Correlation between copy number variations of arm-level result and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1BZ64TH
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/C1BZ64TH
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 490 patients, 124 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 4p gain cnv correlated to 'CN_CNMF'.

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

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

  • 9p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 19p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 6p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 10q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'CN_CNMF'.

  • 20q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • xq loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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, 124 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
1p loss 147 (30%) 343 1e-05
(0.0096) 		3e-05
(0.0266) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.884
(1.00) 		0.173
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00014
(0.12) 		1e-05
(0.0096) 		0.0104
(1.00) 		0.00022
(0.186)
9q loss 239 (49%) 251 3e-05
(0.0266) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.173
(1.00) 		0.0147
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00064
(0.524) 		1e-05
(0.0096)
4p loss 307 (63%) 183 0.00067
(0.547) 		3e-05
(0.0266) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.211
(1.00) 		0.378
(1.00) 		2e-05
(0.0179) 		2e-05
(0.0179) 		0.00014
(0.12) 		0.345
(1.00) 		0.00011
(0.0949) 		7e-05
(0.0609)
7q gain 214 (44%) 276 0.00109
(0.862) 		0.00016
(0.136) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.966
(1.00) 		0.156
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00093
(0.743) 		4e-05
(0.0353) 		0.00466
(1.00) 		1e-05
(0.0096)
10q loss 223 (46%) 267 0.00116
(0.915) 		0.00024
(0.202) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0956
(1.00) 		0.0778
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00015
(0.128) 		1e-05
(0.0096) 		0.00064
(0.524) 		0.00595
(1.00)
14q loss 165 (34%) 325 5e-05
(0.0439) 		0.00029
(0.243) 		0.0605
(1.00) 		0.113
(1.00) 		0.0545
(1.00) 		0.153
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0102
(1.00) 		1e-05
(0.0096)
9q gain 91 (19%) 399 0.0148
(1.00) 		0.00178
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0591
(1.00) 		0.0284
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		4e-05
(0.0353) 		0.00058
(0.477) 		0.00115
(0.908) 		0.00022
(0.186)
17q gain 156 (32%) 334 0.00097
(0.772) 		0.00046
(0.381) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.236
(1.00) 		0.921
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		5e-05
(0.0439) 		0.00083
(0.666) 		1e-05
(0.0096) 		0.00031
(0.259)
10p loss 210 (43%) 280 0.204
(1.00) 		0.218
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.484
(1.00) 		0.184
(1.00) 		1e-05
(0.0096) 		2e-05
(0.0179) 		0.00011
(0.0949) 		1e-05
(0.0096) 		0.0007
(0.568) 		0.00253
(1.00)
7p gain 234 (48%) 256 0.0368
(1.00) 		0.00644
(1.00) 		4e-05
(0.0353) 		0.00013
(0.111) 		0.665
(1.00) 		0.462
(1.00) 		7e-05
(0.0609) 		1e-05
(0.0096) 		0.00475
(1.00) 		0.00072
(0.584) 		0.00333
(1.00) 		3e-05
(0.0266)
2p gain 218 (44%) 272 0.0776
(1.00) 		0.0215
(1.00) 		1e-05
(0.0096) 		2e-05
(0.0179) 		0.419
(1.00) 		0.758
(1.00) 		1e-05
(0.0096) 		2e-05
(0.0179) 		0.00103
(0.818) 		0.0107
(1.00) 		0.00057
(0.469) 		0.0114
(1.00)
9p gain 60 (12%) 430 0.0869
(1.00) 		0.021
(1.00) 		0.00012
(0.103) 		9e-05
(0.0779) 		0.178
(1.00) 		0.0482
