Correlation between copy number variations of arm-level result and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C12V2F1W
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/C12V2F1W
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 501 patients, 118 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 4p gain cnv correlated to 'CN_CNMF'.

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

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

  • 8q gain cnv correlated to 'MRNASEQ_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_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'.

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

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

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

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

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p 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', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'MIRSEQ_CNMF'.

  • 3p loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 5q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • 7p loss cnv correlated to 'CN_CNMF'.

  • 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', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 16q loss cnv correlated to 'MIRSEQ_CNMF'.

  • 17p loss cnv correlated to 'CN_CNMF'.

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

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

  • 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 'CN_CNMF' 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, 118 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
9q loss 245 (49%) 256 2e-05
(0.0179) 		2e-05
(0.0179) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.172
(1.00) 		0.0141
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00426
(1.00) 		0.0001
(0.0867)
1p loss 152 (30%) 349 8e-05
(0.0697) 		1e-05
(0.0096) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.884
(1.00) 		0.172
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00149
(1.00) 		1e-05
(0.0096) 		0.00072
(0.583) 		0.0005
(0.415)
4p loss 315 (63%) 186 0.00147
(1.00) 		6e-05
(0.0525) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.212
(1.00) 		0.374
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00061
(0.498) 		0.0542
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096)
7q gain 221 (44%) 280 0.00327
(1.00) 		0.0002
(0.17) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.903
(1.00) 		0.229
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00058
(0.476) 		0.00018
(0.154) 		0.00108
(0.864) 		0.00071
(0.576)
9q gain 92 (18%) 409 0.00471
(1.00) 		0.00053
(0.437) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0587
(1.00) 		0.027
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00024
(0.203) 		0.00014
(0.121) 		0.00099
(0.795) 		0.00163
(1.00)
10q loss 229 (46%) 272 0.00106
(0.849) 		0.00015
(0.129) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0957
(1.00) 		0.0793
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00041
(0.343) 		1e-05
(0.0096) 		0.0146
(1.00) 		0.00729
(1.00)
2p gain 223 (45%) 278 0.103
(1.00) 		0.0238
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.422
(1.00) 		0.758
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00748
(1.00) 		0.0303
(1.00) 		0.00272
(1.00) 		3e-05
(0.0266)
17q gain 158 (32%) 343 0.00147
(1.00) 		0.00053
(0.437) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.421
(1.00) 		0.978
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0006
(0.491) 		0.0115
(1.00) 		0.00042
(0.351) 		5e-05
(0.044)
10p loss 214 (43%) 287 0.205
(1.00) 		0.219
(1.00) 		8e-05
(0.0697) 		1e-05
(0.0096) 		0.395
(1.00) 		0.16
(1.00) 		2e-05
(0.0179) 		7e-05
