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 71 focal events and 14 molecular subtypes across 579 patients, 76 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' and 'METHLYATION_CNMF'.

  • amp_1q42.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_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_4q13.3 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' and 'METHLYATION_CNMF'.

  • amp_12p12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_12q15 cnv correlated to 'CN_CNMF' and 'METHLYATION_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',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • amp_19q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_19q13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_20p13 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_20q11.21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • amp_20q13.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_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_5q12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_5q13.2 cnv correlated to 'CN_CNMF'.

  • del_6q27 cnv correlated to 'CN_CNMF',  'METHLYATION_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',  'MRNA_CHIERARCHICAL', and 'METHLYATION_CNMF'.

  • 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' and 'METHLYATION_CNMF'.

  • del_14q23.3 cnv correlated to 'CN_CNMF'.

  • del_15q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_15q15.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_16q23.1 cnv correlated to 'CN_CNMF'.

  • del_19q13.33 cnv correlated to 'MRNA_CNMF'.

  • del_19q13.43 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 71 focal events and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 76 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
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 Fisher's exact test Fisher's exact test
amp 19p13 12 315 (54%) 264 0.00019
(0.175) 		0.00025
(0.228) 		0.0371
(1.00) 		0.251
(1.00) 		1e-05
(0.00986) 		1e-05
(0.00986) 		0.00035
(0.318) 		0.0001
(0.0924) 		0.24
(1.00) 		0.465
(1.00) 		0.586
(1.00) 		0.0985
(1.00) 		1
(1.00) 		0.481
(1.00)
amp 8q24 21 461 (80%) 118 1e-05
(0.00986) 		1e-05
(0.00986) 		0.247
(1.00) 		0.00262
(1.00) 		1e-05
(0.00986) 		0.00443
(1.00) 		0.987
(1.00) 		0.325
(1.00) 		1e-05
(0.00986) 		0.00029
(0.264) 		0.161
(1.00) 		0.0976
(1.00) 		0.571
(1.00) 		0.571
(1.00)
amp 20q11 21 348 (60%) 231 0.00271
(1.00) 		0.00303
(1.00) 		0.112
(1.00) 		0.00296
(1.00) 		1e-05
(0.00986) 		1e-05
(0.00986) 		0.13
(1.00) 		0.0193
(1.00) 		0.00019
(0.175) 		0.0474
(1.00) 		0.292
(1.00) 		0.00054
(0.488) 		1
(1.00) 		0.335
(1.00)
del 6q27 380 (66%) 199 0.323
(1.00) 		0.0612
(1.00) 		0.271
(1.00) 		0.103
(1.00) 		1e-05
(0.00986) 		4e-05
(0.0373) 		0.62
(1.00) 		0.56
(1.00) 		2e-05
(0.0188) 		0.0016
(1.00) 		0.561
(1.00) 		0.026
(1.00) 		0.691
(1.00) 		0.436
(1.00)
del 9p24 3 261 (45%) 318 0.00026
(0.237) 		1e-05
(0.00986) 		0.623
(1.00) 		0.0132
(1.00) 		0.0615
(1.00) 		7e-05
(0.065) 		0.321
(1.00) 		0.955
(1.00) 		0.0726
(1.00) 		0.0516
(1.00) 		0.0886
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.514
(1.00)
amp 1q21 3 367 (63%) 212 0.269
(1.00) 		0.163
(1.00) 		0.64
(1.00) 		0.399
(1.00) 		1e-05
(0.00986) 		0.00022
(0.202) 		0.0767
(1.00) 		0.0711
(1.00) 		0.657
(1.00) 		0.371
(1.00) 		0.841
(1.00) 		0.00628
(1.00) 		0.652
(1.00) 		0.695
(1.00)
amp 1q42 2 322 (56%) 257 0.0234
(1.00) 		0.0274
(1.00) 		0.884
(1.00) 		0.00779
(1.00) 		1e-05
(0.00986) 		9e-05
(0.0834) 		0.257
(1.00) 		0.124
(1.00) 		0.506
(1.00) 		0.319
(1.00) 		0.265
(1.00) 		0.00297
(1.00) 		1
(1.00) 		0.51
(1.00)
amp 12p13 33 330 (57%) 249 0.0229
(1.00) 		0.00345
(1.00) 		0.263
(1.00) 		0.0548
(1.00) 		1e-05
(0.00986) 		0.00014
(0.129) 		0.196
(1.00) 		0.151
