10 15 19 12 23

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
2P GAIN MUTATED 76 38 41
2P GAIN WILD-TYPE 115 191 54

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
2P GAIN MUTATED 10 58 32 27
2P GAIN WILD-TYPE 86 67 76 89

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
2P GAIN MUTATED 40 18 26 49 16
2P GAIN WILD-TYPE 98 94 50 57 38

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S6.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
2P GAIN MUTATED 23 11 11 32 8 26 22 0 16
2P GAIN WILD-TYPE 60 46 33 52 38 25 27 18 38

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
2P GAIN MUTATED 40 95 19
2P GAIN WILD-TYPE 149 133 74

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.12

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
2P GAIN MUTATED 16 92 19
2P GAIN WILD-TYPE 87 156 64

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S9.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
2Q GAIN MUTATED 63 38 39
2Q GAIN WILD-TYPE 128 191 56

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

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

Table S10.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
2Q GAIN MUTATED 13 50 32 23
2Q GAIN WILD-TYPE 83 75 76 93

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S11.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
3P GAIN MUTATED 20 0 3 12 5
3P GAIN WILD-TYPE 118 112 73 94 49

Figure S11.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.12

Table S12.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
3P GAIN MUTATED 11 0 4 17 1 2 2 0 3
3P GAIN WILD-TYPE 72 57 40 67 45 49 47 18 51

Figure S12.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.04

Table S13.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
3Q GAIN MUTATED 47 23 22
3Q GAIN WILD-TYPE 144 206 73

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S14.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
3Q GAIN MUTATED 4 31 23 22
3Q GAIN WILD-TYPE 92 94 85 94

Figure S14.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S15.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
3Q GAIN MUTATED 35 2 16 23 10
3Q GAIN WILD-TYPE 103 110 60 83 44

Figure S15.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S16.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
3Q GAIN MUTATED 17 2 10 35 2 6 8 2 4
3Q GAIN WILD-TYPE 66 55 34 49 44 45 41 16 50

Figure S16.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

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

Table S17.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
4P GAIN MUTATED 50 20 13
4P GAIN WILD-TYPE 141 209 82

Figure S17.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S18.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
5P GAIN MUTATED 136 93 45
5P GAIN WILD-TYPE 55 136 50

Figure S18.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S19.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
5P GAIN MUTATED 57 29 17 55 16 31 25 0 30
5P GAIN WILD-TYPE 26 28 27 29 30 20 24 18 24

Figure S19.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.12

Table S20.  Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
5P GAIN MUTATED 37 149 49
5P GAIN WILD-TYPE 66 99 34

Figure S20.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.063

Table S21.  Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
5Q GAIN MUTATED 43 27 21 23
5Q GAIN WILD-TYPE 53 98 87 93

Figure S21.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S22.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
6P GAIN MUTATED 19 59 29 16
6P GAIN WILD-TYPE 77 66 79 100

Figure S22.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S23.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
7P GAIN MUTATED 140 84 40
7P GAIN WILD-TYPE 51 145 55

Figure S23.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S24.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
7P GAIN MUTATED 103 32 38 47 27
7P GAIN WILD-TYPE 35 80 38 59 27

Figure S24.  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 = 0.0095

Table S25.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
7P GAIN MUTATED 53 20 35 51 9 21 27 2 29
7P GAIN WILD-TYPE 30 37 9 33 37 30 22 16 25

Figure S25.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S26.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
7P GAIN MUTATED 71 128 62
7P GAIN WILD-TYPE 118 100 31

Figure S26.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.12

Table S27.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 198 91
7P GAIN MUTATED 61 102 63
7P GAIN WILD-TYPE 84 96 28

Figure S27.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S28.  Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
7P GAIN MUTATED 29 147 50
7P GAIN WILD-TYPE 74 101 33

Figure S28.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S29.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
7Q GAIN MUTATED 114 65 38
7Q GAIN WILD-TYPE 77 164 57

Figure S29.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S30.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
7Q GAIN MUTATED 87 27 33 34 22
7Q GAIN WILD-TYPE 51 85 43 72 32

Figure S30.  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 = 0.0095

Table S31.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
7Q GAIN MUTATED 47 17 30 38 7 16 24 2 22
7Q GAIN WILD-TYPE 36 40 14 46 39 35 25 16 32