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0846
(1.00) 		0.0269
(1.00) 		0.00725
(1.00) 		0.0157
(1.00)
4q loss 290 (59%) 200 0.00107
(0.847) 		0.00099
(0.787) 		1e-05
(0.0096) 		6e-05
(0.0525) 		0.251
(1.00) 		0.497
(1.00) 		2e-05
(0.0179) 		6e-05
(0.0525) 		0.00719
(1.00) 		0.056
(1.00) 		0.0082
(1.00) 		0.0102
(1.00)
6p loss 109 (22%) 381 0.0354
(1.00) 		0.0139
(1.00) 		0.00025
(0.21) 		0.00012
(0.103) 		0.151
(1.00) 		0.149
(1.00) 		2e-05
(0.0179) 		1e-05
(0.0096) 		0.295
(1.00) 		0.0958
(1.00) 		0.00501
(1.00) 		0.294
(1.00)
1q gain 199 (41%) 291 0.681
(1.00) 		0.548
(1.00) 		0.00022
(0.186) 		7e-05
(0.0609) 		0.557
(1.00) 		0.561
(1.00) 		0.00668
(1.00) 		0.00015
(0.128) 		0.0202
(1.00) 		0.00069
(0.561) 		0.064
(1.00) 		0.00166
(1.00)
17p gain 65 (13%) 425 0.00371
(1.00) 		0.103
(1.00) 		1e-05
(0.0096) 		0.00086
(0.69) 		0.84
(1.00) 		0.138
(1.00) 		0.00021
(0.178) 		0.00023
(0.194) 		0.0192
(1.00) 		0.00132
(1.00) 		0.00376
(1.00) 		0.0267
(1.00)
19p gain 109 (22%) 381 0.0352
(1.00) 		0.0811
(1.00) 		1e-05
(0.0096) 		0.00025
(0.21) 		0.0186
(1.00) 		0.0827
(1.00) 		0.00034
(0.283) 		0.00214
(1.00) 		0.0219
(1.00) 		0.00398
(1.00) 		0.0379
(1.00) 		0.00019
(0.161)
9p loss 304 (62%) 186 0.00751
(1.00) 		0.00123
(0.966) 		5e-05
(0.0439) 		0.0184
(1.00) 		0.207
(1.00) 		0.076
(1.00) 		1e-05
(0.0096) 		2e-05
(0.0179) 		0.0515
(1.00) 		0.0009
(0.72) 		0.16
(1.00) 		0.0907
(1.00)
17q loss 90 (18%) 400 0.00463
(1.00) 		0.0053
(1.00) 		0.00062
(0.508) 		0.00011
(0.0949) 		0.32
(1.00) 		0.762
(1.00) 		9e-05
(0.0779) 		2e-05
(0.0179) 		0.176
(1.00) 		0.00944
(1.00) 		0.0521
(1.00) 		0.156
(1.00)
12p gain 224 (46%) 266 0.0185
(1.00) 		0.0336
(1.00) 		1e-05
(0.0096) 		0.00142
(1.00) 		0.218
(1.00) 		0.803
(1.00) 		3e-05
(0.0266) 		0.0222
(1.00) 		0.0238
(1.00) 		0.0403
(1.00) 		0.072
(1.00) 		0.101
(1.00)
12q gain 151 (31%) 339 0.024
(1.00) 		0.309
(1.00) 		1e-05
(0.0096) 		0.00206
(1.00) 		0.536
(1.00) 		0.615
(1.00) 		0.0043
(1.00) 		0.00075
(0.607) 		0.284
(1.00) 		0.0108
(1.00) 		0.0004
(0.332) 		9e-05
(0.0779)
18p gain 147 (30%) 343 0.00769
(1.00) 		0.00136
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.488
(1.00) 		0.714
(1.00) 		0.00051
(0.422) 		0.00068
(0.554) 		0.00206
(1.00) 		0.0676
(1.00) 		0.00235
(1.00) 		0.047
(1.00)
18q gain 105 (21%) 385 0.00853
(1.00) 		0.00762
(1.00) 		1e-05
(0.0096) 		0.0018
(1.00) 		0.405
(1.00) 		0.252
(1.00) 		0.00015
(0.128) 		0.00356
(1.00) 		0.0489
(1.00) 		0.00917
(1.00) 		0.084
(1.00) 		0.0603
(1.00)
7q loss 51 (10%) 439 0.159
(1.00) 		0.0649
(1.00) 		0.0298
(1.00) 		0.216
(1.00) 		0.914
(1.00) 		0.0311
(1.00) 		6e-05
(0.0525) 		1e-05
(0.0096) 		0.0527
(1.00) 		0.101
(1.00) 		0.829
(1.00) 		0.141
(1.00)
22q loss 95 (19%) 395 0.00881
(1.00) 		0.1
(1.00) 		0.106
(1.00) 		0.0384
(1.00) 		0.253
(1.00) 		0.0569
(1.00) 		0.00026
(0.218) 		1e-05
(0.0096) 		0.3
(1.00) 		0.0803
(1.00) 		0.693
(1.00) 		0.145
(1.00)
2q gain 136 (28%) 354 0.344
(1.00) 		0.299
(1.00) 		8e-05
(0.0694) 		0.0308
(1.00) 		0.452
(1.00) 		0.651
(1.00) 		0.00078
(0.63) 		0.0344
(1.00) 		0.101
(1.00) 		0.262
(1.00) 		0.00519
(1.00) 		0.237
(1.00)
4p gain 30 (6%) 460 0.324
(1.00) 		0.102
(1.00) 		4e-05
(0.0353) 		0.153
(1.00) 		0.274
(1.00) 		0.115
(1.00) 		0.0101
(1.00) 		0.0183
(1.00) 		0.255
(1.00) 		0.132
(1.00) 		0.214
(1.00) 		0.107
(1.00)
19q gain 155 (32%) 335 0.114
(1.00) 		0.178
(1.00) 		0.00012
(0.103) 		0.00991
(1.00) 		0.23
(1.00) 		0.12
(1.00) 		0.0252
(1.00) 		0.343
(1.00) 		0.595
(1.00) 		0.516
(1.00) 		0.0766
(1.00) 		0.0995
(1.00)
20p gain 254 (52%) 236 0.0191
