Head and Neck Squamous Cell Carcinoma: Correlation between gene mutation status and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle