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 70 focal events and 10 molecular subtypes across 264 patients, 70 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p34.2 cnv correlated to 'CN_CNMF'.

  • amp_1q21.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_1q23.3 cnv correlated to 'CN_CNMF'.

  • amp_3p25.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3q26.32 cnv correlated to 'CN_CNMF'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • amp_6p22.3 cnv correlated to 'CN_CNMF'.

  • amp_7p21.1 cnv correlated to 'CN_CNMF'.

  • amp_7p11.2 cnv correlated to 'CN_CNMF'.

  • amp_8p11.23 cnv correlated to 'CN_CNMF'.

  • amp_8p11.21 cnv correlated to 'CN_CNMF'.

  • amp_8q22.3 cnv correlated to 'CN_CNMF'.

  • amp_9p24.1 cnv correlated to 'CN_CNMF'.

  • amp_10p14 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_11q13.3 cnv correlated to 'CN_CNMF'.

  • amp_14q11.2 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • amp_16p13.13 cnv correlated to 'CN_CNMF'.

  • amp_17q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

  • amp_19q13.43 cnv correlated to 'CN_CNMF'.

  • amp_20q11.21 cnv correlated to 'CN_CNMF'.

  • del_2q37.1 cnv correlated to 'CN_CNMF'.

  • del_3p21.31 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_3p14.2 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_3p13 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_5q11.2 cnv correlated to 'CN_CNMF'.

  • del_5q35.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_6q21 cnv correlated to 'CN_CNMF'.

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

  • del_8p23.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_8p12 cnv correlated to 'CN_CNMF'.

  • del_8p11.21 cnv correlated to 'CN_CNMF'.

  • del_9p23 cnv correlated to 'CN_CNMF'.

  • del_9p21.3 cnv correlated to 'CN_CNMF'.

  • del_9q33.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_11p15.5 cnv correlated to 'CN_CNMF'.

  • del_11q23.3 cnv correlated to 'CN_CNMF'.

  • del_14q12 cnv correlated to 'CN_CNMF'.

  • del_14q24.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_15q13.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_16q23.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_17p12 cnv correlated to 'CN_CNMF'.

  • del_18q21.2 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • del_22q13.31 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 70 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, 70 significant findings detected.

