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 10 molecular subtypes across 56 patients, 26 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_2q13 cnv correlated to 'MRNASEQ_CNMF'.

  • amp_3p25.1 cnv correlated to 'CN_CNMF'.

  • amp_3q26.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_4p16.3 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

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

  • amp_13q31.3 cnv correlated to 'MIRSEQ_CNMF'.

  • amp_16p11.2 cnv correlated to 'RPPA_CNMF'.

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

  • amp_20q11.21 cnv correlated to 'CN_CNMF'.

  • del_4q22.1 cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • del_4q34.3 cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • del_5q12.1 cnv correlated to 'METHLYATION_CNMF'.

  • del_9p23 cnv correlated to 'RPPA_CNMF'.

  • del_12q24.31 cnv correlated to 'RPPA_CHIERARCHICAL'.

  • del_17p13.1 cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • del_18q22.2 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • del_19p13.3 cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_19q13.33 cnv correlated to 'MRNASEQ_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 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 26 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
del 19p13 3 44 (79%) 12 0.101
(0.427) 		0.102
(0.427) 		0.137
(0.458) 		0.103
(0.427) 		0.00737
(0.232) 		0.0886
(0.399) 		0.00285
(0.214) 		0.00923
(0.239) 		0.00141
(0.163) 		0.0215
(0.319)
amp 3q26 2 37 (66%) 19 0.00052
(0.104) 		0.00569
(0.232) 		0.45
(0.689) 		0.129
(0.451) 		0.262
(0.598) 		0.158
(0.478) 		1
(1.00) 		0.242
(0.573) 		0.0594
(0.39) 		0.184
(0.513)
amp 4p16 3 25 (45%) 31 0.0019
(0.163) 		0.456
(0.689) 		0.71
(0.862) 		0.01
(0.239) 		0.163
(0.48) 		0.187
(0.515) 		0.738
(0.872) 		0.289
(0.61) 		0.845
(0.927) 		0.532
(0.729)
amp 8q24 21 40 (71%) 16 0.00691
(0.232) 		0.446
(0.689) 		0.325
(0.615) 		0.645
(0.813) 		0.009
(0.239) 		0.118
(0.446) 		0.0611
(0.39) 		0.0633
(0.39) 		0.0861
(0.397) 		0.0221
(0.319)
amp 19q12 45 (80%) 11 0.00027
(0.104) 		0.00037
(0.104) 		0.185
(0.513) 		0.248
(0.58) 		0.518
(0.725) 		0.02
(0.319) 		0.457
(0.689) 		0.502
(0.71) 		0.297
(0.612) 		0.433
(0.682)
del 18q22 2 26 (46%) 30 0.147
(0.467) 		0.527
(0.729) 		0.436
(0.682) 		0.537
(0.731) 		0.458
(0.689) 		0.357
(0.63) 		0.0065
(0.232) 		0.0771
(0.397) 		0.00934
(0.239) 		0.0253
(0.32)
amp 2q13 29 (52%) 27 0.432
