Correlation between gene mutation status and selected clinical features
Liver Hepatocellular Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1GH9HDK
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/C1GH9HDK
Overview
Introduction

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

Summary

Testing the association between mutation status of 99 genes and 12 clinical features across 373 patients, 12 significant findings detected with Q value < 0.25.

  • TP53 mutation correlated to 'GENDER' and 'RACE'.

  • CTNNB1 mutation correlated to 'GENDER'.

  • BAP1 mutation correlated to 'GENDER'.

  • MLL4 mutation correlated to 'Time to Death'.

  • ALB mutation correlated to 'YEARS_TO_BIRTH'.

  • BAZ2A mutation correlated to 'Time to Death'.

  • PDZD4 mutation correlated to 'RACE'.

  • SKA3 mutation correlated to 'Time to Death'.

  • CBX4 mutation correlated to 'Time to Death'.

  • NR4A2 mutation correlated to 'Time to Death'.

  • SWAP70 mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 99 genes and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 12 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 		HISTOLOGICAL
TYPE 		RESIDUAL
TUMOR 		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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
TP53 114 (31%) 259 0.0264
(0.666) 		0.138
(0.935) 		0.748
(1.00) 		0.225
(1.00) 		0.581
(1.00) 		0.314
(1.00) 		0.00178
(0.212) 		1
(1.00) 		0.86
(1.00) 		0.682
(1.00) 		8e-05
(0.0238) 		0.602
(1.00)
CTNNB1 97 (26%) 276 0.898
(1.00) 		0.0215
(0.637) 		0.979
(1.00) 		0.864
(1.00) 		1
(1.00) 		1
(1.00) 		7.84e-06
(0.00314) 		0.0572
(0.736) 		0.232
(1.00) 		0.182
(0.975) 		0.579
(1.00) 		0.789
(1.00)
BAP1 21 (6%) 352 0.144
(0.935) 		0.424
(1.00) 		0.0827
(0.819) 		0.152
(0.953) 		0.174
(0.975) 		0.178
(0.975) 		3.56e-06
(0.00314) 		1
(1.00) 		0.104
(0.891) 		1
(1.00) 		0.128
(0.935) 		1
(1.00)
MLL4 19 (5%) 354 0.000659
(0.112) 		0.42
(1.00) 		0.535
(1.00) 		1
(1.00) 		1
(1.00) 		0.228
(1.00) 		0.135
(0.935) 		1
(1.00) 		1
(1.00) 		0.0091
(0.541) 		0.137
(0.935) 		0.612
(1.00)
ALB 43 (12%) 330 0.229
(1.00) 		0.00177
(0.212) 		0.476
(1.00) 		0.119
(0.922) 		1
(1.00) 		1
(1.00) 		0.0154
(0.599) 		1
(1.00) 		0.712
(1.00) 		0.855
(1.00) 		0.295
(1.00) 		1
(1.00)
BAZ2A 11 (3%) 362 0.000221
(0.0438) 		0.447
(1.00) 		0.746
(1.00) 		0.772
(1.00) 		1
(1.00) 		1
(1.00) 		0.514
(1.00) 		1
(1.00) 		1
(1.00) 		0.717
(1.00) 		0.0437
(0.709) 		0.441
(1.00)
PDZD4 4 (1%) 369 0.784
(1.00) 		0.795
(1.00) 		0.157
(0.962) 		0.513
(1.00) 		1
(1.00) 		1
(1.00) 		0.309
(1.00) 		1
(1.00) 		1
(1.00) 		0.364
(1.00) 		0.0021
(0.227) 		1
(1.00)
SKA3 4 (1%) 369 0.00247
(0.245) 		0.426
(1.00) 		0.0679
(0.761) 		0.713
(1.00) 		1
(1.00) 		0.0576