Clinical
Features 		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
amp 3p25 2 127 (48%) 137 1e-05
(0.007) 		4e-05
(0.0261) 		0.0789
(1.00) 		0.0103
(1.00) 		1e-05
(0.007) 		2e-05
(0.0132) 		7e-05
(0.0454) 		2e-05
(0.0132) 		1e-05
(0.007) 		8e-05
(0.0518)
amp 17q11 2 117 (44%) 147 1e-05
(0.007) 		0.00022
(0.141) 		0.0321
(1.00) 		0.0885
(1.00) 		0.00039
(0.246) 		0.00305
(1.00) 		0.0592
(1.00) 		0.00071
(0.441) 		0.00187
(1.00) 		0.0101
(1.00)
del 14q24 1 86 (33%) 178 1e-05
(0.007) 		1e-05
(0.007) 		0.393
(1.00) 		0.346
(1.00) 		0.00283
(1.00) 		1e-05
(0.007) 		0.0464
(1.00) 		0.00063
(0.393) 		0.0846
(1.00) 		0.0841
(1.00)
amp 1q21 3 128 (48%) 136 1e-05
(0.007) 		2e-05
(0.0132) 		0.391
(1.00) 		0.722
(1.00) 		0.0252
(1.00) 		0.0383
(1.00) 		0.0442
(1.00) 		0.00376
(1.00) 		0.335
(1.00) 		0.125
(1.00)
amp 5p15 33 131 (50%) 133 1e-05
(0.007) 		0.0406
(1.00) 		0.0209
(1.00) 		0.18
(1.00) 		0.469
(1.00) 		0.233
(1.00) 		0.0091
(1.00) 		0.00022
(0.141) 		0.215
(1.00) 		0.00429
(1.00)
amp 10p14 116 (44%) 148 1e-05
(0.007) 		1e-05
(0.007) 		0.357
(1.00) 		0.426
(1.00) 		0.515
(1.00) 		0.11
(1.00) 		0.433
(1.00) 		0.162
(1.00) 		0.388
(1.00) 		0.23
(1.00)
amp 17q12 110 (42%) 154 1e-05
(0.007) 		0.163
(1.00) 		0.0779
(1.00) 		0.0187
(1.00) 		0.00511
(1.00) 		0.0153
(1.00) 		0.00363
(1.00) 		0.00177
(1.00) 		0.00017
(0.109) 		0.00112
(0.689)
amp 19q12 109 (41%) 155 1e-05
(0.007) 		0.00021
(0.135) 		0.703
(1.00) 		0.546
(1.00) 		0.0582
(1.00) 		0.159
(1.00) 		0.356
(1.00) 		0.00111
(0.684) 		0.334
(1.00) 		0.0454
(1.00)
del 3p21 31 77 (29%) 187 0.0358
(1.00) 		0.383
(1.00) 		0.0301
(1.00) 		0.00733
(1.00) 		1e-05
(0.007) 		4e-05
(0.0261) 		0.106
(1.00) 		0.0195
(1.00) 		0.134
(1.00) 		0.0626
(1.00)
del 3p14 2 75 (28%) 189 0.0578
(1.00) 		0.499
(1.00) 		0.0337
(1.00) 		0.0172
(1.00) 		2e-05
(0.0132) 		2e-05
(0.0132) 		0.351
(1.00) 		0.00261
(1.00) 		0.0889
(1.00) 		0.0405
(1.00)
del 3p13 71 (27%) 193 0.386
(1.00) 		0.366
(1.00) 		0.12
(1.00) 		0.0023
(1.00) 		2e-05
(0.0132) 		0.00011
(0.0709) 		0.536
(1.00) 		0.041
(1.00) 		0.172
(1.00) 		0.0171
(1.00)
del 5q35 1 126 (48%) 138 3e-05
(0.0197) 		0.00017
(0.109) 		0.472
(1.00) 		0.33
(1.00) 		0.428
(1.00) 		0.0591
(1.00) 		0.393
(1.00) 		0.00872
(1.00) 		0.507
(1.00) 		0.0481
(1.00)
del 6q27 119 (45%) 145 1e-05
(0.007) 		0.0164
(1.00) 		0.661
(1.00) 		0.435
(1.00) 		0.241
(1.00) 		0.011
(1.00) 		0.0805
(1.00) 		3e-05
(0.0197) 		0.166
(1.00) 		0.0669
(1.00)
del 8p23 3 151 (57%) 113 1e-05
(0.007) 		1e-05
(0.007) 		0.553
(1.00) 		0.194
(1.00) 		0.182
(1.00) 		0.857
(1.00) 		0.00239
(1.00) 		0.0125
(1.00) 		0.0381
(1.00) 		0.0333
(1.00)
del 9q33 2 104 (39%) 160 1e-05
(0.007) 		0.0338
(1.00) 		0.0667
(1.00) 		0.00322
(1.00) 		0.0129
(1.00) 		0.00022
(0.141) 		0.464
(1.00) 		0.0994
(1.00) 		0.129
(1.00) 		0.0229
(1.00)
del 15q13 1 107 (41%) 157 0.00026
(0.166) 		0.00127
(0.78) 		0.319
(1.00) 		0.572
(1.00) 		0.947
(1.00) 		0.567
(1.00) 		0.162
(1.00) 		6e-05
(0.0391) 		0.282
(1.00) 		0.165
(1.00)
del 16q23 1 73 (28%) 191 6e-05
(0.0391) 		0.0342
(1.00) 		0.503
(1.00) 		0.0643
(1.00) 		0.0884
(1.00) 		0.182
(1.00) 		0.0314
(1.00) 		0.00031
(0.196) 		0.154
(1.00) 		0.014
(1.00)
amp 1p34 2 70 (27%) 194 1e-05
(0.007) 		0.00164
(0.999) 		0.178
(1.00) 		0.381
(1.00) 		0.792
(1.00) 		0.433
(1.00) 		0.148
(1.00) 		0.302
(1.00) 		0.822
(1.00) 		0.929
(1.00)
amp 1q23 3 135 (51%) 129 1e-05
(0.007) 		0.00162
(0.988) 		0.551
(1.00) 		0.886
(1.00) 		0.123
(1.00) 		0.309
(1.00) 		0.00309
(1.00) 		0.0144
(1.00) 		0.0414
(1.00) 		0.0495
(1.00)
amp 3q26 32 142 (54%) 122 1e-05
(0.007) 		0.57
(1.00) 		0.389
(1.00) 		0.154
(1.00) 		0.739
(1.00) 		0.368
(1.00) 		0.575
(1.00) 		0.00653
(1.00) 		0.417
(1.00) 		0.0909
(1.00)
amp 6p22 3 111 (42%) 153 1e-05
(0.007) 		0.0014
(0.857) 		0.321
(1.00) 		0.487
(1.00) 		0.737
(1.00) 		0.807
(1.00) 		0.294
(1.00) 		0.176
(1.00) 		0.354
(1.00) 		0.125
(1.00)
amp 7p21 1 134 (51%) 130 0.00014
(0.0902) 		0.0131
(1.00) 		0.133
(1.00) 		0.32
(1.00) 		0.888
(1.00) 		0.88
(1.00) 		0.193
(1.00) 		0.0839
(1.00) 		0.728
(1.00) 		0.47
(1.00)
amp 7p11 2 131 (50%) 133 1e-05
(0.007) 		0.0148
(1.00) 		0.0897
(1.00) 		0.6
(1.00) 		0.987
(1.00) 		0.516
(1.00) 		0.404
(1.00) 		0.24
(1.00) 		0.642
(1.00) 		0.543
(1.00)
