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 59 focal events and 12 molecular subtypes across 165 patients, 111 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'CN_CNMF'.

  • amp_1q32.2 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

  • amp_5q22.3 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • amp_6p21.1 cnv correlated to 'CN_CNMF'.

  • amp_8p11.23 cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_8p11.21 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

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

  • amp_11p15.5 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • amp_11q13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_12p13.33 cnv correlated to 'CN_CNMF'.

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

  • amp_13q12.13 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_13q12.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_13q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_16p11.2 cnv correlated to 'CN_CNMF'.

  • amp_17q12 cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • amp_17q24.1 cnv correlated to 'CN_CNMF'.

  • amp_19p13.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_20q11.21 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_20q11.23 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_20q13.31 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_1p36.11 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_1p33 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • del_1p13.2 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_2p12 cnv correlated to 'CN_CNMF'.

  • del_4p13 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • del_4q22.1 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • del_4q35.1 cnv correlated to 'CN_CNMF'.

  • del_5q12.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_5q22.2 cnv correlated to 'MRNA_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.

  • del_6p25.3 cnv correlated to 'METHLYATION_CNMF'.

  • del_6q26 cnv correlated to 'CN_CNMF'.

  • del_8p23.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_8p11.21 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_10q21.1 cnv correlated to 'RPPA_CNMF'.

  • del_10q25.2 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_11q22.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_12q22 cnv correlated to 'CN_CNMF'.

  • del_14q11.2 cnv correlated to 'CN_CNMF'.

  • del_15q21.1 cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • del_15q22.33 cnv correlated to 'CN_CNMF'.

  • del_16p13.3 cnv correlated to 'METHLYATION_CNMF'.

  • del_16q23.1 cnv correlated to 'CN_CNMF'.

  • del_18q21.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_18q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_19p13.3 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • del_20p12.1 cnv correlated to 'CN_CNMF'.