(0.736) 		0.598
(1.00) 		1
(1.00) 		1
(1.00) 		0.0149
(0.599) 		0.11
(0.902) 		1
(1.00)
CBX4 6 (2%) 367 0.00135
(0.201) 		0.147
(0.935) 		0.336
(1.00) 		0.796
(1.00) 		1
(1.00) 		1
(1.00) 		0.668
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.776
(1.00) 		1
(1.00)
NR4A2 6 (2%) 367 7.93e-06
(0.00314) 		0.34
(1.00) 		0.184
(0.975) 		0.0628
(0.747) 		1
(1.00) 		1
(1.00) 		0.668
(1.00) 		1
(1.00) 		1
(1.00) 		0.135
(0.935) 		0.778
(1.00) 		1
(1.00)
SWAP70 5 (1%) 368 0.000139
(0.033) 		0.156
(0.961) 		0.679
(1.00) 		0.76
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.232
(1.00) 		1
(1.00)
AXIN1 24 (6%) 349 0.982
(1.00) 		0.113
(0.917) 		0.226
(1.00) 		0.923
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.824
(1.00) 		1
(1.00) 		1
(1.00) 		0.671
(1.00) 		0.045
(0.709) 		0.102
(0.891)
RB1 21 (6%) 352 0.0349
(0.695) 		0.0223
(0.637) 		0.176
(0.975) 		0.0423
(0.709) 		1
(1.00) 		1
(1.00) 		0.339
(1.00) 		0.431
(1.00) 		0.444
(1.00) 		0.863
(1.00) 		0.135
(0.935) 		0.289
(1.00)
ARID1A 32 (9%) 341 0.00585
(0.431) 		0.923
(1.00) 		0.147
(0.935) 		0.498
(1.00) 		1
(1.00) 		1
(1.00) 		0.432
(1.00) 		0.166
(0.975) 		1
(1.00) 		0.445
(1.00) 		0.156
(0.961) 		1
(1.00)
CDC27 15 (4%) 358 0.466
(1.00) 		0.207
(1.00) 		0.792
(1.00) 		0.964
(1.00) 		0.133
(0.935) 		1
(1.00) 		0.782
(1.00) 		0.252
(1.00) 		1
(1.00) 		0.218
(1.00) 		0.0214
(0.637) 		1
(1.00)
CDKN2A 11 (3%) 362 0.169
(0.975) 		0.621
(1.00) 		0.965
(1.00) 		0.855
(1.00) 		1
(1.00) 		1
(1.00) 		0.514
(1.00) 		0.252
(1.00) 		1
(1.00) 		1
(1.00) 		0.0145
(0.599) 		0.441
(1.00)
KRT2 12 (3%) 361 0.418
(1.00) 		0.689
(1.00) 		0.222
(1.00) 		0.706
(1.00) 		1
(1.00) 		1
(1.00) 		0.215
(1.00) 		1
(1.00) 		0.281
(1.00) 		1
(1.00) 		0.884
(1.00) 		1
(1.00)
NFE2L2 13 (3%) 360 0.96
(1.00) 		0.118
(0.922) 		0.7
(1.00) 		0.435
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.292
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PTEN 11 (3%) 362 0.516
(1.00) 		0.133
(0.935) 		0.517
(1.00) 		0.674
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.715
(1.00) 		0.573
(1.00) 		0.377
(1.00)
ARID2 22 (6%) 351 0.0661
(0.758) 		0.167
(0.975) 		0.594
(1.00) 		0.866
(1.00) 		1
(1.00) 		1
(1.00) 		0.359
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.308
(1.00)
RBM10 8 (2%) 365 0.61
(1.00) 		0.675
(1.00) 		0.889
(1.00) 		0.851
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0568
(0.736)
ZNF512B 8 (2%) 365 0.531
(1.00) 		0.0218
(0.637) 		0.943
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.119
(0.922) 		1
(1.00) 		1
(1.00) 		0.214
(1.00) 		0.142
(0.935) 		0.343
(1.00)
KCNN3 12 (3%) 361 0.307
(1.00) 		0.911
(1.00) 		0.743
(1.00) 		0.411
(1.00) 		1
(1.00) 		1
(1.00) 		0.758
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.47
