Correlation between copy number variations of arm-level result and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1NK3CT8
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/C1NK3CT8
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 493 patients, 203 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' and 'MIRSEQ_CHIERARCHICAL'.

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

  • 4p gain cnv correlated to 'CN_CNMF'.

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

  • 5q gain cnv correlated to 'METHLYATION_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 9p gain cnv correlated to 'MRNASEQ_CNMF'.

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

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

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

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

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

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

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

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

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

  • 21q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

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

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

  • 7p loss cnv correlated to 'CN_CNMF'.

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

  • 8q loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 11p loss cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 21q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', 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, 203 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 131 (27%) 362 0.222
(1.00) 		0.0471
(1.00) 		1e-05
(0.00946) 		2e-05
(0.0167) 		0.0157
(1.00) 		0.0083
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946)
12q gain 126 (26%) 367 0.222
(1.00) 		0.136
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.164
(1.00) 		0.0166
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		2e-05
(0.0167) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946)
20q gain 189 (38%) 304 0.0101
(1.00) 		0.0249
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.224
(1.00) 		0.0345
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		2e-05
(0.0167) 		0.00022
(0.167) 		5e-05
(0.04) 		1e-05
(0.00946)
4q loss 132 (27%) 361 0.00058
(0.422) 		0.00767
(1.00) 		2e-05
(0.0167) 		1e-05
(0.00946) 		0.277
(1.00) 		0.00133
(0.918) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.00027
(0.203) 		1e-05
(0.00946)
5q loss 137 (28%) 356 0.0636
(1.00) 		0.0358
(1.00) 		1e-05
(0.00946) 		2e-05
(0.0167) 		0.00126
(0.874) 		0.00083
(0.592) 		1e-05
(0.00946) 		0.00014
(0.108) 		1e-05
(0.00946) 		1e-05
(0.00946) 		2e-05
(0.0167) 		1e-05
(0.00946)
2p gain 148 (30%) 345 0.302
(1.00) 		0.243
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.454
(1.00) 		0.223
(1.00) 		0.00014
(0.108) 		6e-05
(0.0479) 		1e-05
(0.00946) 		0.00024
(0.182) 		0.00193
(1.00) 		1e-05
(0.00946)
8q gain 235 (48%) 258 0.0241
(1.00) 		0.0467
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.285
(1.00) 		0.00526
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.00077
(0.553) 		0.0003
(0.225) 		1e-05
(0.00946)
17q gain 186 (38%) 307 0.305
(1.00) 		0.876
(1.00) 		1e-05
(0.00946) 		4e-05
(0.0323) 		0.613
(1.00) 		0.0181
(1.00) 		7e-05
(0.0556) 		1e-05
(0.00946) 		2e-05
(0.0167) 		0.00018
(0.138) 		0.057
(1.00) 		0.00024
(0.182)
20p gain 164 (33%) 329 0.0822
(1.00) 		0.142
(1.00) 		0.00012
(0.0938) 		0.00018
(0.138) 		0.426
(1.00) 		0.0438
(1.00) 		0.00026
(0.196) 		1e-05
(0.00946) 		5e-05
(0.04) 		0.00372
(1.00) 		0.00018
(0.138) 		4e-05
(0.0323)
19p loss 235 (48%) 258 0.815
(1.00) 		1
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.337
(1.00) 		0.276
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		6e-05
(0.0479) 		3e-05
(0.0244) 		0.00606
(1.00) 		7e-05
(0.0556)
22q loss 212 (43%) 281 0.129
(1.00) 		0.167
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.806
(1.00) 		0.049
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.00021
(0.16) 		0.00012
(0.0938) 		0.00035
(0.26) 		1e-05
(0.00946)
4p loss 116 (24%) 377 0.184
(1.00) 		0.38
(1.00) 		7e-05
(0.0556) 		1e-05
(0.00946) 		0.196
(1.00) 		0.0155
(1.00) 		9e-05
(0.0707) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.00581
(1.00) 		0.00053
(0.387)
7p gain 251 (51%) 242 0.856
(1.00) 		0.536
(1.00) 		1e-05
(0.00946) 		0.00317
(1.00) 		0.00047
(0.345) 		0.00083
(0.592) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.00059
(0.429) 		0.00038
(0.28) 		1e-05
(0.00946)
15q loss 233 (47%) 260 0.101
(1.00) 		0.282
(1.00) 		1e-05
