Correlation between copy number variation genes (focal events) and molecular subtypes
Skin Cutaneous Melanoma (Metastatic)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1M32TK0
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 variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1M32TK0
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 54 focal events and 10 molecular subtypes across 299 patients, 39 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'CN_CNMF'.

  • amp_1q44 cnv correlated to 'CN_CNMF'.

  • amp_5p15.33 cnv correlated to 'CN_CNMF'.

  • amp_6p24.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • amp_7p22.1 cnv correlated to 'CN_CNMF'.

  • amp_7q34 cnv correlated to 'CN_CNMF'.

  • amp_8q11.21 cnv correlated to 'CN_CNMF'.

  • amp_8q24.21 cnv correlated to 'CN_CNMF'.

  • amp_13q12.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_15q26.2 cnv correlated to 'CN_CNMF'.

  • amp_17q25.3 cnv correlated to 'CN_CNMF'.

  • amp_20q13.33 cnv correlated to 'CN_CNMF'.

  • amp_22q13.2 cnv correlated to 'CN_CNMF'.

  • del_1p36.31 cnv correlated to 'METHLYATION_CNMF'.

  • del_1p22.1 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_6q22.31 cnv correlated to 'CN_CNMF'.

  • del_6q26 cnv correlated to 'CN_CNMF'.

  • del_9p21.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_10p15.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_10q23.31 cnv correlated to 'CN_CNMF'.

  • del_10q26.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_11p11.2 cnv correlated to 'CN_CNMF'.

  • del_11q23.3 cnv correlated to 'CN_CNMF'.

  • del_13q12.11 cnv correlated to 'CN_CNMF'.

  • del_13q34 cnv correlated to 'CN_CNMF'.

  • del_14q23.3 cnv correlated to 'CN_CNMF'.

  • del_14q32.2 cnv correlated to 'CN_CNMF'.

  • del_15q13.3 cnv correlated to 'CN_CNMF'.

  • del_15q14 cnv correlated to 'CN_CNMF'.

