Correlation between copy number variations of arm-level result and molecular subtypes
Rectum Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1VX0F9J
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1VX0F9J
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 78 arm-level events and 12 molecular subtypes across 162 patients, 14 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss 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 78 arm-level 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, 14 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
7p gain 100 (62%) 62 0.00219
(1.00) 		0.00266
(1.00) 		1e-05
(0.00911) 		0.00878
(1.00) 		0.486
(1.00) 		0.375
(1.00) 		0.0197
(1.00) 		0.00019
(0.171) 		0.0409
(1.00) 		0.0965
(1.00) 		0.0363
(1.00) 		0.384
(1.00)
6p gain 40 (25%) 122 0.336
(1.00) 		0.565
(1.00) 		9e-05
(0.0812) 		0.00475
(1.00) 		0.772
(1.00) 		0.256
(1.00) 		0.617
(1.00) 		0.592
(1.00) 		0.239
(1.00) 		0.3
(1.00) 		0.423
(1.00) 		0.625
(1.00)
6q gain 35 (22%) 127 0.671
(1.00) 		0.228
(1.00) 		2e-05
(0.0181) 		0.0107
(1.00) 		0.844
(1.00) 		0.472
(1.00) 		0.664
(1.00) 		0.329
(1.00) 		0.337
(1.00) 		0.581
(1.00) 		0.788
(1.00) 		0.682
(1.00)
7q gain 83 (51%) 79 0.0481
(1.00) 		0.00756
(1.00) 		5e-05
(0.0451) 		0.259
(1.00) 		0.618
(1.00) 		0.949
(1.00) 		0.0412
(1.00) 		0.00266
(1.00) 		0.499
(1.00) 		0.829
(1.00) 		0.379
(1.00) 		0.621
(1.00)
8q gain 88 (54%) 74 0.00775
(1.00) 		0.213
(1.00) 		1e-05
(0.00911) 		0.193
(1.00) 		0.548
(1.00) 		0.785
(1.00) 		0.569
(1.00) 		0.0748
(1.00) 		0.245
(1.00) 		0.066
(1.00) 		0.894
(1.00) 		1
(1.00)
13q gain 110 (68%) 52 0.282
(1.00) 		0.381
(1.00) 		9e-05
(0.0812) 		0.0843
(1.00) 		0.837
(1.00) 		0.321
(1.00) 		0.00436
(1.00) 		0.0264
(1.00) 		0.00278
(1.00) 		0.0659
(1.00) 		0.19
(1.00) 		0.58
(1.00)
16q gain 39 (24%) 123 0.0492
(1.00) 		0.595
(1.00) 		2e-05
(0.0181) 		0.486
(1.00) 		1
(1.00) 		0.67
(1.00) 		0.0294
(1.00) 		0.0431
(1.00) 		0.0209
(1.00) 		0.243
(1.00) 		0.0243
(1.00) 		0.0606
(1.00)
1p loss 44 (27%) 118 0.692
(1.00) 		0.0273
(1.00) 		0.00026
(0.234) 		0.271
(1.00) 		0.935
(1.00) 		0.208
(1.00) 		0.804
(1.00) 		0.0706
(1.00) 		0.44
(1.00) 		0.609
(1.00) 		0.92
(1.00) 		0.192
(1.00)
4p loss 58 (36%) 104 0.666
(1.00) 		0.372
(1.00) 		1e-05