(0.00946) 		2e-05
(0.0167) 		0.124
(1.00) 		0.00246
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.0176
(1.00) 		0.0172
(1.00) 		0.00103
(0.728)
16q loss 137 (28%) 356 0.547
(1.00) 		0.623
(1.00) 		2e-05
(0.0167) 		1e-05
(0.00946) 		0.0819
(1.00) 		0.0322
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.00668
(1.00) 		0.00438
(1.00) 		0.00159
(1.00) 		9e-05
(0.0707)
19q loss 153 (31%) 340 0.345
(1.00) 		0.465
(1.00) 		1e-05
(0.00946) 		2e-05
(0.0167) 		0.272
(1.00) 		0.455
(1.00) 		0.00024
(0.182) 		2e-05
(0.0167) 		0.00059
(0.429) 		0.00141
(0.966) 		0.0252
(1.00) 		0.00021
(0.16)
7q gain 207 (42%) 286 0.481
(1.00) 		0.311
(1.00) 		1e-05
(0.00946) 		0.0287
(1.00) 		0.131
(1.00) 		0.114
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.00275
(1.00) 		0.00695
(1.00) 		0.0122
(1.00) 		7e-05
(0.0556)
10p gain 105 (21%) 388 0.237
(1.00) 		0.295
(1.00) 		0.00071
(0.511) 		1e-05
(0.00946) 		0.0184
(1.00) 		0.00117
(0.82) 		6e-05
(0.0479) 		1e-05
(0.00946) 		0.00924
(1.00) 		0.0018
(1.00) 		0.0379
(1.00) 		6e-05
(0.0479)
11q gain 112 (23%) 381 0.0099
(1.00) 		0.0168
(1.00) 		1e-05
(0.00946) 		0.0595
(1.00) 		0.269
(1.00) 		0.123
(1.00) 		0.00451
(1.00) 		0.00033
(0.246) 		4e-05
(0.0323) 		0.0012
(0.838) 		0.00035
(0.26) 		2e-05
(0.0167)
14q gain 120 (24%) 373 0.804
(1.00) 		0.844
(1.00) 		1e-05
(0.00946) 		0.00419
(1.00) 		0.236
(1.00) 		0.0741
(1.00) 		0.00012
(0.0938) 		2e-05
(0.0167) 		3e-05
(0.0244) 		0.00133
(0.918) 		0.00079
(0.565) 		0.00102
(0.723)
13q loss 243 (49%) 250 0.105
(1.00) 		0.625
(1.00) 		1e-05
(0.00946) 		0.0119
(1.00) 		0.00048
(0.351) 		2e-05
(0.0167) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.0136
(1.00) 		0.0381
(1.00) 		0.0424
(1.00) 		0.0588
(1.00)
21q loss 157 (32%) 336 0.184
(1.00) 		0.143
(1.00) 		1e-05
(0.00946) 		0.00067
(0.485) 		0.0314
(1.00) 		0.00132
(0.912) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.00037
(0.274) 		0.00012
(0.0938) 		0.00747
(1.00) 		0.00248
(1.00)
3q gain 86 (17%) 407 0.0807
(1.00) 		0.126
(1.00) 		0.0012
(0.838) 		3e-05
(0.0244) 		0.0271
(1.00) 		0.0347
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.0167
(1.00) 		0.0586
(1.00) 		0.00957
(1.00) 		0.0384
(1.00)
10q gain 76 (15%) 417 0.0379
(1.00) 		1e-05
(0.00946) 		0.285
(1.00) 		0.0973
(1.00) 		0.00028
(0.21) 		1e-05
(0.00946) 		0.373
(1.00) 		0.0339
(1.00) 		0.218
(1.00) 		0.077
(1.00)
11p gain 92 (19%) 401 0.00924
(1.00) 		0.00991
(1.00) 		2e-05
(0.0167) 		0.342
(1.00) 		0.521
(1.00) 		0.319
(1.00) 		0.215
(1.00) 		0.00045
(0.331) 		0.00054
(0.394) 		1e-05
(0.00946) 		0.00055
(0.401) 		2e-05
(0.0167)
18q gain 66 (13%) 427 0.595
(1.00) 		0.147
(1.00) 		0.00018
(0.138) 		1e-05
(0.00946) 		0.0203
(1.00) 		0.0304
(1.00) 		0.00012
(0.0938) 		0.00118
(0.826) 		0.0104
(1.00) 		0.00071
(0.511) 		0.00236
(1.00) 		0.00122
(0.848)
1p loss 79 (16%) 414 0.0806
(1.00) 		0.126
(1.00) 		2e-05
(0.0167) 		0.00116
(0.817) 		0.888
(1.00) 		0.25
(1.00) 		0.00016
(0.123) 		1e-05
(0.00946) 		0.53
(1.00) 		0.00102
(0.723) 		0.452
(1.00) 		0.102
(1.00)
8p loss 191 (39%) 302 0.134
(1.00) 		0.0781
(1.00) 		1e-05
(0.00946) 		0.0139
(1.00) 		0.0516
(1.00) 		0.0079
(1.00) 		0.00013
(0.101) 		3e-05
(0.0244) 		0.00243
(1.00) 		0.00521
(1.00) 		0.00552
(1.00) 		0.00827
(1.00)
9q loss 238 (48%) 255 0.499
(1.00) 		0.904
(1.00) 		4e-05
(0.0323) 		0.00224
(1.00) 		0.418
(1.00) 		0.00666
(1.00) 		0.14
(1.00) 		0.00031
(0.231) 		0.00616
(1.00) 		3e-05
(0.0244) 		0.024
(1.00) 		0.00891
(1.00)
10p loss 108 (22%) 385 0.817
(1.00) 		0.788
(1.00) 		2e-05
(0.0167) 		0.129
(1.00) 		0.0399
(1.00) 		0.0042
(1.00) 		3e-05
(0.0244) 		1e-05
(0.00946) 		0.00414
(1.00) 		0.00263
(1.00) 		0.00173
(1.00) 		0.00737
(1.00)
10q loss 128 (26%) 365 0.817
(1.00) 		0.784
(1.00) 		2e-05
(0.0167) 		0.0655
(1.00) 		0.0559
(1.00) 		0.0272
(1.00) 		0.00133
(0.918) 		1e-05
(0.00946) 		0.00529
(1.00) 		0.00013
(0.101) 		0.00131
(0.907) 		0.00116
(0.817)
16p loss 108 (22%) 385 0.455
(1.00) 		0.482
(1.00) 		2e-05
(0.0167) 		2e-05
(0.0167) 		0.235
(1.00) 		0.143
(1.00) 		1e-05
(0.00946) 		0.00126
(0.874) 		0.00834
(1.00) 		0.00706
(1.00) 		0.00804
(1.00) 		0.00388
(1.00)
18q loss 207 (42%) 286 0.52
(1.00) 		0.424
(1.00) 		1e-05
(0.00946) 		0.508
(1.00) 		0.0039
(1.00) 		0.00139
(0.954) 		0.0003
(0.225) 		0.00017
(0.131) 		0.0236
(1.00) 		0.943
(1.00) 		0.69
(1.00) 		0.862
(1.00)
1q gain 297 (60%) 196 0.121
(1.00) 		1
(1.00) 		0.0019
(1.00) 		0.00469
(1.00) 		0.00077
(0.553) 		0.0392
(1.00) 		0.127
(1.00) 		0.00015
(0.115) 		0.519
(1.00) 		0.0003
(0.225) 		0.0151
(1.00) 		0.169
(1.00)
2q gain 135 (27%) 358 0.126
(1.00) 		0.288
(1.00) 		2e-05
(0.0167) 		1e-05
(0.00946) 		0.7
(1.00) 		0.793
(1.00) 		0.079