(0.682) 		0.0972
(0.417) 		0.505
(0.711) 		0.488
(0.704) 		0.00773
(0.232) 		0.316
(0.614) 		1
(1.00) 		0.665
(0.828) 		0.721
(0.865) 		0.728
(0.867)
amp 3p25 1 20 (36%) 36 0.0103
(0.239) 		0.754
(0.877) 		0.762
(0.877) 		0.054
(0.39) 		0.32
(0.615) 		0.113
(0.446) 		0.0423
(0.379) 		0.0652
(0.39) 		0.229
(0.562) 		0.0671
(0.39)
amp 13q31 3 25 (45%) 31 0.486
(0.704) 		0.481
(0.703) 		0.228
(0.562) 		0.385
(0.652) 		0.23
(0.562) 		0.116
(0.446) 		0.00716
(0.232) 		0.0371
(0.379) 		0.0246
(0.32) 		0.0534
(0.39)
amp 16p11 2 20 (36%) 36 0.017
(0.309) 		0.0755
(0.397) 		0.00994
(0.239) 		0.0667
(0.39) 		0.766
(0.877) 		0.0727
(0.397) 		0.776
(0.878) 		0.411
(0.677) 		0.585
(0.771) 		0.209
(0.54)
amp 20q11 21 48 (86%) 8 0.00656
(0.232) 		0.0965
(0.417) 		0.113
(0.446) 		0.415
(0.677) 		0.464
(0.689) 		0.423
(0.677) 		0.0817
(0.397) 		0.14
(0.458) 		0.275
(0.6) 		0.275
(0.6)
del 4q22 1 37 (66%) 19 0.0326
(0.377) 		0.0675
(0.39) 		0.138
(0.458) 		0.238
(0.571) 		0.119
(0.446) 		0.154
(0.475) 		0.0203
(0.319) 		0.126
(0.45) 		0.00732
(0.232) 		0.057
(0.39)
del 4q34 3 37 (66%) 19 0.0379
(0.379) 		0.0228
(0.319) 		0.328
(0.615) 		0.135
(0.458) 		0.0413
(0.379) 		0.0409
(0.379) 		0.03
(0.367) 		0.201
(0.533) 		0.00688
(0.232) 		0.125
(0.45)
del 5q12 1 26 (46%) 30 0.207
(0.539) 		0.00516
(0.232) 		0.594
(0.778) 		0.159
(0.478) 		0.63
(0.804) 		0.452
(0.689) 		0.942
(0.98) 		0.297
(0.612) 		0.566
(0.756) 		0.445
(0.689)
del 9p23 34 (61%) 22 0.202
(0.533) 		0.67
(0.832) 		0.00502
(0.232) 		0.0156
(0.303) 		0.31
(0.613) 		0.325
(0.615) 		0.825
(0.915) 		0.426
(0.679) 		0.769
(0.877) 		0.121
(0.446)
del 12q24 31 20 (36%) 36 0.602
(0.781) 		0.756
(0.877) 		0.0234
(0.319) 		0.00166
(0.163) 		0.197
(0.533) 		0.256
(0.592) 		0.775
(0.878) 		0.888
(0.954) 		0.233
(0.562) 		0.931
(0.976)
del 17p13 1 42 (75%) 14 0.286
(0.608) 		0.0442
(0.385) 		0.13
(0.451) 		0.239
(0.571) 		0.0469
(0.387) 		0.423
(0.677) 		0.108
(0.446) 		0.182
(0.509) 		0.00487
(0.232) 		0.0837
(0.397)
del 19q13 33 17 (30%) 39 0.114
(0.446) 		0.0231
(0.319) 		0.247
(0.58) 		0.0636
(0.39) 		0.00182
(0.163) 		0.0353
(0.379) 		0.281
(0.604) 		0.0382
(0.379) 		0.147
(0.467) 		0.0126
(0.28)
amp 1q22 42 (75%) 14 0.68
(0.841) 		0.431
(0.682) 		0.0772
(0.397) 		0.487
(0.704) 		0.459
(0.689) 		0.294
(0.612) 		0.13
(0.451) 		0.187
(0.515) 		0.0589
(0.39) 		0.267
(0.598)
amp 2p14 28 (50%) 28 0.384
(0.652) 		0.0871
(0.397) 		0.947
(0.983) 		0.489
