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 10 molecular subtypes across 577 patients, 132 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',  'METHLYATION_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',  'CN_CNMF', and 'METHLYATION_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',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

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

  • amp_19q12 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_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_3p21.1 cnv correlated to 'CN_CNMF'.

  • del_3q13.31 cnv correlated to 'CN_CNMF'.

  • del_3q22.1 cnv correlated to 'CN_CNMF'.

  • del_4p16.3 cnv correlated to 'METHLYATION_CNMF'.

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

  • del_5q34 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF', and 'METHLYATION_CNMF'.

  • del_6q22.31 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',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

  • del_11p15.5 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_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_13q22.1 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',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • del_18q22.3 cnv correlated to 'CN_CNMF'.

  • del_19q13.41 cnv correlated to 'MRNA_CHIERARCHICAL' and 'METHLYATION_CNMF'.

  • del_22q13.32 cnv correlated to 'CN_CNMF'.

  • del_xp22.2 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, 132 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 2 507 (88%) 70 1e-05
(0.0071) 		1e-05
(0.0071) 		1e-05
(0.0071) 		1e-05
(0.0071) 		1e-05
(0.0071) 		1e-05
(0.0071) 		1e-05
(0.0071) 		7e-05
(0.0421) 		1e-05
(0.0071) 		1e-05
(0.0071)
amp 7q11 21 464 (80%) 113 2e-05
(0.0125) 		1e-05
(0.0071) 		5e-05
(0.0303) 		3e-05
(0.0185) 		1e-05
(0.0071) 		1e-05
(0.0071) 		0.00478
(1.00) 		0.0024
(1.00) 		0.00429
(1.00) 		6e-05
(0.0362)
del 10p13 471 (82%) 106 1e-05
(0.0071) 		1e-05
(0.0071) 		0.00248
(1.00) 		0.00134
(0.752) 		1e-05
(0.0071) 		1e-05
(0.0071) 		0.00018
(0.105) 		0.0001
(0.0592) 		0.088
(1.00) 		0.00275
(1.00)
del 10p11 23 476 (82%) 101 1e-05
(0.0071) 		1e-05
(0.0071) 		5e-05
(0.0303) 		3e-05
(0.0185) 		1e-05
(0.0071) 		1e-05
(0.0071) 		0.00096
(0.547) 		0.00344
(1.00) 		0.044
(1.00) 		0.00127
(0.715)
amp 7q21 2 480 (83%) 97 3e-05
(0.0185) 		1e-05
(0.0071) 		0.05
(1.00) 		0.00012
(0.0708) 		1e-05
(0.0071) 		0.00011
(0.065) 		0.0183
(1.00) 		0.0436
(1.00) 		0.0614
(1.00) 		0.00261
(1.00)
amp 19p13 3 244 (42%) 333 1e-05
(0.0071) 		1e-05
(0.0071) 		0.0377
(1.00) 		0.00148
(0.826) 		1e-05
(0.0071) 		1e-05
(0.0071) 		0.009
(1.00) 		9e-05
(0.0537) 		0.821
(1.00) 		0.969
(1.00)
amp 19p13 2 249 (43%) 328 1e-05
(0.0071) 		1e-05
(0.0071) 		0.147
(1.00) 		0.00116
(0.658) 		1e-05
(0.0071) 		1e-05
(0.0071) 		0.0127
(1.00) 		8e-05
(0.0479) 		0.166
(1.00) 		0.808
(1.00)
del 10p15 3 470 (81%) 107 1e-05
(0.0071) 		1e-05
(0.0071) 		0.00839
(1.00) 		0.00371
(1.00) 		1e-05
(0.0071) 		1e-05
(0.0071) 		0.00508
(1.00) 		0.00202
(1.00) 		0.0147
(1.00) 		0.0002
(0.117)
amp 8q24 21 70 (12%) 507 1e-05
(0.0071) 		2e-05
(0.0125) 		0.0256
(1.00) 		0.289
(1.00) 		1e-05
(0.0071) 		9e-05
(0.0537) 		0.334
(1.00) 		0.292
(1.00) 		0.0875
(1.00) 		0.27
(1.00)
amp 19q12 216 (37%) 361 1e-05
(0.0071) 		2e-05
(0.0125) 		0.281
(1.00) 		0.00492
(1.00) 		1e-05
(0.0071) 		1e-05
(0.0071) 		0.00917
(1.00) 		0.00057
(0.329) 		0.0635
(1.00) 		0.174
(1.00)
del 5q34 70 (12%) 507 4e-05
(0.0244) 		1e-05
(0.0071) 		7e-05
(0.0421) 		0.00521
(1.00) 		0.00698
(1.00) 		2e-05
(0.0125) 		0.698
(1.00) 		0.696
(1.00) 		0.256
