Correlation between copy number variation genes (focal events) and molecular subtypes
Uterine Carcinosarcoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1MK6C0B
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1MK6C0B
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 61 focal events and 10 molecular subtypes across 56 patients, 16 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • amp_5p13.2 cnv correlated to 'CN_CNMF'.

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

  • amp_8q24.21 cnv correlated to 'CN_CNMF'.

  • amp_13q31.3 cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

  • amp_20q11.21 cnv correlated to 'CN_CNMF'.

  • del_4q34.3 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • del_8p23.2 cnv correlated to 'CN_CNMF'.

  • del_12q24.31 cnv correlated to 'RPPA_CHIERARCHICAL'.

  • del_13q14.2 cnv correlated to 'METHLYATION_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 61 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, 16 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 3q26 2 37 (66%) 19 0.00593
(0.226) 		0.00484
(0.223) 		0.33
(0.707) 		0.125
(0.53) 		0.0893
(0.478) 		0.162
(0.594) 		0.345
(0.707) 		0.24
(0.675) 		0.463
(0.768) 		0.182
(0.62)
amp 8q24 21 42 (75%) 14 0.00199
(0.135) 		0.758
(0.909) 		0.746
(0.909) 		0.952
(1.00) 		0.189
(0.624) 		0.34
(0.707) 		0.0387
(0.387) 		0.032
(0.343) 		0.00571
(0.226) 		0.0147
(0.292)
amp 19q12 45 (80%) 11 0.00118
(0.135) 		0.00011
(0.0671) 		0.715
(0.909) 		0.249
(0.678) 		0.193
(0.629) 		0.019
(0.294) 		0.645
(0.869) 		0.501
(0.792) 		0.233
(0.664) 		0.432
(0.745)
del 4q34 3 37 (66%) 19 0.0183
(0.294) 		0.02
(0.294) 		0.121
(0.527) 		0.134
(0.55) 		0.0115
(0.279) 		0.0403
(0.39) 		0.00315
(0.175) 		0.2
(0.642) 		0.00512
(0.223) 		0.125
(0.53)
amp 5p13 2 26 (46%) 30 0.00194
(0.135) 		0.573
(0.812) 		0.0206
(0.294) 		0.309
(0.707) 		0.247
(0.677) 		0.0573
(0.423) 		0.929
(0.992) 		0.0465
(0.405) 		0.477
(0.782) 		0.174
(0.603)
amp 8q24 21 40 (71%) 16 0.00055
(0.0945) 		0.355
(0.707) 		0.758
(0.909) 		0.646
(0.869) 		0.0772
(0.446) 		0.117
(0.527) 		0.0458
(0.405) 		0.0627
(0.423) 		0.00784
(0.266) 		0.0215
(0.294)
amp 13q31 3 25 (45%) 31 0.528
(0.805) 		0.442
(0.753) 		1
(1.00) 		0.387
(0.711) 		0.138
(0.55) 		0.116
(0.527) 		0.0864
(0.467) 		0.0374
(0.386) 		0.00253
(0.154) 		0.0535
(0.423)
amp 20q11 21 48 (86%) 8 0.00423
(0.215) 		0.168
(0.597) 		1
(1.00) 		0.417
