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 40 focal events and 10 molecular subtypes across 292 patients, 25 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q cnv correlated to 'CN_CNMF'.

  • 6p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 6q cnv correlated to 'CN_CNMF'.

  • 7p cnv correlated to 'CN_CNMF'.

  • 7q cnv correlated to 'CN_CNMF'.

  • 8q cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 9p cnv correlated to 'CN_CNMF'.

  • 10p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 10q cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 11q cnv correlated to 'CN_CNMF'.

  • 12p cnv correlated to 'CN_CNMF'.

  • 13q cnv correlated to 'CN_CNMF'.

  • 14q cnv correlated to 'CN_CNMF'.

  • 19p cnv correlated to 'CN_CNMF'.

  • 19q cnv correlated to 'CN_CNMF'.

  • 20p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 20q cnv correlated to 'CN_CNMF'.

  • xq cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 40 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, 25 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
10q 182 (62%) 110 1.9e-09
(7.59e-07) 		0.0509
(1.00) 		0.794
(1.00) 		0.0893
(1.00) 		4.4e-06
(0.00172) 		2.13e-05
(0.00826) 		0.737
(1.00) 		0.0503
(1.00) 		0.561
(1.00) 		0.484
(1.00)
6p 173 (59%) 119 6.65e-07
(0.000264) 		5.69e-05
(0.0219) 		0.793
(1.00) 		0.0729
(1.00) 		0.13
(1.00) 		0.0166
(1.00) 		0.351
(1.00) 		0.1
(1.00) 		0.399
(1.00) 		0.193
(1.00)
8q 155 (53%) 137 4.15e-06
(0.00163) 		0.00511
(1.00) 		0.292
(1.00) 		0.909
(1.00) 		0.000357
(0.135) 		0.0447
(1.00) 		0.345
(1.00) 		0.305
(1.00) 		0.227
(1.00) 		0.566
(1.00)
10p 173 (59%) 119 1.35e-08
(5.37e-06) 		0.0396
(1.00) 		0.905
(1.00) 		0.208
(1.00) 		2.82e-05
(0.0109) 		0.000678
(0.254) 		0.696
(1.00) 		0.00546
(1.00) 		0.686
(1.00) 		0.133
(1.00)
20p 140 (48%) 152 1.74e-05
(0.00677) 		0.014
(1.00) 		0.778
(1.00) 		0.826
(1.00) 		0.00051
(0.192) 		0.0247
(1.00) 		0.316
(1.00) 		0.0273
(1.00) 		0.157
(1.00) 		0.392
(1.00)
xq 103 (35%) 189 0.00259
(0.953) 		1.43e-07
(5.69e-05) 		0.101
(1.00) 		0.165
(1.00) 		7.17e-05
(0.0275) 		0.00258
(0.95) 		0.142
(1.00) 		0.392
(1.00) 		0.326
(1.00) 		0.561
(1.00)
1q 150 (51%) 142 1.89e-06
(0.000746) 		0.061
(1.00) 		0.16
(1.00) 		0.631
(1.00) 		0.00537
(1.00) 		0.153
(1.00) 		0.474
(1.00) 		0.247
(1.00) 		0.181
(1.00) 		0.123
(1.00)
6q 183 (63%) 109 0.000322
(0.123) 		0.204
(1.00) 		0.93
(1.00) 		0.213
(1.00) 		0.0201
(1.00) 		0.112
(1.00) 		0.637
(1.00) 		0.155
(1.00) 		0.88
(1.00) 		0.0849
(1.00)
7p 171 (59%) 121 2.96e-06
(0.00116) 		0.666
(1.00) 		0.0882
(1.00) 		0.718
(1.00) 		0.019
(1.00) 		0.188
(1.00) 		0.354
(1.00) 		0.26
