Correlation between gene mutation status and molecular subtypes
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1W957BH
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1W957BH
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, 11 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 '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, 11 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 0.00102
(0.733) 		7.22e-06
(0.00524) 		1
(1.00) 		0.778
(1.00) 		3e-07
(0.000219) 		5.28e-07
(0.000385) 		0.0199
(1.00) 		0.404
(1.00)
NOTCH1 57 (19%) 249 0.183
(1.00) 		0.000746
(0.537) 		0.0786
(1.00) 		0.362
(1.00) 		0.000428
(0.309) 		2.54e-06
(0.00185) 		4.53e-06
(0.0033) 		0.0837
(1.00)
TP53 214 (70%) 92 7.17e-11
(5.25e-08) 		3.14e-18
(2.3e-15) 		1
(1.00) 		0.608
(1.00) 		0.0113
(1.00) 		0.00143
(1.00) 		0.132
(1.00) 		0.00148
(1.00)
NSD1 33 (11%) 273 0.361
(1.00) 		3.04e-23
(2.23e-20) 		0.168
(1.00) 		0.224
(1.00) 		0.000411
(0.297) 		6.41e-06
(0.00466) 		0.0212
(1.00) 		0.0341
(1.00)
HRAS 10 (3%) 296 6.93e-05
(0.0503) 		0.0612
(1.00) 		0.424
(1.00) 		0.69
(1.00) 		0.00339
(1.00) 		0.0011
(0.787) 		0.142
(1.00) 		1
(1.00)
NFE2L2 17 (6%) 289 0.688
(1.00) 		0.000297
(0.215) 		0.821
(1.00) 		0.828
(1.00) 		1
(1.00) 		0.464
(1.00) 		0.492
(1.00) 		0.146
(1.00)
CDKN2A 65 (21%) 241 0.00337
(1.00) 		0.00306
(1.00) 		0.395
(1.00) 		0.459
(1.00) 		0.201
(1.00) 		0.206
(1.00) 		0.484
(1.00) 		0.124
(1.00)
PIK3CA 64 (21%) 242 0.0486
(1.00) 		0.0554
(1.00) 		0.372
(1.00) 		0.856
(1.00) 		0.119
(1.00) 		0.398
(1.00) 		0.0993
(1.00) 		0.606
(1.00)
FAT1 72 (24%) 234 0.325
(1.00) 		0.227
(1.00) 		0.301
(1.00) 		0.487
(1.00) 		0.152
(1.00) 		0.288
(1.00) 		0.294
(1.00) 		0.172
(1.00)
JUB 18 (6%) 288 0.161
(1.00) 		0.0799
(1.00) 		0.407
(1.00) 		0.0806
(1.00) 		0.305
(1.00) 		0.221
(1.00) 		0.325
(1.00) 		1
(1.00)
MLL2 56 (18%) 250 0.00286
(1.00) 		0.0471
(1.00) 		0.174
(1.00) 		0.311
(1.00) 		0.0532
(1.00) 		0.00795
(1.00) 		0.122
(1.00) 		0.00373
(1.00)
FBXW7 15 (5%) 291 0.777
(1.00) 		0.134
(1.00) 		0.0527
(1.00) 		0.478
(1.00) 		0.881
(1.00) 		0.636
(1.00) 		1
(1.00) 		1
(1.00)
BAGE2 11 (4%) 295 0.522
(1.00) 		0.0999
(1.00) 		0.573
(1.00) 		0.21
(1.00) 		0.253
(1.00) 		0.291
(1.00) 		0.339
(1.00) 		0.139
(1.00)
POTEC 15 (5%) 291 0.167
(1.00) 		0.0364
(1.00) 		0.639
(1.00) 		0.907
(1.00) 		0.17
(1.00) 		0.254
(1.00) 		0.6
(1.00) 		0.169
(1.00)