(1.00) 		0.0215
(1.00) 		1e-05
(0.0096) 		0.00055
(0.453) 		0.888
(1.00) 		0.313
(1.00) 		0.0936
(1.00) 		0.0782
(1.00) 		0.0654
(1.00) 		0.804
(1.00) 		0.404
(1.00) 		0.729
(1.00)
20q gain 243 (50%) 247 0.675
(1.00) 		0.314
(1.00) 		0.00012
(0.103) 		0.149
(1.00) 		0.473
(1.00) 		0.591
(1.00) 		0.351
(1.00) 		0.196
(1.00) 		0.0596
(1.00) 		0.0437
(1.00) 		0.458
(1.00) 		0.636
(1.00)
22q gain 218 (44%) 272 0.00726
(1.00) 		0.0288
(1.00) 		0.00482
(1.00) 		0.0389
(1.00) 		0.965
(1.00) 		0.0682
(1.00) 		0.00174
(1.00) 		0.00021
(0.178) 		0.0737
(1.00) 		0.0859
(1.00) 		0.0879
(1.00) 		0.246
(1.00)
xq gain 77 (16%) 413 0.366
(1.00) 		0.124
(1.00) 		6e-05
(0.0525) 		0.00527
(1.00) 		0.677
(1.00) 		0.621
(1.00) 		0.00465
(1.00) 		0.0421
(1.00) 		0.00151
(1.00) 		0.289
(1.00) 		0.021
(1.00) 		0.0883
(1.00)
19p loss 164 (33%) 326 0.0527
(1.00) 		0.0607
(1.00) 		3e-05
(0.0266) 		0.579
(1.00) 		0.859
(1.00) 		0.265
(1.00) 		0.119
(1.00) 		0.0172
(1.00) 		0.0322
(1.00) 		0.0005
(0.414) 		0.76
(1.00) 		0.24
(1.00)
20q loss 46 (9%) 444 0.0553
(1.00) 		0.0758
(1.00) 		0.00604
(1.00) 		0.0545
(1.00) 		0.266
(1.00) 		0.295
(1.00) 		0.00024
(0.202) 		0.00058
(0.477) 		0.127
(1.00) 		0.518
(1.00) 		0.181
(1.00) 		0.277
(1.00)
21q loss 260 (53%) 230 0.9
(1.00) 		0.321
(1.00) 		1e-05
(0.0096) 		0.0366
(1.00) 		0.526
(1.00) 		0.45
(1.00) 		0.0652
(1.00) 		0.268
(1.00) 		0.00186
(1.00) 		0.0104
(1.00) 		0.189
(1.00) 		0.0932
(1.00)
xq loss 110 (22%) 380 0.202
(1.00) 		0.557
(1.00) 		0.00033
(0.275) 		0.00053
(0.437) 		0.772
(1.00) 		0.824
(1.00) 		0.0206
(1.00) 		0.868
(1.00) 		0.0003
(0.251) 		0.315
(1.00) 		6e-05
(0.0525) 		0.0321
(1.00)
1p gain 88 (18%) 402 0.0869
(1.00) 		0.0885
(1.00) 		0.326
(1.00) 		0.437
(1.00) 		0.489
(1.00) 		0.915
(1.00) 		0.727
(1.00) 		0.476
(1.00) 		0.794
(1.00) 		0.748
(1.00) 		1
(1.00) 		0.112
(1.00)
3p gain 107 (22%) 383 0.978
(1.00) 		0.827
(1.00) 		0.153
(1.00) 		0.0393
(1.00) 		0.846
(1.00) 		0.457
(1.00) 		0.36
(1.00) 		0.231
(1.00) 		0.779
(1.00) 		0.473
(1.00) 		0.687
(1.00) 		0.528
(1.00)
3q gain 307 (63%) 183 0.596
(1.00) 		0.737
(1.00) 		0.00244
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.141
(1.00) 		0.252
(1.00) 		0.363
(1.00) 		0.109
(1.00) 		0.0241
(1.00) 		0.989
(1.00) 		0.241
(1.00)
4q gain 22 (4%) 468 0.585
(1.00) 		0.462
(1.00) 		0.00596
(1.00) 		0.109
(1.00) 		0.677
(1.00) 		0.137
(1.00) 		0.491
(1.00) 		0.751
(1.00) 		0.749
(1.00) 		0.223
(1.00) 		0.436
(1.00) 		0.123
(1.00)
5p gain 304 (62%) 186 0.749
(1.00) 		0.62
(1.00) 		0.00081
(0.652) 		0.801
(1.00) 		0.37
(1.00) 		0.24
(1.00) 		0.33
(1.00) 		0.624
(1.00) 		0.937
(1.00) 		0.0042
(1.00) 		0.345
(1.00) 		0.115
(1.00)
5q gain 93 (19%) 397 0.118
(1.00) 		0.218
(1.00) 		0.0322
(1.00) 		0.186
(1.00) 		0.477
(1.00) 		0.117
(1.00) 		0.301
(1.00) 		0.0951
(1.00) 		0.0397
(1.00) 		0.0496
(1.00) 		0.169
(1.00) 		0.206
(1.00)
6p gain 106 (22%) 384 0.0541
(1.00) 		0.179
(1.00) 		0.00159
(1.00) 		0.943
(1.00) 		0.935
(1.00) 		0.193
(1.00) 		0.00431
(1.00) 		0.00803
(1.00) 		0.747
(1.00) 		0.0794
(1.00) 		0.73
(1.00) 		0.673
(1.00)
6q gain 91 (19%) 399 0.0682
(1.00) 		0.12
(1.00) 		0.00075
(0.607) 		0.518
(1.00) 		0.949
(1.00) 		0.957
(1.00) 		0.0207
(1.00) 		0.0178
(1.00) 		0.644
(1.00) 		0.136
(1.00) 		0.967
(1.00) 		0.252
(1.00)
8p gain 123 (25%) 367 0.598
(1.00) 		0.492
(1.00) 		0.225
(1.00) 		0.102
(1.00) 		0.566
(1.00) 		0.942
(1.00) 		0.0729
(1.00) 		0.0244
(1.00) 		0.505
(1.00) 		0.218
(1.00) 		1
(1.00) 		0.838
(1.00)
8q gain 247 (50%) 243 0.0486
(1.00) 		0.0369
(1.00) 		0.0418
(1.00) 		0.00751
(1.00) 		0.218
(1.00) 		0.785