(0.734) 		0.543
(0.805) 		0.42
(0.737) 		0.162
(0.594) 		0.139
(0.552) 		0.0559
(0.423) 		0.271
(0.691)
del 8p23 2 33 (59%) 23 0.00145
(0.135) 		0.428
(0.742) 		0.245
(0.677) 		0.273
(0.692) 		0.356
(0.707) 		0.357
(0.707) 		0.74
(0.909) 		0.328
(0.707) 		0.599
(0.834) 		0.554
(0.805)
del 12q24 31 20 (36%) 36 0.442
(0.753) 		0.822
(0.946) 		1
(1.00) 		0.00156
(0.135) 		0.155
(0.588) 		0.256
(0.679) 		0.562
(0.805) 		0.888
(0.979) 		0.369
(0.711) 		0.931
(0.993)
del 13q14 2 32 (57%) 24 0.437
(0.749) 		0.00053
(0.0945) 		0.564
(0.805) 		0.414
(0.734) 		0.0131
(0.279) 		0.0202
(0.294) 		0.479
(0.783) 		0.158
(0.592) 		0.0472
(0.405) 		0.194
(0.629)
del 19q13 33 17 (30%) 39 0.317
(0.707) 		0.00918
(0.279) 		0.222
(0.656) 		0.0633
(0.423) 		0.00062
(0.0945) 		0.0366
(0.385) 		0.223
(0.656) 		0.0382
(0.387) 		0.367
(0.711) 		0.0119
(0.279)
amp 1q22 42 (75%) 14 0.507
(0.793) 		0.228
(0.656) 		0.326
(0.707) 		0.485
(0.788) 		0.476
(0.782) 		0.297
(0.707) 		0.188
(0.624) 		0.188
(0.624) 		0.332
(0.707) 		0.269
(0.689)
amp 2p14 28 (50%) 28 0.56
(0.805) 		0.0255
(0.316) 		1
(1.00) 		0.489
(0.788) 		0.00726
(0.261) 		0.0792
(0.451) 		0.488
(0.788) 		0.247
(0.677) 		0.224
(0.656) 		0.36
(0.708)
amp 2q13 29 (52%) 27 0.532
(0.805) 		0.0157
(0.292) 		0.564
(0.805) 		0.487
(0.788) 		0.046
(0.405) 		0.318
(0.707) 		1
(1.00) 		0.664
(0.881) 		0.738
(0.909) 		0.728
(0.909)
amp 3p25 1 20 (36%) 36 0.0121
(0.279) 		0.514
(0.8) 		0.122
(0.527) 		0.0528
(0.423) 		0.3
(0.707) 		0.113
(0.527) 		0.228
(0.656) 		0.0646
(0.423) 		0.122
(0.527) 		0.0673
(0.423)
amp 4p16 3 25 (45%) 31 0.0274
(0.321) 		0.13
(0.543) 		0.566
(0.805) 		0.00982
(0.279) 		0.388
(0.711) 		0.188
(0.624) 		0.976
(1.00) 		0.286
(0.707) 		0.505
(0.792) 		0.53
(0.805)
amp 6p24 2 37 (66%) 19 0.108
(0.527) 		0.972
(1.00) 		0.226
(0.656) 		0.329
(0.707) 		0.689
(0.901) 		0.356
(0.707) 		0.875
(0.976) 		0.498
(0.792) 		0.875
(0.976) 		0.768
(0.909)
amp 8p11 21 33 (59%) 23 0.55
(0.805) 		0.626
(0.855) 		0.564
(0.805) 		0.0918
(0.485) 		0.679
(0.895) 		0.559
(0.805) 		0.625
(0.855) 		1
(1.00) 		0.779
(0.912) 		0.601
(0.835)
amp 8q11 23 38 (68%) 18 0.0133
(0.279) 		0.224
(0.656) 		0.138
(0.55) 		0.202
(0.646) 		0.199
(0.641) 		0.167
(0.597) 		0.772
(0.909) 		0.922
(0.989) 		0.62
(0.855) 		0.858
(0.971)
amp 10q22 2 26 (46%) 30 0.313
(0.707) 		0.491
(0.788) 		0.0189
(0.294) 		0.343
(0.707) 		0.965
(1.00) 		0.923
(0.989) 		0.727
(0.909) 		0.74
