Correlation between copy number variation genes (focal events) and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1348J4T
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1348J4T
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 10 molecular subtypes across 571 patients, 117 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p36.21 cnv correlated to 'CN_CNMF'.

  • amp_1q32.1 cnv correlated to 'CN_CNMF'.

  • amp_1q44 cnv correlated to 'CN_CNMF'.

  • amp_3q26.33 cnv correlated to 'CN_CNMF'.

  • amp_4q12 cnv correlated to 'CN_CNMF'.

  • amp_7p11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_7q11.21 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_7q21.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • amp_7q31.2 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

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

  • amp_12p13.32 cnv correlated to 'CN_CNMF'.

  • amp_12q14.1 cnv correlated to 'CN_CNMF'.

  • amp_12q15 cnv correlated to 'CN_CNMF'.

  • amp_17q25.1 cnv correlated to 'CN_CNMF'.

  • amp_19p13.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • amp_19p13.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • amp_19q12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • amp_21q21.1 cnv correlated to 'CN_CNMF'.

  • del_1p36.23 cnv correlated to 'CN_CNMF'.

  • del_2q22.1 cnv correlated to 'CN_CNMF'.

  • del_3q13.31 cnv correlated to 'CN_CNMF'.

  • del_4q34.3 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • del_5q35.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF', and 'CN_CNMF'.

  • del_6q22.31 cnv correlated to 'CN_CNMF'.

  • del_6q26 cnv correlated to 'CN_CNMF'.

  • del_9p21.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • del_10p15.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_10p13 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

  • del_10p11.23 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • del_10q23.31 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • del_10q26.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • del_11p15.5 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • del_11p11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • del_11q14.1 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • del_12q12 cnv correlated to 'CN_CNMF'.

  • del_12q15 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • del_13q14.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • del_14q13.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • del_14q24.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • del_15q14 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL', and 'CN_CNMF'.

  • del_17p13.2 cnv correlated to 'CN_CNMF'.

  • del_17p13.1 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • del_17q11.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • del_18q22.3 cnv correlated to 'CN_CNMF'.

  • del_19q13.41 cnv correlated to 'MRNA_CHIERARCHICAL'.

  • del_21q22.11 cnv correlated to 'MRNA_CHIERARCHICAL'.

  • del_22q13.32 cnv correlated to 'CN_CNMF'.

  • del_xp22.2 cnv correlated to 'CN_CNMF'.