(1.00) 		0.00608
(1.00) 		0.00647
(1.00) 		0.0269
(1.00) 		0.0246
(1.00) 		0.224
(1.00) 		0.914
(1.00)
10p gain 76 (16%) 414 0.325
(1.00) 		0.701
(1.00) 		0.0686
(1.00) 		0.161
(1.00) 		0.0655
(1.00) 		0.0856
(1.00) 		0.0858
(1.00) 		0.299
(1.00) 		0.0266
(1.00) 		0.00357
(1.00) 		0.511
(1.00) 		0.109
(1.00)
10q gain 43 (9%) 447 0.111
(1.00) 		0.142
(1.00) 		0.0828
(1.00) 		0.571
(1.00) 		0.027
(1.00) 		0.208
(1.00) 		0.134
(1.00) 		0.0348
(1.00) 		0.282
(1.00) 		0.274
(1.00) 		0.591
(1.00) 		0.459
(1.00)
11p gain 72 (15%) 418 0.676
(1.00) 		0.478
(1.00) 		0.0421
(1.00) 		0.231
(1.00) 		0.341
(1.00) 		0.00846
(1.00) 		0.65
(1.00) 		0.826
(1.00) 		0.0106
(1.00) 		0.568
(1.00) 		0.12
(1.00) 		0.929
(1.00)
11q gain 89 (18%) 401 0.0178
(1.00) 		0.212
(1.00) 		0.00064
(0.524) 		0.432
(1.00) 		0.396
(1.00) 		0.0511
(1.00) 		0.253
(1.00) 		0.173
(1.00) 		0.0571
(1.00) 		0.432
(1.00) 		0.146
(1.00) 		0.925
(1.00)
13q gain 39 (8%) 451 0.703
(1.00) 		0.662
(1.00) 		0.454
(1.00) 		0.878
(1.00) 		0.414
(1.00) 		0.664
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.231
(1.00) 		0.424
(1.00) 		0.409
(1.00) 		0.133
(1.00)
14q gain 124 (25%) 366 0.142
(1.00) 		0.0232
(1.00) 		0.231
(1.00) 		0.116
(1.00) 		0.251
(1.00) 		0.331
(1.00) 		0.113
(1.00) 		0.0276
(1.00) 		0.0025
(1.00) 		0.021
(1.00) 		0.21
(1.00) 		0.00185
(1.00)
15q gain 104 (21%) 386 0.838
(1.00) 		0.429
(1.00) 		0.00187
(1.00) 		0.00175
(1.00) 		0.223
(1.00) 		0.66
(1.00) 		0.00081
(0.652) 		0.00116
(0.915) 		0.0123
(1.00) 		0.00651
(1.00) 		0.0255
(1.00) 		0.102
(1.00)
16p gain 86 (18%) 404 0.353
(1.00) 		0.556
(1.00) 		0.042
(1.00) 		0.503
(1.00) 		0.611
(1.00) 		0.782
(1.00) 		0.383
(1.00) 		0.699
(1.00) 		0.0491
(1.00) 		0.468
(1.00) 		0.00178
(1.00) 		0.127
(1.00)
16q gain 85 (17%) 405 0.917
(1.00) 		0.937
(1.00) 		0.0183
(1.00) 		0.331
(1.00) 		0.691
(1.00) 		0.437
(1.00) 		0.0933
(1.00) 		0.41
(1.00) 		0.148
(1.00) 		0.7
(1.00) 		0.0935
(1.00) 		0.103
(1.00)
21q gain 56 (11%) 434 0.894
(1.00) 		0.817
(1.00) 		0.764
(1.00) 		0.0615
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.414
(1.00) 		0.983
(1.00) 		0.215
(1.00) 		0.543
(1.00) 		0.305
(1.00) 		0.178
(1.00)
1q loss 57 (12%) 433 0.554
(1.00) 		0.67
(1.00) 		0.00051
(0.422) 		0.0846
(1.00) 		1
(1.00) 		0.679
(1.00) 		0.0186
(1.00) 		0.0112
(1.00) 		0.297
(1.00) 		0.276
(1.00) 		0.675
(1.00) 		0.252
(1.00)
2p loss 21 (4%) 469 0.046
(1.00) 		0.315
(1.00) 		0.0334
(1.00) 		0.153
(1.00) 		0.141
(1.00) 		0.101
(1.00) 		0.491
(1.00) 		0.144
(1.00) 		0.00359
(1.00) 		0.826
(1.00) 		0.0265
(1.00) 		0.0236
(1.00)
2q loss 41 (8%) 449 0.496
(1.00) 		0.718
(1.00) 		0.102
(1.00) 		0.355
(1.00) 		0.882
(1.00) 		0.143
(1.00) 		0.101
(1.00) 		0.0185
(1.00) 		0.00037
(0.307) 		0.647
(1.00) 		0.00771
(1.00) 		0.0327
(1.00)
3p loss 303 (62%) 187 0.612
(1.00) 		0.133
(1.00) 		0.128
(1.00) 		0.00094
(0.75) 		0.947
(1.00) 		0.161
(1.00) 		0.291
(1.00) 		0.305
(1.00) 		0.0798
(1.00) 		0.246
(1.00) 		0.0529
(1.00) 		0.0317
(1.00)
3q loss 71 (14%) 419 0.942
(1.00) 		0.961
(1.00) 		0.485
(1.00) 		0.663
(1.00) 		0.499
(1.00) 		0.517
(1.00) 		0.876
(1.00) 		0.871
(1.00) 		0.933
(1.00) 		0.779
(1.00) 		0.0508
(1.00) 		0.464
(1.00)
5p loss 76 (16%) 414 0.656
(1.00) 		0.714
(1.00) 		0.0646
(1.00) 		0.00165
(1.00) 		0.468
(1.00) 		0.0146
(1.00) 		0.263
(1.00) 		0.194
(1.00) 		0.184
(1.00) 		0.953
(1.00) 		0.348
(1.00) 		0.07
(1.00)
5q loss 284 (58%) 206 0.168
(1.00) 		0.0562
(1.00) 		0.00124
(0.972) 		0.00667
(1.00) 		0.106
(1.00) 		0.0974
(1.00) 		0.00917
(1.00) 		0.00162
(1.00) 		0.00915
(1.00) 		0.155
(1.00) 		0.154