(0.704) 		0.0137
(0.292) 		0.08
(0.397) 		0.314
(0.613) 		0.248
(0.58) 		0.252
(0.587) 		0.362
(0.635)
amp 5p13 2 26 (46%) 30 0.0919
(0.4) 		0.545
(0.737) 		0.233
(0.562) 		0.308
(0.613) 		0.127
(0.45) 		0.0556
(0.39) 		0.264
(0.598) 		0.0458
(0.387) 		0.327
(0.615) 		0.175
(0.496)
amp 6p24 2 37 (66%) 19 0.449
(0.689) 		0.98
(1.00) 		0.988
(1.00) 		0.326
(0.615) 		0.83
(0.918) 		0.356
(0.63) 		0.723
(0.865) 		0.497
(0.709) 		0.769
(0.877) 		0.768
(0.877)
amp 8p11 21 33 (59%) 23 0.351
(0.629) 		0.727
(0.867) 		0.15
(0.471) 		0.092
(0.4) 		0.435
(0.682) 		0.557
(0.749) 		0.687
(0.846) 		1
(1.00) 		0.641
(0.81) 		0.601
(0.781)
amp 8q11 23 38 (68%) 18 0.061
(0.39) 		0.0823
(0.397) 		0.312
(0.613) 		0.201
(0.533) 		0.0471
(0.387) 		0.166
(0.482) 		1
(1.00) 		0.922
(0.975) 		0.737
(0.872) 		0.857
(0.933)
amp 8q24 21 42 (75%) 14 0.0141
(0.292) 		0.753
(0.877) 		0.464
(0.689) 		0.952
(0.987) 		0.211
(0.54) 		0.337
(0.626) 		0.0504
(0.39) 		0.0326
(0.377) 		0.0598
(0.39) 		0.015
(0.301)
amp 10q22 2 26 (46%) 30 0.21
(0.54) 		0.732
(0.869) 		0.303
(0.613) 		0.344
(0.629) 		0.932
(0.976) 		0.925
(0.976) 		0.352
(0.629) 		0.739
(0.872) 		0.353
(0.629) 		0.428
(0.681)
amp 11q13 1 19 (34%) 37 0.323
(0.615) 		0.788
(0.886) 		0.422
(0.677) 		0.269
(0.598) 		0.109
(0.446) 		0.304
(0.613) 		0.582
(0.77) 		1
(1.00) 		0.514
(0.721) 		0.975
(1.00)
amp 12q12 22 (39%) 34 0.233
(0.562) 		0.232
(0.562) 		0.597
(0.78) 		0.0786
(0.397) 		0.314
(0.613) 		0.409
(0.677) 		0.501
(0.71) 		1
(1.00) 		0.529
(0.729) 		0.954
(0.987)
amp 12q15 17 (30%) 39 0.53
(0.729) 		0.661
(0.826) 		0.831
(0.918) 		0.708
(0.862) 		0.122
(0.446) 		0.698
(0.855) 		0.497
(0.709) 		0.164
(0.482) 		0.571
(0.758) 		0.231
(0.562)
amp 17q12 27 (48%) 29 1
(1.00) 		0.172
(0.493) 		0.934
(0.976) 		0.764
(0.877) 		0.322
(0.615) 		0.461
(0.689) 		0.135
(0.458) 		0.783
(0.883) 		0.498
(0.709) 		1
(1.00)
amp 17q25 1 32 (57%) 24 0.353
(0.629) 		0.123
(0.447) 		0.852
(0.931) 		0.724
(0.865) 		0.6
(0.781) 		0.307
(0.613) 		0.609
(0.787) 		0.719
(0.865) 		0.278
(0.602) 		0.66
(0.826)
amp 19p13 2 19 (34%) 37 0.0874
(0.397) 		0.35
(0.629) 		0.417
(0.677) 		0.663
(0.826) 		0.733
(0.869) 		0.323
(0.615) 		0.2
(0.533) 		0.276
(0.601) 		0.0611
(0.39) 		0.27
(0.598)
amp 20q11 21 48 (86%) 8 0.0861
(0.397) 		0.0704
(0.395) 		0.0468
(0.387) 		0.416
(0.677) 		0.162
(0.48) 		0.317
(0.614) 		0.159
(0.478) 		0.35
(0.629) 		0.273
(0.6) 		0.558
(0.749)
amp xp11 21 28 (50%) 28 0.142