  • del_22q13.31 cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xp22.33 cnv correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 59 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 111 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 13q22 1 120 (73%) 45 0.267
(0.62) 		0.0658
(0.335) 		1e-05
(0.000787) 		0.0351
(0.234) 		0.907
(0.999) 		0.268
(0.62) 		0.00017
(0.00708) 		3e-05
(0.00193) 		0.00448
(0.0647) 		0.0106
(0.112) 		1
(1.00) 		0.4
(0.72)
del 11q22 3 38 (23%) 127 0.0336
(0.231) 		0.03
(0.219) 		0.00269
(0.0477) 		0.0357
(0.234) 		0.69
(0.908) 		0.134
(0.476) 		0.00674
(0.0884) 		0.00732
(0.0894) 		0.452
(0.768) 		0.966
(1.00) 		0.415
(0.738) 		0.664
(0.891)
amp 11q13 3 28 (17%) 137 0.326
(0.686) 		0.33
(0.689) 		0.036
(0.234) 		0.0046
(0.0651) 		0.91
(1.00) 		0.73
(0.919) 		0.00263
(0.0477) 		0.0118
(0.121) 		0.0133
(0.132) 		0.342
(0.701) 		0.0784
(0.371) 		0.135
(0.476)
amp 13q12 13 126 (76%) 39 0.417
(0.738) 		0.173
(0.536) 		1e-05
(0.000787) 		0.172
(0.535) 		0.325
(0.686) 		0.437
(0.755) 		0.00092
(0.0225) 		1e-05
(0.000787) 		0.00294
(0.0496) 		0.00416
(0.0627) 		0.939
(1.00) 		0.781
(0.934)
amp 13q12 2 125 (76%) 40 0.365
(0.703) 		0.234
(0.591) 		1e-05
(0.000787) 		0.117
(0.447) 		0.591
(0.858) 		0.587
(0.857) 		0.0006
(0.0185) 		0.0001
(0.00506) 		0.0216
(0.176) 		0.0218
(0.176) 		0.828
(0.954) 		0.635
(0.875)
amp 20q11 21 146 (88%) 19 0.0079
(0.0917) 		0.162
(0.512) 		0.00074
(0.0202) 		0.0203
(0.171) 		0.194
(0.554) 		0.37
(0.703) 		0.0976
(0.416) 		0.00029
(0.0108) 		0.00732
(0.0894) 		0.397
(0.719) 		0.499
(0.803) 		0.591
(0.858)
amp 19p13 2 36 (22%) 129 0.0196
(0.171) 		0.252
(0.61) 		0.00124
(0.0293) 		0.531
(0.821) 		0.545
(0.825) 		0.0853
(0.39) 		0.0313
(0.222) 		0.0361
(0.234) 		0.588
(0.857) 		0.7
(0.908) 		0.869
(0.972) 		0.869
(0.972)
amp 20q11 23 147 (89%) 18 0.00766
(0.0917) 		0.16
(0.512) 		0.00141
(0.0322) 		0.0476
(0.283) 		0.194
(0.554) 		0.369
(0.703) 		0.162
(0.512) 		0.00015
(0.00664) 		0.0136
(0.132) 		0.278
(0.628) 		0.362
(0.703) 		1
(1.00)
amp 20q13 31 148 (90%) 17 0.00473
(0.0657) 		0.107
(0.432) 		0.00245
(0.0469) 		0.047
(0.283) 		0.195
(0.554) 		0.37
(0.703) 		0.173
(0.536) 		6e-05
(0.00354) 		0.0221
(0.176) 		0.388
(0.713) 		0.36
(0.703) 		1
(1.00)
amp 8p11 23 53 (32%) 112 0.00316
(0.0508) 		0.206
(0.563) 		1e-05
(0.000787) 		0.264
(0.62) 		0.376
(0.708) 		0.131
(0.47) 		0.135
(0.476) 		0.0729
(0.351) 		0.0475
(0.283) 		0.0271
(0.204) 		0.979
(1.00) 		0.119
(0.454)
del 1p13 2 54 (33%) 111 0.476
(0.794) 		0.0236
(0.186) 		0.0027
(0.0477) 		0.578
(0.853) 		0.544
(0.825) 		0.573
(0.851) 		0.476
(0.794) 		0.0191
(0.169) 		0.503
(0.803) 		0.211
(0.569) 		0.648
(0.885) 		0.612
(0.872)
del 5q12 1 53 (32%) 112 0.0665
(0.336) 		0.00187
(0.0368) 		0.207
(0.563) 		0.00391
(0.0602) 		0.782
(0.934) 		0.278
(0.628) 		0.686
(0.908) 		0.0948
(0.414) 		0.536
(0.822) 		0.29
(0.643) 		0.0266
(0.204) 		0.237
(0.591)
del 8p23 2 100 (61%) 65 0.111
(0.436) 		0.09
(0.4) 		0.00015
(0.00664) 		0.457
(0.772) 		1
(1.00) 		0.269
(0.62) 		0.00707
(0.0894) 		0.00992
(0.108) 		0.78
(0.934) 		0.326
(0.686) 		0.558
(0.839) 		0.505
(0.803)
del 8p11 21 45 (27%) 120 0.745
(0.927) 		0.47
(0.789) 		0.00966
(0.107) 		0.236
(0.591) 		0.0701
(0.342) 		0.368
(0.703) 		0.0106
(0.112) 		0.0485
(0.286) 		0.0597
(0.318) 		0.00783
(0.0917) 		0.341
(0.701) 		0.739
(0.925)
del 18q21 2 145 (88%) 20 0.133
(0.475) 		0.334
(0.693) 		2e-05
(0.00142) 		0.0464
(0.283) 		1
(1.00) 		0.768
(0.934) 		0.0313
(0.222) 		0.0284
(0.211) 		0.402
(0.722) 		0.124
(0.464) 		0.899
(0.995) 		0.868
(0.972)
del 18q22 1 141 (85%) 24 0.0672
(0.337) 		0.0898
(0.4) 		1e-05
(0.000787) 		0.0291
(0.215) 		0.779
(0.934) 		0.654
(0.888) 		0.0903
(0.4) 		0.0116
(0.121) 		0.828
(0.954) 		0.299
(0.654) 		0.786
(0.934) 		1
(1.00)
del 22q13 31 68 (41%) 97 0.907
(0.999) 		0.294
(0.647) 		0.00689
(0.0887) 		0.869
(0.972) 		0.404
(0.724) 		0.354
(0.703) 		0.459
(0.773) 		0.273
(0.626) 		0.00662
(0.0884) 		0.116
(0.447) 		0.101
(0.42) 		0.0146
(0.138)
amp 1q32 2 48 (29%) 117 0.829
(0.954) 		0.939
(1.00) 		0.0378
(0.243) 		0.519
(0.816) 		0.188
(0.553) 		0.027
(0.204) 		0.619
(0.874) 		0.821
(0.954) 		0.0808
(0.376) 		0.651
(0.887) 		0.296
(0.649) 		0.116
(0.447)
amp 5q22 3 20 (12%) 145 0.0211
(0.174) 		0.176
(0.538) 		0.00814
(0.093) 		0.222
(0.579) 		0.106
(0.432) 		0.659
(0.888) 		0.675
(0.899) 		0.252
(0.61) 		0.452
(0.768) 		0.661
(0.888) 		1
(1.00) 		0.285
(0.638)
amp 8p11 21 70 (42%) 95 0.0124
(0.125) 		0.211
(0.569) 		1e-05
(0.000787) 		0.233
(0.591) 		0.369
(0.703) 		0.522
(0.819) 		0.628
(0.875) 		0.125
(0.464) 		0.184
(0.553) 		0.274
(0.626) 		0.225
(0.583) 		0.321
(0.684)
amp 8q24 21 109 (66%) 56 0.0166
(0.153) 		0.243
(0.595) 		1e-05
(0.000787) 		0.129
(0.468) 		0.631
(0.875) 		0.887
(0.987) 		0.22
(0.578) 		0.0468
(0.283) 		0.539
(0.823) 		0.261
(0.618) 		0.0752
(0.36) 		0.447
(0.764)
amp 12p12 1 40 (24%) 125 0.696
(0.908) 		0.469
(0.788) 		0.0309
(0.222) 		0.367
(0.703) 		0.0499
(0.287) 		0.0086
(0.0966) 		0.188
(0.553) 		0.366
(0.703) 		0.693
(0.908) 		0.761
(0.93) 		0.434
(0.755) 		0.146
(0.496)
amp 17q12 46 (28%) 119 0.00659
(0.0884) 		0.127
(0.468) 		0.00162
(0.0348) 		0.373
(0.704) 		0.175
(0.538) 		0.917
(1.00) 		0.346
(0.701) 		0.0695
(0.342) 		0.146
(0.496) 		0.599
(0.861) 		0.121
(0.456) 		0.638
(0.877)
del 1p33 53 (32%) 112 0.362
(0.703) 		0.00428
(0.0631) 		0.0173
(0.157) 		0.138
(0.481) 		0.8
(0.944) 		0.31
(0.67) 		0.31
(0.67) 		0.188
(0.553) 		0.445
(0.764) 		0.268
(0.62) 		0.561
(0.84) 		0.569
(0.848)
del 4p13 60 (36%) 105 0.78
(0.934) 		0.0386
(0.246) 		0.00069
(0.0202) 		0.0687
(0.34) 		0.838
(0.959) 		0.506
(0.803) 		0.672
(0.898) 		0.347
(0.701) 		0.979
(1.00) 		0.22
(0.578) 		0.165
(0.517) 		0.502
(0.803)
del 4q22 1 73 (44%) 92 0.617
(0.874) 		0.024
(0.186) 		0.00041
(0.0145) 		0.232
(0.591) 		0.703
(0.908) 		0.478
(0.794) 		0.393
(0.713) 		0.318
(0.68) 		0.986
(1.00) 		0.255
(0.614) 		0.613
(0.872) 		0.704
(0.908)
del 5q22 2 59 (36%) 106 0.185
(0.553) 		0.00089
(0.0225) 		0.176
(0.538) 		0.188
(0.553) 		0.544
(0.825) 		0.728
(0.919) 		0.622
(0.874) 		0.189
(0.553) 		0.738
(0.925) 		0.238
(0.591) 		0.0206
(0.172) 		0.198
(0.554)
del 15q21 1 79 (48%) 86 0.57
(0.848) 		0.111
(0.436) 		0.00072
(0.0202) 		0.788
(0.935) 		0.0328
(0.228) 		0.323
(0.684) 		0.679
(0.9) 		0.415
(0.738) 		0.814
(0.951) 		0.435
(0.755) 		0.424
(0.745) 		0.584
(0.857)
amp 1q21 3 48 (29%) 117 1
(1.00) 		0.852
(0.968) 		0.00276
(0.0477) 		0.926
(1.00) 		0.527
(0.821) 		0.228
(0.588) 		0.421
(0.741) 		0.399
(0.72) 		0.0562
(0.309) 		0.151
(0.501) 		0.93
(1.00) 		0.392
(0.713)
amp 6p21 1 54 (33%) 111 0.0585
(0.314) 		0.106
(0.432) 		0.00054
(0.0177) 		0.0572
(0.309) 		0.809
(0.948) 		0.0452
(0.281) 		0.66
(0.888) 		0.143
(0.491) 		0.191
(0.553) 		0.388
(0.713) 		0.367
(0.703) 		0.781
(0.934)
amp 11p15 5 45 (27%) 120 0.381
(0.711) 		0.0945
(0.414) 		0.0808
(0.376) 		0.62
(0.874) 		0.725
(0.919) 		0.588
(0.857) 		0.289
(0.643) 		0.00357
(0.0562) 		0.0973
(0.416) 		0.537
(0.822) 		0.45
(0.768) 		0.0898
(0.4)
amp 12p13 33 41 (25%) 124 0.688
(0.908) 		0.482
(0.796) 		0.0347
(0.234) 		0.721
(0.918) 		0.114
(0.444) 		0.215
(0.575) 		0.804
(0.947) 		0.488
(0.796) 		0.576
(0.853) 		0.816
(0.951) 		0.436
(0.755) 		0.228
(0.588)
amp 16p11 2 47 (28%) 118 0.123
(0.462) 		0.578
(0.853) 		0.00055
(0.0177) 		0.128
(0.468) 		0.34
(0.701) 		0.666
(0.892) 		0.0396
(0.25) 		0.161
(0.512) 		0.0969
(0.416) 		0.852
(0.968) 		0.645
(0.883) 		0.987
(1.00)
amp 17q24 1 39 (24%) 126 0.291
(0.643) 		0.708
(0.908) 		0.00091
(0.0225) 		0.149
(0.497) 		0.612
(0.872) 		0.748
(0.927) 		0.232
(0.591) 		0.101
(0.42) 		0.61
(0.872) 		0.206
(0.563) 		0.495
(0.799) 		0.94
(1.00)
del 1p36 11 75 (45%) 90 0.114
(0.444) 		0.0641
(0.332) 		0.197
(0.554) 		0.143
(0.491) 		0.706
(0.908) 		0.921
(1.00) 		0.207
(0.563) 		0.0136
(0.132) 		0.493
(0.799) 		0.0647
(0.332) 		0.353
(0.703) 		0.796
(0.943)
del 2p12 13 (8%) 152 0.392
(0.713) 		0.837
(0.959) 		1e-05
(0.000787) 		1
(1.00) 		0.343
(0.701) 		0.148
(0.497) 		0.826
(0.954) 		0.14
(0.485) 		0.152
(0.501) 		0.144
(0.491)
del 4q35 1 72 (44%) 93 0.61
(0.872) 		0.0643
(0.332) 		0.00181
(0.0366) 		0.107
(0.432) 		0.387
(0.713) 		0.655
(0.888) 		0.545
(0.825) 		0.0496
(0.287) 		0.487
(0.796) 		0.0493
(0.287) 		0.551
(0.83) 		0.852
(0.968)
del 6p25 3 24 (15%) 141 1
(1.00) 		0.938
(1.00) 		0.807
(0.948) 		0.0201
(0.171) 		0.654
(0.888) 		0.985
(1.00) 		0.924
(1.00) 		0.696
(0.908) 		0.752
(0.929) 		0.786
(0.934) 		0.57
(0.848) 		0.758
(0.93)
del 6q26 30 (18%) 135 0.157
(0.507) 		0.746
(0.927) 		0.0142
(0.136) 		0.635
(0.875) 		0.0991
(0.42) 		0.2
(0.556) 		0.392
(0.713) 		0.322
(0.684) 		0.0553
(0.308) 		0.334
(0.693) 		0.0785
(0.371) 		0.95
(1.00)
del 10q21 1 41 (25%) 124 0.28
(0.63) 		0.712
(0.909) 		0.257
(0.615) 		0.491
(0.799) 		0.0186
(0.167) 		0.0681
(0.339) 		0.31
(0.67) 		0.539
(0.823) 		0.86
(0.972) 		0.191
(0.553) 		0.965
(1.00) 		0.39
(0.713)
del 10q25 2 48 (29%) 117 0.759
(0.93) 		0.771
(0.934) 		0.736
(0.925) 		0.486
(0.796) 		0.453
(0.768) 		0.243
(0.595) 		0.138
(0.481) 		0.0319
(0.224) 		0.621
(0.874) 		0.276
(0.627) 		0.444
(0.764) 		0.3
(0.655)
del 12q22 26 (16%) 139 0.354
(0.703) 		0.479
(0.794) 		0.0343
(0.233) 		0.774
(0.934) 		0.822
(0.954) 		0.513
(0.813) 		0.657
(0.888) 		0.756
(0.93) 		0.515
(0.813) 		0.707
(0.908) 		0.495
(0.799) 		0.387
(0.713)
del 14q11 2 70 (42%) 95 0.481
(0.796) 		0.131
(0.47) 		0.00021
(0.00826) 		0.932
(1.00) 		0.705
(0.908) 		0.692
(0.908) 		0.436
(0.755) 		0.1
(0.42) 		0.108
(0.432) 		0.344
(0.701) 		0.749
(0.927) 		0.783
(0.934)
del 15q22 33 77 (47%) 88 0.624
(0.875) 		0.154
(0.504) 		7e-05
(0.00381) 		0.598
(0.861) 		0.148
(0.497) 		0.0567
(0.309) 		0.373
(0.704) 		0.101
(0.42) 		0.418
(0.738) 		0.744
(0.927) 		0.858
(0.972) 		0.526
(0.821)
del 16p13 3 13 (8%) 152 0.888
(0.987) 		0.678
(0.9) 		0.204
(0.563) 		0.0203
(0.171) 		0.725
(0.919) 		0.598
(0.861) 		0.191
(0.553) 		0.962
(1.00) 		0.356
(0.703) 		0.634
(0.875) 		0.251
(0.61) 		0.488
(0.796)
del 16q23 1 23 (14%) 142 0.153
(0.501) 		0.351
(0.703) 		0.00305
(0.0502) 		0.126
(0.468) 		0.588
(0.857) 		0.952
(1.00) 		0.363
(0.703) 		0.738
(0.925) 		0.759
(0.93) 		0.841
(0.96) 		0.89
(0.988) 		0.867
(0.972)
del 19p13 3 37 (22%) 128 0.198
(0.554) 		0.885
(0.987) 		0.674
(0.899) 		0.0412
(0.258) 		0.962
(1.00) 		0.829
(0.954) 		0.773
(0.934) 		0.932
(1.00) 		0.356
(0.703) 		0.00176
(0.0366) 		0.53
(0.821) 		0.329
(0.688)
del 20p12 1 49 (30%) 116 0.942
(1.00) 		0.336
(0.696) 		0.0156
(0.145) 		0.494
(0.799) 		0.265
(0.62) 		0.383
(0.713) 		0.528
(0.821) 		0.377
(0.708) 		0.357
(0.703) 		0.256
(0.614) 		0.436
(0.755) 		0.437
(0.755)
del xp22 33 34 (21%) 131 0.778
(0.934) 		0.917
(1.00) 		0.0528
(0.299) 		0.00155
(0.0343) 		0.725
(0.919) 		0.898
(0.995) 		0.972
(1.00) 		0.53
(0.821) 		0.694
(0.908) 		1
(1.00) 		0.627
(0.875) 		0.587
(0.857)
amp 10q22 2 11 (7%) 154 0.503
(0.803) 		0.93
(1.00) 		0.536
(0.822) 		1
(1.00) 		1
(1.00) 		0.971
(1.00) 		0.259
(0.616) 		0.0896
(0.4) 		0.381
(0.711) 		0.187
(0.553)
amp 15q26 1 13 (8%) 152 0.11
(0.436) 		0.21
(0.569) 		1
(1.00) 		0.418
(0.738) 		0.155
(0.505) 		0.346
(0.701) 		0.56
(0.84) 		0.161
(0.512) 		0.906
(0.999) 		1
(1.00) 		0.743
(0.927) 		0.643
(0.882)
amp xp22 2 32 (19%) 133 0.0514
(0.293) 		0.221
(0.578) 		0.598
(0.861) 		0.273
(0.626) 		0.959
(1.00) 		0.235
(0.591) 		0.549
(0.829) 		0.629
(0.875) 		0.813
(0.951) 		0.869
(0.972) 		0.184
(0.553) 		0.948
(1.00)
del 3p14 2 31 (19%) 134 0.799
(0.944) 		0.697
(0.908) 		0.778
(0.934) 		1
(1.00) 		0.22
(0.578) 		0.717
(0.915) 		0.504
(0.803) 		0.861
(0.972) 		0.809
(0.948) 		0.961
(1.00) 		0.259
(0.616) 		0.25
(0.61)
del 3q26 31 18 (11%) 147 1
(1.00) 		0.869
(0.972) 		0.153
(0.501) 		0.478
(0.794) 		0.446
(0.764) 		0.24
(0.592) 		0.314
(0.675) 		0.416
(0.738) 		0.265
(0.62) 		0.0568
(0.309) 		0.785
(0.934) 		0.368
(0.703)
del 7q31 1 4 (2%) 161 0.106
(0.432) 		1
(1.00) 		0.952
(1.00) 		0.164
(0.516) 		0.77
(0.934) 		1
(1.00) 		1
(1.00)
del 12p13 1 33 (20%) 132 1
(1.00) 		0.263
(0.62) 		0.6
(0.861) 		0.199
(0.555) 		0.535
(0.822) 		0.275
(0.627) 		0.617
(0.874) 		0.128
(0.468) 		0.294
(0.647) 		0.526
(0.821) 		0.817
(0.951) 		0.832
(0.954)
del 14q31 1 72 (44%) 93 0.486
(0.796) 		0.239
(0.591) 		0.0539
(0.303) 		0.966
(1.00) 		0.707
(0.908) 		0.198
(0.554) 		0.233
(0.591) 		0.0964
(0.416) 		0.197
(0.554) 		0.236
(0.591) 		0.389
(0.713) 		0.656
(0.888)
del 17p11 2 113 (68%) 52 0.0838
(0.388) 		0.757
(0.93) 		0.0715
(0.347) 		0.29
(0.643) 		0.831
(0.954) 		0.36
(0.703) 		0.627
(0.875) 		0.221
(0.578) 		0.935
(1.00) 		0.351
(0.703) 		0.636
(0.875) 		0.704
(0.908)
del 21q11 2 73 (44%) 92 0.316
(0.678) 		0.0602
(0.318) 		0.0852
(0.39) 		0.872
(0.974) 		0.922
(1.00) 		0.213
(0.572) 		0.517
(0.816) 		0.71
(0.909) 		0.0641
(0.332) 		0.729
(0.919) 		0.219
(0.578) 		0.19
(0.553)
'amp_1q21.3' versus 'CN_CNMF'

P value = 0.00276 (Fisher's exact test), Q value = 0.048

Table S1.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 1(1Q21.3) MUTATED 14 18 6 10
AMP PEAK 1(1Q21.3) WILD-TYPE 52 14 25 26

Figure S1.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.2' versus 'CN_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.24

Table S2.  Gene #2: 'amp_1q32.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 2(1Q32.2) MUTATED 16 16 6 10
AMP PEAK 2(1Q32.2) WILD-TYPE 50 16 25 26

Figure S2.  Get High-res Image Gene #2: 'amp_1q32.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.2

Table S3.  Gene #2: 'amp_1q32.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 23 29 6 29 14
AMP PEAK 2(1Q32.2) MUTATED 2 5 13 2 12 5
AMP PEAK 2(1Q32.2) WILD-TYPE 23 18 16 4 17 9

Figure S3.  Get High-res Image Gene #2: 'amp_1q32.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_5q22.3' versus 'MRNA_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.17

Table S4.  Gene #3: 'amp_5q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 22 22
AMP PEAK 3(5Q22.3) MUTATED 3 0 6
AMP PEAK 3(5Q22.3) WILD-TYPE 22 22 16

Figure S4.  Get High-res Image Gene #3: 'amp_5q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_5q22.3' versus 'CN_CNMF'

P value = 0.00814 (Fisher's exact test), Q value = 0.093

Table S5.  Gene #3: 'amp_5q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 3(5Q22.3) MUTATED 2 7 4 7
AMP PEAK 3(5Q22.3) WILD-TYPE 64 25 27 29

Figure S5.  Get High-res Image Gene #3: 'amp_5q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p21.1' versus 'CN_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.018

Table S6.  Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 4(6P21.1) MUTATED 12 19 12 11
AMP PEAK 4(6P21.1) WILD-TYPE 54 13 19 25

Figure S6.  Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'MRNA_CNMF'

P value = 0.00316 (Fisher's exact test), Q value = 0.051

Table S7.  Gene #5: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 22 22
AMP PEAK 5(8P11.23) MUTATED 2 4 11
AMP PEAK 5(8P11.23) WILD-TYPE 23 18 11

Figure S7.  Get High-res Image Gene #5: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00079

Table S8.  Gene #5: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 5(8P11.23) MUTATED 6 9 10 28
AMP PEAK 5(8P11.23) WILD-TYPE 60 23 21 8

Figure S8.  Get High-res Image Gene #5: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.2

Table S9.  Gene #5: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
AMP PEAK 5(8P11.23) MUTATED 9 26 11
AMP PEAK 5(8P11.23) WILD-TYPE 13 37 45

Figure S9.  Get High-res Image Gene #5: 'amp_8p11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MRNA_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.13

Table S10.  Gene #6: 'amp_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 22 22
AMP PEAK 6(8P11.21) MUTATED 6 6 14
AMP PEAK 6(8P11.21) WILD-TYPE 19 16 8

Figure S10.  Get High-res Image Gene #6: 'amp_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00079

Table S11.  Gene #6: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 6(8P11.21) MUTATED 12 13 13 32
AMP PEAK 6(8P11.21) WILD-TYPE 54 19 18 4

Figure S11.  Get High-res Image Gene #6: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.15

Table S12.  Gene #7: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 22 22
AMP PEAK 7(8Q24.21) MUTATED 12 13 19
AMP PEAK 7(8Q24.21) WILD-TYPE 13 9 3

Figure S12.  Get High-res Image Gene #7: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00079

Table S13.  Gene #7: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 7(8Q24.21) MUTATED 35 14 25 35
AMP PEAK 7(8Q24.21) WILD-TYPE 31 18 6 1

Figure S13.  Get High-res Image Gene #7: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00357 (Fisher's exact test), Q value = 0.056

Table S14.  Gene #9: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
AMP PEAK 9(11P15.5) MUTATED 7 8 2 10 14 2 1
AMP PEAK 9(11P15.5) WILD-TYPE 20 28 10 9 18 16 19

Figure S14.  Get High-res Image Gene #9: 'amp_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.23

Table S15.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 10(11Q13.3) MUTATED 8 5 11 4
AMP PEAK 10(11Q13.3) WILD-TYPE 58 27 20 32

Figure S15.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.0046 (Fisher's exact test), Q value = 0.065

Table S16.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 39 29
AMP PEAK 10(11Q13.3) MUTATED 12 4 4
AMP PEAK 10(11Q13.3) WILD-TYPE 16 35 25

Figure S16.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.00263 (Fisher's exact test), Q value = 0.048

Table S17.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 14 33 28 60
AMP PEAK 10(11Q13.3) MUTATED 9 2 0 8 9
AMP PEAK 10(11Q13.3) WILD-TYPE 20 12 33 20 51

Figure S17.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.12

Table S18.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
AMP PEAK 10(11Q13.3) MUTATED 8 2 2 7 7 1 1
AMP PEAK 10(11Q13.3) WILD-TYPE 19 34 10 12 25 17 19

Figure S18.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.13

Table S19.  Gene #10: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 42 17 8 56
AMP PEAK 10(11Q13.3) MUTATED 5 8 2 4 4
AMP PEAK 10(11Q13.3) WILD-TYPE 13 34 15 4 52

Figure S19.  Get High-res Image Gene #10: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.23

Table S20.  Gene #11: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 11(12P13.33) MUTATED 14 12 3 12
AMP PEAK 11(12P13.33) WILD-TYPE 52 20 28 24

Figure S20.  Get High-res Image Gene #11: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'CN_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.22

Table S21.  Gene #12: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 12(12P12.1) MUTATED 16 11 2 11
AMP PEAK 12(12P12.1) WILD-TYPE 50 21 29 25

Figure S21.  Get High-res Image Gene #12: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0086 (Fisher's exact test), Q value = 0.097

Table S22.  Gene #12: 'amp_12p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 23 29 6 29 14
AMP PEAK 12(12P12.1) MUTATED 9 5 11 0 3 0
AMP PEAK 12(12P12.1) WILD-TYPE 16 18 18 6 26 14

Figure S22.  Get High-res Image Gene #12: 'amp_12p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_13q12.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00079

Table S23.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 13(13Q12.13) MUTATED 38 32 29 27
AMP PEAK 13(13Q12.13) WILD-TYPE 28 0 2 9

Figure S23.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.022

Table S24.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 14 33 28 60
AMP PEAK 13(13Q12.13) MUTATED 23 12 20 28 42
AMP PEAK 13(13Q12.13) WILD-TYPE 6 2 13 0 18

Figure S24.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00079

Table S25.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
AMP PEAK 13(13Q12.13) MUTATED 26 29 7 18 26 5 14
AMP PEAK 13(13Q12.13) WILD-TYPE 1 7 5 1 6 13 6

Figure S25.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.13' versus 'MIRSEQ_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.05

Table S26.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 42 17 8 56
AMP PEAK 13(13Q12.13) MUTATED 15 38 16 5 35
AMP PEAK 13(13Q12.13) WILD-TYPE 3 4 1 3 21

Figure S26.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00416 (Fisher's exact test), Q value = 0.063

Table S27.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
AMP PEAK 13(13Q12.13) MUTATED 19 55 35
AMP PEAK 13(13Q12.13) WILD-TYPE 3 8 21

Figure S27.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00079

Table S28.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 14(13Q12.2) MUTATED 36 32 29 28
AMP PEAK 14(13Q12.2) WILD-TYPE 30 0 2 8

Figure S28.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.018

Table S29.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 14 33 28 60
AMP PEAK 14(13Q12.2) MUTATED 23 12 19 28 42
AMP PEAK 14(13Q12.2) WILD-TYPE 6 2 14 0 18

Figure S29.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0051

Table S30.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
AMP PEAK 14(13Q12.2) MUTATED 26 28 7 17 26 6 14
AMP PEAK 14(13Q12.2) WILD-TYPE 1 8 5 2 6 12 6

Figure S30.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.2' versus 'MIRSEQ_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.18

Table S31.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 42 17 8 56
AMP PEAK 14(13Q12.2) MUTATED 15 38 14 5 36
AMP PEAK 14(13Q12.2) WILD-TYPE 3 4 3 3 20

Figure S31.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.18

Table S32.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
AMP PEAK 14(13Q12.2) MUTATED 19 53 36
AMP PEAK 14(13Q12.2) WILD-TYPE 3 10 20

Figure S32.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00079

Table S33.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 15(13Q22.1) MUTATED 34 32 28 26
AMP PEAK 15(13Q22.1) WILD-TYPE 32 0 3 10

Figure S33.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.23

Table S34.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 39 29
AMP PEAK 15(13Q22.1) MUTATED 26 30 19
AMP PEAK 15(13Q22.1) WILD-TYPE 2 9 10

Figure S34.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0071

Table S35.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 14 33 28 60
AMP PEAK 15(13Q22.1) MUTATED 21 11 17 28 42
AMP PEAK 15(13Q22.1) WILD-TYPE 8 3 16 0 18

Figure S35.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0019

Table S36.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
AMP PEAK 15(13Q22.1) MUTATED 23 26 8 17 28 4 13
AMP PEAK 15(13Q22.1) WILD-TYPE 4 10 4 2 4 14 7

Figure S36.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.065

Table S37.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 42 17 8 56
AMP PEAK 15(13Q22.1) MUTATED 16 38 11 6 34
AMP PEAK 15(13Q22.1) WILD-TYPE 2 4 6 2 22

Figure S37.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.11

Table S38.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
AMP PEAK 15(13Q22.1) MUTATED 18 53 34
AMP PEAK 15(13Q22.1) WILD-TYPE 4 10 22

Figure S38.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.018

Table S39.  Gene #17: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 17(16P11.2) MUTATED 8 14 14 11
AMP PEAK 17(16P11.2) WILD-TYPE 58 18 17 25

Figure S39.  Get High-res Image Gene #17: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'MRNA_CNMF'

P value = 0.00659 (Fisher's exact test), Q value = 0.088

Table S40.  Gene #18: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 22 22
AMP PEAK 18(17Q12) MUTATED 2 10 9
AMP PEAK 18(17Q12) WILD-TYPE 23 12 13

Figure S40.  Get High-res Image Gene #18: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.035

Table S41.  Gene #18: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 18(17Q12) MUTATED 13 4 16 13
AMP PEAK 18(17Q12) WILD-TYPE 53 28 15 23

Figure S41.  Get High-res Image Gene #18: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'CN_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.022

Table S42.  Gene #19: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 19(17Q24.1) MUTATED 13 3 16 7
AMP PEAK 19(17Q24.1) WILD-TYPE 53 29 15 29

Figure S42.  Get High-res Image Gene #19: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'MRNA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.17