(0.00911) 		0.036
(1.00) 		0.97
(1.00) 		0.512
(1.00) 		0.524
(1.00) 		0.643
(1.00) 		0.974
(1.00) 		0.0987
(1.00) 		0.543
(1.00) 		0.623
(1.00)
4q loss 65 (40%) 97 0.781
(1.00) 		0.27
(1.00) 		4e-05
(0.0362) 		0.0408
(1.00) 		0.816
(1.00) 		0.515
(1.00) 		0.702
(1.00) 		0.268
(1.00) 		0.812
(1.00) 		0.217
(1.00) 		0.93
(1.00) 		0.603
(1.00)
11q loss 30 (19%) 132 0.0564
(1.00) 		0.205
(1.00) 		0.00026
(0.234) 		0.0303
(1.00) 		0.605
(1.00) 		0.385
(1.00) 		0.111
(1.00) 		0.00732
(1.00) 		0.206
(1.00) 		0.376
(1.00) 		0.313
(1.00) 		0.0857
(1.00)
18p loss 125 (77%) 37 0.0593
(1.00) 		0.708
(1.00) 		1e-05
(0.00911) 		0.0294
(1.00) 		0.599
(1.00) 		0.153
(1.00) 		0.659
(1.00) 		0.232
(1.00) 		0.17
(1.00) 		0.162
(1.00) 		0.177
(1.00) 		1
(1.00)
18q loss 135 (83%) 27 0.021
(1.00) 		0.173
(1.00) 		3e-05
(0.0271) 		0.0165
(1.00) 		0.797
(1.00) 		0.484
(1.00) 		0.89
(1.00) 		0.68
(1.00) 		0.424
(1.00) 		0.0271
(1.00) 		0.0229
(1.00) 		0.636
(1.00)
1p gain 12 (7%) 150 0.513
(1.00) 		0.941
(1.00) 		0.45
(1.00) 		0.53
(1.00) 		0.0321
(1.00) 		0.0178
(1.00) 		0.22
(1.00) 		0.77
(1.00) 		0.941
(1.00) 		0.458
(1.00) 		0.931
(1.00) 		0.71
(1.00)
1q gain 32 (20%) 130 0.67
(1.00) 		0.614
(1.00) 		0.022
(1.00) 		0.384
(1.00) 		0.033
(1.00) 		0.182
(1.00) 		0.319
(1.00) 		0.784
(1.00) 		0.571
(1.00) 		0.796
(1.00) 		0.15
(1.00) 		0.325
(1.00)
2p gain 39 (24%) 123 0.504
(1.00) 		0.0198
(1.00) 		0.0555
(1.00) 		0.0664
(1.00) 		0.668
(1.00) 		0.639
(1.00) 		0.0457
(1.00) 		0.0414
(1.00) 		0.185
(1.00) 		0.0767
(1.00) 		0.914
(1.00) 		0.471
(1.00)
2q gain 41 (25%) 121 0.0921
(1.00) 		0.0582
(1.00) 		0.0137
(1.00) 		0.163
(1.00) 		0.72
(1.00) 		0.827
(1.00) 		0.0814
(1.00) 		0.00923
(1.00) 		0.216
(1.00) 		0.306
(1.00) 		0.535
(1.00) 		0.239
(1.00)
3p gain 27 (17%) 135 1
(1.00) 		0.904
(1.00) 		0.188
(1.00) 		0.683
(1.00) 		0.0867
(1.00) 		0.456
(1.00) 		0.429
(1.00) 		0.627
(1.00) 		0.378
(1.00) 		0.357
(1.00) 		0.638
(1.00) 		0.561
(1.00)
3q gain 34 (21%) 128 0.604
(1.00) 		0.612
(1.00) 		0.0645
(1.00) 		0.908
(1.00) 		0.253
(1.00) 		0.42
(1.00) 		0.419
(1.00) 		0.226
(1.00) 		0.222
(1.00) 		0.319
(1.00) 		0.935
(1.00) 		0.84
(1.00)
4p gain 9 (6%) 153 1
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.763
(1.00) 		0.0889
(1.00) 		0.171
