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 60 focal events and 12 molecular subtypes across 162 patients, 24 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'CN_CNMF'.

  • amp_6p21.1 cnv correlated to 'CN_CNMF'.

  • amp_8p11.23 cnv correlated to 'CN_CNMF'.

  • amp_8p11.21 cnv correlated to 'CN_CNMF'.

  • amp_8q24.21 cnv correlated to 'CN_CNMF'.

  • amp_12p12.1 cnv correlated to 'CN_CNMF'.

  • amp_13q12.13 cnv correlated to 'CN_CNMF'.

  • amp_13q12.2 cnv correlated to 'CN_CNMF'.

  • amp_13q22.1 cnv correlated to 'CN_CNMF'.

  • amp_16p11.2 cnv correlated to 'CN_CNMF'.

  • amp_17q12 cnv correlated to 'CN_CNMF'.

  • amp_17q24.1 cnv correlated to 'CN_CNMF'.

  • amp_20q11.21 cnv correlated to 'CN_CNMF'.

  • amp_20q11.23 cnv correlated to 'CN_CNMF'.

  • del_1p36.11 cnv correlated to 'CN_CNMF'.

  • del_1p33 cnv correlated to 'CN_CNMF'.

  • del_1p13.2 cnv correlated to 'CN_CNMF'.

  • del_4p13 cnv correlated to 'CN_CNMF'.

  • del_4q22.1 cnv correlated to 'CN_CNMF'.

  • del_4q35.1 cnv correlated to 'CN_CNMF'.

  • del_8p23.2 cnv correlated to 'CN_CNMF'.

  • del_11q22.3 cnv correlated to 'CN_CNMF'.

  • del_18q21.2 cnv correlated to 'CN_CNMF'.