(1.00) 		0.0146
(1.00) 		0.00184
(1.00) 		0.0198
(1.00) 		0.0296
(1.00) 		0.00247
(1.00)
3p gain 40 (8%) 453 0.00344
(1.00) 		0.0186
(1.00) 		0.11
(1.00) 		0.0287
(1.00) 		4e-05
(0.0323) 		0.00022
(0.167) 		0.0684
(1.00) 		0.475
(1.00) 		0.174
(1.00) 		0.343
(1.00)
5p gain 267 (54%) 226 0.8
(1.00) 		0.363
(1.00) 		1e-05
(0.00946) 		0.297
(1.00) 		0.162
(1.00) 		0.845
(1.00) 		0.0239
(1.00) 		1e-05
(0.00946) 		0.0435
(1.00) 		0.305
(1.00) 		0.0921
(1.00) 		0.0042
(1.00)
6p gain 141 (29%) 352 0.353
(1.00) 		0.0885
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.0301
(1.00) 		0.647
(1.00) 		0.108
(1.00) 		0.0122
(1.00) 		0.0268
(1.00) 		0.0681
(1.00) 		0.066
(1.00) 		0.00618
(1.00)
8p gain 123 (25%) 370 0.152
(1.00) 		0.254
(1.00) 		1e-05
(0.00946) 		0.0937
(1.00) 		0.435
(1.00) 		0.511
(1.00) 		0.00167
(1.00) 		0.00026
(0.196) 		0.457
(1.00) 		0.735
(1.00) 		0.845
(1.00) 		0.289
(1.00)
15q gain 35 (7%) 458 0.192
(1.00) 		0.149
(1.00) 		0.388
(1.00) 		0.306
(1.00) 		0.559
(1.00) 		0.464
(1.00) 		1e-05
(0.00946) 		1e-05
(0.00946) 		0.788
(1.00) 		0.504
(1.00) 		0.188
(1.00) 		0.864
(1.00)
17p gain 83 (17%) 410 0.452
(1.00) 		0.687
(1.00) 		8e-05
(0.063) 		0.013
(1.00) 		0.869
(1.00) 		0.0756
(1.00) 		0.00838
(1.00) 		0.0226
(1.00) 		1e-05
(0.00946) 		0.00047
(0.345) 		0.231
(1.00) 		0.0073
(1.00)
18p gain 91 (18%) 402 0.875
(1.00) 		0.633
(1.00) 		7e-05
(0.0556) 		1e-05
(0.00946) 		0.24
(1.00) 		0.595
(1.00) 		0.0214
(1.00) 		0.00309
(1.00) 		0.0151
(1.00) 		0.00194
(1.00) 		0.00579
(1.00) 		0.00041
(0.302)
21q gain 94 (19%) 399 0.54
(1.00) 		0.265
(1.00) 		9e-05
(0.0707) 		0.404
(1.00) 		0.335
(1.00) 		0.0728
(1.00) 		0.0298
(1.00) 		7e-05
(0.0556) 		0.342
(1.00) 		0.308
(1.00) 		0.644
(1.00) 		0.588
(1.00)
3p loss 205 (42%) 288 0.342
(1.00) 		0.114
(1.00) 		4e-05
(0.0323) 		0.00112
(0.79) 		0.262
(1.00) 		0.303
(1.00) 		0.0324
(1.00) 		1e-05
(0.00946) 		0.0213
(1.00) 		0.00786
(1.00) 		0.126
(1.00) 		0.00884
(1.00)
6q loss 208 (42%) 285 0.246
(1.00) 		0.54
(1.00) 		0.03
(1.00) 		0.00014
(0.108) 		0.839
(1.00) 		0.303
(1.00) 		0.0807
(1.00) 		5e-05
(0.04) 		0.342
(1.00) 		0.0299
(1.00) 		0.742
(1.00) 		0.0594
(1.00)
12q loss 93 (19%) 400 0.556
(1.00) 		0.426
(1.00) 		1e-05
(0.00946) 		0.0772
(1.00) 		0.0956
(1.00) 		0.0186
(1.00) 		0.00068
(0.491) 		9e-05
(0.0707) 		0.202
(1.00) 		0.00453
(1.00) 		0.558
(1.00) 		0.476
(1.00)
17p loss 206 (42%) 287 0.549
(1.00) 		0.361
(1.00) 		1e-05
(0.00946) 		0.00017
(0.131) 		0.137
(1.00) 		0.0256
(1.00) 		0.0011
(0.777) 		0.00118
(0.826) 		0.501
(1.00) 		0.182
(1.00) 		0.608
(1.00) 		0.289
(1.00)
1p gain 133 (27%) 360 0.387
(1.00) 		1
(1.00) 		1e-05
(0.00946) 		0.387
(1.00) 		0.0742
(1.00) 		0.00447
(1.00) 		0.129
(1.00) 		0.0314
(1.00) 		0.0715
(1.00) 		0.0496
(1.00) 		0.31
(1.00) 		0.826
(1.00)
4p gain 80 (16%) 413 0.876
(1.00) 		1
(1.00) 		1e-05
(0.00946) 		0.269
(1.00) 		0.299
(1.00) 		0.046
(1.00) 		0.0436
(1.00) 		0.284
(1.00) 		0.0906
(1.00) 		0.435
(1.00) 		0.439
(1.00) 		0.194
(1.00)
5q gain 124 (25%) 369 0.194
(1.00) 		0.285
(1.00) 		0.00571
(1.00) 		0.00031
(0.231) 		0.028
(1.00) 		0.281
(1.00) 		0.00588
(1.00) 		0.028
(1.00) 		0.146
(1.00) 		0.00042
(0.309) 		0.0365
(1.00) 		0.00851
(1.00)
9p gain 42 (9%) 451 0.014
(1.00) 		0.0722
(1.00) 		0.44
(1.00) 		0.216
(1.00) 		0.00019
(0.145) 		0.00509
(1.00) 		0.22
(1.00) 		0.345
(1.00) 		0.206
(1.00) 		0.284
(1.00)
7p loss 33 (7%) 460 1
(1.00) 		1
(1.00) 		3e-05
(0.0244) 		0.043
(1.00) 		0.329
(1.00) 		0.945
(1.00) 		0.00588
(1.00) 		0.00278
(1.00) 		0.273
(1.00) 		0.197
(1.00) 		0.899
(1.00) 		0.323
(1.00)
8q loss 54 (11%) 439 0.00025
(0.188) 		0.93
(1.00) 		0.297
(1.00) 		0.495
(1.00) 		0.174
(1.00) 		0.0637
(1.00) 		0.21
(1.00) 		0.828
(1.00) 		0.42
(1.00) 		0.538
(1.00)
9p loss 254 (52%) 239 0.0512
(1.00) 		0.598
(1.00) 		0.00199
(1.00) 		0.123
(1.00) 		0.217
(1.00) 		0.0251
(1.00) 		0.0009
(0.64) 		8e-05
(0.063) 		0.0617
(1.00) 		0.0106
(1.00) 		0.35
(1.00) 		0.515
(1.00)
11p loss 108 (22%) 385 0.145
(1.00) 		0.0703
(1.00) 		0.00012
(0.0938) 		0.00991
(1.00) 		0.0365
(1.00) 		0.135
(1.00) 		0.00214
(1.00) 		0.00406
(1.00) 		0.0263
(1.00) 		0.0349
(1.00) 		0.0271
(1.00) 		0.00432
(1.00)
17q loss 55 (11%) 438 0.296
(1.00) 		0.473
(1.00) 		0.00013
(0.101) 		0.0163
(1.00) 		0.0101
(1.00) 		0.0247
(1.00) 		0.139
(1.00) 		0.508
(1.00) 		0.417
(1.00) 		0.308
(1.00) 		0.0821
(1.00) 		0.0764
(1.00)
18p loss 169 (34%) 324 0.437
(1.00) 		0.455
(1.00) 		3e-05
(0.0244) 		0.714
(1.00) 		0.0373
(1.00) 		0.00841
(1.00) 		0.0229
(1.00) 		0.00152
(1.00) 		0.029
(1.00) 		0.798
(1.00) 		0.149
(1.00) 		0.504
(1.00)
4q gain 46 (9%) 447 0.333
(1.00) 		0.585
(1.00) 		0.0113
(1.00) 		0.679
(1.00) 		0.4