(1.00)
KRT10 9 (2%) 364 0.0496
(0.736) 		0.0393
(0.709) 		0.472
(1.00) 		0.229
(1.00) 		1
(1.00) 		1
(1.00) 		0.282
(1.00) 		1
(1.00) 		0.218
(1.00) 		1
(1.00) 		0.0551
(0.736) 		1
(1.00)
APOB 39 (10%) 334 0.122
(0.923) 		0.031
(0.695) 		0.297
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.364
(1.00) 		0.859
(1.00) 		0.605
(1.00) 		1
(1.00) 		0.783
(1.00) 		0.328
(1.00) 		0.702
(1.00)
TSC2 12 (3%) 361 0.00657
(0.434) 		0.701
(1.00) 		0.0564
(0.736) 		0.00747
(0.467) 		1
(1.00) 		1
(1.00) 		0.758
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.117
(0.922) 		0.41
(1.00)
IL6ST 12 (3%) 361 0.106
(0.891) 		0.14
(0.935) 		1
(1.00) 		0.953
(1.00) 		1
(1.00) 		1
(1.00) 		0.758
(1.00) 		0.0238
(0.643) 		1
(1.00) 		0.747
(1.00) 		0.605
(1.00) 		1
(1.00)
C19ORF55 6 (2%) 367 0.0612
(0.741) 		0.75
(1.00) 		0.52
(1.00) 		0.487
(1.00) 		1
(1.00) 		1
(1.00) 		0.668
(1.00) 		1
(1.00) 		1
(1.00) 		0.495
(1.00) 		1
(1.00) 		1
(1.00)
PIK3CA 13 (3%) 360 0.83
(1.00) 		0.195
(0.992) 		0.691
(1.00) 		0.587
(1.00) 		1
(1.00) 		1
(1.00) 		0.129
(0.935) 		1
(1.00) 		1
(1.00) 		0.776
(1.00) 		0.271
(1.00) 		1
(1.00)
CELA1 6 (2%) 367 0.477
(1.00) 		0.889
(1.00) 		0.164
(0.975) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.668
(1.00) 		1
(1.00) 		1
(1.00) 		0.498
(1.00) 		0.351
(1.00) 		1
(1.00)
RPS6KA3 14 (4%) 359 0.668
(1.00) 		0.465
(1.00) 		0.0388
(0.709) 		0.306
(1.00) 		1
(1.00) 		1
(1.00) 		0.396
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.524
(1.00)
NRD1 13 (3%) 360 0.0939
(0.858) 		0.805
(1.00) 		0.162
(0.97) 		1
(1.00) 		0.133
(0.935) 		1
(1.00) 		0.56
(1.00) 		1
(1.00) 		0.121
(0.923) 		0.381
(1.00) 		0.07
(0.774) 		1
(1.00)
EEF1A1 9 (2%) 364 0.0663
(0.758) 		0.0446
(0.709) 		0.437
(1.00) 		0.139
(0.935) 		1
(1.00) 		1
(1.00) 		0.724
(1.00) 		1
(1.00) 		1
(1.00) 		0.641
(1.00) 		0.242
(1.00) 		0.343
(1.00)
TCHH 17 (5%) 356 0.972
(1.00) 		0.16
(0.966) 		0.144
(0.935) 		0.0175
(0.63) 		1
(1.00) 		0.191
(0.984) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.552
(1.00) 		0.394
(1.00) 		0.21
(1.00)
COG2 4 (1%) 369 0.138
(0.935) 		0.227
(1.00) 		0.864
(1.00) 		0.838
(1.00) 		1
(1.00) 		1
(1.00) 		0.309
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0346
(0.695) 		1
(1.00)
ATXN1 10 (3%) 363 0.272
(1.00) 		0.302
(1.00) 		0.197
(0.994) 		0.197
(0.994) 		0.0903
(0.838) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.076
(0.796) 		1
(1.00)
KCTD20 5 (1%) 368 0.158
(0.962) 		0.266
(1.00) 		0.0249
(0.657) 		0.15
(0.949) 		0.0757
(0.796) 		0.0717
(0.774) 		0.661
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.525
(1.00) 		1
(1.00)
GPR110 6 (2%) 367 0.641
(1.00) 		0.616
(1.00) 		0.109
(0.9) 		0.0613
(0.741) 		1
(1.00) 		1
