Correlation between gene mutation status and selected clinical features
Esophageal Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1930SJK
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1930SJK
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.

Summary

Testing the association between mutation status of 60 genes and 15 clinical features across 185 patients, 13 significant findings detected with Q value < 0.25.

  • TP53 mutation correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • NFE2L2 mutation correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • ERBB2 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • KIAA2018 mutation correlated to 'YEARS_TO_BIRTH' and 'NUMBER_PACK_YEARS_SMOKED'.

  • DNAH10 mutation correlated to 'PATHOLOGIC_STAGE'.

  • RIC3 mutation correlated to 'YEARS_TO_BIRTH'.

  • IVL mutation correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • LRRC32 mutation correlated to 'RESIDUAL_TUMOR'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 60 genes and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 13 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		NUMBER
PACK
YEARS
SMOKED 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
nMutated (%) nWild-Type logrank test Wilcoxon-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 Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
TP53 153 (83%) 32 0.93
(1.00) 		0.000185
(0.0409) 		0.276
(1.00) 		0.424
(1.00) 		0.443
(1.00) 		1
(1.00) 		0.0946
(0.947) 		0.159
(1.00) 		0.126
(0.992) 		0.0035
(0.242) 		0.975
(1.00) 		0.365
(1.00) 		0.368
(1.00) 		0.00014
(0.0409) 		1
(1.00)
NFE2L2 16 (9%) 169 0.983
(1.00) 		0.0459
(0.774) 		0.189
(1.00) 		0.059
(0.826) 		0.498
(1.00) 		1
(1.00) 		1
(1.00) 		0.742
(1.00) 		0.581
(1.00) 		0.00035
(0.0525) 		0.137
(1.00) 		0.327
(1.00) 		0.245
(1.00) 		4e-05
(0.036) 		0.587
(1.00)
KIAA2018 13 (7%) 172 0.0136
(0.599) 		0.00196
(0.168) 		0.497
(1.00) 		0.795
(1.00) 		0.223
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.733
(1.00) 		0.323
(1.00) 		0.152
(1.00) 		0.00206
(0.168) 		0.45
(1.00) 		0.943
(1.00) 		0.657
(1.00) 		0.334
(1.00)
IVL 15 (8%) 170 0.138
(1.00) 		0.00175
(0.168) 		0.0601
(0.826) 		0.696
(1.00) 		0.186
(1.00) 		0.409
(1.00) 		0.463
(1.00) 		0.119
(0.974) 		0.000208
(0.0409) 		0.0153
(0.599) 		0.569
(1.00) 		0.574
(1.00) 		0.0428
(0.74) 		0.0314
(0.669)
ERBB2 11 (6%) 174 0.222
(1.00) 		0.283
(1.00) 		0.685
(1.00) 		1
(1.00) 		0.391
(1.00) 		1
(1.00) 		0.664