  • del_15q15.2 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 54 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, 39 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 1p22 1 76 (25%) 223 0.00108
(0.53) 		1e-05
(0.0054) 		0.592
(1.00) 		0.213
(1.00) 		2e-05
(0.0104) 		0.00036
(0.181) 		0.193
(1.00) 		0.451
(1.00) 		0.487
(1.00) 		0.573
(1.00)
del 10p15 3 163 (55%) 136 1e-05
(0.0054) 		0.00271
(1.00) 		0.833
(1.00) 		0.156
(1.00) 		7e-05
(0.036) 		0.00011
(0.056) 		0.293
(1.00) 		0.0978
(1.00) 		0.377
(1.00) 		0.792
(1.00)
del 10q26 3 193 (65%) 106 1e-05
(0.0054) 		0.0957
(1.00) 		0.837
(1.00) 		0.309
(1.00) 		3e-05
(0.0155) 		0.00031
(0.157) 		0.116
(1.00) 		0.109
(1.00) 		0.234
(1.00) 		0.881
(1.00)
amp 6p24 3 169 (57%) 130 1e-05
(0.0054) 		0.00098
(0.483) 		0.325
(1.00) 		0.0168
(1.00) 		0.0971
(1.00) 		0.016
(1.00) 		0.00537
(1.00) 		0.00039
(0.196) 		0.00549
(1.00) 		0.00117
(0.572)
amp 13q12 3 85 (28%) 214 1e-05
(0.0054) 		7e-05
(0.036) 		0.388
(1.00) 		0.749
(1.00) 		0.00463
(1.00) 		0.0286
(1.00) 		0.832
(1.00) 		0.662
(1.00) 		0.475
(1.00) 		0.932
(1.00)
del 9p21 3 229 (77%) 70 1e-05
(0.0054) 		0.00114
(0.559) 		0.757
(1.00) 		0.701
(1.00) 		1e-05
(0.0054) 		0.0135
(1.00) 		0.0242
(1.00) 		0.328
(1.00) 		0.471
(1.00) 		0.252
(1.00)
amp 1q21 3 158 (53%) 141 1e-05
(0.0054) 		0.0248
(1.00) 		0.337
(1.00) 		0.523
(1.00) 		0.00969
(1.00) 		0.0902
(1.00) 		0.0827
(1.00) 		0.081
(1.00) 		0.0959
(1.00) 		0.175
(1.00)
amp 1q44 162 (54%) 137 1e-05
(0.0054) 		0.00437
(1.00) 		0.162
(1.00) 		0.143
(1.00) 		0.0318
(1.00) 		0.0151
(1.00) 		0.00782
(1.00) 		0.00838
(1.00) 		0.0731
(1.00) 		0.0103
(1.00)
amp 5p15 33 91 (30%) 208 0.00012
(0.0608) 		0.216
(1.00) 		0.694
(1.00) 		0.739
(1.00) 		0.0949
(1.00) 		0.261
(1.00) 		0.00348
(1.00) 		0.084
(1.00) 		0.00312
(1.00) 		0.283
(1.00)
amp 7p22 1 164 (55%) 135 4e-05
(0.0206) 		0.825
(1.00) 		0.625
(1.00) 		0.215
(1.00) 		0.0258
(1.00) 		0.219
(1.00) 		0.567
(1.00) 		0.506
(1.00) 		0.682
(1.00) 		0.173
(1.00)
amp 7q34 177 (59%) 122 1e-05
(0.0054) 		0.0826
(1.00) 		0.318
(1.00) 		0.953
(1.00) 		0.0624
(1.00) 		0.0198
(1.00) 		0.671
(1.00) 		0.488
(1.00) 		0.357
(1.00) 		0.902
(1.00)
amp 8q11 21 137 (46%) 162 2e-05
(0.0104) 		0.0205
(1.00) 		0.57
(1.00) 		0.246
(1.00) 		0.0159
(1.00) 		0.37
(1.00) 		0.668
(1.00) 		0.772
(1.00) 		0.0499
(1.00) 		0.387
(1.00)
amp 8q24 21 158 (53%) 141 1e-05
(0.0054) 		0.0162
(1.00) 		0.752
(1.00) 		0.936
(1.00) 		0.00983
(1.00) 		0.688
(1.00) 		0.55
