Correlation between gene mutation status and molecular subtypes
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 94 genes and 8 molecular subtypes across 306 patients, 12 significant findings detected with P value < 0.05 and Q value < 0.25.

  • NOTCH1 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CNMF'.

  • HRAS mutation correlated to 'CN_CNMF'.

  • NFE2L2 mutation correlated to 'METHLYATION_CNMF'.

  • TP53 mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • CASP8 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • NSD1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 94 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 12 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nMutated (%) nWild-Type Chi-square 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
CASP8 27 (9%) 279 0.000326
(0.236) 		7.22e-06
(0.00525) 		0.699
(1.00) 		0.739
(1.00) 		3e-07
(0.000219) 		5.28e-07
(0.000385) 		0.329
(1.00) 		0.286
(1.00)
NOTCH1 57 (19%) 249 0.488
(1.00) 		0.000746
(0.536) 		0.0187
(1.00) 		0.279
(1.00) 		0.000428
(0.308) 		2.54e-06
(0.00185) 		7.73e-05
(0.056) 		0.572
(1.00)
TP53 214 (70%) 92 1.84e-16
(1.35e-13) 		3.14e-18
(2.3e-15) 		0.11
(1.00) 		0.776
(1.00) 		0.0113
(1.00) 		0.00143
(1.00) 		0.0426
(1.00) 		0.000589
(0.424)
NSD1 33 (11%) 273 0.377
(1.00) 		3.04e-23
(2.23e-20) 		0.244
(1.00) 		0.73
(1.00) 		0.000411
(0.297) 		6.41e-06
(0.00466) 		0.0133
(1.00) 		0.0339
(1.00)
HRAS 10 (3%) 296 1.33e-05
(0.00968) 		0.0612
(1.00) 		0.168
(1.00) 		0.599
(1.00) 		0.00339
(1.00) 		0.0011
(0.785) 		0.109
(1.00) 		0.504
(1.00)
NFE2L2 17 (6%) 289 0.909
(1.00) 		0.000297
(0.215) 		0.125
(1.00) 		0.765
(1.00) 		1
(1.00) 		0.464
(1.00) 		0.223
(1.00) 		0.11
(1.00)
CDKN2A 65 (21%) 241 0.0451
(1.00) 		0.00306
(1.00) 		0.0349
(1.00) 		0.583
(1.00) 		0.201
(1.00) 		0.206
(1.00) 		0.354
(1.00) 		0.115
(1.00)
PIK3CA 64 (21%) 242 0.0123
(1.00) 		0.0554
(1.00) 		0.0948
(1.00) 		0.928
(1.00) 		0.119
(1.00) 		0.398
(1.00) 		0.0234
(1.00) 		0.152
(1.00)
FAT1 72 (24%) 234 0.308
(1.00) 		0.227
(1.00) 		0.794
(1.00) 		0.487
(1.00) 		0.152
(1.00) 		0.288
(1.00) 		0.82
(1.00) 		0.252
(1.00)
JUB 18 (6%) 288 0.264
(1.00) 		0.0799
(1.00) 		0.0646
(1.00) 		0.0816
(1.00) 		0.305
(1.00) 		0.221
