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 55 focal events and 10 molecular subtypes across 366 patients, 38 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_5q35.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 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_13q31.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_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' and 'MRNASEQ_CNMF'.

  • del_9p23 cnv correlated to 'CN_CNMF'.

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

  • del_10p15.3 cnv correlated to 'CN_CNMF'.

  • del_10q21.1 cnv correlated to 'CN_CNMF'.

  • del_10q23.31 cnv correlated to 'CN_CNMF'.

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

  • del_11q23.3 cnv correlated to 'CN_CNMF'.

  • del_14q23.3 cnv correlated to 'CN_CNMF'.

  • del_14q32.31 cnv correlated to 'CN_CNMF'.

  • del_17p13.3 cnv correlated to 'METHLYATION_CNMF'.

  • del_19p13.3 cnv correlated to 'MRNASEQ_CNMF'.

  • del_xp21.1 cnv correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 55 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, 38 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 13q31 3 104 (28%) 262 1e-05
(0.0055) 		1e-05
(0.0055) 		0.755
(1.00) 		0.27
(1.00) 		0.00023
(0.119) 		0.0536
(1.00) 		0.68
(1.00) 		0.518
(1.00) 		0.0575
(1.00) 		0.791
(1.00)
del 1p22 1 97 (27%) 269 0.00091
(0.459) 		1e-05
(0.0055) 		0.588
(1.00) 		0.208
(1.00) 		9e-05
(0.047) 		0.00021
(0.109) 		0.0779
(1.00) 		0.768
(1.00) 		0.195
(1.00) 		0.256
(1.00)
amp 5q35 3 59 (16%) 307 0.0002
(0.104) 		0.00032
(0.165) 		0.0913
(1.00) 		0.0343
(1.00) 		0.0157
(1.00) 		0.201
(1.00) 		0.269
(1.00) 		0.351
(1.00) 		0.352
(1.00) 		0.46
(1.00)
amp 6p24 3 210 (57%) 156 1e-05
(0.0055) 		2e-05
(0.0105) 		0.323
(1.00) 		0.0165
(1.00) 		0.0282
(1.00) 		0.0327
(1.00) 		0.00085
(0.43) 		0.0167
(1.00) 		0.00093
(0.467) 		0.00165
(0.82)
del 6q26 221 (60%) 145 1e-05
(0.0055) 		0.0107
(1.00) 		0.838
(1.00) 		0.539
(1.00) 		0.00039
(0.2) 		0.0283
(1.00) 		0.323
(1.00) 		0.604
(1.00) 		0.837
(1.00) 		0.455
(1.00)
del 9p21 3 278 (76%) 88 1e-05
(0.0055) 		0.00708
(1.00) 		0.754
(1.00) 		0.702
(1.00) 		2e-05
(0.0105) 		0.00597
(1.00) 		0.0348
(1.00) 		0.797