  • del_xq23 cnv correlated to 'CN_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 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 117 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
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
amp 7p11 2 502 (88%) 69 1e-05
(0.0071) 		1e-05
(0.0071) 		1e-05
(0.0071) 		1e-05
(0.0071) 		1e-05
(0.0071) 		1e-05
(0.0071) 		2e-05
(0.0128) 		8e-05
(0.0489) 		2e-05
(0.0128) 		1e-05
(0.0071)
amp 7q11 21 459 (80%) 112 3e-05
(0.0188) 		1e-05
(0.0071) 		4e-05
(0.0248) 		3e-05
(0.0188) 		1e-05
(0.0071) 		0.0006
(0.354) 		0.00443
(1.00) 		0.00216
(1.00) 		0.00381
(1.00) 		4e-05
(0.0248)
amp 7q21 2 475 (83%) 96 5e-05
(0.0308) 		1e-05
(0.0071) 		0.049
(1.00) 		0.00015
(0.0907) 		1e-05
(0.0071) 		0.00025
(0.149) 		0.0182
(1.00) 		0.0443
(1.00) 		0.0607
(1.00) 		0.00265
(1.00)
del 10p13 466 (82%) 105 1e-05
(0.0071) 		1e-05
(0.0071) 		0.0023
(1.00) 		0.00119
(0.688) 		1e-05
(0.0071) 		0.0285
(1.00) 		0.00015
(0.0907) 		0.00014
(0.0848) 		0.0889
(1.00) 		0.00314
(1.00)
del 10p11 23 471 (82%) 100 1e-05
(0.0071) 		1e-05
(0.0071) 		0.00013
(0.0789) 		1e-05
(0.0071) 		1e-05
(0.0071) 		0.0111
(1.00) 		0.00082
(0.477) 		0.00391
(1.00) 		0.0459
(1.00) 		0.00121
(0.697)
amp 19p13 3 242 (42%) 329 1e-05
(0.0071) 		1e-05
(0.0071) 		0.0375
(1.00) 		0.00157
(0.896) 		1e-05
(0.0071) 		0.00076
(0.445) 		0.00944
(1.00) 		6e-05
(0.0367) 		0.821
(1.00) 		0.971
(1.00)
amp 19p13 2 247 (43%) 324 1e-05
(0.0071) 		1e-05
(0.0071) 		0.149
(1.00) 		0.00111
(0.644) 		1e-05
(0.0071) 		0.00076
(0.445) 		0.013
(1.00) 		0.00011
(0.067) 		0.165
(1.00) 		0.812
(1.00)
del 5q35 3 53 (9%) 518 5e-05
(0.0308) 		1e-05
(0.0071) 		0.00024
(0.144) 		0.0134
(1.00) 		1e-05
(0.0071) 		0.00336
(1.00) 		0.842
(1.00) 		0.545
(1.00) 		0.211
(1.00) 		0.187
(1.00)
del 10p15 3 465 (81%) 106 1e-05
(0.0071) 		1e-05
(0.0071) 		0.00853
(1.00) 		0.00384
(1.00) 		1e-05
(0.0071) 		0.0659
(1.00) 		0.00549
(1.00) 		0.00216
(1.00) 		0.0139
(1.00) 		0.00015
(0.0907)
del 15q14 150 (26%) 421 4e-05
(0.0248) 		2e-05
(0.0128) 		0.00127
(0.729) 		5e-05
(0.0308) 		1e-05
(0.0071) 		0.00924
(1.00) 		0.0574
(1.00) 		0.0492
(1.00) 		0.00102
(0.593) 		0.0169
(1.00)
amp 8q24 21 70 (12%) 501 1e-05
(0.0071) 		2e-05
(0.0128) 		0.0253
(1.00) 		0.29
(1.00) 		1e-05
(0.0071) 		0.0267
(1.00) 		0.334
(1.00) 		0.29
(1.00) 		0.0866
(1.00) 		0.268
(1.00)
amp 19q12 213 (37%) 358 1e-05
(0.0071) 		1e-05
(0.0071) 		0.282
(1.00) 		0.00486
(1.00) 		1e-05
(0.0071) 		0.0568
(1.00) 		0.00919
(1.00) 		0.00051
(0.302) 		0.0632
(1.00) 		0.172
(1.00)
del 9p21 3 416 (73%) 155 2e-05
(0.0128) 		1e-05
(0.0071) 		0.698
(1.00) 		0.0359
(1.00) 		1e-05
(0.0071) 		0.0553
(1.00) 		0.138
(1.00) 		0.0159
(1.00) 		0.0281
(1.00) 		0.00823
(1.00)
del 10q23 31 508 (89%) 63 1e-05
(0.0071) 		1e-05
(0.0071) 		0.0119
(1.00) 		0.00328
(1.00) 		1e-05
(0.0071) 		0.106
(1.00) 		0.0105
(1.00) 		0.0679
(1.00) 		0.369
(1.00) 		0.0423
(1.00)
del 10q26 3 509 (89%) 62 1e-05
(0.0071) 		5e-05
(0.0308) 		0.0424
(1.00) 		0.0012
(0.692) 		1e-05
(0.0071) 		0.00556
(1.00) 		0.117
(1.00) 		0.0441
(1.00) 		0.251
(1.00) 		0.0342
(1.00)
del 11p15 5 127 (22%) 444 1e-05
(0.0071) 		1e-05
(0.0071) 		0.161
(1.00) 		0.00178
(1.00) 		1e-05
(0.0071) 		0.0192
(1.00) 		0.168
(1.00) 		0.0451
(1.00) 		0.0029
(1.00) 		0.00142
(0.814)
del 11p11 2 103 (18%) 468 1e-05
(0.0071) 		1e-05
(0.0071) 		0.505
(1.00) 		0.0184
(1.00) 		1e-05
(0.0071) 		0.103
(1.00) 		0.933
(1.00) 		0.662
(1.00) 		0.0931
(1.00) 		0.0868
(1.00)
del 13q14 2 237 (42%) 334 1e-05
(0.0071) 		2e-05
(0.0128) 		0.353
(1.00) 		0.146
(1.00) 		1e-05
(0.0071) 		0.00663
(1.00) 		0.853
(1.00) 		0.114
(1.00) 		0.0796
(1.00) 		0.0683
(1.00)
del 14q13 1 176 (31%) 395 3e-05
(0.0188) 		0.00017
(0.102) 		0.613
(1.00) 		0.665
(1.00) 		1e-05
(0.0071) 		0.243
(1.00) 		0.62
(1.00) 		0.206
(1.00) 		0.45
(1.00) 		0.943
(1.00)
del 14q24 2 172 (30%) 399 1e-05
(0.0071) 		2e-05
(0.0128) 		0.0576
(1.00) 		0.154
(1.00) 		1e-05
(0.0071) 		0.0346
(1.00) 		0.555
(1.00) 		0.0591
(1.00) 		0.0864
(1.00) 		0.941
(1.00)
del 17q11 2 71 (12%) 500 2e-05
(0.0128) 		2e-05
(0.0128) 		0.00214
(1.00) 		0.0103
(1.00) 		3e-05
(0.0188) 		0.634
(1.00) 		0.00624
(1.00) 		0.00911
(1.00) 		0.538
(1.00) 		0.566
(1.00)
amp 7q31 2 468 (82%) 103 0.00184
(1.00) 		1e-05
(0.0071) 		0.0106
(1.00) 		0.00557
(1.00) 		3e-05
(0.0188) 		0.00123
(0.707) 		0.11
(1.00) 		0.0252
(1.00) 		0.406
(1.00) 		0.00982
(1.00)