(1.00) 		0.495
(1.00) 		0.303
(1.00) 		0.357
(1.00)
amp 15q26 2 99 (33%) 200 0.00034
(0.172) 		0.386
(1.00) 		0.938
(1.00) 		0.807
(1.00) 		0.297
(1.00) 		0.0465
(1.00) 		0.777
(1.00) 		0.0561
(1.00) 		1
(1.00) 		0.37
(1.00)
amp 17q25 3 100 (33%) 199 0.0001
(0.0511) 		0.0125
(1.00) 		0.0307
(1.00) 		0.0745
(1.00) 		0.108
(1.00) 		0.828
(1.00) 		0.844
(1.00) 		0.0514
(1.00) 		0.0305
(1.00) 		0.0182
(1.00)
amp 20q13 33 153 (51%) 146 1e-05
(0.0054) 		0.0125
(1.00) 		0.827
(1.00) 		0.988
(1.00) 		0.00188
(0.91) 		0.0109
(1.00) 		0.261
(1.00) 		0.32
(1.00) 		0.147
(1.00) 		0.24
(1.00)
amp 22q13 2 127 (42%) 172 0.00011
(0.056) 		0.13
(1.00) 		0.973
(1.00) 		0.717
(1.00) 		0.426
(1.00) 		0.118
(1.00) 		0.476
(1.00) 		0.202
(1.00) 		0.317
(1.00) 		0.437
(1.00)
del 1p36 31 70 (23%) 229 0.125
(1.00) 		1e-05
(0.0054) 		0.577
(1.00) 		0.21
(1.00) 		0.0745
(1.00) 		0.00426
(1.00) 		0.0973
(1.00) 		0.118
(1.00) 		0.728
(1.00) 		0.341
(1.00)
del 6q22 31 179 (60%) 120 1e-05
(0.0054) 		0.0214
(1.00) 		0.958
(1.00) 		0.445
(1.00) 		0.00502
(1.00) 		0.193
(1.00) 		0.564
(1.00) 		0.556
(1.00) 		0.748
(1.00) 		0.341
(1.00)
del 6q26 184 (62%) 115 1e-05
(0.0054) 		0.0192
(1.00) 		0.839
(1.00) 		0.537
(1.00) 		0.00142
(0.692) 		0.0544
(1.00) 		0.19
(1.00) 		0.424
(1.00) 		0.861
(1.00) 		0.432
(1.00)
del 10q23 31 188 (63%) 111 1e-05
(0.0054) 		0.0137
(1.00) 		0.88
(1.00) 		0.207
(1.00) 		0.00065
(0.323) 		0.00056
(0.28) 		0.134
(1.00) 		0.0222
(1.00) 		0.908
(1.00) 		0.563
(1.00)
del 11p11 2 96 (32%) 203 0.0001
(0.0511) 		0.00818
(1.00) 		0.65
(1.00) 		0.856
(1.00) 		0.136
(1.00) 		0.00146
(0.71) 		0.582
(1.00) 		0.228
(1.00) 		0.592
(1.00) 		0.697
(1.00)
del 11q23 3 161 (54%) 138 1e-05
(0.0054) 		0.21
(1.00) 		0.902
(1.00) 		0.262
(1.00) 		0.0338
(1.00) 		0.227
(1.00) 		0.296
(1.00) 		0.0173
(1.00) 		0.186
(1.00) 		0.0243
(1.00)
del 13q12 11 68 (23%) 231 8e-05
(0.041) 		0.0696
(1.00) 		0.245
(1.00) 		0.901
(1.00) 		0.984
(1.00) 		0.962
(1.00) 		0.645
(1.00) 		0.442
(1.00) 		0.527
(1.00) 		0.445
(1.00)
del 13q34 68 (23%) 231 0.00036
(0.181) 		0.00443
(1.00) 		0.0676
(1.00) 		0.747
(1.00) 		0.895
(1.00) 		0.261
(1.00) 		0.942
(1.00) 		0.849
(1.00) 		1
(1.00) 		0.39
(1.00)
del 14q23 3 102 (34%) 197 1e-05
(0.0054) 		0.809
(1.00) 		0.553
(1.00) 		0.246
(1.00) 		0.00272
(1.00) 		0.273
(1.00) 		0.0262
(1.00) 		0.663
(1.00) 		0.00346
(1.00) 		0.19
(1.00)
del 14q32 2 100 (33%) 199 1e-05
(0.0054) 		0.769
(1.00) 		0.505
(1.00) 		0.184
(1.00) 		0.00059
(0.294) 		0.386
(1.00) 		0.0201