  • del_18q22.1 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 60 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, 24 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 1q21 3 48 (30%) 114 1
(1.00) 		0.852
(1.00) 		0.0001
(0.0697) 		0.96
(1.00) 		0.53
(1.00) 		0.227
(1.00) 		0.509
(1.00) 		0.36
(1.00) 		0.0577
(1.00) 		0.151
(1.00) 		0.0304
(1.00) 		0.659
(1.00)
amp 6p21 1 53 (33%) 109 0.0595
(1.00) 		0.106
(1.00) 		1e-05
(0.00715) 		0.0699
(1.00) 		0.809
(1.00) 		0.0446
(1.00) 		0.574
(1.00) 		0.337
(1.00) 		0.192
(1.00) 		0.387
(1.00) 		0.392
(1.00) 		0.794
(1.00)
amp 8p11 23 52 (32%) 110 0.00348
(1.00) 		0.206
(1.00) 		1e-05
(0.00715) 		0.31
(1.00) 		0.377
(1.00) 		0.129
(1.00) 		0.123
(1.00) 		0.0353
(1.00) 		0.047
(1.00) 		0.0275
(1.00) 		0.69
(1.00) 		0.468
(1.00)
amp 8p11 21 69 (43%) 93 0.0122
(1.00) 		0.213
(1.00) 		1e-05
(0.00715) 		0.256
(1.00) 		0.373
(1.00) 		0.519
(1.00) 		0.225
(1.00) 		0.134
(1.00) 		0.184
(1.00) 		0.274
(1.00) 		0.432
(1.00) 		0.659
(1.00)
amp 8q24 21 107 (66%) 55 0.017
(1.00) 		0.24
(1.00) 		1e-05
(0.00715) 		0.23
(1.00) 		0.63
(1.00) 		0.887
(1.00) 		0.0308
(1.00) 		0.00707
(1.00) 		0.542
(1.00) 		0.263
(1.00) 		0.938
(1.00) 		0.895
(1.00)
amp 12p12 1 40 (25%) 122 0.698
(1.00) 		0.468
(1.00) 		0.00029
(0.201) 		0.447
(1.00) 		0.0495
(1.00) 		0.00873
(1.00) 		0.705
(1.00) 		0.513
(1.00) 		0.694
(1.00) 		0.76
(1.00) 		0.0282
(1.00) 		0.834
(1.00)
amp 13q12 13 123 (76%) 39 0.415
(1.00) 		0.174
(1.00) 		6e-05
(0.0419) 		0.224
(1.00) 		0.324
(1.00) 		0.433
(1.00) 		0.00163
(1.00) 		0.00212
(1.00) 		0.00253
(1.00) 		0.00422
(1.00) 		0.839
(1.00) 		0.239
(1.00)
amp 13q12 2 122 (75%) 40 0.364
(1.00) 		0.236
(1.00) 		3e-05
(0.0211) 		0.151
(1.00) 		0.594
(1.00) 		0.587
(1.00) 		0.016
(1.00) 		0.012
(1.00) 		0.0215
(1.00) 		0.0218
(1.00) 		0.183
(1.00) 		0.248
(1.00)
amp 13q22 1 117 (72%) 45 0.265
(1.00) 		0.0653
(1.00) 		1e-05
(0.00715) 		0.0507
(1.00) 		0.908
(1.00) 		0.269
(1.00) 		0.00507
(1.00) 		0.00104
(0.714) 		0.00412
(1.00) 		0.0111
(1.00) 		0.156
(1.00) 		0.148
(1.00)
amp 16p11 2 45 (28%) 117 0.124
(1.00) 		0.581
(1.00) 		7e-05
(0.0489) 		0.231
(1.00) 		0.345
(1.00) 		0.668
(1.00) 		0.152
(1.00) 		0.118
(1.00) 		0.0972
(1.00) 		0.852
(1.00) 		0.197
(1.00) 		0.241
(1.00)
amp 17q12 43 (27%) 119 0.00651
(1.00) 		0.127
(1.00) 		2e-05
(0.0141) 		0.535
(1.00) 		0.177
(1.00) 		0.917
(1.00) 		0.433
(1.00) 		0.0251
(1.00) 		0.149
(1.00) 		0.597
(1.00) 		0.582
(1.00) 		0.882
(1.00)
amp 17q24 1 37 (23%) 125 0.291