amp 8p11 23 84 (32%) 180 1e-05
(0.007) 		0.097
(1.00) 		0.746
(1.00) 		0.791
(1.00) 		1
(1.00) 		0.75
(1.00) 		0.244
(1.00) 		0.544
(1.00) 		0.0679
(1.00) 		0.411
(1.00)
amp 8p11 21 86 (33%) 178 1e-05
(0.007) 		0.0274
(1.00) 		0.888
(1.00) 		0.949
(1.00) 		0.522
(1.00) 		0.399
(1.00) 		0.032
(1.00) 		0.00147
(0.898) 		0.0208
(1.00) 		0.0189
(1.00)
amp 8q22 3 169 (64%) 95 1e-05
(0.007) 		0.00075
(0.465) 		0.0243
(1.00) 		0.193
(1.00) 		0.612
(1.00) 		0.629
(1.00) 		0.0802
(1.00) 		0.00064
(0.399) 		0.0179
(1.00) 		0.114
(1.00)
amp 9p24 1 53 (20%) 211 1e-05
(0.007) 		0.284
(1.00) 		0.671
(1.00) 		0.326
(1.00) 		0.33
(1.00) 		0.0795
(1.00) 		0.942
(1.00) 		0.0389
(1.00) 		0.826
(1.00) 		0.276
(1.00)
amp 11q13 3 101 (38%) 163 8e-05
(0.0518) 		0.323
(1.00) 		0.234
(1.00) 		0.0794
(1.00) 		0.183
(1.00) 		0.153
(1.00) 		0.17
(1.00) 		0.00423
(1.00) 		0.653
(1.00) 		0.716
(1.00)
amp 14q11 2 63 (24%) 201 0.742
(1.00) 		0.422
(1.00) 		0.614
(1.00) 		0.0903
(1.00) 		0.355
(1.00) 		0.317
(1.00) 		0.49
(1.00) 		0.00029
(0.184) 		0.573
(1.00) 		1
(1.00)
amp 16p13 13 56 (21%) 208 0.00039
(0.246) 		0.253
(1.00) 		0.52
(1.00) 		0.673
(1.00) 		0.35
(1.00) 		0.782
(1.00) 		0.617
(1.00) 		0.286
(1.00) 		0.504
(1.00) 		0.414
(1.00)
amp 19q13 43 103 (39%) 161 1e-05
(0.007) 		0.00908
(1.00) 		0.167
(1.00) 		0.302
(1.00) 		0.305
(1.00) 		0.945
(1.00) 		0.672
(1.00) 		0.0352
(1.00) 		0.26
(1.00) 		0.0367
(1.00)
amp 20q11 21 171 (65%) 93 0.0003
(0.19) 		0.0459
(1.00) 		0.713
(1.00) 		0.0554
(1.00) 		0.944
(1.00) 		0.32
(1.00) 		0.488
(1.00) 		0.00195
(1.00) 		0.33
(1.00) 		0.575
(1.00)
del 2q37 1 130 (49%) 134 1e-05
(0.007) 		0.0117
(1.00) 		0.593
(1.00) 		0.443
(1.00) 		0.307
(1.00) 		0.122
(1.00) 		0.0685
(1.00) 		0.0762
(1.00) 		0.0841
(1.00) 		0.0636
(1.00)
del 5q11 2 133 (50%) 131 1e-05
(0.007) 		0.00092
(0.569) 		0.958
(1.00) 		0.625
(1.00) 		0.578
(1.00) 		0.0779
(1.00) 		0.172
(1.00) 		0.00279
(1.00) 		0.609
(1.00) 		0.142
(1.00)
del 6q21 117 (44%) 147 1e-05
(0.007) 		0.0255
(1.00) 		0.855
(1.00) 		0.432
(1.00) 		0.645
(1.00) 		0.069
(1.00) 		0.326
(1.00) 		0.00472
(1.00) 		0.415
(1.00) 		0.101
(1.00)
del 8p12 129 (49%) 135 1e-05
(0.007) 		0.00062
(0.388) 		0.553
(1.00) 		0.516
(1.00) 		0.133
(1.00) 		0.885
(1.00) 		0.0383
(1.00) 		0.219
(1.00) 		0.126
(1.00) 		0.0642
(1.00)
del 8p11 21 69 (26%) 195 8e-05
(0.0518) 		0.449
(1.00) 		0.213
(1.00) 		0.248
(1.00) 		0.228
(1.00) 		0.277
(1.00) 		0.0654
(1.00) 		0.395
(1.00) 		0.0546
(1.00) 		0.0547
(1.00)
del 9p23 115 (44%) 149 1e-05
(0.007) 		0.345
(1.00) 		0.22
(1.00) 		0.203
(1.00) 		0.866
(1.00) 		0.0481
(1.00) 		0.402
(1.00) 		0.668
(1.00) 		0.694
(1.00) 		0.691
(1.00)
del 9p21 3 157 (59%) 107 1e-05
(0.007) 		0.863
(1.00) 		0.452
(1.00) 		0.0103
(1.00) 		0.726
(1.00) 		0.0742
(1.00) 		0.884
(1.00) 		0.933
(1.00) 		0.593
(1.00) 		0.833
(1.00)
del 11p15 5 129 (49%) 135 1e-05
(0.007) 		0.00093
(0.574) 		0.365
(1.00) 		0.243
(1.00) 		0.0252
(1.00) 		0.00062
(0.388) 		0.0299
(1.00) 		0.102
(1.00) 		0.0152
(1.00) 		0.119
(1.00)
del 11q23 3 100 (38%) 164 1e-05
(0.007) 		0.124
(1.00) 		0.775
(1.00) 		0.839
(1.00) 		0.032
(1.00) 		0.0841
(1.00) 		0.242
(1.00) 		0.804
(1.00) 		0.316
(1.00) 		0.625
(1.00)
del 14q12 80 (30%) 184 1e-05
(0.007) 		0.00042
(0.264) 		0.121
(1.00) 		0.0709
(1.00) 		0.144
(1.00) 		0.0226
(1.00) 		0.0399
(1.00) 		0.0266
(1.00) 		0.117
(1.00) 		0.352
(1.00)
del 17p12 137 (52%) 127 1e-05
(0.007) 		0.0225
(1.00) 		0.201
(1.00) 		0.609
(1.00) 		0.376
(1.00) 		0.0599
(1.00) 		0.751
(1.00) 		0.0103
(1.00) 		0.869
(1.00) 		0.864
(1.00)
del 18q21 2 115 (44%) 149 0.0571
(1.00) 		0.876
(1.00) 		0.872
(1.00) 		0.745
(1.00) 		0.877
(1.00) 		0.672
(1.00) 		0.00457
(1.00) 		0.00028
(0.178) 		0.0596
(1.00) 		0.0345
(1.00)
del 22q13 31 118 (45%) 146 3e-05
(0.0197) 		0.00178
(1.00) 		0.451
(1.00) 		0.00774
(1.00) 		0.102
(1.00) 		0.462
(1.00) 		0.645
(1.00) 		0.106
(1.00) 		0.0981
(1.00) 		0.499
(1.00)
amp 4p16 3 53 (20%) 211 0.00245
(1.00) 		0.0489
(1.00) 		0.0329
(1.00) 		0.0267
(1.00) 		0.00787
(1.00) 		0.00068
(0.423) 		0.0205
(1.00) 		0.00504
(1.00) 		0.00804
(1.00) 		0.0174
(1.00)
amp 4q13 3 49 (19%) 215 0.00049
(0.308) 		0.00807
(1.00) 		0.581
(1.00) 		0.705
(1.00) 		0.371
(1.00) 		0.317
(1.00) 		0.428
(1.00) 		0.0779
(1.00) 		0.0735