(1.00) 		0.38
(1.00) 		1
(1.00)
MLL2 56 (18%) 250 0.118
(1.00) 		0.0471
(1.00) 		0.687
(1.00) 		0.521
(1.00) 		0.0532
(1.00) 		0.00795
(1.00) 		0.0707
(1.00) 		0.00651
(1.00)
FBXW7 15 (5%) 291 0.21
(1.00) 		0.134
(1.00) 		0.092
(1.00) 		0.303
(1.00) 		0.881
(1.00) 		0.636
(1.00) 		0.945
(1.00) 		0.868
(1.00)
BAGE2 11 (4%) 295 0.279
(1.00) 		0.0999
(1.00) 		0.414
(1.00) 		0.0857
(1.00) 		0.253
(1.00) 		0.291
(1.00) 		0.178
(1.00) 		0.101
(1.00)
POTEC 15 (5%) 291 0.0719
(1.00) 		0.0364
(1.00) 		0.847
(1.00) 		1
(1.00) 		0.17
(1.00) 		0.254
(1.00) 		0.535
(1.00) 		0.21
(1.00)
ZNF750 13 (4%) 293 0.721
(1.00) 		0.159
(1.00) 		0.946
(1.00) 		0.353
(1.00) 		0.119
(1.00) 		0.128
(1.00) 		0.632
(1.00) 		1
(1.00)
EP300 25 (8%) 281 0.0345
(1.00) 		0.151
(1.00) 		0.769
(1.00) 		0.264
(1.00) 		0.00955
(1.00) 		0.00467
(1.00) 		0.338
(1.00) 		0.526
(1.00)
POM121L12 14 (5%) 292 0.0578
(1.00) 		0.304
(1.00) 		0.116
(1.00) 		0.151
(1.00) 		0.658
(1.00) 		0.657
(1.00) 		0.48
(1.00) 		0.454
(1.00)
RHOA 4 (1%) 302 0.0826
(1.00) 		0.54
(1.00) 		0.379
(1.00) 		0.444
(1.00) 		0.245
(1.00) 		0.141
(1.00) 		0.24
(1.00) 		0.254
(1.00)
B2M 7 (2%) 299 0.767
(1.00) 		0.0618
(1.00) 		0.515
(1.00) 		0.517
(1.00) 		0.141
(1.00) 		0.767
(1.00)
RAC1 9 (3%) 297 0.374
(1.00) 		0.585
(1.00) 		1
(1.00) 		0.519
(1.00) 		0.195
(1.00) 		0.192
(1.00) 		0.268
(1.00) 		0.301
(1.00)
ZNF804B 21 (7%) 285 0.825
(1.00) 		0.487
(1.00) 		0.626
(1.00) 		0.514
(1.00) 		0.812
(1.00) 		0.746
(1.00) 		0.92
(1.00) 		0.904
(1.00)
KCNT2 17 (6%) 289 0.197
(1.00) 		0.235
(1.00) 		0.702
(1.00) 		0.562
(1.00) 		0.05
(1.00) 		0.121
(1.00) 		0.052
(1.00) 		0.0388
(1.00)
RASA1 14 (5%) 292 0.0617
(1.00) 		0.24
(1.00) 		1
(1.00) 		0.402
(1.00) 		0.357
(1.00) 		0.271
(1.00) 		0.313
(1.00) 		0.0301
(1.00)
PRIM2 9 (3%) 297 0.0807
(1.00) 		0.305
(1.00) 		0.822
(1.00) 		0.404
(1.00) 		0.4
(1.00) 		0.395
(1.00) 		0.268
(1.00) 		0.301
(1.00)
CDH10 23 (8%) 283 0.326
(1.00) 		0.531
(1.00) 		0.329
(1.00) 		0.695
(1.00) 		0.0743
(1.00) 		0.265
(1.00) 		0.207
(1.00) 		0.694
(1.00)
CNTNAP5 15 (5%) 291 0.0449
(1.00) 		0.115
(1.00) 		0.553
(1.00) 		1
(1.00) 		0.0101
(1.00) 		0.0354
(1.00) 		0.0101
(1.00) 		0.3
(1.00)
POTEG 10 (3%) 296 0.00148
(1.00) 		0.0869