(1.00) 		0.708
(1.00) 		0.00021
(0.146) 		0.124
(1.00) 		0.608
(1.00) 		0.748
(1.00) 		0.638
(1.00) 		0.172
(1.00) 		0.61
(1.00) 		0.209
(1.00) 		0.714
(1.00) 		0.746
(1.00)
amp 20q11 21 143 (88%) 19 0.00761
(1.00) 		0.162
(1.00) 		0.00018
(0.125) 		0.0239
(1.00) 		0.192
(1.00) 		0.368
(1.00) 		0.0578
(1.00) 		0.00319
(1.00) 		0.00761
(1.00) 		0.397
(1.00) 		0.191
(1.00) 		0.31
(1.00)
amp 20q11 23 144 (89%) 18 0.00784
(1.00) 		0.164
(1.00) 		0.00033
(0.228) 		0.056
(1.00) 		0.193
(1.00) 		0.368
(1.00) 		0.0397
(1.00) 		0.00247
(1.00) 		0.0144
(1.00) 		0.28
(1.00) 		0.478
(1.00) 		0.265
(1.00)
del 1p36 11 72 (44%) 90 0.115
(1.00) 		0.0637
(1.00) 		0.00031
(0.215) 		0.256
(1.00) 		0.703
(1.00) 		0.923
(1.00) 		0.726
(1.00) 		0.0212
(1.00) 		0.495
(1.00) 		0.0632
(1.00) 		0.94
(1.00) 		0.293
(1.00)
del 1p33 50 (31%) 112 0.365
(1.00) 		0.00405
(1.00) 		3e-05
(0.0211) 		0.217
(1.00) 		0.801
(1.00) 		0.309
(1.00) 		0.697
(1.00) 		0.164
(1.00) 		0.44
(1.00) 		0.264
(1.00) 		0.871
(1.00) 		0.319
(1.00)
del 1p13 2 52 (32%) 110 0.475
(1.00) 		0.0237
(1.00) 		2e-05
(0.0141) 		0.628
(1.00) 		0.545
(1.00) 		0.569
(1.00) 		0.243
(1.00) 		0.0293
(1.00) 		0.508
(1.00) 		0.21
(1.00) 		0.804
(1.00) 		0.218
(1.00)
del 4p13 59 (36%) 103 0.779
(1.00) 		0.0395
(1.00) 		1e-05
(0.00715) 		0.0843
(1.00) 		0.837
(1.00) 		0.504
(1.00) 		0.712
(1.00) 		0.251
(1.00) 		0.979
(1.00) 		0.221
(1.00) 		0.415
(1.00) 		0.786
(1.00)
del 4q22 1 72 (44%) 90 0.62
(1.00) 		0.0239
(1.00) 		2e-05
(0.0141) 		0.257
(1.00) 		0.703
(1.00) 		0.475
(1.00) 		0.395
(1.00) 		0.312
(1.00) 		0.987
(1.00) 		0.256
(1.00) 		0.797
(1.00) 		0.504
(1.00)
del 4q35 1 71 (44%) 91 0.612
(1.00) 		0.0642
(1.00) 		4e-05
(0.028) 		0.119
(1.00) 		0.385
(1.00) 		0.654
(1.00) 		0.248
(1.00) 		0.0304
(1.00) 		0.486
(1.00) 		0.0513
(1.00) 		0.674
(1.00) 		0.796
(1.00)
del 8p23 2 99 (61%) 63 0.111
(1.00) 		0.0886
(1.00) 		1e-05
(0.00715) 		0.414
(1.00) 		1
(1.00) 		0.269
(1.00) 		0.0623
(1.00) 		0.0268
(1.00) 		0.782
(1.00) 		0.33
(1.00) 		0.289
(1.00) 		0.463
(1.00)
del 11q22 3 38 (23%) 124 0.0328
(1.00) 		0.0302
(1.00) 		1e-05
(0.00715) 		0.0391
(1.00) 		0.688
(1.00) 		0.135
(1.00) 		0.0722
(1.00) 		0.0724
(1.00) 		0.45
(1.00) 		0.966
(1.00) 		0.379
(1.00) 		0.169
(1.00)
del 18q21 2 143 (88%) 19 0.132
(1.00) 		0.334
(1.00) 		1e-05
(0.00715) 		0.112
(1.00) 		1
(1.00) 		0.771
(1.00) 		0.931
(1.00) 		0.719
(1.00) 		0.4
(1.00) 		0.123
(1.00) 		0.0435
(1.00) 		0.709
(1.00)
del 18q22 1 138 (85%) 24 0.0676
(1.00) 		0.0879