(0.462) 		0.308
(0.613) 		0.18
(0.508) 		0.156
(0.478) 		0.242
(0.573) 		0.299
(0.612) 		0.0319
(0.377) 		0.101
(0.427) 		0.498
(0.709) 		0.0653
(0.39)
del 1p36 21 19 (34%) 37 0.188
(0.516) 		0.0638
(0.39) 		0.775
(0.878) 		0.896
(0.959) 		0.598
(0.78) 		0.0816
(0.397) 		0.0513
(0.39) 		0.0242
(0.32) 		0.288
(0.61) 		0.0586
(0.39)
del 2q22 1 11 (20%) 45 0.291
(0.61) 		0.333
(0.621) 		0.755
(0.877) 		0.473
(0.695) 		0.174
(0.495) 		0.168
(0.484) 		0.0184
(0.319) 		0.554
(0.747) 		0.459
(0.689) 		0.919
(0.975)
del 3p14 2 37 (66%) 19 0.419
(0.677) 		0.562
(0.753) 		0.702
(0.857) 		0.769
(0.877) 		0.503
(0.711) 		0.472
(0.695) 		1
(1.00) 		0.769
(0.877) 		0.36
(0.634) 		0.901
(0.959)
del 3q13 31 22 (39%) 34 0.192
(0.524) 		0.521
(0.726) 		0.217
(0.555) 		0.121
(0.446) 		0.64
(0.81) 		0.0666
(0.39) 		0.499
(0.709) 		0.456
(0.689) 		0.876
(0.947) 		0.825
(0.915)
del 6q26 10 (18%) 46 0.13
(0.451) 		0.963
(0.995) 		0.0497
(0.39) 		0.0807
(0.397) 		0.139
(0.458) 		0.697
(0.855) 		1
(1.00) 		0.298
(0.612) 		0.173
(0.495) 		0.314
(0.613)
del 7q11 22 12 (21%) 44 0.542
(0.736) 		0.8
(0.897) 		0.718
(0.865) 		0.721
(0.865) 		0.84
(0.923) 		0.836
(0.922) 		0.84
(0.923) 		0.531
(0.729) 		0.0647
(0.39) 		0.751
(0.877)
del 7q36 2 20 (36%) 36 0.29
(0.61) 		0.268
(0.598) 		0.723
(0.865) 		0.521
(0.726) 		0.422
(0.677) 		0.275
(0.6) 		0.0903
(0.4) 		0.0443
(0.385) 		0.466
(0.689) 		0.0816
(0.397)
del 8p21 3 32 (57%) 24 0.0362
(0.379) 		0.619
(0.796) 		0.489
(0.704) 		0.282
(0.604) 		0.346
(0.629) 		0.33
(0.618) 		0.885
(0.953) 		0.284
(0.607) 		0.402
(0.67) 		0.537
(0.731)
del 9q21 13 39 (70%) 17 0.0366
(0.379) 		0.572
(0.758) 		0.77
(0.877) 		0.452
(0.689) 		0.46
(0.689) 		0.257
(0.592) 		0.757
(0.877) 		0.322
(0.615) 		0.403
(0.67) 		0.399
(0.667)
del 9q33 3 39 (70%) 17 0.462
(0.689) 		0.801
(0.897) 		0.0816
(0.397) 		0.041
(0.379) 		0.227
(0.562) 		0.139
(0.458) 		0.646
(0.813) 		0.113
(0.446) 		0.378
(0.648) 		0.256
(0.592)
del 10q23 31 20 (36%) 36 0.159
(0.478) 		0.148
(0.467) 		0.927
(0.976) 		0.98
(1.00) 		0.375
(0.648) 		0.242
(0.573) 		0.879
(0.949) 		0.852
(0.931) 		0.572
(0.758) 		0.825
(0.915)
del 11q14 1 26 (46%) 30 0.0491
(0.39) 		0.638
(0.809) 		0.161
(0.48) 		0.228
(0.562) 		0.821
(0.915) 		0.923
(0.975) 		0.377
(0.648) 		0.265
(0.598) 		0.199
(0.533) 		0.0751
(0.397)
del 11q23 2 26 (46%) 30 0.437
(0.683) 		0.934
(0.976) 		0.613
(0.791) 		0.225
(0.562) 		0.151
(0.472) 		0.871
(0.943) 		0.514