(1.00) 		0.357
(1.00) 		0.437
(1.00) 		0.222
(1.00) 		0.373
(1.00) 		0.602
(1.00) 		1
(1.00)
4q gain 5 (3%) 157 0.294
(1.00) 		0.65
(1.00) 		1
(1.00) 		0.22
(1.00) 		0.487
(1.00) 		0.555
(1.00) 		1
(1.00) 		0.891
(1.00) 		1
(1.00)
5p gain 34 (21%) 128 0.204
(1.00) 		0.0987
(1.00) 		0.027
(1.00) 		0.125
(1.00) 		0.215
(1.00) 		0.688
(1.00) 		0.0447
(1.00) 		0.004
(1.00) 		0.192
(1.00) 		0.922
(1.00) 		0.2
(1.00) 		0.626
(1.00)
5q gain 22 (14%) 140 0.244
(1.00) 		0.0885
(1.00) 		0.414
(1.00) 		0.0268
(1.00) 		0.0724
(1.00) 		0.918
(1.00) 		0.24
(1.00) 		0.0608
(1.00) 		0.297
(1.00) 		0.611
(1.00) 		0.253
(1.00) 		0.218
(1.00)
8p gain 39 (24%) 123 0.586
(1.00) 		0.358
(1.00) 		0.0138
(1.00) 		0.734
(1.00) 		0.304
(1.00) 		0.0425
(1.00) 		0.214
(1.00) 		0.391
(1.00) 		0.771
(1.00) 		0.203
(1.00) 		0.195
(1.00) 		0.947
(1.00)
9p gain 42 (26%) 120 0.0182
(1.00) 		0.2
(1.00) 		0.626
(1.00) 		0.204
(1.00) 		0.654
(1.00) 		0.229
(1.00) 		0.0221
(1.00) 		0.994
(1.00) 		0.273
(1.00) 		0.331
(1.00) 		0.132
(1.00) 		0.632
(1.00)
9q gain 33 (20%) 129 0.0151
(1.00) 		0.21
(1.00) 		0.328
(1.00) 		0.497
(1.00) 		0.564
(1.00) 		0.0999
(1.00) 		0.244
(1.00) 		0.162
(1.00) 		0.785
(1.00) 		0.622
(1.00) 		0.299
(1.00) 		0.694
(1.00)
10p gain 12 (7%) 150 1
(1.00) 		0.918
(1.00) 		0.155
(1.00) 		0.274
(1.00) 		0.668
(1.00) 		0.748
(1.00) 		0.0895
(1.00) 		0.0415
(1.00) 		0.651
(1.00) 		0.919
(1.00) 		0.386
(1.00) 		0.00654
(1.00)
10q gain 6 (4%) 156 0.516
(1.00) 		0.083
(1.00) 		0.268
(1.00) 		0.78
(1.00) 		1
(1.00) 		0.873
(1.00) 		0.409
(1.00) 		0.0836
(1.00) 		0.772
(1.00) 		0.864
(1.00)
11p gain 30 (19%) 132 0.134
(1.00) 		0.387
(1.00) 		0.0181
(1.00) 		0.393
(1.00) 		0.843
(1.00) 		0.396
(1.00) 		0.191
(1.00) 		0.0273
(1.00) 		0.031
(1.00) 		0.285
(1.00) 		0.129
(1.00) 		0.17
(1.00)
11q gain 25 (15%) 137 0.239
(1.00) 		0.43
(1.00) 		0.00124
(1.00) 		0.0337
(1.00) 		0.574
(1.00) 		0.302
(1.00) 		0.0505
(1.00) 		0.00107
(0.958) 		0.0256
(1.00) 		0.588
(1.00) 		0.233
(1.00) 		1
(1.00)
12p gain 33 (20%) 129 0.693
(1.00) 		0.482
(1.00) 		0.00322
(1.00) 		0.725
(1.00) 		0.183
(1.00) 		0.124
(1.00) 		0.231
(1.00) 		0.323
(1.00) 		0.374
(1.00) 		0.551
(1.00) 		0.379
(1.00) 		0.681
(1.00)
12q gain 23 (14%) 139 0.912
(1.00) 		0.513
(1.00) 		0.0946