(1.00) 		0.0713
(1.00)
amp 4q31 21 29 (11%) 235 0.182
(1.00) 		0.201
(1.00) 		0.123
(1.00) 		0.263
(1.00) 		0.293
(1.00) 		0.18
(1.00) 		0.236
(1.00) 		0.0653
(1.00) 		0.842
(1.00) 		0.332
(1.00)
amp 6q21 23 (9%) 241 0.0418
(1.00) 		0.0918
(1.00) 		0.515
(1.00) 		0.0789
(1.00) 		0.484
(1.00) 		0.605
(1.00) 		0.789
(1.00) 		0.229
(1.00) 		0.74
(1.00) 		0.836
(1.00)
amp 11q22 2 49 (19%) 215 0.151
(1.00) 		0.129
(1.00) 		0.731
(1.00) 		0.413
(1.00) 		0.0676
(1.00) 		0.0145
(1.00) 		0.096
(1.00) 		0.00133
(0.815) 		0.16
(1.00) 		0.161
(1.00)
amp 12q15 77 (29%) 187 0.00703
(1.00) 		0.132
(1.00) 		0.0385
(1.00) 		0.0198
(1.00) 		0.022
(1.00) 		0.0215
(1.00) 		0.188
(1.00) 		0.0174
(1.00) 		0.0357
(1.00) 		0.00833
(1.00)
amp 13q22 1 84 (32%) 180 0.291
(1.00) 		0.75
(1.00) 		0.962
(1.00) 		0.85
(1.00) 		0.886
(1.00) 		0.954
(1.00) 		0.752
(1.00) 		0.683
(1.00) 		0.575
(1.00) 		0.335
(1.00)
amp 16p11 2 64 (24%) 200 0.0101
(1.00) 		0.251
(1.00) 		0.469
(1.00) 		0.368
(1.00) 		0.782
(1.00) 		0.712
(1.00) 		0.867
(1.00) 		0.656
(1.00) 		0.755
(1.00) 		0.962
(1.00)
amp 16q22 1 75 (28%) 189 0.0651
(1.00) 		0.859
(1.00) 		0.0843
(1.00) 		0.0861
(1.00) 		0.0695
(1.00) 		0.0555
(1.00) 		0.413
(1.00) 		0.191
(1.00) 		0.289
(1.00) 		0.5
(1.00)
amp 22q11 23 55 (21%) 209 0.00058
(0.364) 		0.0363
(1.00) 		0.592
(1.00) 		0.61
(1.00) 		0.0279
(1.00) 		0.103
(1.00) 		0.162
(1.00) 		0.235
(1.00) 		0.433
(1.00) 		0.519
(1.00)
del 1p36 11 52 (20%) 212 0.46
(1.00) 		0.177
(1.00) 		0.251
(1.00) 		0.0303
(1.00) 		0.189
(1.00) 		0.603
(1.00) 		0.814
(1.00) 		0.329
(1.00) 		0.52
(1.00) 		0.344
(1.00)
del 1q32 1 47 (18%) 217 0.0973
(1.00) 		0.142
(1.00) 		0.353
(1.00) 		0.601
(1.00) 		0.43
(1.00) 		0.107
(1.00) 		0.157
(1.00) 		0.0102
(1.00) 		0.0973
(1.00) 		0.339
(1.00)
del 2q22 1 80 (30%) 184 0.00331
(1.00) 		0.0896
(1.00) 		0.271
(1.00) 		0.943
(1.00) 		0.137
(1.00) 		0.152
(1.00) 		0.309
(1.00) 		0.254
(1.00) 		0.138
(1.00) 		0.388
(1.00)
del 4q22 1 109 (41%) 155 0.273
(1.00) 		0.258
(1.00) 		0.507
(1.00) 		0.502
(1.00) 		0.0919
(1.00) 		0.0685
(1.00) 		0.304
(1.00) 		0.14
(1.00) 		0.0855
(1.00) 		0.0344
(1.00)
del 4q34 2 119 (45%) 145 0.0127
(1.00) 		0.338
(1.00) 		0.458
(1.00) 		0.795
(1.00) 		0.732
(1.00) 		0.488
(1.00) 		0.0532
(1.00) 		0.146
(1.00) 		0.186
(1.00) 		0.079
(1.00)
del 6p25 3 69 (26%) 195 0.0165
(1.00) 		0.034
(1.00) 		0.839
(1.00) 		0.872
(1.00) 		0.425
(1.00) 		0.0744
(1.00) 		0.604
(1.00) 		0.274
(1.00) 		0.948
(1.00) 		0.544
(1.00)
del 7q36 3 39 (15%) 225 0.449
(1.00) 		0.0545
(1.00) 		0.206
(1.00) 		0.238
(1.00) 		0.291
(1.00) 		0.404
(1.00) 		0.717
(1.00) 		0.0156
(1.00) 		1
(1.00) 		0.894
(1.00)
del 10p12 1 43 (16%) 221 0.954
(1.00) 		0.155
(1.00) 		0.891
(1.00) 		0.43
(1.00) 		0.0157
(1.00) 		0.0367
(1.00) 		0.362
(1.00) 		0.264
(1.00) 		0.363
(1.00) 		0.418
(1.00)
del 10q23 31 106 (40%) 158 0.00251
(1.00) 		0.0159
(1.00) 		0.628
(1.00) 		0.594
(1.00) 		0.0882
(1.00) 		0.635
(1.00) 		0.713
(1.00) 		0.105
(1.00) 		0.67
(1.00) 		0.385
(1.00)
del 13q14 2 103 (39%) 161 0.0004
(0.252) 		0.575
(1.00) 		0.00803
(1.00) 		0.00318
(1.00) 		0.0237
(1.00) 		0.471
(1.00) 		0.782
(1.00) 		0.0252
(1.00) 		0.366
(1.00) 		0.693
(1.00)
del 16p13 3 104 (39%) 160 0.00087
(0.539) 		0.0138
(1.00) 		0.213
(1.00) 		0.466
(1.00) 		0.694
(1.00) 		0.918
(1.00) 		0.947
(1.00) 		0.0361
(1.00) 		0.759
(1.00) 		0.832
(1.00)
del 19p13 3 96 (36%) 168 0.00222
(1.00) 		0.281
(1.00) 		0.855
(1.00) 		0.608
(1.00) 		0.0415
(1.00) 		0.0743
(1.00) 		0.452
(1.00) 		0.0585
(1.00) 		0.178
(1.00) 		0.36
(1.00)
del xp11 3 62 (23%) 202 0.0317
(1.00) 		0.029
(1.00) 		0.735
(1.00) 		0.617
(1.00) 		0.207
(1.00) 		0.962
(1.00) 		0.0941
(1.00) 		0.838
(1.00) 		0.291
(1.00) 		0.785
(1.00)
del xq21 33 53 (20%) 211 0.00276
(1.00) 		0.0198
(1.00) 		0.98
(1.00) 		0.439
(1.00) 		0.0341
(1.00) 		0.239
(1.00) 		0.0493
(1.00) 		0.375
(1.00) 		0.225
(1.00) 		0.056
(1.00)
del xq23 49 (19%) 215 0.0654
(1.00) 		0.0305
(1.00) 		0.995
(1.00) 		0.623
(1.00) 		0.338
(1.00) 		0.655
(1.00) 		0.224
(1.00) 		0.424
(1.00) 		0.18
(1.00) 		0.196
(1.00)
'amp_1p34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S1.  Gene #1: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 1(1P34.2) MUTATED 33 17 20
AMP PEAK 1(1P34.2) WILD-TYPE 34 79 81