Figure S31.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S32.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
7Q GAIN MUTATED 22 120 40
7Q GAIN WILD-TYPE 81 128 43

Figure S32.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S33.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
8P GAIN MUTATED 38 39 49
8P GAIN WILD-TYPE 153 190 46

Figure S33.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.071

Table S34.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
8P GAIN MUTATED 21 6 8 17 14 24 16 0 12
8P GAIN WILD-TYPE 62 51 36 67 32 27 33 18 42

Figure S34.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S35.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
8Q GAIN MUTATED 98 68 80
8Q GAIN WILD-TYPE 93 161 15

Figure S35.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S36.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
8Q GAIN MUTATED 31 82 56 47
8Q GAIN WILD-TYPE 65 43 52 69

Figure S36.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S37.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
8Q GAIN MUTATED 69 33 32 73 21
8Q GAIN WILD-TYPE 69 79 44 33 33

Figure S37.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S38.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
8Q GAIN MUTATED 35 17 28 43 19 40 25 0 21
8Q GAIN WILD-TYPE 48 40 16 41 27 11 24 18 33

Figure S38.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S39.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
8Q GAIN MUTATED 63 131 50
8Q GAIN WILD-TYPE 126 97 43

Figure S39.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S40.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
8Q GAIN MUTATED 32 142 37
8Q GAIN WILD-TYPE 71 106 46

Figure S40.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.18

Table S41.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
9P GAIN MUTATED 14 4 0 16 7
9P GAIN WILD-TYPE 124 108 76 90 47

Figure S41.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S42.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
10P GAIN MUTATED 44 31 37
10P GAIN WILD-TYPE 147 198 58

Figure S42.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S43.  Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
10P GAIN MUTATED 5 44 34 16
10P GAIN WILD-TYPE 91 81 74 100

Figure S43.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.04

Table S44.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
10P GAIN MUTATED 28 10 21 37 9
10P GAIN WILD-TYPE 110 102 55 69 45

Figure S44.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S45.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
10P GAIN MUTATED 13 3 10 16 13 22 17 0 11
10P GAIN WILD-TYPE 70 54 34 68 33 29 32 18 43

Figure S45.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.14

Table S46.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
10P GAIN MUTATED 12 58 15 25
10P GAIN WILD-TYPE 59 140 126 75

Figure S46.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'METHLYATION_CNMF'

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

Table S47.  Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
10Q GAIN MUTATED 4 33 23 10
10Q GAIN WILD-TYPE 92 92 85 106

Figure S47.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S48.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
10Q GAIN MUTATED 10 2 7 7 13 16 13 0 7
10Q GAIN WILD-TYPE 73 55 37 77 33 35 36 18 47

Figure S48.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

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

Table S49.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
11P GAIN MUTATED 48 23 25
11P GAIN WILD-TYPE 143 206 70

Figure S49.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S50.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
11P GAIN MUTATED 4 40 17 34
11P GAIN WILD-TYPE 67 158 124 66

Figure S50.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S51.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
11Q GAIN MUTATED 68 25 25
11Q GAIN WILD-TYPE 123 204 70

Figure S51.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.24

Table S52.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
11Q GAIN MUTATED 22 15 11 27 1 18 9 1 9
11Q GAIN WILD-TYPE 61 42 33 57 45 33 40 17 45

Figure S52.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S53.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
11Q GAIN MUTATED 24 63 28
11Q GAIN WILD-TYPE 165 165 65

Figure S53.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S54.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
11Q GAIN MUTATED 5 52 23 35
11Q GAIN WILD-TYPE 66 146 118 65

Figure S54.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S55.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
12P GAIN MUTATED 56 37 44
12P GAIN WILD-TYPE 135 192 51

Figure S55.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

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

Table S56.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
12P GAIN MUTATED 10 52 28 30
12P GAIN WILD-TYPE 86 73 80 86

Figure S56.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S57.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
12P GAIN MUTATED 41 5 30 42 12
12P GAIN WILD-TYPE 97 107 46 64 42

Figure S57.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S58.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
12P GAIN MUTATED 17 5 16 26 3 27 24 2 10
12P GAIN WILD-TYPE 66 52 28 58 43 24 25 16 44