(1.00) 		0.306
(1.00) 		0.373
(1.00) 		0.258
(1.00) 		0.191
(1.00) 		0.949
(1.00) 		0.299
(1.00) 		0.331
(1.00) 		0.0688
(1.00) 		0.282
(1.00)
14q gain 8 (5%) 154 0.834
(1.00) 		0.916
(1.00) 		0.146
(1.00) 		0.176
(1.00) 		0.519
(1.00) 		0.546
(1.00) 		0.413
(1.00) 		0.399
(1.00) 		0.128
(1.00) 		0.863
(1.00)
15q gain 3 (2%) 159 0.718
(1.00) 		0.484
(1.00) 		0.352
(1.00) 		0.697
(1.00)
16p gain 39 (24%) 123 0.148
(1.00) 		0.851
(1.00) 		0.00133
(1.00) 		0.512
(1.00) 		0.923
(1.00) 		1
(1.00) 		0.254
(1.00) 		0.322
(1.00) 		0.153
(1.00) 		0.676
(1.00) 		0.0585
(1.00) 		0.143
(1.00)
17p gain 8 (5%) 154 0.111
(1.00) 		0.378
(1.00) 		0.0274
(1.00) 		0.376
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.145
(1.00) 		0.556
(1.00) 		0.488
(1.00) 		0.442
(1.00) 		0.229
(1.00) 		0.794
(1.00)
17q gain 30 (19%) 132 0.199
(1.00) 		0.943
(1.00) 		0.00032
(0.287) 		0.387
(1.00) 		0.878
(1.00) 		0.94
(1.00) 		0.42
(1.00) 		0.373
(1.00) 		0.0542
(1.00) 		0.461
(1.00) 		0.415
(1.00) 		1
(1.00)
18p gain 8 (5%) 154 0.519
(1.00) 		0.389
(1.00) 		0.00593
(1.00) 		0.73
(1.00) 		0.807
(1.00) 		0.739
(1.00) 		0.887
(1.00) 		0.924
(1.00) 		0.501
(1.00) 		0.561
(1.00) 		0.621
(1.00) 		0.456
(1.00)
18q gain 6 (4%) 156 0.0795
(1.00) 		0.461
(1.00) 		0.492
(1.00) 		0.892
(1.00) 		0.457
(1.00) 		0.891
(1.00) 		0.653
(1.00) 		0.629
(1.00) 		0.623
(1.00) 		0.458
(1.00)
19p gain 31 (19%) 131 0.0669
(1.00) 		0.418
(1.00) 		0.0106
(1.00) 		1
(1.00) 		0.549
(1.00) 		0.461
(1.00) 		0.881
(1.00) 		0.636
(1.00) 		0.135
(1.00) 		0.956
(1.00) 		0.667
(1.00) 		1
(1.00)
19q gain 30 (19%) 132 0.0811
(1.00) 		0.531
(1.00) 		0.0131
(1.00) 		0.879
(1.00) 		0.957
(1.00) 		0.592
(1.00) 		0.26
(1.00) 		0.353
(1.00) 		0.356
(1.00) 		0.579
(1.00) 		0.256
(1.00) 		0.408
(1.00)
20p gain 104 (64%) 58 0.0963
(1.00) 		0.725
(1.00) 		0.382
(1.00) 		0.562
(1.00) 		0.0563
(1.00) 		0.501
(1.00) 		0.486
(1.00) 		0.28
(1.00) 		0.428
(1.00) 		0.0738
(1.00) 		0.575
(1.00) 		0.208
(1.00)
20q gain 142 (88%) 20 0.00819
(1.00) 		0.162
(1.00) 		0.00041
(0.367) 		0.34
(1.00) 		0.162
(1.00) 		0.337
(1.00) 		0.123
(1.00) 		0.0202
(1.00) 		0.0437
(1.00) 		0.362
(1.00) 		0.337
(1.00) 		0.31
(1.00)
21q gain 10 (6%) 152 0.538
(1.00) 		0.658
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.622
(1.00) 		0.794
(1.00) 		0.887
(1.00) 		0.739
(1.00) 		0.291
(1.00) 		0.724
(1.00) 		0.694
(1.00) 		0.706
(1.00)
22q gain 9 (6%) 153 0.729
(1.00) 		0.0608
(1.00) 		0.279
(1.00) 		1
(1.00) 		0.425
(1.00) 		0.237
(1.00) 		0.476
(1.00) 		0.0819
(1.00) 		1
(1.00) 		1
(1.00) 		0.688
(1.00) 		0.0883
(1.00)
xq gain 32 (20%) 130 0.106
(1.00) 		0.335
(1.00) 		0.0501
(1.00) 		0.437
(1.00) 		0.78
(1.00) 		0.442
(1.00) 		0.158
(1.00) 		0.436
(1.00) 		0.965
(1.00) 		0.958
(1.00) 		0.72
(1.00) 		0.703
(1.00)
1q loss 25 (15%) 137 0.911
(1.00) 		0.0576
(1.00) 		0.0219
(1.00) 		0.0442
(1.00) 		0.726
(1.00) 		0.383
(1.00) 		0.718
(1.00) 		0.603
(1.00) 		0.517
(1.00) 		0.238
(1.00) 		0.805
(1.00) 		0.109
(1.00)
2p loss 11 (7%) 151 0.637
(1.00) 		0.752
(1.00) 		0.0111
(1.00) 		0.482
(1.00) 		0.908
(1.00) 		0.54
(1.00) 		0.123
(1.00) 		0.242
(1.00) 		0.435
(1.00) 		0.604
(1.00) 		1
(1.00) 		1
(1.00)
2q loss 6 (4%) 156 1
(1.00) 		0.57
(1.00) 		0.152
(1.00) 		0.102
(1.00) 		0.304
(1.00) 		0.198
(1.00) 		0.225
(1.00) 		0.203
(1.00) 		0.467
(1.00)
3p loss 15 (9%) 147 1
(1.00) 		0.365
(1.00) 		0.124
(1.00) 		0.842
(1.00) 		0.256
(1.00) 		0.897
(1.00) 		0.159
(1.00) 		0.537
(1.00) 		0.454
(1.00) 		0.135
(1.00) 		0.114
(1.00) 		1
(1.00)
3q loss 10 (6%) 152 0.517
(1.00) 		0.792
(1.00) 		0.0626
(1.00) 		0.407
(1.00) 		0.328
(1.00) 		0.659
(1.00) 		0.0376
(1.00) 		0.287
(1.00) 		0.496
(1.00) 		0.00962
(1.00) 		0.292
(1.00) 		1
(1.00)
5p loss 26 (16%) 136 0.239
(1.00) 		0.817
(1.00) 		0.232
(1.00) 		0.196
(1.00) 		0.527
(1.00) 		0.0663
(1.00) 		0.696
(1.00) 		0.226
(1.00) 		0.724
(1.00) 		0.578
(1.00) 		0.316
(1.00) 		0.255
(1.00)
5q loss 40 (25%) 122 0.0908
(1.00) 		0.0113
(1.00) 		0.0061
(1.00) 		0.347
(1.00) 		1
(1.00) 		0.669
(1.00) 		0.969
(1.00) 		0.205
(1.00) 		0.944
(1.00) 		0.207
(1.00) 		0.645
(1.00) 		0.801
(1.00)
6p loss 13 (8%) 149 0.544
(1.00) 		0.928
(1.00) 		0.852
(1.00) 		0.142
(1.00) 		0.307
(1.00) 		0.359
(1.00) 		0.725
(1.00) 		0.242
(1.00) 		0.566
(1.00) 		0.256
(1.00) 		0.384
(1.00) 		0.147
(1.00)
6q loss 22 (14%) 140 0.169
(1.00) 		0.643
(1.00) 		0.134
(1.00) 		0.502
(1.00) 		0.451
(1.00) 		0.605
(1.00) 		0.134
(1.00) 		0.0384
(1.00) 		0.261
(1.00) 		0.41
(1.00) 		0.17
(1.00) 		0.345
(1.00)
7q loss 3 (2%) 159 0.204