(1.00) 		0.229
(1.00) 		0.754
(1.00) 		0.16
(1.00) 		0.143
(1.00) 		0.728
(1.00) 		0.504
(1.00)
ZNF99 22 (7%) 284 0.229
(1.00) 		0.126
(1.00) 		0.322
(1.00) 		0.402
(1.00) 		0.0343
(1.00) 		0.0116
(1.00) 		0.00606
(1.00) 		0.00653
(1.00)
OR2T12 11 (4%) 295 0.0236
(1.00) 		0.12
(1.00) 		0.512
(1.00) 		0.599
(1.00) 		0.552
(1.00) 		0.502
(1.00) 		0.593
(1.00) 		0.672
(1.00)
REG1A 8 (3%) 298 0.168
(1.00) 		0.102
(1.00) 		0.496
(1.00) 		0.36
(1.00) 		0.058
(1.00) 		0.00131
(0.938) 		0.0569
(1.00) 		0.0617
(1.00)
PABPC5 9 (3%) 297 0.207
(1.00) 		0.407
(1.00) 		0.692
(1.00) 		0.779
(1.00) 		0.089
(1.00) 		0.237
(1.00) 		0.268
(1.00) 		1
(1.00)
IL32 4 (1%) 302 0.116
(1.00) 		0.00177
(1.00) 		0.561
(1.00) 		1
(1.00) 		0.563
(1.00) 		0.68
(1.00)
PRAMEF11 10 (3%) 296 0.0932
(1.00) 		0.438
(1.00) 		0.963
(1.00) 		0.777
(1.00) 		0.669
(1.00) 		0.606
(1.00) 		0.551
(1.00) 		1
(1.00)
EPHA2 14 (5%) 292 0.0127
(1.00) 		0.00256
(1.00) 		0.811
(1.00) 		0.906
(1.00) 		0.499
(1.00) 		0.57
(1.00) 		0.774
(1.00) 		0.071
(1.00)
FCRL4 13 (4%) 293 0.12
(1.00) 		0.0179
(1.00) 		0.788
(1.00) 		1
(1.00) 		0.405
(1.00) 		0.106
(1.00) 		0.46
(1.00) 		0.847
(1.00)
LCP1 12 (4%) 294 0.463
(1.00) 		0.000851
(0.61) 		0.667
(1.00) 		0.0436
(1.00) 		0.873
(1.00) 		0.758
(1.00) 		0.498
(1.00) 		0.842
(1.00)
LRFN5 13 (4%) 293 0.00104
(0.748) 		0.07
(1.00) 		0.766
(1.00) 		0.865
(1.00) 		0.279
(1.00) 		0.0765
(1.00) 		0.0196
(1.00) 		0.424
(1.00)
MAPK1 4 (1%) 302 0.725
(1.00) 		0.924
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.691
(1.00) 		0.686
(1.00) 		0.691
(1.00) 		0.132
(1.00)
PEG3 23 (8%) 283 0.172
(1.00) 		0.022
(1.00) 		0.0827
(1.00) 		0.103
(1.00) 		0.0217
(1.00) 		0.053
(1.00) 		0.253
(1.00) 		0.241
(1.00)
PRSS1 8 (3%) 298 0.014
(1.00) 		0.478
(1.00) 		0.0589
(1.00) 		1
(1.00) 		1
(1.00) 		0.89
(1.00) 		0.82
(1.00) 		0.205
(1.00)
DOK6 8 (3%) 298 0.375
(1.00) 		0.582
(1.00) 		0.705
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.666
(1.00) 		1
(1.00)
GABRB3 11 (4%) 295 0.222
(1.00) 		0.0147
(1.00) 		0.148
(1.00) 		0.541
(1.00) 		0.253
(1.00) 		0.192
(1.00) 		0.593
(1.00) 		0.672
(1.00)
STEAP4 10 (3%) 296 0.174
(1.00) 		0.636
(1.00) 		0.175
(1.00) 		0.656
(1.00) 		0.0813
(1.00) 		0.0997
(1.00) 		0.0893
(1.00) 		1