(1.00) 		0.183
(0.975) 		0.146
(0.935) 		1
(1.00) 		1
(1.00) 		0.582
(1.00) 		1
(1.00)
CEP164 9 (2%) 364 0.427
(1.00) 		0.983
(1.00) 		0.0522
(0.736) 		0.546
(1.00) 		0.105
(0.891) 		0.126
(0.935) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0263
(0.666) 		0.0559
(0.736) 		1
(1.00)
TCEAL6 4 (1%) 369 0.138
(0.935) 		0.227
(1.00) 		0.866
(1.00) 		0.837
(1.00) 		1
(1.00) 		1
(1.00) 		0.309
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0327
(0.695) 		1
(1.00)
DNAJC28 4 (1%) 369 0.0332
(0.695) 		0.0848
(0.819) 		0.817
(1.00) 		0.36
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0655
(0.758) 		0.698
(1.00) 		1
(1.00)
FOXI1 5 (1%) 368 0.0857
(0.821) 		0.941
(1.00) 		0.887
(1.00) 		0.866
(1.00) 		1
(1.00) 		1
(1.00) 		0.179
(0.975) 		1
(1.00) 		1
(1.00) 		0.433
(1.00) 		0.0455
(0.709) 		1
(1.00)
KRTAP5-7 4 (1%) 369 0.339
(1.00) 		0.264
(1.00) 		0.0121
(0.598) 		0.0156
(0.599) 		1
(1.00) 		0.0576
(0.736) 		0.102
(0.891) 		1
(1.00) 		1
(1.00) 		0.363
(1.00) 		0.0736
(0.788) 		0.189
(0.984)
JAK1 14 (4%) 359 0.913
(1.00) 		0.285
(1.00) 		0.341
(1.00) 		0.832
(1.00) 		1
(1.00) 		0.165
(0.975) 		0.562
(1.00) 		0.272
(1.00) 		1
(1.00) 		0.0656
(0.758) 		0.00295
(0.27) 		0.498
(1.00)
DENND4B 12 (3%) 361 0.00617
(0.431) 		0.18
(0.975) 		0.805
(1.00) 		0.795
(1.00) 		1
(1.00) 		1
(1.00) 		0.536
(1.00) 		1
(1.00) 		1
(1.00) 		0.381
(1.00) 		0.0798
(0.811) 		1
(1.00)
BRD7 10 (3%) 363 0.178
(0.975) 		0.0439
(0.709) 		0.385
(1.00) 		0.886
(1.00) 		1
(1.00) 		1
(1.00) 		0.304
(1.00) 		1
(1.00) 		1
(1.00) 		0.46
(1.00) 		0.203
(1.00) 		1
(1.00)
IDH1 8 (2%) 365 0.55
(1.00) 		0.18
(0.975) 		0.105
(0.891) 		0.108
(0.895) 		0.0903
(0.838) 		1
(1.00) 		0.718
(1.00) 		1
(1.00) 		1
(1.00) 		0.0466
(0.71) 		0.826
(1.00) 		1
(1.00)
CNGA3 11 (3%) 362 0.411
(1.00) 		0.254
(1.00) 		0.713
(1.00) 		0.507
(1.00) 		1
(1.00) 		1
(1.00) 		0.514
(1.00) 		1
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.869
(1.00) 		0.41
(1.00)
PLA2G3 6 (2%) 367 0.0346
(0.695) 		0.265
(1.00) 		0.716
(1.00) 		0.709
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.352
(1.00) 		1
(1.00)
HLA-DPB1 5 (1%) 368 0.792
(1.00) 		0.0868
(0.825) 		0.259
(1.00) 		0.133
(0.935) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0542
(0.736) 		1
(1.00)
ALMS1 24 (6%) 349 0.265
(1.00) 		0.944
(1.00) 		0.503
(1.00) 		0.26
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.586
(1.00) 		1
(1.00) 		1
(1.00)
NUCB2 3 (1%) 370 0.00367
(0.311) 		0.843
(1.00) 		0.0442
(0.709) 		0.272
(1.00) 		1
(1.00) 		0.0435
(0.709) 		0.554
(1.00) 		1
(1.00) 		1
(1.00) 		0.0146
(0.599) 		0.66
(1.00) 		1
(1.00)
TAF1B 6 (2%) 367 0.106
(0.891) 		0.195
(0.992) 		1
(1.00) 		0.897
(1.00) 		1
(1.00) 		1
(1.00) 		0.183
(0.975) 		1
(1.00) 		0.151