(1.00) 		0.133
(1.00) 		0.00744
(1.00) 		0.00358
(1.00) 		0.0173
(1.00) 		0.0492
(1.00) 		0.163
(1.00) 		0.247
(1.00)
6q gain 60 (12%) 433 1
(1.00) 		1
(1.00) 		0.0125
(1.00) 		0.00539
(1.00) 		0.168
(1.00) 		0.903
(1.00) 		0.217
(1.00) 		0.0199
(1.00) 		0.00218
(1.00) 		0.0161
(1.00) 		0.284
(1.00) 		0.00545
(1.00)
9q gain 30 (6%) 463 0.268
(1.00) 		0.547
(1.00) 		0.572
(1.00) 		0.629
(1.00) 		0.0775
(1.00) 		0.0666
(1.00) 		0.481
(1.00) 		0.933
(1.00) 		0.445
(1.00) 		0.35
(1.00)
13q gain 43 (9%) 450 0.413
(1.00) 		0.543
(1.00) 		0.758
(1.00) 		0.0152
(1.00) 		0.0512
(1.00) 		0.5
(1.00) 		0.0605
(1.00) 		0.128
(1.00) 		0.976
(1.00) 		0.131
(1.00) 		0.796
(1.00) 		0.664
(1.00)
16p gain 127 (26%) 366 0.534
(1.00) 		0.336
(1.00) 		0.00307
(1.00) 		0.0619
(1.00) 		0.312
(1.00) 		0.123
(1.00) 		0.175
(1.00) 		0.00691
(1.00) 		0.0102
(1.00) 		0.0715
(1.00) 		0.0472
(1.00) 		0.0303
(1.00)
16q gain 94 (19%) 399 0.436
(1.00) 		0.153
(1.00) 		0.00265
(1.00) 		0.0898
(1.00) 		0.0706
(1.00) 		0.0227
(1.00) 		0.424
(1.00) 		0.0249
(1.00) 		0.00201
(1.00) 		0.0129
(1.00) 		0.0207
(1.00) 		0.0282
(1.00)
19p gain 32 (6%) 461 0.192
(1.00) 		0.0398
(1.00) 		0.188
(1.00) 		0.766
(1.00) 		1
(1.00) 		0.852
(1.00) 		0.994
(1.00) 		0.743
(1.00) 		0.453
(1.00) 		0.886
(1.00) 		0.0195
(1.00) 		0.71
(1.00)
19q gain 71 (14%) 422 0.0513
(1.00) 		0.0415
(1.00) 		0.00313
(1.00) 		0.0146
(1.00) 		0.941
(1.00) 		0.614
(1.00) 		0.182
(1.00) 		0.0162
(1.00) 		0.368
(1.00) 		0.0922
(1.00) 		0.0716
(1.00) 		0.0241
(1.00)
22q gain 61 (12%) 432 0.107
(1.00) 		0.121
(1.00) 		0.00333
(1.00) 		0.764
(1.00) 		0.236
(1.00) 		0.19
(1.00) 		0.178
(1.00) 		0.0964
(1.00) 		0.607
(1.00) 		0.78
(1.00) 		0.477
(1.00) 		0.298
(1.00)
xq gain 68 (14%) 425 0.656
(1.00) 		0.248
(1.00) 		0.00067
(0.485) 		0.31
(1.00) 		0.273
(1.00) 		0.403
(1.00) 		0.0288
(1.00) 		0.00639
(1.00) 		0.117
(1.00) 		0.421
(1.00) 		0.217
(1.00) 		0.0763
(1.00)
1q loss 28 (6%) 465 0.18
(1.00) 		0.0128
(1.00) 		0.194
(1.00) 		0.156
(1.00) 		0.0478
(1.00) 		0.166
(1.00) 		0.747
(1.00) 		0.323
(1.00) 		0.305
(1.00) 		0.162
(1.00)
2p loss 24 (5%) 469 0.75
(1.00) 		0.581
(1.00) 		0.124
(1.00) 		0.339
(1.00) 		0.61
(1.00) 		0.93
(1.00) 		0.978
(1.00) 		0.902
(1.00) 		0.083
(1.00) 		0.789
(1.00) 		0.0719
(1.00) 		0.355
(1.00)
2q loss 23 (5%) 470 0.00136
(0.934) 		0.111
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.292
(1.00) 		0.388
(1.00) 		0.353
(1.00) 		0.388
(1.00) 		0.447
(1.00) 		0.166
(1.00)
3q loss 140 (28%) 353 0.554
(1.00) 		0.141
(1.00) 		0.0151
(1.00) 		0.00719
(1.00) 		0.918
(1.00) 		0.914
(1.00) 		0.0663
(1.00) 		0.00078
(0.558) 		0.689
(1.00) 		0.0656
(1.00) 		0.855
(1.00) 		0.498
(1.00)
5p loss 40 (8%) 453 0.593
(1.00) 		0.309
(1.00) 		0.695
(1.00) 		0.0225
(1.00) 		0.406
(1.00) 		0.0994
(1.00) 		0.0134
(1.00) 		0.0012
(0.838) 		0.0649
(1.00) 		0.0813
(1.00) 		0.0164
(1.00) 		0.00795
(1.00)
6p loss 101 (20%) 392 0.0122
(1.00) 		0.00439
(1.00) 		0.0511
(1.00) 		0.126
(1.00) 		0.534
(1.00) 		0.477
(1.00) 		0.188
(1.00) 		0.277
(1.00) 		0.542
(1.00) 		0.183
(1.00) 		0.498
(1.00) 		0.706
(1.00)
7q loss 39 (8%) 454 0.802
(1.00) 		0.256
(1.00) 		0.00715
(1.00) 		0.074
(1.00) 		0.905
(1.00) 		0.155
(1.00) 		0.104
(1.00) 		0.0332
(1.00) 		0.375
(1.00) 		0.0559
(1.00) 		0.273
(1.00) 		0.84
(1.00)
11q loss 88 (18%) 405 0.84
(1.00) 		0.484
(1.00) 		0.00645
(1.00) 		0.00435
(1.00) 		0.00334
(1.00) 		0.277
(1.00) 		0.00093
(0.66) 		0.00602
(1.00) 		0.0557
(1.00) 		0.103
(1.00) 		0.0293
(1.00) 		0.0332
(1.00)
12p loss 106 (22%) 387 0.631
(1.00) 		0.882
(1.00) 		0.00638
(1.00) 		0.262
(1.00) 		0.0457
(1.00) 		0.0589
(1.00) 		0.00442
(1.00) 		0.00035
(0.26) 		0.264
(1.00) 		0.113
(1.00) 		0.613
(1.00) 		0.812
(1.00)
14q loss 111 (23%) 382 0.931
(1.00) 		0.408
(1.00) 		0.0601
(1.00) 		0.142
(1.00) 		0.174
(1.00) 		0.282
(1.00) 		0.0318
(1.00) 		0.00486
(1.00) 		0.0734
(1.00) 		0.00623
(1.00) 		0.0008
(0.571) 		0.00565
(1.00)
20p loss 114 (23%) 379 0.335
(1.00) 		0.454
(1.00) 		0.00037
(0.274) 		0.00116
(0.817) 		0.00059
(0.429) 		0.00187
(1.00) 		0.0159
(1.00) 		0.0053
(1.00) 		0.967
(1.00) 		0.732
(1.00) 		0.129
(1.00) 		0.857
(1.00)
20q loss 67 (14%) 426 0.513
(1.00) 		0.876
(1.00) 		0.396
(1.00) 		0.515
(1.00) 		0.26
(1.00) 		0.404
(1.00) 		0.663
(1.00) 		0.735
(1.00) 		0.608
(1.00) 		0.72
(1.00) 		0.132
(1.00) 		0.669
(1.00)
xq loss 64 (13%) 429 0.272
(1.00) 		0.0541
(1.00) 		0.0007
(0.505) 		0.0083
(1.00) 		0.434
(1.00) 		0.643
(1.00) 		0.425
(1.00) 		0.572
(1.00) 		0.349
(1.00) 		0.473
(1.00) 		0.506
(1.00) 		0.597
(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 186 216 91
1P GAIN MUTATED 79 35 19
1P GAIN WILD-TYPE 107 181 72