ZNF750 13 (4%) 293 0.897
(1.00) 		0.159
(1.00) 		0.325
(1.00) 		0.248
(1.00) 		0.119
(1.00) 		0.128
(1.00) 		0.88
(1.00) 		1
(1.00)
EP300 25 (8%) 281 0.433
(1.00) 		0.151
(1.00) 		0.939
(1.00) 		0.302
(1.00) 		0.00955
(1.00) 		0.00467
(1.00) 		0.249
(1.00) 		0.856
(1.00)
POM121L12 14 (5%) 292 0.195
(1.00) 		0.304
(1.00) 		0.105
(1.00) 		0.109
(1.00) 		0.658
(1.00) 		0.657
(1.00) 		0.481
(1.00) 		0.207
(1.00)
RHOA 4 (1%) 302 0.114
(1.00) 		0.54
(1.00) 		0.231
(1.00) 		0.424
(1.00) 		0.245
(1.00) 		0.141
(1.00) 		0.237
(1.00) 		0.395
(1.00)
B2M 7 (2%) 299 0.547
(1.00) 		0.0618
(1.00) 		0.515
(1.00) 		0.517
(1.00) 		0.571
(1.00) 		0.767
(1.00)
RAC1 9 (3%) 297 0.83
(1.00) 		0.585
(1.00) 		1
(1.00) 		0.379
(1.00) 		0.195
(1.00) 		0.192
(1.00) 		0.324
(1.00) 		0.497
(1.00)
ZNF804B 21 (7%) 285 0.482
(1.00) 		0.487
(1.00) 		0.939
(1.00) 		0.915
(1.00) 		0.812
(1.00) 		0.746
(1.00) 		0.959
(1.00) 		0.759
(1.00)
KCNT2 17 (6%) 289 0.148
(1.00) 		0.235
(1.00) 		0.727
(1.00) 		0.478
(1.00) 		0.05
(1.00) 		0.121
(1.00) 		0.0579
(1.00) 		0.0117
(1.00)
RASA1 14 (5%) 292 0.306
(1.00) 		0.24
(1.00) 		0.485
(1.00) 		0.786
(1.00) 		0.357
(1.00) 		0.271
(1.00) 		0.272
(1.00) 		0.0425
(1.00)
PRIM2 9 (3%) 297 0.214
(1.00) 		0.305
(1.00) 		1
(1.00) 		0.5
(1.00) 		0.4
(1.00) 		0.395
(1.00) 		0.53
(1.00) 		0.497
(1.00)
CDH10 23 (8%) 283 0.171
(1.00) 		0.531
(1.00) 		0.593
(1.00) 		0.558
(1.00) 		0.0743
(1.00) 		0.265
(1.00) 		0.242
(1.00) 		0.483
(1.00)
CNTNAP5 15 (5%) 291 0.0655
(1.00) 		0.115
(1.00) 		0.37
(1.00) 		1
(1.00) 		0.0101
(1.00) 		0.0354
(1.00) 		0.0164
(1.00) 		0.169
(1.00)
POTEG 10 (3%) 296 0.0959
(1.00) 		0.0869
(1.00) 		0.0285
(1.00) 		0.741
(1.00) 		0.16
(1.00) 		0.143
(1.00) 		0.79
(1.00) 		0.436
(1.00)
ZNF99 22 (7%) 284 0.687
(1.00) 		0.126
(1.00) 		0.233
(1.00) 		0.436
(1.00) 		0.0343
(1.00) 		0.0116
(1.00) 		0.0131
(1.00) 		0.00332
(1.00)
OR2T12 11 (4%) 295 0.106
(1.00) 		0.12
(1.00) 		0.884
(1.00) 		0.69
(1.00) 		0.552
(1.00) 		0.502
(1.00) 		0.64
(1.00) 		0.68
(1.00)
REG1A 8 (3%) 298 0.375
(1.00) 		0.102
(1.00) 		1
(1.00) 		0.339
(1.00) 		0.058
(1.00) 		0.00131
(0.94) 		0.0765
(1.00) 		0.0515
(1.00)
PABPC5 9 (3%) 297 0.698
(1.00) 		0.407
(1.00) 		0.843
(1.00) 		0.602
(1.00) 		0.089
(1.00) 		0.237
(1.00) 		0.324
(1.00) 		0.81
(1.00)
IL32 4 (1%) 302 0.0781
(1.00) 		0.00177
(1.00) 		0.561
(1.00) 		1
(1.00) 		0.474
(1.00) 		1
(1.00)
PRAMEF11 10 (3%) 296 0.421