(1.00) 		0.412
(1.00) 		0.12
(1.00)
del 10q26 3 236 (64%) 130 1e-05
(0.0055) 		0.435
(1.00) 		0.834
(1.00) 		0.305
(1.00) 		0.00012
(0.0625) 		0.00092
(0.463) 		0.0777
(1.00) 		0.512
(1.00) 		0.186
(1.00) 		0.394
(1.00)
amp 1q21 3 203 (55%) 163 1e-05
(0.0055) 		0.0561
(1.00) 		0.338
(1.00) 		0.524
(1.00) 		0.00207
(1.00) 		0.218
(1.00) 		0.0238
(1.00) 		0.0606
(1.00) 		0.172
(1.00) 		0.0826
(1.00)
amp 1q44 201 (55%) 165 1e-05
(0.0055) 		0.00722
(1.00) 		0.162
(1.00) 		0.141
(1.00) 		0.00526
(1.00) 		0.118
(1.00) 		0.00445
(1.00) 		0.00575
(1.00) 		0.0194
(1.00) 		0.00221
(1.00)
amp 5p15 33 110 (30%) 256 2e-05
(0.0105) 		0.11
(1.00) 		0.692
(1.00) 		0.74
(1.00) 		0.0818
(1.00) 		0.59
(1.00) 		0.00478
(1.00) 		0.737
(1.00) 		0.249
(1.00) 		0.0242
(1.00)
amp 7p22 1 208 (57%) 158 1e-05
(0.0055) 		0.781
(1.00) 		0.63
(1.00) 		0.215
(1.00) 		0.0192
(1.00) 		0.0227
(1.00) 		0.0732
(1.00) 		0.41
(1.00) 		0.912
(1.00) 		0.475
(1.00)
amp 7q34 224 (61%) 142 2e-05
(0.0105) 		0.426
(1.00) 		0.237
(1.00) 		0.938
(1.00) 		0.139
(1.00) 		0.0946
(1.00) 		0.0965
(1.00) 		0.26
(1.00) 		0.0788
(1.00) 		0.419
(1.00)
amp 8q11 21 163 (45%) 203 1e-05
(0.0055) 		0.00262
(1.00) 		0.573
(1.00) 		0.245
(1.00) 		0.0184
(1.00) 		0.00468
(1.00) 		0.834
(1.00) 		0.858
(1.00) 		0.761
(1.00) 		0.743
(1.00)
amp 8q24 21 191 (52%) 175 1e-05
(0.0055) 		0.00606
(1.00) 		0.753
(1.00) 		0.936
(1.00) 		0.0122
(1.00) 		0.0562
(1.00) 		0.802
(1.00) 		0.751
(1.00) 		0.617
(1.00) 		0.767
(1.00)
amp 17q25 3 122 (33%) 244 0.00015
(0.078) 		0.0458
(1.00) 		0.0294
(1.00) 		0.0749
(1.00) 		0.412
(1.00) 		0.0894
(1.00) 		0.562
(1.00) 		0.0666
(1.00) 		0.239
(1.00) 		0.195
(1.00)
amp 20q13 33 187 (51%) 179 1e-05
(0.0055) 		0.00202
(1) 		0.827
(1.00) 		0.989
(1.00) 		0.00512
(1.00) 		0.0589
(1.00) 		0.179
(1.00) 		0.588
(1.00) 		0.797
(1.00) 		0.366
(1.00)
amp 22q13 2 151 (41%) 215 3e-05
(0.0157) 		0.0593
(1.00) 		0.973
(1.00) 		0.716
(1.00) 		0.336
(1.00) 		0.324
(1.00) 		0.808
(1.00) 		0.0862
(1.00) 		0.26
(1.00) 		0.316
(1.00)
del 1p36 31 81 (22%) 285 0.0359
(1.00) 		1e-05
(0.0055) 		0.58
(1.00) 		0.21
(1.00) 		0.0254
(1.00) 		0.00967
(1.00) 		0.062
(1.00) 		0.0603
(1.00) 		0.404
(1.00) 		0.857
(1.00)
del 6q22 31 215 (59%) 151 1e-05