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

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 45 36 37 30 6 31
1Q GAIN WILD-TYPE 29 19 29 39 10 14 19 12 23

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

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.22

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
1Q GAIN MUTATED 52 37 63 77 50 15
1Q GAIN WILD-TYPE 19 7 55 60 33 20

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
2P GAIN MUTATED 74 36 38
2P GAIN WILD-TYPE 112 180 53

Figure S4.  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 S5.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
2P GAIN MUTATED 9 57 34 24
2P GAIN WILD-TYPE 83 68 81 75

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.11

Table S6.  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 25 49 16
2P GAIN WILD-TYPE 98 94 51 57 38

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S7.  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 21 0 16
2P GAIN WILD-TYPE 60 46 33 52 38 25 28 18 38

Figure S7.  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 S8.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
2P GAIN MUTATED 37 96 14
2P GAIN WILD-TYPE 142 135 64

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
2P GAIN MUTATED 13 18 42 32 37 5
2P GAIN WILD-TYPE 58 26 76 105 46 30

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
2P GAIN MUTATED 37 82 4
2P GAIN WILD-TYPE 149 127 26

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

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

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
2Q GAIN MUTATED 60 37 38
2Q GAIN WILD-TYPE 126 179 53

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

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

Table S12.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
2Q GAIN MUTATED 10 49 35 20
2Q GAIN WILD-TYPE 82 76 80 79

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.032

Table S13.  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 S13.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S14.  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 S14.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.024

Table S15.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
3Q GAIN MUTATED 3 32 23 19
3Q GAIN WILD-TYPE 89 93 92 80

Figure S15.  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 S16.  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 34 2 16 23 10
3Q GAIN WILD-TYPE 104 110 60 83 44

Figure S16.  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 S17.  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 34 2 6 8 2 4
3Q GAIN WILD-TYPE 66 55 34 50 44 45 41 16 50

Figure S17.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

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

Table S18.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
4P GAIN MUTATED 48 18 14
4P GAIN WILD-TYPE 138 198 77

Figure S18.  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 S19.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
5P GAIN MUTATED 135 84 48
5P GAIN WILD-TYPE 51 132 43

Figure S19.  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 S20.  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 58 29 18 55 16 31 25 0 30
5P GAIN WILD-TYPE 25 28 26 29 30 20 24 18 24

Figure S20.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
5Q GAIN MUTATED 40 27 24 19
5Q GAIN WILD-TYPE 52 98 91 80

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

'6p gain' versus 'CN_CNMF'

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

Table S22.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
6P GAIN MUTATED 62 40 39
6P GAIN WILD-TYPE 124 176 52

Figure S22.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

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

Table S23.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
6P GAIN MUTATED 18 58 31 14
6P GAIN WILD-TYPE 74 67 84 85

Figure S23.  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 S24.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
7P GAIN MUTATED 145 72 34
7P GAIN WILD-TYPE 41 144 57

Figure S24.  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 S25.  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 S25.  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 S26.  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 S26.  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 S27.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
7P GAIN MUTATED 66 130 52
7P GAIN WILD-TYPE 113 101 26

Figure S27.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_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 186 209 30
7P GAIN MUTATED 69 122 23
7P GAIN WILD-TYPE 117 87 7

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 186 216 91
7Q GAIN MUTATED 114 63 30
7Q GAIN WILD-TYPE 72 153 61

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
7Q GAIN MUTATED 56 100 18
7Q GAIN WILD-TYPE 130 109 12

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 186 216 91
8P GAIN MUTATED 33 41 49
8P GAIN WILD-TYPE 153 175 42

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

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.2

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 22 6 8 17 14 23 16 0 12
8P GAIN WILD-TYPE 61 51 36 67 32 28 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 186 216 91
8Q GAIN MUTATED 92 64 79
8Q GAIN WILD-TYPE 94 152 12

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 92 125 115 99
8Q GAIN MUTATED 27 81 61 38
8Q GAIN WILD-TYPE 65 44 54 61

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 68 33 32 74 21
8Q GAIN WILD-TYPE 70 79 44 32 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 42 19 41 25 0 21
8Q GAIN WILD-TYPE 48 40 16 42 27 10 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 179 231 78
8Q GAIN MUTATED 60 134 39
8Q GAIN WILD-TYPE 119 97 39

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

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.22

Table S40.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
8Q GAIN MUTATED 56 112 37
8Q GAIN WILD-TYPE 99 80 41

Figure S40.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S41.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
8Q GAIN MUTATED 67 127 11
8Q GAIN WILD-TYPE 119 82 19

Figure S41.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.14

Table S42.  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 S42.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_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 92 125 115 99
10P GAIN MUTATED 3 43 34 13
10P GAIN WILD-TYPE 89 82 81 86

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

'10p gain' versus 'MRNASEQ_CNMF'

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

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 27 10 20 37 9
10P GAIN WILD-TYPE 111 102 56 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 9 16 13 22 17 0 10
10P GAIN WILD-TYPE 70 54 35 68 33 29 32 18 44

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

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S46.  Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
10P GAIN MUTATED 26 64 3
10P GAIN WILD-TYPE 160 145 27

Figure S46.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
10Q GAIN MUTATED 3 33 22 9
10Q GAIN WILD-TYPE 89 92 93 90

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

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.21

Table S48.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
10Q GAIN MUTATED 17 7 16 28 6
10Q GAIN WILD-TYPE 121 105 60 78 48

Figure S48.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S49.  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 6
10Q GAIN WILD-TYPE 73 55 37 77 33 35 36 18 48