Figure S1.  Get High-res Image Gene #1: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S2.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 2(1Q21.3) MUTATED 55 35 38
AMP PEAK 2(1Q21.3) WILD-TYPE 12 61 63

Figure S2.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 60 54 47
AMP PEAK 2(1Q21.3) MUTATED 34 46 23 20
AMP PEAK 2(1Q21.3) WILD-TYPE 55 14 31 27

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

'amp_1q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S4.  Gene #3: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 3(1Q23.3) MUTATED 57 37 41
AMP PEAK 3(1Q23.3) WILD-TYPE 10 59 60

Figure S4.  Get High-res Image Gene #3: 'amp_1q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S5.  Gene #4: 'amp_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 4(3P25.2) MUTATED 53 28 46
AMP PEAK 4(3P25.2) WILD-TYPE 14 68 55

Figure S5.  Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p25.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S6.  Gene #4: 'amp_3p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 60 54 47
AMP PEAK 4(3P25.2) MUTATED 29 43 25 25
AMP PEAK 4(3P25.2) WILD-TYPE 60 17 29 22

Figure S6.  Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3p25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S7.  Gene #4: 'amp_3p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 72 73
AMP PEAK 4(3P25.2) MUTATED 72 37 18
AMP PEAK 4(3P25.2) WILD-TYPE 46 35 55