(1.00) 		0.438
(1.00) 		1
(1.00) 		0.874
(1.00) 		0.669
(1.00) 		0.606
(1.00) 		0.853
(1.00) 		1
(1.00)
EPHA2 14 (5%) 292 0.296
(1.00) 		0.00256
(1.00) 		0.639
(1.00) 		1
(1.00) 		0.499
(1.00) 		0.57
(1.00) 		0.348
(1.00) 		0.186
(1.00)
FCRL4 13 (4%) 293 0.0784
(1.00) 		0.0179
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.405
(1.00) 		0.106
(1.00) 		0.281
(1.00) 		0.724
(1.00)
LCP1 12 (4%) 294 0.133
(1.00) 		0.000851
(0.612) 		0.555
(1.00) 		0.0359
(1.00) 		0.873
(1.00) 		0.758
(1.00) 		1
(1.00) 		0.244
(1.00)
LRFN5 13 (4%) 293 0.0175
(1.00) 		0.07
(1.00) 		0.521
(1.00) 		0.855
(1.00) 		0.279
(1.00) 		0.0765
(1.00) 		0.0332
(1.00) 		0.387
(1.00)
MAPK1 4 (1%) 302 0.787
(1.00) 		0.924
(1.00) 		0.842
(1.00) 		1
(1.00) 		0.691
(1.00) 		0.686
(1.00) 		0.825
(1.00) 		1
(1.00)
PEG3 23 (8%) 283 0.101
(1.00) 		0.022
(1.00) 		0.371
(1.00) 		0.0892
(1.00) 		0.0217
(1.00) 		0.053
(1.00) 		0.124
(1.00) 		0.296
(1.00)
PRSS1 8 (3%) 298 0.788
(1.00) 		0.478
(1.00) 		0.842
(1.00) 		1
(1.00) 		1
(1.00) 		0.89
(1.00) 		1
(1.00) 		1
(1.00)
DOK6 8 (3%) 298 0.235
(1.00) 		0.582
(1.00) 		0.447
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.605
(1.00) 		0.786
(1.00)
GABRB3 11 (4%) 295 0.559
(1.00) 		0.0147
(1.00) 		0.469
(1.00) 		1
(1.00) 		0.253
(1.00) 		0.192
(1.00) 		0.339
(1.00) 		0.68
(1.00)
STEAP4 10 (3%) 296 0.187
(1.00) 		0.636
(1.00) 		0.653
(1.00) 		0.633
(1.00) 		0.0813
(1.00) 		0.0997
(1.00) 		0.0687
(1.00) 		1
(1.00)
ASXL3 21 (7%) 285 0.712
(1.00) 		0.632
(1.00) 		0.409
(1.00) 		0.331
(1.00) 		0.96
(1.00) 		0.714
(1.00) 		1
(1.00) 		0.359
(1.00)
NTM 7 (2%) 299 0.948
(1.00) 		0.24
(1.00) 		0.128
(1.00) 		0.0226
(1.00) 		0.182
(1.00) 		0.0877
(1.00) 		0.141
(1.00) 		0.405
(1.00)
FAM155A 11 (4%) 295 0.253
(1.00) 		0.0585
(1.00) 		0.332
(1.00) 		0.077
(1.00) 		0.233
(1.00) 		0.175
(1.00) 		0.146
(1.00) 		0.277
(1.00)
HLA-A 9 (3%) 297 0.586
(1.00) 		0.335
(1.00) 		0.44
(1.00) 		1
(1.00) 		0.072
(1.00) 		0.0311
(1.00) 		0.296
(1.00) 		0.386
(1.00)
KRTAP1-5 3 (1%) 303 0.838
(1.00) 		0.807
(1.00) 		0.78
(1.00) 		0.63
(1.00) 		0.0525
(1.00) 		1
(1.00)
CTCF 11 (4%) 295 0.386
(1.00) 		0.401
(1.00) 		0.121
(1.00) 		0.617
(1.00) 		0.636
(1.00) 		0.632
(1.00) 		0.929
(1.00) 		1
(1.00)
BRWD3 16 (5%) 290 0.891
(1.00) 		0.532
(1.00) 		0.205
(1.00) 		1
(1.00) 		0.256
(1.00) 		0.136
(1.00) 		0.316
(1.00) 		0.0456
(1.00)
CNPY3 3 (1%) 303 0.336
(1.00) 		0.48
