Correlation between copy number variation genes (focal events) and molecular subtypes
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 68 focal events and 13 molecular subtypes across 569 patients, 56 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p34.3 cnv correlated to 'CN_CNMF'.

  • amp_1q21.3 cnv correlated to 'CN_CNMF'.

  • amp_1q42.2 cnv correlated to 'CN_CNMF'.

  • amp_2p23.2 cnv correlated to 'CN_CNMF'.

  • amp_2q31.2 cnv correlated to 'CN_CNMF'.

  • amp_3q26.2 cnv correlated to 'CN_CNMF'.

  • amp_4p16.3 cnv correlated to 'CN_CNMF'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF'.

  • amp_6p22.3 cnv correlated to 'CN_CNMF'.

  • amp_7q36.3 cnv correlated to 'CN_CNMF'.

  • amp_8p11.21 cnv correlated to 'CN_CNMF'.

  • amp_8q24.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CNMF'.

  • amp_10p15.3 cnv correlated to 'CN_CNMF'.

  • amp_11q14.1 cnv correlated to 'CN_CNMF'.

  • amp_12p13.33 cnv correlated to 'CN_CNMF'.

  • amp_12p12.1 cnv correlated to 'CN_CNMF'.

  • amp_14q32.33 cnv correlated to 'CN_CNMF'.

  • amp_15q26.3 cnv correlated to 'CN_CNMF'.

  • amp_18q11.2 cnv correlated to 'CN_CNMF'.

  • amp_19p13.12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

  • amp_19q12 cnv correlated to 'CN_CNMF'.

  • amp_19q13.2 cnv correlated to 'CN_CNMF'.

  • amp_20p13 cnv correlated to 'CN_CNMF'.

  • amp_20q11.21 cnv correlated to 'CN_CNMF'.

  • amp_20q13.33 cnv correlated to 'CN_CNMF'.

  • amp_xp11.23 cnv correlated to 'CN_CNMF'.

  • del_1p36.11 cnv correlated to 'CN_CNMF'.

  • del_1q41 cnv correlated to 'CN_CNMF'.

  • del_2q37.3 cnv correlated to 'CN_CNMF'.

  • del_3p26.2 cnv correlated to 'CN_CNMF'.

  • del_5q11.2 cnv correlated to 'CN_CNMF'.

  • del_5q13.2 cnv correlated to 'CN_CNMF'.

  • del_6q27 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_7p22.1 cnv correlated to 'CN_CNMF'.

  • del_8p23.3 cnv correlated to 'CN_CNMF'.

  • del_8p21.2 cnv correlated to 'CN_CNMF'.

  • del_9p24.3 cnv correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

  • del_9q34.13 cnv correlated to 'CN_CNMF'.

  • del_10q24.2 cnv correlated to 'CN_CNMF'.

  • del_11p15.5 cnv correlated to 'CN_CNMF'.

  • del_12q24.33 cnv correlated to 'CN_CNMF'.

  • del_13q14.2 cnv correlated to 'CN_CNMF'.

  • del_14q23.3 cnv correlated to 'CN_CNMF'.

  • del_15q15.1 cnv correlated to 'CN_CNMF'.

  • del_16q22.1 cnv correlated to 'CN_CNMF'.

  • del_16q23.1 cnv correlated to 'CN_CNMF'.

  • del_19q13.33 cnv correlated to 'MRNA_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 68 focal events and 13 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 56 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		CN
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 Fisher's exact test
amp 19p13 12 308 (54%) 261 0.00027
(0.225) 		0.00024
(0.2) 		0.0375
(1.00) 		0.251
(1.00) 		1e-05
(0.00884) 		0.00028
(0.233) 		0.00011
(0.0922) 		0.24
(1.00) 		0.461
(1.00) 		0.585
(1.00) 		0.0952
(1.00) 		0.985
(1.00) 		0.287
(1.00)
amp 8q24 21 451 (79%) 118 1e-05
(0.00884) 		1e-05
(0.00884) 		0.25
(1.00) 		0.00232
(1.00) 		1e-05
(0.00884) 		0.986
(1.00) 		0.327
(1.00) 		1e-05
(0.00884) 		0.00031
(0.257) 		0.162
(1.00) 		0.0998
(1.00) 		0.0634
(1.00) 		0.0667
(1.00)
del 6q27 381 (67%) 188 0.169
(1.00) 		0.046
(1.00) 		0.265
(1.00) 		0.145
(1.00) 		1e-05
(0.00884) 		0.452
(1.00) 		0.247
(1.00) 		3e-05
(0.0254) 		0.00094
(0.77) 		0.371
(1.00) 		0.0287
(1.00) 		0.34
(1.00) 		0.491
(1.00)
del 9p24 3 257 (45%) 312 0.00028
(0.233) 		5e-05
(0.042) 		0.62
(1.00) 		0.0132
(1.00) 		0.0395
(1.00) 		0.325
(1.00) 		0.955
(1.00) 		0.073
(1.00) 		0.0519
(1.00) 		0.0878
(1.00) 		0.125
(1.00) 		0.0632
(1.00) 		0.158
(1.00)
amp 1p34 3 287 (50%) 282 0.431
(1.00) 		0.0815
(1.00) 		0.125
(1.00) 		0.0889
(1.00) 		1e-05
(0.00884) 		0.112
(1.00) 		0.386
(1.00) 		0.559
(1.00) 		0.186
(1.00) 		0.0869
(1.00) 		0.166
(1.00) 		0.0664
(1.00) 		0.413
(1.00)
amp 1q21 3 361 (63%) 208 0.268
(1.00) 		0.162
(1.00) 		0.642
(1.00) 		0.397
(1.00) 		1e-05
(0.00884) 		0.0766
(1.00) 		0.0709
(1.00) 		0.66
(1.00) 		0.372
(1.00) 		0.844
(1.00) 		0.00584
(1.00) 		0.744
(1.00) 		0.35
(1.00)
amp 1q42 2 314 (55%) 255 0.0233
(1.00) 		0.0269
(1.00) 		0.885
(1.00) 		0.00751
(1.00) 		1e-05
(0.00884) 		0.256
(1.00) 		0.124
(1.00) 		0.503
(1.00) 		0.323
(1.00) 		0.267
(1.00) 		0.00291
(1.00) 		0.364
(1.00) 		0.327
(1.00)
amp 2p23 2 245 (43%) 324 0.33
(1.00) 		0.0132
(1.00) 		0.758
(1.00) 		0.171
(1.00) 		1e-05
(0.00884) 		0.143
(1.00) 		0.215
(1.00) 		0.033
(1.00) 		0.0203
(1.00) 		0.919
(1.00) 		0.2
(1.00) 		0.939
(1.00) 		0.628
(1.00)
amp 2q31 2 259 (46%) 310 0.112
(1.00) 		0.173
(1.00) 		0.0325
(1.00) 		0.0302
(1.00) 		1e-05
(0.00884) 		0.0494
(1.00) 		0.324
(1.00) 		0.152
(1.00) 		0.271
(1.00) 		0.289
(1.00) 		0.0848
(1.00) 		0.082
(1.00) 		0.449
(1.00)
amp 3q26 2 476 (84%) 93 0.00905
(1.00) 		0.0268
(1.00) 		0.817
(1.00) 		0.279
(1.00) 		1e-05
(0.00884) 		0.407
(1.00) 		0.278
(1.00) 		0.00664
(1.00) 		0.0115
(1.00) 		0.126
(1.00) 		0.068
(1.00) 		0.478
(1.00) 		0.764
(1.00)
amp 4p16 3 157 (28%) 412 1
(1.00) 		0.321
(1.00) 		0.0299
(1.00) 		0.479
(1.00) 		0.00028
(0.233) 		0.273
(1.00) 		0.691
(1.00) 		0.691
(1.00) 		0.983
(1.00) 		0.627
(1.00) 		0.0193
(1.00) 		0.753
(1.00) 		0.963
(1.00)
amp 5p15 33 304 (53%) 265 1
(1.00) 		0.0543
(1.00) 		0.627
(1.00) 		0.249
(1.00) 		1e-05
(0.00884) 		0.982
(1.00) 		0.238
(1.00) 		0.244
(1.00) 		0.389
(1.00) 		0.0252
(1.00) 		0.146
(1.00) 		0.105
(1.00) 		0.264
(1.00)
amp 6p22 3 300 (53%) 269 0.173
(1.00) 		0.031
(1.00) 		0.275
(1.00) 		0.0745
(1.00) 		1e-05
(0.00884) 		0.0735
(1.00) 		0.056
(1.00) 		0.866
(1.00) 		0.213
(1.00) 		0.378
(1.00) 		0.616
(1.00) 		0.168
(1.00) 		0.514
(1.00)
amp 7q36 3 311 (55%) 258 0.107
(1.00) 		0.177
(1.00) 		0.358
(1.00) 		0.988
(1.00) 		3e-05
(0.0254) 		0.0318
(1.00) 		0.204
(1.00) 		0.845
(1.00) 		0.971
(1.00) 		0.21
(1.00) 		0.501
(1.00) 		0.0237
(1.00) 		0.442
(1.00)
amp 8p11 21 207 (36%) 362 0.11
(1.00) 		0.354
(1.00) 		0.101
(1.00) 		0.533
(1.00) 		4e-05
(0.0337) 		0.0109
(1.00) 		0.425
(1.00) 		0.276
(1.00) 		0.173
(1.00) 		0.769
(1.00) 		0.325
(1.00) 		0.673
(1.00) 		0.975
(1.00)
amp 10p15 3 246 (43%) 323 0.824
(1.00) 		0.1
(1.00) 		0.0532
(1.00) 		0.168
(1.00) 		1e-05
(0.00884) 		0.486
(1.00) 		0.504
(1.00) 		0.241
(1.00) 		0.121
(1.00) 		0.376
(1.00) 		0.0665
(1.00) 		0.601
(1.00) 		0.581
(1.00)
amp 11q14 1 253 (44%) 316 0.0053
(1.00) 		0.004
(1.00) 		0.772
(1.00) 		0.308
(1.00) 		1e-05
(0.00884) 		0.383
(1.00) 		0.226
(1.00) 		0.00434
(1.00) 		0.0279
(1.00) 		0.132
(1.00) 		0.922
(1.00) 		0.214
(1.00) 		0.912
(1.00)
amp 12p13 33 323 (57%) 246 0.0236
(1.00) 		0.00349
(1.00) 		0.265
(1.00) 		0.0546
(1.00) 		1e-05
(0.00884) 		0.193
(1.00) 		0.157
(1.00) 		0.0147
(1.00) 		0.032
(1.00) 		0.535
(1.00) 		0.0078
(1.00) 		0.833
(1.00) 		0.817
(1.00)
amp 12p12 1 306 (54%) 263 0.131
(1.00) 		0.308
(1.00) 		0.902
(1.00) 		0.0415
(1.00) 		1e-05
(0.00884) 		0.616
(1.00) 		0.0912
(1.00) 		0.0126
(1.00) 		0.303
(1.00) 		0.442
(1.00) 		0.00475
(1.00) 		0.734
(1.00) 		0.18
(1.00)
amp 14q32 33 153 (27%) 416 0.437
(1.00) 		0.649
(1.00) 		0.197
(1.00) 		0.017
(1.00) 		0.00028
(0.233) 		1
(1.00) 		0.203
(1.00) 		0.166
(1.00) 		0.242
(1.00) 		0.373
(1.00) 		0.421
(1.00) 		0.476
(1.00) 		0.561
(1.00)
amp 15q26 3 161 (28%) 408 0.0854
(1.00) 		0.422
(1.00) 		0.509
(1.00) 		0.424
(1.00) 		1e-05
(0.00884) 		0.979
(1.00) 		0.185
(1.00) 		0.205
(1.00) 		0.546
(1.00) 		0.153
(1.00) 		0.066
(1.00) 		0.164
(1.00) 		0.428
(1.00)
amp 18q11 2 142 (25%) 427 0.823
(1.00) 		0.779
(1.00) 		0.953
(1.00) 		0.22
(1.00) 		7e-05
(0.0587) 		0.156
(1.00) 		0.418
(1.00) 		0.0422
(1.00) 		0.0769
(1.00) 		0.148
(1.00) 		0.514
(1.00) 		0.171
(1.00) 		0.277
(1.00)
amp 19q12 319 (56%) 250 0.125
(1.00) 		0.00654
(1.00) 		0.0283
(1.00) 		0.516
(1.00) 		1e-05
(0.00884) 		0.0476
(1.00) 		0.213
(1.00) 		0.553
(1.00) 		0.376
(1.00) 		0.349
(1.00) 		0.06
(1.00) 		0.83
(1.00) 		0.106
(1.00)
amp 19q13 2 241 (42%) 328 0.946
(1.00) 		0.54
(1.00) 		0.661
(1.00) 		0.39
(1.00) 		1e-05
(0.00884) 		0.445
(1.00) 		0.148
(1.00) 		0.381
(1.00) 		0.0873
(1.00) 		0.977
(1.00) 		0.551
(1.00) 		0.711
(1.00) 		0.358
(1.00)
amp 20p13 313 (55%) 256 0.47
(1.00) 		0.0166
(1.00) 		0.142
(1.00) 		0.04
(1.00) 		1e-05
(0.00884) 		0.198
(1.00) 		0.419
(1.00) 		0.0818
(1.00) 		0.702
(1.00) 		0.189
(1.00) 		0.00852
(1.00) 		0.663
(1.00) 		0.94
(1.00)
amp 20q11 21 340 (60%) 229 0.00283
(1.00) 		0.0035
(1.00) 		0.112
(1.00) 		0.00286
(1.00) 		1e-05
(0.00884) 		0.133
(1.00) 		0.019
(1.00) 		0.00037
(0.306) 		0.048
(1.00) 		0.289
(1.00) 		0.00057
(0.469) 		0.736
(1.00) 		0.865
(1.00)
amp 20q13 33 393 (69%) 176 0.00996
(1.00) 		0.00084
(0.689) 		0.683
(1.00) 		0.00142
(1.00) 		1e-05
(0.00884) 		0.851
(1.00) 		0.282
(1.00) 		0.00768
(1.00) 		0.00468
(1.00) 		0.477
(1.00) 		0.0497
(1.00) 		0.691
(1.00) 		0.65
(1.00)
amp xp11 23 154 (27%) 415 0.665
(1.00) 		0.865
(1.00) 		0.419
(1.00) 		0.634
(1.00) 		5e-05
(0.042) 		0.719
(1.00) 		0.904
(1.00) 		0.445
(1.00) 		0.929
(1.00) 		0.276
(1.00) 		0.031
(1.00) 		0.454
(1.00) 		0.91
(1.00)
del 1p36 11 267 (47%) 302 0.739
(1.00) 		0.0677
(1.00) 		0.0288
(1.00) 		0.117
(1.00) 		2e-05
(0.017) 		0.123
(1.00) 		0.391
(1.00) 		0.854
(1.00) 		0.419
(1.00) 		0.22
(1.00) 		0.17
(1.00) 		0.347
(1.00) 		0.0585
(1.00)
del 1q41 95 (17%) 474 0.0882
(1.00) 		0.624
(1.00) 		0.297
(1.00) 		0.836
(1.00) 		1e-05
(0.00884) 		0.486
(1.00) 		0.0191
(1.00) 		0.28
(1.00) 		0.247
(1.00) 		0.921
(1.00) 		0.97
(1.00) 		0.76
(1.00) 		0.672
(1.00)
del 2q37 3 173 (30%) 396 0.0161
(1.00) 		0.526
(1.00) 		0.767
(1.00) 		0.0172
(1.00) 		3e-05
(0.0254) 		0.815
(1.00) 		0.69
(1.00) 		0.0163
(1.00) 		0.00424
(1.00) 		0.0137
(1.00) 		0.015
(1.00) 		0.054
(1.00) 		0.0259
(1.00)
del 3p26 2 209 (37%) 360 0.154
(1.00) 		0.00052
(0.429) 		0.00562
(1.00) 		0.0045
(1.00) 		2e-05
(0.017) 		0.97
(1.00) 		0.239
(1.00) 		0.00326
(1.00) 		0.00953
(1.00) 		0.634
(1.00) 		0.123
(1.00) 		0.975
(1.00) 		0.827
(1.00)
del 5q11 2 347 (61%) 222 0.923
(1.00) 		0.828
(1.00) 		0.638
(1.00) 		0.0421
(1.00) 		1e-05
(0.00884) 		0.745
(1.00) 		0.87
(1.00) 		0.209
(1.00) 		0.0407
(1.00) 		0.0924
(1.00) 		0.182
(1.00) 		0.0659
(1.00) 		0.0561
(1.00)
del 5q13 2 412 (72%) 157 0.747
(1.00) 		0.623
(1.00) 		0.898
(1.00) 		0.259
(1.00) 		1e-05
(0.00884) 		0.791
(1.00) 		0.831
(1.00) 		0.517
(1.00) 		0.0925
(1.00) 		0.157
(1.00) 		0.108
(1.00) 		0.212
(1.00) 		0.175
(1.00)
del 7p22 1 248 (44%) 321 0.397
(1.00) 		0.517
(1.00) 		0.772
(1.00) 		0.0629
(1.00) 		1e-05
(0.00884) 		0.818
(1.00) 		0.605
(1.00) 		0.346
(1.00) 		0.126
(1.00) 		0.346
(1.00) 		0.906
(1.00) 		0.698
(1.00) 		0.293
(1.00)
del 8p23 3 382 (67%) 187 0.0443
(1.00) 		0.152
(1.00) 		0.573
(1.00) 		0.0114
(1.00) 		1e-05
(0.00884) 		0.893
(1.00) 		0.451
(1.00) 		0.893
(1.00) 		0.912
(1.00) 		0.244
(1.00) 		0.246
(1.00) 		0.171
(1.00) 		0.332
(1.00)
del 8p21 2 400 (70%) 169 0.0434
(1.00) 		0.0904
(1.00) 		0.181
(1.00) 		0.00554
(1.00) 		1e-05
(0.00884) 		0.876
(1.00) 		0.994
(1.00) 		0.457
(1.00) 		0.701
(1.00) 		0.581
(1.00) 		0.513
(1.00) 		0.919
(1.00) 		0.0752
(1.00)
del 9q34 13 337 (59%) 232 0.0286
(1.00) 		0.00122
(0.997) 		0.963
(1.00) 		0.454
(1.00) 		2e-05
(0.017) 		0.418
(1.00) 		0.0881
(1.00) 		0.207
(1.00) 		0.144
(1.00) 		0.0349
(1.00) 		0.198
(1.00) 		0.132
(1.00) 		0.078
(1.00)
del 10q24 2 246 (43%) 323 0.00181
(1.00) 		0.00279
(1.00) 		0.00633
(1.00) 		0.214
(1.00) 		4e-05
(0.0337) 		0.0108
(1.00) 		0.00203
(1.00) 		0.444
(1.00) 		0.295
(1.00) 		0.00187
(1.00) 		0.453
(1.00) 		0.0103
(1.00) 		0.00578
(1.00)
del 11p15 5 338 (59%) 231 0.111
(1.00) 		0.971
(1.00) 		0.618
(1.00) 		0.0848
(1.00) 		1e-05
(0.00884) 		0.945
(1.00) 		0.712
(1.00) 		0.698
(1.00) 		0.504
(1.00) 		0.105
(1.00) 		0.00913
(1.00) 		0.156
(1.00) 		0.195
(1.00)
del 12q24 33 217 (38%) 352 0.00096
(0.785) 		0.0998
(1.00) 		0.164
(1.00) 		0.0145
(1.00) 		1e-05
(0.00884) 		0.295
(1.00) 		0.224
(1.00) 		0.052
(1.00) 		0.0318
(1.00) 		0.0151
(1.00) 		0.0046
(1.00) 		0.0189
(1.00) 		0.0267
(1.00)
del 13q14 2 358 (63%) 211 0.01
(1.00) 		0.0158
(1.00) 		0.613
(1.00) 		0.0427
(1.00) 		1e-05
(0.00884) 		0.00174
(1.00) 		0.0513
(1.00) 		0.0988
(1.00) 		0.681
(1.00) 		0.377
(1.00) 		0.367
(1.00) 		0.452
(1.00) 		0.387
(1.00)
del 14q23 3 299 (53%) 270 0.0656
(1.00) 		0.505
(1.00) 		0.655
(1.00) 		0.612
(1.00) 		0.00013
(0.109) 		0.227
(1.00) 		0.511
(1.00) 		0.856
(1.00) 		0.283
(1.00) 		0.899
(1.00) 		0.592
(1.00) 		0.711
(1.00) 		0.798
(1.00)
del 15q15 1 360 (63%) 209 0.0262
(1.00) 		0.0601
(1.00) 		0.0222
(1.00) 		0.00285
(1.00) 		1e-05
(0.00884) 		0.157
(1.00) 		0.151
(1.00) 		0.0109
(1.00) 		0.497
(1.00) 		0.396
(1.00) 		0.00206
(1.00) 		0.204
(1.00) 		0.0237
(1.00)
del 16q22 1 453 (80%) 116 0.497
(1.00) 		0.704
(1.00) 		0.0309
(1.00) 		0.449
(1.00) 		0.00017
(0.142) 		0.697
(1.00) 		0.143
(1.00) 		0.223
(1.00) 		0.291
(1.00) 		0.313
(1.00) 		0.0475
(1.00) 		0.0601
(1.00) 		0.0899
(1.00)
del 16q23 1 444 (78%) 125 0.108
(1.00) 		0.245
(1.00) 		0.101
(1.00) 		0.0611
(1.00) 		3e-05
(0.0254) 		0.813
(1.00) 		0.222
(1.00) 		0.273
(1.00) 		0.168
(1.00) 		0.057
(1.00) 		0.0482
(1.00) 		0.0407
(1.00) 		0.00628
(1.00)
del 19q13 33 295 (52%) 274 0.00026
(0.217) 		0.00229
(1.00) 		0.0458
(1.00) 		0.021
(1.00) 		0.0957
(1.00) 		0.0293
(1.00) 		0.301
(1.00) 		0.00675
(1.00) 		0.122
(1.00) 		0.321
(1.00) 		0.129
(1.00) 		0.292
(1.00) 		0.475
(1.00)
amp 4q13 3 110 (19%) 459 0.952
(1.00) 		0.429
(1.00) 		0.345
(1.00) 		0.987
(1.00) 		0.00038
(0.314) 		0.554
(1.00) 		0.423
(1.00) 		0.125
(1.00) 		0.478
(1.00) 		1
(1.00) 		0.723
(1.00) 		0.876
(1.00) 		0.835
(1.00)
amp 10q22 3 181 (32%) 388 0.471
(1.00) 		0.298
(1.00) 		0.542
(1.00) 		0.964
(1.00) 		0.219
(1.00) 		0.656
(1.00) 		0.845
(1.00) 		0.194
(1.00) 		0.765
(1.00) 		0.268
(1.00) 		0.517
(1.00) 		0.907
(1.00) 		0.412
(1.00)
amp 14q11 2 146 (26%) 423 0.0166
(1.00) 		0.0589
(1.00) 		0.293
(1.00) 		0.00687
(1.00) 		0.04
(1.00) 		0.536
(1.00) 		0.467
(1.00) 		0.343
(1.00) 		0.408
(1.00) 		0.301
(1.00) 		0.822
(1.00) 		0.217
(1.00) 		0.298
(1.00)
amp 17q25 3 212 (37%) 357 0.47
(1.00) 		0.0577
(1.00) 		0.981
(1.00) 		0.666
(1.00) 		0.00219
(1.00) 		0.072
(1.00) 		0.131
(1.00) 		0.0116
(1.00) 		0.0261
(1.00) 		0.323
(1.00) 		0.127
(1.00) 		0.297
(1.00) 		0.0506
(1.00)
amp 22q12 2 89 (16%) 480 0.624
(1.00) 		0.155
(1.00) 		0.0717
(1.00) 		0.0342
(1.00) 		0.00128
(1.00) 		0.984
(1.00) 		0.0878
(1.00) 		0.0596
(1.00) 		0.0597
(1.00) 		0.109
(1.00) 		0.0145
(1.00) 		0.0374
(1.00) 		0.0165
(1.00)
amp xq28 217 (38%) 352 0.242
(1.00) 		0.846
(1.00) 		0.558
(1.00) 		0.123
(1.00) 		0.00131
(1.00) 		0.454
(1.00) 		0.445
(1.00) 		0.625
(1.00) 		0.938
(1.00) 		0.881
(1.00) 		0.806
(1.00) 		0.868
(1.00) 		0.991
(1.00)
del 2p25 3 120 (21%) 449 0.88
(1.00) 		0.269
(1.00) 		0.421
(1.00) 		0.157
(1.00) 		0.244
(1.00) 		0.26
(1.00) 		0.541
(1.00) 		0.0625
(1.00) 		0.237
(1.00) 		0.875
(1.00) 		0.951
(1.00) 		0.892
(1.00) 		1
(1.00)
del 2q22 1 136 (24%) 433 0.107
(1.00) 		0.272
(1.00) 		0.566
(1.00) 		0.00356
(1.00) 		0.0851
(1.00) 		0.602
(1.00) 		0.721
(1.00) 		0.921
(1.00) 		0.301
(1.00) 		0.481
(1.00) 		0.599
(1.00) 		0.418
(1.00) 		0.414
(1.00)
del 4q22 1 388 (68%) 181 0.0522
(1.00) 		0.0228
(1.00) 		1
(1.00) 		0.166
(1.00) 		0.0203
(1.00) 		0.19
(1.00) 		0.0609
(1.00) 		0.0703
(1.00) 		0.389
(1.00) 		0.306
(1.00) 		0.253
(1.00) 		0.0296
(1.00) 		0.224
(1.00)
del 4q34 3 415 (73%) 154 0.0532
(1.00) 		0.00062
(0.509) 		0.0627
(1.00) 		0.0277
(1.00) 		0.151
(1.00) 		0.669
(1.00) 		0.199
(1.00) 		0.0834
(1.00) 		0.0179
(1.00) 		0.423
(1.00) 		0.529
(1.00) 		0.161
(1.00) 		0.279
(1.00)
del 10p15 3 120 (21%) 449 0.177
(1.00) 		0.708
(1.00) 		0.0887
(1.00) 		0.322
(1.00) 		0.148
(1.00) 		0.289
(1.00) 		0.0397
(1.00) 		0.0144
(1.00) 		0.0887
(1.00) 		0.252
(1.00) 		0.264
(1.00) 		0.113
(1.00) 		0.41
(1.00)
del 11q25 195 (34%) 374 0.714
(1.00) 		0.636
(1.00) 		0.173
(1.00) 		0.0634
(1.00) 		0.147
(1.00) 		0.317
(1.00) 		0.197
(1.00) 		0.932
(1.00) 		0.31
(1.00) 		0.634
(1.00) 		0.18
(1.00) 		0.683
(1.00) 		0.19
(1.00)
del 16p13 3 307 (54%) 262 0.608
(1.00) 		0.0727
(1.00) 		0.274
(1.00) 		0.0292
(1.00) 		0.0536
(1.00) 		0.84
(1.00) 		0.818
(1.00) 		0.366
(1.00) 		0.431
(1.00) 		0.221
(1.00) 		0.485
(1.00) 		0.112
(1.00) 		0.455
(1.00)
del 17p12 483 (85%) 86 0.142
(1.00) 		0.333
(1.00) 		0.594
(1.00) 		0.691
(1.00) 		0.737
(1.00) 		0.907
(1.00) 		0.369
(1.00) 		0.153
(1.00) 		0.194
(1.00) 		0.508
(1.00) 		0.21
(1.00) 		0.467
(1.00) 		0.415
(1.00)
del 17q11 2 466 (82%) 103 0.92
(1.00) 		0.193
(1.00) 		0.733
(1.00) 		0.216
(1.00) 		0.00057
(0.469) 		0.765
(1.00) 		0.036
(1.00) 		0.373
(1.00) 		0.441
(1.00) 		0.15
(1.00) 		0.164
(1.00) 		0.0251
(1.00) 		0.762
(1.00)
del 18q23 377 (66%) 192 0.986
(1.00) 		0.992
(1.00) 		0.147
(1.00) 		0.807
(1.00) 		0.0158
(1.00) 		0.335
(1.00) 		0.203
(1.00) 		0.126
(1.00) 		0.367
(1.00) 		0.484
(1.00) 		0.176
(1.00) 		0.0745
(1.00) 		0.743
(1.00)
del 19p13 3 502 (88%) 67 0.159
(1.00) 		0.0896
(1.00) 		0.84
(1.00) 		0.546
(1.00) 		0.00053
(0.437) 		0.624
(1.00) 		0.404
(1.00) 		0.333
(1.00) 		0.52
(1.00) 		0.478
(1.00) 		0.731
(1.00) 		0.442
(1.00) 		0.19
(1.00)
del 19q13 43 279 (49%) 290 0.0115
(1.00) 		0.0642
(1.00) 		0.0966
(1.00) 		0.388
(1.00) 		0.00281
(1.00) 		0.18
(1.00) 		0.416
(1.00) 		0.475
(1.00) 		0.941
(1.00) 		0.523
(1.00) 		0.139
(1.00) 		0.369
(1.00) 		0.654
(1.00)
del 21q22 3 224 (39%) 345 0.369
(1.00) 		0.0418
(1.00) 		0.692
(1.00) 		0.204
(1.00) 		0.815
(1.00) 		0.661
(1.00) 		0.717
(1.00) 		0.244
(1.00) 		0.127
(1.00) 		0.821
(1.00) 		0.732
(1.00) 		0.198
(1.00) 		0.453
(1.00)
del 22q13 32 495 (87%) 74 0.166
(1.00) 		0.124
(1.00) 		0.0221
(1.00) 		0.31
(1.00) 		0.00486
(1.00) 		0.102
(1.00) 		0.0446
(1.00) 		0.106
(1.00) 		0.0139
(1.00) 		0.0308
(1.00) 		0.6
(1.00) 		0.027
(1.00) 		0.11
(1.00)
del xp21 1 350 (62%) 219 0.405
(1.00) 		0.646
(1.00) 		0.0984
(1.00) 		0.797
(1.00) 		0.123
(1.00) 		0.461
(1.00) 		0.106
(1.00) 		0.883
(1.00) 		0.242
(1.00) 		0.976
(1.00) 		0.718
(1.00) 		0.861
(1.00) 		0.108
(1.00)
'amp_1p34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S1.  Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 1(1P34.3) MUTATED 59 120 108
AMP PEAK 1(1P34.3) WILD-TYPE 115 86 81

Figure S1.  Get High-res Image Gene #1: 'amp_1p34.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S2.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 2(1Q21.3) MUTATED 90 115 156
AMP PEAK 2(1Q21.3) WILD-TYPE 84 91 33

Figure S2.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q42.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S3.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 3(1Q42.2) MUTATED 90 86 138
AMP PEAK 3(1Q42.2) WILD-TYPE 84 120 51

Figure S3.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S4.  Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 4(2P23.2) MUTATED 48 86 111
AMP PEAK 4(2P23.2) WILD-TYPE 126 120 78

Figure S4.  Get High-res Image Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S5.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 5(2Q31.2) MUTATED 47 102 110
AMP PEAK 5(2Q31.2) WILD-TYPE 127 104 79

Figure S5.  Get High-res Image Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S6.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 6(3Q26.2) MUTATED 118 182 176
AMP PEAK 6(3Q26.2) WILD-TYPE 56 24 13

Figure S6.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4p16.3' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.23

Table S7.  Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 7(4P16.3) MUTATED 34 77 46
AMP PEAK 7(4P16.3) WILD-TYPE 140 129 143

Figure S7.  Get High-res Image Gene #7: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S8.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 9(5P15.33) MUTATED 64 125 115
AMP PEAK 9(5P15.33) WILD-TYPE 110 81 74

Figure S8.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_6p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S9.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 10(6P22.3) MUTATED 63 124 113
AMP PEAK 10(6P22.3) WILD-TYPE 111 82 76

Figure S9.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q36.3' versus 'CN_CNMF'

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

Table S10.  Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 11(7Q36.3) MUTATED 70 125 116
AMP PEAK 11(7Q36.3) WILD-TYPE 104 81 73