(0.0055) 		0.00829
(1.00) 		0.959
(1.00) 		0.446
(1.00) 		0.00059
(0.301) 		0.117
(1.00) 		0.48
(1.00) 		0.534
(1.00) 		0.469
(1.00) 		0.27
(1.00)
del 9p23 249 (68%) 117 1e-05
(0.0055) 		0.0869
(1.00) 		0.455
(1.00) 		0.612
(1.00) 		0.00962
(1.00) 		0.193
(1.00) 		0.0344
(1.00) 		0.168
(1.00) 		0.824
(1.00) 		0.156
(1.00)
del 10p15 3 199 (54%) 167 1e-05
(0.0055) 		0.04
(1.00) 		0.884
(1.00) 		0.219
(1.00) 		0.00062
(0.316) 		0.00163
(0.812) 		0.0711
(1.00) 		0.456
(1.00) 		0.331
(1.00) 		0.272
(1.00)
del 10q21 1 217 (59%) 149 1e-05
(0.0055) 		0.493
(1.00) 		0.713
(1.00) 		0.149
(1.00) 		0.0113
(1.00) 		0.0224
(1.00) 		0.062
(1.00) 		0.251
(1.00) 		0.227
(1.00) 		0.762
(1.00)
del 10q23 31 230 (63%) 136 1e-05
(0.0055) 		0.144
(1.00) 		0.882
(1.00) 		0.208
(1.00) 		0.00259
(1.00) 		0.00157
(0.783) 		0.0306
(1.00) 		0.687
(1.00) 		0.343
(1.00) 		0.775
(1.00)
del 11q23 3 202 (55%) 164 1e-05
(0.0055) 		0.307
(1.00) 		0.902
(1.00) 		0.264
(1.00) 		0.122
(1.00) 		0.398
(1.00) 		0.443
(1.00) 		0.0338
(1.00) 		0.00986
(1.00) 		0.0856
(1.00)
del 14q23 3 120 (33%) 246 1e-05
(0.0055) 		0.9
(1.00) 		0.551
(1.00) 		0.246
(1.00) 		0.00672
(1.00) 		0.036
(1.00) 		0.00057
(0.291) 		0.179
(1.00) 		0.113
(1.00) 		0.0393
(1.00)
del 14q32 31 117 (32%) 249 1e-05
(0.0055) 		0.774
(1.00) 		0.589
(1.00) 		0.187
(1.00) 		0.00476
(1.00) 		0.0431
(1.00) 		0.00419
(1.00) 		0.187
(1.00) 		0.424
(1.00) 		0.186
(1.00)
del 17p13 3 135 (37%) 231 0.253
(1.00) 		0.00036
(0.185) 		0.364
(1.00) 		0.637
(1.00) 		0.0844
(1.00) 		0.231
(1.00) 		0.848
(1.00) 		0.361
(1.00) 		0.385
(1.00) 		0.216
(1.00)
del 19p13 3 104 (28%) 262 0.0204
(1.00) 		0.646
(1.00) 		0.00264
(1.00) 		0.0626
(1.00) 		0.00044
(0.226) 		0.206
(1.00) 		0.787
(1.00) 		0.0992
(1.00) 		0.185
(1.00) 		0.462
(1.00)
del xp21 1 87 (24%) 279 0.122
(1.00) 		1e-05
(0.0055) 		0.0461
(1.00) 		0.109
(1.00) 		0.00535
(1.00) 		0.00087
(0.439) 		0.00071
(0.361) 		0.0477
(1.00) 		0.00137
(0.686) 		0.24
(1.00)
amp 1p12 121 (33%) 245 0.0357
(1.00) 		0.881
(1.00) 		0.708
(1.00) 		0.882
(1.00) 		0.275
(1.00) 		0.383
(1.00) 		0.62
(1.00) 		0.527
(1.00) 		0.779
(1.00) 		0.613
(1.00)
amp 3p13 103 (28%) 263 0.123
(1.00) 		0.499
(1.00) 		0.0651
(1.00) 		0.0531