Figure S49.  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 S50.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
11P GAIN MUTATED 45 21 26
11P GAIN WILD-TYPE 141 195 65

Figure S50.  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 S51.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
11P GAIN MUTATED 5 11 16 18 30 11
11P GAIN WILD-TYPE 66 33 102 119 53 24

Figure S51.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S52.  Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
11P GAIN MUTATED 18 49 12
11P GAIN WILD-TYPE 168 160 18

Figure S52.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

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

Table S53.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
11Q GAIN MUTATED 63 23 26
11Q GAIN WILD-TYPE 123 193 65

Figure S53.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.25

Table S54.  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 21 15 11 28 1 17 9 1 9
11Q GAIN WILD-TYPE 62 42 33 56 45 34 40 17 45

Figure S54.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.032

Table S55.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
11Q GAIN MUTATED 21 65 23
11Q GAIN WILD-TYPE 158 166 55

Figure S55.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S56.  Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
11Q GAIN MUTATED 23 59 13
11Q GAIN WILD-TYPE 163 150 17

Figure S56.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

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

Table S57.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
12P GAIN MUTATED 50 38 43
12P GAIN WILD-TYPE 136 178 48

Figure S57.  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 S58.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
12P GAIN MUTATED 8 51 29 28
12P GAIN WILD-TYPE 84 74 86 71

Figure S58.  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 S59.  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 40 5 30 42 12
12P GAIN WILD-TYPE 98 107 46 64 42

Figure S59.  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 S60.  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 16 5 16 26 3 27 24 2 10
12P GAIN WILD-TYPE 67 52 28 58 43 24 25 16 44

Figure S60.  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 S61.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
12P GAIN MUTATED 28 83 18
12P GAIN WILD-TYPE 151 148 60

Figure S61.  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 S62.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
12P GAIN MUTATED 9 20 33 22 37 8
12P GAIN WILD-TYPE 62 24 85 115 46 27

Figure S62.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S63.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
12P GAIN MUTATED 18 73 23
12P GAIN WILD-TYPE 137 119 55

Figure S63.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S64.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
12P GAIN MUTATED 25 82 7
12P GAIN WILD-TYPE 161 127 23

Figure S64.  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 S65.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
12Q GAIN MUTATED 41 39 46
12Q GAIN WILD-TYPE 145 177 45

Figure S65.  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 S66.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
12Q GAIN MUTATED 5 49 29 28
12Q GAIN WILD-TYPE 87 76 86 71

Figure S66.  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 S67.  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 31 6 29 49 9
12Q GAIN WILD-TYPE 107 106 47 57 45

Figure S67.  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 S68.  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 15 6 15 20 3 32 25 2 6
12Q GAIN WILD-TYPE 68 51 29 64 43 19 24 16 48

Figure S68.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

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

Table S69.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
12Q GAIN MUTATED 27 81 16
12Q GAIN WILD-TYPE 152 150 62

Figure S69.  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 S70.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
12Q GAIN MUTATED 12 23 28 15 36 10
12Q GAIN WILD-TYPE 59 21 90 122 47 25

Figure S70.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S71.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
12Q GAIN MUTATED 17 68 24
12Q GAIN WILD-TYPE 138 124 54

Figure S71.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S72.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
12Q GAIN MUTATED 22 78 9
12Q GAIN WILD-TYPE 164 131 21

Figure S72.  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 S73.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
14Q GAIN MUTATED 47 30 43
14Q GAIN WILD-TYPE 139 186 48

Figure S73.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.094

Table S74.  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 S74.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S75.  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 S75.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.024

Table S76.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
14Q GAIN MUTATED 23 69 25
14Q GAIN WILD-TYPE 156 162 53

Figure S76.  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 S77.  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 S77.  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 S78.  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 S78.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

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

Table S79.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
17P GAIN MUTATED 28 25 30
17P GAIN WILD-TYPE 158 191 61

Figure S79.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MIRSEQ_CNMF'

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

Table S80.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
17P GAIN MUTATED 16 58 7
17P GAIN WILD-TYPE 163 173 71

Figure S80.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'CN_CNMF'

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

Table S81.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
17Q GAIN MUTATED 91 50 45
17Q GAIN WILD-TYPE 95 166 46

Figure S81.  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 = 0.032

Table S82.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
17Q GAIN MUTATED 19 56 57 31
17Q GAIN WILD-TYPE 73 69 58 68

Figure S82.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

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

Table S83.  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 S83.  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 S84.  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 S84.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

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

Table S85.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
17Q GAIN MUTATED 46 112 26
17Q GAIN WILD-TYPE 133 119 52

Figure S85.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S86.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
17Q GAIN MUTATED 19 25 48 37 43 12
17Q GAIN WILD-TYPE 52 19 70 100 40 23

Figure S86.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S87.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
17Q GAIN MUTATED 52 100 10
17Q GAIN WILD-TYPE 134 109 20

Figure S87.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

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

Table S88.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
18P GAIN MUTATED 47 21 23
18P GAIN WILD-TYPE 139 195 68

Figure S88.  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 S89.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
18P GAIN MUTATED 5 41 24 9
18P GAIN WILD-TYPE 87 84 91 90

Figure S89.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'CN_CNMF'

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

Table S90.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
18Q GAIN MUTATED 29 15 22
18Q GAIN WILD-TYPE 157 201 69

Figure S90.  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 S91.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
18Q GAIN MUTATED 3 33 16 4
18Q GAIN WILD-TYPE 89 92 99 95

Figure S91.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.094

Table S92.  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 14 8 9 30 4
18Q GAIN WILD-TYPE 124 104 67 76 50

Figure S92.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.094

Table S93.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
20P GAIN MUTATED 62 55 47
20P GAIN WILD-TYPE 124 161 44

Figure S93.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

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

Table S94.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
20P GAIN MUTATED 19 59 30 34
20P GAIN WILD-TYPE 73 66 85 65

Figure S94.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.2

Table S95.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
20P GAIN MUTATED 45 27 24 53 11
20P GAIN WILD-TYPE 93 85 52 53 43

Figure S95.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S96.  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 20 45 14 25 15 1 12
20P GAIN WILD-TYPE 65 47 24 39 32 26 34 17 42

Figure S96.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

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

Table S97.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
20P GAIN MUTATED 37 92 33
20P GAIN WILD-TYPE 142 139 45

Figure S97.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S98.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
20P GAIN MUTATED 33 75 34
20P GAIN WILD-TYPE 122 117 44

Figure S98.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.032

Table S99.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
20P GAIN MUTATED 41 88 13
20P GAIN WILD-TYPE 145 121 17

Figure S99.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

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

Table S100.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
20Q GAIN MUTATED 80 56 53
20Q GAIN WILD-TYPE 106 160 38

Figure S100.  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 S101.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
20Q GAIN MUTATED 19 69 42 35
20Q GAIN WILD-TYPE 73 56 73 64