(1.00) 		0.525
(1.00) 		0.535
(1.00)
7q 169 (58%) 123 1.02e-06
(0.000404) 		0.887
(1.00) 		0.326
(1.00) 		0.874
(1.00) 		0.0307
(1.00) 		0.28
(1.00) 		0.807
(1.00) 		0.202
(1.00) 		0.79
(1.00) 		0.51
(1.00)
9p 208 (71%) 84 8.3e-07
(0.000329) 		0.0064
(1.00) 		0.269
(1.00) 		0.473
(1.00) 		0.00271
(0.996) 		0.0178
(1.00) 		0.587
(1.00) 		0.122
(1.00) 		0.882
(1.00) 		0.509
(1.00)
11q 141 (48%) 151 0.000113
(0.0434) 		0.209
(1.00) 		0.804
(1.00) 		0.526
(1.00) 		0.0325
(1.00) 		0.197
(1.00) 		0.504
(1.00) 		0.21
(1.00) 		0.773
(1.00) 		0.892
(1.00)
12p 93 (32%) 199 0.000449
(0.17) 		0.04
(1.00) 		0.898
(1.00) 		0.768
(1.00) 		0.0104
(1.00) 		0.0256
(1.00) 		0.978
(1.00) 		0.568
(1.00) 		0.393
(1.00) 		0.746
(1.00)
13q 136 (47%) 156 0.000234
(0.0893) 		0.12
(1.00) 		0.0903
(1.00) 		0.965
(1.00) 		0.0389
(1.00) 		0.372
(1.00) 		0.496
(1.00) 		0.236
(1.00) 		0.771
(1.00) 		0.119
(1.00)
14q 123 (42%) 169 3.26e-05
(0.0126) 		0.302
(1.00) 		0.864
(1.00) 		0.682
(1.00) 		0.00804
(1.00) 		0.107
(1.00) 		0.441
(1.00) 		0.367
(1.00) 		0.559
(1.00) 		0.8
(1.00)
19p 103 (35%) 189 0.000357
(0.135) 		0.0154
(1.00) 		0.633
(1.00) 		0.233
(1.00) 		0.0156
(1.00) 		0.224
(1.00) 		0.382
(1.00) 		0.989
(1.00) 		0.241
(1.00) 		0.774
(1.00)
19q 102 (35%) 190 0.00053
(0.199) 		0.00572
(1.00) 		0.513
(1.00) 		0.102
(1.00) 		0.00751
(1.00) 		0.0164
(1.00) 		0.297
(1.00) 		0.965
(1.00) 		0.358
(1.00) 		0.774
(1.00)
20q 152 (52%) 140 1.52e-05
(0.00594) 		0.0274
(1.00) 		0.831
(1.00) 		0.764
(1.00) 		0.0111
(1.00) 		0.225
(1.00) 		0.762
(1.00) 		0.0267
(1.00) 		0.243
(1.00) 		0.56
(1.00)
1p 102 (35%) 190 0.0411
(1.00) 		0.153
(1.00) 		0.756
(1.00) 		0.823
(1.00) 		0.00332
(1.00) 		0.0275
(1.00) 		0.273
(1.00) 		0.16
(1.00) 		0.207
(1.00) 		0.831
(1.00)
2p 94 (32%) 198 0.0301
(1.00) 		0.185
(1.00) 		0.21
(1.00) 		0.18
(1.00) 		0.331
(1.00) 		0.189
(1.00) 		0.861
(1.00) 		0.401
(1.00) 		0.566
(1.00) 		0.375
(1.00)
2q 92 (32%) 200 0.0555
(1.00) 		0.16
(1.00) 		0.271
(1.00) 		0.497
(1.00) 		0.17
(1.00) 		0.0785
(1.00) 		0.736
(1.00) 		0.348
(1.00) 		0.392
(1.00) 		0.213
(1.00)
3p 93 (32%) 199 0.713
(1.00) 		0.672
(1.00) 		0.67
(1.00) 		0.195
(1.00) 		0.0664
(1.00) 		0.0737
(1.00) 		0.271
(1.00) 		0.0243
(1.00) 		0.0283
(1.00) 		0.472
(1.00)
3q 92 (32%) 200 0.391
(1.00) 		0.825
(1.00) 		0.379
(1.00) 		0.124
(1.00) 		0.0359
(1.00) 		0.114
(1.00) 		0.448
(1.00) 		0.00797
(1.00) 		0.0932
(1.00) 		0.752
(1.00)
4p 106 (36%) 186 0.0649
(1.00) 		0.265
(1.00) 		0.691
(1.00) 		0.27
(1.00) 		0.255
(1.00) 		0.0689
(1.00) 		0.828
(1.00) 		0.757
(1.00) 		0.893
(1.00) 		0.9
(1.00)
4q 101 (35%) 191 0.162
(1.00) 		0.63
(1.00) 		0.306