(0.909) 		1
(1.00) 		0.426
(0.74)
amp 11q13 1 19 (34%) 37 0.779
(0.912) 		0.648
(0.871) 		0.758
(0.909) 		0.269
(0.689) 		0.328
(0.707) 		0.301
(0.707) 		0.761
(0.909) 		1
(1.00) 		0.821
(0.946) 		0.974
(1.00)
amp 12q12 22 (39%) 34 0.0313
(0.343) 		0.105
(0.527) 		0.374
(0.711) 		0.0775
(0.446) 		0.255
(0.679) 		0.402
(0.723) 		0.927
(0.992) 		1
(1.00) 		0.883
(0.979) 		0.953
(1.00)
amp 12q15 17 (30%) 39 0.587
(0.821) 		0.377
(0.711) 		0.211
(0.65) 		0.707
(0.909) 		0.256
(0.679) 		0.702
(0.909) 		0.799
(0.93) 		0.168
(0.597) 		1
(1.00) 		0.228
(0.656)
amp 16p11 2 20 (36%) 36 0.0271
(0.321) 		0.279
(0.696) 		0.758
(0.909) 		0.0666
(0.423) 		0.655
(0.876) 		0.0725
(0.439) 		0.762
(0.909) 		0.413
(0.734) 		0.517
(0.803) 		0.208
(0.648)
amp 17q12 27 (48%) 29 0.446
(0.755) 		0.189
(0.624) 		1
(1.00) 		0.761
(0.909) 		0.336
(0.707) 		0.457
(0.766) 		0.342
(0.707) 		0.784
(0.916) 		0.607
(0.842) 		1
(1.00)
amp 17q25 1 32 (57%) 24 0.495
(0.789) 		0.0115
(0.279) 		0.388
(0.711) 		0.724
(0.909) 		0.634
(0.859) 		0.308
(0.707) 		0.687
(0.901) 		0.719
(0.909) 		0.322
(0.707) 		0.657
(0.877)
amp 19p13 2 19 (34%) 37 0.333
(0.707) 		0.273
(0.692) 		0.758
(0.909) 		0.663
(0.881) 		0.796
(0.929) 		0.322
(0.707) 		0.347
(0.707) 		0.279
(0.696) 		0.147
(0.567) 		0.268
(0.689)
amp 20q11 21 48 (86%) 8 0.0999
(0.512) 		0.256
(0.679) 		0.436
(0.749) 		0.415
(0.734) 		0.194
(0.629) 		0.314
(0.707) 		0.178
(0.612) 		0.352
(0.707) 		0.372
(0.711) 		0.558
(0.805)
amp xp11 21 28 (50%) 28 0.0588
(0.423) 		0.566
(0.805) 		0.381
(0.711) 		0.158
(0.592) 		0.047
(0.405) 		0.302
(0.707) 		0.0279
(0.321) 		0.102
(0.519) 		0.112
(0.527) 		0.0642
(0.423)
del 1p36 21 19 (34%) 37 0.725
(0.909) 		0.379
(0.711) 		0.355
(0.707) 		0.897
(0.979) 		0.347
(0.707) 		0.0822
(0.456) 		0.133
(0.547) 		0.0242
(0.316) 		0.0732
(0.439) 		0.0589
(0.423)
del 2q22 1 11 (20%) 45 0.915
(0.989) 		0.543
(0.805) 		0.731
(0.909) 		0.475
(0.782) 		0.529
(0.805) 		0.168
(0.597) 		0.556
(0.805) 		0.554
(0.805) 		0.257
(0.679) 		0.922
(0.989)
del 3p14 2 37 (66%) 19 0.726
(0.909) 		0.702
(0.909) 		1
(1.00) 		0.767
(0.909) 		0.809
(0.94) 		0.473
(0.782) 		0.627
(0.855) 		0.768
(0.909) 		0.87
(0.974) 		0.901
(0.979)
del 3q13 31 22 (39%) 34 0.204
(0.648) 		0.045
(0.405) 		0.245
(0.677) 		0.12
(0.527) 		0.88
(0.978) 		0.0672
(0.423) 		1
(1.00) 		0.459
(0.766) 		0.356
(0.707) 		0.824
(0.946)
del 4q22 1 37 (66%) 19 0.164
(0.597) 		0.056
