Correlation between gene mutation status and selected clinical features
Adrenocortical Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C16W992X
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C16W992X
Overview
Introduction

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

Summary

Testing the association between mutation status of 119 genes and 7 clinical features across 62 patients, 2 significant findings detected with Q value < 0.25.

  • IER5 mutation correlated to 'Time to Death'.

  • PTX4 mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 119 genes and 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		GENDER 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
IER5 3 (5%) 59 0.000211
(0.0877) 		0.588
(1.00) 		0.088
(1.00) 		0.0336
(0.956) 		0.275
(1.00) 		0.546
(1.00) 		1
(1.00)
PTX4 3 (5%) 59 0.000151
(0.0877) 		0.301
(1.00) 		0.0103
(0.858) 		0.0341
(0.956) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ZFPM1 24 (39%) 38 0.202
(1.00) 		0.534
(1.00) 		0.319
(1.00) 		0.974
(1.00) 		0.666
(1.00) 		1
(1.00) 		0.677
(1.00)
LACTB 19 (31%) 43 0.782
(1.00) 		0.945
(1.00) 		0.194
(1.00) 		0.108
(1.00) 		1
(1.00) 		0.568
(1.00) 		0.656
(1.00)
CCDC102A 17 (27%) 45 0.174
(1.00) 		0.477
(1.00) 		0.146
(1.00) 		0.208
(1.00) 		0.17
(1.00) 		1
(1.00) 		1
(1.00)
ZNF517 13 (21%) 49 0.992
(1.00) 		0.0421
(0.956) 		0.736
(1.00) 		0.75
(1.00) 		1
(1.00) 		0.756
(1.00) 		0.306
(1.00)
MAL2 11 (18%) 51 0.753
(1.00) 		0.0708
(1.00) 		0.452
(1.00) 		0.0453
(0.956) 		0.302
(1.00) 		0.0789
(1.00) 		0.3
(1.00)
CLDN23 10 (16%) 52 0.934
(1.00) 		0.716
(1.00) 		0.623
(1.00) 		0.755
(1.00) 		0.259
(1.00) 		0.472
(1.00) 		0.559
(1.00)
TOR3A 12 (19%) 50 0.568
(1.00) 		0.533
(1.00) 		0.187
(1.00) 		0.137
(1.00) 		0.581
(1.00) 		0.74
(1.00) 		1
(1.00)
USP42 15 (24%) 47 0.75
(1.00) 		0.681
(1.00) 		0.528
(1.00) 		0.791
(1.00) 		0.634
(1.00) 		0.541
(1.00) 		1
(1.00)
TP53 12 (19%) 50 0.0415
(0.956) 		0.782
(1.00) 		0.0958
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.58
(1.00)
APOE 7 (11%) 55 0.879
(1.00) 		0.133
(1.00) 		1
(1.00) 		0.919
(1.00) 		1
(1.00) 		0.0861
(1.00) 		1
(1.00)
ZAR1 11 (18%) 51 0.23
(1.00) 		0.672
(1.00) 		0.655
(1.00) 		0.33
(1.00) 		0.302
(1.00) 		0.0789
(1.00) 		0.559
(1.00)
ASPDH 8 (13%) 54 0.333
(1.00) 		0.983
(1.00) 		0.00299
(0.83) 		0.31
(1.00) 		0.105
(1.00) 		0.7
(1.00) 		1
(1.00)
KCNK17 9 (15%) 53 0.281
(1.00) 		0.719
(1.00) 		0.852
(1.00) 		0.429
(1.00) 		0.585
(1.00) 		0.709
(1.00) 		0.18
(1.00)
LZTR1 6 (10%) 56 0.48