(1.00) 		0.258
(1.00) 		0.0705
(1.00) 		0.0678
(1.00) 		0.192
(1.00) 		0.382
(1.00) 		0.349
(1.00) 		0.482
(1.00)
5p 123 (42%) 169 0.011
(1.00) 		0.227
(1.00) 		0.96
(1.00) 		0.56
(1.00) 		0.846
(1.00) 		0.913
(1.00) 		0.132
(1.00) 		0.267
(1.00) 		0.229
(1.00) 		0.364
(1.00)
5q 118 (40%) 174 0.102
(1.00) 		0.194
(1.00) 		0.196
(1.00) 		0.166
(1.00) 		0.856
(1.00) 		0.757
(1.00) 		0.15
(1.00) 		0.318
(1.00) 		0.0558
(1.00) 		0.376
(1.00)
8p 146 (50%) 146 0.00113
(0.422) 		0.195
(1.00) 		0.397
(1.00) 		0.828
(1.00) 		0.00475
(1.00) 		0.142
(1.00) 		0.549
(1.00) 		0.221
(1.00) 		0.483
(1.00) 		0.649
(1.00)
9q 170 (58%) 122 0.113
(1.00) 		0.0692
(1.00) 		0.222
(1.00) 		0.0156
(1.00) 		0.0329
(1.00) 		0.284
(1.00) 		0.466
(1.00) 		0.447
(1.00) 		0.803
(1.00) 		0.346
(1.00)
11p 131 (45%) 161 0.0028
(1.00) 		0.124
(1.00) 		0.835
(1.00) 		0.728
(1.00) 		0.00171
(0.635) 		0.0267
(1.00) 		0.809
(1.00) 		0.212
(1.00) 		0.719
(1.00) 		0.991
(1.00)
12q 81 (28%) 211 0.0153
(1.00) 		0.15
(1.00) 		0.974
(1.00) 		0.689
(1.00) 		0.0979
(1.00) 		0.149
(1.00) 		0.981
(1.00) 		0.863
(1.00) 		0.811
(1.00) 		0.976
(1.00)
15q 107 (37%) 185 0.0181
(1.00) 		0.329
(1.00) 		0.234
(1.00) 		0.738
(1.00) 		0.0213
(1.00) 		0.0324
(1.00) 		0.231
(1.00) 		0.00229
(0.846) 		0.253
(1.00) 		0.162
(1.00)
16p 98 (34%) 194 0.00513
(1.00) 		0.00184
(0.682) 		0.103
(1.00) 		0.552
(1.00) 		0.0525
(1.00) 		0.206
(1.00) 		0.979
(1.00) 		0.299
(1.00) 		0.931
(1.00) 		0.983
(1.00)
16q 120 (41%) 172 0.0143
(1.00) 		0.0436
(1.00) 		0.0809
(1.00) 		0.72
(1.00) 		0.287
(1.00) 		0.486
(1.00) 		0.837
(1.00) 		0.405
(1.00) 		0.794
(1.00) 		0.822
(1.00)
17p 131 (45%) 161 0.417
(1.00) 		0.723
(1.00) 		0.673
(1.00) 		0.741
(1.00) 		0.478
(1.00) 		0.897
(1.00) 		0.809
(1.00) 		0.973
(1.00) 		0.852
(1.00) 		0.924
(1.00)
17q 105 (36%) 187 0.298
(1.00) 		0.399
(1.00) 		0.217
(1.00) 		0.17
(1.00) 		0.525
(1.00) 		0.66
(1.00) 		0.808
(1.00) 		0.842
(1.00) 		0.285
(1.00) 		0.182
(1.00)
18p 131 (45%) 161 0.0371
(1.00) 		0.437
(1.00) 		0.926
(1.00) 		0.634
(1.00) 		0.125
(1.00) 		0.281
(1.00) 		0.77
(1.00) 		0.595
(1.00) 		0.212
(1.00) 		0.935
(1.00)
18q 117 (40%) 175 0.105
(1.00) 		0.624
(1.00) 		0.988
(1.00) 		0.588
(1.00) 		0.474
(1.00) 		0.521
(1.00) 		0.824
(1.00) 		0.441
(1.00) 		0.65
(1.00) 		0.896
(1.00)
21q 108 (37%) 184 0.231
(1.00) 		0.107
(1.00) 		0.323
(1.00) 		0.963
(1.00) 		0.144
(1.00) 		0.205
(1.00) 		0.459
(1.00) 		0.574
(1.00) 		0.208
(1.00) 		0.555
(1.00)
22q 136 (47%) 156 0.00161
(0.6) 		0.103
(1.00) 		0.929
(1.00) 		0.971
(1.00) 		0.316
(1.00) 		0.387
(1.00) 		0.716
(1.00) 		0.397
(1.00) 		0.676
(1.00) 		0.855
(1.00)
'1q' versus 'CN_CNMF'