(1.00) 		0.13
(1.00)
del 10q26 3 515 (89%) 62 1e-05
(0.0071) 		1e-05
(0.0071) 		0.0422
(1.00) 		0.00148
(0.826) 		1e-05
(0.0071) 		3e-05
(0.0185) 		0.119
(1.00) 		0.0448
(1.00) 		0.251
(1.00) 		0.0357
(1.00)
del 11p15 5 129 (22%) 448 1e-05
(0.0071) 		1e-05
(0.0071) 		0.163
(1.00) 		0.00136
(0.762) 		1e-05
(0.0071) 		2e-05
(0.0125) 		0.169
(1.00) 		0.0455
(1.00) 		0.00279
(1.00) 		0.00152
(0.845)
del 15q14 154 (27%) 423 3e-05
(0.0185) 		1e-05
(0.0071) 		0.00121
(0.684) 		6e-05
(0.0362) 		1e-05
(0.0071) 		0.00502
(1.00) 		0.0576
(1.00) 		0.0479
(1.00) 		0.00097
(0.552) 		0.0174
(1.00)
del 17q11 2 72 (12%) 505 2e-05
(0.0125) 		3e-05
(0.0185) 		0.00257
(1.00) 		0.0106
(1.00) 		1e-05
(0.0071) 		0.00028
(0.163) 		0.00602
(1.00) 		0.00878
(1.00) 		0.536
(1.00) 		0.565
(1.00)
del 9p21 3 421 (73%) 156 1e-05
(0.0071) 		1e-05
(0.0071) 		0.696
(1.00) 		0.0364
(1.00) 		1e-05
(0.0071) 		0.14
(1.00) 		0.14
(1.00) 		0.0163
(1.00) 		0.0274
(1.00) 		0.0076
(1.00)
del 10q23 31 514 (89%) 63 1e-05
(0.0071) 		1e-05
(0.0071) 		0.0118
(1.00) 		0.0032
(1.00) 		1e-05
(0.0071) 		0.00053
(0.306) 		0.0098
(1.00) 		0.0683
(1.00) 		0.366
(1.00) 		0.0421
(1.00)
del 11p11 2 105 (18%) 472 1e-05
(0.0071) 		1e-05
(0.0071) 		0.504
(1.00) 		0.0185
(1.00) 		1e-05
(0.0071) 		0.00251
(1.00) 		0.934
(1.00) 		0.661
(1.00) 		0.0936
(1.00) 		0.0883
(1.00)
del 13q14 2 241 (42%) 336 1e-05
(0.0071) 		5e-05
(0.0303) 		0.352
(1.00) 		0.147
(1.00) 		1e-05
(0.0071) 		0.00061
(0.351) 		0.854
(1.00) 		0.115
(1.00) 		0.0788
(1.00) 		0.07
(1.00)
del 13q22 1 230 (40%) 347 1e-05
(0.0071) 		0.00012
(0.0708) 		0.507
(1.00) 		0.338
(1.00) 		1e-05
(0.0071) 		0.0717
(1.00) 		0.606
(1.00) 		0.0144
(1.00) 		0.522
(1.00) 		0.285
(1.00)
del 14q13 1 178 (31%) 399 2e-05
(0.0125) 		0.00024
(0.14) 		0.612
(1.00) 		0.663
(1.00) 		1e-05
(0.0071) 		0.0436
(1.00) 		0.625
(1.00) 		0.205
(1.00) 		0.447
(1.00) 		0.943
(1.00)
del 14q24 2 173 (30%) 404 1e-05
(0.0071) 		1e-05
(0.0071) 		0.057
(1.00) 		0.155
(1.00) 		1e-05
(0.0071) 		0.0043
(1.00) 		0.552
(1.00) 		0.0588
(1.00) 		0.0871
(1.00) 		0.939
(1.00)
amp 7q31 2 473 (82%) 104 0.00192
(1.00) 		1e-05
(0.0071) 		0.0104
(1.00) 		0.00593
(1.00) 		2e-05
(0.0125) 		0.0104
(1.00) 		0.11
(1.00) 		0.0256
(1.00) 		0.409
(1.00) 		0.00998
(1.00)
del 4q34 3 93 (16%) 484 0.00513
(1.00) 		0.00033
(0.191) 		0.0751
(1.00) 		0.0993
(1.00) 		1e-05
(0.0071) 		0.00723
(1.00) 		0.0975
(1.00) 		0.919
(1.00) 		0.124
(1.00) 		0.136
(1.00)
del 11q14 1 96 (17%) 481 1e-05
(0.0071) 		0.00063
(0.362) 		0.878
(1.00) 		0.139
(1.00) 		1e-05
(0.0071) 		0.331
(1.00) 		0.749
(1.00) 		0.676
(1.00) 		0.121
(1.00) 		0.162
(1.00)
del 12q15 79 (14%) 498 0.00012
(0.0708) 		0.0019
(1.00) 		0.485
(1.00) 		0.427
(1.00) 		1e-05
(0.0071) 		0.243
(1.00) 		0.55
(1.00) 		0.718
(1.00) 		0.714
(1.00) 		0.394
(1.00)
del 17p13 1 98 (17%) 479 0.0002
(0.117) 		0.00194
(1.00) 		0.628
(1.00) 		0.897
(1.00) 		1e-05
(0.0071) 		0.11
(1.00) 		0.646
(1.00) 		0.259
(1.00) 		0.646
(1.00) 		0.664
(1.00)
del 19q13 41 99 (17%) 478 0.004
(1.00) 		4e-05
(0.0244) 		0.0767
(1.00) 		0.0442
(1.00) 		0.0012
(0.679) 		1e-05
(0.0071) 		0.053
(1.00) 		0.334
(1.00) 		0.0353
(1.00) 		0.0935
(1.00)
amp 1p36 21 92 (16%) 485 0.589
(1.00) 		0.424
(1.00) 		0.402
(1.00) 		0.114
(1.00) 		1e-05
(0.0071) 		0.57
(1.00) 		0.0267
(1.00) 		0.0952
(1.00) 		0.0121
(1.00) 		0.02
(1.00)
amp 1q32 1 160 (28%) 417 0.819
(1.00) 		0.0614
(1.00) 		0.334
(1.00) 		0.148
(1.00) 		1e-05
(0.0071) 		0.306
(1.00) 		0.914
(1.00) 		0.668
(1.00) 		0.551
(1.00) 		0.0899
(1.00)
amp 1q44 99 (17%) 478 0.144
(1.00) 		0.62
(1.00) 		0.608
(1.00) 		0.308
(1.00) 		1e-05