del 4q34 3 91 (16%) 480 0.00541
(1.00) 		0.00023
(0.138) 		0.0741
(1.00) 		0.0978
(1.00) 		1e-05
(0.0071) 		0.0119
(1.00) 		0.0967
(1.00) 		0.919
(1.00) 		0.123
(1.00) 		0.135
(1.00)
del 11q14 1 95 (17%) 476 1e-05
(0.0071) 		0.00057
(0.337) 		0.878
(1.00) 		0.138
(1.00) 		1e-05
(0.0071) 		0.523
(1.00) 		0.756
(1.00) 		0.679
(1.00) 		0.12
(1.00) 		0.162
(1.00)
del 12q15 77 (13%) 494 0.00016
(0.0963) 		0.00179
(1.00) 		0.49
(1.00) 		0.426
(1.00) 		1e-05
(0.0071) 		0.0424
(1.00) 		0.55
(1.00) 		0.718
(1.00) 		0.714
(1.00) 		0.396
(1.00)
del 17p13 1 95 (17%) 476 0.00041
(0.244) 		0.00282
(1.00) 		0.686
(1.00) 		0.894
(1.00) 		1e-05
(0.0071) 		0.0114
(1.00) 		0.708
(1.00) 		0.35
(1.00) 		0.645
(1.00) 		0.665
(1.00)
amp 1p36 21 92 (16%) 479 0.587
(1.00) 		0.428
(1.00) 		0.405
(1.00) 		0.115
(1.00) 		1e-05
(0.0071) 		0.821
(1.00) 		0.0264
(1.00) 		0.0958
(1.00) 		0.0119
(1.00) 		0.0194
(1.00)
amp 1q32 1 159 (28%) 412 0.821
(1.00) 		0.0622
(1.00) 		0.334
(1.00) 		0.149
(1.00) 		1e-05
(0.0071) 		0.832
(1.00) 		0.916
(1.00) 		0.665
(1.00) 		0.555
(1.00) 		0.0898
(1.00)
amp 1q44 99 (17%) 472 0.146
(1.00) 		0.62
(1.00) 		0.607
(1.00) 		0.308
(1.00) 		1e-05
(0.0071) 		0.426
(1.00) 		0.32
(1.00) 		0.0828
(1.00) 		0.962
(1.00) 		0.554
(1.00)
amp 3q26 33 111 (19%) 460 0.00829
(1.00) 		0.209
(1.00) 		0.442
(1.00) 		0.0555
(1.00) 		1e-05
(0.0071) 		0.00989
(1.00) 		0.0874
(1.00) 		0.662
(1.00) 		0.278
(1.00) 		0.697
(1.00)
amp 4q12 107 (19%) 464 0.00071
(0.417) 		0.00306
(1.00) 		0.54
(1.00) 		0.47
(1.00) 		1e-05
(0.0071) 		0.11
(1.00) 		0.469
(1.00) 		0.604
(1.00) 		0.156
(1.00) 		0.417
(1.00)
amp 12p13 32 82 (14%) 489 0.662
(1.00) 		0.385
(1.00) 		0.344
(1.00) 		0.43
(1.00) 		1e-05
(0.0071) 		0.413
(1.00) 		0.392
(1.00) 		0.372
(1.00) 		0.315
(1.00) 		0.548
(1.00)
amp 12q14 1 133 (23%) 438 0.0672
(1.00) 		0.148
(1.00) 		0.0981
(1.00) 		0.0881
(1.00) 		1e-05
(0.0071) 		0.311
(1.00) 		0.0939
(1.00) 		0.25
(1.00) 		0.0435
(1.00) 		0.138
(1.00)
amp 12q15 92 (16%) 479 0.73
(1.00) 		0.317
(1.00) 		0.708
(1.00) 		0.278
(1.00) 		1e-05
(0.0071) 		0.846
(1.00) 		0.293
(1.00) 		0.301
(1.00) 		0.314
(1.00) 		0.902
(1.00)
amp 17q25 1 84 (15%) 487 0.0137
(1.00) 		0.255
(1.00) 		0.279
(1.00) 		0.728
(1.00) 		0.0001
(0.061) 		0.81
(1.00) 		0.137
(1.00) 		0.19
(1.00) 		0.865
(1.00) 		0.694
(1.00)
amp 21q21 1 69 (12%) 502 0.00515
(1.00) 		0.0598
(1.00) 		0.0178
(1.00) 		0.00799
(1.00) 		0.0004
(0.238) 		0.228
(1.00) 		0.668
(1.00) 		0.0821
(1.00) 		0.0972
(1.00) 		0.406
(1.00)
del 1p36 23 136 (24%) 435 0.0709
(1.00) 		0.186
(1.00) 		0.56
(1.00) 		0.503
(1.00) 		3e-05
(0.0188) 		0.263
(1.00) 		0.278
(1.00) 		0.293
(1.00) 		0.017
(1.00) 		0.0939
(1.00)
del 2q22 1 45 (8%) 526 0.00566
(1.00) 		0.0295
(1.00) 		0.39
(1.00) 		0.549
(1.00) 		2e-05
(0.0128) 		0.0348
(1.00) 		0.476
(1.00) 		0.338
(1.00) 		0.183
(1.00) 		0.433
(1.00)
del 3q13 31 58 (10%) 513 0.513
(1.00) 		0.388
(1.00) 		0.693
(1.00) 		0.666
(1.00) 		3e-05
(0.0188) 		0.617
(1.00) 		0.975
(1.00) 		0.206
(1.00) 		1
(1.00) 		0.178
(1.00)
del 6q22 31 157 (27%) 414 0.632
(1.00) 		0.991
(1.00) 		0.294
(1.00) 		0.287
(1.00) 		1e-05
(0.0071) 		0.0836
(1.00) 		0.346
(1.00) 		0.19
(1.00) 		0.798
(1.00) 		0.109
(1.00)
del 6q26 178 (31%) 393 0.744
(1.00) 		0.755
(1.00) 		0.477
(1.00) 		0.547
(1.00) 		0.00028
(0.167) 		0.227
(1.00) 		0.0347
(1.00) 		0.345
(1.00) 		0.764
(1.00) 		0.0185
(1.00)
del 12q12 76 (13%) 495 0.0135
(1.00) 		0.00067
(0.395) 		0.266
(1.00) 		0.0861
(1.00) 		0.00011
(0.067) 		0.0395
(1.00) 		0.0973
(1.00) 		0.27
(1.00) 		1
(1.00) 		0.664
(1.00)
del 17p13 2 86 (15%) 485 0.00317
(1.00) 		0.0261
(1.00) 		0.95
(1.00) 		0.948
(1.00) 		1e-05
(0.0071) 		0.0801
(1.00) 		0.631
(1.00) 		0.411
(1.00) 		0.586
(1.00) 		0.819
(1.00)
del 18q22 3 81 (14%) 490 0.127
(1.00) 		0.0846
(1.00) 		0.787
(1.00) 		0.39
(1.00) 		4e-05
(0.0248) 		0.0346
(1.00) 		0.0109
(1.00) 		0.0072
(1.00) 		0.197
(1.00) 		0.273
(1.00)
del 19q13 41 99 (17%) 472 0.00358
(1.00) 		1e-05
(0.0071) 		0.0407
(1.00) 		0.0214
(1.00) 		0.00161
(0.918) 		0.111
(1.00) 		0.053
(1.00) 		0.335
(1.00) 		0.0346
(1.00) 		0.0956
(1.00)
del 21q22 11 46 (8%) 525 0.00153
(0.875) 		0.00016
(0.0963) 		0.00496
(1.00) 		0.126
(1.00) 		0.00197
(1.00) 		0.296
(1.00) 		0.156
(1.00) 		0.11
(1.00) 		0.682
(1.00) 		1
(1.00)
del 22q13 32 211 (37%) 360 0.716
(1.00) 		0.971
(1.00) 		0.0397
(1.00) 		0.41
(1.00) 		4e-05
(0.0248) 		0.275
(1.00) 		0.794
(1.00) 		0.325