(1.00) 		0.581
(1.00) 		0.0153
(1.00) 		0.109
(1.00)
del 15q13 3 73 (24%) 226 2e-05
(0.0104) 		0.0159
(1.00) 		0.0896
(1.00) 		0.305
(1.00) 		0.276
(1.00) 		0.0474
(1.00) 		0.944
(1.00) 		0.797
(1.00) 		0.6
(1.00) 		0.707
(1.00)
del 15q14 73 (24%) 226 1e-05
(0.0054) 		0.0116
(1.00) 		0.808
(1.00) 		0.683
(1.00) 		0.132
(1.00) 		0.0247
(1.00) 		0.892
(1.00) 		0.305
(1.00) 		0.641
(1.00) 		0.393
(1.00)
del 15q15 2 78 (26%) 221 1e-05
(0.0054) 		0.00964
(1.00) 		0.476
(1.00) 		0.431
(1.00) 		0.252
(1.00) 		0.0458
(1.00) 		0.891
(1.00) 		0.449
(1.00) 		0.864
(1.00) 		0.349
(1.00)
amp 1p12 96 (32%) 203 0.0135
(1.00) 		0.764
(1.00) 		0.706
(1.00) 		0.883
(1.00) 		0.158
(1.00) 		0.611
(1.00) 		0.0845
(1.00) 		0.782
(1.00) 		0.524
(1.00) 		0.399
(1.00)
amp 3p13 78 (26%) 221 0.153
(1.00) 		0.166
(1.00) 		0.0689
(1.00) 		0.113
(1.00) 		0.785
(1.00) 		0.146
(1.00) 		0.572
(1.00) 		0.0111
(1.00) 		0.823
(1.00) 		0.67
(1.00)
amp 4q12 53 (18%) 246 0.00058
(0.289) 		0.201
(1.00) 		0.0828
(1.00) 		0.532
(1.00) 		0.31
(1.00) 		0.121
(1.00) 		0.0407
(1.00) 		0.00127
(0.62) 		0.0081
(1.00) 		0.0393
(1.00)
amp 5q35 3 48 (16%) 251 0.00675
(1.00) 		0.00218
(1.00) 		0.0933
(1.00) 		0.0732
(1.00) 		0.0365
(1.00) 		0.226
(1.00) 		0.224
(1.00) 		0.098
(1.00) 		0.00457
(1.00) 		0.124
(1.00)
amp 6q12 64 (21%) 235 0.00509
(1.00) 		0.793
(1.00) 		0.529
(1.00) 		0.081
(1.00) 		0.113
(1.00) 		0.144
(1.00) 		0.0877
(1.00) 		0.0972
(1.00) 		0.515
(1.00) 		0.396
(1.00)
amp 11q13 3 58 (19%) 241 0.0265
(1.00) 		0.312
(1.00) 		0.905
(1.00) 		0.84
(1.00) 		0.406
(1.00) 		0.31
(1.00) 		0.366
(1.00) 		0.0927
(1.00) 		0.981
(1.00) 		0.349
(1.00)
amp 11q13 4 54 (18%) 245 0.00103
(0.507) 		0.0959
(1.00) 		0.917
(1.00) 		0.873
(1.00) 		0.148
(1.00) 		0.757
(1.00) 		0.119
(1.00) 		0.0349
(1.00) 		0.872
(1.00) 		0.237
(1.00)
amp 12q14 1 51 (17%) 248 0.0111
(1.00) 		0.33
(1.00) 		0.87
(1.00) 		0.286
(1.00) 		0.0558
(1.00) 		0.114
(1.00) 		0.787
(1.00) 		0.42
(1.00) 		0.138
(1.00) 		0.853
(1.00)
amp 12q15 50 (17%) 249 0.0116
(1.00) 		0.682
(1.00) 		0.642
(1.00) 		0.558
(1.00) 		0.272
(1.00) 		0.444
(1.00) 		0.688
(1.00) 		0.566
(1.00) 		0.463
(1.00) 		0.753
(1.00)
amp 19p13 2 56 (19%) 243 0.107
(1.00) 		0.366
(1.00) 		0.44
(1.00) 		0.956
(1.00) 		0.0124
(1.00) 		0.101
(1.00) 		0.982
(1.00) 		0.371
(1.00) 		0.841
(1.00) 		0.21
(1.00)
del 2q37 3 74 (25%) 225 0.715
(1.00) 		0.0557
(1.00) 		0.0912
(1.00) 		0.00418
(1.00) 		0.00251
(1.00) 		0.062
(1.00) 		0.00643
(1.00) 		0.099
(1.00) 		0.217