(1.00) 		0.46
(1.00) 		1
(1.00) 		1
(1.00) 		0.484
(1.00) 		1
(1.00) 		1
(1.00)
ERCC2 10 (16%) 52 0.841
(1.00) 		0.833
(1.00) 		0.601
(1.00) 		0.636
(1.00) 		0.259
(1.00) 		1
(1.00) 		0.511
(1.00)
RINL 8 (13%) 54 0.359
(1.00) 		0.622
(1.00) 		0.617
(1.00) 		0.515
(1.00) 		1
(1.00) 		0.7
(1.00) 		0.268
(1.00)
SYT8 8 (13%) 54 0.143
(1.00) 		0.407
(1.00) 		0.23
(1.00) 		0.693
(1.00) 		0.585
(1.00) 		1
(1.00) 		0.559
(1.00)
LRIG1 16 (26%) 46 0.792
(1.00) 		0.459
(1.00) 		0.913
(1.00) 		0.745
(1.00) 		0.159
(1.00) 		0.375
(1.00) 		0.644
(1.00)
C1ORF106 9 (15%) 53 0.148
(1.00) 		0.384
(1.00) 		0.515
(1.00) 		0.306
(1.00) 		0.218
(1.00) 		0.14
(1.00) 		0.559
(1.00)
GPRIN2 8 (13%) 54 0.567
(1.00) 		0.401
(1.00) 		0.944
(1.00) 		0.58
(1.00) 		0.585
(1.00) 		1
(1.00) 		1
(1.00)
CTNNB1 7 (11%) 55 0.285
(1.00) 		0.266
(1.00) 		0.684
(1.00) 		0.934
(1.00) 		0.14
(1.00) 		0.0443
(0.956) 		0.559
(1.00)
C16ORF3 5 (8%) 57 0.434
(1.00) 		0.756
(1.00) 		0.238
(1.00) 		0.561
(1.00) 		0.421
(1.00) 		0.151
(1.00) 		1
(1.00)
CCDC105 6 (10%) 56 0.444
(1.00) 		0.432
(1.00) 		0.281
(1.00) 		0.103
(1.00) 		0.484
(1.00) 		0.0808
(1.00) 		0.511
(1.00)
RGS9BP 8 (13%) 54 0.439
(1.00) 		0.983
(1.00) 		0.938
(1.00) 		0.0347
(0.956) 		0.541
(1.00) 		0.438
(1.00) 		0.511
(1.00)
HHIPL1 6 (10%) 56 0.779
(1.00) 		0.6
(1.00) 		0.73
(1.00) 		0.639
(1.00) 		0.484
(1.00) 		0.657
(1.00) 		1
(1.00)
C10ORF95 6 (10%) 56 0.946
(1.00) 		0.536
(1.00) 		0.358
(1.00) 		0.707
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
TSC22D2 8 (13%) 54 0.0252
(0.956) 		0.629
(1.00) 		0.275
(1.00) 		0.112
(1.00) 		1
(1.00) 		0.7
(1.00) 		0.511
(1.00)
NOXA1 5 (8%) 57 0.655
(1.00) 		0.99
(1.00) 		0.897
(1.00) 		0.797
(1.00) 		0.421
(1.00) 		0.151
(1.00) 		1
(1.00)
THEM4 5 (8%) 57 0.426
(1.00) 		0.313
(1.00) 		0.479
(1.00) 		0.387
(1.00) 		0.351
(1.00) 		0.647
(1.00) 		1
(1.00)
ATXN1 10 (16%) 52 0.717
(1.00) 		0.263
(1.00) 		0.749
(1.00) 		0.433
(1.00) 		1
(1.00) 		0.082
(1.00) 		1
(1.00)
PLIN5 5 (8%) 57 0.405
(1.00) 		0.587
(1.00) 		1
(1.00) 		0.894
(1.00) 		0.421
(1.00) 		0.647
(1.00) 		0.374
(1.00)
OPRD1 12 (19%) 50 0.926
(1.00) 		0.139
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.512
(1.00) 		1
(1.00)
KRTAP4-5 5 (8%) 57 0.134
(1.00) 		0.477
(1.00) 		0.573
(1.00) 		0.311
(1.00) 		1
(1.00) 		0.647
(1.00) 		1
(1.00)
C19ORF10 7 (11%) 55 0.932
(1.00) 		0.533
(1.00) 		0.144
(1.00) 		0.476
(1.00) 		0.541
(1.00) 		0.405
(1.00) 		1
(1.00)
AATK 6 (10%) 56 0.336
(1.00) 		0.034
(0.956) 		0.681
(1.00) 		0.709