(1.00) 		0.113
(0.964) 		0.000227
(0.0409) 		0.796
(1.00) 		1
(1.00) 		0.525
(1.00) 		0.107
(0.947) 		0.286
(1.00)
DNAH10 19 (10%) 166 0.241
(1.00) 		0.291
(1.00) 		0.00162
(0.168) 		0.395
(1.00) 		0.567
(1.00) 		0.598
(1.00) 		1
(1.00) 		1
(1.00) 		0.226
(1.00) 		0.226
(1.00) 		0.887
(1.00) 		0.101
(0.947) 		0.191
(1.00) 		1
(1.00)
RIC3 4 (2%) 181 0.359
(1.00) 		0.00288
(0.216) 		0.213
(1.00) 		0.836
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.471
(1.00) 		1
(1.00) 		0.353
(1.00) 		0.0317
(0.669) 		0.237
(1.00) 		0.595
(1.00) 		0.628
(1.00)
LRRC32 9 (5%) 176 0.0946
(0.947) 		0.146
(1.00) 		0.935
(1.00) 		0.372
(1.00) 		0.817
(1.00) 		1
(1.00) 		0.361
(1.00) 		0.681
(1.00) 		0.74
(1.00) 		0.238
(1.00) 		0.00074
(0.0951) 		0.136
(1.00) 		0.739
(1.00) 		1
(1.00)
SMAD4 13 (7%) 172 0.389
(1.00) 		0.946
(1.00) 		0.159
(1.00) 		0.605
(1.00) 		0.0387
(0.74) 		1
(1.00) 		0.696
(1.00) 		0.731
(1.00) 		0.0426
(0.74) 		0.716
(1.00) 		0.149
(1.00) 		0.124
(0.989) 		0.42
(1.00) 		1
(1.00)
CDKN2A 19 (10%) 166 0.342
(1.00) 		0.559
(1.00) 		0.225
(1.00) 		1
(1.00) 		0.065
(0.826) 		0.6
(1.00) 		0.489
(1.00) 		0.032
(0.669) 		0.836
(1.00) 		0.0274
(0.669) 		0.518
(1.00) 		0.624
(1.00) 		0.283
(1.00) 		0.365
(1.00) 		0.38
(1.00)
MLL2 32 (17%) 153 0.692
(1.00) 		0.738
(1.00) 		0.27
(1.00) 		0.515
(1.00) 		0.585
(1.00) 		0.685
(1.00) 		0.0946
(0.947) 		0.0645
(0.826) 		0.115
(0.967) 		0.119
(0.974) 		0.234
(1.00) 		0.468
(1.00) 		0.818
(1.00) 		0.0182
(0.602) 		1
(1.00)
ZNF750 10 (5%) 175 0.849
(1.00) 		0.727
(1.00) 		0.546
(1.00) 		0.35
(1.00) 		0.306
(1.00) 		1
(1.00) 		1
(1.00) 		0.238
(1.00) 		0.0869
(0.938) 		0.0191
(0.602) 		0.582
(1.00) 		0.57
(1.00) 		0.905
(1.00) 		0.0173
(0.599) 		1
(1.00)
TGFBR2 15 (8%) 170 0.57
(1.00) 		0.183
(1.00) 		0.188
(1.00) 		0.887
(1.00) 		0.081
(0.9) 		0.519
(1.00) 		0.241
(1.00) 		1
(1.00) 		0.356
(1.00) 		0.596
(1.00) 		0.128
(1.00) 		0.847
(1.00) 		0.428
(1.00) 		0.842
(1.00) 		1
(1.00)
FBXW7 13 (7%) 172 0.253
(1.00) 		0.303
(1.00) 		0.622
(1.00) 		0.567
(1.00) 		0.089
(0.942) 		0.448
(1.00) 		0.102
(0.947) 		0.518
(1.00) 		0.061
(0.826) 		0.152
(1.00) 		0.557
(1.00) 		0.78
(1.00) 		0.284
(1.00) 		0.424
(1.00) 		0.0621
(0.826)
PKD2 7 (4%) 178 0.389
(1.00) 		0.166
(1.00) 		0.982
(1.00) 		0.602
(1.00) 		0.779
(1.00) 		1
(1.00) 		0.596
(1.00) 		0.0388
(0.74) 		0.0732
(0.834) 		0.446
(1.00) 		0.984
(1.00) 		1
(1.00) 		0.933
(1.00) 		0.282
(1.00) 		1
(1.00)
ARID1A 15 (8%) 170 0.874
(1.00) 		0.0612