(0.0071) 		0.6
(1.00) 		0.318
(1.00) 		0.0829
(1.00) 		0.962
(1.00) 		0.551
(1.00)
amp 3q26 33 111 (19%) 466 0.0076
(1.00) 		0.213
(1.00) 		0.449
(1.00) 		0.0564
(1.00) 		1e-05
(0.0071) 		0.0663
(1.00) 		0.0871
(1.00) 		0.666
(1.00) 		0.277
(1.00) 		0.699
(1.00)
amp 4q12 108 (19%) 469 0.00079
(0.451) 		0.00312
(1.00) 		0.537
(1.00) 		0.472
(1.00) 		3e-05
(0.0185) 		0.00998
(1.00) 		0.471
(1.00) 		0.603
(1.00) 		0.158
(1.00) 		0.418
(1.00)
amp 12p13 32 84 (15%) 493 0.666
(1.00) 		0.384
(1.00) 		0.342
(1.00) 		0.429
(1.00) 		0.00014
(0.0822) 		0.469
(1.00) 		0.391
(1.00) 		0.37
(1.00) 		0.317
(1.00) 		0.55
(1.00)
amp 12q14 1 134 (23%) 443 0.0663
(1.00) 		0.148
(1.00) 		0.0967
(1.00) 		0.0884
(1.00) 		1e-05
(0.0071) 		0.482
(1.00) 		0.0928
(1.00) 		0.248
(1.00) 		0.0431
(1.00) 		0.14
(1.00)
amp 12q15 93 (16%) 484 0.729
(1.00) 		0.317
(1.00) 		0.706
(1.00) 		0.278
(1.00) 		1e-05
(0.0071) 		0.491
(1.00) 		0.295
(1.00) 		0.301
(1.00) 		0.315
(1.00) 		0.899
(1.00)
amp 17q25 1 84 (15%) 493 0.0133
(1.00) 		0.255
(1.00) 		0.283
(1.00) 		0.728
(1.00) 		1e-05
(0.0071) 		0.172
(1.00) 		0.136
(1.00) 		0.189
(1.00) 		0.865
(1.00) 		0.696
(1.00)
amp 21q21 1 70 (12%) 507 0.00524
(1.00) 		0.0608
(1.00) 		0.018
(1.00) 		0.00761
(1.00) 		8e-05
(0.0479) 		0.0182
(1.00) 		0.669
(1.00) 		0.0836
(1.00) 		0.097
(1.00) 		0.407
(1.00)
del 1p36 23 136 (24%) 441 0.0688
(1.00) 		0.184
(1.00) 		0.57
(1.00) 		0.553
(1.00) 		0.00024
(0.14) 		0.551
(1.00) 		0.279
(1.00) 		0.295
(1.00) 		0.0157
(1.00) 		0.0693
(1.00)
del 2q22 1 47 (8%) 530 0.0057
(1.00) 		0.0299
(1.00) 		0.389
(1.00) 		0.55
(1.00) 		1e-05
(0.0071) 		0.453
(1.00) 		0.478
(1.00) 		0.339
(1.00) 		0.181
(1.00) 		0.432
(1.00)
del 3p21 1 53 (9%) 524 0.244
(1.00) 		0.134
(1.00) 		0.675
(1.00) 		0.484
(1.00) 		7e-05
(0.0421) 		0.0469
(1.00) 		0.136
(1.00) 		0.914
(1.00) 		0.459
(1.00) 		0.107
(1.00)
del 3q13 31 56 (10%) 521 0.575
(1.00) 		0.346
(1.00) 		0.608
(1.00) 		0.511
(1.00) 		3e-05
(0.0185) 		0.0248
(1.00) 		0.975
(1.00) 		0.203
(1.00) 		1
(1.00) 		0.177
(1.00)
del 3q22 1 58 (10%) 519 0.793
(1.00) 		0.628
(1.00) 		0.956
(1.00) 		1
(1.00) 		0.0004
(0.232) 		0.083
(1.00) 		0.962
(1.00) 		0.319
(1.00) 		1
(1.00) 		0.217
(1.00)
del 4p16 3 78 (14%) 499 0.0477
(1.00) 		0.00478
(1.00) 		0.321
(1.00) 		0.249
(1.00) 		0.00195
(1.00) 		9e-05
(0.0537) 		0.834
(1.00) 		0.453
(1.00) 		0.872
(1.00) 		0.945
(1.00)
del 6q22 31 158 (27%) 419 0.633
(1.00) 		0.991
(1.00) 		0.291
(1.00) 		0.287
(1.00) 		1e-05
(0.0071) 		0.252
(1.00) 		0.345
(1.00) 		0.189
(1.00) 		0.796
(1.00) 		0.111
(1.00)
del 12q12 77 (13%) 500 0.0135
(1.00) 		0.00065
(0.372) 		0.27
(1.00) 		0.084
(1.00) 		9e-05
(0.0537) 		0.0632
(1.00) 		0.0968
(1.00) 		0.271
(1.00) 		1
(1.00) 		0.661
(1.00)
del 17p13 2 88 (15%) 489 0.00283
(1.00) 		0.0255
(1.00) 		0.952
(1.00) 		0.948
(1.00) 		1e-05
(0.0071) 		0.0744
(1.00) 		0.633
(1.00) 		0.41
(1.00) 		0.587
(1.00) 		0.819
(1.00)
del 18q22 3 82 (14%) 495 0.127
(1.00) 		0.0875
(1.00) 		0.788
(1.00) 		0.391
(1.00) 		9e-05
(0.0537) 		0.19
(1.00) 		0.0102
(1.00) 		0.00793
(1.00) 		0.197
(1.00) 		0.273
(1.00)
del 22q13 32 212 (37%) 365 0.714
(1.00) 		0.972
(1.00) 		0.0405
(1.00) 		0.411
(1.00) 		2e-05
(0.0125) 		0.264
(1.00) 		0.794
(1.00) 		0.325
(1.00) 		0.0491
(1.00) 		0.0855
(1.00)
del xp22 2 118 (20%) 459 0.006
(1.00) 		0.0018
(0.999) 		0.113
(1.00) 		0.171
(1.00) 		1e-05
(0.0071) 		0.00129
(0.725) 		0.685
(1.00) 		0.248
(1.00) 		0.305
(1.00) 		0.668
(1.00)
amp 2p24 3 49 (8%) 528 0.0994
(1.00) 		0.0173
(1.00) 		0.432
(1.00) 		0.979
(1.00) 		0.00123
(0.694) 		0.0159
(1.00) 		0.433
(1.00) 		0.365
(1.00) 		0.885
(1.00) 		0.625