(0.952) 		1
(1.00) 		0.0305
(0.695) 		1
(1.00)
C1ORF125 11 (3%) 362 0.412
(1.00) 		0.428
(1.00) 		0.467
(1.00) 		0.467
(1.00) 		1
(1.00) 		1
(1.00) 		0.753
(1.00) 		1
(1.00) 		1
(1.00) 		0.496
(1.00) 		0.458
(1.00) 		1
(1.00)
AR 10 (3%) 363 0.0778
(0.796) 		0.878
(1.00) 		0.736
(1.00) 		0.64
(1.00) 		1
(1.00) 		1
(1.00) 		0.0838
(0.819) 		1
(1.00) 		1
(1.00) 		0.682
(1.00) 		0.536
(1.00) 		0.41
(1.00)
SPHK1 6 (2%) 367 0.104
(0.891) 		0.39
(1.00) 		0.283
(1.00) 		0.368
(1.00) 		1
(1.00) 		1
(1.00) 		0.183
(0.975) 		0.146
(0.935) 		1
(1.00) 		1
(1.00) 		0.0613
(0.741) 		1
(1.00)
CREB3L3 5 (1%) 368 0.551
(1.00) 		0.894
(1.00) 		0.504
(1.00) 		0.355
(1.00) 		1
(1.00) 		1
(1.00) 		0.661
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.746
(1.00) 		1
(1.00)
LFNG 7 (2%) 366 0.0421
(0.709) 		0.614
(1.00) 		0.571
(1.00) 		0.439
(1.00) 		1
(1.00) 		1
(1.00) 		0.435
(1.00) 		1
(1.00) 		0.0617
(0.741) 		1
(1.00) 		0.28
(1.00) 		0.307
(1.00)
FZR1 6 (2%) 367 0.525
(1.00) 		0.443
(1.00) 		1
(1.00) 		0.898
(1.00) 		1
(1.00) 		1
(1.00) 		0.183
(0.975) 		0.146
(0.935) 		1
(1.00) 		0.0847
(0.819) 		0.215
(1.00) 		1
(1.00)
TRIOBP 11 (3%) 362 0.784
(1.00) 		0.113
(0.917) 		1
(1.00) 		0.901
(1.00) 		1
(1.00) 		1
(1.00) 		0.514
(1.00) 		1
(1.00) 		1
(1.00) 		0.68
(1.00) 		0.859
(1.00) 		0.41
(1.00)
GJB1 3 (1%) 370 0.0351
(0.695) 		0.402
(1.00) 		0.136
(0.935) 		0.649
(1.00) 		0.046
(0.709) 		1
(1.00) 		0.247
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
DYRK1A 7 (2%) 366 0.0283
(0.695) 		0.03
(0.695) 		0.929
(1.00) 		0.759
(1.00) 		1
(1.00) 		1
(1.00) 		0.435
(1.00) 		1
(1.00) 		0.174
(0.975) 		1
(1.00) 		1
(1.00) 		1
(1.00)
TNPO1 9 (2%) 364 0.872
(1.00) 		0.246
(1.00) 		0.426
(1.00) 		0.673
(1.00) 		1
(1.00) 		1
(1.00) 		0.724
(1.00) 		0.211
(1.00) 		1
(1.00) 		0.0586
(0.741) 		0.498
(1.00) 		1
(1.00)
CCNA2 5 (1%) 368 0.057
(0.736) 		0.75
(1.00) 		0.0213
(0.637) 		0.454
(1.00) 		1
(1.00) 		0.0717
(0.774) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0225
(0.637) 		1
(1.00) 		0.23
(1.00)
AHCTF1 8 (2%) 365 0.812
(1.00) 		0.456
(1.00) 		0.715
(1.00) 		0.923
(1.00) 		1
(1.00) 		1
(1.00) 		0.28
(1.00) 		0.19
(0.984) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
RXRB 8 (2%) 365 0.0403
(0.709) 		0.0875
(0.825) 		0.405
(1.00) 		0.589
(1.00) 		0.0609
(0.741) 		1
(1.00) 		0.28
(1.00) 		0.19
(0.984) 		1
(1.00) 		1
(1.00) 		0.17
(0.975) 		1
(1.00)
PARP1 5 (1%) 368 0.535
(1.00) 		0.305
(1.00) 		0.341
(1.00) 		0.314
(1.00) 		1
(1.00) 		1
(1.00) 		0.661
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0112
(0.576) 		1
(1.00)
NBEA 21 (6%) 352 0.226
(1.00) 		0.489
(1.00) 		0.8
(1.00) 		0.597
(1.00) 		1
(1.00) 		1
(1.00) 		0.813
(1.00) 		1
(1.00) 		1
(1.00) 		0.547
(1.00) 		0.938