Figure S7.  Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3p25.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S8.  Gene #4: 'amp_3p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 44 64 59
AMP PEAK 4(3P25.2) MUTATED 57 20 38 12
AMP PEAK 4(3P25.2) WILD-TYPE 39 24 26 47

Figure S8.  Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.2' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.045

Table S9.  Gene #4: 'amp_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 115 85
AMP PEAK 4(3P25.2) MUTATED 45 50 31
AMP PEAK 4(3P25.2) WILD-TYPE 18 65 54

Figure S9.  Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3p25.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S10.  Gene #4: 'amp_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 24 31 34 47 36 47
AMP PEAK 4(3P25.2) MUTATED 34 11 23 13 22 10 13
AMP PEAK 4(3P25.2) WILD-TYPE 10 13 8 21 25 26 34

Figure S10.  Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S11.  Gene #4: 'amp_3p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 112 104
AMP PEAK 4(3P25.2) MUTATED 36 41 49
AMP PEAK 4(3P25.2) WILD-TYPE 11 71 55

Figure S11.  Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.052

Table S12.  Gene #4: 'amp_3p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 132 88
AMP PEAK 4(3P25.2) MUTATED 33 51 42
AMP PEAK 4(3P25.2) WILD-TYPE 10 81 46

Figure S12.  Get High-res Image Gene #4: 'amp_3p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S13.  Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 5(3Q26.32) MUTATED 51 36 55
AMP PEAK 5(3Q26.32) WILD-TYPE 16 60 46

Figure S13.  Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S14.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 9(5P15.33) MUTATED 51 36 44
AMP PEAK 9(5P15.33) WILD-TYPE 16 60 57

Figure S14.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S15.  Gene #9: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 24 31 34 47 36 47
AMP PEAK 9(5P15.33) MUTATED 28 14 19 17 27 16 9
AMP PEAK 9(5P15.33) WILD-TYPE 16 10 12 17 20 20 38

Figure S15.  Get High-res Image Gene #9: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S16.  Gene #10: 'amp_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 10(6P22.3) MUTATED 52 32 27
AMP PEAK 10(6P22.3) WILD-TYPE 15 64 74

Figure S16.  Get High-res Image Gene #10: 'amp_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p21.1' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.09

Table S17.  Gene #12: 'amp_7p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 12(7P21.1) MUTATED 46 34 54
AMP PEAK 12(7P21.1) WILD-TYPE 21 62 47

Figure S17.  Get High-res Image Gene #12: 'amp_7p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S18.  Gene #13: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 13(7P11.2) MUTATED 48 28 55
AMP PEAK 13(7P11.2) WILD-TYPE 19 68 46

Figure S18.  Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S19.  Gene #14: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 14(8P11.23) MUTATED 27 7 50
AMP PEAK 14(8P11.23) WILD-TYPE 40 89 51

Figure S19.  Get High-res Image Gene #14: 'amp_8p11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S20.  Gene #15: 'amp_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 15(8P11.21) MUTATED 29 8 49
AMP PEAK 15(8P11.21) WILD-TYPE 38 88 52

Figure S20.  Get High-res Image Gene #15: 'amp_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S21.  Gene #16: 'amp_8q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 16(8Q22.3) MUTATED 54 41 74
AMP PEAK 16(8Q22.3) WILD-TYPE 13 55 27

Figure S21.  Get High-res Image Gene #16: 'amp_8q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S22.  Gene #17: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 17(9P24.1) MUTATED 21 26 6
AMP PEAK 17(9P24.1) WILD-TYPE 46 70 95

Figure S22.  Get High-res Image Gene #17: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p14' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S23.  Gene #18: 'amp_10p14' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 18(10P14) MUTATED 50 28 38
AMP PEAK 18(10P14) WILD-TYPE 17 68 63

Figure S23.  Get High-res Image Gene #18: 'amp_10p14' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p14' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S24.  Gene #18: 'amp_10p14' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 60 54 47
AMP PEAK 18(10P14) MUTATED 32 45 17 18
AMP PEAK 18(10P14) WILD-TYPE 57 15 37 29

Figure S24.  Get High-res Image Gene #18: 'amp_10p14' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.052

Table S25.  Gene #19: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 19(11Q13.3) MUTATED 31 20 50
AMP PEAK 19(11Q13.3) WILD-TYPE 36 76 51

Figure S25.  Get High-res Image Gene #19: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.18

Table S26.  Gene #23: 'amp_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 24 31 34 47 36 47
AMP PEAK 23(14Q11.2) MUTATED 12 8 12 11 2 12 5
AMP PEAK 23(14Q11.2) WILD-TYPE 32 16 19 23 45 24 42

Figure S26.  Get High-res Image Gene #23: 'amp_14q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_16p13.13' versus 'CN_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.25

Table S27.  Gene #24: 'amp_16p13.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 24(16P13.13) MUTATED 25 11 20
AMP PEAK 24(16P13.13) WILD-TYPE 42 85 81

Figure S27.  Get High-res Image Gene #24: 'amp_16p13.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S28.  Gene #27: 'amp_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 27(17Q11.2) MUTATED 45 17 55
AMP PEAK 27(17Q11.2) WILD-TYPE 22 79 46