Table S43.  Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 22 22
AMP PEAK 20(19P13.2) MUTATED 2 4 9
AMP PEAK 20(19P13.2) WILD-TYPE 23 18 13

Figure S43.  Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.029

Table S44.  Gene #20: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 20(19P13.2) MUTATED 5 11 11 9
AMP PEAK 20(19P13.2) WILD-TYPE 61 21 20 27

Figure S44.  Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.22

Table S45.  Gene #20: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 14 33 28 60
AMP PEAK 20(19P13.2) MUTATED 5 2 3 12 14
AMP PEAK 20(19P13.2) WILD-TYPE 24 12 30 16 46

Figure S45.  Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.23

Table S46.  Gene #20: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
AMP PEAK 20(19P13.2) MUTATED 11 6 0 4 8 1 6
AMP PEAK 20(19P13.2) WILD-TYPE 16 30 12 15 24 17 14

Figure S46.  Get High-res Image Gene #20: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 0.0079 (Fisher's exact test), Q value = 0.092

Table S47.  Gene #21: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 22 22
AMP PEAK 21(20Q11.21) MUTATED 22 15 22
AMP PEAK 21(20Q11.21) WILD-TYPE 3 7 0

Figure S47.  Get High-res Image Gene #21: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.02

Table S48.  Gene #21: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 21(20Q11.21) MUTATED 52 32 31 31
AMP PEAK 21(20Q11.21) WILD-TYPE 14 0 0 5

Figure S48.  Get High-res Image Gene #21: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.17

Table S49.  Gene #21: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 39 29
AMP PEAK 21(20Q11.21) MUTATED 28 36 23
AMP PEAK 21(20Q11.21) WILD-TYPE 0 3 6

Figure S49.  Get High-res Image Gene #21: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.011

Table S50.  Gene #21: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
AMP PEAK 21(20Q11.21) MUTATED 26 32 9 19 31 10 18
AMP PEAK 21(20Q11.21) WILD-TYPE 1 4 3 0 1 8 2

Figure S50.  Get High-res Image Gene #21: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CNMF'

P value = 0.00732 (Fisher's exact test), Q value = 0.089

Table S51.  Gene #21: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 42 17 8 56
AMP PEAK 21(20Q11.21) MUTATED 17 42 13 7 46
AMP PEAK 21(20Q11.21) WILD-TYPE 1 0 4 1 10

Figure S51.  Get High-res Image Gene #21: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q11.23' versus 'MRNA_CNMF'

P value = 0.00766 (Fisher's exact test), Q value = 0.092

Table S52.  Gene #22: 'amp_20q11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 22 22
AMP PEAK 22(20Q11.23) MUTATED 22 15 22
AMP PEAK 22(20Q11.23) WILD-TYPE 3 7 0

Figure S52.  Get High-res Image Gene #22: 'amp_20q11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.23' versus 'CN_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.032

Table S53.  Gene #22: 'amp_20q11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 22(20Q11.23) MUTATED 53 32 31 31
AMP PEAK 22(20Q11.23) WILD-TYPE 13 0 0 5

Figure S53.  Get High-res Image Gene #22: 'amp_20q11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0066

Table S54.  Gene #22: 'amp_20q11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
AMP PEAK 22(20Q11.23) MUTATED 26 33 9 19 31 10 18
AMP PEAK 22(20Q11.23) WILD-TYPE 1 3 3 0 1 8 2

Figure S54.  Get High-res Image Gene #22: 'amp_20q11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.23' versus 'MIRSEQ_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.13

Table S55.  Gene #22: 'amp_20q11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 42 17 8 56
AMP PEAK 22(20Q11.23) MUTATED 17 42 14 7 46
AMP PEAK 22(20Q11.23) WILD-TYPE 1 0 3 1 10

Figure S55.  Get High-res Image Gene #22: 'amp_20q11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.31' versus 'MRNA_CNMF'

P value = 0.00473 (Fisher's exact test), Q value = 0.066

Table S56.  Gene #23: 'amp_20q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 22 22
AMP PEAK 23(20Q13.31) MUTATED 23 15 22
AMP PEAK 23(20Q13.31) WILD-TYPE 2 7 0

Figure S56.  Get High-res Image Gene #23: 'amp_20q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.31' versus 'CN_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.047

Table S57.  Gene #23: 'amp_20q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
AMP PEAK 23(20Q13.31) MUTATED 54 32 31 31
AMP PEAK 23(20Q13.31) WILD-TYPE 12 0 0 5

Figure S57.  Get High-res Image Gene #23: 'amp_20q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.0035

Table S58.  Gene #23: 'amp_20q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
AMP PEAK 23(20Q13.31) MUTATED 26 33 9 19 32 10 18
AMP PEAK 23(20Q13.31) WILD-TYPE 1 3 3 0 0 8 2

Figure S58.  Get High-res Image Gene #23: 'amp_20q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.31' versus 'MIRSEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.18

Table S59.  Gene #23: 'amp_20q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 42 17 8 56
AMP PEAK 23(20Q13.31) MUTATED 17 42 14 7 47
AMP PEAK 23(20Q13.31) WILD-TYPE 1 0 3 1 9

Figure S59.  Get High-res Image Gene #23: 'amp_20q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.13

Table S60.  Gene #25: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
DEL PEAK 1(1P36.11) MUTATED 15 14 3 8 23 5 7
DEL PEAK 1(1P36.11) WILD-TYPE 12 22 9 11 9 13 13

Figure S60.  Get High-res Image Gene #25: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00428 (Fisher's exact test), Q value = 0.063

Table S61.  Gene #26: 'del_1p33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 13 9 8 9 8 3
DEL PEAK 2(1P33) MUTATED 1 1 4 5 6 0 3 0
DEL PEAK 2(1P33) WILD-TYPE 5 12 9 4 2 9 5 3

Figure S61.  Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p33' versus 'CN_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.16

Table S62.  Gene #26: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 2(1P33) MUTATED 14 13 16 10
DEL PEAK 2(1P33) WILD-TYPE 52 19 15 26

Figure S62.  Get High-res Image Gene #26: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.19

Table S63.  Gene #27: 'del_1p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 13 9 8 9 8 3
DEL PEAK 3(1P13.2) MUTATED 1 2 4 4 6 0 2 0
DEL PEAK 3(1P13.2) WILD-TYPE 5 11 9 5 2 9 6 3

Figure S63.  Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 0.0027 (Fisher's exact test), Q value = 0.048

Table S64.  Gene #27: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 3(1P13.2) MUTATED 11 15 14 14
DEL PEAK 3(1P13.2) WILD-TYPE 55 17 17 22

Figure S64.  Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.17

Table S65.  Gene #27: 'del_1p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
DEL PEAK 3(1P13.2) MUTATED 16 7 3 8 12 3 5
DEL PEAK 3(1P13.2) WILD-TYPE 11 29 9 11 20 15 15

Figure S65.  Get High-res Image Gene #27: 'del_1p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00079