(1.00) 		0.0504
(1.00) 		0.085
(1.00)
del xp22 2 116 (20%) 455 0.00574
(1.00) 		0.00162
(0.922) 		0.112
(1.00) 		0.171
(1.00) 		1e-05
(0.0071) 		0.02
(1.00) 		0.682
(1.00) 		0.248
(1.00) 		0.307
(1.00) 		0.672
(1.00)
del xq23 107 (19%) 464 0.0192
(1.00) 		0.00969
(1.00) 		0.0979
(1.00) 		0.193
(1.00) 		1e-05
(0.0071) 		0.0588
(1.00) 		0.912
(1.00) 		0.441
(1.00) 		0.172
(1.00) 		0.506
(1.00)
amp 2p24 3 49 (9%) 522 0.0994
(1.00) 		0.0163
(1.00) 		0.429
(1.00) 		0.979
(1.00) 		0.00118
(0.683) 		0.1
(1.00) 		0.433
(1.00) 		0.363
(1.00) 		0.884
(1.00) 		0.624
(1.00)
amp 4p16 3 48 (8%) 523 0.308
(1.00) 		0.729
(1.00) 		0.859
(1.00) 		0.0841
(1.00) 		0.322
(1.00) 		0.528
(1.00) 		0.705
(1.00) 		0.474
(1.00) 		1
(1.00) 		1
(1.00)
amp 11p13 31 (5%) 540 0.786
(1.00) 		0.35
(1.00) 		0.551
(1.00) 		0.248
(1.00) 		0.395
(1.00) 		0.242
(1.00) 		0.712
(1.00) 		0.343
(1.00) 		1
(1.00) 		0.887
(1.00)
amp 13q34 32 (6%) 539 0.262
(1.00) 		0.2
(1.00) 		0.0286
(1.00) 		0.484
(1.00) 		0.0559
(1.00) 		0.624
(1.00) 		0.02
(1.00) 		0.235
(1.00) 		0.491
(1.00) 		0.804
(1.00)
amp 13q34 30 (5%) 541 0.141
(1.00) 		0.209
(1.00) 		0.215
(1.00) 		0.786
(1.00) 		0.127
(1.00) 		0.624
(1.00) 		0.0529
(1.00) 		0.3
(1.00) 		0.369
(1.00) 		0.792
(1.00)
amp 14q32 33 36 (6%) 535 0.187
(1.00) 		0.658
(1.00) 		0.0887
(1.00) 		0.919
(1.00) 		0.823
(1.00) 		0.496
(1.00) 		0.0244
(1.00) 		0.34
(1.00) 		0.0385
(1.00) 		0.067
(1.00)
amp 17p13 2 51 (9%) 520 0.00054
(0.32) 		0.0137
(1.00) 		0.0486
(1.00) 		0.112
(1.00) 		0.00071
(0.417) 		0.0469
(1.00) 		0.126
(1.00) 		0.514
(1.00) 		0.403
(1.00) 		0.571
(1.00)
del 1p36 32 100 (18%) 471 0.918
(1.00) 		0.714
(1.00) 		0.584
(1.00) 		0.175
(1.00) 		0.351
(1.00) 		0.287
(1.00) 		0.603
(1.00) 		0.305
(1.00) 		0.253
(1.00) 		0.58
(1.00)
del 1p32 3 61 (11%) 510 0.243
(1.00) 		0.368
(1.00) 		0.83
(1.00) 		0.157
(1.00) 		0.387
(1.00) 		0.926
(1.00) 		0.706
(1.00) 		0.478
(1.00) 		0.802
(1.00) 		0.104
(1.00)
del 1p22 1 48 (8%) 523 0.976
(1.00) 		0.554
(1.00) 		0.814
(1.00) 		0.00479
(1.00) 		0.135
(1.00) 		0.842
(1.00) 		0.888
(1.00) 		0.721
(1.00) 		1
(1.00) 		0.32
(1.00)
del 1q42 11 51 (9%) 520 0.219
(1.00) 		0.825
(1.00) 		0.514
(1.00) 		0.286
(1.00) 		0.676
(1.00) 		0.0662
(1.00) 		0.141
(1.00) 		0.0165
(1.00) 		0.688
(1.00) 		0.193
(1.00)
del 1q44 35 (6%) 536 0.813
(1.00) 		0.471
(1.00) 		0.727
(1.00) 		0.247
(1.00) 		0.259
(1.00) 		0.0717
(1.00) 		0.663
(1.00) 		0.439
(1.00) 		0.54
(1.00) 		0.324
(1.00)
del 2q37 1 54 (9%) 517 0.102
(1.00) 		0.00584
(1.00) 		0.317
(1.00) 		0.822
(1.00) 		0.0484
(1.00) 		0.0704
(1.00) 		0.784
(1.00) 		0.273
(1.00) 		0.183
(1.00) 		0.0514
(1.00)
del 3p21 1 52 (9%) 519 0.241
(1.00) 		0.133
(1.00) 		0.677
(1.00) 		0.483
(1.00) 		0.0008
(0.466) 		0.0692
(1.00) 		0.136
(1.00) 		0.915
(1.00) 		0.462
(1.00) 		0.107
(1.00)
del 3q22 1 58 (10%) 513 0.791
(1.00) 		0.626
(1.00) 		0.956
(1.00) 		1
(1.00) 		0.0007
(0.412) 		0.238
(1.00) 		0.962
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.22
(1.00)
del 3q29 65 (11%) 506 0.089
(1.00) 		0.186
(1.00) 		0.537
(1.00) 		0.876
(1.00) 		0.0457
(1.00) 		0.803
(1.00) 		0.449
(1.00) 		0.0609
(1.00) 		0.954
(1.00) 		0.791
(1.00)
del 4p16 3 77 (13%) 494 0.0483
(1.00) 		0.00493
(1.00) 		0.322
(1.00) 		0.249
(1.00) 		0.00613
(1.00) 		1
(1.00) 		0.83
(1.00) 		0.454
(1.00) 		0.873
(1.00) 		0.946
(1.00)
del 8p23 2 65 (11%) 506 0.375
(1.00) 		0.247
(1.00) 		0.177
(1.00) 		0.275
(1.00) 		0.12
(1.00) 		1
(1.00) 		0.944
(1.00) 		0.903
(1.00) 		0.722
(1.00) 		0.437
(1.00)
del 9q34 2 78 (14%) 493 0.214
(1.00) 		0.106
(1.00) 		0.518
(1.00) 		0.23
(1.00) 		0.344
(1.00) 		0.281
(1.00) 		0.229
(1.00) 		0.224
(1.00) 		0.444
(1.00) 		0.305
(1.00)
del 12p13 1 72 (13%) 499 0.0493
(1.00) 		0.0133
(1.00) 		0.252
(1.00) 		0.235
(1.00) 		0.063
(1.00) 		0.425
(1.00) 		0.679
(1.00) 		0.56
(1.00) 		1
(1.00) 		0.933
(1.00)
del 16p12 2 92 (16%) 479 0.409
(1.00) 		0.203
(1.00) 		0.284
(1.00) 		0.87
(1.00) 		0.222
(1.00) 		0.104
(1.00) 		0.403
(1.00) 		0.0702
(1.00) 		0.441
(1.00) 		0.334
(1.00)
del 16q23 3 97 (17%) 474 0.0222
(1.00) 		0.575
(1.00) 		0.865
(1.00) 		0.412
(1.00) 		0.00603
(1.00) 		0.651
(1.00) 		0.0386
(1.00) 		0.00257
(1.00) 		0.528
(1.00) 		0.722
(1.00)
'amp_1p36.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S1.  Gene #1: 'amp_1p36.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 1(1P36.21) MUTATED 52 19 21
AMP PEAK 1(1P36.21) WILD-TYPE 107 193 179