Figure S10.  Get High-res Image Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

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

Table S11.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 12(8P11.21) MUTATED 43 73 91
AMP PEAK 12(8P11.21) WILD-TYPE 131 133 98

Figure S11.  Get High-res Image Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S12.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 13(8Q24.21) MUTATED 144 188 110
AMP PEAK 13(8Q24.21) WILD-TYPE 71 28 16

Figure S12.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S13.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 13(8Q24.21) MUTATED 245 144 53
AMP PEAK 13(8Q24.21) WILD-TYPE 65 14 36

Figure S13.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S14.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 13(8Q24.21) MUTATED 118 199 134
AMP PEAK 13(8Q24.21) WILD-TYPE 56 7 55

Figure S14.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S15.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 67 91
AMP PEAK 13(8Q24.21) MUTATED 90 61 56
AMP PEAK 13(8Q24.21) WILD-TYPE 10 6 35

Figure S15.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CNMF'

'amp_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S16.  Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 14(10P15.3) MUTATED 46 80 120
AMP PEAK 14(10P15.3) WILD-TYPE 128 126 69

Figure S16.  Get High-res Image Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S17.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 16(11Q14.1) MUTATED 57 121 75
AMP PEAK 16(11Q14.1) WILD-TYPE 117 85 114

Figure S17.  Get High-res Image Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S18.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 17(12P13.33) MUTATED 72 114 137
AMP PEAK 17(12P13.33) WILD-TYPE 102 92 52

Figure S18.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S19.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 18(12P12.1) MUTATED 67 99 140
AMP PEAK 18(12P12.1) WILD-TYPE 107 107 49

Figure S19.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_14q32.33' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.23

Table S20.  Gene #20: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 20(14Q32.33) MUTATED 43 75 35
AMP PEAK 20(14Q32.33) WILD-TYPE 131 131 154

Figure S20.  Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S21.  Gene #21: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 21(15Q26.3) MUTATED 35 91 35
AMP PEAK 21(15Q26.3) WILD-TYPE 139 115 154

Figure S21.  Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

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

Table S22.  Gene #23: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 23(18Q11.2) MUTATED 26 48 68
AMP PEAK 23(18Q11.2) WILD-TYPE 148 158 121

Figure S22.  Get High-res Image Gene #23: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.12' versus 'MRNA_CNMF'

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

Table S23.  Gene #24: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 24(19P13.12) MUTATED 136 115 51
AMP PEAK 24(19P13.12) WILD-TYPE 79 101 75

Figure S23.  Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

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

Table S24.  Gene #24: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 24(19P13.12) MUTATED 186 64 52
AMP PEAK 24(19P13.12) WILD-TYPE 124 94 37

Figure S24.  Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S25.  Gene #24: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 24(19P13.12) MUTATED 72 95 141
AMP PEAK 24(19P13.12) WILD-TYPE 102 111 48

Figure S25.  Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.12' versus 'RPPA_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.23

Table S26.  Gene #24: 'amp_19p13.12' versus Molecular Subtype #6: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 196 82
AMP PEAK 24(19P13.12) MUTATED 59 125 32
AMP PEAK 24(19P13.12) WILD-TYPE 61 71 50

Figure S26.  Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #6: 'RPPA_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.092

Table S27.  Gene #24: 'amp_19p13.12' versus Molecular Subtype #7: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 96 128 58
AMP PEAK 24(19P13.12) MUTATED 44 55 86 31
AMP PEAK 24(19P13.12) WILD-TYPE 72 41 42 27

Figure S27.  Get High-res Image Gene #24: 'amp_19p13.12' versus Molecular Subtype #7: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S28.  Gene #25: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 25(19Q12) MUTATED 66 88 165
AMP PEAK 25(19Q12) WILD-TYPE 108 118 24

Figure S28.  Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S29.  Gene #26: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 26(19Q13.2) MUTATED 51 71 119
AMP PEAK 26(19Q13.2) WILD-TYPE 123 135 70

Figure S29.  Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S30.  Gene #27: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 27(20P13) MUTATED 72 100 141
AMP PEAK 27(20P13) WILD-TYPE 102 106 48

Figure S30.  Get High-res Image Gene #27: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S31.  Gene #28: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 28(20Q11.21) MUTATED 78 97 165
AMP PEAK 28(20Q11.21) WILD-TYPE 96 109 24

Figure S31.  Get High-res Image Gene #28: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S32.  Gene #29: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 29(20Q13.33) MUTATED 88 136 169
AMP PEAK 29(20Q13.33) WILD-TYPE 86 70 20

Figure S32.  Get High-res Image Gene #29: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_xp11.23' versus 'CN_CNMF'

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

Table S33.  Gene #31: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
AMP PEAK 31(XP11.23) MUTATED 28 55 71
AMP PEAK 31(XP11.23) WILD-TYPE 146 151 118

Figure S33.  Get High-res Image Gene #31: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.11' versus 'CN_CNMF'

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

Table S34.  Gene #33: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 1(1P36.11) MUTATED 92 113 62
DEL PEAK 1(1P36.11) WILD-TYPE 82 93 127

Figure S34.  Get High-res Image Gene #33: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

'del_1q41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S35.  Gene #34: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 2(1Q41) MUTATED 15 58 22
DEL PEAK 2(1Q41) WILD-TYPE 159 148 167

Figure S35.  Get High-res Image Gene #34: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q37.3' versus 'CN_CNMF'