(1.00) 		0.613
(1.00)
H6PD 5 (1%) 368 0.568
(1.00) 		0.0775
(0.796) 		0.193
(0.989) 		0.397
(1.00) 		1
(1.00) 		1
(1.00) 		0.661
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
VPS4B 5 (1%) 368 0.428
(1.00) 		0.132
(0.935) 		0.888
(1.00) 		0.866
(1.00) 		1
(1.00) 		1
(1.00) 		0.179
(0.975) 		0.123
(0.923) 		1
(1.00) 		1
(1.00) 		0.524
(1.00) 		0.23
(1.00)
HNRNPL 8 (2%) 365 0.0399
(0.709) 		0.378
(1.00) 		0.703
(1.00) 		0.634
(1.00) 		1
(1.00) 		1
(1.00) 		0.718
(1.00) 		1
(1.00) 		1
(1.00) 		0.377
(1.00) 		0.45
(1.00) 		1
(1.00)
FILIP1 13 (3%) 360 0.022
(0.637) 		0.392
(1.00) 		0.599
(1.00) 		0.394
(1.00) 		1
(1.00) 		1
(1.00) 		0.56
(1.00) 		0.292
(1.00) 		1
(1.00) 		0.298
(1.00) 		0.185
(0.976) 		0.498
(1.00)
FAM22F 4 (1%) 369 0.0843
(0.819) 		0.944
(1.00) 		0.0768
(0.796) 		0.426
(1.00) 		1
(1.00) 		0.0576
(0.736) 		0.598
(1.00) 		1
(1.00) 		1
(1.00) 		0.0142
(0.599) 		1
(1.00) 		1
(1.00)
GPSM2 4 (1%) 369 0.0537
(0.736) 		0.0294
(0.695) 		0.547
(1.00) 		0.713
(1.00) 		1
(1.00) 		1
(1.00) 		0.598
(1.00) 		1
(1.00) 		1
(1.00) 		0.364
(1.00) 		0.295
(1.00) 		1
(1.00)
RCCD1 5 (1%) 368 0.423
(1.00) 		0.807
(1.00) 		0.593
(1.00) 		0.519
(1.00) 		1
(1.00) 		1
(1.00) 		0.179
(0.975) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.746
(1.00) 		1
(1.00)
PTGR1 5 (1%) 368 0.656
(1.00) 		0.566
(1.00) 		0.433
(1.00) 		0.278
(1.00) 		1
(1.00) 		1
(1.00) 		0.179
(0.975) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.746
(1.00) 		1
(1.00)
SAMM50 3 (1%) 370 0.26
(1.00) 		0.43
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.554
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0224
(0.637) 		1
(1.00)
PBRM1 9 (2%) 364 0.804
(1.00) 		0.337
(1.00) 		0.587
(1.00) 		0.762
(1.00) 		1
(1.00) 		1
(1.00) 		0.724
(1.00) 		0.211
(1.00) 		0.219
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SGK269 8 (2%) 365 0.331
(1.00) 		0.443
(1.00) 		0.531
(1.00) 		0.354
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.597
(1.00) 		0.628
(1.00) 		1
(1.00)
LEO1 5 (1%) 368 0.0381
(0.709) 		0.486
(1.00) 		0.156
(0.961) 		0.0558
(0.736) 		1
(1.00) 		1
(1.00) 		0.179
(0.975) 		0.123
(0.923) 		1
(1.00) 		0.431
(1.00) 		0.379
(1.00) 		1
(1.00)
CD97 5 (1%) 368 0.559
(1.00) 		0.884
(1.00) 		0.889
(1.00) 		0.865
(1.00) 		1
(1.00) 		1
(1.00) 		0.334
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0454
(0.709) 		1
(1.00)
MTA1 6 (2%) 367 0.0163
(0.606) 		0.629
(1.00) 		0.656
(1.00) 		0.71
(1.00) 		1
(1.00) 		1
(1.00) 		0.183
(0.975) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.159
(0.964) 		1
(1.00)
CRIP3 6 (2%) 367 0.66
(1.00) 		0.556
(1.00) 		0.916
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.668
(1.00) 		1
(1.00) 		1
(1.00) 		0.286
(1.00) 		1
(1.00) 		1
(1.00)