(1.00) 		0.5
(1.00) 		0.499
(1.00) 		0.38
(1.00) 		0.61
(1.00)
FAM101A 4 (1%) 302 0.477
(1.00) 		0.374
(1.00) 		0.691
(1.00) 		1
(1.00) 		0.825
(1.00) 		0.692
(1.00)
HLA-B 9 (3%) 297 0.253
(1.00) 		0.0957
(1.00) 		0.0877
(1.00) 		0.69
(1.00) 		0.00341
(1.00) 		0.00425
(1.00) 		0.0708
(1.00) 		0.16
(1.00)
PSG8 9 (3%) 297 0.165
(1.00) 		0.618
(1.00) 		0.703
(1.00) 		0.571
(1.00) 		0.483
(1.00) 		0.484
(1.00) 		0.918
(1.00) 		0.386
(1.00)
OR56A1 8 (3%) 298 0.37
(1.00) 		0.0158
(1.00) 		0.751
(1.00) 		0.812
(1.00) 		0.357
(1.00) 		0.352
(1.00) 		0.201
(1.00) 		0.287
(1.00)
OR2M2 8 (3%) 298 0.00675
(1.00) 		0.126
(1.00) 		0.181
(1.00) 		0.0118
(1.00) 		0.498
(1.00) 		0.0946
(1.00)
OR4M2 8 (3%) 298 0.799
(1.00) 		0.88
(1.00) 		0.34
(1.00) 		0.379
(1.00) 		0.643
(1.00) 		0.639
(1.00) 		0.403
(1.00) 		0.603
(1.00)
CPXCR1 7 (2%) 299 0.622
(1.00) 		0.536
(1.00) 		0.206
(1.00) 		0.192
(1.00) 		0.345
(1.00) 		0.498
(1.00) 		0.723
(1.00) 		0.131
(1.00)
EYA1 10 (3%) 296 0.105
(1.00) 		0.636
(1.00) 		0.191
(1.00) 		0.831
(1.00) 		0.0274
(1.00) 		0.0263
(1.00) 		0.919
(1.00) 		0.187
(1.00)
LINGO2 10 (3%) 296 0.268
(1.00) 		0.82
(1.00) 		0.00359
(1.00) 		1
(1.00) 		0.015
(1.00) 		0.0144
(1.00) 		0.0894
(1.00) 		0.117
(1.00)
SEMA5A 19 (6%) 287 0.000736
(0.531) 		0.00318
(1.00) 		1
(1.00) 		1
(1.00) 		0.00661
(1.00) 		0.0234
(1.00) 		0.379
(1.00) 		0.0635
(1.00)
TGFBR2 10 (3%) 296 0.353
(1.00) 		0.201
(1.00) 		0.903
(1.00) 		1
(1.00) 		0.313
(1.00) 		0.785
(1.00) 		0.666
(1.00) 		1
(1.00)
PLSCR1 5 (2%) 301 0.0057
(1.00) 		0.23
(1.00) 		0.802
(1.00) 		1
(1.00) 		0.524
(1.00) 		0.526
(1.00) 		0.737
(1.00) 		0.494
(1.00)
LIN28B 6 (2%) 300 0.409
(1.00) 		0.938
(1.00) 		0.802
(1.00) 		1
(1.00) 		0.737
(1.00) 		0.739
(1.00) 		0.514
(1.00) 		0.515
(1.00)
AGTR1 8 (3%) 298 0.616
(1.00) 		0.401
(1.00) 		0.169
(1.00) 		0.106
(1.00) 		0.181
(1.00) 		0.2
(1.00) 		0.0765
(1.00) 		0.603
(1.00)
C6 12 (4%) 294 0.734
(1.00) 		0.591
(1.00) 		0.157
(1.00) 		1
(1.00) 		0.0762
(1.00) 		0.222
(1.00) 		0.534
(1.00) 		0.582
(1.00)
MS4A14 9 (3%) 297 0.397
(1.00) 		0.418
(1.00) 		0.0584
(1.00) 		1
(1.00) 		0.4
(1.00) 		0.484
(1.00) 		0.268
(1.00) 		0.497
(1.00)
HIST1H4E 5 (2%) 301 0.732
(1.00) 		0.731
(1.00) 		0.156
(1.00) 		0.741
(1.00) 		0.866
(1.00) 		0.386
(1.00) 		0.193
(1.00) 		0.224
(1.00)
LBP 7 (2%) 299 0.76
(1.00) 		0.837
(1.00) 		0.775
(1.00) 		0.771
(1.00) 		1
(1.00) 		0.565
(1.00)