(0.721) 		0.863
(0.938) 		0.0844
(0.397) 		0.357
(0.63)
del 12q23 1 20 (36%) 36 0.638
(0.809) 		0.943
(0.98) 		0.121
(0.446) 		0.0629
(0.39) 		0.629
(0.804) 		0.751
(0.877) 		1
(1.00) 		0.338
(0.626) 		0.622
(0.797) 		0.545
(0.737)
del 13q12 11 30 (54%) 26 0.165
(0.482) 		0.145
(0.467) 		0.435
(0.682) 		0.0692
(0.393) 		0.153
(0.475) 		0.206
(0.539) 		0.351
(0.629) 		0.0256
(0.32) 		0.127
(0.45) 		0.0619
(0.39)
del 13q14 2 32 (57%) 24 0.296
(0.612) 		0.0401
(0.379) 		0.227
(0.562) 		0.414
(0.677) 		0.0356
(0.379) 		0.0204
(0.319) 		0.303
(0.613) 		0.158
(0.478) 		0.0868
(0.397) 		0.193
(0.525)
del 14q21 1 28 (50%) 28 0.788
(0.886) 		0.115
(0.446) 		0.592
(0.777) 		0.132
(0.455) 		0.0676
(0.39) 		0.0545
(0.39) 		0.313
(0.613) 		0.381
(0.651) 		0.089
(0.399) 		0.369
(0.641)
del 15q15 1 43 (77%) 13 0.166
(0.482) 		0.0227
(0.319) 		0.447
(0.689) 		0.0395
(0.379) 		0.398
(0.667) 		0.771
(0.877) 		0.0712
(0.395) 		0.347
(0.629) 		0.115
(0.446) 		0.206
(0.539)
del 16p13 3 33 (59%) 23 0.421
(0.677) 		0.631
(0.804) 		0.708
(0.862) 		0.263
(0.598) 		0.366
(0.639) 		0.23
(0.562) 		0.0163
(0.306) 		0.388
(0.655) 		0.679
(0.841) 		0.716
(0.865)
del 16q23 1 39 (70%) 17 0.207
(0.539) 		0.14
(0.458) 		0.463
(0.689) 		0.279
(0.603) 		0.682
(0.841) 		0.393
(0.661) 		0.3
(0.613) 		0.814
(0.91) 		0.935
(0.976) 		0.621
(0.797)
del 17q21 31 27 (48%) 29 0.364
(0.636) 		0.0631
(0.39) 		0.525
(0.729) 		0.0914
(0.4) 		0.297
(0.612) 		0.347
(0.629) 		0.314
(0.613) 		0.085
(0.397) 		0.0564
(0.39) 		0.141
(0.458)
del 19p13 3 47 (84%) 9 0.138
(0.458) 		0.0417
(0.379) 		0.422
(0.677) 		0.121
(0.446) 		0.12
(0.446) 		0.378
(0.648) 		0.0817
(0.397) 		0.0846
(0.397) 		0.0401
(0.379) 		0.114
(0.446)
del 20p12 1 9 (16%) 47 0.534
(0.73) 		0.697
(0.855) 		0.0747
(0.397) 		0.0204
(0.319) 		0.42
(0.677) 		0.528
(0.729) 		0.269
(0.598) 		0.342
(0.629) 		0.766
(0.877) 		0.466
(0.689)
del 22q13 31 40 (71%) 16 0.485
(0.704) 		0.372
(0.644) 		0.115
(0.446) 		0.307
(0.613) 		0.481
(0.703) 		0.458
(0.689) 		1
(1.00) 		0.351
(0.629) 		0.974
(1.00) 		0.588
(0.773)
del xp21 1 18 (32%) 38 0.383
(0.652) 		0.659
(0.826) 		0.912
(0.969) 		0.895
(0.959) 		0.886
(0.953) 		0.868
(0.942) 		1
(1.00) 		1
(1.00) 		0.854
(0.931) 		0.901
(0.959)
del xq25 23 (41%) 33 0.783
(0.883) 		0.219
(0.557) 		0.265
(0.598) 		0.0694
(0.393) 		0.147
(0.467) 		0.898
(0.959) 		0.482
(0.703) 		0.567
(0.756) 		0.12
(0.446) 		0.386
(0.652)
'amp_2q13' versus 'MRNASEQ_CNMF'