HNF1A 8 (2%) 365 0.697
(1.00) 		0.293
(1.00) 		0.0932
(0.858) 		0.14
(0.935) 		1
(1.00) 		1
(1.00) 		0.119
(0.922) 		1
(1.00) 		1
(1.00) 		0.597
(1.00) 		0.264
(1.00) 		1
(1.00)
KRAS 6 (2%) 367 1
(1.00) 		0.974
(1.00) 		0.552
(1.00) 		0.406
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0522
(0.736) 		1
(1.00) 		0.775
(1.00) 		1
(1.00)
PGBD1 3 (1%) 370 0.138
(0.935) 		0.929
(1.00) 		0.82
(1.00) 		0.649
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.66
(1.00) 		1
(1.00)
LATS1 7 (2%) 366 0.404
(1.00) 		0.249
(1.00) 		0.871
(1.00) 		0.835
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0676
(0.761) 		1
(1.00) 		1
(1.00)
KEAP1 17 (5%) 356 0.213
(1.00) 		0.583
(1.00) 		0.45
(1.00) 		0.0984
(0.891) 		1
(1.00) 		1
(1.00) 		0.597
(1.00) 		1
(1.00) 		1
(1.00) 		0.55
(1.00) 		0.28
(1.00) 		0.21
(1.00)
SENP6 11 (3%) 362 0.00981
(0.555) 		0.651
(1.00) 		0.617
(1.00) 		0.9
(1.00) 		1
(1.00) 		1
(1.00) 		0.019
(0.637) 		1
(1.00) 		1
(1.00) 		0.34
(1.00) 		0.0714
(0.774) 		1
(1.00)
FKBP4 4 (1%) 369 0.893
(1.00) 		0.919
(1.00) 		0.339
(1.00) 		0.229
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0103
(0.555) 		1
(1.00)
FOXK2 6 (2%) 367 0.0132
(0.599) 		0.0411
(0.709) 		0.63
(1.00) 		0.586
(1.00) 		1
(1.00) 		1
(1.00) 		0.668
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.527
(1.00) 		1
(1.00)
DSPP 21 (6%) 352 0.492
(1.00) 		0.103
(0.891) 		0.183
(0.975) 		0.843
(1.00) 		1
(1.00) 		1
(1.00) 		0.813
(1.00) 		1
(1.00) 		1
(1.00) 		0.461
(1.00) 		0.12
(0.922) 		1
(1.00)
C10ORF28 4 (1%) 369 0.621
(1.00) 		0.242
(1.00) 		0.565
(1.00) 		0.513
(1.00) 		1
(1.00) 		1
(1.00) 		0.309
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.47
(1.00) 		1
(1.00)
PRAMEF4 4 (1%) 369 0.00576
(0.431) 		0.797
(1.00) 		0.191
(0.984) 		0.107
(0.895) 		1
(1.00) 		1
(1.00) 		0.598
(1.00) 		1
(1.00) 		1
(1.00) 		0.365
(1.00) 		1
(1.00) 		0.145
(0.935)
RPS6KA5 5 (1%) 368 0.51
(1.00) 		0.115
(0.922) 		0.539
(1.00) 		0.451
(1.00) 		1
(1.00) 		1
(1.00) 		0.661
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
DDX42 6 (2%) 367 0.0819
(0.819) 		0.234
(1.00) 		0.835
(1.00) 		0.798
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.775
(1.00) 		1
(1.00)
RHCG 4 (1%) 369 0.0232
(0.642) 		0.668
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.309
(1.00) 		1
(1.00) 		1
(1.00) 		0.191
(0.984) 		0.231
(1.00) 		1
(1.00)
BIN1 4 (1%) 369 0.72
(1.00) 		0.297
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0994
(0.891) 		1
(1.00) 		1
(1.00) 		0.0333
(0.695) 		1
(1.00)
SMARCA4 11 (3%) 362 0.0296
(0.695) 		0.442
(1.00) 		0.485
(1.00) 		0.382
(1.00) 		1
(1.00) 		1
(1.00) 		0.753
(1.00) 		1
(1.00) 		1
(1.00) 		0.501
(1.00) 		1
(1.00) 		1
(1.00)
'TP53 MUTATION STATUS' versus 'GENDER'