Figure S28.  Get High-res Image Gene #27: 'amp_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S29.  Gene #27: 'amp_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 60 54 47
AMP PEAK 27(17Q11.2) MUTATED 24 36 30 21
AMP PEAK 27(17Q11.2) WILD-TYPE 65 24 24 26

Figure S29.  Get High-res Image Gene #27: 'amp_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.25

Table S30.  Gene #27: 'amp_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 72 73
AMP PEAK 27(17Q11.2) MUTATED 68 27 22
AMP PEAK 27(17Q11.2) WILD-TYPE 50 45 51

Figure S30.  Get High-res Image Gene #27: 'amp_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S31.  Gene #28: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 28(17Q12) MUTATED 40 19 51
AMP PEAK 28(17Q12) WILD-TYPE 27 77 50

Figure S31.  Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S32.  Gene #28: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 112 104
AMP PEAK 28(17Q12) MUTATED 30 33 46
AMP PEAK 28(17Q12) WILD-TYPE 17 79 58

Figure S32.  Get High-res Image Gene #28: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S33.  Gene #29: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 29(19Q12) MUTATED 46 22 41
AMP PEAK 29(19Q12) WILD-TYPE 21 74 60

Figure S33.  Get High-res Image Gene #29: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.13

Table S34.  Gene #29: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 60 54 47
AMP PEAK 29(19Q12) MUTATED 28 39 17 20
AMP PEAK 29(19Q12) WILD-TYPE 61 21 37 27

Figure S34.  Get High-res Image Gene #29: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S35.  Gene #30: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 30(19Q13.43) MUTATED 38 21 44
AMP PEAK 30(19Q13.43) WILD-TYPE 29 75 57

Figure S35.  Get High-res Image Gene #30: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.19

Table S36.  Gene #31: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
AMP PEAK 31(20Q11.21) MUTATED 55 50 66
AMP PEAK 31(20Q11.21) WILD-TYPE 12 46 35

Figure S36.  Get High-res Image Gene #31: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S37.  Gene #36: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 4(2Q37.1) MUTATED 49 34 47
DEL PEAK 4(2Q37.1) WILD-TYPE 18 62 54

Figure S37.  Get High-res Image Gene #36: 'del_2q37.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S38.  Gene #37: 'del_3p21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 72 73
DEL PEAK 5(3P21.31) MUTATED 27 12 38
DEL PEAK 5(3P21.31) WILD-TYPE 91 60 35

Figure S38.  Get High-res Image Gene #37: 'del_3p21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.026

Table S39.  Gene #37: 'del_3p21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 44 64 59
DEL PEAK 5(3P21.31) MUTATED 21 9 14 33
DEL PEAK 5(3P21.31) WILD-TYPE 75 35 50 26

Figure S39.  Get High-res Image Gene #37: 'del_3p21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MRNASEQ_CNMF'

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

Table S40.  Gene #38: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 72 73
DEL PEAK 6(3P14.2) MUTATED 25 13 36
DEL PEAK 6(3P14.2) WILD-TYPE 93 59 37

Figure S40.  Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S41.  Gene #38: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 44 64 59
DEL PEAK 6(3P14.2) MUTATED 19 8 15 32
DEL PEAK 6(3P14.2) WILD-TYPE 77 36 49 27

Figure S41.  Get High-res Image Gene #38: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MRNASEQ_CNMF'

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

Table S42.  Gene #39: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 72 73
DEL PEAK 7(3P13) MUTATED 23 12 35
DEL PEAK 7(3P13) WILD-TYPE 95 60 38

Figure S42.  Get High-res Image Gene #39: 'del_3p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.071

Table S43.  Gene #39: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 44 64 59
DEL PEAK 7(3P13) MUTATED 18 8 14 30
DEL PEAK 7(3P13) WILD-TYPE 78 36 50 29

Figure S43.  Get High-res Image Gene #39: 'del_3p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S44.  Gene #42: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 10(5Q11.2) MUTATED 51 33 49
DEL PEAK 10(5Q11.2) WILD-TYPE 16 63 52

Figure S44.  Get High-res Image Gene #42: 'del_5q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S45.  Gene #43: 'del_5q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 11(5Q35.1) MUTATED 45 30 51
DEL PEAK 11(5Q35.1) WILD-TYPE 22 66 50

Figure S45.  Get High-res Image Gene #43: 'del_5q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q35.1' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S46.  Gene #43: 'del_5q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 60 54 47
DEL PEAK 11(5Q35.1) MUTATED 38 42 27 13
DEL PEAK 11(5Q35.1) WILD-TYPE 51 18 27 34

Figure S46.  Get High-res Image Gene #43: 'del_5q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S47.  Gene #45: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 13(6Q21) MUTATED 43 19 55
DEL PEAK 13(6Q21) WILD-TYPE 24 77 46

Figure S47.  Get High-res Image Gene #45: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S48.  Gene #46: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 14(6Q27) MUTATED 44 25 50
DEL PEAK 14(6Q27) WILD-TYPE 23 71 51

Figure S48.  Get High-res Image Gene #46: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S49.  Gene #46: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 24 31 34 47 36 47
DEL PEAK 14(6Q27) MUTATED 26 13 21 17 23 10 9
DEL PEAK 14(6Q27) WILD-TYPE 18 11 10 17 24 26 38