(0.061) 		0.00035
(0.294) 		1e-05
(0.0096) 		0.0479
(1.00) 		0.00392
(1.00)
14q loss 166 (33%) 335 0.00013
(0.112) 		0.00036
(0.302) 		0.0178
(1.00) 		0.152
(1.00) 		0.0543
(1.00) 		0.153
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.00017
(0.146) 		1e-05
(0.0096) 		0.00286
(1.00) 		0.00196
(1.00)
7p gain 243 (49%) 258 0.0603
(1.00) 		0.0127
(1.00) 		3e-05
(0.0266) 		0.00016
(0.137) 		0.569
(1.00) 		0.656
(1.00) 		0.0001
(0.0867) 		1e-05
(0.0096) 		0.00061
(0.498) 		0.00039
(0.327) 		0.0132
(1.00) 		0.0817
(1.00)
9p gain 62 (12%) 439 0.0857
(1.00) 		0.0208
(1.00) 		6e-05
(0.0525) 		0.00014
(0.121) 		0.177
(1.00) 		0.0486
(1.00) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.0137
(1.00) 		0.0492
(1.00) 		0.00088
(0.708) 		0.0732
(1.00)
4q loss 298 (59%) 203 0.00226
(1.00) 		0.0012
(0.955) 		1e-05
(0.0096) 		3e-05
(0.0266) 		0.295
(1.00) 		0.546
(1.00) 		2e-05
(0.0179) 		0.00032
(0.269) 		0.00329
(1.00) 		0.0308
(1.00) 		0.00061
(0.498) 		5e-05
(0.044)
18p gain 150 (30%) 351 0.00843
(1.00) 		0.00113
(0.902) 		1e-05
(0.0096) 		1e-05
(0.0096) 		0.492
(1.00) 		0.713
(1.00) 		0.00116
(0.925) 		1e-05
(0.0096) 		0.0175
(1.00) 		0.28
(1.00) 		0.0868
(1.00) 		0.00049
(0.408)
19p gain 111 (22%) 390 0.0456
(1.00) 		0.123
(1.00) 		1e-05
(0.0096) 		0.00023
(0.195) 		0.0221
(1.00) 		0.0669
(1.00) 		0.00015
(0.129) 		0.00203
(1.00) 		0.131
(1.00) 		0.00143
(1.00) 		0.0683
(1.00) 		0.00559
(1.00)
6p loss 112 (22%) 389 0.0351
(1.00) 		0.0146
(1.00) 		0.00428
(1.00) 		0.00024
(0.203) 		0.148
(1.00) 		0.144
(1.00) 		2e-05
(0.0179) 		2e-05
(0.0179) 		0.196
(1.00) 		0.163
(1.00) 		0.179
(1.00) 		0.405
(1.00)
9p loss 310 (62%) 191 0.0075
(1.00) 		0.00122
(0.97) 		1e-05
(0.0096) 		0.0188
(1.00) 		0.207
(1.00) 		0.077
(1.00) 		1e-05
(0.0096) 		4e-05
(0.0353) 		0.0443
(1.00) 		0.00042
(0.351) 		0.434
(1.00) 		0.0264
(1.00)
1q gain 203 (41%) 298 0.681
(1.00) 		0.55
(1.00) 		1e-05
(0.0096) 		0.00017
(0.146) 		0.491
(1.00) 		0.456
(1.00) 		0.00364
(1.00) 		0.00068
(0.553) 		0.0011
(0.879) 		0.00404
(1.00) 		0.0424
(1.00) 		0.0391
(1.00)
12p gain 229 (46%) 272 0.0182
(1.00) 		0.0344
(1.00) 		1e-05
(0.0096) 		0.00249
(1.00) 		0.221
(1.00) 		0.802
(1.00) 		5e-05
(0.044) 		0.00226
(1.00) 		0.0315
(1.00) 		0.00956
(1.00) 		0.0226
(1.00) 		0.00138
(1.00)
12q gain 153 (31%) 348 0.0235
(1.00) 		0.31
(1.00) 		1e-05
(0.0096) 		0.0035
(1.00) 		0.537
(1.00) 		0.612
(1.00) 		0.0032
(1.00) 		0.00122
(0.97) 		0.117
(1.00) 		0.126
(1.00) 		0.00935
(1.00) 		5e-05
(0.044)
18q gain 104 (21%) 397 0.0158
(1.00) 		0.0147
(1.00) 		1e-05
(0.0096) 		0.00347
(1.00) 		0.519
(1.00) 		0.333
(1.00) 		0.0006
(0.491) 		0.00018
(0.154) 		0.0585
(1.00) 		0.0329
(1.00) 		0.262
(1.00) 		0.00249
(1.00)
7q loss 51 (10%) 450 0.162
(1.00) 		0.0905
(1.00) 		0.00317
(1.00) 		0.331
(1.00) 		0.83
(1.00) 		0.0631
(1.00) 		2e-05
(0.0179) 		2e-05
(0.0179) 		0.107
(1.00) 		0.0336
(1.00) 		0.809
(1.00) 		0.404
(1.00)
17q loss 94 (19%) 407 0.0103
(1.00) 		0.0048
(1.00) 		0.00057
(0.468) 		0.0004
(0.335) 		0.662
(1.00) 		0.969
(1.00) 		0.00023
(0.195) 		1e-05
(0.0096) 		0.076
(1.00) 		0.01
(1.00) 		0.697
(1.00) 		0.0424
(1.00)
19p loss 167 (33%) 334 0.0388
(1.00) 		0.0533
(1.00) 		5e-05
(0.044) 		0.6
(1.00) 		0.891
(1.00) 		0.317
(1.00) 		0.0446
(1.00) 		0.0193
(1.00) 		0.101
(1.00) 		0.00019
(0.162) 		0.837
(1.00) 		0.162
(1.00)
22q loss 98 (20%) 403 0.00834
(1.00) 		0.101
(1.00) 		0.173
(1.00) 		0.0393
(1.00) 		0.253
(1.00) 		0.0572
(1.00) 		0.00013
(0.112) 		1e-05
(0.0096) 		0.79
(1.00) 		0.00901
(1.00) 		0.193
(1.00) 		0.201
(1.00)
xq loss 115 (23%) 386 0.201
(1.00) 		0.56
(1.00) 		1e-05
(0.0096) 		0.00052
(0.43) 		0.774
(1.00) 		0.823
(1.00) 		0.016
(1.00) 		0.982
(1.00) 		0.0113
(1.00) 		0.0118
(1.00) 		0.00602
(1.00) 		1e-05
(0.0096)
4p gain 32 (6%) 469 0.56
(1.00) 		0.203
(1.00) 		0.00016
(0.137) 		0.0917
(1.00) 		0.576
(1.00) 		0.41
(1.00) 		0.0287
(1.00) 		0.0062
(1.00) 		0.00539
(1.00) 		0.311
(1.00) 		0.0124
(1.00) 		0.0155
(1.00)
8q gain 257 (51%) 244 0.0481
(1.00) 		0.0376
(1.00) 		0.0217
(1.00) 		0.00907
(1.00) 		0.262
(1.00) 		0.756
(1.00) 		0.00637
(1.00) 		0.00026
(0.219) 		0.0662
(1.00) 		0.00445
(1.00) 		0.418
(1.00) 		0.46
(1.00)
17p gain 68 (14%) 433 0.00383
(1.00) 		0.101
(1.00) 		1e-05
(0.0096) 		0.00316
(1.00) 		0.841
(1.00) 		0.138
(1.00) 		0.00058
(0.476) 		0.00073
(0.591) 		0.0161
(1.00) 		0.094
(1.00) 		0.0501
(1.00) 		0.00749
(1.00)
19q gain 159 (32%) 342 0.115
(1.00) 		0.179
(1.00) 		9e-05
(0.0782) 		0.0098
(1.00) 		0.23
(1.00) 		0.12
(1.00) 		0.023
(1.00) 		0.509
(1.00) 		0.943
(1.00) 		0.418
(1.00) 		0.363
(1.00) 		0.147
(1.00)
20p gain 261 (52%) 240 0.0196
(1.00) 		0.0221
(1.00) 		1e-05
(0.0096) 		0.0005
(0.415) 		0.888
(1.00) 		0.313
(1.00) 		0.228
(1.00) 		0.144
(1.00) 		0.076
(1.00) 		0.717
(1.00) 		0.635
(1.00) 		0.928
(1.00)
22q gain 221 (44%) 280 0.00802
(1.00) 		0.0298
(1.00) 		0.00391
(1.00) 		0.038
(1.00) 		0.967
(1.00) 		0.0672
(1.00) 		0.00052
(0.43) 		6e-05
(0.0525) 		0.799
(1.00) 		0.111
(1.00) 		0.989
(1.00) 		0.756
(1.00)
xq gain 78 (16%) 423 0.363
(1.00) 		0.124
(1.00) 		3e-05
(0.0266) 		0.00478
(1.00) 		0.679
(1.00) 		0.623
(1.00) 		0.00973
(1.00) 		0.0283
(1.00) 		0.0586
(1.00) 		0.331
(1.00) 		0.417
(1.00) 		0.209
(1.00)
2q loss 42 (8%) 459 0.71
(1.00) 		1
(1.00) 		0.275
(1.00) 		0.358
(1.00) 		0.882
(1.00) 		0.142
(1.00) 		0.0646
(1.00) 		0.0248
(1.00) 		9e-05
(0.0782) 		0.196
(1.00) 		0.128
(1.00) 		0.00133
(1.00)
3p loss 309 (62%) 192 0.368
(1.00) 		0.0516
(1.00) 		0.13
(1.00) 		0.00194
(1.00) 		0.931
(1.00) 		0.104
(1.00) 		0.398
(1.00) 		0.383
(1.00) 		0.274
(1.00) 		0.00017
(0.146) 		0.031
(1.00) 		0.11
(1.00)
5q loss 291 (58%) 210 0.133
(1.00) 		0.0537
(1.00) 		0.00031
(0.261) 		0.00868
(1.00) 		0.268
(1.00) 		0.124
(1.00) 		0.00574
(1.00) 		0.00028
(0.236) 		0.133
(1.00) 		0.0191
(1.00) 		0.0141
(1.00) 		0.0939
(1.00)
7p loss 58 (12%) 443 0.397
(1.00) 		1
(1.00) 		0.0001
(0.0867) 		0.274
(1.00) 		0.482
(1.00) 		0.124
(1.00) 		0.402
(1.00) 		0.0928
(1.00) 		0.0907
(1.00) 		0.00545
(1.00) 		0.927
(1.00) 		0.296
(1.00)
16q loss 182 (36%) 319 0.776
(1.00) 		0.124
(1.00) 		0.0173
(1.00) 		0.16
(1.00) 		0.131
(1.00) 		0.85
(1.00) 		0.0525
(1.00) 		0.0533
(1.00) 		0.00019
(0.162) 		0.393
(1.00) 		0.00253
(1.00) 		0.00152
(1.00)
17p loss 291 (58%) 210 0.00473
(1.00) 		0.171
(1.00) 		4e-05
(0.0353) 		0.0102
(1.00) 		0.435
(1.00) 		0.00638
(1.00) 		0.00155
(1.00) 		0.00147
(1.00) 		0.096
(1.00) 		0.00073
(0.591) 		0.134
(1.00) 		0.0934
(1.00)
20q loss 46 (9%) 455 0.0579
(1.00) 		0.0765
(1.00) 		0.00201
(1.00) 		0.0194
(1.00) 		0.435
(1.00) 		0.425
(1.00) 		5e-05
(0.044) 		0.00161
(1.00) 		0.0105
(1.00) 		0.0974
(1.00) 		0.464
(1.00) 		0.268
(1.00)
21q loss 265 (53%) 236 0.902
(1.00) 		0.318
(1.00) 		2e-05
(0.0179) 		0.0363
(1.00) 		0.523
(1.00) 		0.449
(1.00) 		0.0599
(1.00) 		0.0393
(1.00) 		0.0162
(1.00) 		0.00052
(0.43) 		0.0239
(1.00) 		0.0123
(1.00)
1p gain 89 (18%) 412 0.133
(1.00) 		0.154
(1.00) 		0.745
(1.00) 		0.437
(1.00) 		0.488
(1.00) 		0.916
(1.00) 		0.799
(1.00) 		0.435
(1.00) 		0.35
(1.00) 		0.746
(1.00) 		0.353
(1.00) 		0.324
(1.00)
2q gain 140 (28%) 361 0.473
(1.00) 		0.362
(1.00) 		0.0005
(0.415) 		0.0316
(1.00) 		0.451
(1.00) 		0.647
(1.00) 		0.00142
(1.00) 		0.0213
(1.00) 		0.147
(1.00) 		0.269
(1.00) 		0.00217
(1.00) 		0.0122
(1.00)
3p gain 109 (22%) 392 0.977
(1.00) 		0.85
(1.00) 		0.22
(1.00) 		0.0838
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.314
(1.00) 		0.149
(1.00) 		0.921
(1.00) 		0.692
(1.00) 		0.972
(1.00) 		0.501
(1.00)
3q gain 316 (63%) 185 0.601
(1.00) 		0.737
(1.00) 		0.0138
(1.00) 		0.315
(1.00) 		1
(1.00) 		0.111
(1.00) 		0.308
(1.00) 		0.309
(1.00) 		0.447
(1.00) 		0.0273
(1.00) 		0.69
(1.00) 		0.189
(1.00)
4q gain 23 (5%) 478 0.742
(1.00) 		0.73
(1.00) 		0.0103
(1.00) 		0.0786
(1.00) 		0.875
(1.00) 		0.172
(1.00) 		0.842
(1.00) 		0.89
(1.00) 		0.095
(1.00) 		0.351
(1.00) 		0.146
(1.00) 		0.19
(1.00)
5p gain 309 (62%) 192 0.776
(1.00) 		0.855
(1.00) 		0.0301
(1.00) 		0.708
(1.00) 		0.312
(1.00) 		0.23
(1.00) 		0.319
(1.00) 		0.476
(1.00) 		0.232
(1.00) 		0.0538
(1.00) 		0.0417
(1.00) 		0.127
(1.00)
5q gain 93 (19%) 408 0.237
(1.00) 		0.21
(1.00) 		0.377
(1.00) 		0.322
(1.00) 		0.713
(1.00) 		0.147
(1.00) 		0.317
(1.00) 		0.0181
(1.00) 		0.521
(1.00) 		0.283
(1.00) 		0.113
(1.00) 		0.0364
(1.00)
6p gain 109 (22%) 392 0.0532
(1.00) 		0.182
(1.00) 		0.00068
(0.553) 		0.944
(1.00) 		0.935
(1.00) 		0.19
(1.00) 		0.00163
(1.00) 		0.00619
(1.00) 		0.951
(1.00) 		0.339
(1.00) 		0.172
(1.00) 		0.156
(1.00)
6q gain 94 (19%) 407 0.0678
(1.00) 		0.121
(1.00) 		0.00179
(1.00) 		0.61
(1.00) 		0.878
(1.00) 		0.963
(1.00) 		0.0163
(1.00) 		0.0169
(1.00) 		0.803
(1.00) 		0.18
(1.00) 		0.468
(1.00) 		0.0394
(1.00)
8p gain 129 (26%) 372 0.405
(1.00) 		0.55
(1.00) 		0.403
(1.00) 		0.15
(1.00) 		0.257
(1.00) 		0.95
(1.00) 		0.0372
(1.00) 		0.024
(1.00) 		0.391
(1.00) 		0.0156
(1.00) 		0.854
(1.00) 		0.862
(1.00)
10p gain 79 (16%) 422 0.321
(1.00) 		0.702
(1.00) 		0.11
(1.00) 		0.161
(1.00) 		0.0651
(1.00) 		0.0844
(1.00) 		0.071
(1.00) 		0.0546
(1.00) 		0.0456
(1.00) 		0.00054
(0.444) 		0.902
(1.00) 		0.182
(1.00)
10q gain 45 (9%) 456 0.113
(1.00) 		0.139
(1.00) 		0.0517
(1.00) 		0.573
(1.00) 		0.0272
(1.00) 		0.208
(1.00) 		0.0603
(1.00) 		0.011
(1.00) 		0.413
(1.00) 		0.132
(1.00) 		0.762
(1.00) 		0.352
(1.00)
11p gain 74 (15%) 427 0.678
(1.00) 		0.478
(1.00) 		0.0602
(1.00) 		0.306
(1.00) 		0.243
(1.00) 		0.00974
(1.00) 		0.656
(1.00) 		0.924
(1.00) 		0.131
(1.00) 		0.0758
(1.00) 		0.186
(1.00) 		0.038
(1.00)
11q gain 91 (18%) 410 0.0178
(1.00) 		0.209
(1.00) 		0.00103
(0.826) 		0.43
(1.00) 		0.393
(1.00) 		0.0525
(1.00) 		0.251
(1.00) 		0.064
(1.00) 		0.143
(1.00) 		0.111
(1.00) 		0.642
(1.00) 		0.0717
(1.00)
13q gain 39 (8%) 462 0.7
(1.00) 		0.663
(1.00) 		0.797
(1.00) 		0.967
(1.00) 		0.414
(1.00) 		0.664
(1.00) 		0.509
(1.00) 		0.709
(1.00) 		0.23
(1.00) 		0.59
(1.00) 		0.892
(1.00) 		0.913
(1.00)
14q gain 129 (26%) 372 0.145
(1.00) 		0.0231
(1.00) 		0.0388
(1.00) 		0.0969
(1.00) 		0.253
(1.00) 		0.332
(1.00) 		0.181
(1.00) 		0.00441
(1.00) 		0.0727
(1.00) 		0.168
(1.00) 		0.571
(1.00) 		0.906
(1.00)
15q gain 105 (21%) 396 0.838
(1.00) 		0.427
(1.00) 		0.00087
(0.7) 		0.00168
(1.00) 		0.22
(1.00) 		0.659
(1.00) 		0.00166
(1.00) 		0.0112
(1.00) 		0.109
(1.00) 		0.0376
(1.00) 		0.0861
(1.00) 		0.00236
(1.00)
16p gain 86 (17%) 415 0.353
(1.00) 		0.557
(1.00) 		0.117
(1.00) 		0.504
(1.00) 		0.613
(1.00) 		0.785
(1.00) 		0.688
(1.00) 		0.768
(1.00) 		0.481
(1.00) 		0.02
(1.00) 		0.474
(1.00) 		0.289
(1.00)
16q gain 87 (17%) 414 0.918
(1.00) 		0.936
(1.00) 		0.025
(1.00) 		0.331
(1.00) 		0.69
(1.00) 		0.437
(1.00) 		0.159
(1.00) 		0.65
(1.00) 		0.214
(1.00) 		0.0267
(1.00) 		0.418
(1.00) 		0.42
(1.00)
20q gain 251 (50%) 250 0.675
(1.00) 		0.318
(1.00) 		0.00045
(0.375) 		0.231
(1.00) 		0.56
(1.00) 		0.584
(1.00) 		0.309
(1.00) 		0.117
(1.00) 		0.0962
(1.00) 		0.029
(1.00) 		0.846
(1.00) 		0.351
(1.00)
21q gain 57 (11%) 444 0.894
(1.00) 		0.816
(1.00) 		0.968
(1.00) 		0.0618
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.41
(1.00) 		0.777
(1.00) 		0.513
(1.00) 		0.467
(1.00) 		0.219
(1.00) 		0.525
(1.00)
1q loss 60 (12%) 441 0.551
(1.00) 		0.668
(1.00) 		0.00216
(1.00) 		0.0435
(1.00) 		0.959
(1.00) 		0.615
(1.00) 		0.0346
(1.00) 		0.0278
(1.00) 		0.246
(1.00) 		0.0832
(1.00) 		0.225
(1.00) 		0.529
(1.00)
2p loss 21 (4%) 480 0.129
(1.00) 		0.191
(1.00) 		0.38
(1.00) 		0.153
(1.00) 		0.142
(1.00) 		0.101
(1.00) 		0.448
(1.00) 		0.0284
(1.00) 		0.00609
(1.00) 		0.528
(1.00) 		0.0374
(1.00) 		0.00049
(0.408)
3q loss 69 (14%) 432 0.944
(1.00) 		0.928
(1.00) 		0.493
(1.00) 		0.693
(1.00) 		0.633
(1.00) 		0.409
(1.00) 		0.905
(1.00) 		0.317
(1.00) 		0.609
(1.00) 		0.238
(1.00) 		0.162
(1.00) 		0.343
(1.00)
5p loss 78 (16%) 423 0.827
(1.00) 		0.935
(1.00) 		0.0043
(1.00) 		0.00289
(1.00) 		0.432
(1.00) 		0.0347
(1.00) 		0.228
(1.00) 		0.285
(1.00) 		0.0403
(1.00) 		0.372
(1.00) 		0.0157
(1.00) 		0.094
(1.00)
6q loss 113 (23%) 388 0.00505
(1.00) 		0.00082
(0.661) 		0.026
(1.00) 		0.00178
(1.00) 		0.701
(1.00) 		0.397
(1.00) 		0.00154
(1.00) 		0.0233
(1.00) 		0.553
(1.00) 		0.759
(1.00) 		0.115
(1.00) 		0.345
(1.00)
8p loss 244 (49%) 257 0.923
(1.00) 		0.959
(1.00) 		0.00517
(1.00) 		0.00206
(1.00) 		0.1
(1.00) 		0.443
(1.00) 		0.113
(1.00) 		0.0861
(1.00) 		0.39
(1.00) 		0.015
(1.00) 		0.187
(1.00) 		0.622
(1.00)
8q loss 48 (10%) 453 0.347
(1.00) 		0.357
(1.00) 		0.393
(1.00) 		0.00598
(1.00) 		0.0713
(1.00) 		0.877
(1.00) 		0.267
(1.00) 		0.0414
(1.00) 		0.0999
(1.00) 		0.125
(1.00) 		0.259
(1.00) 		0.909
(1.00)
11p loss 171 (34%) 330 0.253
(1.00) 		0.249
(1.00) 		0.00557
(1.00) 		0.00214
(1.00) 		0.141
(1.00) 		0.00319
(1.00) 		0.121
(1.00) 		0.627
(1.00) 		0.0554
(1.00) 		0.583
(1.00) 		0.474
(1.00) 		0.0648
(1.00)
11q loss 141 (28%) 360 0.987
(1.00) 		0.757
(1.00) 		0.00613
(1.00) 		0.00139
(1.00) 		0.542
(1.00) 		0.868
(1.00) 		0.125
(1.00) 		0.705
(1.00) 		0.0668
(1.00) 		0.232
(1.00) 		0.421
(1.00) 		0.0947
(1.00)
12p loss 39 (8%) 462 0.0237
(1.00) 		0.00517
(1.00) 		0.265
(1.00) 		0.882
(1.00) 		0.0999
(1.00) 		0.886
(1.00) 		0.981
(1.00) 		0.112
(1.00) 		0.187
(1.00) 		0.0833
(1.00) 		0.067
(1.00) 		0.192
(1.00)
12q loss 48 (10%) 453 0.366
(1.00) 		0.143
(1.00) 		0.811
(1.00) 		0.673
(1.00) 		0.0272
(1.00) 		0.752
(1.00) 		0.703
(1.00) 		0.791
(1.00) 		0.806
(1.00) 		0.116
(1.00) 		0.543
(1.00) 		0.15
(1.00)
13q loss 311 (62%) 190 0.62
(1.00) 		0.71
(1.00) 		0.0772
(1.00) 		0.0453
(1.00) 		0.704
(1.00) 		0.37
(1.00) 		0.278
(1.00) 		0.702
(1.00) 		0.0745
(1.00) 		0.108
(1.00) 		0.00077
(0.621) 		0.025
(1.00)
15q loss 142 (28%) 359 0.719
(1.00) 		0.743
(1.00) 		0.123
(1.00) 		0.0509
(1.00) 		0.328
(1.00) 		0.00182
(1.00) 		0.0905
(1.00) 		0.289
(1.00) 		0.0296
(1.00) 		0.156
(1.00) 		0.532
(1.00) 		0.412
(1.00)
16p loss 163 (33%) 338 0.978
(1.00) 		0.702
(1.00) 		0.0036
(1.00) 		0.116
(1.00) 		0.12
(1.00) 		0.268
(1.00) 		0.328
(1.00) 		0.443
(1.00) 		0.199
(1.00) 		0.832
(1.00) 		0.0276
(1.00) 		0.0848
(1.00)
18p loss 140 (28%) 361 0.857
(1.00) 		0.653
(1.00) 		0.092
(1.00) 		0.0859
(1.00) 		0.628
(1.00) 		0.918
(1.00) 		0.196
(1.00) 		0.0731
(1.00) 		0.419
(1.00) 		0.0776
(1.00) 		0.0683
(1.00) 		0.618
(1.00)
18q loss 189 (38%) 312 0.224
(1.00) 		0.331
(1.00) 		0.0531
(1.00) 		0.273
(1.00) 		0.704
(1.00) 		0.389
(1.00) 		0.487
(1.00) 		0.147
(1.00) 		0.0736
(1.00) 		0.124
(1.00) 		0.0807
(1.00) 		0.621
(1.00)
19q loss 112 (22%) 389 0.613
(1.00) 		0.511
(1.00) 		0.0413
(1.00) 		0.048
(1.00) 		0.341
(1.00) 		0.693
(1.00) 		0.821
(1.00) 		0.342
(1.00) 		0.478
(1.00) 		0.121
(1.00) 		0.459
(1.00) 		0.569
(1.00)
20p loss 42 (8%) 459 0.144
(1.00) 		0.141
(1.00) 		0.0252
(1.00) 		0.00732
(1.00) 		0.112
(1.00) 		0.144
(1.00) 		0.2
(1.00) 		0.0303
(1.00) 		0.441
(1.00) 		0.0641
(1.00) 		0.962
(1.00) 		0.338
(1.00)
'1q gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
1Q GAIN MUTATED 65 92 46
1Q GAIN WILD-TYPE 117 74 107