(0.423) 		0.226
(0.656) 		0.236
(0.667) 		0.025
(0.316) 		0.155
(0.588) 		0.0126
(0.279) 		0.126
(0.53) 		0.0311
(0.343) 		0.0579
(0.423)
del 5q12 1 26 (46%) 30 0.63
(0.857) 		0.0923
(0.485) 		1
(1.00) 		0.16
(0.594) 		0.586
(0.821) 		0.453
(0.762) 		0.547
(0.805) 		0.294
(0.707) 		0.257
(0.679) 		0.447
(0.755)
del 6q26 10 (18%) 46 0.415
(0.734) 		0.539
(0.805) 		1
(1.00) 		0.0808
(0.456) 		0.122
(0.527) 		0.7
(0.909) 		0.329
(0.707) 		0.295
(0.707) 		0.816
(0.944) 		0.314
(0.707)
del 7q11 22 12 (21%) 44 0.714
(0.909) 		0.509
(0.794) 		1
(1.00) 		0.722
(0.909) 		0.758
(0.909) 		0.836
(0.953) 		0.861
(0.973) 		0.531
(0.805) 		0.842
(0.959) 		0.749
(0.909)
del 7q36 2 20 (36%) 36 0.328
(0.707) 		0.17
(0.598) 		0.758
(0.909) 		0.519
(0.803) 		0.494
(0.789) 		0.277
(0.696) 		0.403
(0.723) 		0.0446
(0.405) 		0.325
(0.707) 		0.0822
(0.456)
del 9p23 34 (61%) 22 0.3
(0.707) 		0.123
(0.527) 		0.763
(0.909) 		0.0158
(0.292) 		0.637
(0.862) 		0.323
(0.707) 		0.505
(0.792) 		0.43
(0.742) 		0.49
(0.788) 		0.12
(0.527)
del 9q21 13 39 (70%) 17 0.342
(0.707) 		0.324
(0.707) 		0.528
(0.805) 		0.449
(0.757) 		0.209
(0.648) 		0.256
(0.679) 		0.48
(0.783) 		0.318
(0.707) 		0.742
(0.909) 		0.398
(0.719)
del 9q33 3 39 (70%) 17 0.672
(0.889) 		0.0745
(0.442) 		0.746
(0.909) 		0.0401
(0.39) 		0.114
(0.527) 		0.138
(0.55) 		0.967
(1.00) 		0.114
(0.527) 		1
(1.00) 		0.258
(0.679)
del 10q23 31 20 (36%) 36 0.151
(0.578) 		0.107
(0.527) 		0.562
(0.805) 		0.981
(1.00) 		0.123
(0.527) 		0.243
(0.677) 		0.76
(0.909) 		0.853
(0.969) 		0.77
(0.909) 		0.825
(0.946)
del 11p15 5 25 (45%) 31 0.587
(0.821) 		0.767
(0.909) 		0.564
(0.805) 		0.492
(0.788) 		0.9
(0.979) 		0.894
(0.979) 		0.726
(0.909) 		0.895
(0.979) 		0.829
(0.948) 		0.917
(0.989)
del 11q14 1 26 (46%) 30 0.446
(0.755) 		0.172
(0.603) 		0.566
(0.805) 		0.229
(0.657) 		1
(1.00) 		0.923
(0.989) 		0.267
(0.689) 		0.263
(0.686) 		0.226
(0.656) 		0.0734
(0.439)
del 11q23 2 26 (46%) 30 1
(1.00) 		0.116
(0.527) 		0.774
(0.91) 		0.227
(0.656) 		0.346
(0.707) 		0.867
(0.974) 		0.361
(0.708) 		0.863
(0.973) 		0.395
(0.717) 		0.357
(0.707)
del 12q23 1 20 (36%) 36 0.88
(0.978) 		0.899
(0.979) 		0.375
(0.711) 		0.0627
(0.423) 		0.653
(0.876) 		0.751
(0.909) 		0.95
(1.00) 		0.338
(0.707) 		1
(1.00) 		0.548
(0.805)
del 13q12 11 30 (54%) 26 0.297
(0.707) 		0.0192
(0.294) 		0.244
(0.677) 		0.0713
(0.439) 		0.372
(0.711) 		0.206
(0.648) 		0.726
(0.909) 		0.0259