(1.00) 		0.786
(1.00) 		0.772
(1.00) 		0.599
(1.00) 		1
(1.00) 		0.859
(1.00) 		1
(1.00)
8p loss 75 (46%) 87 0.184
(1.00) 		0.368
(1.00) 		0.017
(1.00) 		0.669
(1.00) 		0.704
(1.00) 		0.238
(1.00) 		0.282
(1.00) 		0.328
(1.00) 		0.848
(1.00) 		0.974
(1.00) 		0.0189
(1.00) 		0.432
(1.00)
8q loss 11 (7%) 151 0.179
(1.00) 		0.74
(1.00) 		0.161
(1.00) 		0.377
(1.00) 		0.796
(1.00) 		0.277
(1.00) 		0.186
(1.00) 		0.192
(1.00) 		0.865
(1.00) 		0.303
(1.00) 		0.741
(1.00) 		0.806
(1.00)
9p loss 22 (14%) 140 0.632
(1.00) 		0.617
(1.00) 		0.243
(1.00) 		0.226
(1.00) 		0.747
(1.00) 		0.567
(1.00) 		0.822
(1.00) 		0.955
(1.00) 		0.31
(1.00) 		0.0472
(1.00) 		0.153
(1.00) 		0.122
(1.00)
9q loss 22 (14%) 140 0.208
(1.00) 		0.447
(1.00) 		0.367
(1.00) 		0.239
(1.00) 		0.942
(1.00) 		0.902
(1.00) 		0.988
(1.00) 		0.38
(1.00) 		0.0698
(1.00) 		0.00181
(1.00) 		0.162
(1.00) 		0.0564
(1.00)
10p loss 32 (20%) 130 0.142
(1.00) 		0.173
(1.00) 		0.604
(1.00) 		0.0965
(1.00) 		0.146
(1.00) 		0.24
(1.00) 		0.875
(1.00) 		0.502
(1.00) 		0.838
(1.00) 		0.115
(1.00) 		0.893
(1.00) 		0.221
(1.00)
10q loss 37 (23%) 125 0.176
(1.00) 		0.155
(1.00) 		0.0974
(1.00) 		0.143
(1.00) 		0.13
(1.00) 		0.0331
(1.00) 		0.494
(1.00) 		0.163
(1.00) 		0.682
(1.00) 		0.0872
(1.00) 		0.852
(1.00) 		0.29
(1.00)
11p loss 24 (15%) 138 0.244
(1.00) 		0.373
(1.00) 		0.00314
(1.00) 		0.139
(1.00) 		0.203
(1.00) 		0.181
(1.00) 		0.306
(1.00) 		0.0857
(1.00) 		0.994
(1.00) 		0.712
(1.00) 		0.489
(1.00) 		0.0542
(1.00)
12p loss 22 (14%) 140 0.425
(1.00) 		0.283
(1.00) 		0.155
(1.00) 		0.43
(1.00) 		0.695
(1.00) 		0.0792
(1.00) 		0.92
(1.00) 		0.215
(1.00) 		0.45
(1.00) 		0.775
(1.00) 		0.236
(1.00) 		0.797
(1.00)
12q loss 20 (12%) 142 0.281
(1.00) 		0.407
(1.00) 		0.0595
(1.00) 		0.931
(1.00) 		0.643
(1.00) 		0.328
(1.00) 		0.937
(1.00) 		0.072
(1.00) 		0.458
(1.00) 		0.206
(1.00) 		0.267
(1.00) 		0.611
(1.00)
13q loss 8 (5%) 154 0.517
(1.00) 		1
(1.00) 		0.247
(1.00) 		0.107
(1.00) 		0.0558
(1.00) 		0.433
(1.00) 		1
(1.00) 		0.891
(1.00) 		0.175
(1.00) 		1
(1.00) 		0.744
(1.00) 		0.567
(1.00)
14q loss 65 (40%) 97 0.497
(1.00) 		0.248
(1.00) 		0.0116
(1.00) 		0.646
(1.00) 		0.803
(1.00) 		0.491
(1.00) 		0.108
(1.00) 		0.164
(1.00) 		0.337
(1.00) 		0.199
(1.00) 		0.792
(1.00) 		0.481