Figure S58.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S59.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
12P GAIN MUTATED 29 82 24
12P GAIN WILD-TYPE 160 146 69

Figure S59.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S60.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
12P GAIN MUTATED 10 58 20 47
12P GAIN WILD-TYPE 61 140 121 53

Figure S60.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S61.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
12P GAIN MUTATED 10 89 18
12P GAIN WILD-TYPE 93 159 65

Figure S61.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S62.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
12Q GAIN MUTATED 46 36 48
12Q GAIN WILD-TYPE 145 193 47

Figure S62.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S63.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
12Q GAIN MUTATED 7 50 28 29
12Q GAIN WILD-TYPE 89 75 80 87

Figure S63.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S64.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
12Q GAIN MUTATED 32 6 29 49 9
12Q GAIN WILD-TYPE 106 106 47 57 45

Figure S64.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S65.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
12Q GAIN MUTATED 16 6 15 20 3 32 25 2 6
12Q GAIN WILD-TYPE 67 51 29 64 43 19 24 16 48

Figure S65.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S66.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
12Q GAIN MUTATED 27 82 19
12Q GAIN WILD-TYPE 162 146 74

Figure S66.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S67.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
12Q GAIN MUTATED 13 58 14 43
12Q GAIN WILD-TYPE 58 140 127 57

Figure S67.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S68.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
12Q GAIN MUTATED 8 84 19
12Q GAIN WILD-TYPE 95 164 64

Figure S68.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S69.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
14Q GAIN MUTATED 50 34 42
14Q GAIN WILD-TYPE 141 195 53

Figure S69.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.12

Table S70.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
14Q GAIN MUTATED 37 19 9 42 11
14Q GAIN WILD-TYPE 101 93 67 64 43

Figure S70.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.04

Table S71.  Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
14Q GAIN MUTATED 14 12 11 38 8 19 8 0 8
14Q GAIN WILD-TYPE 69 45 33 46 38 32 41 18 46

Figure S71.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.056

Table S72.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
14Q GAIN MUTATED 27 62 34
14Q GAIN WILD-TYPE 162 166 59

Figure S72.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S73.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
15Q GAIN MUTATED 3 5 19 6 2
15Q GAIN WILD-TYPE 135 107 57 100 52

Figure S73.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S74.  Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
15Q GAIN MUTATED 2 1 0 3 3 4 15 3 4
15Q GAIN WILD-TYPE 81 56 44 81 43 47 34 15 50

Figure S74.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S75.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
17P GAIN MUTATED 33 22 30
17P GAIN WILD-TYPE 158 207 65

Figure S75.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S76.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
17Q GAIN MUTATED 99 47 45
17Q GAIN WILD-TYPE 92 182 50

Figure S76.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S77.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
17Q GAIN MUTATED 20 55 56 35
17Q GAIN WILD-TYPE 76 70 52 81

Figure S77.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S78.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
17Q GAIN MUTATED 72 28 20 44 18
17Q GAIN WILD-TYPE 66 84 56 62 36

Figure S78.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S79.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
17Q GAIN MUTATED 40 19 21 41 5 26 14 0 16
17Q GAIN WILD-TYPE 43 38 23 43 41 25 35 18 38

Figure S79.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.093

Table S80.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
17Q GAIN MUTATED 49 104 36
17Q GAIN WILD-TYPE 140 124 57

Figure S80.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S81.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
17Q GAIN MUTATED 19 87 34 49
17Q GAIN WILD-TYPE 52 111 107 51

Figure S81.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.22

Table S82.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
17Q GAIN MUTATED 22 107 35
17Q GAIN WILD-TYPE 81 141 48

Figure S82.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S83.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
18P GAIN MUTATED 45 22 26
18P GAIN WILD-TYPE 146 207 69

Figure S83.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S84.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
18P GAIN MUTATED 7 40 23 11
18P GAIN WILD-TYPE 89 85 85 105

Figure S84.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.19

Table S85.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
18P GAIN MUTATED 6 57 16
18P GAIN WILD-TYPE 97 191 67

Figure S85.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S86.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
18Q GAIN MUTATED 30 14 27
18Q GAIN WILD-TYPE 161 215 68

Figure S86.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S87.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
18Q GAIN MUTATED 4 37 14 6
18Q GAIN WILD-TYPE 92 88 94 110

Figure S87.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

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

Table S88.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
18Q GAIN MUTATED 13 8 9 31 4
18Q GAIN WILD-TYPE 125 104 67 75 50

Figure S88.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.093

Table S89.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
20P GAIN MUTATED 22 61 27 38
20P GAIN WILD-TYPE 74 64 81 78

Figure S89.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S90.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
20P GAIN MUTATED 18 10 19 45 14 25 15 1 13
20P GAIN WILD-TYPE 65 47 25 39 32 26 34 17 41

Figure S90.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S91.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
20P GAIN MUTATED 41 90 40
20P GAIN WILD-TYPE 148 138 53

Figure S91.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S92.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
20Q GAIN MUTATED 87 60 52
20Q GAIN WILD-TYPE 104 169 43

Figure S92.  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 = 0.0095

Table S93.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
20Q GAIN MUTATED 22 71 39 39
20Q GAIN WILD-TYPE 74 54 69 77

Figure S93.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

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

Table S94.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
20Q GAIN MUTATED 58 24 27 60 17
20Q GAIN WILD-TYPE 80 88 49 46 37

Figure S94.  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 = 0.0095

Table S95.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
20Q GAIN MUTATED 26 10 24 52 14 27 18 1 14
20Q GAIN WILD-TYPE 57 47 20 32 32 24 31 17 40

Figure S95.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

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

Table S96.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
20Q GAIN MUTATED 47 107 41
20Q GAIN WILD-TYPE 142 121 52

Figure S96.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.093

Table S97.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
20Q GAIN MUTATED 16 85 42 52
20Q GAIN WILD-TYPE 55 113 99 48

Figure S97.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S98.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
20Q GAIN MUTATED 19 121 31
20Q GAIN WILD-TYPE 84 127 52

Figure S98.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.056

Table S99.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
21Q GAIN MUTATED 25 17 5 24 3 4 7 0 8
21Q GAIN WILD-TYPE 58 40 39 60 43 47 42 18 46

Figure S99.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S100.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
1P LOSS MUTATED 17 31 34
1P LOSS WILD-TYPE 174 198 61

Figure S100.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.12

Table S101.  Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
1P LOSS MUTATED 19 10 15 29 2
1P LOSS WILD-TYPE 119 102 61 77 52

Figure S101.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S102.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
1P LOSS MUTATED 7 7 10 5 10 20 12 1 3
1P LOSS WILD-TYPE 76 50 34 79 36 31 37 17 51

Figure S102.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S103.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
3P LOSS MUTATED 89 71 53
3P LOSS WILD-TYPE 102 158 42

Figure S103.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S104.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
3P LOSS MUTATED 33 73 41 38
3P LOSS WILD-TYPE 63 52 67 78

Figure S104.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S105.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
3P LOSS MUTATED 28 25 14 42 17 34 26 0 18
3P LOSS WILD-TYPE 55 32 30 42 29 17 23 18 36

Figure S105.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S106.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
4P LOSS MUTATED 55 31 34
4P LOSS WILD-TYPE 136 198 61

Figure S106.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S107.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
4P LOSS MUTATED 6 44 22 28
4P LOSS WILD-TYPE 90 81 86 88

Figure S107.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.079

Table S108.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
4P LOSS MUTATED 30 12 22 40 11
4P LOSS WILD-TYPE 108 100 54 66 43

Figure S108.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S109.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
4P LOSS MUTATED 16 9 7 35 2 20 14 2 10
4P LOSS WILD-TYPE 67 48 37 49 44 31 35 16 44

Figure S109.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

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

Table S110.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
4P LOSS MUTATED 22 75 22
4P LOSS WILD-TYPE 167 153 71

Figure S110.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S111.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
4P LOSS MUTATED 6 54 22 37
4P LOSS WILD-TYPE 65 144 119 63

Figure S111.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.079

Table S112.  Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
4P LOSS MUTATED 12 75 12
4P LOSS WILD-TYPE 91 173 71

Figure S112.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S113.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
4Q LOSS MUTATED 61 35 40
4Q LOSS WILD-TYPE 130 194 55