(1.00) 		0.215
(1.00)
6q loss 109 (22%) 381 0.00523
(1.00) 		0.00103
(0.818) 		0.00127
(0.994) 		0.00087
(0.697) 		0.569
(1.00) 		0.313
(1.00) 		0.00094
(0.75) 		0.0012
(0.944) 		0.122
(1.00) 		0.309
(1.00) 		0.143
(1.00) 		0.59
(1.00)
7p loss 58 (12%) 432 0.565
(1.00) 		1
(1.00) 		0.00078
(0.63) 		0.276
(1.00) 		0.687
(1.00) 		0.0878
(1.00) 		0.304
(1.00) 		0.022
(1.00) 		0.421
(1.00) 		0.00782
(1.00) 		0.839
(1.00) 		0.952
(1.00)
8p loss 237 (48%) 253 0.91
(1.00) 		0.938
(1.00) 		0.0712
(1.00) 		0.00197
(1.00) 		0.134
(1.00) 		0.559
(1.00) 		0.203
(1.00) 		0.00817
(1.00) 		0.0414
(1.00) 		0.953
(1.00) 		0.375
(1.00) 		0.00622
(1.00)
8q loss 49 (10%) 441 0.348
(1.00) 		0.359
(1.00) 		0.27
(1.00) 		0.00301
(1.00) 		0.0405
(1.00) 		0.944
(1.00) 		0.143
(1.00) 		0.0008
(0.645) 		0.439
(1.00) 		0.0936
(1.00) 		0.818
(1.00) 		0.551
(1.00)
11p loss 168 (34%) 322 0.252
(1.00) 		0.252
(1.00) 		0.00297
(1.00) 		0.00336
(1.00) 		0.133
(1.00) 		0.00273
(1.00) 		0.156
(1.00) 		0.394
(1.00) 		0.385
(1.00) 		0.783
(1.00) 		0.111
(1.00) 		0.0628
(1.00)
11q loss 139 (28%) 351 0.987
(1.00) 		0.76
(1.00) 		0.0024
(1.00) 		0.00148
(1.00) 		0.54
(1.00) 		0.866
(1.00) 		0.182
(1.00) 		0.671
(1.00) 		0.0186
(1.00) 		0.54
(1.00) 		0.219
(1.00) 		0.411
(1.00)
12p loss 38 (8%) 452 0.0236
(1.00) 		0.00504
(1.00) 		0.313
(1.00) 		0.881
(1.00) 		0.0992
(1.00) 		0.885
(1.00) 		0.949
(1.00) 		0.058
(1.00) 		0.133
(1.00) 		0.178
(1.00) 		0.587
(1.00) 		0.171
(1.00)
12q loss 48 (10%) 442 0.368
(1.00) 		0.141
(1.00) 		0.981
(1.00) 		0.675
(1.00) 		0.0283
(1.00) 		0.752
(1.00) 		0.739
(1.00) 		0.543
(1.00) 		0.181
(1.00) 		0.0175
(1.00) 		0.559
(1.00) 		0.65
(1.00)
13q loss 305 (62%) 185 0.618
(1.00) 		0.708
(1.00) 		0.0168
(1.00) 		0.0544
(1.00) 		0.703
(1.00) 		0.37
(1.00) 		0.402
(1.00) 		0.375
(1.00) 		0.311
(1.00) 		0.0264
(1.00) 		0.00169
(1.00) 		0.0173
(1.00)
15q loss 137 (28%) 353 0.721
(1.00) 		0.744
(1.00) 		0.247
(1.00) 		0.0514
(1.00) 		0.326
(1.00) 		0.002
(1.00) 		0.0572
(1.00) 		0.141
(1.00) 		0.0485
(1.00) 		0.0311
(1.00) 		0.0114
(1.00) 		0.0148
(1.00)
16p loss 155 (32%) 335 0.917
(1.00) 		0.759
(1.00) 		0.00122
(0.959) 		0.118
(1.00) 		0.119
(1.00) 		0.273
(1.00) 		0.456
(1.00) 		0.279
(1.00) 		0.09
(1.00) 		0.776
(1.00) 		0.0926
(1.00) 		0.196
(1.00)
16q loss 177 (36%) 313 0.776
(1.00) 		0.128
(1.00) 		0.00532
(1.00) 		0.161
(1.00) 		0.133
(1.00) 		0.852
(1.00) 		0.0634
(1.00) 		0.114
(1.00) 		0.0119
(1.00) 		0.178
(1.00) 		0.00378
(1.00) 		0.00606
(1.00)
17p loss 285 (58%) 205 0.00517
(1.00) 		0.171
(1.00) 		0.00154
(1.00) 		0.0112
(1.00) 		0.435
(1.00) 		0.00621
(1.00) 		0.0003
(0.251) 		0.00587
(1.00) 		0.0282
(1.00) 		0.00067
(0.547) 		0.709
(1.00) 		0.094
(1.00)
18p loss 139 (28%) 351 0.858
(1.00) 		0.656
(1.00) 		0.0195
(1.00) 		0.0874
(1.00) 		0.624
(1.00) 		0.919
(1.00) 		0.178
(1.00) 		0.0435
(1.00) 		0.389
(1.00) 		0.03
(1.00) 		0.00829
(1.00) 		0.767
(1.00)
18q loss 182 (37%) 308 0.178
(1.00) 		0.25
(1.00) 		0.0802
(1.00) 		0.324
(1.00) 		0.648
(1.00) 		0.3
(1.00) 		0.39
(1.00) 		0.179
(1.00) 		0.204
(1.00) 		0.138
(1.00) 		0.0613
(1.00) 		0.4
(1.00)
19q loss 110 (22%) 380 0.617
(1.00) 		0.509
(1.00) 		0.00959
(1.00) 		0.0459
(1.00) 		0.341
(1.00) 		0.692
(1.00) 		0.721
(1.00) 		0.916
(1.00) 		0.28
(1.00) 		0.636
(1.00) 		0.608
(1.00) 		0.417
(1.00)
20p loss 41 (8%) 449 0.144
(1.00) 		0.139
(1.00) 		0.00242
(1.00) 		0.00744
(1.00) 		0.113
(1.00) 		0.142
(1.00) 		0.166
(1.00) 		0.193
(1.00) 		0.0487
(1.00) 		0.74
(1.00) 		0.201
(1.00) 		0.0184
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.19

