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 221 patients, 30 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 2p cnv correlated to 'CN_CNMF'.

  • 2q cnv correlated to 'CN_CNMF'.

  • 3p cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 3q cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 4p cnv correlated to 'CN_CNMF'.

  • 4q cnv correlated to 'CN_CNMF'.

  • 5p cnv correlated to 'CN_CNMF'.

  • 5q cnv correlated to 'CN_CNMF'.

  • 6q cnv correlated to 'CN_CNMF'.

  • 7p cnv correlated to 'CN_CNMF'.

  • 7q cnv correlated to 'CN_CNMF'.

  • 8p cnv correlated to 'CN_CNMF'.

  • 10p cnv correlated to 'CN_CNMF'.

  • 10q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 11p cnv correlated to 'CN_CNMF'.

  • 11q cnv correlated to 'CN_CNMF'.

  • 12p cnv correlated to 'CN_CNMF'.

  • 16p cnv correlated to 'CN_CNMF'.

  • 16q cnv correlated to 'CN_CNMF'.

  • 17p cnv correlated to 'CN_CNMF'.

  • 18p cnv correlated to 'CN_CNMF'.

  • 18q cnv correlated to 'CN_CNMF'.

  • 19p cnv correlated to 'CN_CNMF'.

  • 19q cnv correlated to 'CN_CNMF'.

  • 20q cnv correlated to 'CN_CNMF'.

  • 21q cnv correlated to 'CN_CNMF'.