(1.00) 		0.581
(1.00) 		0.26
(1.00) 		0.48
(1.00) 		0.67
(1.00) 		0.841
(1.00) 		0.871
(1.00)
amp 4q12 65 (18%) 301 0.00296
(1.00) 		0.156
(1.00) 		0.0808
(1.00) 		0.535
(1.00) 		0.817
(1.00) 		0.183
(1.00) 		0.0614
(1.00) 		0.029
(1.00) 		0.275
(1.00) 		0.51
(1.00)
amp 6q12 80 (22%) 286 0.548
(1.00) 		0.535
(1.00) 		0.527
(1.00) 		0.0814
(1.00) 		0.515
(1.00) 		0.204
(1.00) 		0.214
(1.00) 		0.167
(1.00) 		0.35
(1.00) 		0.105
(1.00)
amp 11q13 3 69 (19%) 297 0.126
(1.00) 		0.0808
(1.00) 		0.907
(1.00) 		0.84
(1.00) 		0.18
(1.00) 		0.781
(1.00) 		0.158
(1.00) 		0.111
(1.00) 		0.558
(1.00) 		0.247
(1.00)
amp 12q14 1 58 (16%) 308 0.00314
(1.00) 		0.36
(1.00) 		0.87
(1.00) 		0.287
(1.00) 		0.0229
(1.00) 		0.0988
(1.00) 		0.769
(1.00) 		0.215
(1.00) 		0.171
(1.00) 		0.644
(1.00)
amp 12q15 59 (16%) 307 0.0742
(1.00) 		0.14
(1.00) 		0.609
(1.00) 		0.427
(1.00) 		0.0474
(1.00) 		0.0136
(1.00) 		0.663
(1.00) 		0.293
(1.00) 		0.37
(1.00) 		0.315
(1.00)
amp 15q26 2 119 (33%) 247 0.00053
(0.271) 		0.182
(1.00) 		0.937
(1.00) 		0.808
(1.00) 		0.131
(1.00) 		0.245
(1.00) 		0.808
(1.00) 		0.237
(1.00) 		0.164
(1.00) 		0.443
(1.00)
amp 19p13 2 69 (19%) 297 0.00081
(0.411) 		0.131
(1.00) 		0.443
(1.00) 		0.957
(1.00) 		0.00171
(0.848) 		0.0162
(1.00) 		0.951
(1.00) 		0.285
(1.00) 		0.132
(1.00) 		0.738
(1.00)
del 2q37 3 93 (25%) 273 0.42
(1.00) 		0.136
(1.00) 		0.167
(1.00) 		0.02
(1.00) 		0.00598
(1.00) 		0.00644
(1.00) 		0.0315
(1.00) 		0.00943
(1.00) 		0.263
(1.00) 		0.308
(1.00)
del 3p25 1 71 (19%) 295 0.175
(1.00) 		0.244
(1.00) 		0.423
(1.00) 		0.216
(1.00) 		0.793
(1.00) 		0.542
(1.00) 		0.356
(1.00) 		0.395
(1.00) 		0.322
(1.00) 		0.169
(1.00)
del 3q13 31 62 (17%) 304 0.162
(1.00) 		0.0683
(1.00) 		0.408
(1.00) 		0.116
(1.00) 		0.0208
(1.00) 		0.345
(1.00) 		0.254
(1.00) 		0.279
(1.00) 		0.078
(1.00) 		0.55
(1.00)
del 4p16 3 91 (25%) 275 0.549
(1.00) 		0.0915
(1.00) 		0.65
(1.00) 		0.708
(1.00) 		0.129
(1.00) 		0.0377
(1.00) 		0.666
(1.00) 		0.251
(1.00) 		0.431
(1.00) 		0.982
(1.00)
del 4q34 3 110 (30%) 256 0.267
(1.00) 		0.056
(1.00) 		0.516
(1.00) 		0.555
(1.00) 		0.0802
(1.00) 		0.0194
(1.00) 		0.679
(1.00) 		0.00916
(1.00) 		0.122
(1.00) 		0.174
(1.00)