(1.00) 		0.0146
(1.00) 		0.0311
(1.00) 		0.535
(1.00) 		0.00771
(1.00) 		0.378
(1.00) 		0.529
(1.00)
amp 12p12 1 313 (54%) 266 0.127
(1.00) 		0.306
(1.00) 		0.9
(1.00) 		0.0412
(1.00) 		1e-05
(0.00986) 		3e-05
(0.0281) 		0.615
(1.00) 		0.0905
(1.00) 		0.0117
(1.00) 		0.301
(1.00) 		0.442
(1.00) 		0.00492
(1.00) 		0.391
(1.00) 		0.0414
(1.00)
amp 12q15 222 (38%) 357 0.0028
(1.00) 		0.242
(1.00) 		0.574
(1.00) 		0.0023
(1.00) 		1e-05
(0.00986) 		1e-05
(0.00986) 		0.0731
(1.00) 		0.249
(1.00) 		0.00141
(1.00) 		0.0714
(1.00) 		0.968
(1.00) 		0.101
(1.00) 		0.231
(1.00) 		0.269
(1.00)
amp 19q12 322 (56%) 257 0.125
(1.00) 		0.00619
(1.00) 		0.0295
(1.00) 		0.513
(1.00) 		1e-05
(0.00986) 		1e-05
(0.00986) 		0.0471
(1.00) 		0.213
(1.00) 		0.552
(1.00) 		0.375
(1.00) 		0.346
(1.00) 		0.06
(1.00) 		1
(1.00) 		0.782
(1.00)
amp 19q13 2 245 (42%) 334 0.945
(1.00) 		0.537
(1.00) 		0.665
(1.00) 		0.39
(1.00) 		1e-05
(0.00986) 		0.00011
(0.102) 		0.447
(1.00) 		0.146
(1.00) 		0.382
(1.00) 		0.0869
(1.00) 		0.977
(1.00) 		0.552
(1.00) 		0.675
(1.00) 		0.612
(1.00)
amp 20p13 317 (55%) 262 0.188
(1.00) 		0.00571
(1.00) 		0.207
(1.00) 		0.0332
(1.00) 		1e-05
(0.00986) 		1e-05
(0.00986) 		0.321
(1.00) 		0.573
(1.00) 		0.0165
(1.00) 		0.348
(1.00) 		0.248
(1.00) 		0.00082
(0.736) 		1
(1.00) 		0.936
(1.00)
amp 20q13 33 402 (69%) 177 0.0107
(1.00) 		0.00088
(0.789) 		0.683
(1.00) 		0.00125
(1.00) 		1e-05
(0.00986) 		1e-05
(0.00986) 		0.851
(1.00) 		0.279
(1.00) 		0.00841
(1.00) 		0.00475
(1.00) 		0.477
(1.00) 		0.0491
(1.00) 		0.624
(1.00) 		0.0139
(1.00)
del 5q12 1 355 (61%) 224 0.883
(1.00) 		0.874
(1.00) 		0.577
(1.00) 		0.0558
(1.00) 		1e-05
(0.00986) 		0.0002
(0.183) 		0.685
(1.00) 		0.863
(1.00) 		0.295
(1.00) 		0.0541
(1.00) 		0.162
(1.00) 		0.253
(1.00) 		1
(1.00) 		0.263
(1.00)
del 13q14 2 364 (63%) 215 0.0105
(1.00) 		0.0155
(1.00) 		0.613
(1.00) 		0.0429
(1.00) 		0.00024
(0.219) 		1e-05
(0.00986) 		0.00219
(1.00) 		0.052
(1.00) 		0.0991
(1.00) 		0.677
(1.00) 		0.377
(1.00) 		0.367
(1.00) 		0.675
(1.00) 		0.249
(1.00)
del 15q11 2 299 (52%) 280 0.00546
(1.00) 		0.0354
(1.00) 		0.0106
(1.00) 		0.0062
(1.00) 		1e-05
(0.00986) 		3e-05
(0.0281) 		0.468
(1.00) 		0.766
(1.00) 		0.00509
(1.00) 		0.159
(1.00) 		0.0258
(1.00) 		0.00973
(1.00) 		1
(1.00) 		0.372
(1.00)
del 15q15 1 363 (63%) 216 0.0259
(1.00) 		0.0596
(1.00) 		0.0211
(1.00) 		0.00285
(1.00) 		1e-05
(0.00986) 		1e-05
(0.00986) 		0.156
(1.00) 		0.152
(1.00) 		0.0115
(1.00) 		0.5
(1.00) 		0.395
(1.00) 		0.00184
(1.00) 		0.204
(1.00) 		0.144
(1.00)
del 19q13 43 285 (49%) 294 0.0167
(1.00) 		0.0817
(1.00) 		0.0799
(1.00) 		0.386
(1.00) 		0.00011
(0.102) 		5e-05
(0.0466) 		0.161
(1.00) 		0.488
(1.00) 		0.564
(1.00) 		0.985
(1.00) 		0.518
(1.00) 		0.121
(1.00) 		0.0427
(1.00) 		0.0214
(1.00)
amp 1p34 3 292 (50%) 287 0.431
(1.00) 		0.0813
(1.00) 		0.125
(1.00) 		0.0851
(1.00) 		1e-05
(0.00986) 		0.195
(1.00) 		0.112
(1.00) 		0.388
(1.00) 		0.555
(1.00) 		0.184
(1.00) 		0.0882
(1.00) 		0.163
(1.00) 		0.0743
(1.00) 		0.927
(1.00)
amp 2p23 2 252 (44%) 327 0.326
(1.00) 		0.0135
(1.00) 		0.759
(1.00) 		0.171
(1.00) 		1e-05
(0.00986) 		0.00441
(1.00) 		0.145
(1.00) 		0.213
(1.00) 		0.0317
(1.00) 		0.0202
(1.00) 		0.92
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.671
(1.00)
amp 2q31 2 262 (45%) 317 0.114
(1.00) 		0.173
(1.00) 		0.0341
(1.00) 		0.0298
(1.00) 		1e-05
(0.00986) 		0.00754
(1.00) 		0.0491
(1.00) 		0.321
(1.00) 		0.151
(1.00) 		0.271
(1.00) 		0.286
(1.00) 		0.0869
(1.00) 		0.67
(1.00) 		0.888
(1.00)
amp 3q26 2 485 (84%) 94 0.00906
(1.00) 		0.0255
(1.00) 		0.818
(1.00) 		0.28
(1.00) 		1e-05
(0.00986) 		0.0356
(1.00) 		0.405
(1.00) 		0.28
(1.00) 		0.00703
(1.00) 		0.0114
(1.00) 		0.125
(1.00) 		0.0679
(1.00) 		1
(1.00) 		0.578
(1.00)
amp 4q13 3 113 (20%) 466 0.905