(1.00) 		1e-05
(0.00715) 		0.0311
(1.00) 		0.777
(1.00) 		0.653
(1.00) 		0.619
(1.00) 		0.676
(1.00) 		0.828
(1.00) 		0.299
(1.00) 		0.00126
(0.864) 		0.499
(1.00)
amp 1q32 2 48 (30%) 114 0.826
(1.00) 		0.938
(1.00) 		0.00273
(1.00) 		0.577
(1.00) 		0.186
(1.00) 		0.027
(1.00) 		0.508
(1.00) 		0.54
(1.00) 		0.0818
(1.00) 		0.65
(1.00) 		0.0303
(1.00) 		0.332
(1.00)
amp 5q22 3 20 (12%) 142 0.0227
(1.00) 		0.175
(1.00) 		0.36
(1.00) 		0.283
(1.00) 		0.105
(1.00) 		0.658
(1.00) 		0.719
(1.00) 		0.682
(1.00) 		0.454
(1.00) 		0.662
(1.00) 		0.0615
(1.00) 		0.664
(1.00)
amp 10q22 2 11 (7%) 151 0.499
(1.00) 		0.931
(1.00) 		0.817
(1.00) 		1
(1.00) 		1
(1.00) 		0.972
(1.00) 		0.222
(1.00) 		0.191
(1.00) 		0.38
(1.00) 		0.187
(1.00) 		0.229
(1.00) 		1
(1.00)
amp 11p15 5 44 (27%) 118 0.382
(1.00) 		0.0961
(1.00) 		0.0278
(1.00) 		0.695
(1.00) 		0.726
(1.00) 		0.588
(1.00) 		0.137
(1.00) 		0.034
(1.00) 		0.0966
(1.00) 		0.538
(1.00) 		0.344
(1.00) 		0.104
(1.00)
amp 11q13 3 27 (17%) 135 0.329
(1.00) 		0.332
(1.00) 		0.00527
(1.00) 		0.00753
(1.00) 		0.911
(1.00) 		0.731
(1.00) 		0.141
(1.00) 		0.00204
(1.00) 		0.0132
(1.00) 		0.341
(1.00) 		0.43
(1.00) 		0.534
(1.00)
amp 12p13 33 41 (25%) 121 0.689
(1.00) 		0.483
(1.00) 		0.00184
(1.00) 		0.654
(1.00) 		0.116
(1.00) 		0.214
(1.00) 		0.809
(1.00) 		0.836
(1.00) 		0.579
(1.00) 		0.815
(1.00) 		0.207
(1.00) 		0.511
(1.00)
amp 15q26 1 13 (8%) 149 0.111
(1.00) 		0.212
(1.00) 		0.151
(1.00) 		0.507
(1.00) 		0.156
(1.00) 		0.348
(1.00) 		0.0921
(1.00) 		0.122
(1.00) 		0.908
(1.00) 		1
(1.00) 		0.79
(1.00) 		0.104
(1.00)
amp 19p13 2 34 (21%) 128 0.0206
(1.00) 		0.25
(1.00) 		0.00158
(1.00) 		0.854
(1.00) 		0.545
(1.00) 		0.0852
(1.00) 		0.0577
(1.00) 		0.704
(1.00) 		0.588
(1.00) 		0.696
(1.00) 		0.977
(1.00) 		0.322
(1.00)
amp 20q13 33 143 (88%) 19 0.0365
(1.00) 		0.234
(1.00) 		0.0196
(1.00) 		0.242
(1.00) 		0.259
(1.00) 		0.562
(1.00) 		0.173
(1.00) 		0.0452
(1.00) 		0.0777
(1.00) 		0.396
(1.00) 		0.338
(1.00) 		0.711
(1.00)
amp xp22 2 31 (19%) 131 0.0503
(1.00) 		0.219
(1.00) 		0.646
(1.00) 		0.317
(1.00) 		0.96
(1.00) 		0.235
(1.00) 		0.708
(1.00) 		0.175
(1.00) 		0.813
(1.00) 		0.87
(1.00) 		0.414
(1.00) 		0.184
(1.00)
amp xq27 3 36 (22%) 126 0.362
(1.00) 		0.325
(1.00) 		0.0148
(1.00) 		0.0202
(1.00) 		0.648
(1.00) 		0.21
(1.00) 		0.0197
(1.00) 		0.123
(1.00) 		0.383
(1.00) 		0.278
(1.00) 		0.291
(1.00) 		0.305
(1.00)
del 2p12 18 (11%) 144 0.354
(1.00) 		0.821
(1.00) 		0.00143
(0.978) 		0.406
(1.00) 		0.449
(1.00) 		0.142