(0.316) 		0.345
(0.707) 		0.0634
(0.423)
del 14q21 1 28 (50%) 28 0.891
(0.979) 		0.0495
(0.419) 		0.77
(0.909) 		0.136
(0.55) 		0.0641
(0.423) 		0.0561
(0.423) 		0.376
(0.711) 		0.383
(0.711) 		0.831
(0.95) 		0.365
(0.71)
del 15q11 2 41 (73%) 15 0.747
(0.909) 		0.0973
(0.507) 		1
(1.00) 		0.588
(0.821) 		0.552
(0.805) 		0.625
(0.855) 		0.144
(0.559) 		0.907
(0.982) 		0.325
(0.707) 		0.707
(0.909)
del 15q15 1 43 (77%) 13 0.168
(0.597) 		0.0316
(0.343) 		0.33
(0.707) 		0.041
(0.391) 		0.346
(0.707) 		0.768
(0.909) 		0.119
(0.527) 		0.348
(0.707) 		0.0669
(0.423) 		0.208
(0.648)
del 16p13 3 33 (59%) 23 0.664
(0.881) 		0.551
(0.805) 		1
(1.00) 		0.261
(0.684) 		0.568
(0.806) 		0.228
(0.656) 		0.349
(0.707) 		0.387
(0.711) 		0.383
(0.711) 		0.714
(0.909)
del 16q23 1 39 (70%) 17 0.628
(0.855) 		0.421
(0.737) 		1
(1.00) 		0.278
(0.696) 		0.396
(0.717) 		0.394
(0.717) 		0.867
(0.974) 		0.812
(0.942) 		0.174
(0.603) 		0.622
(0.855)
del 17p13 1 42 (75%) 14 0.141
(0.554) 		0.0559
(0.423) 		0.505
(0.792) 		0.236
(0.667) 		0.0606
(0.423) 		0.423
(0.737) 		0.133
(0.547) 		0.183
(0.621) 		0.0203
(0.294) 		0.0865
(0.467)
del 17q21 32 19 (34%) 37 0.143
(0.559) 		0.764
(0.909) 		1
(1.00) 		0.754
(0.909) 		0.179
(0.612) 		0.0667
(0.423) 		0.226
(0.656) 		0.208
(0.648) 		0.385
(0.711) 		0.74
(0.909)
del 18q22 2 26 (46%) 30 0.331
(0.707) 		0.341
(0.707) 		0.561
(0.805) 		0.535
(0.805) 		0.504
(0.792) 		0.361
(0.708) 		0.0217
(0.294) 		0.0774
(0.446) 		0.0132
(0.279) 		0.0244
(0.316)
del 19p13 3 47 (84%) 9 0.0632
(0.423) 		0.0202
(0.294) 		0.684
(0.899) 		0.121
(0.527) 		0.0998
(0.512) 		0.377
(0.711) 		0.0152
(0.292) 		0.0841
(0.462) 		0.00907
(0.279) 		0.114
(0.527)
del 20p12 1 9 (16%) 47 0.537
(0.805) 		0.7
(0.909) 		0.678
(0.895) 		0.0207
(0.294) 		0.392
(0.717) 		0.527
(0.805) 		0.223
(0.656) 		0.339
(0.707) 		0.366
(0.71) 		0.464
(0.768)
del 22q13 31 40 (71%) 16 0.298
(0.707) 		0.408
(0.73) 		0.0517
(0.423) 		0.31
(0.707) 		0.894
(0.979) 		0.459
(0.766) 		0.577
(0.815) 		0.353
(0.707) 		0.857
(0.971) 		0.588
(0.821)
del xp21 1 18 (32%) 38 0.936
(0.996) 		0.422
(0.737) 		1
(1.00) 		0.896
(0.979) 		0.819
(0.946) 		0.87
(0.974) 		0.362
(0.708) 		1
(1.00) 		1
(1.00) 		0.902
(0.979)
del xq25 23 (41%) 33 0.623
(0.855) 		0.307
(0.707) 		0.566
(0.805) 		0.068
(0.423) 		0.113
(0.527) 		0.898
(0.979) 		0.726
(0.909) 		0.566
(0.805) 		0.281
(0.697) 		0.385
(0.711)
'amp_3q26.2' versus 'CN_CNMF'