Figure S113.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S114.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
4Q LOSS MUTATED 6 56 20 32
4Q LOSS WILD-TYPE 90 69 88 84

Figure S114.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S115.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
4Q LOSS MUTATED 33 12 25 49 11
4Q LOSS WILD-TYPE 105 100 51 57 43

Figure S115.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S116.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
4Q LOSS MUTATED 17 6 6 38 5 28 19 1 10
4Q LOSS WILD-TYPE 66 51 38 46 41 23 30 17 44

Figure S116.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S117.  Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
4Q LOSS MUTATED 25 85 25
4Q LOSS WILD-TYPE 164 143 68

Figure S117.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S118.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
4Q LOSS MUTATED 8 61 20 46
4Q LOSS WILD-TYPE 63 137 121 54

Figure S118.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S119.  Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
4Q LOSS MUTATED 13 84 16
4Q LOSS WILD-TYPE 90 164 67

Figure S119.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S120.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
5Q LOSS MUTATED 68 34 39
5Q LOSS WILD-TYPE 123 195 56

Figure S120.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S121.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
5Q LOSS MUTATED 9 50 34 26
5Q LOSS WILD-TYPE 87 75 74 90

Figure S121.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

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

Table S122.  Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
5Q LOSS MUTATED 44 12 22 44 9
5Q LOSS WILD-TYPE 94 100 54 62 45

Figure S122.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.079

Table S123.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
5Q LOSS MUTATED 24 5 11 32 7 20 18 1 13
5Q LOSS WILD-TYPE 59 52 33 52 39 31 31 17 41

Figure S123.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S124.  Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
5Q LOSS MUTATED 29 87 23
5Q LOSS WILD-TYPE 160 141 70

Figure S124.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S125.  Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
5Q LOSS MUTATED 9 62 21 47
5Q LOSS WILD-TYPE 62 136 120 53

Figure S125.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S126.  Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
5Q LOSS MUTATED 12 91 18
5Q LOSS WILD-TYPE 91 157 65

Figure S126.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.086

Table S127.  Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
6Q LOSS MUTATED 47 56 57 29
6Q LOSS WILD-TYPE 49 69 51 87

Figure S127.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.17

Table S128.  Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
6Q LOSS MUTATED 43 20 22 23 28 29 16 4 21
6Q LOSS WILD-TYPE 40 37 22 61 18 22 33 14 33

Figure S128.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S129.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
8P LOSS MUTATED 114 58 30
8P LOSS WILD-TYPE 77 171 65

Figure S129.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S130.  Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
8P LOSS MUTATED 77 36 23 40 14
8P LOSS WILD-TYPE 61 76 53 66 40

Figure S130.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S131.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
8P LOSS MUTATED 39 23 25 46 8 15 14 2 18
8P LOSS WILD-TYPE 44 34 19 38 38 36 35 16 36

Figure S131.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S132.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
9P LOSS MUTATED 36 30 18 51 19 24 41 8 23
9P LOSS WILD-TYPE 47 27 26 33 27 27 8 10 31

Figure S132.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.086

Table S133.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
9Q LOSS MUTATED 108 87 53
9Q LOSS WILD-TYPE 83 142 42

Figure S133.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.17

Table S134.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
9Q LOSS MUTATED 36 79 44 48
9Q LOSS WILD-TYPE 60 46 64 68

Figure S134.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S135.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
9Q LOSS MUTATED 29 92 54 70
9Q LOSS WILD-TYPE 42 106 87 30

Figure S135.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S136.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
10P LOSS MUTATED 67 29 14
10P LOSS WILD-TYPE 124 200 81

Figure S136.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S137.  Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
10P LOSS MUTATED 46 18 5 23 15
10P LOSS WILD-TYPE 92 94 71 83 39

Figure S137.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S138.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
10P LOSS MUTATED 18 16 10 36 0 10 4 2 11
10P LOSS WILD-TYPE 65 41 34 48 46 41 45 16 43

Figure S138.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S139.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
10Q LOSS MUTATED 70 39 23
10Q LOSS WILD-TYPE 121 190 72

Figure S139.  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 = 0.0095

Table S140.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
10Q LOSS MUTATED 23 16 12 44 0 10 9 2 11
10Q LOSS WILD-TYPE 60 41 32 40 46 41 40 16 43