del 5p15 31 79 (22%) 287 0.65
(1.00) 		0.391
(1.00) 		0.548
(1.00) 		0.541
(1.00) 		0.54
(1.00) 		0.257
(1.00) 		0.675
(1.00) 		0.364
(1.00) 		0.0913
(1.00) 		0.904
(1.00)
del 5q12 1 97 (27%) 269 0.234
(1.00) 		0.292
(1.00) 		0.388
(1.00) 		0.115
(1.00) 		0.396
(1.00) 		0.144
(1.00) 		0.301
(1.00) 		0.524
(1.00) 		0.34
(1.00) 		0.652
(1.00)
del 5q31 3 131 (36%) 235 0.275
(1.00) 		0.00149
(0.745) 		0.622
(1.00) 		0.303
(1.00) 		0.71
(1.00) 		0.337
(1.00) 		0.832
(1.00) 		0.638
(1.00) 		0.391
(1.00) 		0.474
(1.00)
del 8p23 3 89 (24%) 277 0.0091
(1.00) 		0.0776
(1.00) 		0.207
(1.00) 		0.159
(1.00) 		0.0439
(1.00) 		0.725
(1.00) 		0.372
(1.00) 		0.252
(1.00) 		0.0848
(1.00) 		0.0819
(1.00)
del 11p15 5 114 (31%) 252 0.0198
(1.00) 		0.0479
(1.00) 		0.621
(1.00) 		0.714
(1.00) 		0.595
(1.00) 		0.168
(1.00) 		0.479
(1.00) 		0.25
(1.00) 		0.0294
(1.00) 		0.338
(1.00)
del 12q23 3 92 (25%) 274 0.013
(1.00) 		0.0283
(1.00) 		0.966
(1.00) 		0.818
(1.00) 		0.49
(1.00) 		0.404
(1.00) 		0.299
(1.00) 		0.243
(1.00) 		0.469
(1.00) 		0.456
(1.00)
del 13q34 85 (23%) 281 0.951
(1.00) 		0.0204
(1.00) 		0.0656
(1.00) 		0.744
(1.00) 		0.774
(1.00) 		0.498
(1.00) 		0.649
(1.00) 		0.099
(1.00) 		0.293
(1.00) 		0.698
(1.00)
del 15q13 3 84 (23%) 282 0.0488
(1.00) 		0.0086
(1.00) 		0.0916
(1.00) 		0.308
(1.00) 		0.473
(1.00) 		0.0116
(1.00) 		0.652
(1.00) 		0.869
(1.00) 		0.0156
(1.00) 		0.762
(1.00)
del 15q21 1 91 (25%) 275 0.0767
(1.00) 		0.1
(1.00) 		0.539
(1.00) 		0.334
(1.00) 		0.646
(1.00) 		0.0593
(1.00) 		0.861
(1.00) 		0.519
(1.00) 		0.116
(1.00) 		0.849
(1.00)
del 16p13 3 62 (17%) 304 0.559
(1.00) 		0.0975
(1.00) 		0.0123
(1.00) 		0.338
(1.00) 		0.158
(1.00) 		0.919
(1.00) 		0.366
(1.00) 		0.333
(1.00) 		0.0451
(1.00) 		0.0892
(1.00)
del 16q12 1 117 (32%) 249 0.263
(1.00) 		0.343
(1.00) 		0.0206
(1.00) 		0.681
(1.00) 		0.018
(1.00) 		0.496
(1.00) 		0.186
(1.00) 		0.0217
(1.00) 		0.264
(1.00) 		0.0597
(1.00)
del 16q24 3 133 (36%) 233 0.11
(1.00) 		0.67
(1.00) 		0.144
(1.00) 		0.908
(1.00) 		0.00599
(1.00) 		0.106
(1.00) 		0.0841
(1.00) 		0.0908
(1.00) 		0.0134
(1.00) 		0.0402
(1.00)
'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 2(1Q21.3) MUTATED 92 51 60
AMP PEAK 2(1Q21.3) WILD-TYPE 9 88 66