Figure S1.  Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S2.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 2(1Q32.1) MUTATED 75 43 41
AMP PEAK 2(1Q32.1) WILD-TYPE 84 169 159

Figure S2.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S3.  Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 3(1Q44) MUTATED 57 20 22
AMP PEAK 3(1Q44) WILD-TYPE 102 192 178

Figure S3.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #5: 'CN_CNMF'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S4.  Gene #5: 'amp_3q26.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 5(3Q26.33) MUTATED 59 22 30
AMP PEAK 5(3Q26.33) WILD-TYPE 100 190 170

Figure S4.  Get High-res Image Gene #5: 'amp_3q26.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S5.  Gene #7: 'amp_4q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 7(4Q12) MUTATED 53 22 32
AMP PEAK 7(4Q12) WILD-TYPE 106 190 168

Figure S5.  Get High-res Image Gene #7: 'amp_4q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7p11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S6.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 8(7P11.2) MUTATED 139 68 147 89
AMP PEAK 8(7P11.2) WILD-TYPE 8 28 5 24

Figure S6.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S7.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 8(7P11.2) MUTATED 136 60 99 148
AMP PEAK 8(7P11.2) WILD-TYPE 12 42 1 10

Figure S7.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p11.2' versus 'MIR_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S8.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
AMP PEAK 8(7P11.2) MUTATED 151 146 73 110
AMP PEAK 8(7P11.2) WILD-TYPE 5 37 14 10

Figure S8.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7p11.2' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S9.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
AMP PEAK 8(7P11.2) MUTATED 234 120 126
AMP PEAK 8(7P11.2) WILD-TYPE 59 4 3

Figure S9.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S10.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 8(7P11.2) MUTATED 150 211 141
AMP PEAK 8(7P11.2) WILD-TYPE 9 1 59

Figure S10.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S11.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 47 33
AMP PEAK 8(7P11.2) MUTATED 40 47 20
AMP PEAK 8(7P11.2) WILD-TYPE 0 0 13

Figure S11.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S12.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 58 44 45
AMP PEAK 8(7P11.2) MUTATED 49 42 44 44
AMP PEAK 8(7P11.2) WILD-TYPE 5 16 0 1

Figure S12.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.049

Table S13.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 76 56
AMP PEAK 8(7P11.2) MUTATED 64 59 56
AMP PEAK 8(7P11.2) WILD-TYPE 5 17 0

Figure S13.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S14.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 67 36
AMP PEAK 8(7P11.2) MUTATED 31 66 34
AMP PEAK 8(7P11.2) WILD-TYPE 13 1 2

Figure S14.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S15.  Gene #8: 'amp_7p11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
AMP PEAK 8(7P11.2) MUTATED 17 90 24
AMP PEAK 8(7P11.2) WILD-TYPE 13 2 1

Figure S15.  Get High-res Image Gene #8: 'amp_7p11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q11.21' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S16.  Gene #9: 'amp_7q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 9(7Q11.21) MUTATED 133 64 124 82
AMP PEAK 9(7Q11.21) WILD-TYPE 14 32 28 31

Figure S16.  Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S17.  Gene #9: 'amp_7q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 9(7Q11.21) MUTATED 129 55 82 137
AMP PEAK 9(7Q11.21) WILD-TYPE 19 47 18 21

Figure S17.  Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q11.21' versus 'MIR_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

Table S18.  Gene #9: 'amp_7q11.21' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
AMP PEAK 9(7Q11.21) MUTATED 141 133 63 103
AMP PEAK 9(7Q11.21) WILD-TYPE 15 50 24 17

Figure S18.  Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7q11.21' versus 'MIR_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S19.  Gene #9: 'amp_7q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
AMP PEAK 9(7Q11.21) MUTATED 216 114 110
AMP PEAK 9(7Q11.21) WILD-TYPE 77 10 19

Figure S19.  Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S20.  Gene #9: 'amp_7q11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 9(7Q11.21) MUTATED 143 182 134
AMP PEAK 9(7Q11.21) WILD-TYPE 16 30 66

Figure S20.  Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

Table S21.  Gene #9: 'amp_7q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
AMP PEAK 9(7Q11.21) MUTATED 15 82 21
AMP PEAK 9(7Q11.21) WILD-TYPE 15 10 4

Figure S21.  Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.031

Table S22.  Gene #10: 'amp_7q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 10(7Q21.2) MUTATED 131 64 134 89
AMP PEAK 10(7Q21.2) WILD-TYPE 16 32 18 24

Figure S22.  Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S23.  Gene #10: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 10(7Q21.2) MUTATED 126 62 89 141
AMP PEAK 10(7Q21.2) WILD-TYPE 22 40 11 17

Figure S23.  Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q21.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.091

Table S24.  Gene #10: 'amp_7q21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
AMP PEAK 10(7Q21.2) MUTATED 224 111 117
AMP PEAK 10(7Q21.2) WILD-TYPE 69 13 12

Figure S24.  Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S25.  Gene #10: 'amp_7q21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 10(7Q21.2) MUTATED 142 192 141
AMP PEAK 10(7Q21.2) WILD-TYPE 17 20 59

Figure S25.  Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.15

Table S26.  Gene #10: 'amp_7q21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 47 33
AMP PEAK 10(7Q21.2) MUTATED 39 44 22
AMP PEAK 10(7Q21.2) WILD-TYPE 1 3 11

Figure S26.  Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S27.  Gene #11: 'amp_7q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 11(7Q31.2) MUTATED 131 63 83 136
AMP PEAK 11(7Q31.2) WILD-TYPE 17 39 17 22

Figure S27.  Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S28.  Gene #11: 'amp_7q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 11(7Q31.2) MUTATED 138 186 144
AMP PEAK 11(7Q31.2) WILD-TYPE 21 26 56

Figure S28.  Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S29.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 12(8Q24.21) MUTATED 9 25 7 21
AMP PEAK 12(8Q24.21) WILD-TYPE 138 71 145 92

Figure S29.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S30.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 12(8Q24.21) MUTATED 10 29 6 17
AMP PEAK 12(8Q24.21) WILD-TYPE 138 73 94 141

Figure S30.  Get High-res Image Gene #12: '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 = 0.0071

Table S31.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 12(8Q24.21) MUTATED 35 8 27
AMP PEAK 12(8Q24.21) WILD-TYPE 124 204 173

Figure S31.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12p13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S32.  Gene #14: 'amp_12p13.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 14(12P13.32) MUTATED 39 16 27
AMP PEAK 14(12P13.32) WILD-TYPE 120 196 173

Figure S32.  Get High-res Image Gene #14: 'amp_12p13.32' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S33.  Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 15(12Q14.1) MUTATED 64 36 33
AMP PEAK 15(12Q14.1) WILD-TYPE 95 176 167

Figure S33.  Get High-res Image Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S34.  Gene #16: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 16(12Q15) MUTATED 48 23 21
AMP PEAK 16(12Q15) WILD-TYPE 111 189 179

Figure S34.  Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'amp_17q25.1' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.061

Table S35.  Gene #21: 'amp_17q25.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 21(17Q25.1) MUTATED 40 20 24
AMP PEAK 21(17Q25.1) WILD-TYPE 119 192 176

Figure S35.  Get High-res Image Gene #21: 'amp_17q25.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S36.  Gene #22: 'amp_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 22(19P13.3) MUTATED 58 34 95 28
AMP PEAK 22(19P13.3) WILD-TYPE 89 62 57 85

Figure S36.  Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S37.  Gene #22: 'amp_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 22(19P13.3) MUTATED 67 30 62 56
AMP PEAK 22(19P13.3) WILD-TYPE 81 72 38 102

Figure S37.  Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S38.  Gene #22: 'amp_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 22(19P13.3) MUTATED 42 149 51
AMP PEAK 22(19P13.3) WILD-TYPE 117 63 149

Figure S38.  Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.037

Table S39.  Gene #22: 'amp_19p13.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 76 56
AMP PEAK 22(19P13.3) MUTATED 23 23 37
AMP PEAK 22(19P13.3) WILD-TYPE 46 53 19

Figure S39.  Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S40.  Gene #23: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 23(19P13.2) MUTATED 57 38 101 25
AMP PEAK 23(19P13.2) WILD-TYPE 90 58 51 88

Figure S40.  Get High-res Image Gene #23: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S41.  Gene #23: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 23(19P13.2) MUTATED 66 32 66 57
AMP PEAK 23(19P13.2) WILD-TYPE 82 70 34 101

Figure S41.  Get High-res Image Gene #23: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S42.  Gene #23: 'amp_19p13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 23(19P13.2) MUTATED 45 152 50
AMP PEAK 23(19P13.2) WILD-TYPE 114 60 150

Figure S42.  Get High-res Image Gene #23: 'amp_19p13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.067

Table S43.  Gene #23: 'amp_19p13.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 76 56
AMP PEAK 23(19P13.2) MUTATED 25 23 37
AMP PEAK 23(19P13.2) WILD-TYPE 44 53 19

Figure S43.  Get High-res Image Gene #23: 'amp_19p13.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S44.  Gene #24: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
AMP PEAK 24(19Q12) MUTATED 55 31 85 17
AMP PEAK 24(19Q12) WILD-TYPE 92 65 67 96

Figure S44.  Get High-res Image Gene #24: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S45.  Gene #24: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
AMP PEAK 24(19Q12) MUTATED 62 21 54 51
AMP PEAK 24(19Q12) WILD-TYPE 86 81 46 107

Figure S45.  Get High-res Image Gene #24: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S46.  Gene #24: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 24(19Q12) MUTATED 40 131 42
AMP PEAK 24(19Q12) WILD-TYPE 119 81 158

Figure S46.  Get High-res Image Gene #24: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_21q21.1' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.24

Table S47.  Gene #25: 'amp_21q21.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
AMP PEAK 25(21Q21.1) MUTATED 29 12 28
AMP PEAK 25(21Q21.1) WILD-TYPE 130 200 172

Figure S47.  Get High-res Image Gene #25: 'amp_21q21.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.23' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S48.  Gene #27: 'del_1p36.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 2(1P36.23) MUTATED 36 71 29
DEL PEAK 2(1P36.23) WILD-TYPE 123 141 171

Figure S48.  Get High-res Image Gene #27: 'del_1p36.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S49.  Gene #32: 'del_2q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 7(2Q22.1) MUTATED 26 5 14
DEL PEAK 7(2Q22.1) WILD-TYPE 133 207 186

Figure S49.  Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_3q13.31' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S50.  Gene #35: 'del_3q13.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 10(3Q13.31) MUTATED 26 7 25
DEL PEAK 10(3Q13.31) WILD-TYPE 133 205 175

Figure S50.  Get High-res Image Gene #35: 'del_3q13.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.14

Table S51.  Gene #39: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 14(4Q34.3) MUTATED 17 31 10 23
DEL PEAK 14(4Q34.3) WILD-TYPE 131 71 90 135

Figure S51.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S52.  Gene #39: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 14(4Q34.3) MUTATED 45 17 29
DEL PEAK 14(4Q34.3) WILD-TYPE 114 195 171

Figure S52.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q35.3' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.031

Table S53.  Gene #40: 'del_5q35.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 15(5Q35.3) MUTATED 8 21 6 14
DEL PEAK 15(5Q35.3) WILD-TYPE 139 75 146 99

Figure S53.  Get High-res Image Gene #40: 'del_5q35.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q35.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S54.  Gene #40: 'del_5q35.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 15(5Q35.3) MUTATED 9 26 3 11
DEL PEAK 15(5Q35.3) WILD-TYPE 139 76 97 147

Figure S54.  Get High-res Image Gene #40: 'del_5q35.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q35.3' versus 'MIR_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.14

Table S55.  Gene #40: 'del_5q35.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
DEL PEAK 15(5Q35.3) MUTATED 6 30 8 6
DEL PEAK 15(5Q35.3) WILD-TYPE 150 153 79 114

Figure S55.  Get High-res Image Gene #40: 'del_5q35.3' versus Molecular Subtype #3: 'MIR_CNMF'

'del_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S56.  Gene #40: 'del_5q35.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 15(5Q35.3) MUTATED 18 5 30
DEL PEAK 15(5Q35.3) WILD-TYPE 141 207 170

Figure S56.  Get High-res Image Gene #40: 'del_5q35.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S57.  Gene #41: 'del_6q22.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 16(6Q22.31) MUTATED 72 46 39
DEL PEAK 16(6Q22.31) WILD-TYPE 87 166 161

Figure S57.  Get High-res Image Gene #41: 'del_6q22.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.17

Table S58.  Gene #42: 'del_6q26' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 17(6Q26) MUTATED 68 65 45
DEL PEAK 17(6Q26) WILD-TYPE 91 147 155

Figure S58.  Get High-res Image Gene #42: 'del_6q26' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S59.  Gene #44: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 19(9P21.3) MUTATED 100 61 133 75
DEL PEAK 19(9P21.3) WILD-TYPE 47 35 19 38

Figure S59.  Get High-res Image Gene #44: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S60.  Gene #44: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 19(9P21.3) MUTATED 102 61 91 115
DEL PEAK 19(9P21.3) WILD-TYPE 46 41 9 43