P value = 1.89e-06 (Fisher's exact test), Q value = 0.00075

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
1Q MUTATED 76 39 35
1Q WILD-TYPE 34 41 67

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

'6p' versus 'CN_CNMF'

P value = 6.65e-07 (Fisher's exact test), Q value = 0.00026

Table S2.  Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
6P MUTATED 86 42 45
6P WILD-TYPE 24 38 57

Figure S2.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

'6p' versus 'METHLYATION_CNMF'

P value = 5.69e-05 (Fisher's exact test), Q value = 0.022

Table S3.  Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 108 112
6P MUTATED 56 66 51
6P WILD-TYPE 16 42 61

Figure S3.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q' versus 'CN_CNMF'

P value = 0.000322 (Fisher's exact test), Q value = 0.12

Table S4.  Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
6Q MUTATED 79 56 48
6Q WILD-TYPE 31 24 54

Figure S4.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'CN_CNMF'

P value = 2.96e-06 (Fisher's exact test), Q value = 0.0012

Table S5.  Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
7P MUTATED 65 63 43
7P WILD-TYPE 45 17 59

Figure S5.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

'7q' versus 'CN_CNMF'

P value = 1.02e-06 (Fisher's exact test), Q value = 4e-04

Table S6.  Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
7Q MUTATED 62 64 43
7Q WILD-TYPE 48 16 59

Figure S6.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

'8q' versus 'CN_CNMF'

P value = 4.15e-06 (Fisher's exact test), Q value = 0.0016

Table S7.  Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
8Q MUTATED 69 52 34
8Q WILD-TYPE 41 28 68

Figure S7.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

'8q' versus 'MRNASEQ_CNMF'

P value = 0.000357 (Fisher's exact test), Q value = 0.14

Table S8.  Gene #16: '8q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 79 110
8Q MUTATED 64 30 57
8Q WILD-TYPE 30 49 53

Figure S8.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p' versus 'CN_CNMF'

P value = 8.3e-07 (Fisher's exact test), Q value = 0.00033

Table S9.  Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
9P MUTATED 82 71 55
9P WILD-TYPE 28 9 47

Figure S9.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'CN_CNMF'

P value = 1.35e-08 (Fisher's exact test), Q value = 5.4e-06

Table S10.  Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
10P MUTATED 67 66 40
10P WILD-TYPE 43 14 62

Figure S10.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.011

Table S11.  Gene #19: '10p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 79 110
10P MUTATED 73 37 58
10P WILD-TYPE 21 42 52

Figure S11.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q' versus 'CN_CNMF'

P value = 1.9e-09 (Fisher's exact test), Q value = 7.6e-07

Table S12.  Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
10Q MUTATED 68 70 44
10Q WILD-TYPE 42 10 58

Figure S12.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'MRNASEQ_CNMF'

P value = 4.4e-06 (Fisher's exact test), Q value = 0.0017

Table S13.  Gene #20: '10q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 79 110
10Q MUTATED 77 41 58
10Q WILD-TYPE 17 38 52

Figure S13.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.13e-05 (Fisher's exact test), Q value = 0.0083

Table S14.  Gene #20: '10q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 122 87
10Q MUTATED 62 65 49
10Q WILD-TYPE 12 57 38

Figure S14.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q' versus 'CN_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.043

Table S15.  Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
11Q MUTATED 63 46 32
11Q WILD-TYPE 47 34 70

Figure S15.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

'12p' versus 'CN_CNMF'

P value = 0.000449 (Fisher's exact test), Q value = 0.17

Table S16.  Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
12P MUTATED 42 33 18
12P WILD-TYPE 68 47 84

Figure S16.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'CN_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.089

Table S17.  Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
13Q MUTATED 61 44 31
13Q WILD-TYPE 49 36 71

Figure S17.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

'14q' versus 'CN_CNMF'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.013

Table S18.  Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
14Q MUTATED 43 50 30
14Q WILD-TYPE 67 30 72

Figure S18.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

'19p' versus 'CN_CNMF'

P value = 0.000357 (Fisher's exact test), Q value = 0.14

Table S19.  Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
19P MUTATED 45 37 21
19P WILD-TYPE 65 43 81

Figure S19.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

'19q' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.2

Table S20.  Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
19Q MUTATED 45 36 21
19Q WILD-TYPE 65 44 81

Figure S20.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

'20p' versus 'CN_CNMF'

P value = 1.74e-05 (Fisher's exact test), Q value = 0.0068

Table S21.  Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
20P MUTATED 58 51 31
20P WILD-TYPE 52 29 71

Figure S21.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

'20p' versus 'MRNASEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.19

Table S22.  Gene #36: '20p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 79 110
20P MUTATED 60 29 46
20P WILD-TYPE 34 50 64

Figure S22.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q' versus 'CN_CNMF'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.0059

Table S23.  Gene #37: '20q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 80 102
20Q MUTATED 68 50 34
20Q WILD-TYPE 42 30 68

Figure S23.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #1: 'CN_CNMF'

'xq' versus 'METHLYATION_CNMF'

P value = 1.43e-07 (Fisher's exact test), Q value = 5.7e-05

Table S24.  Gene #40: 'xq' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 108 112
XQ MUTATED 32 53 18
XQ WILD-TYPE 40 55 94

Figure S24.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq' versus 'MRNASEQ_CNMF'

P value = 7.17e-05 (Fisher's exact test), Q value = 0.028

Table S25.  Gene #40: 'xq' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 79 110
XQ MUTATED 42 13 46
XQ WILD-TYPE 52 66 64

Figure S25.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 292

  • Number of significantly focal cnvs = 40

  • 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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