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.15

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 61 37
1Q GAIN WILD-TYPE 103 53 63

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

'2p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
2P GAIN MUTATED 53 108 62
2P GAIN WILD-TYPE 129 58 91

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

'2p gain' versus 'METHLYATION_CNMF'

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

Table S4.  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 S4.  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 S5.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
2P GAIN MUTATED 36 94 67 24
2P GAIN WILD-TYPE 77 58 87 55

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
2P GAIN MUTATED 62 111 48
2P GAIN WILD-TYPE 116 78 83

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

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
2P GAIN MUTATED 17 90 47
2P GAIN WILD-TYPE 22 61 97

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

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

Table S8.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
4P GAIN MUTATED 9 3 20
4P GAIN WILD-TYPE 173 163 133

Figure S8.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
7P GAIN MUTATED 73 105 65
7P GAIN WILD-TYPE 109 61 88

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

'7p gain' versus 'METHLYATION_CNMF'

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

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

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.087

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
7P GAIN MUTATED 50 96 68 27
7P GAIN WILD-TYPE 63 56 86 52

Figure S11.  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 S12.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
7P GAIN MUTATED 68 121 52
7P GAIN WILD-TYPE 110 68 79

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

'7q gain' versus 'MRNA_CHIERARCHICAL'

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

Table S13.  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 15
7Q GAIN WILD-TYPE 24 18 36

Figure S13.  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 S14.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
7Q GAIN MUTATED 52 109 60
7Q GAIN WILD-TYPE 130 57 93

Figure S14.  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 S15.  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 68 42
7Q GAIN WILD-TYPE 104 46 58

Figure S15.  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 S16.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
7Q GAIN MUTATED 43 100 48 28
7Q GAIN WILD-TYPE 70 52 106 51

Figure S16.  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 S17.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
7Q GAIN MUTATED 56 123 40
7Q GAIN WILD-TYPE 122 66 91

Figure S17.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S18.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
7Q GAIN MUTATED 59 48 81 26
7Q GAIN WILD-TYPE 30 70 118 43

Figure S18.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S19.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
8Q GAIN MUTATED 106 75 74
8Q GAIN WILD-TYPE 72 114 57

Figure S19.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

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

Table S20.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
9P GAIN MUTATED 21 34 7
9P GAIN WILD-TYPE 161 132 146

Figure S20.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

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

Table S21.  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 S21.  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 S22.  Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
9P GAIN MUTATED 3 36 15 8
9P GAIN WILD-TYPE 110 116 139 71

Figure S22.  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 S23.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
9P GAIN MUTATED 6 39 17
9P GAIN WILD-TYPE 172 150 114

Figure S23.  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 S24.  Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
9Q GAIN MUTATED 23 61 8
9Q GAIN WILD-TYPE 159 105 145

Figure S24.  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 S25.  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 S25.  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 S26.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
9Q GAIN MUTATED 5 60 21 6
9Q GAIN WILD-TYPE 108 92 133 73

Figure S26.  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 S27.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
9Q GAIN MUTATED 6 65 21
9Q GAIN WILD-TYPE 172 124 110

Figure S27.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
9Q GAIN MUTATED 24 31 9 20 4
9Q GAIN WILD-TYPE 97 103 112 42 33

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

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S29.  Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
9Q GAIN MUTATED 30 26 24 8
9Q GAIN WILD-TYPE 59 92 175 61

Figure S29.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

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

Table S30.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
12P GAIN MUTATED 49 100 80
12P GAIN WILD-TYPE 133 66 73

Figure S30.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

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

Table S31.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
12P GAIN MUTATED 36 86 79 26
12P GAIN WILD-TYPE 77 66 75 53

Figure S31.  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 S32.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
12Q GAIN MUTATED 33 75 45
12Q GAIN WILD-TYPE 149 91 108

Figure S32.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S33.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
12Q GAIN MUTATED 3 58 32
12Q GAIN WILD-TYPE 36 93 112

Figure S33.  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 S34.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
17P GAIN MUTATED 11 41 16
17P GAIN WILD-TYPE 171 125 137

Figure S34.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

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

Table S35.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
17Q GAIN MUTATED 32 91 35
17Q GAIN WILD-TYPE 150 75 118

Figure S35.  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 S36.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
17Q GAIN MUTATED 25 61 29
17Q GAIN WILD-TYPE 117 53 71