(1.00) 		0.0567
(1.00)
del 3p24 3 60 (20%) 239 0.478
(1.00) 		0.375
(1.00) 		0.374
(1.00) 		0.523
(1.00) 		0.192
(1.00) 		0.391
(1.00) 		0.268
(1.00) 		0.437
(1.00) 		0.0991
(1.00) 		0.117
(1.00)
del 3q23 48 (16%) 251 0.144
(1.00) 		0.0532
(1.00) 		0.351
(1.00) 		0.431
(1.00) 		0.207
(1.00) 		0.543
(1.00) 		0.363
(1.00) 		0.458
(1.00) 		0.606
(1.00) 		0.447
(1.00)
del 4q34 3 85 (28%) 214 0.0196
(1.00) 		0.0127
(1.00) 		0.513
(1.00) 		0.552
(1.00) 		0.0561
(1.00) 		0.0129
(1.00) 		0.541
(1.00) 		0.00302
(1.00) 		0.215
(1.00) 		0.00725
(1.00)
del 5p15 31 61 (20%) 238 0.784
(1.00) 		0.345
(1.00) 		0.548
(1.00) 		0.538
(1.00) 		0.651
(1.00) 		0.67
(1.00) 		0.994
(1.00) 		0.583
(1.00) 		0.78
(1.00) 		0.42
(1.00)
del 5q11 2 80 (27%) 219 0.0015
(0.727) 		0.178
(1.00) 		0.573
(1.00) 		0.178
(1.00) 		0.468
(1.00) 		0.106
(1.00) 		0.851
(1.00) 		0.333
(1.00) 		0.613
(1.00) 		0.535
(1.00)
del 5q31 3 111 (37%) 188 0.00052
(0.261) 		0.00092
(0.454) 		0.62
(1.00) 		0.3
(1.00) 		0.39
(1.00) 		0.0942
(1.00) 		0.932
(1.00) 		0.352
(1.00) 		0.515
(1.00) 		0.398
(1.00)
del 8p23 3 69 (23%) 230 0.0799
(1.00) 		0.16
(1.00) 		0.202
(1.00) 		0.162
(1.00) 		0.0796
(1.00) 		0.793
(1.00) 		0.454
(1.00) 		0.321
(1.00) 		0.21
(1.00) 		0.782
(1.00)
del 9p23 206 (69%) 93 0.00083
(0.411) 		0.0199
(1.00) 		0.455
(1.00) 		0.613
(1.00) 		0.00422
(1.00) 		0.141
(1.00) 		0.0237
(1.00) 		0.0805
(1.00) 		0.568
(1.00) 		0.0589
(1.00)
del 12q23 3 73 (24%) 226 0.00068
(0.337) 		0.0206
(1.00) 		0.965
(1.00) 		0.822
(1.00) 		0.513
(1.00) 		0.283
(1.00) 		0.288
(1.00) 		0.224
(1.00) 		0.909
(1.00) 		0.764
(1.00)
del 16p13 3 56 (19%) 243 0.366
(1.00) 		0.022
(1.00) 		0.0124
(1.00) 		0.337
(1.00) 		0.0489
(1.00) 		0.874
(1.00) 		0.466
(1.00) 		0.59
(1.00) 		0.136
(1.00) 		0.238
(1.00)
del 16q12 1 97 (32%) 202 0.0912
(1.00) 		0.541
(1.00) 		0.0212
(1.00) 		0.685
(1.00) 		0.154
(1.00) 		0.262
(1.00) 		0.0861
(1.00) 		0.193
(1.00) 		0.22
(1.00) 		0.15
(1.00)
del 16q24 3 107 (36%) 192 0.0321
(1.00) 		0.652
(1.00) 		0.146
(1.00) 		0.907
(1.00) 		0.013
(1.00) 		0.051
(1.00) 		0.176
(1.00) 		0.0522
(1.00) 		0.0353
(1.00) 		0.042
(1.00)
del 19p13 3 83 (28%) 216 0.00677
(1.00) 		0.407
(1.00) 		0.00239
(1.00) 		0.0624
(1.00) 		0.00342
(1.00) 		0.221
(1.00) 		0.896
(1.00) 		0.443
(1.00) 		0.665
(1.00) 		0.125
(1.00)
'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S1.  Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 2(1Q21.3) MUTATED 76 13 37 32
AMP PEAK 2(1Q21.3) WILD-TYPE 9 44 14 74