  • 22q cnv correlated to 'CN_CNMF' and 'METHLYATION_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, 30 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 Chi-square test Fisher's exact test Chi-square 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
3q 109 (49%) 112 0.000573
(0.213) 		0.841
(1.00) 		0.582
(1.00) 		0.707
(1.00) 		0.548
(1.00) 		0.622
(1.00) 		0.015
(1.00) 		0.0304
(1.00) 		0.000117
(0.0445) 		0.0105
(1.00)
10q 93 (42%) 128 9.94e-06
(0.00388) 		0.000278
(0.104) 		0.41
(1.00) 		0.944
(1.00) 		0.237
(1.00) 		0.145
(1.00) 		0.2
(1.00) 		0.0956
(1.00) 		0.458
(1.00) 		0.19
(1.00)
22q 116 (52%) 105 4.24e-10
(1.7e-07) 		0.000263
(0.0986) 		0.825
(1.00) 		0.0768
(1.00) 		0.0509
(1.00) 		0.458
(1.00) 		0.34
(1.00) 		0.0995
(1.00) 		0.254
(1.00) 		0.0272
(1.00)
2p 89 (40%) 132 5.84e-08
(2.31e-05) 		0.02
(1.00) 		0.532
(1.00) 		0.888
(1.00) 		0.0279
(1.00) 		0.0433
(1.00) 		0.107
(1.00) 		0.0692
(1.00) 		0.359
(1.00) 		0.0063
(1.00)
2q 81 (37%) 140 2.27e-06
(0.000894) 		0.00492
(1.00) 		0.777
(1.00) 		0.824
(1.00) 		0.0413
(1.00) 		0.0585
(1.00) 		0.808
(1.00) 		0.636
(1.00) 		0.851
(1.00) 		0.082
(1.00)
3p 104 (47%) 117 0.000836
(0.309) 		0.635
(1.00) 		0.0968
(1.00) 		0.351
(1.00) 		0.6
(1.00) 		0.366
(1.00) 		0.0387
(1.00) 		0.112
(1.00) 		0.000175
(0.0662) 		0.0322
(1.00)
4p 100 (45%) 121 4.8e-05
(0.0184) 		0.0886
(1.00) 		0.852
(1.00) 		0.8
(1.00) 		0.364
(1.00) 		0.22
(1.00) 		0.575
(1.00) 		0.377
(1.00) 		0.421
(1.00) 		0.815
(1.00)
4q 94 (43%) 127 1.59e-05
(0.00617) 		0.0729
(1.00) 		0.533
(1.00) 		0.631
(1.00) 		0.214
(1.00) 		0.131
(1.00) 		0.236
(1.00) 		0.394
(1.00) 		0.0793
(1.00) 		0.631
(1.00)
5p 125 (57%) 96 0.000115
(0.0437) 		0.0819
(1.00) 		0.348
(1.00) 		0.134
(1.00) 		0.149
(1.00) 		0.139
(1.00) 		0.163
(1.00) 		0.245
(1.00) 		0.25
(1.00) 		0.22
(1.00)
5q 115 (52%) 106 0.000297
(0.111) 		0.0732
(1.00) 		0.334
(1.00) 		0.751
(1.00) 		0.0243
(1.00) 		0.00391
(1.00) 		0.113
(1.00) 		0.068
(1.00) 		0.0457
(1.00) 		0.137
(1.00)
6q 99 (45%) 122 3.25e-06
(0.00127) 		0.00685
(1.00) 		0.87
(1.00) 		0.97
(1.00) 		0.635
(1.00) 		0.59
(1.00) 		0.279
(1.00) 		0.075
(1.00) 		0.214
(1.00) 		0.481
(1.00)
7p 102 (46%) 119 5.75e-05
(0.022) 		0.00113
(0.413) 		0.0461
(1.00) 		0.917
(1.00) 		0.391
(1.00) 		0.683
(1.00) 		0.159
(1.00) 		0.183
(1.00) 		0.059
(1.00) 		0.208
(1.00)
7q 95 (43%) 126 0.000103
(0.0392) 		0.00724
(1.00) 		0.306
(1.00) 		0.9
(1.00) 		0.532
(1.00) 		0.21
(1.00) 		0.334
(1.00) 		0.258
(1.00) 		0.164
(1.00) 		0.694
(1.00)
8p 143 (65%) 78 0.000213
(0.0803) 		0.00577
(1.00) 		0.896
(1.00) 		0.502
(1.00) 		0.00333
(1.00) 		0.291
(1.00) 		0.0809
(1.00) 		0.117
(1.00) 		0.0156
(1.00) 		0.0677
(1.00)
10p 105 (48%) 116 2.22e-09
(8.88e-07) 		0.00994
(1.00) 		0.389
(1.00) 		0.72
(1.00) 		0.0442
(1.00) 		0.808
(1.00) 		0.361
(1.00) 		0.417
(1.00) 		0.0718
(1.00) 		0.105
(1.00)
11p 110 (50%) 111 2.23e-07
(8.79e-05) 		0.00436
(1.00) 		0.301
(1.00) 		0.554
(1.00) 		0.199
(1.00) 		0.192
(1.00) 		0.126
(1.00) 		0.308
(1.00) 		0.259
(1.00) 		0.899
(1.00)
11q 98 (44%) 123 6.17e-09
(2.45e-06) 		0.0361
(1.00) 		0.0661
(1.00) 		0.22
(1.00) 		0.0681
(1.00) 		0.703
(1.00) 		0.637
(1.00) 		0.892
(1.00) 		0.306
(1.00) 		0.853
(1.00)
12p 88 (40%) 133 0.000286
(0.107) 		0.0822
(1.00) 		0.831
(1.00) 		0.669
(1.00) 		0.521
(1.00) 		0.504
(1.00) 		0.567
(1.00) 		0.264
(1.00) 		0.606
(1.00) 		0.142
(1.00)
16p 96 (43%) 125 2.14e-05
(0.00829) 		0.0398
(1.00) 		0.298
(1.00) 		0.227
(1.00) 		0.166
(1.00) 		0.463
(1.00) 		0.845
(1.00) 		0.394
(1.00) 		0.332
(1.00) 		0.414
(1.00)
16q 100 (45%) 121 2.97e-06