(1.00) 		0.465
(1.00) 		0.387
(1.00) 		0.986
(1.00) 		0.00025
(0.228) 		0.522
(1.00) 		0.617
(1.00) 		0.539
(1.00) 		0.182
(1.00) 		0.484
(1.00) 		0.966
(1.00) 		0.693
(1.00) 		0.323
(1.00) 		0.696
(1.00)
amp 5p15 33 309 (53%) 270 1
(1.00) 		0.0553
(1.00) 		0.626
(1.00) 		0.25
(1.00) 		1e-05
(0.00986) 		0.0972
(1.00) 		0.981
(1.00) 		0.237
(1.00) 		0.243
(1.00) 		0.391
(1.00) 		0.0245
(1.00) 		0.148
(1.00) 		0.231
(1.00) 		0.268
(1.00)
amp 6p22 3 306 (53%) 273 0.176
(1.00) 		0.0301
(1.00) 		0.275
(1.00) 		0.0728
(1.00) 		1e-05
(0.00986) 		0.012
(1.00) 		0.0736
(1.00) 		0.0566
(1.00) 		0.867
(1.00) 		0.213
(1.00) 		0.378
(1.00) 		0.614
(1.00) 		1
(1.00) 		0.254
(1.00)
amp 7q36 3 320 (55%) 259 0.106
(1.00) 		0.178
(1.00) 		0.36
(1.00) 		0.989
(1.00) 		3e-05
(0.0281) 		0.455
(1.00) 		0.0319
(1.00) 		0.201
(1.00) 		0.845
(1.00) 		0.97
(1.00) 		0.211
(1.00) 		0.502
(1.00) 		0.198
(1.00) 		0.263
(1.00)
amp 8p11 21 211 (36%) 368 0.11
(1.00) 		0.352
(1.00) 		0.102
(1.00) 		0.533
(1.00) 		1e-05
(0.00986) 		0.0161
(1.00) 		0.011
(1.00) 		0.42
(1.00) 		0.279
(1.00) 		0.172
(1.00) 		0.769
(1.00) 		0.326
(1.00) 		0.231
(1.00) 		0.858
(1.00)
amp 10p15 3 252 (44%) 327 0.823
(1.00) 		0.102
(1.00) 		0.0536
(1.00) 		0.165
(1.00) 		1e-05
(0.00986) 		0.00043
(0.39) 		0.488
(1.00) 		0.501
(1.00) 		0.242
(1.00) 		0.121
(1.00) 		0.378
(1.00) 		0.0675
(1.00) 		1
(1.00) 		0.608
(1.00)
amp 11q14 1 257 (44%) 322 0.00528
(1.00) 		0.00385
(1.00) 		0.773
(1.00) 		0.31
(1.00) 		1e-05
(0.00986) 		0.00263
(1.00) 		0.38
(1.00) 		0.228
(1.00) 		0.00457
(1.00) 		0.0268
(1.00) 		0.131
(1.00) 		0.923
(1.00) 		0.0427
(1.00) 		0.435
(1.00)
amp 14q32 33 156 (27%) 423 0.437
(1.00) 		0.653
(1.00) 		0.198
(1.00) 		0.0172
(1.00) 		5e-05
(0.0466) 		0.289
(1.00) 		1
(1.00) 		0.203
(1.00) 		0.166
(1.00) 		0.241
(1.00) 		0.373
(1.00) 		0.423
(1.00) 		0.0964
(1.00) 		0.139
(1.00)
amp 15q26 3 163 (28%) 416 0.084
(1.00) 		0.426
(1.00) 		0.507
(1.00) 		0.426
(1.00) 		1e-05
(0.00986) 		0.805
(1.00) 		0.978
(1.00) 		0.18
(1.00) 		0.203
(1.00) 		0.548
(1.00) 		0.155
(1.00) 		0.0648
(1.00) 		0.675
(1.00) 		0.785
(1.00)
amp 18q11 2 143 (25%) 436 0.823
(1.00) 		0.782
(1.00) 		0.953
(1.00) 		0.222
(1.00) 		1e-05
(0.00986) 		0.00386
(1.00) 		0.156
(1.00) 		0.42
(1.00) 		0.0422
(1.00) 		0.0761
(1.00) 		0.148
(1.00) 		0.511
(1.00) 		0.381
(1.00) 		0.093
(1.00)
amp xp11 23 159 (27%) 420 0.664
(1.00) 		0.867
(1.00) 		0.418
(1.00) 		0.632
(1.00) 		1e-05
(0.00986) 		0.00169
(1.00) 		0.718
(1.00) 		0.902
(1.00) 		0.448
(1.00) 		0.929
(1.00) 		0.277
(1.00) 		0.0318
(1.00) 		0.675
(1.00) 		0.634
(1.00)
del 1p36 11 269 (46%) 310 0.738
(1.00) 		0.0687
(1.00) 		0.0294
(1.00) 		0.117
(1.00) 		6e-05
(0.0558) 		0.0889
(1.00) 		0.125
(1.00) 		0.392
(1.00) 		0.852
(1.00) 		0.42
(1.00) 		0.22
(1.00) 		0.171
(1.00) 		0.675
(1.00) 		0.978
(1.00)
del 1q41 97 (17%) 482 0.0884
(1.00) 		0.625
(1.00) 		0.299
(1.00) 		0.837
(1.00) 		1e-05
(0.00986) 		0.135
(1.00) 		0.487
(1.00) 		0.0179
(1.00) 		0.282
(1.00) 		0.246
(1.00) 		0.921
(1.00) 		0.97
(1.00) 		0.455
(1.00)
del 2q37 3 175 (30%) 404 0.0159
(1.00) 		0.464
(1.00) 		0.635
(1.00) 		0.0269
(1.00) 		2e-05
(0.0188) 		0.0882
(1.00) 		0.748
(1.00) 		0.588
(1.00) 		0.014
(1.00) 		0.00236
(1.00) 		0.0229
(1.00) 		0.0192
(1.00) 		0.323
(1.00) 		0.966
(1.00)
del 3p26 2 209 (36%) 370 0.156
(1.00) 		0.00057
(0.515) 		0.00582
(1.00) 		0.00437
(1.00) 		9e-05
(0.0834) 		0.00057
(0.515) 		0.97
(1.00) 		0.24
(1.00) 		0.00293
(1.00) 		0.00982
(1.00) 		0.63
(1.00) 		0.123
(1.00) 		0.415
(1.00) 		0.94
(1.00)
del 5q13 2 419 (72%) 160 0.747
(1.00) 		0.623
(1.00) 		0.9
(1.00) 		0.257
(1.00) 		1e-05
(0.00986) 		0.104
(1.00) 		0.791
(1.00) 		0.831
(1.00) 		0.517
(1.00) 		0.0924
(1.00) 		0.155
(1.00) 		0.107
(1.00) 		1
(1.00) 		0.723
(1.00)