Figure S1.  Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S2.  Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 3(1Q44) MUTATED 77 14 37 34
AMP PEAK 3(1Q44) WILD-TYPE 8 43 14 72

Figure S2.  Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.061

Table S3.  Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 6(5P15.33) MUTATED 32 25 18 16
AMP PEAK 6(5P15.33) WILD-TYPE 53 32 33 90

Figure S3.  Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S4.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 8(6P24.3) MUTATED 67 45 15 42
AMP PEAK 8(6P24.3) WILD-TYPE 18 12 36 64

Figure S4.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.2

Table S5.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 80 36 95
AMP PEAK 8(6P24.3) MUTATED 51 30 19 62
AMP PEAK 8(6P24.3) WILD-TYPE 25 50 17 33

Figure S5.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.021

Table S6.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 10(7P22.1) MUTATED 47 34 41 42
AMP PEAK 10(7P22.1) WILD-TYPE 38 23 10 64

Figure S6.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S7.  Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 11(7Q34) MUTATED 45 35 47 50
AMP PEAK 11(7Q34) WILD-TYPE 40 22 4 56

Figure S7.  Get High-res Image Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S8.  Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 12(8Q11.21) MUTATED 44 37 29 27
AMP PEAK 12(8Q11.21) WILD-TYPE 41 20 22 79

Figure S8.  Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S9.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 13(8Q24.21) MUTATED 53 41 30 34
AMP PEAK 13(8Q24.21) WILD-TYPE 32 16 21 72

Figure S9.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S10.  Gene #18: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 18(13Q12.3) MUTATED 32 32 10 11
AMP PEAK 18(13Q12.3) WILD-TYPE 53 25 41 95

Figure S10.  Get High-res Image Gene #18: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.036

Table S11.  Gene #18: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 112 111 76
AMP PEAK 18(13Q12.3) MUTATED 29 20 36
AMP PEAK 18(13Q12.3) WILD-TYPE 83 91 40

Figure S11.  Get High-res Image Gene #18: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.2' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.17

Table S12.  Gene #19: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 19(15Q26.2) MUTATED 27 16 30 26
AMP PEAK 19(15Q26.2) WILD-TYPE 58 41 21 80

Figure S12.  Get High-res Image Gene #19: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.051

Table S13.  Gene #20: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 20(17Q25.3) MUTATED 39 23 19 19
AMP PEAK 20(17Q25.3) WILD-TYPE 46 34 32 87

Figure S13.  Get High-res Image Gene #20: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S14.  Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 22(20Q13.33) MUTATED 47 36 36 34
AMP PEAK 22(20Q13.33) WILD-TYPE 38 21 15 72

Figure S14.  Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q13.2' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.056

Table S15.  Gene #23: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
AMP PEAK 23(22Q13.2) MUTATED 44 20 32 31
AMP PEAK 23(22Q13.2) WILD-TYPE 41 37 19 75

Figure S15.  Get High-res Image Gene #23: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S16.  Gene #24: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 112 111 76
DEL PEAK 1(1P36.31) MUTATED 20 16 34
DEL PEAK 1(1P36.31) WILD-TYPE 92 95 42

Figure S16.  Get High-res Image Gene #24: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S17.  Gene #25: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 112 111 76
DEL PEAK 2(1P22.1) MUTATED 19 22 35
DEL PEAK 2(1P22.1) WILD-TYPE 93 89 41

Figure S17.  Get High-res Image Gene #25: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S18.  Gene #25: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 87 112
DEL PEAK 2(1P22.1) MUTATED 40 9 27
DEL PEAK 2(1P22.1) WILD-TYPE 59 78 85

Figure S18.  Get High-res Image Gene #25: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.18

Table S19.  Gene #25: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 178 50
DEL PEAK 2(1P22.1) MUTATED 18 34 24
DEL PEAK 2(1P22.1) WILD-TYPE 52 144 26

Figure S19.  Get High-res Image Gene #25: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S20.  Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 10(6Q22.31) MUTATED 55 46 40 38
DEL PEAK 10(6Q22.31) WILD-TYPE 30 11 11 68

Figure S20.  Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S21.  Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 11(6Q26) MUTATED 60 46 40 38
DEL PEAK 11(6Q26) WILD-TYPE 25 11 11 68

Figure S21.  Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S22.  Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 14(9P21.3) MUTATED 65 55 44 65
DEL PEAK 14(9P21.3) WILD-TYPE 20 2 7 41

Figure S22.  Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S23.  Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 87 112
DEL PEAK 14(9P21.3) MUTATED 90 54 84
DEL PEAK 14(9P21.3) WILD-TYPE 9 33 28