P value = 0.00593 (Fisher's exact test), Q value = 0.23

Table S1.  Gene #5: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
AMP PEAK 5(3Q26.2) MUTATED 17 11 9
AMP PEAK 5(3Q26.2) WILD-TYPE 1 10 8

Figure S1.  Get High-res Image Gene #5: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 0.00484 (Fisher's exact test), Q value = 0.22

Table S2.  Gene #5: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 9 10 13 13
AMP PEAK 5(3Q26.2) MUTATED 11 5 4 11 6
AMP PEAK 5(3Q26.2) WILD-TYPE 0 4 6 2 7

Figure S2.  Get High-res Image Gene #5: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p13.2' versus 'CN_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.13

Table S3.  Gene #7: 'amp_5p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
AMP PEAK 7(5P13.2) MUTATED 9 4 13
AMP PEAK 7(5P13.2) WILD-TYPE 9 17 4

Figure S3.  Get High-res Image Gene #7: 'amp_5p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.13

Table S4.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
AMP PEAK 11(8Q24.21) MUTATED 9 16 17
AMP PEAK 11(8Q24.21) WILD-TYPE 9 5 0

Figure S4.  Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00571 (Fisher's exact test), Q value = 0.23

Table S5.  Gene #11: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 23 20
AMP PEAK 11(8Q24.21) MUTATED 11 12 18
AMP PEAK 11(8Q24.21) WILD-TYPE 1 11 2

Figure S5.  Get High-res Image Gene #11: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.095

Table S6.  Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
AMP PEAK 12(8Q24.21) MUTATED 8 15 17
AMP PEAK 12(8Q24.21) WILD-TYPE 10 6 0

Figure S6.  Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q31.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.15

Table S7.  Gene #17: 'amp_13q31.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 23 20
AMP PEAK 17(13Q31.3) MUTATED 7 15 3
AMP PEAK 17(13Q31.3) WILD-TYPE 5 8 17

Figure S7.  Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'CN_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.13

Table S8.  Gene #22: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
AMP PEAK 22(19Q12) MUTATED 18 12 15
AMP PEAK 22(19Q12) WILD-TYPE 0 9 2

Figure S8.  Get High-res Image Gene #22: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.067

Table S9.  Gene #22: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 9 10 13 13
AMP PEAK 22(19Q12) MUTATED 11 7 3 11 13
AMP PEAK 22(19Q12) WILD-TYPE 0 2 7 2 0

Figure S9.  Get High-res Image Gene #22: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'CN_CNMF'

P value = 0.00423 (Fisher's exact test), Q value = 0.22

Table S10.  Gene #23: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
AMP PEAK 23(20Q11.21) MUTATED 18 14 16
AMP PEAK 23(20Q11.21) WILD-TYPE 0 7 1

Figure S10.  Get High-res Image Gene #23: 'amp_20q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.17

Table S11.  Gene #31: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 22 4 19
DEL PEAK 6(4Q34.3) MUTATED 10 17 1 9
DEL PEAK 6(4Q34.3) WILD-TYPE 0 5 3 10

Figure S11.  Get High-res Image Gene #31: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00512 (Fisher's exact test), Q value = 0.22

Table S12.  Gene #31: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 23 20
DEL PEAK 6(4Q34.3) MUTATED 11 18 8
DEL PEAK 6(4Q34.3) WILD-TYPE 1 5 12

Figure S12.  Get High-res Image Gene #31: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.13

Table S13.  Gene #36: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
DEL PEAK 11(8P23.2) MUTATED 13 6 14
DEL PEAK 11(8P23.2) WILD-TYPE 5 15 3

Figure S13.  Get High-res Image Gene #36: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00156 (Fisher's exact test), Q value = 0.13

Table S14.  Gene #45: '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 20(12Q24.31) MUTATED 2 7 5 3 1 0 0
DEL PEAK 20(12Q24.31) WILD-TYPE 6 1 2 4 6 5 5

Figure S14.  Get High-res Image Gene #45: 'del_12q24.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.095

Table S15.  Gene #47: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 9 10 13 13
DEL PEAK 22(13Q14.2) MUTATED 3 7 7 12 3
DEL PEAK 22(13Q14.2) WILD-TYPE 8 2 3 1 10

Figure S15.  Get High-res Image Gene #47: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.33' versus 'MRNASEQ_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.095

Table S16.  Gene #57: 'del_19q13.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 20 12 10
DEL PEAK 32(19Q13.33) MUTATED 9 2 1 5
DEL PEAK 32(19Q13.33) WILD-TYPE 5 18 11 5

Figure S16.  Get High-res Image Gene #57: '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/15107627/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/15115115/UCS-TP.transferedmergedcluster.txt

  • Number of patients = 56

  • Number of significantly focal cnvs = 61

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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