del 7p22 1 253 (44%) 326 0.394
(1.00) 		0.514
(1.00) 		0.771
(1.00) 		0.0614
(1.00) 		1e-05
(0.00986) 		0.626
(1.00) 		0.818
(1.00) 		0.602
(1.00) 		0.347
(1.00) 		0.127
(1.00) 		0.349
(1.00) 		0.905
(1.00) 		0.231
(1.00) 		0.784
(1.00)
del 8p23 3 388 (67%) 191 0.0448
(1.00) 		0.152
(1.00) 		0.572
(1.00) 		0.0115
(1.00) 		1e-05
(0.00986) 		0.0515
(1.00) 		0.892
(1.00) 		0.449
(1.00) 		0.895
(1.00) 		0.912
(1.00) 		0.247
(1.00) 		0.249
(1.00) 		1
(1.00)
del 8p21 2 406 (70%) 173 0.0425
(1.00) 		0.0919
(1.00) 		0.183
(1.00) 		0.00522
(1.00) 		1e-05
(0.00986) 		0.147
(1.00) 		0.875
(1.00) 		0.994
(1.00) 		0.458
(1.00) 		0.701
(1.00) 		0.58
(1.00) 		0.518
(1.00) 		1
(1.00)
del 9q34 13 342 (59%) 237 0.017
(1.00) 		0.00089
(0.797) 		0.698
(1.00) 		0.41
(1.00) 		1e-05
(0.00986) 		0.0183
(1.00) 		0.675
(1.00) 		0.163
(1.00) 		0.0774
(1.00) 		0.0806
(1.00) 		0.0503
(1.00) 		0.1
(1.00) 		1
(1.00) 		0.793
(1.00)
del 10q24 2 251 (43%) 328 0.00318
(1.00) 		0.00276
(1.00) 		0.0073
(1.00) 		0.236
(1.00) 		9e-05
(0.0834) 		0.00196
(1.00) 		0.0162
(1.00) 		0.00243
(1.00) 		0.532
(1.00) 		0.365
(1.00) 		0.00187
(1.00) 		0.368
(1.00) 		1
(1.00) 		0.784
(1.00)
del 11p15 5 346 (60%) 233 0.111
(1.00) 		0.971
(1.00) 		0.619
(1.00) 		0.0855
(1.00) 		1e-05
(0.00986) 		0.00758
(1.00) 		0.946
(1.00) 		0.711
(1.00) 		0.7
(1.00) 		0.506
(1.00) 		0.106
(1.00) 		0.00864
(1.00) 		0.204
(1.00) 		0.927
(1.00)
del 12q24 33 220 (38%) 359 0.00112
(1.00) 		0.0992
(1.00) 		0.163
(1.00) 		0.0146
(1.00) 		1e-05
(0.00986) 		0.0198
(1.00) 		0.292
(1.00) 		0.224
(1.00) 		0.0503
(1.00) 		0.0321
(1.00) 		0.0155
(1.00) 		0.00464
(1.00) 		0.646
(1.00) 		1
(1.00)
del 14q23 3 305 (53%) 274 0.0656
(1.00) 		0.506
(1.00) 		0.651
(1.00) 		0.609
(1.00) 		6e-05
(0.0558) 		0.737
(1.00) 		0.23
(1.00) 		0.508
(1.00) 		0.856
(1.00) 		0.282
(1.00) 		0.9
(1.00) 		0.595
(1.00) 		0.666
(1.00) 		0.14
(1.00)
del 16q23 1 452 (78%) 127 0.108
(1.00) 		0.243
(1.00) 		0.103
(1.00) 		0.0606
(1.00) 		0.00015
(0.138) 		0.538
(1.00) 		0.812
(1.00) 		0.227
(1.00) 		0.274
(1.00) 		0.169
(1.00) 		0.0568
(1.00) 		0.0484
(1.00) 		1
(1.00) 		0.902
(1.00)
del 19q13 33 299 (52%) 280 0.00023
(0.21) 		0.00229
(1.00) 		0.0457
(1.00) 		0.0199
(1.00) 		0.0143
(1.00) 		0.00278
(1.00) 		0.0289
(1.00) 		0.301
(1.00) 		0.00628
(1.00) 		0.123
(1.00) 		0.321
(1.00) 		0.13
(1.00) 		0.391
(1.00) 		0.112
(1.00)
amp 4p16 3 160 (28%) 419 1
(1.00) 		0.32
(1.00) 		0.0293
(1.00) 		0.479
(1.00) 		0.00042
(0.381) 		0.0277
(1.00) 		0.27
(1.00) 		0.688
(1.00) 		0.687
(1.00) 		0.983
(1.00) 		0.629
(1.00) 		0.0187
(1.00) 		0.652
(1.00) 		0.579
(1.00)
amp 10q22 3 184 (32%) 395 0.371
(1.00) 		0.265
(1.00) 		0.608
(1.00) 		0.949
(1.00) 		0.0788
(1.00) 		0.843
(1.00) 		0.772
(1.00) 		0.82
(1.00) 		0.342
(1.00) 		0.898
(1.00) 		0.228
(1.00) 		0.648
(1.00) 		0.67
(1.00) 		0.303
(1.00)
amp 14q11 2 148 (26%) 431 0.0168
(1.00) 		0.0592
(1.00) 		0.29
(1.00) 		0.00669
(1.00) 		0.0687
(1.00) 		0.193
(1.00) 		0.532
(1.00) 		0.47
(1.00) 		0.34
(1.00) 		0.411
(1.00) 		0.3
(1.00) 		0.822
(1.00) 		0.323
(1.00) 		0.277
(1.00)
amp 17q25 3 215 (37%) 364 0.468
(1.00) 		0.0561
(1.00) 		0.982
(1.00) 		0.665
(1.00) 		0.00382
(1.00) 		0.774
(1.00) 		0.0727
(1.00) 		0.128
(1.00) 		0.0119
(1.00) 		0.0259
(1.00) 		0.326
(1.00) 		0.129
(1.00) 		1
(1.00) 		0.709
(1.00)
amp 22q12 2 91 (16%) 488 0.623
(1.00) 		0.157
(1.00) 		0.0698
(1.00) 		0.0359
(1.00) 		0.00762
(1.00) 		0.00061
(0.55) 		0.983
(1.00) 		0.0911
(1.00) 		0.0591
(1.00) 		0.0595
(1.00) 		0.108
(1.00) 		0.0144
(1.00) 		1
(1.00) 		0.0865
(1.00)
amp xq28 220 (38%) 359 0.245
(1.00) 		0.848
(1.00) 		0.555
(1.00) 		0.123
(1.00) 		0.00047
(0.425) 		0.178
(1.00) 		0.456
(1.00) 		0.444
(1.00) 		0.627
(1.00) 		0.939
(1.00) 		0.878
(1.00) 		0.802
(1.00) 		0.0427
(1.00) 		0.624
(1.00)