Figure S23.  Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S24.  Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 15(10P15.3) MUTATED 50 37 41 35
DEL PEAK 15(10P15.3) WILD-TYPE 35 20 10 71

Figure S24.  Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.036

Table S25.  Gene #38: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 87 112
DEL PEAK 15(10P15.3) MUTATED 72 38 53
DEL PEAK 15(10P15.3) WILD-TYPE 27 49 59

Figure S25.  Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.056

Table S26.  Gene #38: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 178 50
DEL PEAK 15(10P15.3) MUTATED 40 83 40
DEL PEAK 15(10P15.3) WILD-TYPE 30 95 10

Figure S26.  Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S27.  Gene #39: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 16(10Q23.31) MUTATED 51 42 48 47
DEL PEAK 16(10Q23.31) WILD-TYPE 34 15 3 59

Figure S27.  Get High-res Image Gene #39: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S28.  Gene #40: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 17(10Q26.3) MUTATED 49 45 48 51
DEL PEAK 17(10Q26.3) WILD-TYPE 36 12 3 55

Figure S28.  Get High-res Image Gene #40: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S29.  Gene #40: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 87 112
DEL PEAK 17(10Q26.3) MUTATED 82 47 64
DEL PEAK 17(10Q26.3) WILD-TYPE 17 40 48

Figure S29.  Get High-res Image Gene #40: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.16

Table S30.  Gene #40: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 178 50
DEL PEAK 17(10Q26.3) MUTATED 43 106 44
DEL PEAK 17(10Q26.3) WILD-TYPE 27 72 6

Figure S30.  Get High-res Image Gene #40: 'del_10q26.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p11.2' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.051

Table S31.  Gene #41: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 18(11P11.2) MUTATED 42 13 19 22
DEL PEAK 18(11P11.2) WILD-TYPE 43 44 32 84

Figure S31.  Get High-res Image Gene #41: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S32.  Gene #42: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 19(11Q23.3) MUTATED 66 24 32 39
DEL PEAK 19(11Q23.3) WILD-TYPE 19 33 19 67

Figure S32.  Get High-res Image Gene #42: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.041

Table S33.  Gene #44: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 21(13Q12.11) MUTATED 20 6 24 18
DEL PEAK 21(13Q12.11) WILD-TYPE 65 51 27 88

Figure S33.  Get High-res Image Gene #44: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q34' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.18

Table S34.  Gene #45: 'del_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 22(13Q34) MUTATED 20 5 22 21
DEL PEAK 22(13Q34) WILD-TYPE 65 52 29 85

Figure S34.  Get High-res Image Gene #45: 'del_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S35.  Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 23(14Q23.3) MUTATED 21 32 29 20
DEL PEAK 23(14Q23.3) WILD-TYPE 64 25 22 86

Figure S35.  Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S36.  Gene #47: 'del_14q32.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 24(14Q32.2) MUTATED 23 32 27 18
DEL PEAK 24(14Q32.2) WILD-TYPE 62 25 24 88

Figure S36.  Get High-res Image Gene #47: 'del_14q32.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q13.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.01

Table S37.  Gene #48: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 25(15Q13.3) MUTATED 33 20 4 16
DEL PEAK 25(15Q13.3) WILD-TYPE 52 37 47 90

Figure S37.  Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q14' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S38.  Gene #49: 'del_15q14' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 26(15Q14) MUTATED 35 20 1 17
DEL PEAK 26(15Q14) WILD-TYPE 50 37 50 89

Figure S38.  Get High-res Image Gene #49: 'del_15q14' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0054

Table S39.  Gene #50: 'del_15q15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 85 57 51 106
DEL PEAK 27(15Q15.2) MUTATED 37 23 1 17
DEL PEAK 27(15Q15.2) WILD-TYPE 48 34 50 89

Figure S39.  Get High-res Image Gene #50: 'del_15q15.2' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

  • Molecular subtype file = SKCM-TM.transferedmergedcluster.txt

  • Number of patients = 299

  • Number of significantly focal cnvs = 54

  • 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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