Figure S60.  Get High-res Image Gene #44: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S61.  Gene #44: 'del_9p21.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 19(9P21.3) MUTATED 104 191 121
DEL PEAK 19(9P21.3) WILD-TYPE 55 21 79

Figure S61.  Get High-res Image Gene #44: 'del_9p21.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p15.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S62.  Gene #46: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 21(10P15.3) MUTATED 129 63 134 82
DEL PEAK 21(10P15.3) WILD-TYPE 18 33 18 31

Figure S62.  Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p15.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S63.  Gene #46: 'del_10p15.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 21(10P15.3) MUTATED 125 59 89 135
DEL PEAK 21(10P15.3) WILD-TYPE 23 43 11 23

Figure S63.  Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S64.  Gene #46: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 21(10P15.3) MUTATED 146 199 120
DEL PEAK 21(10P15.3) WILD-TYPE 13 13 80

Figure S64.  Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.091

Table S65.  Gene #46: 'del_10p15.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 92 25
DEL PEAK 21(10P15.3) MUTATED 19 83 25
DEL PEAK 21(10P15.3) WILD-TYPE 11 9 0

Figure S65.  Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S66.  Gene #47: 'del_10p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 22(10P13) MUTATED 131 65 135 79
DEL PEAK 22(10P13) WILD-TYPE 16 31 17 34

Figure S66.  Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S67.  Gene #47: 'del_10p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 22(10P13) MUTATED 129 58 89 134
DEL PEAK 22(10P13) WILD-TYPE 19 44 11 24

Figure S67.  Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S68.  Gene #47: 'del_10p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 22(10P13) MUTATED 146 201 119
DEL PEAK 22(10P13) WILD-TYPE 13 11 81

Figure S68.  Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p13' versus 'RPPA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.091

Table S69.  Gene #47: 'del_10p13' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 54 58 44 45
DEL PEAK 22(10P13) MUTATED 50 38 42 37
DEL PEAK 22(10P13) WILD-TYPE 4 20 2 8

Figure S69.  Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_10p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.085

Table S70.  Gene #47: 'del_10p13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 76 56
DEL PEAK 22(10P13) MUTATED 60 53 54
DEL PEAK 22(10P13) WILD-TYPE 9 23 2

Figure S70.  Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10p11.23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S71.  Gene #48: 'del_10p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 23(10P11.23) MUTATED 130 61 142 83
DEL PEAK 23(10P11.23) WILD-TYPE 17 35 10 30

Figure S71.  Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p11.23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S72.  Gene #48: 'del_10p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 23(10P11.23) MUTATED 127 60 93 136
DEL PEAK 23(10P11.23) WILD-TYPE 21 42 7 22

Figure S72.  Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p11.23' versus 'MIR_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.079

Table S73.  Gene #48: 'del_10p11.23' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
DEL PEAK 23(10P11.23) MUTATED 145 139 67 99
DEL PEAK 23(10P11.23) WILD-TYPE 11 44 20 21

Figure S73.  Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p11.23' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S74.  Gene #48: 'del_10p11.23' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 23(10P11.23) MUTATED 223 106 121
DEL PEAK 23(10P11.23) WILD-TYPE 70 18 8

Figure S74.  Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S75.  Gene #48: 'del_10p11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 23(10P11.23) MUTATED 147 205 119
DEL PEAK 23(10P11.23) WILD-TYPE 12 7 81

Figure S75.  Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S76.  Gene #49: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 24(10Q23.31) MUTATED 136 75 147 91
DEL PEAK 24(10Q23.31) WILD-TYPE 11 21 5 22

Figure S76.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S77.  Gene #49: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 24(10Q23.31) MUTATED 132 75 98 144
DEL PEAK 24(10Q23.31) WILD-TYPE 16 27 2 14

Figure S77.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S78.  Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 24(10Q23.31) MUTATED 152 210 146
DEL PEAK 24(10Q23.31) WILD-TYPE 7 2 54

Figure S78.  Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S79.  Gene #50: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 25(10Q26.3) MUTATED 136 75 148 91
DEL PEAK 25(10Q26.3) WILD-TYPE 11 21 4 22

Figure S79.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.031

Table S80.  Gene #50: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 25(10Q26.3) MUTATED 132 77 97 144
DEL PEAK 25(10Q26.3) WILD-TYPE 16 25 3 14

Figure S80.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S81.  Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 25(10Q26.3) MUTATED 149 210 150
DEL PEAK 25(10Q26.3) WILD-TYPE 10 2 50

Figure S81.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.5' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S82.  Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 26(11P15.5) MUTATED 32 42 13 31
DEL PEAK 26(11P15.5) WILD-TYPE 115 54 139 82

Figure S82.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S83.  Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 26(11P15.5) MUTATED 30 48 9 31
DEL PEAK 26(11P15.5) WILD-TYPE 118 54 91 127

Figure S83.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S84.  Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 26(11P15.5) MUTATED 59 13 55
DEL PEAK 26(11P15.5) WILD-TYPE 100 199 145

Figure S84.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S85.  Gene #52: 'del_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 27(11P11.2) MUTATED 27 35 10 23
DEL PEAK 27(11P11.2) WILD-TYPE 120 61 142 90

Figure S85.  Get High-res Image Gene #52: 'del_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S86.  Gene #52: 'del_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 27(11P11.2) MUTATED 27 36 5 27
DEL PEAK 27(11P11.2) WILD-TYPE 121 66 95 131

Figure S86.  Get High-res Image Gene #52: 'del_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S87.  Gene #52: 'del_11p11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 27(11P11.2) MUTATED 53 11 39
DEL PEAK 27(11P11.2) WILD-TYPE 106 201 161

Figure S87.  Get High-res Image Gene #52: 'del_11p11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_11q14.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S88.  Gene #53: 'del_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 28(11Q14.1) MUTATED 30 33 12 13
DEL PEAK 28(11Q14.1) WILD-TYPE 117 63 140 100

Figure S88.  Get High-res Image Gene #53: 'del_11q14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S89.  Gene #53: 'del_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 28(11Q14.1) MUTATED 59 10 26
DEL PEAK 28(11Q14.1) WILD-TYPE 100 202 174

Figure S89.  Get High-res Image Gene #53: 'del_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q12' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.067

Table S90.  Gene #55: 'del_12q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 30(12Q12) MUTATED 33 13 30
DEL PEAK 30(12Q12) WILD-TYPE 126 199 170

Figure S90.  Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q15' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.096

Table S91.  Gene #56: 'del_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 31(12Q15) MUTATED 21 21 7 20
DEL PEAK 31(12Q15) WILD-TYPE 126 75 145 93