(1.00) 		0.646
(1.00) 		0.432
(1.00) 		0.359
(1.00) 		0.545
(1.00) 		0.267
(1.00) 		0.884
(1.00)
del 3p14 2 29 (18%) 133 0.801
(1.00) 		0.701
(1.00) 		0.783
(1.00) 		1
(1.00) 		0.218
(1.00) 		0.716
(1.00) 		0.342
(1.00) 		0.764
(1.00) 		0.81
(1.00) 		0.96
(1.00) 		0.72
(1.00) 		0.768
(1.00)
del 3q26 31 16 (10%) 146 1
(1.00) 		0.497
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.725
(1.00) 		0.836
(1.00) 		0.799
(1.00) 		0.295
(1.00) 		0.0834
(1.00) 		0.372
(1.00) 		0.0671
(1.00) 		0.865
(1.00)
del 5q11 2 51 (31%) 111 0.066
(1.00) 		0.00202
(1.00) 		0.0119
(1.00) 		0.00184
(1.00) 		0.857
(1.00) 		0.341
(1.00) 		0.557
(1.00) 		0.0342
(1.00) 		0.552
(1.00) 		0.289
(1.00) 		0.675
(1.00) 		0.252
(1.00)
del 5q22 2 57 (35%) 105 0.183
(1.00) 		0.00082
(0.564) 		0.0556
(1.00) 		0.323
(1.00) 		0.546
(1.00) 		0.728
(1.00) 		1
(1.00) 		0.0982
(1.00) 		0.739
(1.00) 		0.238
(1.00) 		0.213
(1.00) 		0.444
(1.00)
del 6p25 3 24 (15%) 138 1
(1.00) 		0.939
(1.00) 		0.264
(1.00) 		0.0217
(1.00) 		0.653
(1.00) 		0.985
(1.00) 		0.95
(1.00) 		0.867
(1.00) 		0.753
(1.00) 		0.783
(1.00) 		0.469
(1.00) 		0.173
(1.00)
del 6q26 30 (19%) 132 0.158
(1.00) 		0.744
(1.00) 		0.213
(1.00) 		0.682
(1.00) 		0.101
(1.00) 		0.199
(1.00) 		0.265
(1.00) 		0.119
(1.00) 		0.0558
(1.00) 		0.334
(1.00) 		0.0967
(1.00) 		0.114
(1.00)
del 7q31 1 4 (2%) 158 0.0623
(1.00) 		1
(1.00) 		0.952
(1.00) 		0.759
(1.00) 		0.767
(1.00) 		1
(1.00) 		1
(1.00)
del 8p11 21 24 (15%) 138 0.317
(1.00) 		0.823
(1.00) 		0.00427
(1.00) 		0.203
(1.00) 		0.112
(1.00) 		0.702
(1.00) 		0.166
(1.00) 		0.0989
(1.00) 		0.0463
(1.00) 		0.0685
(1.00) 		0.378
(1.00) 		0.163
(1.00)
del 10q21 1 37 (23%) 125 0.37
(1.00) 		0.417
(1.00) 		0.0293
(1.00) 		0.302
(1.00) 		0.0605
(1.00) 		0.186
(1.00) 		0.431
(1.00) 		0.793
(1.00) 		0.833
(1.00) 		0.28
(1.00) 		0.822
(1.00) 		0.315
(1.00)
del 10q25 2 47 (29%) 115 0.761
(1.00) 		0.772
(1.00) 		0.0715
(1.00) 		0.671
(1.00) 		0.456
(1.00) 		0.241
(1.00) 		0.687
(1.00) 		0.223
(1.00) 		0.624
(1.00) 		0.275
(1.00) 		0.713
(1.00) 		0.349
(1.00)
del 12p13 1 33 (20%) 129 1
(1.00) 		0.261
(1.00) 		0.26
(1.00) 		0.287
(1.00) 		0.536
(1.00) 		0.276
(1.00) 		0.532
(1.00) 		0.149
(1.00) 		0.295
(1.00) 		0.528
(1.00) 		0.771
(1.00) 		0.537
(1.00)
del 12q22 24 (15%) 138 0.607
(1.00) 		0.408
(1.00) 		0.0227
(1.00) 		0.774
(1.00) 		0.9
(1.00) 		0.315
(1.00) 		0.851
(1.00) 		0.403
(1.00) 		0.365
(1.00) 		0.617
(1.00) 		0.304
(1.00) 		0.362
(1.00)
del 14q11 2 68 (42%) 94 0.483
(1.00) 		0.128