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

Table S36.  Gene #37: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 5(2Q37.3) MUTATED 39 88 46
DEL PEAK 5(2Q37.3) WILD-TYPE 135 118 143

Figure S36.  Get High-res Image Gene #37: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_3p26.2' versus 'CN_CNMF'

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

Table S37.  Gene #38: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 6(3P26.2) MUTATED 45 71 93
DEL PEAK 6(3P26.2) WILD-TYPE 129 135 96

Figure S37.  Get High-res Image Gene #38: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S38.  Gene #41: 'del_5q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 9(5Q11.2) MUTATED 74 146 127
DEL PEAK 9(5Q11.2) WILD-TYPE 100 60 62

Figure S38.  Get High-res Image Gene #41: 'del_5q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S39.  Gene #42: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 10(5Q13.2) MUTATED 95 178 139
DEL PEAK 10(5Q13.2) WILD-TYPE 79 28 50

Figure S39.  Get High-res Image Gene #42: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S40.  Gene #43: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 11(6Q27) MUTATED 127 162 92
DEL PEAK 11(6Q27) WILD-TYPE 47 44 97

Figure S40.  Get High-res Image Gene #43: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'MRNASEQ_CNMF'

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

Table S41.  Gene #43: 'del_6q27' versus Molecular Subtype #8: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 67 91
DEL PEAK 11(6Q27) MUTATED 67 52 39
DEL PEAK 11(6Q27) WILD-TYPE 33 15 52

Figure S41.  Get High-res Image Gene #43: 'del_6q27' versus Molecular Subtype #8: 'MRNASEQ_CNMF'

'del_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S42.  Gene #44: 'del_7p22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 12(7P22.1) MUTATED 51 133 64
DEL PEAK 12(7P22.1) WILD-TYPE 123 73 125

Figure S42.  Get High-res Image Gene #44: 'del_7p22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S43.  Gene #45: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 13(8P23.3) MUTATED 80 164 138
DEL PEAK 13(8P23.3) WILD-TYPE 94 42 51

Figure S43.  Get High-res Image Gene #45: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S44.  Gene #46: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 14(8P21.2) MUTATED 91 166 143
DEL PEAK 14(8P21.2) WILD-TYPE 83 40 46

Figure S44.  Get High-res Image Gene #46: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p24.3' versus 'MRNA_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.23

Table S45.  Gene #47: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 15(9P24.3) MUTATED 109 73 66
DEL PEAK 15(9P24.3) WILD-TYPE 106 143 60

Figure S45.  Get High-res Image Gene #47: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p24.3' versus 'MRNA_CHIERARCHICAL'

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

Table S46.  Gene #47: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 15(9P24.3) MUTATED 120 69 59
DEL PEAK 15(9P24.3) WILD-TYPE 190 89 30

Figure S46.  Get High-res Image Gene #47: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.13' versus 'CN_CNMF'

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

Table S47.  Gene #48: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 16(9Q34.13) MUTATED 91 105 141
DEL PEAK 16(9Q34.13) WILD-TYPE 83 101 48

Figure S47.  Get High-res Image Gene #48: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q24.2' versus 'CN_CNMF'

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

Table S48.  Gene #50: 'del_10q24.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 18(10Q24.2) MUTATED 55 113 78
DEL PEAK 18(10Q24.2) WILD-TYPE 119 93 111

Figure S48.  Get High-res Image Gene #50: 'del_10q24.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S49.  Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 19(11P15.5) MUTATED 81 158 99
DEL PEAK 19(11P15.5) WILD-TYPE 93 48 90

Figure S49.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S50.  Gene #53: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 21(12Q24.33) MUTATED 58 112 47
DEL PEAK 21(12Q24.33) WILD-TYPE 116 94 142

Figure S50.  Get High-res Image Gene #53: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S51.  Gene #54: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 22(13Q14.2) MUTATED 88 156 114
DEL PEAK 22(13Q14.2) WILD-TYPE 86 50 75

Figure S51.  Get High-res Image Gene #54: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q23.3' versus 'CN_CNMF'

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

Table S52.  Gene #55: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 23(14Q23.3) MUTATED 75 102 122
DEL PEAK 23(14Q23.3) WILD-TYPE 99 104 67

Figure S52.  Get High-res Image Gene #55: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0088

Table S53.  Gene #56: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 24(15Q15.1) MUTATED 83 122 155
DEL PEAK 24(15Q15.1) WILD-TYPE 91 84 34

Figure S53.  Get High-res Image Gene #56: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_16q22.1' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.14

Table S54.  Gene #58: 'del_16q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 26(16Q22.1) MUTATED 120 171 162
DEL PEAK 26(16Q22.1) WILD-TYPE 54 35 27

Figure S54.  Get High-res Image Gene #58: 'del_16q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

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

Table S55.  Gene #59: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 174 206 189
DEL PEAK 27(16Q23.1) MUTATED 114 168 162
DEL PEAK 27(16Q23.1) WILD-TYPE 60 38 27

Figure S55.  Get High-res Image Gene #59: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.33' versus 'MRNA_CNMF'

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

Table S56.  Gene #64: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 32(19Q13.33) MUTATED 127 117 46
DEL PEAK 32(19Q13.33) WILD-TYPE 88 99 80

Figure S56.  Get High-res Image Gene #64: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

Methods & Data
Input

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

  • Molecular subtype file = OV-TP.transferedmergedcluster.txt

  • Number of patients = 569

  • Number of significantly focal cnvs = 68

  • Number of molecular subtypes = 13

  • Exclude genes that fewer than K tumors have alterations, 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.

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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