Figure S49.  Get High-res Image Gene #46: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S50.  Gene #48: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 16(8P23.3) MUTATED 56 54 41
DEL PEAK 16(8P23.3) WILD-TYPE 11 42 60

Figure S50.  Get High-res Image Gene #48: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S51.  Gene #48: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 60 54 47
DEL PEAK 16(8P23.3) MUTATED 57 49 20 17
DEL PEAK 16(8P23.3) WILD-TYPE 32 11 34 30

Figure S51.  Get High-res Image Gene #48: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S52.  Gene #49: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 17(8P12) MUTATED 50 50 29
DEL PEAK 17(8P12) WILD-TYPE 17 46 72

Figure S52.  Get High-res Image Gene #49: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p11.21' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.052

Table S53.  Gene #50: 'del_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 18(8P11.21) MUTATED 23 34 12
DEL PEAK 18(8P11.21) WILD-TYPE 44 62 89

Figure S53.  Get High-res Image Gene #50: 'del_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S54.  Gene #51: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 19(9P23) MUTATED 24 19 72
DEL PEAK 19(9P23) WILD-TYPE 43 77 29

Figure S54.  Get High-res Image Gene #51: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S55.  Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 20(9P21.3) MUTATED 32 37 88
DEL PEAK 20(9P21.3) WILD-TYPE 35 59 13

Figure S55.  Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q33.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S56.  Gene #53: 'del_9q33.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 21(9Q33.2) MUTATED 24 20 60
DEL PEAK 21(9Q33.2) WILD-TYPE 43 76 41

Figure S56.  Get High-res Image Gene #53: 'del_9q33.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q33.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S57.  Gene #53: 'del_9q33.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 44 64 59
DEL PEAK 21(9Q33.2) MUTATED 43 12 36 13
DEL PEAK 21(9Q33.2) WILD-TYPE 53 32 28 46

Figure S57.  Get High-res Image Gene #53: 'del_9q33.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S58.  Gene #56: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 24(11P15.5) MUTATED 43 21 65
DEL PEAK 24(11P15.5) WILD-TYPE 24 75 36

Figure S58.  Get High-res Image Gene #56: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S59.  Gene #57: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 25(11Q23.3) MUTATED 33 17 50
DEL PEAK 25(11Q23.3) WILD-TYPE 34 79 51

Figure S59.  Get High-res Image Gene #57: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S60.  Gene #59: 'del_14q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 27(14Q12) MUTATED 33 12 35
DEL PEAK 27(14Q12) WILD-TYPE 34 84 66

Figure S60.  Get High-res Image Gene #59: 'del_14q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S61.  Gene #60: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 28(14Q24.1) MUTATED 39 14 33
DEL PEAK 28(14Q24.1) WILD-TYPE 28 82 68

Figure S61.  Get High-res Image Gene #60: 'del_14q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S62.  Gene #60: 'del_14q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 89 60 54 47
DEL PEAK 28(14Q24.1) MUTATED 21 36 10 16
DEL PEAK 28(14Q24.1) WILD-TYPE 68 24 44 31

Figure S62.  Get High-res Image Gene #60: 'del_14q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S63.  Gene #60: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 96 44 64 59
DEL PEAK 28(14Q24.1) MUTATED 35 8 34 9
DEL PEAK 28(14Q24.1) WILD-TYPE 61 36 30 50

Figure S63.  Get High-res Image Gene #60: 'del_14q24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.1' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.17

Table S64.  Gene #61: 'del_15q13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 29(15Q13.1) MUTATED 41 35 31
DEL PEAK 29(15Q13.1) WILD-TYPE 26 61 70

Figure S64.  Get High-res Image Gene #61: 'del_15q13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.039

Table S65.  Gene #61: 'del_15q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 24 31 34 47 36 47
DEL PEAK 29(15Q13.1) MUTATED 23 13 19 18 15 12 7
DEL PEAK 29(15Q13.1) WILD-TYPE 21 11 12 16 32 24 40

Figure S65.  Get High-res Image Gene #61: 'del_15q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.039

Table S66.  Gene #63: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 31(16Q23.1) MUTATED 33 22 18
DEL PEAK 31(16Q23.1) WILD-TYPE 34 74 83

Figure S66.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.2

Table S67.  Gene #63: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 24 31 34 47 36 47
DEL PEAK 31(16Q23.1) MUTATED 20 5 13 8 6 15 6
DEL PEAK 31(16Q23.1) WILD-TYPE 24 19 18 26 41 21 41

Figure S67.  Get High-res Image Gene #63: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.007

Table S68.  Gene #64: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 32(17P12) MUTATED 48 25 64
DEL PEAK 32(17P12) WILD-TYPE 19 71 37

Figure S68.  Get High-res Image Gene #64: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.18

Table S69.  Gene #65: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 24 31 34 47 36 47
DEL PEAK 33(18Q21.2) MUTATED 25 17 16 18 19 9 11
DEL PEAK 33(18Q21.2) WILD-TYPE 19 7 15 16 28 27 36

Figure S69.  Get High-res Image Gene #65: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.02

Table S70.  Gene #67: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 101
DEL PEAK 35(22Q13.31) MUTATED 46 42 30
DEL PEAK 35(22Q13.31) WILD-TYPE 21 54 71

Figure S70.  Get High-res Image Gene #67: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 264

  • Number of significantly focal cnvs = 70

  • 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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