P value = 0.00773 (Fisher's exact test), Q value = 0.23

Table S1.  Gene #3: 'amp_2q13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 19 12 10
AMP PEAK 3(2Q13) MUTATED 8 7 11 3
AMP PEAK 3(2Q13) WILD-TYPE 7 12 1 7

Figure S1.  Get High-res Image Gene #3: 'amp_2q13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3p25.1' versus 'CN_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.24

Table S2.  Gene #4: 'amp_3p25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
AMP PEAK 4(3P25.1) MUTATED 7 4 9
AMP PEAK 4(3P25.1) WILD-TYPE 14 18 4

Figure S2.  Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.1

Table S3.  Gene #5: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
AMP PEAK 5(3Q26.2) MUTATED 20 10 7
AMP PEAK 5(3Q26.2) WILD-TYPE 1 12 6

Figure S3.  Get High-res Image Gene #5: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.23

Table S4.  Gene #5: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 13 13 11
AMP PEAK 5(3Q26.2) MUTATED 16 4 11 6
AMP PEAK 5(3Q26.2) WILD-TYPE 3 9 2 5

Figure S4.  Get High-res Image Gene #5: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'CN_CNMF'

P value = 0.0019 (Fisher's exact test), Q value = 0.16

Table S5.  Gene #6: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
AMP PEAK 6(4P16.3) MUTATED 15 4 6
AMP PEAK 6(4P16.3) WILD-TYPE 6 18 7

Figure S5.  Get High-res Image Gene #6: 'amp_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.24

Table S6.  Gene #6: 'amp_4p16.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 8 8 7 7 7 5 5
AMP PEAK 6(4P16.3) MUTATED 7 3 0 1 3 3 3
AMP PEAK 6(4P16.3) WILD-TYPE 1 5 7 6 4 2 2

Figure S6.  Get High-res Image Gene #6: 'amp_4p16.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 0.00691 (Fisher's exact test), Q value = 0.23

Table S7.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
AMP PEAK 12(8Q24.21) MUTATED 11 16 13
AMP PEAK 12(8Q24.21) WILD-TYPE 10 6 0

Figure S7.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.009 (Fisher's exact test), Q value = 0.24

Table S8.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 19 12 10
AMP PEAK 12(8Q24.21) MUTATED 11 17 4 8
AMP PEAK 12(8Q24.21) WILD-TYPE 4 2 8 2

Figure S8.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q31.3' versus 'MIRSEQ_CNMF'

P value = 0.00716 (Fisher's exact test), Q value = 0.23

Table S9.  Gene #17: 'amp_13q31.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 24 17
AMP PEAK 17(13Q31.3) MUTATED 6 16 3
AMP PEAK 17(13Q31.3) WILD-TYPE 8 8 14

Figure S9.  Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_16p11.2' versus 'RPPA_CNMF'

P value = 0.00994 (Fisher's exact test), Q value = 0.24

Table S10.  Gene #18: 'amp_16p11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 9 12 6 9
AMP PEAK 18(16P11.2) MUTATED 7 3 1 4 1
AMP PEAK 18(16P11.2) WILD-TYPE 4 6 11 2 8

Figure S10.  Get High-res Image Gene #18: 'amp_16p11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.1

Table S11.  Gene #22: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
AMP PEAK 22(19Q12) MUTATED 21 12 12
AMP PEAK 22(19Q12) WILD-TYPE 0 10 1

Figure S11.  Get High-res Image Gene #22: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.1

Table S12.  Gene #22: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 13 13 11
AMP PEAK 22(19Q12) MUTATED 17 5 12 11
AMP PEAK 22(19Q12) WILD-TYPE 2 8 1 0

Figure S12.  Get High-res Image Gene #22: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 0.00656 (Fisher's exact test), Q value = 0.23

Table S13.  Gene #23: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
AMP PEAK 23(20Q11.21) MUTATED 21 15 12
AMP PEAK 23(20Q11.21) WILD-TYPE 0 7 1

Figure S13.  Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00732 (Fisher's exact test), Q value = 0.23

Table S14.  Gene #30: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 14 14 18
DEL PEAK 5(4Q22.1) MUTATED 9 10 11 7
DEL PEAK 5(4Q22.1) WILD-TYPE 0 4 3 11

Figure S14.  Get High-res Image Gene #30: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00688 (Fisher's exact test), Q value = 0.23