(0.00117) 		0.038
(1.00) 		0.388
(1.00) 		0.418
(1.00) 		0.131
(1.00) 		0.793
(1.00) 		0.397
(1.00) 		0.183
(1.00) 		0.717
(1.00) 		0.233
(1.00)
17p 129 (58%) 92 2.75e-05
(0.0106) 		0.199
(1.00) 		0.907
(1.00) 		0.627
(1.00) 		0.0504
(1.00) 		0.808
(1.00) 		0.269
(1.00) 		0.0386
(1.00) 		0.935
(1.00) 		0.66
(1.00)
18p 117 (53%) 104 9.03e-09
(3.59e-06) 		0.00557
(1.00) 		0.552
(1.00) 		0.651
(1.00) 		0.0331
(1.00) 		0.716
(1.00) 		1
(1.00) 		0.648
(1.00) 		0.375
(1.00) 		0.573
(1.00)
18q 110 (50%) 111 3.67e-05
(0.0141) 		0.0215
(1.00) 		0.281
(1.00) 		0.333
(1.00) 		0.356
(1.00) 		0.854
(1.00) 		0.351
(1.00) 		0.0611
(1.00) 		0.351
(1.00) 		0.753
(1.00)
19p 101 (46%) 120 2.94e-05
(0.0114) 		0.0834
(1.00) 		0.92
(1.00) 		0.7
(1.00) 		0.0802
(1.00) 		0.137
(1.00) 		0.147
(1.00) 		0.0205
(1.00) 		0.534
(1.00) 		0.651
(1.00)
19q 108 (49%) 113 6.35e-07
(0.00025) 		0.00586
(1.00) 		0.649
(1.00) 		0.87
(1.00) 		0.712
(1.00) 		0.414
(1.00) 		0.236
(1.00) 		0.186
(1.00) 		0.66
(1.00) 		0.354
(1.00)
20q 133 (60%) 88 0.000249
(0.0936) 		0.0321
(1.00) 		0.578
(1.00) 		0.379
(1.00) 		0.683
(1.00) 		0.232
(1.00) 		0.294
(1.00) 		0.0458
(1.00) 		0.0376
(1.00) 		0.291
(1.00)
21q 102 (46%) 119 3.34e-05
(0.0129) 		0.0373
(1.00) 		0.88
(1.00) 		0.334
(1.00) 		0.323
(1.00) 		0.971
(1.00) 		0.00742
(1.00) 		0.0016
(0.578) 		0.315
(1.00) 		0.0674
(1.00)
1p 69 (31%) 152 0.0259
(1.00) 		0.513
(1.00) 		0.375
(1.00) 		0.12
(1.00) 		0.781
(1.00) 		0.523
(1.00) 		0.447
(1.00) 		0.0435
(1.00) 		0.933
(1.00) 		0.611
(1.00)
1q 90 (41%) 131 0.286
(1.00) 		0.851
(1.00) 		0.879
(1.00) 		0.754
(1.00) 		0.783
(1.00) 		0.202
(1.00) 		0.698
(1.00) 		0.152
(1.00) 		0.982
(1.00) 		0.697
(1.00)
6p 87 (39%) 134 0.000866
(0.32) 		0.016
(1.00) 		0.763
(1.00) 		0.362
(1.00) 		0.789
(1.00) 		0.631
(1.00) 		0.109
(1.00) 		0.149
(1.00) 		0.482
(1.00) 		0.722
(1.00)
8q 122 (55%) 99 0.0636
(1.00) 		0.0138
(1.00) 		0.405
(1.00) 		0.19
(1.00) 		0.402
(1.00) 		0.864
(1.00) 		0.478
(1.00) 		0.0905
(1.00) 		0.306
(1.00) 		0.521
(1.00)
9p 128 (58%) 93 0.0275
(1.00) 		0.249
(1.00) 		0.0641
(1.00) 		0.277
(1.00) 		0.558
(1.00) 		0.118
(1.00) 		0.789
(1.00) 		0.396
(1.00) 		0.88
(1.00) 		0.936
(1.00)
9q 116 (52%) 105 0.0729
(1.00) 		0.354
(1.00) 		0.173
(1.00) 		0.546
(1.00) 		0.437
(1.00) 		0.0344
(1.00) 		0.767
(1.00) 		0.709
(1.00) 		0.648
(1.00) 		0.551
(1.00)
12q 77 (35%) 144 0.00155
(0.561) 		0.0905
(1.00) 		0.645
(1.00) 		0.245
(1.00) 		0.753
(1.00) 		0.512
(1.00) 		0.154
(1.00) 		0.0506
(1.00) 		0.427
(1.00) 		0.185
(1.00)
13q 104 (47%) 117 0.00725
(1.00) 		0.337
(1.00) 		0.0223
(1.00) 		0.0364
(1.00) 		0.0818
(1.00) 		0.852
(1.00) 		0.853
(1.00) 		0.36
(1.00) 		0.627
(1.00) 		0.388
(1.00)
14q 99 (45%) 122 0.000999
(0.367) 		0.0178
(1.00) 		0.458
(1.00) 		0.224
(1.00) 		0.0381
(1.00) 		0.76
(1.00) 		0.0508
(1.00) 		0.227
(1.00) 		0.298
(1.00) 		0.759
(1.00)
15q 96 (43%) 125 0.0314
(1.00) 		0.0922
(1.00) 		0.2
(1.00) 		0.705
(1.00) 		0.0768
(1.00) 		0.384
(1.00) 		0.189
(1.00) 		0.258
(1.00) 		0.201
(1.00) 		0.26
(1.00)
17q 103 (47%) 118 0.000917
(0.337) 		0.065
(1.00) 		0.148
(1.00) 		0.451
(1.00) 		0.0417
(1.00) 		0.0957
(1.00) 		0.0293
(1.00) 		0.00593
(1.00) 		0.0429
(1.00) 		0.0384
(1.00)
20p 128 (58%) 93 0.00111
(0.406) 		0.093
(1.00) 		0.844
(1.00) 		0.208
(1.00) 		0.895
(1.00) 		0.0737
(1.00) 		0.257
(1.00) 		0.00934
(1.00) 		0.0214
(1.00) 		0.0505
(1.00)
xq 71 (32%) 150 0.00113
(0.413) 		0.00729
(1.00) 		0.84
(1.00) 		0.847
(1.00) 		0.0186
(1.00) 		0.414
(1.00) 		0.0755
(1.00) 		0.548
(1.00) 		0.352
(1.00) 		0.409
(1.00)
'2p' versus 'CN_CNMF'