RGS17 5 (2%) 301 0.603
(1.00) 		0.81
(1.00) 		0.157
(1.00) 		0.155
(1.00) 		0.193
(1.00) 		0.224
(1.00)
LILRB1 12 (4%) 294 0.302
(1.00) 		0.166
(1.00) 		0.653
(1.00) 		0.812
(1.00) 		0.861
(1.00) 		0.929
(1.00) 		0.754
(1.00) 		0.423
(1.00)
MAGEL2 12 (4%) 294 0.209
(1.00) 		0.00566
(1.00) 		0.469
(1.00) 		0.352
(1.00) 		0.538
(1.00) 		0.341
(1.00) 		0.659
(1.00) 		0.582
(1.00)
OR8D4 6 (2%) 300 0.992
(1.00) 		0.119
(1.00) 		0.51
(1.00) 		0.42
(1.00) 		0.387
(1.00) 		1
(1.00) 		0.444
(1.00) 		0.748
(1.00)
HIST1H1B 7 (2%) 299 0.429
(1.00) 		0.356
(1.00) 		0.447
(1.00) 		0.812
(1.00) 		0.802
(1.00) 		0.717
(1.00) 		0.723
(1.00) 		0.131
(1.00)
C3ORF59 8 (3%) 298 0.142
(1.00) 		0.476
(1.00) 		0.169
(1.00) 		0.00687
(1.00) 		1
(1.00) 		1
(1.00) 		0.82
(1.00) 		1
(1.00)
C8ORF34 7 (2%) 299 0.847
(1.00) 		0.0892
(1.00) 		0.177
(1.00) 		0.42
(1.00) 		0.802
(1.00) 		1
(1.00) 		0.429
(1.00) 		0.565
(1.00)
OR8J1 9 (3%) 297 0.224
(1.00) 		0.319
(1.00) 		0.128
(1.00) 		0.0226
(1.00) 		0.245
(1.00) 		0.265
(1.00) 		0.268
(1.00) 		0.207
(1.00)
RAB32 3 (1%) 303 0.453
(1.00) 		0.825
(1.00) 		0.613
(1.00) 		0.106
(1.00) 		0.114
(1.00) 		0.116
(1.00) 		0.492
(1.00) 		0.342
(1.00)
TMEM195 8 (3%) 298 0.713
(1.00) 		0.448
(1.00) 		0.531
(1.00) 		0.571
(1.00) 		0.821
(1.00) 		0.905
(1.00) 		1
(1.00) 		1
(1.00)
PCDH11X 21 (7%) 285 0.764
(1.00) 		0.71
(1.00) 		0.401
(1.00) 		0.0572
(1.00) 		0.346
(1.00) 		0.377
(1.00) 		0.882
(1.00) 		0.759
(1.00)
SLITRK4 12 (4%) 294 0.468
(1.00) 		0.178
(1.00) 		0.587
(1.00) 		0.596
(1.00) 		0.092
(1.00) 		0.0896
(1.00) 		0.273
(1.00) 		0.2
(1.00)
FRG2B 6 (2%) 300 0.76
(1.00) 		0.692
(1.00) 		1
(1.00) 		0.664
(1.00) 		0.291
(1.00) 		0.289
(1.00) 		0.0943
(1.00) 		0.748
(1.00)
OR2L13 7 (2%) 299 0.452
(1.00) 		0.101
(1.00) 		0.843
(1.00) 		1
(1.00) 		0.345
(1.00) 		0.498
(1.00) 		0.723
(1.00) 		0.131
(1.00)
CUL3 10 (3%) 296 0.423
(1.00) 		0.124
(1.00) 		0.903
(1.00) 		0.518
(1.00) 		0.403
(1.00) 		0.852
(1.00) 		0.853
(1.00) 		0.52
(1.00)
FOSL2 7 (2%) 299 0.178
(1.00) 		0.611
(1.00) 		0.843
(1.00) 		1
(1.00) 		0.345
(1.00) 		0.717
(1.00) 		0.0869
(1.00) 		0.565
(1.00)
GPR158 12 (4%) 294 0.635
(1.00) 		0.131
(1.00) 		0.469
(1.00) 		0.855
(1.00) 		0.538
(1.00) 		0.531
(1.00) 		0.754
(1.00) 		0.582
(1.00)
PTPRT 19 (6%) 287 0.202
(1.00) 		0.0925
(1.00) 		1
(1.00) 		0.749
(1.00) 		0.0996
(1.00) 		0.693
(1.00) 		0.501
(1.00) 		0.199
(1.00)