(1.00)
15q loss 72 (44%) 90 0.452
(1.00) 		0.11
(1.00) 		0.00146
(1.00) 		1
(1.00) 		0.0888
(1.00) 		0.252
(1.00) 		0.866
(1.00) 		0.501
(1.00) 		0.817
(1.00) 		0.633
(1.00) 		0.976
(1.00) 		0.833
(1.00)
16p loss 9 (6%) 153 0.379
(1.00) 		0.757
(1.00) 		0.196
(1.00) 		0.0621
(1.00) 		0.653
(1.00) 		0.633
(1.00) 		0.963
(1.00) 		0.963
(1.00) 		0.564
(1.00) 		1
(1.00) 		0.678
(1.00) 		0.57
(1.00)
16q loss 14 (9%) 148 0.28
(1.00) 		0.677
(1.00) 		0.00202
(1.00) 		0.148
(1.00) 		0.643
(1.00) 		0.713
(1.00) 		0.754
(1.00) 		0.73
(1.00) 		0.567
(1.00) 		0.858
(1.00) 		0.792
(1.00) 		0.552
(1.00)
17p loss 104 (64%) 58 0.203
(1.00) 		0.375
(1.00) 		0.0437
(1.00) 		0.169
(1.00) 		0.971
(1.00) 		0.32
(1.00) 		0.8
(1.00) 		0.962
(1.00) 		0.981
(1.00) 		0.395
(1.00) 		0.526
(1.00) 		0.516
(1.00)
17q loss 25 (15%) 137 0.903
(1.00) 		0.737
(1.00) 		0.00354
(1.00) 		0.0774
(1.00) 		0.749
(1.00) 		0.974
(1.00) 		0.316
(1.00) 		0.626
(1.00) 		0.869
(1.00) 		0.945
(1.00) 		0.393
(1.00) 		1
(1.00)
19p loss 22 (14%) 140 0.728
(1.00) 		0.835
(1.00) 		0.0506
(1.00) 		0.046
(1.00) 		0.7
(1.00) 		0.833
(1.00) 		0.222
(1.00) 		0.212
(1.00) 		0.273
(1.00) 		0.0213
(1.00) 		0.676
(1.00) 		1
(1.00)
19q loss 21 (13%) 141 0.833
(1.00) 		0.501
(1.00) 		0.391
(1.00) 		0.137
(1.00) 		0.882
(1.00) 		0.776
(1.00) 		0.332
(1.00) 		0.265
(1.00) 		0.0453
(1.00) 		0.00962
(1.00) 		0.759
(1.00) 		0.93
(1.00)
20p loss 25 (15%) 137 1
(1.00) 		0.953
(1.00) 		0.0744
(1.00) 		0.412
(1.00) 		0.206
(1.00) 		0.687
(1.00) 		0.675
(1.00) 		0.682
(1.00) 		0.111
(1.00) 		0.0612
(1.00) 		0.0297
(1.00) 		0.166
(1.00)
21q loss 66 (41%) 96 0.286
(1.00) 		0.247
(1.00) 		0.0267
(1.00) 		0.965
(1.00) 		0.972
(1.00) 		0.53
(1.00) 		0.578
(1.00) 		0.833
(1.00) 		0.0152
(1.00) 		0.184
(1.00) 		0.427
(1.00) 		0.471
(1.00)
22q loss 57 (35%) 105 0.853
(1.00) 		0.311
(1.00) 		0.0649
(1.00) 		0.738
(1.00) 		0.748
(1.00) 		0.299
(1.00) 		0.0664
(1.00) 		0.0946
(1.00) 		0.00603
(1.00) 		0.179
(1.00) 		0.369
(1.00) 		0.411
(1.00)
xq loss 25 (15%) 137 1
(1.00) 		0.714
(1.00) 		0.115
(1.00) 		0.469
(1.00) 		0.567
(1.00) 		0.972
(1.00) 		0.744
(1.00) 		0.903
(1.00) 		0.935
(1.00) 		0.681
(1.00) 		0.972
(1.00) 		0.516
(1.00)
'6p gain' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.081