(1.00)
ASXL3 21 (7%) 285 0.618
(1.00) 		0.632
(1.00) 		0.225
(1.00) 		0.356
(1.00) 		0.96
(1.00) 		0.714
(1.00) 		0.501
(1.00) 		0.383
(1.00)
NTM 7 (2%) 299 0.238
(1.00) 		0.24
(1.00) 		0.0949
(1.00) 		0.0238
(1.00) 		0.182
(1.00) 		0.0877
(1.00) 		0.104
(1.00) 		0.0893
(1.00)
FAM155A 11 (4%) 295 0.151
(1.00) 		0.0585
(1.00) 		0.0106
(1.00) 		0.0694
(1.00) 		0.233
(1.00) 		0.175
(1.00) 		0.119
(1.00) 		0.0667
(1.00)
HLA-A 9 (3%) 297 0.528
(1.00) 		0.335
(1.00) 		1
(1.00) 		1
(1.00) 		0.072
(1.00) 		0.0311
(1.00) 		0.633
(1.00) 		0.612
(1.00)
KRTAP1-5 3 (1%) 303 0.826
(1.00) 		0.807
(1.00) 		0.78
(1.00) 		0.63
(1.00) 		0.0245
(1.00) 		1
(1.00)
CTCF 11 (4%) 295 0.551
(1.00) 		0.401
(1.00) 		0.393
(1.00) 		0.541
(1.00) 		0.636
(1.00) 		0.632
(1.00) 		0.86
(1.00) 		0.366
(1.00)
BRWD3 16 (5%) 290 0.88
(1.00) 		0.532
(1.00) 		0.537
(1.00) 		1
(1.00) 		0.256
(1.00) 		0.136
(1.00) 		0.584
(1.00) 		0.234
(1.00)
CNPY3 3 (1%) 303 0.598
(1.00) 		0.48
(1.00) 		0.5
(1.00) 		0.499
(1.00) 		0.495
(1.00) 		0.599
(1.00)
FAM101A 4 (1%) 302 0.581
(1.00) 		0.374
(1.00) 		0.691
(1.00) 		1
(1.00) 		0.0707
(1.00) 		1
(1.00)
HLA-B 9 (3%) 297 0.194
(1.00) 		0.0957
(1.00) 		0.952
(1.00) 		0.599
(1.00) 		0.00341
(1.00) 		0.00425
(1.00) 		0.361
(1.00) 		0.301
(1.00)
PSG8 9 (3%) 297 0.221
(1.00) 		0.618
(1.00) 		1
(1.00) 		0.71
(1.00) 		0.483
(1.00) 		0.484
(1.00) 		0.918
(1.00) 		0.362
(1.00)
OR56A1 8 (3%) 298 0.558
(1.00) 		0.0158
(1.00) 		0.894
(1.00) 		0.822
(1.00) 		0.357
(1.00) 		0.352
(1.00) 		0.201
(1.00) 		0.341
(1.00)
OR2M2 8 (3%) 298 0.005
(1.00) 		0.126
(1.00) 		0.181
(1.00) 		0.0118
(1.00) 		0.605
(1.00) 		0.116
(1.00)
OR4M2 8 (3%) 298 0.373
(1.00) 		0.88
(1.00) 		0.746
(1.00) 		0.519
(1.00) 		0.643
(1.00) 		0.639
(1.00) 		0.605
(1.00) 		0.776
(1.00)
CPXCR1 7 (2%) 299 0.767
(1.00) 		0.536
(1.00) 		0.202
(1.00) 		0.209
(1.00) 		0.345
(1.00) 		0.498
(1.00) 		0.5
(1.00) 		0.399
(1.00)
EYA1 10 (3%) 296 0.215
(1.00) 		0.636
(1.00) 		0.79
(1.00) 		0.843
(1.00) 		0.0274
(1.00) 		0.0263
(1.00) 		0.728
(1.00) 		0.215
(1.00)
LINGO2 10 (3%) 296 0.316
(1.00) 		0.82
(1.00) 		0.284
(1.00) 		1
(1.00) 		0.015
(1.00) 		0.0144
(1.00) 		0.172
(1.00) 		0.138
(1.00)
SEMA5A 19 (6%) 287 0.000737
(0.53) 		0.00318
(1.00) 		0.936