Figure S91.  Get High-res Image Gene #56: 'del_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S92.  Gene #56: 'del_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 31(12Q15) MUTATED 37 11 29
DEL PEAK 31(12Q15) WILD-TYPE 122 201 171

Figure S92.  Get High-res Image Gene #56: 'del_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S93.  Gene #57: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 32(13Q14.2) MUTATED 81 45 36 53
DEL PEAK 32(13Q14.2) WILD-TYPE 66 51 116 60

Figure S93.  Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S94.  Gene #57: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 32(13Q14.2) MUTATED 68 50 21 76
DEL PEAK 32(13Q14.2) WILD-TYPE 80 52 79 82

Figure S94.  Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S95.  Gene #57: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 32(13Q14.2) MUTATED 108 37 92
DEL PEAK 32(13Q14.2) WILD-TYPE 51 175 108

Figure S95.  Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q13.1' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S96.  Gene #58: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 33(14Q13.1) MUTATED 54 39 25 43
DEL PEAK 33(14Q13.1) WILD-TYPE 93 57 127 70

Figure S96.  Get High-res Image Gene #58: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.1

Table S97.  Gene #58: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 33(14Q13.1) MUTATED 49 42 15 55
DEL PEAK 33(14Q13.1) WILD-TYPE 99 60 85 103

Figure S97.  Get High-res Image Gene #58: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S98.  Gene #58: 'del_14q13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 33(14Q13.1) MUTATED 93 26 57
DEL PEAK 33(14Q13.1) WILD-TYPE 66 186 143

Figure S98.  Get High-res Image Gene #58: 'del_14q13.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q24.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S99.  Gene #59: 'del_14q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 34(14Q24.2) MUTATED 51 43 22 45
DEL PEAK 34(14Q24.2) WILD-TYPE 96 53 130 68

Figure S99.  Get High-res Image Gene #59: 'del_14q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q24.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S100.  Gene #59: 'del_14q24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 34(14Q24.2) MUTATED 48 46 14 53
DEL PEAK 34(14Q24.2) WILD-TYPE 100 56 86 105

Figure S100.  Get High-res Image Gene #59: 'del_14q24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S101.  Gene #59: 'del_14q24.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 34(14Q24.2) MUTATED 95 16 61
DEL PEAK 34(14Q24.2) WILD-TYPE 64 196 139

Figure S101.  Get High-res Image Gene #59: 'del_14q24.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q14' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

Table S102.  Gene #60: 'del_15q14' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 35(15Q14) MUTATED 36 37 23 42
DEL PEAK 35(15Q14) WILD-TYPE 111 59 129 71

Figure S102.  Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q14' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S103.  Gene #60: 'del_15q14' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 35(15Q14) MUTATED 34 47 12 45
DEL PEAK 35(15Q14) WILD-TYPE 114 55 88 113

Figure S103.  Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q14' versus 'MIR_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.031

Table S104.  Gene #60: 'del_15q14' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 35(15Q14) MUTATED 95 15 33
DEL PEAK 35(15Q14) WILD-TYPE 198 109 96

Figure S104.  Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_15q14' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S105.  Gene #60: 'del_15q14' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 35(15Q14) MUTATED 66 36 48
DEL PEAK 35(15Q14) WILD-TYPE 93 176 152

Figure S105.  Get High-res Image Gene #60: 'del_15q14' versus Molecular Subtype #5: 'CN_CNMF'

'del_17p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S106.  Gene #63: 'del_17p13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 38(17P13.2) MUTATED 41 10 35
DEL PEAK 38(17P13.2) WILD-TYPE 118 202 165

Figure S106.  Get High-res Image Gene #63: 'del_17p13.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_17p13.1' versus 'MRNA_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.24

Table S107.  Gene #64: 'del_17p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 39(17P13.1) MUTATED 32 26 13 16
DEL PEAK 39(17P13.1) WILD-TYPE 115 70 139 97

Figure S107.  Get High-res Image Gene #64: 'del_17p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S108.  Gene #64: 'del_17p13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 39(17P13.1) MUTATED 50 8 37
DEL PEAK 39(17P13.1) WILD-TYPE 109 204 163

Figure S108.  Get High-res Image Gene #64: 'del_17p13.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S109.  Gene #65: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 40(17Q11.2) MUTATED 35 9 12 5
DEL PEAK 40(17Q11.2) WILD-TYPE 112 87 140 108

Figure S109.  Get High-res Image Gene #65: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.013

Table S110.  Gene #65: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 40(17Q11.2) MUTATED 35 7 9 10
DEL PEAK 40(17Q11.2) WILD-TYPE 113 95 91 148

Figure S110.  Get High-res Image Gene #65: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.019

Table S111.  Gene #65: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 40(17Q11.2) MUTATED 31 10 30
DEL PEAK 40(17Q11.2) WILD-TYPE 128 202 170

Figure S111.  Get High-res Image Gene #65: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_18q22.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

Table S112.  Gene #66: 'del_18q22.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 41(18Q22.3) MUTATED 37 14 30
DEL PEAK 41(18Q22.3) WILD-TYPE 122 198 170

Figure S112.  Get High-res Image Gene #66: 'del_18q22.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.41' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S113.  Gene #67: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 42(19Q13.41) MUTATED 24 34 7 25
DEL PEAK 42(19Q13.41) WILD-TYPE 124 68 93 133

Figure S113.  Get High-res Image Gene #67: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_21q22.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.096

Table S114.  Gene #68: 'del_21q22.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 43(21Q22.11) MUTATED 5 20 5 12
DEL PEAK 43(21Q22.11) WILD-TYPE 143 82 95 146

Figure S114.  Get High-res Image Gene #68: 'del_21q22.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.025

Table S115.  Gene #69: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 44(22Q13.32) MUTATED 82 61 68
DEL PEAK 44(22Q13.32) WILD-TYPE 77 151 132

Figure S115.  Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S116.  Gene #70: 'del_xp22.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 45(XP22.2) MUTATED 58 25 33
DEL PEAK 45(XP22.2) WILD-TYPE 101 187 167

Figure S116.  Get High-res Image Gene #70: 'del_xp22.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_xq23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0071

Table S117.  Gene #71: 'del_xq23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 212 200
DEL PEAK 46(XQ23) MUTATED 60 27 20
DEL PEAK 46(XQ23) WILD-TYPE 99 185 180

Figure S117.  Get High-res Image Gene #71: 'del_xq23' versus Molecular Subtype #5: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 571

  • Number of significantly focal cnvs = 71

  • Number of molecular subtypes = 10

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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