(1.00)
amp 4p16 3 48 (8%) 529 0.31
(1.00) 		0.726
(1.00) 		0.858
(1.00) 		0.0831
(1.00) 		0.184
(1.00) 		0.558
(1.00) 		0.705
(1.00) 		0.476
(1.00) 		1
(1.00) 		1
(1.00)
amp 11p13 31 (5%) 546 0.786
(1.00) 		0.351
(1.00) 		0.552
(1.00) 		0.247
(1.00) 		0.349
(1.00) 		0.904
(1.00) 		0.712
(1.00) 		0.34
(1.00) 		1
(1.00) 		0.888
(1.00)
amp 13q34 32 (6%) 545 0.261
(1.00) 		0.199
(1.00) 		0.0288
(1.00) 		0.481
(1.00) 		0.0582
(1.00) 		0.236
(1.00) 		0.021
(1.00) 		0.237
(1.00) 		0.49
(1.00) 		0.802
(1.00)
amp 13q34 30 (5%) 547 0.14
(1.00) 		0.209
(1.00) 		0.216
(1.00) 		0.786
(1.00) 		0.0619
(1.00) 		0.488
(1.00) 		0.0534
(1.00) 		0.301
(1.00) 		0.366
(1.00) 		0.79
(1.00)
amp 14q32 33 36 (6%) 541 0.189
(1.00) 		0.658
(1.00) 		0.0903
(1.00) 		0.92
(1.00) 		0.254
(1.00) 		0.542
(1.00) 		0.0252
(1.00) 		0.34
(1.00) 		0.0374
(1.00) 		0.0681
(1.00)
amp 17p13 2 51 (9%) 526 0.00063
(0.362) 		0.0134
(1.00) 		0.0481
(1.00) 		0.112
(1.00) 		0.00206
(1.00) 		0.0119
(1.00) 		0.126
(1.00) 		0.513
(1.00) 		0.405
(1.00) 		0.569
(1.00)
del 1p36 32 100 (17%) 477 0.92
(1.00) 		0.711
(1.00) 		0.586
(1.00) 		0.174
(1.00) 		0.509
(1.00) 		0.182
(1.00) 		0.601
(1.00) 		0.309
(1.00) 		0.25
(1.00) 		0.578
(1.00)
del 1p32 3 61 (11%) 516 0.243
(1.00) 		0.365
(1.00) 		0.831
(1.00) 		0.16
(1.00) 		0.491
(1.00) 		0.84
(1.00) 		0.706
(1.00) 		0.475
(1.00) 		0.803
(1.00) 		0.105
(1.00)
del 1p22 1 48 (8%) 529 0.976
(1.00) 		0.552
(1.00) 		0.812
(1.00) 		0.00514
(1.00) 		0.141
(1.00) 		0.0889
(1.00) 		0.888
(1.00) 		0.721
(1.00) 		1
(1.00) 		0.321
(1.00)
del 1q42 11 51 (9%) 526 0.22
(1.00) 		0.823
(1.00) 		0.513
(1.00) 		0.282
(1.00) 		0.606
(1.00) 		0.557
(1.00) 		0.139
(1.00) 		0.0164
(1.00) 		0.684
(1.00) 		0.193
(1.00)
del 1q44 35 (6%) 542 0.815
(1.00) 		0.473
(1.00) 		0.732
(1.00) 		0.247
(1.00) 		0.217
(1.00) 		1
(1.00) 		0.663
(1.00) 		0.44
(1.00) 		0.54
(1.00) 		0.321
(1.00)
del 2q37 1 55 (10%) 522 0.102
(1.00) 		0.00557
(1.00) 		0.311
(1.00) 		0.825
(1.00) 		0.0194
(1.00) 		0.222
(1.00) 		0.782
(1.00) 		0.27
(1.00) 		0.184
(1.00) 		0.0526
(1.00)
del 3q29 65 (11%) 512 0.0896
(1.00) 		0.187
(1.00) 		0.537
(1.00) 		0.876
(1.00) 		0.045
(1.00) 		0.328
(1.00) 		0.453
(1.00) 		0.0595
(1.00) 		0.954
(1.00) 		0.795
(1.00)
del 6q26 179 (31%) 398 0.741
(1.00) 		0.755
(1.00) 		0.479
(1.00) 		0.546
(1.00) 		0.00136
(0.762) 		0.0168
(1.00) 		0.0347
(1.00) 		0.341
(1.00) 		0.762
(1.00) 		0.0182
(1.00)
del 8p23 2 66 (11%) 511 0.375
(1.00) 		0.247
(1.00) 		0.179
(1.00) 		0.276
(1.00) 		0.489
(1.00) 		0.325
(1.00) 		0.945
(1.00) 		0.902
(1.00) 		0.721
(1.00) 		0.437
(1.00)
del 9q34 2 79 (14%) 498 0.213
(1.00) 		0.105
(1.00) 		0.519
(1.00) 		0.231
(1.00) 		0.395
(1.00) 		0.845
(1.00) 		0.228
(1.00) 		0.225
(1.00) 		0.442
(1.00) 		0.302
(1.00)
del 12p13 1 72 (12%) 505 0.0504
(1.00) 		0.0136
(1.00) 		0.253
(1.00) 		0.231
(1.00) 		0.0839
(1.00) 		0.154
(1.00) 		0.682
(1.00) 		0.558
(1.00) 		1
(1.00) 		0.929
(1.00)
del 16p12 2 92 (16%) 485 0.247
(1.00) 		0.232
(1.00) 		0.395
(1.00) 		0.872
(1.00) 		0.173
(1.00) 		0.0702
(1.00) 		0.441
(1.00) 		0.114
(1.00) 		0.444
(1.00) 		0.332
(1.00)
del 16q23 1 101 (18%) 476 0.0148
(1.00) 		0.491
(1.00) 		0.875
(1.00) 		0.538
(1.00) 		0.0126
(1.00) 		0.858
(1.00) 		0.0555
(1.00) 		0.00602
(1.00) 		0.879
(1.00) 		0.784
(1.00)
del 21q21 1 56 (10%) 521 0.0113
(1.00) 		0.00111
(0.63) 		0.0157
(1.00) 		0.208
(1.00) 		0.0907
(1.00) 		0.00078
(0.446) 		0.00324
(1.00) 		0.0328
(1.00) 		0.662
(1.00) 		1
(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 162 218 197
AMP PEAK 1(1P36.21) MUTATED 52 22 18
AMP PEAK 1(1P36.21) WILD-TYPE 110 196 179