(0.826) 		0.575
(1.00) 		0.55
(1.00) 		0.211
(1.00) 		1
(1.00) 		0.0482
(0.774) 		0.0225
(0.642) 		0.0136
(0.599) 		0.709
(1.00) 		0.371
(1.00) 		0.284
(1.00) 		0.175
(1.00) 		0.181
(1.00)
PTCH1 12 (6%) 173 0.393
(1.00) 		0.639
(1.00) 		0.66
(1.00) 		0.792
(1.00) 		0.335
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.476
(1.00) 		0.288
(1.00) 		0.136
(1.00) 		0.589
(1.00) 		0.496
(1.00) 		0.843
(1.00) 		0.0652
(0.826) 		0.235
(1.00)
FAM108A1 4 (2%) 181 0.0693
(0.832) 		0.748
(1.00) 		0.877
(1.00) 		0.58
(1.00) 		1
(1.00) 		1
(1.00) 		0.102
(0.947) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.545
(1.00) 		1
(1.00) 		1
(1.00)
PAXIP1 10 (5%) 175 0.552
(1.00) 		0.192
(1.00) 		0.296
(1.00) 		0.136
(1.00) 		0.747
(1.00) 		0.0984
(0.947) 		0.642
(1.00) 		0.696
(1.00) 		0.853
(1.00) 		0.749
(1.00) 		0.251
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.785
(1.00) 		1
(1.00)
MGC29506 4 (2%) 181 0.244
(1.00) 		0.671
(1.00) 		0.281
(1.00) 		0.686
(1.00) 		0.4
(1.00) 		0.228
(1.00) 		0.471
(1.00) 		0.573
(1.00) 		1
(1.00) 		1
(1.00) 		0.287
(1.00) 		0.268
(1.00)
C10ORF76 6 (3%) 179 0.397
(1.00) 		0.52
(1.00) 		0.257
(1.00) 		0.262
(1.00) 		0.166
(1.00) 		1
(1.00) 		0.0413
(0.74) 		1
(1.00) 		0.684
(1.00) 		0.472
(1.00) 		0.592
(1.00) 		0.756
(1.00) 		0.732
(1.00) 		1
(1.00)
IPP 6 (3%) 179 0.49
(1.00) 		0.00907
(0.544) 		0.777
(1.00) 		0.29
(1.00) 		0.302
(1.00) 		1
(1.00) 		1
(1.00) 		0.34
(1.00) 		0.43
(1.00) 		0.489
(1.00) 		1
(1.00) 		0.603
(1.00) 		0.629
(1.00) 		1
(1.00)
HMMR 4 (2%) 181 0.651
(1.00) 		0.428
(1.00) 		0.536
(1.00) 		0.689
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.454
(1.00) 		0.409
(1.00) 		1
(1.00) 		1
(1.00)
PIAS1 5 (3%) 180 0.665
(1.00) 		0.879
(1.00) 		0.292
(1.00) 		0.209
(1.00) 		0.365
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.673
(1.00) 		0.364
(1.00) 		1
(1.00) 		0.82
(1.00) 		0.629
(1.00) 		1
(1.00)
ITGA6 7 (4%) 178 0.529
(1.00) 		0.0409
(0.74) 		0.852
(1.00) 		0.548
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0388
(0.74) 		0.0385
(0.74) 		1
(1.00) 		0.396
(1.00) 		0.288
(1.00) 		0.4
(1.00) 		0.465
(1.00) 		1
(1.00)
ASTE1 5 (3%) 180 0.299
(1.00) 		0.0167
(0.599) 		0.209
(1.00) 		0.416
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.155
(1.00) 		0.573
(1.00) 		0.0243
(0.643) 		0.511
(1.00) 		0.299
(1.00) 		0.256
(1.00) 		0.628
(1.00) 		1
(1.00)
KPNA1 6 (3%) 179 0.4
(1.00) 		0.898
(1.00) 		0.591
(1.00) 		0.499
(1.00) 		0.391