Table S15.  Gene #31: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 14 14 18
DEL PEAK 6(4Q34.3) MUTATED 9 11 10 7
DEL PEAK 6(4Q34.3) WILD-TYPE 0 3 4 11

Figure S15.  Get High-res Image Gene #31: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 0.00516 (Fisher's exact test), Q value = 0.23

Table S16.  Gene #32: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 13 13 11
DEL PEAK 7(5Q12.1) MUTATED 11 1 6 8
DEL PEAK 7(5Q12.1) WILD-TYPE 8 12 7 3

Figure S16.  Get High-res Image Gene #32: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.00502 (Fisher's exact test), Q value = 0.23

Table S17.  Gene #37: 'del_9p23' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 9 12 6 9
DEL PEAK 12(9P23) MUTATED 11 5 7 4 2
DEL PEAK 12(9P23) WILD-TYPE 0 4 5 2 7

Figure S17.  Get High-res Image Gene #37: 'del_9p23' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_12q24.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.16

Table S18.  Gene #44: 'del_12q24.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 8 8 7 7 7 5 5
DEL PEAK 19(12Q24.31) MUTATED 2 7 5 3 1 0 0
DEL PEAK 19(12Q24.31) WILD-TYPE 6 1 2 4 6 5 5

Figure S18.  Get High-res Image Gene #44: 'del_12q24.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00487 (Fisher's exact test), Q value = 0.23

Table S19.  Gene #51: 'del_17p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 14 14 18
DEL PEAK 26(17P13.1) MUTATED 8 14 11 9
DEL PEAK 26(17P13.1) WILD-TYPE 1 0 3 9

Figure S19.  Get High-res Image Gene #51: 'del_17p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q22.2' versus 'MIRSEQ_CNMF'

P value = 0.0065 (Fisher's exact test), Q value = 0.23

Table S20.  Gene #53: 'del_18q22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 24 17
DEL PEAK 28(18Q22.2) MUTATED 5 17 4
DEL PEAK 28(18Q22.2) WILD-TYPE 9 7 13

Figure S20.  Get High-res Image Gene #53: 'del_18q22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00934 (Fisher's exact test), Q value = 0.24

Table S21.  Gene #53: 'del_18q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 14 14 18
DEL PEAK 28(18Q22.2) MUTATED 6 4 11 5
DEL PEAK 28(18Q22.2) WILD-TYPE 3 10 3 13

Figure S21.  Get High-res Image Gene #53: 'del_18q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00737 (Fisher's exact test), Q value = 0.23

Table S22.  Gene #55: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 19 12 10
DEL PEAK 30(19P13.3) MUTATED 13 10 12 9
DEL PEAK 30(19P13.3) WILD-TYPE 2 9 0 1

Figure S22.  Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.21

Table S23.  Gene #55: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 24 17
DEL PEAK 30(19P13.3) MUTATED 12 23 9
DEL PEAK 30(19P13.3) WILD-TYPE 2 1 8

Figure S23.  Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00923 (Fisher's exact test), Q value = 0.24

Table S24.  Gene #55: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 8 18 6
DEL PEAK 30(19P13.3) MUTATED 16 7 18 3
DEL PEAK 30(19P13.3) WILD-TYPE 7 1 0 3

Figure S24.  Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.16

Table S25.  Gene #55: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 14 14 18
DEL PEAK 30(19P13.3) MUTATED 8 13 14 9
DEL PEAK 30(19P13.3) WILD-TYPE 1 1 0 9

Figure S25.  Get High-res Image Gene #55: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.33' versus 'MRNASEQ_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.16

Table S26.  Gene #56: 'del_19q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 19 12 10
DEL PEAK 31(19Q13.33) MUTATED 9 2 1 5
DEL PEAK 31(19Q13.33) WILD-TYPE 6 17 11 5

Figure S26.  Get High-res Image Gene #56: 'del_19q13.33' versus Molecular Subtype #5: 'MRNASEQ_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/UCS-TP/22533741/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/22541488/UCS-TP.transferedmergedcluster.txt

  • Number of patients = 56

  • Number of significantly focal cnvs = 60

  • 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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