Figure S36.  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 S37.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
17Q GAIN MUTATED 19 76 44 18
17Q GAIN WILD-TYPE 94 76 110 61

Figure S37.  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 S38.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
17Q GAIN MUTATED 32 88 37
17Q GAIN WILD-TYPE 146 101 94

Figure S38.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S39.  Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
17Q GAIN MUTATED 8 66 30
17Q GAIN WILD-TYPE 31 85 114

Figure S39.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

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

Table S40.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
18P GAIN MUTATED 33 76 41
18P GAIN WILD-TYPE 149 90 112

Figure S40.  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 S41.  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 S41.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S42.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
18P GAIN MUTATED 35 81 33
18P GAIN WILD-TYPE 143 108 98

Figure S42.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

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

Table S43.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
18Q GAIN MUTATED 23 57 24
18Q GAIN WILD-TYPE 159 109 129

Figure S43.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S44.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
18Q GAIN MUTATED 22 56 24
18Q GAIN WILD-TYPE 156 133 107

Figure S44.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

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

Table S45.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
19P GAIN MUTATED 30 65 16
19P GAIN WILD-TYPE 152 101 137

Figure S45.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.2

Table S46.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
19P GAIN MUTATED 22 43 20
19P GAIN WILD-TYPE 120 71 80

Figure S46.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

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

Table S47.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
19P GAIN MUTATED 18 52 31 9
19P GAIN WILD-TYPE 95 100 123 70

Figure S47.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
19Q GAIN MUTATED 42 74 43
19Q GAIN WILD-TYPE 140 92 110

Figure S48.  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 S49.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
20P GAIN MUTATED 68 107 86
20P GAIN WILD-TYPE 114 59 67

Figure S49.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S50.  Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
22Q GAIN MUTATED 84 98 37
22Q GAIN WILD-TYPE 94 91 94

Figure S50.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

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

Table S51.  Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
XQ GAIN MUTATED 13 41 24
XQ GAIN WILD-TYPE 169 125 129

Figure S51.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.07

Table S52.  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 29 8 3
1P LOSS WILD-TYPE 34 23 24 25

Figure S52.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S53.  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 31 9
1P LOSS WILD-TYPE 39 25 42

Figure S53.  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 S54.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
1P LOSS MUTATED 31 97 24
1P LOSS WILD-TYPE 151 69 129

Figure S54.  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 S55.  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 60 24
1P LOSS WILD-TYPE 122 54 76

Figure S55.  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 S56.  Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
1P LOSS MUTATED 19 83 31 18
1P LOSS WILD-TYPE 94 69 123 61

Figure S56.  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 S57.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
1P LOSS MUTATED 28 98 25
1P LOSS WILD-TYPE 150 91 106

Figure S57.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S58.  Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
1P LOSS MUTATED 49 32 52 10
1P LOSS WILD-TYPE 40 86 147 59

Figure S58.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

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

Table S59.  Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
2Q LOSS MUTATED 15 18 0 5 3
2Q LOSS WILD-TYPE 106 116 121 57 34

Figure S59.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.15

Table S60.  Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
3P LOSS MUTATED 62 79 123 26
3P LOSS WILD-TYPE 27 39 76 43

Figure S60.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MRNA_CHIERARCHICAL'

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

Table S61.  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 44 20
4P LOSS WILD-TYPE 14 12 31

Figure S61.  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 S62.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
4P LOSS MUTATED 85 139 91
4P LOSS WILD-TYPE 97 27 62

Figure S62.  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 S63.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 114 100
4P LOSS MUTATED 63 90 67
4P LOSS WILD-TYPE 79 24 33

Figure S63.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

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

Table S64.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
4P LOSS MUTATED 74 119 81 40
4P LOSS WILD-TYPE 39 33 73 39

Figure S64.  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 = 0.0096

Table S65.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
4P LOSS MUTATED 98 150 66
4P LOSS WILD-TYPE 80 39 65

Figure S65.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S66.  Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 129 116
4P LOSS MUTATED 39 79 92
4P LOSS WILD-TYPE 50 50 24

Figure S66.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S67.  Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
4P LOSS MUTATED 17 118 75
4P LOSS WILD-TYPE 22 33 69

Figure S67.  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 S68.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
4Q LOSS MUTATED 86 132 80
4Q LOSS WILD-TYPE 96 34 73

Figure S68.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

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

Table S69.  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 87 57
4Q LOSS WILD-TYPE 74 27 43

Figure S69.  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 S70.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
4Q LOSS MUTATED 64 114 85 34
4Q LOSS WILD-TYPE 49 38 69 45

Figure S70.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S71.  Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
4Q LOSS MUTATED 22 110 67
4Q LOSS WILD-TYPE 17 41 77

Figure S71.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.24

Table S72.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
5Q LOSS MUTATED 90 131 67
5Q LOSS WILD-TYPE 88 58 64

Figure S72.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

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

Table S73.  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 41 21
6P LOSS WILD-TYPE 122 73 79

Figure S73.  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 S74.  Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
6P LOSS MUTATED 20 56 21 14
6P LOSS WILD-TYPE 93 96 133 65

Figure S74.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S75.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
6P LOSS MUTATED 29 65 17
6P LOSS WILD-TYPE 149 124 114

Figure S75.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.087

Table S76.  Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
7P LOSS MUTATED 10 17 31
7P LOSS WILD-TYPE 172 149 122

Figure S76.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

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

Table S77.  Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
7Q LOSS MUTATED 10 5 30 6
7Q LOSS WILD-TYPE 103 147 124 73

Figure S77.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S78.  Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
7Q LOSS MUTATED 17 7 27
7Q LOSS WILD-TYPE 161 182 104