del 2p25 3 120 (21%) 459 0.881
(1.00) 		0.267
(1.00) 		0.422
(1.00) 		0.159
(1.00) 		0.401
(1.00) 		0.638
(1.00) 		0.261
(1.00) 		0.542
(1.00) 		0.0632
(1.00) 		0.239
(1.00) 		0.876
(1.00) 		0.95
(1.00) 		0.381
(1.00) 		0.426
(1.00)
del 2q22 1 137 (24%) 442 0.106
(1.00) 		0.273
(1.00) 		0.568
(1.00) 		0.00388
(1.00) 		0.0767
(1.00) 		0.665
(1.00) 		0.604
(1.00) 		0.719
(1.00) 		0.919
(1.00) 		0.301
(1.00) 		0.479
(1.00) 		0.603
(1.00) 		1
(1.00) 		0.266
(1.00)
del 3q13 31 84 (15%) 495 0.328
(1.00) 		0.227
(1.00) 		0.568
(1.00) 		0.626
(1.00) 		0.11
(1.00) 		0.0825
(1.00) 		0.25
(1.00) 		0.453
(1.00) 		0.407
(1.00) 		0.396
(1.00) 		0.519
(1.00) 		0.523
(1.00) 		1
(1.00)
del 4q22 1 394 (68%) 185 0.0535
(1.00) 		0.0237
(1.00) 		1
(1.00) 		0.166
(1.00) 		0.0155
(1.00) 		0.225
(1.00) 		0.191
(1.00) 		0.0615
(1.00) 		0.071
(1.00) 		0.388
(1.00) 		0.303
(1.00) 		0.255
(1.00) 		0.675
(1.00) 		0.413
(1.00)
del 4q34 3 421 (73%) 158 0.0533
(1.00) 		0.00075
(0.674) 		0.0626
(1.00) 		0.0281
(1.00) 		0.184
(1.00) 		0.58
(1.00) 		0.669
(1.00) 		0.199
(1.00) 		0.0839
(1.00) 		0.0193
(1.00) 		0.42
(1.00) 		0.53
(1.00) 		1
(1.00) 		0.56
(1.00)
del 10p15 3 120 (21%) 459 0.179
(1.00) 		0.709
(1.00) 		0.087
(1.00) 		0.319
(1.00) 		0.0972
(1.00) 		0.351
(1.00) 		0.29
(1.00) 		0.0409
(1.00) 		0.0143
(1.00) 		0.0889
(1.00) 		0.253
(1.00) 		0.266
(1.00) 		0.594
(1.00) 		0.105
(1.00)
del 11q25 201 (35%) 378 0.623
(1.00) 		0.652
(1.00) 		0.209
(1.00) 		0.0532
(1.00) 		0.273
(1.00) 		0.417
(1.00) 		0.322
(1.00) 		0.267
(1.00) 		0.931
(1.00) 		0.454
(1.00) 		0.708
(1.00) 		0.274
(1.00) 		1
(1.00) 		0.768
(1.00)
del 16p13 3 313 (54%) 266 0.602
(1.00) 		0.0718
(1.00) 		0.274
(1.00) 		0.0295
(1.00) 		0.108
(1.00) 		0.419
(1.00) 		0.84
(1.00) 		0.821
(1.00) 		0.37
(1.00) 		0.426
(1.00) 		0.224
(1.00) 		0.485
(1.00) 		0.675
(1.00) 		0.787
(1.00)
del 16q22 1 461 (80%) 118 0.499
(1.00) 		0.706
(1.00) 		0.0319
(1.00) 		0.449
(1.00) 		0.00089
(0.797) 		0.64
(1.00) 		0.694
(1.00) 		0.143
(1.00) 		0.221
(1.00) 		0.285
(1.00) 		0.313
(1.00) 		0.0482
(1.00) 		1
(1.00) 		0.385
(1.00)
del 17p12 491 (85%) 88 0.143
(1.00) 		0.336
(1.00) 		0.595
(1.00) 		0.69
(1.00) 		0.709
(1.00) 		0.322
(1.00) 		0.907
(1.00) 		0.371
(1.00) 		0.154
(1.00) 		0.194
(1.00) 		0.504
(1.00) 		0.21
(1.00) 		1
(1.00)
del 17q11 2 472 (82%) 107 0.921
(1.00) 		0.19
(1.00) 		0.734
(1.00) 		0.217
(1.00) 		0.00072
(0.648) 		0.00276
(1.00) 		0.767
(1.00) 		0.0359
(1.00) 		0.373
(1.00) 		0.439
(1.00) 		0.151
(1.00) 		0.164
(1.00) 		1
(1.00) 		0.339
(1.00)
del 18q23 381 (66%) 198 0.883
(1.00) 		0.854
(1.00) 		0.369
(1.00) 		0.957
(1.00) 		0.00275
(1.00) 		0.587
(1.00) 		0.48
(1.00) 		0.185
(1.00) 		0.152
(1.00) 		0.362
(1.00) 		0.66
(1.00) 		0.492
(1.00) 		0.646
(1.00) 		0.794
(1.00)
del 19p13 3 512 (88%) 67 0.158
(1.00) 		0.091
(1.00) 		0.839
(1.00) 		0.547
(1.00) 		0.00034
(0.309) 		0.0181
(1.00) 		0.622
(1.00) 		0.405
(1.00) 		0.335
(1.00) 		0.517
(1.00) 		0.477
(1.00) 		0.732
(1.00) 		1
(1.00)
del 21q22 3 227 (39%) 352 0.371
(1.00) 		0.0417
(1.00) 		0.693
(1.00) 		0.205
(1.00) 		0.795
(1.00) 		0.263
(1.00) 		0.659
(1.00) 		0.714
(1.00) 		0.246
(1.00) 		0.127
(1.00) 		0.82
(1.00) 		0.727
(1.00) 		0.162
(1.00) 		0.928
(1.00)
del 22q13 32 503 (87%) 76 0.209
(1.00) 		0.123
(1.00) 		0.0352
(1.00) 		0.285
(1.00) 		0.0175
(1.00) 		0.159
(1.00) 		0.122
(1.00) 		0.0447
(1.00) 		0.169
(1.00) 		0.0136
(1.00) 		0.0366
(1.00) 		0.577
(1.00)
del xp21 1 355 (61%) 224 0.405
(1.00) 		0.644
(1.00) 		0.0998
(1.00) 		0.8
(1.00) 		0.167
(1.00) 		0.0203
(1.00) 		0.461
(1.00) 		0.108
(1.00) 		0.885
(1.00) 		0.238
(1.00) 		0.976
(1.00) 		0.716
(1.00) 		0.594
(1.00) 		0.282
(1.00)
'amp_1p34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 1(1P34.3) MUTATED 58 114 120
AMP PEAK 1(1P34.3) WILD-TYPE 113 92 82