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
1Q GAIN MUTATED 68 87 44
1Q GAIN WILD-TYPE 125 75 91

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.061

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
1Q GAIN MUTATED 39 62 36
1Q GAIN WILD-TYPE 103 52 64

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
1Q GAIN MUTATED 61 78 60
1Q GAIN WILD-TYPE 141 71 75

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
2P GAIN MUTATED 56 107 55
2P GAIN WILD-TYPE 137 55 80

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
2P GAIN MUTATED 49 74 42
2P GAIN WILD-TYPE 93 40 58

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
2P GAIN MUTATED 34 90 70 22
2P GAIN WILD-TYPE 76 55 83 56

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
2P GAIN MUTATED 72 90 54
2P GAIN WILD-TYPE 130 59 81

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.069

Table S8.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
2Q GAIN MUTATED 37 65 34
2Q GAIN WILD-TYPE 156 97 101

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.035

Table S9.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
4P GAIN MUTATED 9 2 19
4P GAIN WILD-TYPE 184 160 116

Figure S9.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.035

Table S10.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
7P GAIN MUTATED 74 101 59
7P GAIN WILD-TYPE 119 61 76

Figure S10.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

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

Table S11.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
7P GAIN MUTATED 50 70 46
7P GAIN WILD-TYPE 92 44 54

Figure S11.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.061

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
7P GAIN MUTATED 47 92 66 27
7P GAIN WILD-TYPE 63 53 87 51

Figure S12.  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 = 0.0096

Table S13.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
7P GAIN MUTATED 83 96 53
7P GAIN WILD-TYPE 119 53 82

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.027

Table S14.  Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 53 34 28 26 38 59 31 21 38
7P GAIN MUTATED 31 10 7 16 11 21 24 10 21
7P GAIN WILD-TYPE 22 24 21 10 27 38 7 11 17

Figure S14.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.14

Table S15.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
7Q GAIN MUTATED 23 38 14
7Q GAIN WILD-TYPE 24 18 37

Figure S15.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S16.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
7Q GAIN MUTATED 55 105 54
7Q GAIN WILD-TYPE 138 57 81

Figure S16.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S17.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
7Q GAIN MUTATED 38 69 42
7Q GAIN WILD-TYPE 104 45 58

Figure S17.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
7Q GAIN MUTATED 41 96 47 28
7Q GAIN WILD-TYPE 69 49 106 50

Figure S18.  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 = 0.0096

Table S19.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
7Q GAIN MUTATED 72 98 42
7Q GAIN WILD-TYPE 130 51 93

Figure S19.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.035

Table S20.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 193 197
7Q GAIN MUTATED 50 76 81
7Q GAIN WILD-TYPE 24 117 116

Figure S20.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S21.  Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 53 34 28 26 38 59 31 21 38
7Q GAIN MUTATED 25 7 5 15 10 17 21 12 24
7Q GAIN WILD-TYPE 28 27 23 11 28 42 10 9 14

Figure S21.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

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

Table S22.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
9P GAIN MUTATED 19 34 7
9P GAIN WILD-TYPE 174 128 128

Figure S22.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.078

Table S23.  Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
9P GAIN MUTATED 10 28 8
9P GAIN WILD-TYPE 132 86 92

Figure S23.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S24.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
9P GAIN MUTATED 3 35 15 7
9P GAIN WILD-TYPE 107 110 138 71

Figure S24.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S25.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
9P GAIN MUTATED 7 36 17
9P GAIN WILD-TYPE 195 113 118

Figure S25.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S26.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
9Q GAIN MUTATED 22 60 9
9Q GAIN WILD-TYPE 171 102 126

Figure S26.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S27.  Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
9Q GAIN MUTATED 10 44 11
9Q GAIN WILD-TYPE 132 70 89

Figure S27.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S28.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
9Q GAIN MUTATED 5 59 22 5
9Q GAIN WILD-TYPE 105 86 131 73

Figure S28.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S29.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
9Q GAIN MUTATED 8 59 24
9Q GAIN WILD-TYPE 194 90 111

Figure S29.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.035

Table S30.  Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
9Q GAIN MUTATED 32 19 12 24
9Q GAIN WILD-TYPE 113 111 113 40

Figure S30.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.19

Table S31.  Gene #18: '9q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 53 34 28 26 38 59 31 21 38
9Q GAIN MUTATED 8 1 1 4 7 6 14 6 9
9Q GAIN WILD-TYPE 45 33 27 22 31 53 17 15 29

Figure S31.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S32.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
12P GAIN MUTATED 54 98 72
12P GAIN WILD-TYPE 139 64 63

Figure S32.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.027

Table S33.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
12P GAIN MUTATED 34 82 80 26
12P GAIN WILD-TYPE 76 63 73 52

Figure S33.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S34.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
12Q GAIN MUTATED 37 73 41
12Q GAIN WILD-TYPE 156 89 94

Figure S34.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.078

Table S35.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 53 34 28 26 38 59 31 21 38
12Q GAIN MUTATED 14 1 6 11 14 10 16 7 14
12Q GAIN WILD-TYPE 39 33 22 15 24 49 15 14 24

Figure S35.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S36.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
17P GAIN MUTATED 9 40 16
17P GAIN WILD-TYPE 184 122 119

Figure S36.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.18

Table S37.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
17P GAIN MUTATED 8 35 16 6
17P GAIN WILD-TYPE 102 110 137 72

Figure S37.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.19

Table S38.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
17P GAIN MUTATED 14 33 18
17P GAIN WILD-TYPE 188 116 117

Figure S38.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S39.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
17Q GAIN MUTATED 29 90 37
17Q GAIN WILD-TYPE 164 72 98

Figure S39.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S40.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
17Q GAIN MUTATED 23 62 30
17Q GAIN WILD-TYPE 119 52 70

Figure S40.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S41.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
17Q GAIN MUTATED 19 76 44 16
17Q GAIN WILD-TYPE 91 69 109 62

Figure S41.  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 = 0.0096

Table S42.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
17Q GAIN MUTATED 37 76 42
17Q GAIN WILD-TYPE 165 73 93

Figure S42.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.044

Table S43.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
17Q GAIN MUTATED 46 55 20 24
17Q GAIN WILD-TYPE 99 75 105 40

Figure S43.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S44.  Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
17Q GAIN MUTATED 61 18 25
17Q GAIN WILD-TYPE 64 94 66

Figure S44.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S45.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
18P GAIN MUTATED 36 78 33
18P GAIN WILD-TYPE 157 84 102