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 = 0.0055

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 3(1Q44) MUTATED 90 50 61
AMP PEAK 3(1Q44) WILD-TYPE 11 89 65

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

'amp_5p15.33' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 6(5P15.33) MUTATED 31 24 55
AMP PEAK 6(5P15.33) WILD-TYPE 70 115 71

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

'amp_5q35.3' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.1

Table S4.  Gene #7: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 7(5Q35.3) MUTATED 21 9 29
AMP PEAK 7(5Q35.3) WILD-TYPE 80 130 97

Figure S4.  Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.17

Table S5.  Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 142 92
AMP PEAK 7(5Q35.3) MUTATED 19 13 27
AMP PEAK 7(5Q35.3) WILD-TYPE 110 129 65

Figure S5.  Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S6.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 8(6P24.3) MUTATED 78 57 75
AMP PEAK 8(6P24.3) WILD-TYPE 23 82 51

Figure S6.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p24.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S7.  Gene #8: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 142 92
AMP PEAK 8(6P24.3) MUTATED 79 59 69
AMP PEAK 8(6P24.3) WILD-TYPE 50 83 23

Figure S7.  Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S8.  Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 10(7P22.1) MUTATED 62 55 91
AMP PEAK 10(7P22.1) WILD-TYPE 39 84 35

Figure S8.  Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q34' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S9.  Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 11(7Q34) MUTATED 64 66 94
AMP PEAK 11(7Q34) WILD-TYPE 37 73 32

Figure S9.  Get High-res Image Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S10.  Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 12(8Q11.21) MUTATED 35 39 89
AMP PEAK 12(8Q11.21) WILD-TYPE 66 100 37

Figure S10.  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 = 0.0055

Table S11.  Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 13(8Q24.21) MUTATED 47 48 96
AMP PEAK 13(8Q24.21) WILD-TYPE 54 91 30

Figure S11.  Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q31.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S12.  Gene #17: 'amp_13q31.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 17(13Q31.3) MUTATED 34 19 51
AMP PEAK 17(13Q31.3) WILD-TYPE 67 120 75

Figure S12.  Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q31.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S13.  Gene #17: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 142 92
AMP PEAK 17(13Q31.3) MUTATED 36 22 44
AMP PEAK 17(13Q31.3) WILD-TYPE 93 120 48

Figure S13.  Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q31.3' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.12

Table S14.  Gene #17: 'amp_13q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 102 121
AMP PEAK 17(13Q31.3) MUTATED 33 20 51
AMP PEAK 17(13Q31.3) WILD-TYPE 109 82 70

Figure S14.  Get High-res Image Gene #17: 'amp_13q31.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.078

Table S15.  Gene #19: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 19(17Q25.3) MUTATED 50 33 39
AMP PEAK 19(17Q25.3) WILD-TYPE 51 106 87

Figure S15.  Get High-res Image Gene #19: '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 = 0.0055

Table S16.  Gene #21: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 21(20Q13.33) MUTATED 64 41 82
AMP PEAK 21(20Q13.33) WILD-TYPE 37 98 44

Figure S16.  Get High-res Image Gene #21: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q13.2' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S17.  Gene #22: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
AMP PEAK 22(22Q13.2) MUTATED 54 37 60
AMP PEAK 22(22Q13.2) WILD-TYPE 47 102 66

Figure S17.  Get High-res Image Gene #22: '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 = 0.0055

Table S18.  Gene #23: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 142 92
DEL PEAK 1(1P36.31) MUTATED 19 22 39
DEL PEAK 1(1P36.31) WILD-TYPE 110 120 53

Figure S18.  Get High-res Image Gene #23: '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 = 0.0055

Table S19.  Gene #24: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 142 92
DEL PEAK 2(1P22.1) MUTATED 21 31 44
DEL PEAK 2(1P22.1) WILD-TYPE 108 111 48

Figure S19.  Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.047

Table S20.  Gene #24: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 102 121
DEL PEAK 2(1P22.1) MUTATED 36 14 47
DEL PEAK 2(1P22.1) WILD-TYPE 106 88 74

Figure S20.  Get High-res Image Gene #24: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.11

Table S21.  Gene #24: 'del_1p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 166 91
DEL PEAK 2(1P22.1) MUTATED 27 31 39
DEL PEAK 2(1P22.1) WILD-TYPE 81 135 52