Figure S101.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

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

Table S102.  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 59 24 27 59 16
20Q GAIN WILD-TYPE 79 88 49 47 38

Figure S102.  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 S103.  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 25 51 14 27 18 1 13
20Q GAIN WILD-TYPE 57 47 19 33 32 24 31 17 41

Figure S103.  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 S104.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
20Q GAIN MUTATED 42 109 34
20Q GAIN WILD-TYPE 137 122 44

Figure S104.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S105.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
20Q GAIN MUTATED 15 16 51 44 47 12
20Q GAIN WILD-TYPE 56 28 67 93 36 23

Figure S105.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S106.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
20Q GAIN MUTATED 38 92 35
20Q GAIN WILD-TYPE 117 100 43

Figure S106.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S107.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
20Q GAIN MUTATED 45 106 14
20Q GAIN WILD-TYPE 141 103 16

Figure S107.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

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

Table S108.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
21Q GAIN MUTATED 54 31 9
21Q GAIN WILD-TYPE 132 185 82

Figure S108.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S109.  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 S109.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

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

Table S110.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
1P LOSS MUTATED 17 33 29
1P LOSS WILD-TYPE 169 183 62

Figure S110.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

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

Table S111.  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 14 30 2
1P LOSS WILD-TYPE 119 102 62 76 52

Figure S111.  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 S112.  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 6 10 20 11 1 3
1P LOSS WILD-TYPE 76 50 34 78 36 31 38 17 51

Figure S112.  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 = 0.032

Table S113.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
3P LOSS MUTATED 83 68 54
3P LOSS WILD-TYPE 103 148 37

Figure S113.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S114.  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 41 17 34 26 0 18
3P LOSS WILD-TYPE 55 32 30 43 29 17 23 18 36

Figure S114.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

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

Table S115.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
4P LOSS MUTATED 50 32 34
4P LOSS WILD-TYPE 136 184 57

Figure S115.  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 S116.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
4P LOSS MUTATED 6 43 23 25
4P LOSS WILD-TYPE 86 82 92 74

Figure S116.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

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

Table S117.  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 S117.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S118.  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 S118.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

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

Table S119.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
4P LOSS MUTATED 23 76 16
4P LOSS WILD-TYPE 156 155 62

Figure S119.  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 S120.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
4P LOSS MUTATED 6 14 39 24 29 3
4P LOSS WILD-TYPE 65 30 79 113 54 32

Figure S120.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

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

Table S121.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
4Q LOSS MUTATED 56 36 40
4Q LOSS WILD-TYPE 130 180 51

Figure S121.  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 S122.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
4Q LOSS MUTATED 5 55 22 29
4Q LOSS WILD-TYPE 87 70 93 70

Figure S122.  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 S123.  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 S123.  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 S124.  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 S124.  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 S125.  Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
4Q LOSS MUTATED 26 85 20
4Q LOSS WILD-TYPE 153 146 58

Figure S125.  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 S126.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
4Q LOSS MUTATED 9 16 39 23 38 6
4Q LOSS WILD-TYPE 62 28 79 114 45 29

Figure S126.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.2

Table S127.  Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
4Q LOSS MUTATED 26 68 17
4Q LOSS WILD-TYPE 129 124 61

Figure S127.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S128.  Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
4Q LOSS MUTATED 30 77 4
4Q LOSS WILD-TYPE 156 132 26

Figure S128.  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 S129.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
5Q LOSS MUTATED 69 30 38
5Q LOSS WILD-TYPE 117 186 53

Figure S129.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

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

Table S130.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
5Q LOSS MUTATED 8 49 36 26
5Q LOSS WILD-TYPE 84 76 79 73

Figure S130.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

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

Table S131.  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 47 12 22 44 9
5Q LOSS WILD-TYPE 91 100 54 62 45

Figure S131.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.11

Table S132.  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 25 5 13 32 7 20 18 1 13
5Q LOSS WILD-TYPE 58 52 31 52 39 31 31 17 41

Figure S132.  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 S133.  Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
5Q LOSS MUTATED 27 88 20
5Q LOSS WILD-TYPE 152 143 58

Figure S133.  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 S134.  Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
5Q LOSS MUTATED 10 16 39 25 40 5
5Q LOSS WILD-TYPE 61 28 79 112 43 30

Figure S134.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S135.  Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
5Q LOSS MUTATED 25 75 18
5Q LOSS WILD-TYPE 130 117 60

Figure S135.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S136.  Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
5Q LOSS MUTATED 28 85 5
5Q LOSS WILD-TYPE 158 124 25

Figure S136.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.11

Table S137.  Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
6Q LOSS MUTATED 41 57 62 24
6Q LOSS WILD-TYPE 51 68 53 75

Figure S137.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S138.  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 15 3 21
6Q LOSS WILD-TYPE 40 37 22 61 18 22 34 15 33

Figure S138.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.024

Table S139.  Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
7P LOSS MUTATED 5 11 17
7P LOSS WILD-TYPE 181 205 74

Figure S139.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

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

Table S140.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
8P LOSS MUTATED 119 45 27
8P LOSS WILD-TYPE 67 171 64

Figure S140.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

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

Table S141.  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 76 36 23 41 14
8P LOSS WILD-TYPE 62 76 53 65 40

Figure S141.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.024

Table S142.  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 38 23 25 46 8 16 14 2 18
8P LOSS WILD-TYPE 45 34 19 38 38 35 35 16 36

Figure S142.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

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

Table S143.  Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
8Q LOSS MUTATED 34 16 4
8Q LOSS WILD-TYPE 152 200 87

Figure S143.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S144.  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 37 30 18 51 19 24 41 8 23
9P LOSS WILD-TYPE 46 27 26 33 27 27 8 10 31

Figure S144.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.032

Table S145.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
9Q LOSS MUTATED 101 80 57
9Q LOSS WILD-TYPE 85 136 34

Figure S145.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S146.  Gene #58: '9q 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
9Q LOSS MUTATED 36 27 18 52 13 29 33 4 24
9Q LOSS WILD-TYPE 47 30 26 32 33 22 16 14 30

Figure S146.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.024

Table S147.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
9Q LOSS MUTATED 29 26 52 52 59 17
9Q LOSS WILD-TYPE 42 18 66 85 24 18

Figure S147.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

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

Table S148.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
10P LOSS MUTATED 64 27 17
10P LOSS WILD-TYPE 122 189 74

Figure S148.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.024

Table S149.  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 S149.  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 S150.  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 S150.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

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

Table S151.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
10Q LOSS MUTATED 69 36 23
10Q LOSS WILD-TYPE 117 180 68

Figure S151.  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 S152.  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 S152.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S153.  Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
10Q LOSS MUTATED 10 8 28 29 34 17
10Q LOSS WILD-TYPE 61 36 90 108 49 18