(1.00) 		1
(1.00) 		0.00661
(1.00) 		0.0234
(1.00) 		0.299
(1.00) 		0.0351
(1.00)
TGFBR2 10 (3%) 296 0.46
(1.00) 		0.201
(1.00) 		0.469
(1.00) 		1
(1.00) 		0.313
(1.00) 		0.785
(1.00) 		0.79
(1.00) 		1
(1.00)
PLSCR1 5 (2%) 301 0.141
(1.00) 		0.23
(1.00) 		1
(1.00) 		1
(1.00) 		0.524
(1.00) 		0.526
(1.00) 		0.155
(1.00) 		0.463
(1.00)
LIN28B 6 (2%) 300 0.634
(1.00) 		0.938
(1.00) 		0.513
(1.00) 		1
(1.00) 		0.737
(1.00) 		0.739
(1.00) 		0.515
(1.00) 		0.139
(1.00)
AGTR1 8 (3%) 298 0.398
(1.00) 		0.401
(1.00) 		0.173
(1.00) 		0.108
(1.00) 		0.181
(1.00) 		0.2
(1.00) 		0.0569
(1.00) 		0.776
(1.00)
C6 12 (4%) 294 0.58
(1.00) 		0.591
(1.00) 		0.062
(1.00) 		1
(1.00) 		0.0762
(1.00) 		0.222
(1.00) 		0.535
(1.00) 		1
(1.00)
MS4A14 9 (3%) 297 0.238
(1.00) 		0.418
(1.00) 		0.588
(1.00) 		1
(1.00) 		0.4
(1.00) 		0.484
(1.00) 		0.486
(1.00) 		1
(1.00)
HIST1H4E 5 (2%) 301 0.658
(1.00) 		0.731
(1.00) 		0.255
(1.00) 		0.754
(1.00) 		0.866
(1.00) 		0.386
(1.00) 		0.333
(1.00) 		0.278
(1.00)
LBP 7 (2%) 299 0.426
(1.00) 		0.837
(1.00) 		0.775
(1.00) 		0.771
(1.00) 		1
(1.00) 		1
(1.00)
RGS17 5 (2%) 301 0.706
(1.00) 		0.81
(1.00) 		0.157
(1.00) 		0.155
(1.00) 		0.155
(1.00) 		0.278
(1.00)
LILRB1 12 (4%) 294 0.269
(1.00) 		0.166
(1.00) 		0.419
(1.00) 		0.822
(1.00) 		0.861
(1.00) 		0.929
(1.00) 		0.704
(1.00) 		0.462
(1.00)
MAGEL2 12 (4%) 294 0.228
(1.00) 		0.00566
(1.00) 		0.17
(1.00) 		0.446
(1.00) 		0.538
(1.00) 		0.341
(1.00) 		0.397
(1.00) 		0.573
(1.00)
OR8D4 6 (2%) 300 0.902
(1.00) 		0.119
(1.00) 		0.894
(1.00) 		0.438
(1.00) 		0.387
(1.00) 		1
(1.00) 		0.386
(1.00) 		0.732
(1.00)
HIST1H1B 7 (2%) 299 0.627
(1.00) 		0.356
(1.00) 		0.705
(1.00) 		0.822
(1.00) 		0.802
(1.00) 		0.717
(1.00) 		0.183
(1.00) 		0.125
(1.00)
C3ORF59 8 (3%) 298 0.459
(1.00) 		0.476
(1.00) 		0.173
(1.00) 		0.00863
(1.00) 		1
(1.00) 		1
(1.00) 		0.908
(1.00) 		1
(1.00)
C8ORF34 7 (2%) 299 0.931
(1.00) 		0.0892
(1.00) 		0.419
(1.00) 		0.0617
(1.00) 		0.802
(1.00) 		1
(1.00) 		0.345
(1.00) 		1
(1.00)
OR8J1 9 (3%) 297 0.161
(1.00) 		0.319
(1.00) 		0.0346
(1.00) 		0.0238
(1.00) 		0.245
(1.00) 		0.265
(1.00) 		0.296
(1.00) 		0.612
(1.00)
RAB32 3 (1%) 303 0.0793
(1.00) 		0.825
(1.00) 		0.856
(1.00) 		0.672
(1.00) 		0.114