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.648
(1.00) 		0.43
(1.00) 		0.844
(1.00) 		0.598
(1.00) 		0.857
(1.00) 		1
(1.00) 		1
(1.00)
LIMA1 8 (4%) 177 0.639
(1.00) 		0.107
(0.947) 		0.0875
(0.938) 		0.0468
(0.774) 		1
(1.00) 		0.409
(1.00) 		0.0941
(0.947) 		0.681
(1.00) 		0.157
(1.00) 		0.843
(1.00) 		1
(1.00) 		0.368
(1.00) 		0.568
(1.00) 		1
(1.00)
FAM65B 8 (4%) 177 0.513
(1.00) 		0.326
(1.00) 		0.668
(1.00) 		0.596
(1.00) 		0.903
(1.00) 		0.368
(1.00) 		1
(1.00) 		0.192
(1.00) 		0.722
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.633
(1.00) 		1
(1.00) 		1
(1.00)
CORO7 7 (4%) 178 0.0714
(0.834) 		0.382
(1.00) 		0.623
(1.00) 		0.358
(1.00) 		0.562
(1.00) 		1
(1.00) 		0.271
(1.00) 		0.329
(1.00) 		0.264
(1.00) 		0.316
(1.00) 		0.0296
(0.669) 		0.768
(1.00) 		0.321
(1.00) 		1
(1.00)
ANAPC1 5 (3%) 180 0.203
(1.00) 		0.226
(1.00) 		0.438
(1.00) 		1
(1.00) 		0.366
(1.00) 		1
(1.00) 		0.0229
(0.642) 		0.329
(1.00) 		0.673
(1.00) 		1
(1.00) 		0.558
(1.00) 		1
(1.00) 		1
(1.00)
PIK3CA 19 (10%) 166 0.672
(1.00) 		0.0205
(0.615) 		0.953
(1.00) 		0.0718
(0.834) 		0.822
(1.00) 		1
(1.00) 		0.744
(1.00) 		0.771
(1.00) 		0.415
(1.00) 		0.151
(1.00) 		0.152
(1.00) 		0.875
(1.00) 		0.498
(1.00) 		0.593
(1.00) 		0.57
(1.00)
RB1 7 (4%) 178 0.0669
(0.83) 		0.695
(1.00) 		0.515
(1.00) 		0.37
(1.00) 		0.334
(1.00) 		1
(1.00) 		0.271
(1.00) 		0.192
(1.00) 		0.458
(1.00) 		1
(1.00) 		0.289
(1.00) 		1
(1.00) 		0.911
(1.00) 		1
(1.00) 		1
(1.00)
EIF4EBP2 3 (2%) 182 0.677
(1.00) 		0.119
(0.974) 		1
(1.00) 		1
(1.00) 		0.57
(1.00) 		0.109
(0.947) 		0.596
(1.00) 		1
(1.00)
SCD 3 (2%) 182 0.993
(1.00) 		0.105
(0.947) 		0.153
(1.00) 		0.474
(1.00) 		0.0291
(0.669) 		1
(1.00) 		0.379
(1.00) 		1
(1.00) 		0.609
(1.00) 		1
(1.00) 		0.0159
(0.599) 		1
(1.00)
MKL2 6 (3%) 179 0.675
(1.00) 		0.0146
(0.599) 		0.305
(1.00) 		1
(1.00) 		0.365
(1.00) 		1
(1.00) 		1
(1.00) 		0.329
(1.00) 		0.107
(0.947) 		0.0301
(0.669) 		0.302
(1.00) 		0.558
(1.00) 		0.325
(1.00) 		1
(1.00)
NOTCH1 18 (10%) 167 0.924
(1.00) 		0.311
(1.00) 		0.465
(1.00) 		0.35
(1.00) 		0.627
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.365
(1.00) 		0.893
(1.00) 		0.0252
(0.648) 		0.367
(1.00) 		0.537
(1.00) 		0.244
(1.00) 		0.0758
(0.853) 		0.57
(1.00)
KLF3 3 (2%) 182 0.66
(1.00) 		0.0128
(0.599) 		0.422
(1.00) 		1
(1.00) 		0.0649
(0.826) 		1
(1.00) 		0.379
(1.00) 		0.57
(1.00) 		0.109
(0.947) 		1
(1.00) 		0.54
(1.00) 		0.598
(1.00)
IL10RA 3 (2%) 182 0.952
(1.00) 		0.849