Figure S78.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

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

Table S79.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
9P LOSS MUTATED 99 90 121
9P LOSS WILD-TYPE 83 76 32

Figure S79.  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 S80.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
9P LOSS MUTATED 89 74 104 40
9P LOSS WILD-TYPE 24 78 50 39

Figure S80.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S81.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
9P LOSS MUTATED 133 96 78
9P LOSS WILD-TYPE 45 93 53

Figure S81.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

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

Table S82.  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 29 11 21 13
9Q LOSS WILD-TYPE 13 41 11 15

Figure S82.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S83.  Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 56 51
9Q LOSS MUTATED 32 12 30
9Q LOSS WILD-TYPE 15 44 21

Figure S83.  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 S84.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
9Q LOSS MUTATED 89 44 112
9Q LOSS WILD-TYPE 93 122 41

Figure S84.  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 S85.  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 S85.  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 S86.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
9Q LOSS MUTATED 78 28 95 42
9Q LOSS WILD-TYPE 35 124 59 37

Figure S86.  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 S87.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
9Q LOSS MUTATED 127 42 74
9Q LOSS WILD-TYPE 51 147 57

Figure S87.  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 S88.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
9Q LOSS MUTATED 57 59 72 14 29
9Q LOSS WILD-TYPE 64 75 49 48 8

Figure S88.  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 S89.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
9Q LOSS MUTATED 18 54 128 31
9Q LOSS WILD-TYPE 71 64 71 38

Figure S89.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.087

Table S90.  Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
9Q LOSS MUTATED 31 63 72
9Q LOSS WILD-TYPE 8 88 72

Figure S90.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.07

Table S91.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
10P LOSS MUTATED 55 90 69
10P LOSS WILD-TYPE 127 76 84

Figure S91.  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 S92.  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 72 37
10P LOSS WILD-TYPE 102 42 63

Figure S92.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

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

Table S93.  Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
10P LOSS MUTATED 39 91 56 27
10P LOSS WILD-TYPE 74 61 98 52

Figure S93.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S94.  Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
10P LOSS MUTATED 67 104 42
10P LOSS WILD-TYPE 111 85 89

Figure S94.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S95.  Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
10P LOSS MUTATED 58 41 90 15
10P LOSS WILD-TYPE 31 77 109 54

Figure S95.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MRNA_CHIERARCHICAL'

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

Table S96.  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 18
10Q LOSS WILD-TYPE 35 20 33

Figure S96.  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 S97.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
10Q LOSS MUTATED 62 99 68
10Q LOSS WILD-TYPE 120 67 85

Figure S97.  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 S98.  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 S98.  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 S99.  Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
10Q LOSS MUTATED 44 102 56 26
10Q LOSS WILD-TYPE 69 50 98 53

Figure S99.  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 S100.  Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
10Q LOSS MUTATED 69 119 40
10Q LOSS WILD-TYPE 109 70 91

Figure S100.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S101.  Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
10Q LOSS MUTATED 61 43 96 18
10Q LOSS WILD-TYPE 28 75 103 51

Figure S101.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

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

Table S102.  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 20 12 12
14Q LOSS WILD-TYPE 40 32 20 16

Figure S102.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

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

Table S103.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
14Q LOSS MUTATED 16 63 69 16
14Q LOSS WILD-TYPE 97 89 85 63

Figure S103.  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 S104.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
14Q LOSS MUTATED 28 75 61
14Q LOSS WILD-TYPE 150 114 70

Figure S104.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.15

Table S105.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
14Q LOSS MUTATED 34 44 28 35 15
14Q LOSS WILD-TYPE 87 90 93 27 22

Figure S105.  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 S106.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
14Q LOSS MUTATED 51 34 58 13
14Q LOSS WILD-TYPE 38 84 141 56

Figure S106.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

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

Table S107.  Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 121 134 121 62 37
16Q LOSS MUTATED 39 53 32 24 25
16Q LOSS WILD-TYPE 82 81 89 38 12

Figure S107.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'CN_CNMF'

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

Table S108.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
17P LOSS MUTATED 93 87 111
17P LOSS WILD-TYPE 89 79 42

Figure S108.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.2

Table S109.  Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
17Q LOSS MUTATED 32 13 31 18
17Q LOSS WILD-TYPE 81 139 123 61

Figure S109.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S110.  Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
17Q LOSS MUTATED 55 17 22
17Q LOSS WILD-TYPE 123 172 109

Figure S110.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

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

Table S111.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
19P LOSS MUTATED 47 47 73
19P LOSS WILD-TYPE 135 119 80

Figure S111.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S112.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 118 199 69
19P LOSS MUTATED 17 39 84 15
19P LOSS WILD-TYPE 72 79 115 54

Figure S112.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MRNASEQ_CNMF'

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

Table S113.  Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
20Q LOSS MUTATED 3 28 12 3
20Q LOSS WILD-TYPE 110 124 142 76

Figure S113.  Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

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

Table S114.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
21Q LOSS MUTATED 69 106 90
21Q LOSS WILD-TYPE 113 60 63

Figure S114.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

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

Table S115.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 113 152 154 79
22Q LOSS MUTATED 22 15 47 14
22Q LOSS WILD-TYPE 91 137 107 65

Figure S115.  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 S116.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 189 131
22Q LOSS MUTATED 26 24 48
22Q LOSS WILD-TYPE 152 165 83

Figure S116.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

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

Table S117.  Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 182 166 153
XQ LOSS MUTATED 21 41 53
XQ LOSS WILD-TYPE 161 125 100

Figure S117.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S118.  Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 151 144
XQ LOSS MUTATED 9 51 16
XQ LOSS WILD-TYPE 30 100 128

Figure S118.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 501

  • 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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