(1.00) 		0.116
(1.00) 		0.381
(1.00) 		0.35
(1.00)
TMEM195 8 (3%) 298 0.508
(1.00) 		0.448
(1.00) 		0.79
(1.00) 		0.71
(1.00) 		0.821
(1.00) 		0.905
(1.00) 		0.82
(1.00) 		1
(1.00)
PCDH11X 21 (7%) 285 0.422
(1.00) 		0.71
(1.00) 		0.697
(1.00) 		0.0248
(1.00) 		0.346
(1.00) 		0.377
(1.00) 		0.78
(1.00) 		0.904
(1.00)
SLITRK4 12 (4%) 294 0.147
(1.00) 		0.178
(1.00) 		0.465
(1.00) 		0.613
(1.00) 		0.092
(1.00) 		0.0896
(1.00) 		0.194
(1.00) 		0.283
(1.00)
FRG2B 6 (2%) 300 0.773
(1.00) 		0.692
(1.00) 		0.324
(1.00) 		0.672
(1.00) 		0.291
(1.00) 		0.289
(1.00) 		0.291
(1.00) 		0.732
(1.00)
OR2L13 7 (2%) 299 0.239
(1.00) 		0.101
(1.00) 		0.00821
(1.00) 		1
(1.00) 		0.345
(1.00) 		0.498
(1.00) 		0.5
(1.00) 		0.00432
(1.00)
CUL3 10 (3%) 296 0.0463
(1.00) 		0.124
(1.00) 		0.737
(1.00) 		0.636
(1.00) 		0.403
(1.00) 		0.852
(1.00) 		0.551
(1.00) 		0.403
(1.00)
FOSL2 7 (2%) 299 0.395
(1.00) 		0.611
(1.00) 		0.644
(1.00) 		1
(1.00) 		0.345
(1.00) 		0.717
(1.00) 		0.345
(1.00) 		0.281
(1.00)
GPR158 12 (4%) 294 0.454
(1.00) 		0.131
(1.00) 		1
(1.00) 		0.865
(1.00) 		0.538
(1.00) 		0.531
(1.00) 		0.934
(1.00) 		0.573
(1.00)
PTPRT 19 (6%) 287 0.743
(1.00) 		0.0925
(1.00) 		0.576
(1.00) 		0.752
(1.00) 		0.0996
(1.00) 		0.693
(1.00) 		0.477
(1.00) 		0.501
(1.00)
POTEH 7 (2%) 299 0.892
(1.00) 		0.55
(1.00) 		0.152
(1.00) 		0.155
(1.00) 		0.123
(1.00) 		0.103
(1.00) 		0.57
(1.00) 		0.767
(1.00)
OR5D13 7 (2%) 299 0.756
(1.00) 		0.16
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.767
(1.00)
PRB1 7 (2%) 299 0.5
(1.00) 		0.177
(1.00) 		0.757
(1.00) 		0.672
(1.00) 		0.89
(1.00) 		0.639
(1.00) 		0.104
(1.00) 		1
(1.00)
NEUROD6 7 (2%) 299 0.892
(1.00) 		0.862
(1.00) 		0.502
(1.00) 		0.563
(1.00) 		1
(1.00) 		1
(1.00)
DPP10 16 (5%) 290 0.0613
(1.00) 		0.12
(1.00) 		0.115
(1.00) 		0.26
(1.00) 		0.17
(1.00) 		0.0574
(1.00) 		0.0128
(1.00) 		0.0731
(1.00)
DPPA4 7 (2%) 299 0.0625
(1.00) 		0.0035
(1.00) 		0.442
(1.00) 		0.0845
(1.00) 		0.123
(1.00) 		0.0461
(1.00) 		0.5
(1.00) 		0.767
(1.00)
EPDR1 6 (2%) 300 0.773
(1.00) 		0.799
(1.00) 		0.561
(1.00) 		0.779
(1.00) 		0.327
(1.00) 		0.675
(1.00) 		0.881
(1.00) 		1
(1.00)
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.54e-06 (Fisher's exact test), Q value = 0.0019