(1.00) 		0.466
(1.00) 		0.629
(1.00) 		0.727
(1.00) 		1
(1.00) 		1
(1.00) 		0.163
(1.00) 		0.609
(1.00) 		1
(1.00) 		0.719
(1.00) 		0.596
(1.00) 		1
(1.00)
RAD17 4 (2%) 181 0.186
(1.00) 		0.962
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.611
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.926
(1.00) 		0.622
(1.00) 		0.861
(1.00) 		0.24
(1.00) 		0.624
(1.00) 		1
(1.00) 		1
(1.00)
KPNB1 6 (3%) 179 0.541
(1.00) 		0.0838
(0.919) 		0.945
(1.00) 		0.695
(1.00) 		0.639
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.648
(1.00) 		0.164
(1.00) 		0.213
(1.00) 		0.808
(1.00) 		0.596
(1.00) 		0.4
(1.00) 		0.111
(0.949) 		1
(1.00)
ZBED4 5 (3%) 180 0.7
(1.00) 		0.909
(1.00) 		1
(1.00) 		0.754
(1.00) 		0.672
(1.00) 		1
(1.00) 		1
(1.00) 		0.273
(1.00) 		0.164
(1.00) 		0.37
(1.00) 		0.935
(1.00) 		0.302
(1.00) 		0.269
(1.00) 		1
(1.00)
NAA16 6 (3%) 179 0.777
(1.00) 		0.941
(1.00) 		0.287
(1.00) 		0.0482
(0.774) 		0.0566
(0.826) 		1
(1.00) 		0.595
(1.00) 		0.648
(1.00) 		0.43
(1.00) 		0.733
(1.00) 		0.23
(1.00) 		0.269
(1.00) 		1
(1.00) 		1
(1.00)
CNNM2 7 (4%) 178 0.26
(1.00) 		0.0648
(0.826) 		0.634
(1.00) 		0.341
(1.00) 		0.369
(1.00) 		0.324
(1.00) 		1
(1.00) 		0.679
(1.00) 		0.264
(1.00) 		0.0235
(0.642) 		1
(1.00) 		0.25
(1.00) 		0.736
(1.00) 		1
(1.00)
HLA-B 7 (4%) 178 0.232
(1.00) 		0.871
(1.00) 		0.188
(1.00) 		1
(1.00) 		0.641
(1.00) 		1
(1.00) 		0.271
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.265
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.352
(1.00) 		1
(1.00)
PLXNB2 12 (6%) 173 0.689
(1.00) 		0.641
(1.00) 		0.491
(1.00) 		0.531
(1.00) 		0.319
(1.00) 		1
(1.00) 		1
(1.00) 		0.476
(1.00) 		0.299
(1.00) 		1
(1.00) 		0.658
(1.00) 		1
(1.00) 		0.558
(1.00) 		0.505
(1.00) 		0.463
(1.00)
PTEN 7 (4%) 178 0.371
(1.00) 		0.392
(1.00) 		0.765
(1.00) 		0.243
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.271
(1.00) 		0.679
(1.00) 		0.535
(1.00) 		0.446
(1.00) 		0.984
(1.00) 		1
(1.00) 		0.891
(1.00) 		0.528
(1.00) 		1
(1.00)
CPT1B 5 (3%) 180 0.413
(1.00) 		0.973
(1.00) 		0.748
(1.00) 		0.36
(1.00) 		0.145
(1.00) 		1
(1.00) 		0.55
(1.00) 		1
(1.00) 		1
(1.00) 		0.596
(1.00) 		1
(1.00) 		0.131
(1.00) 		0.166
(1.00) 		0.124
(0.989)
CAMTA1 9 (5%) 176 0.816
(1.00) 		0.153
(1.00) 		0.345
(1.00) 		0.861
(1.00) 		0.141
(1.00) 		1
(1.00) 		0.622
(1.00) 		1
(1.00) 		0.316
(1.00) 		0.378
(1.00) 		0.396
(1.00) 		0.664
(1.00) 		0.738
(1.00) 		1
(1.00)
OTUD7B 7 (4%) 178 0.392
(1.00) 		0.326
(1.00) 		0.617
(1.00) 		0.289
(1.00) 		0.494
(1.00) 		1
(1.00) 		0.0652
(0.826) 		0.648
(1.00) 		0.712
(1.00) 		0.314
(1.00) 		0.599
(1.00) 		0.805
(1.00) 		0.0682
(0.83) 		1
(1.00)
ARRB1 5 (3%) 180 0.759
(1.00) 		0.976
(1.00) 		0.642
(1.00) 		0.578
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.673
(1.00) 		0.337
(1.00) 		0.452
(1.00) 		0.783
(1.00) 		1
(1.00) 		1
(1.00)
KIAA1704 3 (2%) 182 0.231
(1.00) 		0.147
(1.00) 		0.19
(1.00) 		1
(1.00) 		0.0286
(0.669) 		1
(1.00) 		0.379
(1.00) 		0.57
(1.00) 		0.609
(1.00) 		1
(1.00) 		0.188
(1.00) 		1
(1.00)
RNF169 6 (3%) 179 0.724
(1.00) 		0.753
(1.00) 		0.679
(1.00) 		0.561
(1.00) 		1
(1.00) 		0.278
(1.00) 		0.595
(1.00) 		0.108
(0.947) 		0.0732
(0.834) 		0.43
(1.00) 		0.679
(1.00) 		1
(1.00) 		0.519
(1.00) 		1
(1.00) 		1
(1.00)
RBPJL 6 (3%) 179 0.165
(1.00) 		0.16
(1.00) 		1
(1.00) 		0.448
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.212
(1.00) 		0.108
(0.947) 		0.684
(1.00) 		0.369
(1.00) 		0.359
(1.00) 		0.563
(1.00) 		1
(1.00) 		1
(1.00)
MGAT5B 8 (4%) 177 0.0533
(0.826) 		0.468
(1.00) 		0.189
(1.00) 		0.341
(1.00) 		0.016
(0.599) 		0.278
(1.00) 		1
(1.00) 		1
(1.00) 		0.362
(1.00) 		1
(1.00) 		0.605
(1.00) 		0.414
(1.00) 		0.336
(1.00) 		0.739
(1.00) 		0.0194
(0.602)
TCHH 14 (8%) 171 0.24
(1.00) 		0.954
(1.00) 		0.952
(1.00) 		0.124
(0.989) 		0.866
(1.00) 		1
(1.00) 		1
(1.00) 		0.0501
(0.791) 		0.602
(1.00) 		0.784
(1.00) 		0.82
(1.00) 		1
(1.00) 		0.521
(1.00) 		0.0675
(0.83) 		1
(1.00)
SLC22A2 4 (2%) 181 0.85
(1.00) 		0.0984
(0.947) 		0.363
(1.00) 		0.26
(1.00) 		0.477
(1.00) 		0.228
(1.00) 		0.471
(1.00) 		0.163
(1.00) 		0.353
(1.00) 		1
(1.00) 		0.302
(1.00) 		0.405
(1.00) 		1
(1.00)
PCDH15 21 (11%) 164 0.769
(1.00) 		0.509
(1.00) 		0.0985
(0.947) 		0.572
(1.00) 		0.0143
(0.599) 		1
(1.00) 		0.321
(1.00) 		1
(1.00) 		0.591
(1.00) 		0.246
(1.00) 		0.221
(1.00) 		0.484
(1.00) 		0.0122
(0.599) 		0.324
(1.00) 		0.536
(1.00)
KIAA1549 8 (4%) 177 0.733
(1.00) 		0.168
(1.00) 		0.749
(1.00) 		0.0607
(0.826) 		0.409
(1.00) 		1
(1.00) 		0.33
(1.00) 		0.679
(1.00) 		1
(1.00) 		0.187
(1.00) 		1
(1.00) 		0.834
(1.00) 		0.565
(1.00) 		0.181
(1.00)
SETBP1 14 (8%) 171 0.3
(1.00) 		0.00572
(0.368) 		0.615
(1.00) 		0.291
(1.00) 		0.868
(1.00) 		0.581
(1.00) 		1
(1.00) 		1
(1.00) 		0.557
(1.00) 		0.0949
(0.947) 		0.211
(1.00) 		0.429
(1.00) 		0.536
(1.00) 		0.0415
(0.74) 		0.334
(1.00)
'TP53 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000185 (Wilcoxon-test), Q value = 0.041