P value = 5.84e-08 (Chi-square test), Q value = 2.3e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
2P MUTATED 8 11 8 9 23 13 12 5
2P WILD-TYPE 10 68 15 5 15 12 2 5

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

'2q' versus 'CN_CNMF'

P value = 2.27e-06 (Chi-square test), Q value = 0.00089

Table S2.  Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
2Q MUTATED 9 10 9 6 23 9 10 5
2Q WILD-TYPE 9 69 14 8 15 16 4 5

Figure S2.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

'3p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000175 (Fisher's exact test), Q value = 0.066

Table S3.  Gene #5: '3p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 60 67 49
3P MUTATED 23 35 20 18
3P WILD-TYPE 10 25 47 31

Figure S3.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q' versus 'CN_CNMF'

P value = 0.000573 (Chi-square test), Q value = 0.21

Table S4.  Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
3Q MUTATED 11 28 6 9 19 19 11 6
3Q WILD-TYPE 7 51 17 5 19 6 3 4

Figure S4.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

'3q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.045

Table S5.  Gene #6: '3q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 60 67 49
3Q MUTATED 26 33 23 19
3Q WILD-TYPE 7 27 44 30

Figure S5.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p' versus 'CN_CNMF'

P value = 4.8e-05 (Chi-square test), Q value = 0.018

Table S6.  Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
4P MUTATED 10 18 9 11 24 15 7 6
4P WILD-TYPE 8 61 14 3 14 10 7 4

Figure S6.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

'4q' versus 'CN_CNMF'

P value = 1.59e-05 (Chi-square test), Q value = 0.0062

Table S7.  Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
4Q MUTATED 11 14 11 9 24 13 8 4
4Q WILD-TYPE 7 65 12 5 14 12 6 6

Figure S7.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

'5p' versus 'CN_CNMF'

P value = 0.000115 (Chi-square test), Q value = 0.044

Table S8.  Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
5P MUTATED 14 28 14 10 24 19 12 4
5P WILD-TYPE 4 51 9 4 14 6 2 6

Figure S8.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

'5q' versus 'CN_CNMF'

P value = 0.000297 (Chi-square test), Q value = 0.11

Table S9.  Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
5Q MUTATED 14 24 15 10 24 15 9 4
5Q WILD-TYPE 4 55 8 4 14 10 5 6

Figure S9.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

'6q' versus 'CN_CNMF'

P value = 3.25e-06 (Chi-square test), Q value = 0.0013

Table S10.  Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
6Q MUTATED 12 16 11 8 25 10 9 8
6Q WILD-TYPE 6 63 12 6 13 15 5 2

Figure S10.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'CN_CNMF'

P value = 5.75e-05 (Chi-square test), Q value = 0.022

Table S11.  Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
7P MUTATED 10 19 8 9 25 15 9 7
7P WILD-TYPE 8 60 15 5 13 10 5 3

Figure S11.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

'7q' versus 'CN_CNMF'

P value = 0.000103 (Chi-square test), Q value = 0.039

Table S12.  Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
7Q MUTATED 9 18 8 5 25 14 9 7
7Q WILD-TYPE 9 61 15 9 13 11 5 3

Figure S12.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

'8p' versus 'CN_CNMF'

P value = 0.000213 (Chi-square test), Q value = 0.08

Table S13.  Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
8P MUTATED 15 34 17 12 28 21 9 7
8P WILD-TYPE 3 45 6 2 10 4 5 3

Figure S13.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'CN_CNMF'

P value = 2.22e-09 (Chi-square test), Q value = 8.9e-07

Table S14.  Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
10P MUTATED 11 12 12 9 26 18 10 7
10P WILD-TYPE 7 67 11 5 12 7 4 3

Figure S14.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'CN_CNMF'

P value = 9.94e-06 (Chi-square test), Q value = 0.0039

Table S15.  Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
10Q MUTATED 9 13 11 9 23 14 9 5
10Q WILD-TYPE 9 66 12 5 15 11 5 5

Figure S15.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 0.000278 (Fisher's exact test), Q value = 0.1

Table S16.  Gene #20: '10q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 88 52
10Q MUTATED 48 31 14
10Q WILD-TYPE 33 57 38

Figure S16.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p' versus 'CN_CNMF'

P value = 2.23e-07 (Chi-square test), Q value = 8.8e-05

Table S17.  Gene #21: '11p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
11P MUTATED 15 20 9 8 28 14 7 9
11P WILD-TYPE 3 59 14 6 10 11 7 1

Figure S17.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #1: 'CN_CNMF'

'11q' versus 'CN_CNMF'

P value = 6.17e-09 (Chi-square test), Q value = 2.5e-06

Table S18.  Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
11Q MUTATED 14 13 8 8 25 13 8 9
11Q WILD-TYPE 4 66 15 6 13 12 6 1

Figure S18.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

'12p' versus 'CN_CNMF'

P value = 0.000286 (Chi-square test), Q value = 0.11

Table S19.  Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
12P MUTATED 11 16 9 9 20 12 4 7
12P WILD-TYPE 7 63 14 5 18 13 10 3

Figure S19.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

'16p' versus 'CN_CNMF'

P value = 2.14e-05 (Chi-square test), Q value = 0.0083

Table S20.  Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
16P MUTATED 11 15 16 8 19 13 7 7
16P WILD-TYPE 7 64 7 6 19 12 7 3

Figure S20.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

'16q' versus 'CN_CNMF'

P value = 2.97e-06 (Chi-square test), Q value = 0.0012

Table S21.  Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
16Q MUTATED 12 15 14 8 23 14 6 8
16Q WILD-TYPE 6 64 9 6 15 11 8 2

Figure S21.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'CN_CNMF'

P value = 2.75e-05 (Chi-square test), Q value = 0.011

Table S22.  Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
17P MUTATED 16 29 12 7 27 19 11 8
17P WILD-TYPE 2 50 11 7 11 6 3 2

Figure S22.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

'18p' versus 'CN_CNMF'

P value = 9.03e-09 (Chi-square test), Q value = 3.6e-06

Table S23.  Gene #32: '18p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
18P MUTATED 10 17 17 11 28 17 10 7
18P WILD-TYPE 8 62 6 3 10 8 4 3

Figure S23.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #1: 'CN_CNMF'

'18q' versus 'CN_CNMF'

P value = 3.67e-05 (Chi-square test), Q value = 0.014

Table S24.  Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
18Q MUTATED 11 21 16 12 24 12 8 6
18Q WILD-TYPE 7 58 7 2 14 13 6 4

Figure S24.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

'19p' versus 'CN_CNMF'

P value = 2.94e-05 (Chi-square test), Q value = 0.011

Table S25.  Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
19P MUTATED 5 20 10 9 24 15 11 7
19P WILD-TYPE 13 59 13 5 14 10 3 3

Figure S25.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

'19q' versus 'CN_CNMF'

P value = 6.35e-07 (Chi-square test), Q value = 0.00025

Table S26.  Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
19Q MUTATED 7 19 10 9 28 17 11 7
19Q WILD-TYPE 11 60 13 5 10 8 3 3

Figure S26.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

'20q' versus 'CN_CNMF'

P value = 0.000249 (Chi-square test), Q value = 0.094

Table S27.  Gene #37: '20q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
20Q MUTATED 14 30 15 10 26 19 10 9
20Q WILD-TYPE 4 49 8 4 12 6 4 1

Figure S27.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #1: 'CN_CNMF'

'21q' versus 'CN_CNMF'

P value = 3.34e-05 (Chi-square test), Q value = 0.013

Table S28.  Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
21Q MUTATED 10 17 14 10 21 17 7 6
21Q WILD-TYPE 8 62 9 4 17 8 7 4

Figure S28.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'CN_CNMF'

P value = 4.24e-10 (Chi-square test), Q value = 1.7e-07

Table S29.  Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 18 79 23 14 38 25 14 10
22Q MUTATED 12 16 18 8 26 20 7 9
22Q WILD-TYPE 6 63 5 6 12 5 7 1

Figure S29.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'METHLYATION_CNMF'

P value = 0.000263 (Fisher's exact test), Q value = 0.099

Table S30.  Gene #39: '22q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 88 52
22Q MUTATED 54 46 16
22Q WILD-TYPE 27 42 36

Figure S30.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input

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

  • Molecular subtype file = BLCA-TP.transferedmergedcluster.txt

  • Number of patients = 221

  • Number of significantly focal cnvs = 40

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have alterations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[3] 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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