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 162 218 197
AMP PEAK 2(1Q32.1) MUTATED 75 47 38
AMP PEAK 2(1Q32.1) WILD-TYPE 87 171 159

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 162 218 197
AMP PEAK 3(1Q44) MUTATED 57 22 20
AMP PEAK 3(1Q44) WILD-TYPE 105 196 177

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 162 218 197
AMP PEAK 5(3Q26.33) MUTATED 61 24 26
AMP PEAK 5(3Q26.33) WILD-TYPE 101 194 171

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

'amp_4q12' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
AMP PEAK 7(4Q12) MUTATED 50 26 32
AMP PEAK 7(4Q12) WILD-TYPE 112 192 165

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 162 218 197
AMP PEAK 8(7P11.2) MUTATED 153 217 137
AMP PEAK 8(7P11.2) WILD-TYPE 9 1 60

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 89 108 78
AMP PEAK 8(7P11.2) MUTATED 85 106 50
AMP PEAK 8(7P11.2) WILD-TYPE 4 2 28

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

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 = 7e-05 (Fisher's exact test), Q value = 0.042

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

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

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 = 5e-05 (Fisher's exact test), Q value = 0.03

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 162 218 197
AMP PEAK 9(7Q11.21) MUTATED 145 189 130
AMP PEAK 9(7Q11.21) WILD-TYPE 17 29 67

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

'amp_7q11.21' versus 'METHLYATION_CNMF'

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

Table S21.  Gene #9: 'amp_7q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
AMP PEAK 9(7Q11.21) MUTATED 83 91 46
AMP PEAK 9(7Q11.21) WILD-TYPE 6 17 32

Figure S21.  Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.036

Table S22.  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 S22.  Get High-res Image Gene #9: 'amp_7q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MRNA_CNMF'

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

Table S23.  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 S23.  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 S24.  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 S24.  Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q21.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.071

Table S25.  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 S25.  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 S26.  Gene #10: 'amp_7q21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
AMP PEAK 10(7Q21.2) MUTATED 144 199 137
AMP PEAK 10(7Q21.2) WILD-TYPE 18 19 60

Figure S26.  Get High-res Image Gene #10: 'amp_7q21.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.065

Table S27.  Gene #10: 'amp_7q21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
AMP PEAK 10(7Q21.2) MUTATED 80 93 50
AMP PEAK 10(7Q21.2) WILD-TYPE 9 15 28

Figure S27.  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 S28.  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 S28.  Get High-res Image Gene #11: 'amp_7q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

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

Table S29.  Gene #11: 'amp_7q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
AMP PEAK 11(7Q31.2) MUTATED 140 193 140
AMP PEAK 11(7Q31.2) WILD-TYPE 22 25 57

Figure S29.  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 S30.  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 S30.  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 S31.  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 S31.  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 S32.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
AMP PEAK 12(8Q24.21) MUTATED 39 8 23
AMP PEAK 12(8Q24.21) WILD-TYPE 123 210 174

Figure S32.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.054

Table S33.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
AMP PEAK 12(8Q24.21) MUTATED 5 12 23
AMP PEAK 12(8Q24.21) WILD-TYPE 84 96 55

Figure S33.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12p13.32' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.082

Table S34.  Gene #14: 'amp_12p13.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
AMP PEAK 14(12P13.32) MUTATED 40 18 26
AMP PEAK 14(12P13.32) WILD-TYPE 122 200 171

Figure S34.  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 S35.  Gene #15: 'amp_12q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
AMP PEAK 15(12Q14.1) MUTATED 65 39 30
AMP PEAK 15(12Q14.1) WILD-TYPE 97 179 167

Figure S35.  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 S36.  Gene #16: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
AMP PEAK 16(12Q15) MUTATED 48 25 20
AMP PEAK 16(12Q15) WILD-TYPE 114 193 177

Figure S36.  Get High-res Image Gene #16: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'amp_17q25.1' versus 'CN_CNMF'

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

Table S37.  Gene #21: 'amp_17q25.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
AMP PEAK 21(17Q25.1) MUTATED 42 20 22
AMP PEAK 21(17Q25.1) WILD-TYPE 120 198 175