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 = 0.0099

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 2(1Q21.3) MUTATED 86 114 167
AMP PEAK 2(1Q21.3) WILD-TYPE 85 92 35

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.2

Table S3.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 2(1Q21.3) MUTATED 128 92 141
AMP PEAK 2(1Q21.3) WILD-TYPE 44 83 80

Figure S3.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q42.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S4.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 3(1Q42.2) MUTATED 88 87 147
AMP PEAK 3(1Q42.2) WILD-TYPE 83 119 55

Figure S4.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q42.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.083

Table S5.  Gene #3: 'amp_1q42.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 3(1Q42.2) MUTATED 119 87 108
AMP PEAK 3(1Q42.2) WILD-TYPE 53 88 113

Figure S5.  Get High-res Image Gene #3: 'amp_1q42.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_2p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S6.  Gene #4: 'amp_2p23.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 4(2P23.2) MUTATED 47 87 118
AMP PEAK 4(2P23.2) WILD-TYPE 124 119 84

Figure S6.  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 = 0.0099

Table S7.  Gene #5: 'amp_2q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 5(2Q31.2) MUTATED 46 102 114
AMP PEAK 5(2Q31.2) WILD-TYPE 125 104 88

Figure S7.  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 = 0.0099

Table S8.  Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 6(3Q26.2) MUTATED 113 181 191
AMP PEAK 6(3Q26.2) WILD-TYPE 58 25 11

Figure S8.  Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4q13.3' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.23

Table S9.  Gene #8: 'amp_4q13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 8(4Q13.3) MUTATED 17 54 42
AMP PEAK 8(4Q13.3) WILD-TYPE 154 152 160

Figure S9.  Get High-res Image Gene #8: 'amp_4q13.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S10.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 9(5P15.33) MUTATED 60 123 126
AMP PEAK 9(5P15.33) WILD-TYPE 111 83 76

Figure S10.  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 = 0.0099

Table S11.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 10(6P22.3) MUTATED 59 124 123
AMP PEAK 10(6P22.3) WILD-TYPE 112 82 79

Figure S11.  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 = 0.028

Table S12.  Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 11(7Q36.3) MUTATED 69 124 127
AMP PEAK 11(7Q36.3) WILD-TYPE 102 82 75

Figure S12.  Get High-res Image Gene #11: 'amp_7q36.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S13.  Gene #12: 'amp_8p11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 12(8P11.21) MUTATED 42 70 99
AMP PEAK 12(8P11.21) WILD-TYPE 129 136 103

Figure S13.  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 = 0.0099

Table S14.  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 S14.  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 = 0.0099

Table S15.  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 S15.  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 = 0.0099

Table S16.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 13(8Q24.21) MUTATED 113 200 148
AMP PEAK 13(8Q24.21) WILD-TYPE 58 6 54

Figure S16.  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 = 0.0099

Table S17.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: '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 S17.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S18.  Gene #14: 'amp_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 14(10P15.3) MUTATED 45 81 126
AMP PEAK 14(10P15.3) WILD-TYPE 126 125 76

Figure S18.  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 = 0.0099

Table S19.  Gene #16: 'amp_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 16(11Q14.1) MUTATED 54 117 86
AMP PEAK 16(11Q14.1) WILD-TYPE 117 89 116

Figure S19.  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 = 0.0099

Table S20.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 17(12P13.33) MUTATED 71 111 148
AMP PEAK 17(12P13.33) WILD-TYPE 100 95 54

Figure S20.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.13

Table S21.  Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 17(12P13.33) MUTATED 119 96 108
AMP PEAK 17(12P13.33) WILD-TYPE 53 79 113

Figure S21.  Get High-res Image Gene #17: 'amp_12p13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S22.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 18(12P12.1) MUTATED 66 98 149
AMP PEAK 18(12P12.1) WILD-TYPE 105 108 53

Figure S22.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.028

Table S23.  Gene #18: 'amp_12p12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 18(12P12.1) MUTATED 117 87 102
AMP PEAK 18(12P12.1) WILD-TYPE 55 88 119