Figure S140.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S141.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
11P LOSS MUTATED 55 28 29
11P LOSS WILD-TYPE 136 201 66

Figure S141.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.15

Table S142.  Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
12P LOSS MUTATED 22 17 5 28 11 3 4 2 14
12P LOSS WILD-TYPE 61 40 39 56 35 48 45 16 40

Figure S142.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.033

Table S143.  Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
12Q LOSS MUTATED 55 36 8
12Q LOSS WILD-TYPE 136 193 87

Figure S143.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.063

Table S144.  Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
12Q LOSS MUTATED 23 12 4 24 10 1 3 2 14
12Q LOSS WILD-TYPE 60 45 40 60 36 50 46 16 40

Figure S144.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S145.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
13Q LOSS MUTATED 125 66 61
13Q LOSS WILD-TYPE 66 163 34

Figure S145.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S146.  Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
13Q LOSS MUTATED 86 40 24 66 23
13Q LOSS WILD-TYPE 52 72 52 40 31

Figure S146.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S147.  Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
13Q LOSS MUTATED 52 22 25 48 10 36 19 1 26
13Q LOSS WILD-TYPE 31 35 19 36 36 15 30 17 28

Figure S147.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S148.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
15Q LOSS MUTATED 113 73 56
15Q LOSS WILD-TYPE 78 156 39

Figure S148.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S149.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
15Q LOSS MUTATED 27 65 63 53
15Q LOSS WILD-TYPE 69 60 45 63

Figure S149.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S150.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
15Q LOSS MUTATED 92 37 13 61 26
15Q LOSS WILD-TYPE 46 75 63 45 28

Figure S150.  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 = 0.0095

Table S151.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
15Q LOSS MUTATED 48 23 31 49 7 34 9 0 28
15Q LOSS WILD-TYPE 35 34 13 35 39 17 40 18 26

Figure S151.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S152.  Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
15Q LOSS MUTATED 63 122 55
15Q LOSS WILD-TYPE 126 106 38

Figure S152.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S153.  Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
15Q LOSS MUTATED 27 133 46
15Q LOSS WILD-TYPE 76 115 37

Figure S153.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S154.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
16P LOSS MUTATED 50 28 33
16P LOSS WILD-TYPE 141 201 62

Figure S154.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.056

Table S155.  Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
16P LOSS MUTATED 7 36 35 20
16P LOSS WILD-TYPE 89 89 73 96

Figure S155.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.063

Table S156.  Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
16P LOSS MUTATED 42 10 14 35 8
16P LOSS WILD-TYPE 96 102 62 71 46

Figure S156.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S157.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
16Q LOSS MUTATED 62 39 39
16Q LOSS WILD-TYPE 129 190 56

Figure S157.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S158.  Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
16Q LOSS MUTATED 12 42 42 24
16Q LOSS WILD-TYPE 84 83 66 92

Figure S158.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S159.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
16Q LOSS MUTATED 59 15 16 39 9
16Q LOSS WILD-TYPE 79 97 60 67 45

Figure S159.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S160.  Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
16Q LOSS MUTATED 35 7 20 29 9 17 10 0 11
16Q LOSS WILD-TYPE 48 50 24 55 37 34 39 18 43

Figure S160.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S161.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
17P LOSS MUTATED 117 58 40
17P LOSS WILD-TYPE 74 171 55

Figure S161.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.079

Table S162.  Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
17P LOSS MUTATED 28 53 63 39
17P LOSS WILD-TYPE 68 72 45 77

Figure S162.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S163.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
18P LOSS MUTATED 92 61 28
18P LOSS WILD-TYPE 99 168 67

Figure S163.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S164.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
18Q LOSS MUTATED 116 74 26
18Q LOSS WILD-TYPE 75 155 69

Figure S164.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S165.  Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 40 33 45 31 32
18Q LOSS MUTATED 17 6 34 15 12
18Q LOSS WILD-TYPE 23 27 11 16 20

Figure S165.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.086

Table S166.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
18Q LOSS MUTATED 80 39 33 32 20
18Q LOSS WILD-TYPE 58 73 43 74 34