(1.00) 		0.029
(1.00) 		0.931
(1.00) 		0.702
(1.00) 		0.694
(1.00) 		0.0662
(1.00) 		0.277
(1.00) 		0.109
(1.00) 		0.343
(1.00) 		0.576
(1.00) 		0.343
(1.00)
del 14q31 1 70 (43%) 92 0.483
(1.00) 		0.237
(1.00) 		0.0297
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.2
(1.00) 		0.08
(1.00) 		0.141
(1.00) 		0.2
(1.00) 		0.239
(1.00) 		0.87
(1.00) 		0.632
(1.00)
del 15q22 33 76 (47%) 86 0.623
(1.00) 		0.154
(1.00) 		0.00078
(0.537) 		0.697
(1.00) 		0.148
(1.00) 		0.0578
(1.00) 		0.784
(1.00) 		0.187
(1.00) 		0.421
(1.00) 		0.744
(1.00) 		0.932
(1.00) 		0.724
(1.00)
del 16p13 3 13 (8%) 149 0.887
(1.00) 		0.677
(1.00) 		0.0158
(1.00) 		0.0204
(1.00) 		0.724
(1.00) 		0.6
(1.00) 		0.912
(1.00) 		0.832
(1.00) 		0.355
(1.00) 		0.633
(1.00) 		0.675
(1.00) 		0.573
(1.00)
del 16q23 1 23 (14%) 139 0.152
(1.00) 		0.351
(1.00) 		0.0411
(1.00) 		0.136
(1.00) 		0.588
(1.00) 		0.952
(1.00) 		0.586
(1.00) 		0.658
(1.00) 		0.76
(1.00) 		0.843
(1.00) 		0.511
(1.00) 		0.307
(1.00)
del 17p11 2 110 (68%) 52 0.0848
(1.00) 		0.757
(1.00) 		0.00582
(1.00) 		0.281
(1.00) 		0.829
(1.00) 		0.358
(1.00) 		0.864
(1.00) 		0.972
(1.00) 		0.935
(1.00) 		0.352
(1.00) 		0.634
(1.00) 		0.807
(1.00)
del 19p13 3 36 (22%) 126 0.273
(1.00) 		0.952
(1.00) 		0.0183
(1.00) 		0.0303
(1.00) 		1
(1.00) 		0.705
(1.00) 		0.809
(1.00) 		0.518
(1.00) 		0.46
(1.00) 		0.00606
(1.00) 		0.759
(1.00) 		0.579
(1.00)
del 20p12 1 60 (37%) 102 0.622
(1.00) 		0.0322
(1.00) 		0.00051
(0.352) 		0.788
(1.00) 		0.541
(1.00) 		0.179
(1.00) 		0.707
(1.00) 		0.0382
(1.00) 		0.0411
(1.00) 		0.0727
(1.00) 		0.984
(1.00) 		0.612
(1.00)
del 20p12 1 60 (37%) 102 0.619
(1.00) 		0.0323
(1.00) 		0.00058
(0.4) 		0.788
(1.00) 		0.54
(1.00) 		0.182
(1.00) 		0.706
(1.00) 		0.0394
(1.00) 		0.0424
(1.00) 		0.0751
(1.00) 		0.984
(1.00) 		0.614
(1.00)
del 21q11 2 71 (44%) 91 0.315
(1.00) 		0.0609
(1.00) 		0.0194
(1.00) 		0.836
(1.00) 		0.922
(1.00) 		0.214
(1.00) 		0.249
(1.00) 		0.482
(1.00) 		0.0639
(1.00) 		0.726
(1.00) 		0.273
(1.00) 		0.316
(1.00)
del 22q13 31 67 (41%) 95 0.906
(1.00) 		0.293
(1.00) 		0.00611
(1.00) 		0.834
(1.00) 		0.409
(1.00) 		0.352
(1.00) 		0.0623
(1.00) 		0.123
(1.00) 		0.00608
(1.00) 		0.113
(1.00) 		0.23
(1.00) 		0.123
(1.00)
del xp22 33 33 (20%) 129 0.774
(1.00) 		0.916
(1.00) 		0.00131
(0.897) 		0.00318
(1.00) 		0.726
(1.00) 		0.897
(1.00) 		0.674
(1.00) 		0.5
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.731
(1.00) 		0.934
(1.00)
'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.07