Figure S23.  Get High-res Image Gene #18: 'amp_12p12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S24.  Gene #19: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 19(12Q15) MUTATED 52 58 112
AMP PEAK 19(12Q15) WILD-TYPE 119 148 90

Figure S24.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S25.  Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 19(12Q15) MUTATED 90 62 65
AMP PEAK 19(12Q15) WILD-TYPE 82 113 156

Figure S25.  Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_14q32.33' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.047

Table S26.  Gene #21: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 21(14Q32.33) MUTATED 41 77 38
AMP PEAK 21(14Q32.33) WILD-TYPE 130 129 164

Figure S26.  Get High-res Image Gene #21: '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 = 0.0099

Table S27.  Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 22(15Q26.3) MUTATED 34 90 39
AMP PEAK 22(15Q26.3) WILD-TYPE 137 116 163

Figure S27.  Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S28.  Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 24(18Q11.2) MUTATED 25 44 74
AMP PEAK 24(18Q11.2) WILD-TYPE 146 162 128

Figure S28.  Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.17

Table S29.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
AMP PEAK 25(19P13.12) MUTATED 136 115 51
AMP PEAK 25(19P13.12) WILD-TYPE 79 101 75

Figure S29.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.23

Table S30.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
AMP PEAK 25(19P13.12) MUTATED 186 64 52
AMP PEAK 25(19P13.12) WILD-TYPE 124 94 37

Figure S30.  Get High-res Image Gene #25: '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 = 0.0099

Table S31.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 25(19P13.12) MUTATED 72 92 151
AMP PEAK 25(19P13.12) WILD-TYPE 99 114 51

Figure S31.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S32.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 25(19P13.12) MUTATED 118 73 116
AMP PEAK 25(19P13.12) WILD-TYPE 54 102 105

Figure S32.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.092

Table S33.  Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 116 96 128 58
AMP PEAK 25(19P13.12) MUTATED 44 55 86 31
AMP PEAK 25(19P13.12) WILD-TYPE 72 41 42 27

Figure S33.  Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S34.  Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 26(19Q12) MUTATED 67 83 172
AMP PEAK 26(19Q12) WILD-TYPE 104 123 30

Figure S34.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S35.  Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 26(19Q12) MUTATED 128 70 121
AMP PEAK 26(19Q12) WILD-TYPE 44 105 100

Figure S35.  Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S36.  Gene #27: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 27(19Q13.2) MUTATED 51 71 123
AMP PEAK 27(19Q13.2) WILD-TYPE 120 135 79

Figure S36.  Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q13.2' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.1

Table S37.  Gene #27: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 27(19Q13.2) MUTATED 94 56 91
AMP PEAK 27(19Q13.2) WILD-TYPE 78 119 130

Figure S37.  Get High-res Image Gene #27: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S38.  Gene #28: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 28(20P13) MUTATED 69 97 151
AMP PEAK 28(20P13) WILD-TYPE 102 109 51

Figure S38.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S39.  Gene #28: 'amp_20p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 28(20P13) MUTATED 123 81 103
AMP PEAK 28(20P13) WILD-TYPE 49 94 118

Figure S39.  Get High-res Image Gene #28: 'amp_20p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S40.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 29(20Q11.21) MUTATED 79 95 174
AMP PEAK 29(20Q11.21) WILD-TYPE 92 111 28

Figure S40.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S41.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 29(20Q11.21) MUTATED 140 91 109
AMP PEAK 29(20Q11.21) WILD-TYPE 32 84 112

Figure S41.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.17

Table S42.  Gene #29: 'amp_20q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 67 91
AMP PEAK 29(20Q11.21) MUTATED 63 28 67
AMP PEAK 29(20Q11.21) WILD-TYPE 37 39 24

Figure S42.  Get High-res Image Gene #29: 'amp_20q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S43.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 30(20Q13.33) MUTATED 87 132 183
AMP PEAK 30(20Q13.33) WILD-TYPE 84 74 19

Figure S43.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S44.  Gene #30: 'amp_20q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
AMP PEAK 30(20Q13.33) MUTATED 144 109 140
AMP PEAK 30(20Q13.33) WILD-TYPE 28 66 81

Figure S44.  Get High-res Image Gene #30: 'amp_20q13.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_xp11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S45.  Gene #32: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
AMP PEAK 32(XP11.23) MUTATED 25 55 79
AMP PEAK 32(XP11.23) WILD-TYPE 146 151 123

Figure S45.  Get High-res Image Gene #32: 'amp_xp11.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.056

Table S46.  Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 1(1P36.11) MUTATED 87 113 69
DEL PEAK 1(1P36.11) WILD-TYPE 84 93 133

Figure S46.  Get High-res Image Gene #34: 'del_1p36.11' versus Molecular Subtype #5: 'CN_CNMF'

'del_1q41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S47.  Gene #35: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 2(1Q41) MUTATED 14 60 23
DEL PEAK 2(1Q41) WILD-TYPE 157 146 179

Figure S47.  Get High-res Image Gene #35: 'del_1q41' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q37.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S48.  Gene #38: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 5(2Q37.3) MUTATED 35 86 54
DEL PEAK 5(2Q37.3) WILD-TYPE 136 120 148

Figure S48.  Get High-res Image Gene #38: 'del_2q37.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_3p26.2' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.083

Table S49.  Gene #39: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 6(3P26.2) MUTATED 47 66 96
DEL PEAK 6(3P26.2) WILD-TYPE 124 140 106

Figure S49.  Get High-res Image Gene #39: 'del_3p26.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S50.  Gene #43: 'del_5q12.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 10(5Q12.1) MUTATED 73 145 137
DEL PEAK 10(5Q12.1) WILD-TYPE 98 61 65

Figure S50.  Get High-res Image Gene #43: 'del_5q12.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.18

Table S51.  Gene #43: 'del_5q12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 10(5Q12.1) MUTATED 117 85 146
DEL PEAK 10(5Q12.1) WILD-TYPE 55 90 75