Figure S153.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.094

Table S154.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
11P LOSS MUTATED 53 28 27
11P LOSS WILD-TYPE 133 188 64

Figure S154.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

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

Table S155.  Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
12Q LOSS MUTATED 54 32 7
12Q LOSS WILD-TYPE 132 184 84

Figure S155.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S156.  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 23 10 1 3 2 14
12Q LOSS WILD-TYPE 60 45 40 61 36 50 46 16 40

Figure S156.  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 S157.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
13Q LOSS MUTATED 122 59 62
13Q LOSS WILD-TYPE 64 157 29

Figure S157.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S158.  Gene #65: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 112 71 52
13Q LOSS MUTATED 66 16 29
13Q LOSS WILD-TYPE 46 55 23

Figure S158.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

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

Table S159.  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 87 40 24 66 24
13Q LOSS WILD-TYPE 51 72 52 40 30

Figure S159.  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 S160.  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 53 22 25 49 10 36 19 1 26
13Q LOSS WILD-TYPE 30 35 19 35 36 15 30 17 28

Figure S160.  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 S161.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
15Q LOSS MUTATED 107 73 53
15Q LOSS WILD-TYPE 79 143 38

Figure S161.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

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

Table S162.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
15Q LOSS MUTATED 23 66 67 47
15Q LOSS WILD-TYPE 69 59 48 52

Figure S162.  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 S163.  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 36 13 61 26
15Q LOSS WILD-TYPE 46 76 63 45 28

Figure S163.  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 S164.  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 47 23 31 49 7 34 9 0 28
15Q LOSS WILD-TYPE 36 34 13 35 39 17 40 18 26

Figure S164.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

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

Table S165.  Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
15Q LOSS MUTATED 60 126 45
15Q LOSS WILD-TYPE 119 105 33

Figure S165.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'CN_CNMF'

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

Table S166.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
16P LOSS MUTATED 49 27 32
16P LOSS WILD-TYPE 137 189 59

Figure S166.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

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

Table S167.  Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
16P LOSS MUTATED 5 37 36 18
16P LOSS WILD-TYPE 87 88 79 81

Figure S167.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

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

Table S168.  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 34 8
16P LOSS WILD-TYPE 96 102 62 72 46

Figure S168.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'CN_CNMF'

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

Table S169.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
16Q LOSS MUTATED 64 37 36
16Q LOSS WILD-TYPE 122 179 55

Figure S169.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

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

Table S170.  Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
16Q LOSS MUTATED 8 45 44 21
16Q LOSS WILD-TYPE 84 80 71 78

Figure S170.  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 S171.  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 8
16Q LOSS WILD-TYPE 79 97 60 67 46

Figure S171.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S172.  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 10
16Q LOSS WILD-TYPE 48 50 24 55 37 34 39 18 44

Figure S172.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S173.  Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
16Q LOSS MUTATED 33 77 6
16Q LOSS WILD-TYPE 153 132 24

Figure S173.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

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

Table S174.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
17P LOSS MUTATED 111 55 40
17P LOSS WILD-TYPE 75 161 51

Figure S174.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.13

Table S175.  Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
17P LOSS MUTATED 27 53 66 33
17P LOSS WILD-TYPE 65 72 49 66

Figure S175.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'CN_CNMF'

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

Table S176.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
17Q LOSS MUTATED 30 10 15
17Q LOSS WILD-TYPE 156 206 76

Figure S176.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.024

Table S177.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
18P LOSS MUTATED 88 55 26
18P LOSS WILD-TYPE 98 161 65

Figure S177.  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 S178.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
18Q LOSS MUTATED 113 68 26
18Q LOSS WILD-TYPE 73 148 65

Figure S178.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.22

Table S179.  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 79 39 33 33 20
18Q LOSS WILD-TYPE 59 73 43 73 34

Figure S179.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.13

Table S180.  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 24 43 7 14 24 9 17
18Q LOSS WILD-TYPE 44 30 20 41 39 37 25 9 37

Figure S180.  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 S181.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
19P LOSS MUTATED 99 74 62
19P LOSS WILD-TYPE 87 142 29

Figure S181.  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 S182.  Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
19P LOSS MUTATED 26 88 49 37
19P LOSS WILD-TYPE 66 37 66 62

Figure S182.  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 S183.  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 S183.  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 S184.  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 S184.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

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

Table S185.  Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
19P LOSS MUTATED 65 134 31
19P LOSS WILD-TYPE 114 97 47

Figure S185.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.024

Table S186.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
19P LOSS MUTATED 31 24 64 44 54 13
19P LOSS WILD-TYPE 40 20 54 93 29 22

Figure S186.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S187.  Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
19P LOSS MUTATED 68 121 10
19P LOSS WILD-TYPE 118 88 20

Figure S187.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

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

Table S188.  Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
19Q LOSS MUTATED 76 39 38
19Q LOSS WILD-TYPE 110 177 53

Figure S188.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

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

Table S189.  Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
19Q LOSS MUTATED 14 54 39 23
19Q LOSS WILD-TYPE 78 71 76 76

Figure S189.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

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

Table S190.  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 48 23 22 50 10
19Q LOSS WILD-TYPE 90 89 54 56 44

Figure S190.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S191.  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 35 17 23 20 0 8
19Q LOSS WILD-TYPE 63 44 27 49 29 28 29 18 46

Figure S191.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.16

Table S192.  Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
19Q LOSS MUTATED 38 82 8
19Q LOSS WILD-TYPE 148 127 22

Figure S192.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

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

Table S193.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
21Q LOSS MUTATED 50 56 51
21Q LOSS WILD-TYPE 136 160 40

Figure S193.  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 S194.  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 S194.  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 S195.  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 S195.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.094

Table S196.  Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
21Q LOSS MUTATED 16 18 42 30 41 7
21Q LOSS WILD-TYPE 55 26 76 107 42 28

Figure S196.  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 S197.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
22Q LOSS MUTATED 94 60 58
22Q LOSS WILD-TYPE 92 156 33

Figure S197.  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 S198.  Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 125 115 99
22Q LOSS MUTATED 18 70 61 38
22Q LOSS WILD-TYPE 74 55 54 61

Figure S198.  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 S199.  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 63 11
22Q LOSS WILD-TYPE 68 82 42 43 43

Figure S199.  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 S200.  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 34 24 4 11
22Q LOSS WILD-TYPE 36 43 24 44 32 17 25 14 43

Figure S200.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.16

Table S201.  Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
22Q LOSS MUTATED 56 119 33
22Q LOSS WILD-TYPE 123 112 45

Figure S201.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.094

Table S202.  Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 44 118 137 83 35
22Q LOSS MUTATED 22 25 63 44 44 10
22Q LOSS WILD-TYPE 49 19 55 93 39 25

Figure S202.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S203.  Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 209 30
22Q LOSS MUTATED 60 115 8
22Q LOSS WILD-TYPE 126 94 22

Figure S203.  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 = 493

  • 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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