Figure S21.  Get High-res Image Gene #24: '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 = 0.0055

Table S22.  Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 11(6Q22.31) MUTATED 81 47 87
DEL PEAK 11(6Q22.31) WILD-TYPE 20 92 39

Figure S22.  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 = 0.0055

Table S23.  Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 12(6Q26) MUTATED 82 50 89
DEL PEAK 12(6Q26) WILD-TYPE 19 89 37

Figure S23.  Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

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

Table S24.  Gene #34: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 102 121
DEL PEAK 12(6Q26) MUTATED 92 45 84
DEL PEAK 12(6Q26) WILD-TYPE 50 57 37

Figure S24.  Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S25.  Gene #36: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 14(9P23) MUTATED 63 80 106
DEL PEAK 14(9P23) WILD-TYPE 38 59 20

Figure S25.  Get High-res Image Gene #36: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S26.  Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 15(9P21.3) MUTATED 77 86 115
DEL PEAK 15(9P21.3) WILD-TYPE 24 53 11

Figure S26.  Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S27.  Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 102 121
DEL PEAK 15(9P21.3) MUTATED 106 64 107
DEL PEAK 15(9P21.3) WILD-TYPE 36 38 14

Figure S27.  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 = 0.0055

Table S28.  Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 16(10P15.3) MUTATED 54 48 97
DEL PEAK 16(10P15.3) WILD-TYPE 47 91 29

Figure S28.  Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S29.  Gene #39: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 17(10Q21.1) MUTATED 48 61 108
DEL PEAK 17(10Q21.1) WILD-TYPE 53 78 18

Figure S29.  Get High-res Image Gene #39: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S30.  Gene #40: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 18(10Q23.31) MUTATED 53 66 111
DEL PEAK 18(10Q23.31) WILD-TYPE 48 73 15

Figure S30.  Get High-res Image Gene #40: '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 = 0.0055

Table S31.  Gene #41: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 19(10Q26.3) MUTATED 51 71 114
DEL PEAK 19(10Q26.3) WILD-TYPE 50 68 12

Figure S31.  Get High-res Image Gene #41: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.063

Table S32.  Gene #41: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 102 121
DEL PEAK 19(10Q26.3) MUTATED 81 59 96
DEL PEAK 19(10Q26.3) WILD-TYPE 61 43 25

Figure S32.  Get High-res Image Gene #41: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S33.  Gene #43: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 21(11Q23.3) MUTATED 77 63 62
DEL PEAK 21(11Q23.3) WILD-TYPE 24 76 64

Figure S33.  Get High-res Image Gene #43: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S34.  Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 24(14Q23.3) MUTATED 30 29 61
DEL PEAK 24(14Q23.3) WILD-TYPE 71 110 65

Figure S34.  Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S35.  Gene #47: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
DEL PEAK 25(14Q32.31) MUTATED 28 27 62
DEL PEAK 25(14Q32.31) WILD-TYPE 73 112 64

Figure S35.  Get High-res Image Gene #47: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.19

Table S36.  Gene #53: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 142 92
DEL PEAK 31(17P13.3) MUTATED 59 57 19
DEL PEAK 31(17P13.3) WILD-TYPE 70 85 73

Figure S36.  Get High-res Image Gene #53: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.23

Table S37.  Gene #54: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 102 121
DEL PEAK 32(19P13.3) MUTATED 57 22 25
DEL PEAK 32(19P13.3) WILD-TYPE 85 80 96

Figure S37.  Get High-res Image Gene #54: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0055

Table S38.  Gene #55: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 142 92
DEL PEAK 33(XP21.1) MUTATED 47 15 24
DEL PEAK 33(XP21.1) WILD-TYPE 82 127 68

Figure S38.  Get High-res Image Gene #55: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 366

  • Number of significantly focal cnvs = 55

  • 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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