Table S1.  Gene #11: '6p gain' 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
6P GAIN MUTATED 5 11 4 6 13 1
6P GAIN WILD-TYPE 5 23 38 24 11 21

Figure S1.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S2.  Gene #12: '6q gain' 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
6Q GAIN MUTATED 4 12 3 3 12 1
6Q GAIN WILD-TYPE 6 22 39 27 12 21

Figure S2.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S3.  Gene #13: '7p gain' 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
7P GAIN MUTATED 7 31 16 12 18 16
7P GAIN WILD-TYPE 3 3 26 18 6 6

Figure S3.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.17

Table S4.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 35 41 30
7P GAIN MUTATED 45 17 17 20
7P GAIN WILD-TYPE 10 18 24 10

Figure S4.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.045

Table S5.  Gene #14: '7q gain' 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
7Q GAIN MUTATED 4 25 13 9 18 14
7Q GAIN WILD-TYPE 6 9 29 21 6 8

Figure S5.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S6.  Gene #16: '8q gain' 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
8Q GAIN MUTATED 6 21 12 17 11 21
8Q GAIN WILD-TYPE 4 13 30 13 13 1

Figure S6.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.081

Table S7.  Gene #25: '13q gain' 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
13Q GAIN MUTATED 8 28 18 17 22 17
13Q GAIN WILD-TYPE 2 6 24 13 2 5

Figure S7.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S8.  Gene #29: '16q gain' 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
16Q GAIN MUTATED 5 13 1 3 11 6
16Q GAIN WILD-TYPE 5 21 41 27 13 16

Figure S8.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.23

Table S9.  Gene #41: '1p loss' 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
1P LOSS MUTATED 5 14 3 10 10 2
1P LOSS WILD-TYPE 5 20 39 20 14 20

Figure S9.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S10.  Gene #47: '4p loss' 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
4P LOSS MUTATED 4 13 5 15 17 4
4P LOSS WILD-TYPE 6 21 37 15 7 18

Figure S10.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.036

Table S11.  Gene #48: '4q loss' 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
4Q LOSS MUTATED 5 16 6 17 17 4
4Q LOSS WILD-TYPE 5 18 36 13 7 18

Figure S11.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.23

Table S12.  Gene #61: '11q loss' 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
11Q LOSS MUTATED 2 0 5 11 8 4
11Q LOSS WILD-TYPE 8 34 37 19 16 18

Figure S12.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0091

Table S13.  Gene #71: '18p loss' 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
18P LOSS MUTATED 10 33 23 18 20 21
18P LOSS WILD-TYPE 0 1 19 12 4 1

Figure S13.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.027

Table S14.  Gene #72: '18q loss' 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
18Q LOSS MUTATED 10 34 25 23 22 21
18Q LOSS WILD-TYPE 0 0 17 7 2 1

Figure S14.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 162

  • Number of significantly arm-level cnvs = 78

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, 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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