P value = 0.00178 (Fisher's exact test), Q value = 0.21

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 121 252
TP53 MUTATED 24 90
TP53 WILD-TYPE 97 162

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

'TP53 MUTATION STATUS' versus 'RACE'

P value = 8e-05 (Fisher's exact test), Q value = 0.024

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 160 17 184
TP53 MUTATED 1 58 12 41
TP53 WILD-TYPE 1 102 5 143

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'RACE'

'CTNNB1 MUTATION STATUS' versus 'GENDER'

P value = 7.84e-06 (Fisher's exact test), Q value = 0.0031

Table S3.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 121 252
CTNNB1 MUTATED 14 83
CTNNB1 WILD-TYPE 107 169

Figure S3.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

'BAP1 MUTATION STATUS' versus 'GENDER'

P value = 3.56e-06 (Fisher's exact test), Q value = 0.0031

Table S4.  Gene #6: 'BAP1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 121 252
BAP1 MUTATED 17 4
BAP1 WILD-TYPE 104 248

Figure S4.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

'MLL4 MUTATION STATUS' versus 'Time to Death'

P value = 0.000659 (logrank test), Q value = 0.11

Table S5.  Gene #18: 'MLL4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 367 130 0.0 - 120.8 (19.8)
MLL4 MUTATED 19 10 0.2 - 45.1 (8.6)
MLL4 WILD-TYPE 348 120 0.0 - 120.8 (20.2)

Figure S5.  Get High-res Image Gene #18: 'MLL4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'ALB MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00177 (Wilcoxon-test), Q value = 0.21

Table S6.  Gene #19: 'ALB MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 369 59.1 (13.4)
ALB MUTATED 42 64.9 (11.5)
ALB WILD-TYPE 327 58.4 (13.5)

Figure S6.  Get High-res Image Gene #19: 'ALB MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'BAZ2A MUTATION STATUS' versus 'Time to Death'

P value = 0.000221 (logrank test), Q value = 0.044

Table S7.  Gene #47: 'BAZ2A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 367 130 0.0 - 120.8 (19.8)
BAZ2A MUTATED 11 9 5.6 - 25.1 (19.1)
BAZ2A WILD-TYPE 356 121 0.0 - 120.8 (20.0)

Figure S7.  Get High-res Image Gene #47: 'BAZ2A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PDZD4 MUTATION STATUS' versus 'RACE'

P value = 0.0021 (Fisher's exact test), Q value = 0.23

Table S8.  Gene #59: 'PDZD4 MUTATION STATUS' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 160 17 184
PDZD4 MUTATED 1 0 1 2
PDZD4 WILD-TYPE 1 160 16 182

Figure S8.  Get High-res Image Gene #59: 'PDZD4 MUTATION STATUS' versus Clinical Feature #11: 'RACE'

'SKA3 MUTATION STATUS' versus 'Time to Death'

P value = 0.00247 (logrank test), Q value = 0.24

Table S9.  Gene #78: 'SKA3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 367 130 0.0 - 120.8 (19.8)
SKA3 MUTATED 4 3 0.5 - 18.2 (11.1)
SKA3 WILD-TYPE 363 127 0.0 - 120.8 (20.0)

Figure S9.  Get High-res Image Gene #78: 'SKA3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'CBX4 MUTATION STATUS' versus 'Time to Death'

P value = 0.00135 (logrank test), Q value = 0.2

Table S10.  Gene #79: 'CBX4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 367 130 0.0 - 120.8 (19.8)
CBX4 MUTATED 6 4 1.8 - 20.8 (8.1)
CBX4 WILD-TYPE 361 126 0.0 - 120.8 (20.0)

Figure S10.  Get High-res Image Gene #79: 'CBX4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'NR4A2 MUTATION STATUS' versus 'Time to Death'

P value = 7.93e-06 (logrank test), Q value = 0.0031

Table S11.  Gene #82: 'NR4A2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 367 130 0.0 - 120.8 (19.8)
NR4A2 MUTATED 6 5 0.7 - 25.8 (6.3)
NR4A2 WILD-TYPE 361 125 0.0 - 120.8 (20.0)

Figure S11.  Get High-res Image Gene #82: 'NR4A2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'SWAP70 MUTATION STATUS' versus 'Time to Death'

P value = 0.000139 (logrank test), Q value = 0.033

Table S12.  Gene #97: 'SWAP70 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 367 130 0.0 - 120.8 (19.8)
SWAP70 MUTATED 5 4 0.2 - 20.8 (7.7)
SWAP70 WILD-TYPE 362 126 0.0 - 120.8 (19.9)

Figure S12.  Get High-res Image Gene #97: 'SWAP70 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

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/LIHC-TP/22623049/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/22506983/LIHC-TP.merged_data.txt

  • Number of patients = 373

  • Number of significantly mutated genes = 99

  • Number of selected clinical features = 12

  • 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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