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 185 62.5 (11.9)
TP53 MUTATED 153 60.9 (11.6)
TP53 WILD-TYPE 32 69.8 (10.7)

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.0035 (Fisher's exact test), Q value = 0.24

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA, NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 89 96
TP53 MUTATED 66 87
TP53 WILD-TYPE 23 9

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'TP53 MUTATION STATUS' versus 'RACE'

P value = 0.00014 (Fisher's exact test), Q value = 0.041

Table S3.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
TP53 MUTATED 46 4 87
TP53 WILD-TYPE 0 1 27

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #14: 'RACE'

'NFE2L2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00035 (Fisher's exact test), Q value = 0.052

Table S4.  Gene #4: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA, NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 89 96
NFE2L2 MUTATED 1 15
NFE2L2 WILD-TYPE 88 81

Figure S4.  Get High-res Image Gene #4: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'NFE2L2 MUTATION STATUS' versus 'RACE'

P value = 4e-05 (Fisher's exact test), Q value = 0.036

Table S5.  Gene #4: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
NFE2L2 MUTATED 12 0 3
NFE2L2 WILD-TYPE 34 5 111

Figure S5.  Get High-res Image Gene #4: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #14: 'RACE'

'ERBB2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.000227 (Fisher's exact test), Q value = 0.041

Table S6.  Gene #11: 'ERBB2 MUTATION STATUS' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA, NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 89 96
ERBB2 MUTATED 11 0
ERBB2 WILD-TYPE 78 96

Figure S6.  Get High-res Image Gene #11: 'ERBB2 MUTATION STATUS' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'KIAA2018 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00196 (Wilcoxon-test), Q value = 0.17

Table S7.  Gene #13: 'KIAA2018 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 185 62.5 (11.9)
KIAA2018 MUTATED 13 72.7 (10.0)
KIAA2018 WILD-TYPE 172 61.7 (11.7)

Figure S7.  Get High-res Image Gene #13: 'KIAA2018 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'KIAA2018 MUTATION STATUS' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00206 (Wilcoxon-test), Q value = 0.17

Table S8.  Gene #13: 'KIAA2018 MUTATION STATUS' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 98 34.5 (21.5)
KIAA2018 MUTATED 7 56.9 (12.7)
KIAA2018 WILD-TYPE 91 32.8 (21.1)

Figure S8.  Get High-res Image Gene #13: 'KIAA2018 MUTATION STATUS' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'DNAH10 MUTATION STATUS' versus 'PATHOLOGIC_STAGE'

P value = 0.00162 (Fisher's exact test), Q value = 0.17

Table S9.  Gene #19: 'DNAH10 MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 8 5 6 1 47 31 26 14 9 7 5 4
DNAH10 MUTATED 3 0 1 0 1 11 1 1 0 1 0 0
DNAH10 WILD-TYPE 5 5 5 1 46 20 25 13 9 6 5 4

Figure S9.  Get High-res Image Gene #19: 'DNAH10 MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'RIC3 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00288 (Wilcoxon-test), Q value = 0.22

Table S10.  Gene #20: 'RIC3 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 185 62.5 (11.9)
RIC3 MUTATED 4 82.2 (6.1)
RIC3 WILD-TYPE 181 62.0 (11.6)

Figure S10.  Get High-res Image Gene #20: 'RIC3 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'IVL MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00175 (Wilcoxon-test), Q value = 0.17

Table S11.  Gene #30: 'IVL MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 185 62.5 (11.9)
IVL MUTATED 15 71.8 (10.0)
IVL WILD-TYPE 170 61.6 (11.7)

Figure S11.  Get High-res Image Gene #30: 'IVL MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'IVL MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.000208 (Fisher's exact test), Q value = 0.041

Table S12.  Gene #30: 'IVL MUTATION STATUS' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA, NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 89 96
IVL MUTATED 14 1
IVL WILD-TYPE 75 95

Figure S12.  Get High-res Image Gene #30: 'IVL MUTATION STATUS' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'LRRC32 MUTATION STATUS' versus 'RESIDUAL_TUMOR'

P value = 0.00074 (Fisher's exact test), Q value = 0.095

Table S13.  Gene #55: 'LRRC32 MUTATION STATUS' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 137 13 2 7
LRRC32 MUTATED 3 2 0 3
LRRC32 WILD-TYPE 134 11 2 4

Figure S13.  Get High-res Image Gene #55: 'LRRC32 MUTATION STATUS' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/22588509/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/22506419/ESCA-TP.merged_data.txt

  • Number of patients = 185

  • Number of significantly mutated genes = 60

  • Number of selected clinical features = 15

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

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[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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