Table S66.  Gene #28: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 4(2P12) MUTATED 0 8 0 5
DEL PEAK 4(2P12) WILD-TYPE 66 24 31 31

Figure S66.  Get High-res Image Gene #28: 'del_2p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p13' versus 'MRNA_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.25

Table S67.  Gene #31: 'del_4p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 13 9 8 9 8 3
DEL PEAK 7(4P13) MUTATED 1 7 4 5 4 0 5 0
DEL PEAK 7(4P13) WILD-TYPE 5 6 9 4 4 9 3 3

Figure S67.  Get High-res Image Gene #31: 'del_4p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p13' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.02

Table S68.  Gene #31: 'del_4p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 7(4P13) MUTATED 15 21 12 12
DEL PEAK 7(4P13) WILD-TYPE 51 11 19 24

Figure S68.  Get High-res Image Gene #31: 'del_4p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.19

Table S69.  Gene #32: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 13 9 8 9 8 3
DEL PEAK 8(4Q22.1) MUTATED 1 6 6 8 3 1 4 0
DEL PEAK 8(4Q22.1) WILD-TYPE 5 7 7 1 5 8 4 3

Figure S69.  Get High-res Image Gene #32: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.015

Table S70.  Gene #32: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 8(4Q22.1) MUTATED 18 23 15 17
DEL PEAK 8(4Q22.1) WILD-TYPE 48 9 16 19

Figure S70.  Get High-res Image Gene #32: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'CN_CNMF'

P value = 0.00181 (Fisher's exact test), Q value = 0.037

Table S71.  Gene #33: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 9(4Q35.1) MUTATED 19 22 16 15
DEL PEAK 9(4Q35.1) WILD-TYPE 47 10 15 21

Figure S71.  Get High-res Image Gene #33: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00187 (Fisher's exact test), Q value = 0.037

Table S72.  Gene #34: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 13 9 8 9 8 3
DEL PEAK 10(5Q12.1) MUTATED 0 4 1 7 2 0 3 0
DEL PEAK 10(5Q12.1) WILD-TYPE 6 9 12 2 6 9 5 3

Figure S72.  Get High-res Image Gene #34: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.06

Table S73.  Gene #34: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 39 29
DEL PEAK 10(5Q12.1) MUTATED 17 8 12
DEL PEAK 10(5Q12.1) WILD-TYPE 11 31 17

Figure S73.  Get High-res Image Gene #34: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.2

Table S74.  Gene #34: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 14 14 13
DEL PEAK 10(5Q12.1) MUTATED 8 5 4 7
DEL PEAK 10(5Q12.1) WILD-TYPE 1 9 10 6

Figure S74.  Get High-res Image Gene #34: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q22.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.022

Table S75.  Gene #35: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 13 9 8 9 8 3
DEL PEAK 11(5Q22.2) MUTATED 0 4 3 8 3 0 4 0
DEL PEAK 11(5Q22.2) WILD-TYPE 6 9 10 1 5 9 4 3

Figure S75.  Get High-res Image Gene #35: 'del_5q22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.17

Table S76.  Gene #35: 'del_5q22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 14 14 13
DEL PEAK 11(5Q22.2) MUTATED 7 4 4 9
DEL PEAK 11(5Q22.2) WILD-TYPE 2 10 10 4

Figure S76.  Get High-res Image Gene #35: 'del_5q22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.17

Table S77.  Gene #36: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 39 29
DEL PEAK 12(6P25.3) MUTATED 0 8 6
DEL PEAK 12(6P25.3) WILD-TYPE 28 31 23

Figure S77.  Get High-res Image Gene #36: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.14

Table S78.  Gene #37: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 13(6Q26) MUTATED 10 8 1 11
DEL PEAK 13(6Q26) WILD-TYPE 56 24 30 25

Figure S78.  Get High-res Image Gene #37: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0066

Table S79.  Gene #39: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 15(8P23.2) MUTATED 28 21 20 31
DEL PEAK 15(8P23.2) WILD-TYPE 38 11 11 5

Figure S79.  Get High-res Image Gene #39: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 0.00707 (Fisher's exact test), Q value = 0.089

Table S80.  Gene #39: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 14 33 28 60
DEL PEAK 15(8P23.2) MUTATED 20 8 11 17 43
DEL PEAK 15(8P23.2) WILD-TYPE 9 6 22 11 17

Figure S80.  Get High-res Image Gene #39: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00992 (Fisher's exact test), Q value = 0.11

Table S81.  Gene #39: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
DEL PEAK 15(8P23.2) MUTATED 22 16 8 8 24 8 13
DEL PEAK 15(8P23.2) WILD-TYPE 5 20 4 11 8 10 7

Figure S81.  Get High-res Image Gene #39: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p11.21' versus 'CN_CNMF'

P value = 0.00966 (Fisher's exact test), Q value = 0.11

Table S82.  Gene #40: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 16(8P11.21) MUTATED 23 12 7 3
DEL PEAK 16(8P11.21) WILD-TYPE 43 20 24 33

Figure S82.  Get High-res Image Gene #40: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p11.21' versus 'MRNASEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.11

Table S83.  Gene #40: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 14 33 28 60
DEL PEAK 16(8P11.21) MUTATED 4 3 5 6 26
DEL PEAK 16(8P11.21) WILD-TYPE 25 11 28 22 34

Figure S83.  Get High-res Image Gene #40: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00783 (Fisher's exact test), Q value = 0.092

Table S84.  Gene #40: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
DEL PEAK 16(8P11.21) MUTATED 8 9 21
DEL PEAK 16(8P11.21) WILD-TYPE 14 54 35

Figure S84.  Get High-res Image Gene #40: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q21.1' versus 'RPPA_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.17

Table S85.  Gene #41: 'del_10q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 40 53
DEL PEAK 17(10Q21.1) MUTATED 5 5 19
DEL PEAK 17(10Q21.1) WILD-TYPE 28 35 34

Figure S85.  Get High-res Image Gene #41: 'del_10q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.22

Table S86.  Gene #42: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
DEL PEAK 18(10Q25.2) MUTATED 14 6 2 3 8 8 6
DEL PEAK 18(10Q25.2) WILD-TYPE 13 30 10 16 24 10 14

Figure S86.  Get High-res Image Gene #42: 'del_10q25.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.3' versus 'MRNA_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.23

Table S87.  Gene #43: 'del_11q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 22 22
DEL PEAK 19(11Q22.3) MUTATED 6 8 1
DEL PEAK 19(11Q22.3) WILD-TYPE 19 14 21

Figure S87.  Get High-res Image Gene #43: 'del_11q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.22

Table S88.  Gene #43: 'del_11q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 13 9 8 9 8 3
DEL PEAK 19(11Q22.3) MUTATED 0 7 4 0 2 2 0 0
DEL PEAK 19(11Q22.3) WILD-TYPE 6 6 9 9 6 7 8 3

Figure S88.  Get High-res Image Gene #43: 'del_11q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11q22.3' versus 'CN_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.048