Figure S45.  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 = 0.0096

Table S46.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
18P GAIN MUTATED 24 52 33
18P GAIN WILD-TYPE 118 62 67

Figure S46.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S47.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
18Q GAIN MUTATED 24 58 23
18Q GAIN WILD-TYPE 169 104 112

Figure S47.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

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

Table S48.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
18Q GAIN MUTATED 15 47 33 8
18Q GAIN WILD-TYPE 95 98 120 70

Figure S48.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S49.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
19P GAIN MUTATED 30 63 16
19P GAIN WILD-TYPE 163 99 119

Figure S49.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

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

Table S50.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
19P GAIN MUTATED 23 43 20
19P GAIN WILD-TYPE 119 71 80

Figure S50.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S51.  Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 53 34 28 26 38 59 31 21 38
19P GAIN MUTATED 18 2 2 8 11 6 14 6 10
19P GAIN WILD-TYPE 35 32 26 18 27 53 17 15 28

Figure S51.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

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

Table S52.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
19Q GAIN MUTATED 44 71 40
19Q GAIN WILD-TYPE 149 91 95

Figure S52.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S53.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
20P GAIN MUTATED 73 107 74
20P GAIN WILD-TYPE 120 55 61

Figure S53.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
20Q GAIN MUTATED 75 84 84
20Q GAIN WILD-TYPE 118 78 51

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

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.18

Table S55.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
22Q GAIN MUTATED 98 78 40
22Q GAIN WILD-TYPE 104 71 95

Figure S55.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.052

Table S56.  Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
XQ GAIN MUTATED 15 40 22
XQ GAIN WILD-TYPE 178 122 113

Figure S56.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S57.  Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
1P LOSS MUTATED 8 30 8 3
1P LOSS WILD-TYPE 34 22 24 25

Figure S57.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.027

Table S58.  Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
1P LOSS MUTATED 8 32 9
1P LOSS WILD-TYPE 39 24 42

Figure S58.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S59.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
1P LOSS MUTATED 32 95 20
1P LOSS WILD-TYPE 161 67 115

Figure S59.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S60.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
1P LOSS MUTATED 20 59 24
1P LOSS WILD-TYPE 122 55 76

Figure S60.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S61.  Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
1P LOSS MUTATED 20 80 28 18
1P LOSS WILD-TYPE 90 65 125 60

Figure S61.  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 = 0.0096

Table S62.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
1P LOSS MUTATED 39 82 25
1P LOSS WILD-TYPE 163 67 110

Figure S62.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

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

Table S63.  Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
1P LOSS MUTATED 44 41 22 31
1P LOSS WILD-TYPE 101 89 103 33

Figure S63.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S64.  Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 193 197
1P LOSS MUTATED 40 46 52
1P LOSS WILD-TYPE 34 147 145

Figure S64.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.19

Table S65.  Gene #41: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 53 34 28 26 38 59 31 21 38
1P LOSS MUTATED 16 5 2 6 8 13 15 10 19
1P LOSS WILD-TYPE 37 29 26 20 30 46 16 11 19

Figure S65.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.027

Table S66.  Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
4P LOSS MUTATED 33 45 20
4P LOSS WILD-TYPE 14 11 31

Figure S66.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
4P LOSS MUTATED 90 136 81
4P LOSS WILD-TYPE 103 26 54

Figure S67.  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 = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
4P LOSS MUTATED 64 90 67
4P LOSS WILD-TYPE 78 24 33

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

'4p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S69.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
4P LOSS MUTATED 72 114 80 40
4P LOSS WILD-TYPE 38 31 73 38

Figure S69.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S70.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
4P LOSS MUTATED 122 117 67
4P LOSS WILD-TYPE 80 32 68

Figure S70.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

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

Table S71.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
4P LOSS MUTATED 97 92 58 46
4P LOSS WILD-TYPE 48 38 67 18

Figure S71.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.095

Table S72.  Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
4P LOSS MUTATED 96 60 49
4P LOSS WILD-TYPE 29 52 42

Figure S72.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.061

Table S73.  Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 53 34 28 26 38 59 31 21 38
4P LOSS MUTATED 41 15 10 14 25 30 23 17 30
4P LOSS WILD-TYPE 12 19 18 12 13 29 8 4 8

Figure S73.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S74.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
4Q LOSS MUTATED 91 130 69
4Q LOSS WILD-TYPE 102 32 66

Figure S74.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.052

Table S75.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
4Q LOSS MUTATED 68 86 57
4Q LOSS WILD-TYPE 74 28 43

Figure S75.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S76.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
4Q LOSS MUTATED 63 110 82 34
4Q LOSS WILD-TYPE 47 35 71 44

Figure S76.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.052

Table S77.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
4Q LOSS MUTATED 111 110 68
4Q LOSS WILD-TYPE 91 39 67

Figure S77.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

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

Table S78.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
6P LOSS MUTATED 31 54 24
6P LOSS WILD-TYPE 162 108 111

Figure S78.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

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

Table S79.  Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
6P LOSS MUTATED 20 42 20
6P LOSS WILD-TYPE 122 72 80

Figure S79.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S80.  Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
6P LOSS MUTATED 20 55 20 13
6P LOSS WILD-TYPE 90 90 133 65

Figure S80.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S81.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
6P LOSS MUTATED 37 54 17
6P LOSS WILD-TYPE 165 95 118

Figure S81.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.052

Table S82.  Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
7Q LOSS MUTATED 9 5 31 6
7Q LOSS WILD-TYPE 101 140 122 72

Figure S82.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S83.  Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
7Q LOSS MUTATED 17 5 29
7Q LOSS WILD-TYPE 185 144 106

Figure S83.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.044

Table S84.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
9P LOSS MUTATED 109 89 106
9P LOSS WILD-TYPE 84 73 29

Figure S84.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S85.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
9P LOSS MUTATED 86 69 106 40
9P LOSS WILD-TYPE 24 76 47 38