POTEH 7 (2%) 299 0.211
(1.00) 		0.55
(1.00) 		0.102
(1.00) 		0.602
(1.00) 		0.123
(1.00) 		0.103
(1.00) 		0.647
(1.00) 		0.767
(1.00)
OR5D13 7 (2%) 299 0.591
(1.00) 		0.16
(1.00) 		0.685
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.767
(1.00)
PRB1 7 (2%) 299 0.554
(1.00) 		0.177
(1.00) 		0.613
(1.00) 		0.664
(1.00) 		0.89
(1.00) 		0.639
(1.00) 		0.141
(1.00) 		0.186
(1.00)
NEUROD6 7 (2%) 299 0.668
(1.00) 		0.862
(1.00) 		0.502
(1.00) 		0.563
(1.00) 		1
(1.00) 		1
(1.00)
DPP10 16 (5%) 290 0.161
(1.00) 		0.12
(1.00) 		0.783
(1.00) 		0.21
(1.00) 		0.17
(1.00) 		0.0574
(1.00) 		0.0154
(1.00) 		0.0456
(1.00)
DPPA4 7 (2%) 299 0.0108
(1.00) 		0.0035
(1.00) 		0.575
(1.00) 		0.119
(1.00) 		0.123
(1.00) 		0.0461
(1.00) 		0.723
(1.00) 		0.767
(1.00)
EPDR1 6 (2%) 300 0.584
(1.00) 		0.799
(1.00) 		0.277
(1.00) 		0.602
(1.00) 		0.327
(1.00) 		0.675
(1.00) 		0.774
(1.00) 		0.748
(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 = 4.53e-06 (Fisher's exact test), Q value = 0.0033

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 122 89
NOTCH1 MUTATED 30 8 18
NOTCH1 WILD-TYPE 63 114 71

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 = 6.93e-05 (Chi-square test), Q value = 0.05

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 CLUS_7
ALL 63 41 44 80 19 9 46
HRAS MUTATED 0 0 0 10 0 0 0
HRAS WILD-TYPE 63 41 44 70 19 9 46

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 = 7.17e-11 (Chi-square test), Q value = 5.2e-08

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 CLUS_7
ALL 63 41 44 80 19 9 46
TP53 MUTATED 53 36 37 30 16 6 34
TP53 WILD-TYPE 10 5 7 50 3 3 12

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 'METHLYATION_CNMF'

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

Table S7.  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 S7.  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 S8.  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 S8.  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 S9.  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 S9.  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 S10.  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 S10.  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 S11.  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 S11.  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)
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