Table S1.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 118
NOTCH1 MUTATED 20 29 8
NOTCH1 WILD-TYPE 77 55 110

Figure S1.  Get High-res Image Gene #1: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 7.73e-05 (Fisher's exact test), Q value = 0.056

Table S2.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 121 94
NOTCH1 MUTATED 26 9 21
NOTCH1 WILD-TYPE 63 112 73

Figure S2.  Get High-res Image Gene #1: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 1.33e-05 (Chi-square test), Q value = 0.0097

Table S3.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 36 44 77 65 9
HRAS MUTATED 0 0 0 10 0 0
HRAS WILD-TYPE 71 36 44 67 65 9

Figure S3.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000297 (Chi-square test), Q value = 0.21

Table S4.  Gene #4: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 42 47 39 43 58 53 5 19
NFE2L2 MUTATED 0 0 2 0 10 2 0 3
NFE2L2 WILD-TYPE 42 47 37 43 48 51 5 16

Figure S4.  Get High-res Image Gene #4: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.84e-16 (Chi-square test), Q value = 1.3e-13

Table S5.  Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 36 44 77 65 9
TP53 MUTATED 60 33 38 23 50 8
TP53 WILD-TYPE 11 3 6 54 15 1

Figure S5.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.14e-18 (Chi-square test), Q value = 2.3e-15

Table S6.  Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 42 47 39 43 58 53 5 19
TP53 MUTATED 34 43 29 4 51 36 3 14
TP53 WILD-TYPE 8 4 10 39 7 17 2 5

Figure S6.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000326 (Chi-square test), Q value = 0.24

Table S7.  Gene #7: 'CASP8 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 36 44 77 65 9
CASP8 MUTATED 1 1 1 16 6 1
CASP8 WILD-TYPE 70 35 43 61 59 8

Figure S7.  Get High-res Image Gene #7: 'CASP8 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 7.22e-06 (Chi-square test), Q value = 0.0052

Table S8.  Gene #7: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 42 47 39 43 58 53 5 19
CASP8 MUTATED 1 3 8 0 0 9 0 6
CASP8 WILD-TYPE 41 44 31 43 58 44 5 13

Figure S8.  Get High-res Image Gene #7: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3e-07 (Fisher's exact test), Q value = 0.00022

Table S9.  Gene #7: 'CASP8 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 93 89
CASP8 MUTATED 1 5 19
CASP8 WILD-TYPE 116 88 70

Figure S9.  Get High-res Image Gene #7: 'CASP8 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.28e-07 (Fisher's exact test), Q value = 0.00039

Table S10.  Gene #7: 'CASP8 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 118
CASP8 MUTATED 6 18 1
CASP8 WILD-TYPE 91 66 117

Figure S10.  Get High-res Image Gene #7: 'CASP8 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.04e-23 (Chi-square test), Q value = 2.2e-20

Table S11.  Gene #12: 'NSD1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 42 47 39 43 58 53 5 19
NSD1 MUTATED 25 1 2 3 0 2 0 0
NSD1 WILD-TYPE 17 46 37 40 58 51 5 19

Figure S11.  Get High-res Image Gene #12: 'NSD1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.41e-06 (Fisher's exact test), Q value = 0.0047

Table S12.  Gene #12: 'NSD1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 118
NSD1 MUTATED 3 4 26
NSD1 WILD-TYPE 94 80 92

Figure S12.  Get High-res Image Gene #12: 'NSD1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

  • Mutation data file = HNSC-TP.mutsig.cluster.txt

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

  • Number of patients = 306

  • Number of significantly mutated genes = 94

  • Number of Molecular subtypes = 8

  • Exclude genes that fewer than K tumors have mutations, 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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