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 1(1Q21.3) MUTATED 7 7 6 16 9 3
AMP PEAK 1(1Q21.3) WILD-TYPE 3 27 36 14 15 19

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

'amp_6p21.1' versus 'CN_CNMF'

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

Table S2.  Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 4(6P21.1) MUTATED 6 16 4 10 15 2
AMP PEAK 4(6P21.1) WILD-TYPE 4 18 38 20 9 20

Figure S2.  Get High-res Image Gene #4: 'amp_6p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'CN_CNMF'

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

Table S3.  Gene #5: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 5(8P11.23) MUTATED 3 15 4 5 8 17
AMP PEAK 5(8P11.23) WILD-TYPE 7 19 38 25 16 5

Figure S3.  Get High-res Image Gene #5: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

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

Table S4.  Gene #6: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 6(8P11.21) MUTATED 5 17 6 10 9 22
AMP PEAK 6(8P11.21) WILD-TYPE 5 17 36 20 15 0

Figure S4.  Get High-res Image Gene #6: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

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

Table S5.  Gene #7: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 7(8Q24.21) MUTATED 6 29 14 24 12 22
AMP PEAK 7(8Q24.21) WILD-TYPE 4 5 28 6 12 0

Figure S5.  Get High-res Image Gene #7: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.2

Table S6.  Gene #12: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 12(12P12.1) MUTATED 1 5 7 18 6 3
AMP PEAK 12(12P12.1) WILD-TYPE 9 29 35 12 18 19

Figure S6.  Get High-res Image Gene #12: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.13' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.042

Table S7.  Gene #13: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 13(13Q12.13) MUTATED 8 29 23 19 24 20
AMP PEAK 13(13Q12.13) WILD-TYPE 2 5 19 11 0 2

Figure S7.  Get High-res Image Gene #13: 'amp_13q12.13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q12.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S8.  Gene #14: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 14(13Q12.2) MUTATED 8 29 21 20 24 20
AMP PEAK 14(13Q12.2) WILD-TYPE 2 5 21 10 0 2

Figure S8.  Get High-res Image Gene #14: 'amp_13q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q22.1' versus 'CN_CNMF'

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

Table S9.  Gene #15: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 15(13Q22.1) MUTATED 8 29 19 18 24 19
AMP PEAK 15(13Q22.1) WILD-TYPE 2 5 23 12 0 3

Figure S9.  Get High-res Image Gene #15: 'amp_13q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S10.  Gene #17: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 17(16P11.2) MUTATED 3 17 2 6 11 6
AMP PEAK 17(16P11.2) WILD-TYPE 7 17 40 24 13 16

Figure S10.  Get High-res Image Gene #17: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S11.  Gene #18: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 18(17Q12) MUTATED 2 19 7 10 0 5
AMP PEAK 18(17Q12) WILD-TYPE 8 15 35 20 24 17

Figure S11.  Get High-res Image Gene #18: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q24.1' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.15

Table S12.  Gene #19: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 19(17Q24.1) MUTATED 1 17 7 8 0 4
AMP PEAK 19(17Q24.1) WILD-TYPE 9 17 35 22 24 18

Figure S12.  Get High-res Image Gene #19: 'amp_17q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.13

Table S13.  Gene #21: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 21(20Q11.21) MUTATED 10 34 31 23 24 21
AMP PEAK 21(20Q11.21) WILD-TYPE 0 0 11 7 0 1

Figure S13.  Get High-res Image Gene #21: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.23' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.23

Table S14.  Gene #22: 'amp_20q11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
AMP PEAK 22(20Q11.23) MUTATED 10 34 32 23 24 21
AMP PEAK 22(20Q11.23) WILD-TYPE 0 0 10 7 0 1

Figure S14.  Get High-res Image Gene #22: 'amp_20q11.23' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.21

Table S15.  Gene #26: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
DEL PEAK 1(1P36.11) MUTATED 4 19 10 21 13 5
DEL PEAK 1(1P36.11) WILD-TYPE 6 15 32 9 11 17

Figure S15.  Get High-res Image Gene #26: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p33' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.021

Table S16.  Gene #27: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
DEL PEAK 2(1P33) MUTATED 7 17 3 11 10 2
DEL PEAK 2(1P33) WILD-TYPE 3 17 39 19 14 20

Figure S16.  Get High-res Image Gene #27: 'del_1p33' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S17.  Gene #28: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
DEL PEAK 3(1P13.2) MUTATED 7 15 2 12 10 6
DEL PEAK 3(1P13.2) WILD-TYPE 3 19 40 18 14 16

Figure S17.  Get High-res Image Gene #28: 'del_1p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p13' versus 'CN_CNMF'

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

Table S18.  Gene #32: 'del_4p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
DEL PEAK 7(4P13) MUTATED 4 13 5 16 17 4
DEL PEAK 7(4P13) WILD-TYPE 6 21 37 14 7 18

Figure S18.  Get High-res Image Gene #32: 'del_4p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.014

Table S19.  Gene #33: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
DEL PEAK 8(4Q22.1) MUTATED 5 19 8 18 18 4
DEL PEAK 8(4Q22.1) WILD-TYPE 5 15 34 12 6 18

Figure S19.  Get High-res Image Gene #33: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.028

Table S20.  Gene #34: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
DEL PEAK 9(4Q35.1) MUTATED 4 17 8 19 18 5
DEL PEAK 9(4Q35.1) WILD-TYPE 6 17 34 11 6 17

Figure S20.  Get High-res Image Gene #34: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'CN_CNMF'

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

Table S21.  Gene #40: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
DEL PEAK 15(8P23.2) MUTATED 7 24 11 23 15 19
DEL PEAK 15(8P23.2) WILD-TYPE 3 10 31 7 9 3

Figure S21.  Get High-res Image Gene #40: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q22.3' versus 'CN_CNMF'

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

Table S22.  Gene #44: 'del_11q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
DEL PEAK 19(11Q22.3) MUTATED 2 0 7 16 8 5
DEL PEAK 19(11Q22.3) WILD-TYPE 8 34 35 14 16 17

Figure S22.  Get High-res Image Gene #44: 'del_11q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'CN_CNMF'

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

Table S23.  Gene #53: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
DEL PEAK 28(18Q21.2) MUTATED 10 34 27 27 23 22
DEL PEAK 28(18Q21.2) WILD-TYPE 0 0 15 3 1 0

Figure S23.  Get High-res Image Gene #53: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q22.1' versus 'CN_CNMF'

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

Table S24.  Gene #54: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 34 42 30 24 22
DEL PEAK 29(18Q22.1) MUTATED 10 34 25 25 23 21
DEL PEAK 29(18Q22.1) WILD-TYPE 0 0 17 5 1 1

Figure S24.  Get High-res Image Gene #54: 'del_18q22.1' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 162

  • Number of significantly focal cnvs = 60

  • 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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