Figure S166.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S167.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
18Q LOSS MUTATED 39 27 25 42 7 14 24 9 17
18Q LOSS WILD-TYPE 44 30 19 42 39 37 25 9 37

Figure S167.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S168.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
19P LOSS MUTATED 109 72 63
19P LOSS WILD-TYPE 82 157 32

Figure S168.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S169.  Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
19P LOSS MUTATED 31 87 46 43
19P LOSS WILD-TYPE 65 38 62 73

Figure S169.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S170.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
19P LOSS MUTATED 63 39 42 73 17
19P LOSS WILD-TYPE 75 73 34 33 37

Figure S170.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S171.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
19P LOSS MUTATED 29 17 21 50 31 35 33 4 14
19P LOSS WILD-TYPE 54 40 23 34 15 16 16 14 40

Figure S171.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S172.  Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
19P LOSS MUTATED 65 135 39
19P LOSS WILD-TYPE 124 93 54

Figure S172.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S173.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
19P LOSS MUTATED 31 97 43 68
19P LOSS WILD-TYPE 40 101 98 32

Figure S173.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S174.  Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
19Q LOSS MUTATED 82 38 39
19Q LOSS WILD-TYPE 109 191 56

Figure S174.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.093

Table S175.  Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
19Q LOSS MUTATED 17 54 37 26
19Q LOSS WILD-TYPE 79 71 71 90

Figure S175.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.12

Table S176.  Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
19Q LOSS MUTATED 47 23 23 50 10
19Q LOSS WILD-TYPE 91 89 53 56 44

Figure S176.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.04

Table S177.  Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
19Q LOSS MUTATED 20 13 17 34 17 23 21 0 8
19Q LOSS WILD-TYPE 63 44 27 50 29 28 28 18 46

Figure S177.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.04

Table S178.  Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
19Q LOSS MUTATED 38 90 27
19Q LOSS WILD-TYPE 151 138 66

Figure S178.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S179.  Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
19Q LOSS MUTATED 18 64 25 48
19Q LOSS WILD-TYPE 53 134 116 52

Figure S179.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.063

Table S180.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
20P LOSS MUTATED 62 33 22
20P LOSS WILD-TYPE 129 196 73

Figure S180.  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 = 0.0095

Table S181.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
21Q LOSS MUTATED 52 59 54
21Q LOSS WILD-TYPE 139 170 41

Figure S181.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S182.  Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
21Q LOSS MUTATED 40 14 30 58 11
21Q LOSS WILD-TYPE 98 98 46 48 43

Figure S182.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S183.  Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
21Q LOSS MUTATED 14 8 17 31 11 32 24 4 12
21Q LOSS WILD-TYPE 69 49 27 53 35 19 25 14 42

Figure S183.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

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

Table S184.  Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
21Q LOSS MUTATED 39 96 27
21Q LOSS WILD-TYPE 150 132 66

Figure S184.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.071

Table S185.  Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
21Q LOSS MUTATED 15 66 32 49
21Q LOSS WILD-TYPE 56 132 109 51

Figure S185.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S186.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 191 229 95
22Q LOSS MUTATED 99 60 61
22Q LOSS WILD-TYPE 92 169 34

Figure S186.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S187.  Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 125 108 116
22Q LOSS MUTATED 24 69 56 41
22Q LOSS WILD-TYPE 72 56 52 75

Figure S187.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S188.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
22Q LOSS MUTATED 70 30 34 62 11
22Q LOSS WILD-TYPE 68 82 42 44 43

Figure S188.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0095

Table S189.  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 CLUS_8 CLUS_9
ALL 83 57 44 84 46 51 49 18 54
22Q LOSS MUTATED 47 14 20 40 14 33 24 4 11
22Q LOSS WILD-TYPE 36 43 24 44 32 18 25 14 43

Figure S189.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.056

Table S190.  Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 189 228 93
22Q LOSS MUTATED 58 119 39
22Q LOSS WILD-TYPE 131 109 54

Figure S190.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.025

Table S191.  Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 198 141 100
22Q LOSS MUTATED 21 100 41 54
22Q LOSS WILD-TYPE 50 98 100 46

Figure S191.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.12

Table S192.  Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 248 83
22Q LOSS MUTATED 28 128 31
22Q LOSS WILD-TYPE 75 120 52

Figure S192.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 515

  • 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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