Figure S37.  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 S38.  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 S38.  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 S39.  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 S39.  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 S40.  Gene #22: 'amp_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
AMP PEAK 22(19P13.3) MUTATED 46 148 50
AMP PEAK 22(19P13.3) WILD-TYPE 116 70 147

Figure S40.  Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.3' versus 'METHLYATION_CNMF'

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

Table S41.  Gene #22: 'amp_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
AMP PEAK 22(19P13.3) MUTATED 29 72 17
AMP PEAK 22(19P13.3) WILD-TYPE 60 36 61

Figure S41.  Get High-res Image Gene #22: 'amp_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.054

Table S42.  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 S42.  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 S43.  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 S43.  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 S44.  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 S44.  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 S45.  Gene #23: 'amp_19p13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
AMP PEAK 23(19P13.2) MUTATED 50 150 49
AMP PEAK 23(19P13.2) WILD-TYPE 112 68 148

Figure S45.  Get High-res Image Gene #23: 'amp_19p13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

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

Table S46.  Gene #23: 'amp_19p13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
AMP PEAK 23(19P13.2) MUTATED 31 74 19
AMP PEAK 23(19P13.2) WILD-TYPE 58 34 59

Figure S46.  Get High-res Image Gene #23: 'amp_19p13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.048

Table S47.  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 S47.  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 S48.  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 S48.  Get High-res Image Gene #24: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

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

Table S49.  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 S49.  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 S50.  Gene #24: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
AMP PEAK 24(19Q12) MUTATED 44 132 40
AMP PEAK 24(19Q12) WILD-TYPE 118 86 157

Figure S50.  Get High-res Image Gene #24: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

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

Table S51.  Gene #24: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
AMP PEAK 24(19Q12) MUTATED 31 64 10
AMP PEAK 24(19Q12) WILD-TYPE 58 44 68

Figure S51.  Get High-res Image Gene #24: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_21q21.1' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.048

Table S52.  Gene #25: 'amp_21q21.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
AMP PEAK 25(21Q21.1) MUTATED 34 13 23
AMP PEAK 25(21Q21.1) WILD-TYPE 128 205 174

Figure S52.  Get High-res Image Gene #25: 'amp_21q21.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.23' versus 'CN_CNMF'

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

Table S53.  Gene #27: 'del_1p36.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 2(1P36.23) MUTATED 34 71 31
DEL PEAK 2(1P36.23) WILD-TYPE 128 147 166

Figure S53.  Get High-res Image Gene #27: 'del_1p36.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q22.1' versus 'CN_CNMF'

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

Table S54.  Gene #32: 'del_2q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 7(2Q22.1) MUTATED 29 6 12
DEL PEAK 7(2Q22.1) WILD-TYPE 133 212 185

Figure S54.  Get High-res Image Gene #32: 'del_2q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_3p21.1' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.042

Table S55.  Gene #34: 'del_3p21.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 9(3P21.1) MUTATED 25 7 21
DEL PEAK 9(3P21.1) WILD-TYPE 137 211 176

Figure S55.  Get High-res Image Gene #34: 'del_3p21.1' 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 S56.  Gene #35: 'del_3q13.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 10(3Q13.31) MUTATED 26 7 23
DEL PEAK 10(3Q13.31) WILD-TYPE 136 211 174

Figure S56.  Get High-res Image Gene #35: 'del_3q13.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_3q22.1' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.23

Table S57.  Gene #36: 'del_3q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 11(3Q22.1) MUTATED 24 9 25
DEL PEAK 11(3Q22.1) WILD-TYPE 138 209 172

Figure S57.  Get High-res Image Gene #36: 'del_3q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.054

Table S58.  Gene #38: 'del_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
DEL PEAK 13(4P16.3) MUTATED 2 13 18
DEL PEAK 13(4P16.3) WILD-TYPE 87 95 60

Figure S58.  Get High-res Image Gene #38: 'del_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.19

Table S59.  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 S59.  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 S60.  Gene #39: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 14(4Q34.3) MUTATED 47 20 26
DEL PEAK 14(4Q34.3) WILD-TYPE 115 198 171

Figure S60.  Get High-res Image Gene #39: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q34' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S61.  Gene #40: 'del_5q34' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 15(5Q34) MUTATED 8 26 12 17
DEL PEAK 15(5Q34) WILD-TYPE 139 70 140 96

Figure S61.  Get High-res Image Gene #40: 'del_5q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q34' versus 'MRNA_CHIERARCHICAL'

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

Table S62.  Gene #40: 'del_5q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 15(5Q34) MUTATED 10 31 11 11
DEL PEAK 15(5Q34) WILD-TYPE 138 71 89 147

Figure S62.  Get High-res Image Gene #40: 'del_5q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q34' versus 'MIR_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.042

Table S63.  Gene #40: 'del_5q34' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 156 183 87 120
DEL PEAK 15(5Q34) MUTATED 6 36 9 11
DEL PEAK 15(5Q34) WILD-TYPE 150 147 78 109

Figure S63.  Get High-res Image Gene #40: 'del_5q34' versus Molecular Subtype #3: 'MIR_CNMF'

'del_5q34' versus 'METHLYATION_CNMF'

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

Table S64.  Gene #40: 'del_5q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
DEL PEAK 15(5Q34) MUTATED 2 11 22
DEL PEAK 15(5Q34) WILD-TYPE 87 97 56

Figure S64.  Get High-res Image Gene #40: 'del_5q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6q22.31' versus 'CN_CNMF'

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

Table S65.  Gene #41: 'del_6q22.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 16(6Q22.31) MUTATED 71 48 39
DEL PEAK 16(6Q22.31) WILD-TYPE 91 170 158

Figure S65.  Get High-res Image Gene #41: 'del_6q22.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p21.3' versus 'MRNA_CNMF'

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

Table S66.  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 S66.  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 S67.  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 S67.  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 S68.  Gene #44: 'del_9p21.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 19(9P21.3) MUTATED 102 195 124
DEL PEAK 19(9P21.3) WILD-TYPE 60 23 73

Figure S68.  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 S69.  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 S69.  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 S70.  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 S70.  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 S71.  Gene #46: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 21(10P15.3) MUTATED 147 206 117
DEL PEAK 21(10P15.3) WILD-TYPE 15 12 80

Figure S71.  Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

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

Table S72.  Gene #46: 'del_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
DEL PEAK 21(10P15.3) MUTATED 78 97 45
DEL PEAK 21(10P15.3) WILD-TYPE 11 11 33

Figure S72.  Get High-res Image Gene #46: 'del_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S73.  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 S73.  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 S74.  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 S74.  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 S75.  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 S75.  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 S76.  Gene #47: 'del_10p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 22(10P13) MUTATED 147 208 116
DEL PEAK 22(10P13) WILD-TYPE 15 10 81

Figure S76.  Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p13' versus 'METHLYATION_CNMF'

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

Table S77.  Gene #47: 'del_10p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
DEL PEAK 22(10P13) MUTATED 78 96 44
DEL PEAK 22(10P13) WILD-TYPE 11 12 34

Figure S77.  Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p13' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.11

Table S78.  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 S78.  Get High-res Image Gene #47: 'del_10p13' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_10p13' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.059

Table S79.  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 S79.  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 S80.  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 S80.  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 S81.  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 S81.  Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p11.23' versus 'MIR_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S82.  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 S82.  Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p11.23' versus 'MIR_CHIERARCHICAL'

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

Table S83.  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 S83.  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 S84.  Gene #48: 'del_10p11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 23(10P11.23) MUTATED 148 212 116
DEL PEAK 23(10P11.23) WILD-TYPE 14 6 81

Figure S84.  Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p11.23' versus 'METHLYATION_CNMF'

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

Table S85.  Gene #48: 'del_10p11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
DEL PEAK 23(10P11.23) MUTATED 79 96 45
DEL PEAK 23(10P11.23) WILD-TYPE 10 12 33

Figure S85.  Get High-res Image Gene #48: 'del_10p11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNA_CNMF'

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

Table S86.  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 S86.  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 S87.  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 S87.  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 S88.  Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 24(10Q23.31) MUTATED 154 216 144
DEL PEAK 24(10Q23.31) WILD-TYPE 8 2 53

Figure S88.  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 S89.  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 S89.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q26.3' versus 'MRNA_CHIERARCHICAL'

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

Table S90.  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 S90.  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 S91.  Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 25(10Q26.3) MUTATED 151 216 148
DEL PEAK 25(10Q26.3) WILD-TYPE 11 2 49

Figure S91.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

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

Table S92.  Gene #50: 'del_10q26.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
DEL PEAK 25(10Q26.3) MUTATED 79 105 58
DEL PEAK 25(10Q26.3) WILD-TYPE 10 3 20

Figure S92.  Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNA_CNMF'

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

Table S93.  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 S93.  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 S94.  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 S94.  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 S95.  Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 26(11P15.5) MUTATED 64 13 52
DEL PEAK 26(11P15.5) WILD-TYPE 98 205 145

Figure S95.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

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

Table S96.  Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
DEL PEAK 26(11P15.5) MUTATED 13 20 36
DEL PEAK 26(11P15.5) WILD-TYPE 76 88 42

Figure S96.  Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11p11.2' versus 'MRNA_CNMF'

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

Table S97.  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 S97.  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 S98.  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 S98.  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 S99.  Gene #52: 'del_11p11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 27(11P11.2) MUTATED 58 11 36
DEL PEAK 27(11P11.2) WILD-TYPE 104 207 161

Figure S99.  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 S100.  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 S100.  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 S101.  Gene #53: 'del_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 28(11Q14.1) MUTATED 63 10 23
DEL PEAK 28(11Q14.1) WILD-TYPE 99 208 174

Figure S101.  Get High-res Image Gene #53: 'del_11q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q12' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.054

Table S102.  Gene #55: 'del_12q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 30(12Q12) MUTATED 35 15 27
DEL PEAK 30(12Q12) WILD-TYPE 127 203 170

Figure S102.  Get High-res Image Gene #55: 'del_12q12' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q15' versus 'MRNA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.071

Table S103.  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 S103.  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 S104.  Gene #56: 'del_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 31(12Q15) MUTATED 40 14 25
DEL PEAK 31(12Q15) WILD-TYPE 122 204 172

Figure S104.  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 S105.  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 S105.  Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.03

Table S106.  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 S106.  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 S107.  Gene #57: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 32(13Q14.2) MUTATED 123 37 81
DEL PEAK 32(13Q14.2) WILD-TYPE 39 181 116

Figure S107.  Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q22.1' versus 'MRNA_CNMF'

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

Table S108.  Gene #58: 'del_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 96 152 113
DEL PEAK 33(13Q22.1) MUTATED 81 40 34 50
DEL PEAK 33(13Q22.1) WILD-TYPE 66 56 118 63

Figure S108.  Get High-res Image Gene #58: 'del_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.071

Table S109.  Gene #58: 'del_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 33(13Q22.1) MUTATED 68 45 21 71
DEL PEAK 33(13Q22.1) WILD-TYPE 80 57 79 87

Figure S109.  Get High-res Image Gene #58: 'del_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q22.1' versus 'CN_CNMF'

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

Table S110.  Gene #58: 'del_13q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 33(13Q22.1) MUTATED 123 35 72
DEL PEAK 33(13Q22.1) WILD-TYPE 39 183 125

Figure S110.  Get High-res Image Gene #58: 'del_13q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q13.1' versus 'MRNA_CNMF'