Figure S51.  Get High-res Image Gene #43: 'del_5q12.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S52.  Gene #44: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 11(5Q13.2) MUTATED 92 180 147
DEL PEAK 11(5Q13.2) WILD-TYPE 79 26 55

Figure S52.  Get High-res Image Gene #44: 'del_5q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S53.  Gene #45: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 12(6Q27) MUTATED 121 162 97
DEL PEAK 12(6Q27) WILD-TYPE 50 44 105

Figure S53.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.037

Table S54.  Gene #45: 'del_6q27' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 12(6Q27) MUTATED 91 132 152
DEL PEAK 12(6Q27) WILD-TYPE 81 43 69

Figure S54.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6q27' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S55.  Gene #45: 'del_6q27' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 67 91
DEL PEAK 12(6Q27) MUTATED 66 52 38
DEL PEAK 12(6Q27) WILD-TYPE 34 15 53

Figure S55.  Get High-res Image Gene #45: 'del_6q27' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S56.  Gene #46: 'del_7p22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 13(7P22.1) MUTATED 48 135 70
DEL PEAK 13(7P22.1) WILD-TYPE 123 71 132

Figure S56.  Get High-res Image Gene #46: '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 = 0.0099

Table S57.  Gene #47: 'del_8p23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 14(8P23.3) MUTATED 78 162 148
DEL PEAK 14(8P23.3) WILD-TYPE 93 44 54

Figure S57.  Get High-res Image Gene #47: '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 = 0.0099

Table S58.  Gene #48: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 15(8P21.2) MUTATED 88 166 152
DEL PEAK 15(8P21.2) WILD-TYPE 83 40 50

Figure S58.  Get High-res Image Gene #48: 'del_8p21.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p24.3' versus 'MRNA_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.24

Table S59.  Gene #49: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 16(9P24.3) MUTATED 109 73 66
DEL PEAK 16(9P24.3) WILD-TYPE 106 143 60

Figure S59.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p24.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S60.  Gene #49: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
DEL PEAK 16(9P24.3) MUTATED 120 69 59
DEL PEAK 16(9P24.3) WILD-TYPE 190 89 30

Figure S60.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p24.3' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.065

Table S61.  Gene #49: 'del_9p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 16(9P24.3) MUTATED 92 90 75
DEL PEAK 16(9P24.3) WILD-TYPE 80 85 146

Figure S61.  Get High-res Image Gene #49: 'del_9p24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_9q34.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S62.  Gene #50: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 17(9Q34.13) MUTATED 93 98 151
DEL PEAK 17(9Q34.13) WILD-TYPE 78 108 51

Figure S62.  Get High-res Image Gene #50: 'del_9q34.13' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q24.2' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.083

Table S63.  Gene #52: 'del_10q24.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 19(10Q24.2) MUTATED 53 111 87
DEL PEAK 19(10Q24.2) WILD-TYPE 118 95 115

Figure S63.  Get High-res Image Gene #52: '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 = 0.0099

Table S64.  Gene #53: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 20(11P15.5) MUTATED 77 163 106
DEL PEAK 20(11P15.5) WILD-TYPE 94 43 96

Figure S64.  Get High-res Image Gene #53: '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 = 0.0099

Table S65.  Gene #55: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 22(12Q24.33) MUTATED 56 113 51
DEL PEAK 22(12Q24.33) WILD-TYPE 115 93 151

Figure S65.  Get High-res Image Gene #55: 'del_12q24.33' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.22

Table S66.  Gene #56: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 23(13Q14.2) MUTATED 90 150 124
DEL PEAK 23(13Q14.2) WILD-TYPE 81 56 78

Figure S66.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S67.  Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 23(13Q14.2) MUTATED 109 88 161
DEL PEAK 23(13Q14.2) WILD-TYPE 63 87 60

Figure S67.  Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.056

Table S68.  Gene #57: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 24(14Q23.3) MUTATED 70 104 131
DEL PEAK 24(14Q23.3) WILD-TYPE 101 102 71

Figure S68.  Get High-res Image Gene #57: 'del_14q23.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S69.  Gene #58: 'del_15q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 25(15Q11.2) MUTATED 68 76 155
DEL PEAK 25(15Q11.2) WILD-TYPE 103 130 47

Figure S69.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.028

Table S70.  Gene #58: 'del_15q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 25(15Q11.2) MUTATED 114 82 100
DEL PEAK 25(15Q11.2) WILD-TYPE 58 93 121

Figure S70.  Get High-res Image Gene #58: 'del_15q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S71.  Gene #59: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 26(15Q15.1) MUTATED 81 115 167
DEL PEAK 26(15Q15.1) WILD-TYPE 90 91 35

Figure S71.  Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0099

Table S72.  Gene #59: 'del_15q15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 26(15Q15.1) MUTATED 134 97 129
DEL PEAK 26(15Q15.1) WILD-TYPE 38 78 92

Figure S72.  Get High-res Image Gene #59: 'del_15q15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.14

Table S73.  Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 29(16Q23.1) MUTATED 114 168 170
DEL PEAK 29(16Q23.1) WILD-TYPE 57 38 32

Figure S73.  Get High-res Image Gene #62: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.33' versus 'MRNA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.21

Table S74.  Gene #67: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
DEL PEAK 34(19Q13.33) MUTATED 127 117 46
DEL PEAK 34(19Q13.33) WILD-TYPE 88 99 80

Figure S74.  Get High-res Image Gene #67: 'del_19q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.43' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.1

Table S75.  Gene #68: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
DEL PEAK 35(19Q13.43) MUTATED 84 80 121
DEL PEAK 35(19Q13.43) WILD-TYPE 87 126 81

Figure S75.  Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.047

Table S76.  Gene #68: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
DEL PEAK 35(19Q13.43) MUTATED 105 64 111
DEL PEAK 35(19Q13.43) WILD-TYPE 67 111 110

Figure S76.  Get High-res Image Gene #68: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 579

  • Number of significantly focal cnvs = 71

  • Number of molecular subtypes = 14

  • 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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