Figure S85.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S86.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
9P LOSS MUTATED 148 71 82
9P LOSS WILD-TYPE 54 78 53

Figure S86.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.027

Table S87.  Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
9Q LOSS MUTATED 28 11 21 13
9Q LOSS WILD-TYPE 14 41 11 15

Figure S87.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S88.  Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
9Q LOSS MUTATED 31 12 30
9Q LOSS WILD-TYPE 16 44 21

Figure S88.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S89.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
9Q LOSS MUTATED 100 39 100
9Q LOSS WILD-TYPE 93 123 35

Figure S89.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S90.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
9Q LOSS MUTATED 81 29 65
9Q LOSS WILD-TYPE 61 85 35

Figure S90.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S91.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
9Q LOSS MUTATED 76 24 95 42
9Q LOSS WILD-TYPE 34 121 58 36

Figure S91.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S92.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
9Q LOSS MUTATED 138 24 75
9Q LOSS WILD-TYPE 64 125 60

Figure S92.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S93.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
9Q LOSS MUTATED 62 80 71 12
9Q LOSS WILD-TYPE 83 50 54 52

Figure S93.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S94.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 193 197
9Q LOSS MUTATED 12 90 123
9Q LOSS WILD-TYPE 62 103 74

Figure S94.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S95.  Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 53 34 28 26 38 59 31 21 38
9Q LOSS MUTATED 22 28 11 13 21 37 4 11 16
9Q LOSS WILD-TYPE 31 6 17 13 17 22 27 10 22

Figure S95.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S96.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
10P LOSS MUTATED 59 92 59
10P LOSS WILD-TYPE 134 70 76

Figure S96.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S97.  Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
10P LOSS MUTATED 40 73 37
10P LOSS WILD-TYPE 102 41 63

Figure S97.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S98.  Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
10P LOSS MUTATED 37 89 56 27
10P LOSS WILD-TYPE 73 56 97 51

Figure S98.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S99.  Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
10P LOSS MUTATED 75 90 44
10P LOSS WILD-TYPE 127 59 91

Figure S99.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.095

Table S100.  Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
10P LOSS MUTATED 61 63 36 40
10P LOSS WILD-TYPE 84 67 89 24

Figure S100.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S101.  Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 193 197
10P LOSS MUTATED 51 58 91
10P LOSS WILD-TYPE 23 135 106

Figure S101.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.2

Table S102.  Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
10Q LOSS MUTATED 12 36 19
10Q LOSS WILD-TYPE 35 20 32

Figure S102.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S103.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
10Q LOSS MUTATED 64 98 61
10Q LOSS WILD-TYPE 129 64 74

Figure S103.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S104.  Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
10Q LOSS MUTATED 44 74 45
10Q LOSS WILD-TYPE 98 40 55

Figure S104.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S105.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
10Q LOSS MUTATED 42 97 57 26
10Q LOSS WILD-TYPE 68 48 96 52

Figure S105.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S106.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
10Q LOSS MUTATED 81 98 43
10Q LOSS WILD-TYPE 121 51 92

Figure S106.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

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

Table S107.  Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
10Q LOSS MUTATED 58 68 44 42
10Q LOSS WILD-TYPE 87 62 81 22

Figure S107.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S108.  Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 193 197
10Q LOSS MUTATED 52 64 96
10Q LOSS WILD-TYPE 22 129 101

Figure S108.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.044

Table S109.  Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 52 32 28
14Q LOSS MUTATED 2 21 12 12
14Q LOSS WILD-TYPE 40 31 20 16

Figure S109.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.24

Table S110.  Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
14Q LOSS MUTATED 4 23 20
14Q LOSS WILD-TYPE 43 33 31

Figure S110.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S111.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
14Q LOSS MUTATED 15 63 70 15
14Q LOSS WILD-TYPE 95 82 83 63

Figure S111.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S112.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
14Q LOSS MUTATED 36 64 63
14Q LOSS WILD-TYPE 166 85 72

Figure S112.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S113.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 145 130 125 64
14Q LOSS MUTATED 46 37 30 42
14Q LOSS WILD-TYPE 99 93 95 22

Figure S113.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S114.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 193 197
14Q LOSS MUTATED 44 49 62
14Q LOSS WILD-TYPE 30 144 135

Figure S114.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S115.  Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 53 34 28 26 38 59 31 21 38
14Q LOSS MUTATED 14 7 7 4 25 21 21 4 11
14Q LOSS WILD-TYPE 39 27 21 22 13 38 10 17 27

Figure S115.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.095

Table S116.  Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
17Q LOSS MUTATED 38 8 20
17Q LOSS WILD-TYPE 104 106 80

Figure S116.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.078

Table S117.  Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
17Q LOSS MUTATED 31 11 30 18
17Q LOSS WILD-TYPE 79 134 123 60

Figure S117.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S118.  Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
17Q LOSS MUTATED 56 13 21
17Q LOSS WILD-TYPE 146 136 114

Figure S118.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.027

Table S119.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
19P LOSS MUTATED 48 49 67
19P LOSS WILD-TYPE 145 113 68

Figure S119.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.2

Table S120.  Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
20Q LOSS MUTATED 4 27 11 4
20Q LOSS WILD-TYPE 106 118 142 74

Figure S120.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S121.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 193 162 135
21Q LOSS MUTATED 75 105 80
21Q LOSS WILD-TYPE 118 57 55

Figure S121.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.22

Table S122.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 145 153 78
22Q LOSS MUTATED 22 14 45 14
22Q LOSS WILD-TYPE 88 131 108 64

Figure S122.  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 = 0.0096

Table S123.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 202 149 135
22Q LOSS MUTATED 29 17 49
22Q LOSS WILD-TYPE 173 132 86

Figure S123.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.052

Table S124.  Gene #80: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 112 91
XQ LOSS MUTATED 44 19 11
XQ LOSS WILD-TYPE 81 93 80

Figure S124.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 490

  • 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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