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

Table S111.  Gene #59: '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 34(14Q13.1) MUTATED 54 39 25 43
DEL PEAK 34(14Q13.1) WILD-TYPE 93 57 127 70

Figure S111.  Get High-res Image Gene #59: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q13.1' versus 'MRNA_CHIERARCHICAL'

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

Table S112.  Gene #59: '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 34(14Q13.1) MUTATED 49 42 15 55
DEL PEAK 34(14Q13.1) WILD-TYPE 99 60 85 103

Figure S112.  Get High-res Image Gene #59: '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 S113.  Gene #59: 'del_14q13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 34(14Q13.1) MUTATED 91 29 58
DEL PEAK 34(14Q13.1) WILD-TYPE 71 189 139

Figure S113.  Get High-res Image Gene #59: '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 S114.  Gene #60: '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 35(14Q24.2) MUTATED 51 43 22 45
DEL PEAK 35(14Q24.2) WILD-TYPE 96 53 130 68

Figure S114.  Get High-res Image Gene #60: 'del_14q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q24.2' versus 'MRNA_CHIERARCHICAL'

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

Table S115.  Gene #60: '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 35(14Q24.2) MUTATED 48 46 14 53
DEL PEAK 35(14Q24.2) WILD-TYPE 100 56 86 105

Figure S115.  Get High-res Image Gene #60: '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 S116.  Gene #60: 'del_14q24.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 35(14Q24.2) MUTATED 91 21 61
DEL PEAK 35(14Q24.2) WILD-TYPE 71 197 136

Figure S116.  Get High-res Image Gene #60: 'del_14q24.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q14' versus 'MRNA_CNMF'

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

Table S117.  Gene #61: 'del_15q14' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S117.  Get High-res Image Gene #61: 'del_15q14' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q14' versus 'MRNA_CHIERARCHICAL'

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

Table S118.  Gene #61: 'del_15q14' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 102 100 158
DEL PEAK 36(15Q14) MUTATED 34 47 12 45
DEL PEAK 36(15Q14) WILD-TYPE 114 55 88 113

Figure S118.  Get High-res Image Gene #61: 'del_15q14' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q14' versus 'MIR_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.036

Table S119.  Gene #61: 'del_15q14' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 293 124 129
DEL PEAK 36(15Q14) MUTATED 95 15 33
DEL PEAK 36(15Q14) WILD-TYPE 198 109 96

Figure S119.  Get High-res Image Gene #61: '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 S120.  Gene #61: 'del_15q14' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 36(15Q14) MUTATED 72 38 44
DEL PEAK 36(15Q14) WILD-TYPE 90 180 153

Figure S120.  Get High-res Image Gene #61: '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 S121.  Gene #64: 'del_17p13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 39(17P13.2) MUTATED 47 9 32
DEL PEAK 39(17P13.2) WILD-TYPE 115 209 165

Figure S121.  Get High-res Image Gene #64: 'del_17p13.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_17p13.1' versus 'MRNA_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S122.  Gene #65: '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 40(17P13.1) MUTATED 32 27 13 16
DEL PEAK 40(17P13.1) WILD-TYPE 115 69 139 97

Figure S122.  Get High-res Image Gene #65: '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 S123.  Gene #65: 'del_17p13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 40(17P13.1) MUTATED 55 8 35
DEL PEAK 40(17P13.1) WILD-TYPE 107 210 162

Figure S123.  Get High-res Image Gene #65: '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 S124.  Gene #66: '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 41(17Q11.2) MUTATED 35 9 12 5
DEL PEAK 41(17Q11.2) WILD-TYPE 112 87 140 108

Figure S124.  Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

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

Table S125.  Gene #66: '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 41(17Q11.2) MUTATED 35 7 9 10
DEL PEAK 41(17Q11.2) WILD-TYPE 113 95 91 148

Figure S125.  Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

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

Table S126.  Gene #66: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 41(17Q11.2) MUTATED 33 9 30
DEL PEAK 41(17Q11.2) WILD-TYPE 129 209 167

Figure S126.  Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.16

Table S127.  Gene #66: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
DEL PEAK 41(17Q11.2) MUTATED 18 4 4
DEL PEAK 41(17Q11.2) WILD-TYPE 71 104 74

Figure S127.  Get High-res Image Gene #66: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_18q22.3' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.054

Table S128.  Gene #67: 'del_18q22.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 42(18Q22.3) MUTATED 36 15 31
DEL PEAK 42(18Q22.3) WILD-TYPE 126 203 166

Figure S128.  Get High-res Image Gene #67: 'del_18q22.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.41' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.024

Table S129.  Gene #68: '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 43(19Q13.41) MUTATED 23 34 8 25
DEL PEAK 43(19Q13.41) WILD-TYPE 125 68 92 133

Figure S129.  Get High-res Image Gene #68: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.41' versus 'METHLYATION_CNMF'

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

Table S130.  Gene #68: 'del_19q13.41' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 108 78
DEL PEAK 43(19Q13.41) MUTATED 12 8 29
DEL PEAK 43(19Q13.41) WILD-TYPE 77 100 49

Figure S130.  Get High-res Image Gene #68: 'del_19q13.41' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_22q13.32' versus 'CN_CNMF'

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

Table S131.  Gene #70: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 45(22Q13.32) MUTATED 85 63 64
DEL PEAK 45(22Q13.32) WILD-TYPE 77 155 133

Figure S131.  Get High-res Image Gene #70: '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 S132.  Gene #71: 'del_xp22.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 218 197
DEL PEAK 46(XP22.2) MUTATED 59 26 33
DEL PEAK 46(XP22.2) WILD-TYPE 103 192 164

Figure S132.  Get High-res Image Gene #71: 'del_xp22.2' 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 = 577

  • 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.

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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