Table S89.  Gene #43: 'del_11q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 19(11Q22.3) MUTATED 14 9 1 14
DEL PEAK 19(11Q22.3) WILD-TYPE 52 23 30 22

Figure S89.  Get High-res Image Gene #43: 'del_11q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q22.3' versus 'METHLYATION_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.23

Table S90.  Gene #43: 'del_11q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 39 29
DEL PEAK 19(11Q22.3) MUTATED 2 11 10
DEL PEAK 19(11Q22.3) WILD-TYPE 26 28 19

Figure S90.  Get High-res Image Gene #43: 'del_11q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00674 (Fisher's exact test), Q value = 0.088

Table S91.  Gene #43: 'del_11q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 14 33 28 60
DEL PEAK 19(11Q22.3) MUTATED 5 6 12 1 14
DEL PEAK 19(11Q22.3) WILD-TYPE 24 8 21 27 46

Figure S91.  Get High-res Image Gene #43: 'del_11q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00732 (Fisher's exact test), Q value = 0.089

Table S92.  Gene #43: 'del_11q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
DEL PEAK 19(11Q22.3) MUTATED 1 13 5 2 6 7 4
DEL PEAK 19(11Q22.3) WILD-TYPE 26 23 7 17 26 11 16

Figure S92.  Get High-res Image Gene #43: 'del_11q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q22' versus 'CN_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.23

Table S93.  Gene #45: 'del_12q22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 21(12Q22) MUTATED 5 9 4 8
DEL PEAK 21(12Q22) WILD-TYPE 61 23 27 28

Figure S93.  Get High-res Image Gene #45: 'del_12q22' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q11.2' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0083

Table S94.  Gene #46: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 22(14Q11.2) MUTATED 19 22 18 11
DEL PEAK 22(14Q11.2) WILD-TYPE 47 10 13 25

Figure S94.  Get High-res Image Gene #46: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'CN_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.02

Table S95.  Gene #48: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 24(15Q21.1) MUTATED 19 21 18 21
DEL PEAK 24(15Q21.1) WILD-TYPE 47 11 13 15

Figure S95.  Get High-res Image Gene #48: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'RPPA_CNMF'

P value = 0.0328 (Fisher's exact test), Q value = 0.23

Table S96.  Gene #48: 'del_15q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 40 53
DEL PEAK 24(15Q21.1) MUTATED 10 17 31
DEL PEAK 24(15Q21.1) WILD-TYPE 23 23 22

Figure S96.  Get High-res Image Gene #48: 'del_15q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q22.33' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0038

Table S97.  Gene #49: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 25(15Q22.33) MUTATED 17 22 17 21
DEL PEAK 25(15Q22.33) WILD-TYPE 49 10 14 15

Figure S97.  Get High-res Image Gene #49: 'del_15q22.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.17

Table S98.  Gene #50: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 39 29
DEL PEAK 26(16P13.3) MUTATED 0 1 5
DEL PEAK 26(16P13.3) WILD-TYPE 28 38 24

Figure S98.  Get High-res Image Gene #50: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00305 (Fisher's exact test), Q value = 0.05

Table S99.  Gene #51: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 27(16Q23.1) MUTATED 5 6 1 11
DEL PEAK 27(16Q23.1) WILD-TYPE 61 26 30 25

Figure S99.  Get High-res Image Gene #51: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S100.  Gene #53: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 29(18Q21.2) MUTATED 48 30 31 36
DEL PEAK 29(18Q21.2) WILD-TYPE 18 2 0 0

Figure S100.  Get High-res Image Gene #53: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.22

Table S101.  Gene #53: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 14 33 28 60
DEL PEAK 29(18Q21.2) MUTATED 27 13 23 26 55
DEL PEAK 29(18Q21.2) WILD-TYPE 2 1 10 2 5

Figure S101.  Get High-res Image Gene #53: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.21

Table S102.  Gene #53: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
DEL PEAK 29(18Q21.2) MUTATED 27 32 8 17 29 13 18
DEL PEAK 29(18Q21.2) WILD-TYPE 0 4 4 2 3 5 2

Figure S102.  Get High-res Image Gene #53: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00079

Table S103.  Gene #54: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 30(18Q22.1) MUTATED 44 30 31 36
DEL PEAK 30(18Q22.1) WILD-TYPE 22 2 0 0

Figure S103.  Get High-res Image Gene #54: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q22.1' versus 'METHLYATION_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.21

Table S104.  Gene #54: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 39 29
DEL PEAK 30(18Q22.1) MUTATED 28 31 24
DEL PEAK 30(18Q22.1) WILD-TYPE 0 8 5

Figure S104.  Get High-res Image Gene #54: 'del_18q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.12

Table S105.  Gene #54: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 36 12 19 32 18 20
DEL PEAK 30(18Q22.1) MUTATED 27 30 7 17 29 13 17
DEL PEAK 30(18Q22.1) WILD-TYPE 0 6 5 2 3 5 3

Figure S105.  Get High-res Image Gene #54: 'del_18q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00176 (Fisher's exact test), Q value = 0.037

Table S106.  Gene #55: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 63 56
DEL PEAK 31(19P13.3) MUTATED 12 15 8
DEL PEAK 31(19P13.3) WILD-TYPE 10 48 48

Figure S106.  Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.15

Table S107.  Gene #56: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 32(20P12.1) MUTATED 13 7 12 17
DEL PEAK 32(20P12.1) WILD-TYPE 53 25 19 19

Figure S107.  Get High-res Image Gene #56: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 0.089

Table S108.  Gene #58: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 32 31 36
DEL PEAK 34(22Q13.31) MUTATED 19 21 13 15
DEL PEAK 34(22Q13.31) WILD-TYPE 47 11 18 21

Figure S108.  Get High-res Image Gene #58: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.00662 (Fisher's exact test), Q value = 0.088

Table S109.  Gene #58: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 18 42 17 8 56
DEL PEAK 34(22Q13.31) MUTATED 5 27 3 4 23
DEL PEAK 34(22Q13.31) WILD-TYPE 13 15 14 4 33

Figure S109.  Get High-res Image Gene #58: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.14

Table S110.  Gene #58: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 13 18 5 5
DEL PEAK 34(22Q13.31) MUTATED 7 4 12 2 0
DEL PEAK 34(22Q13.31) WILD-TYPE 2 9 6 3 5

Figure S110.  Get High-res Image Gene #58: 'del_22q13.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.33' versus 'METHLYATION_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.034

Table S111.  Gene #59: 'del_xp22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 39 29
DEL PEAK 35(XP22.33) MUTATED 5 12 0
DEL PEAK 35(XP22.33) WILD-TYPE 23 27 29

Figure S111.  Get High-res Image Gene #59: 'del_xp22.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/15096454/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/READ-TP/15107799/READ-TP.transferedmergedcluster.txt

  • Number of patients = 165

  • Number of significantly focal cnvs = 59

  • Number of molecular subtypes = 12

  • 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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