(1.00) 		0.484
(1.00) 		0.409
(1.00) 		1
(1.00)
SARM1 6 (10%) 56 0.224
(1.00) 		0.739
(1.00) 		0.632
(1.00) 		0.234
(1.00) 		1
(1.00) 		0.657
(1.00) 		0.101
(1.00)
TRIOBP 10 (16%) 52 0.796
(1.00) 		0.767
(1.00) 		0.953
(1.00) 		1
(1.00) 		0.0524
(0.981) 		0.082
(1.00) 		1
(1.00)
ZNF598 12 (19%) 50 0.345
(1.00) 		0.021
(0.956) 		0.513
(1.00) 		0.866
(1.00) 		0.581
(1.00) 		0.0186
(0.956) 		0.58
(1.00)
WDR34 5 (8%) 57 0.539
(1.00) 		0.679
(1.00) 		1
(1.00) 		0.735
(1.00) 		1
(1.00) 		0.0493
(0.956) 		1
(1.00)
ZNF628 7 (11%) 55 0.0281
(0.956) 		0.755
(1.00) 		0.434
(1.00) 		0.415
(1.00) 		1
(1.00) 		1
(1.00) 		0.511
(1.00)
BTBD11 6 (10%) 56 0.707
(1.00) 		0.868
(1.00) 		0.0369
(0.956) 		0.143
(1.00) 		0.484
(1.00) 		0.409
(1.00) 		1
(1.00)
IRX3 5 (8%) 57 0.906
(1.00) 		0.313
(1.00) 		0.236
(1.00) 		0.505
(1.00) 		1
(1.00) 		0.647
(1.00) 		1
(1.00)
FPGS 5 (8%) 57 0.113
(1.00) 		0.319
(1.00) 		0.237
(1.00) 		0.56
(1.00) 		0.421
(1.00) 		1
(1.00) 		1
(1.00)
MEN1 5 (8%) 57 0.0772
(1.00) 		0.688
(1.00) 		0.0332
(0.956) 		0.153
(1.00) 		0.351
(1.00) 		1
(1.00) 		0.511
(1.00)
BHLHE22 5 (8%) 57 0.198
(1.00) 		0.928
(1.00) 		0.287
(1.00) 		0.895
(1.00) 		0.0735
(1.00) 		0.647
(1.00) 		0.18
(1.00)
DMKN 3 (5%) 59 0.199
(1.00) 		0.384
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
OBSCN 18 (29%) 44 0.797
(1.00) 		0.0453
(0.956) 		0.436
(1.00) 		0.838
(1.00) 		0.338
(1.00) 		0.561
(1.00) 		1
(1.00)
PANK2 5 (8%) 57 0.00733
(0.858) 		0.166
(1.00) 		0.897
(1.00) 		0.621
(1.00) 		1
(1.00) 		0.0493
(0.956) 		1
(1.00)
RREB1 5 (8%) 57 0.824
(1.00) 		0.938
(1.00) 		0.634
(1.00) 		0.235
(1.00) 		0.0735
(1.00) 		1
(1.00) 		0.374
(1.00)
RNF149 4 (6%) 58 0.189
(1.00) 		0.0709
(1.00) 		0.23
(1.00) 		0.387
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
GLTPD2 6 (10%) 56 0.389
(1.00) 		0.1
(1.00) 		0.634
(1.00) 		0.619
(1.00) 		1
(1.00) 		0.657
(1.00) 		0.206
(1.00)
SNED1 5 (8%) 57 0.353
(1.00) 		0.737
(1.00) 		0.129
(1.00) 		0.162
(1.00) 		0.0735
(1.00) 		0.647
(1.00) 		1
(1.00)
TPO 12 (19%) 50 0.764
(1.00) 		0.852
(1.00) 		0.865
(1.00) 		0.952
(1.00) 		0.0879
(1.00) 		1
(1.00) 		1
(1.00)
PTPLA 4 (6%) 58 0.681
(1.00) 		0.72
(1.00) 		0.607
(1.00) 		0.641
(1.00) 		1
(1.00) 		0.61
(1.00) 		0.511
(1.00)
PRSS27 3 (5%) 59 0.235
(1.00) 		0.412
(1.00) 		0.468
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.285
(1.00) 		0.0374
(0.956)
CD320 4 (6%) 58 0.364
(1.00) 		0.282
(1.00) 		0.152
(1.00) 		0.274
(1.00) 		1
(1.00) 		1
(1.00) 		0.101
(1.00)
SEMA5B 8 (13%) 54 0.778
(1.00) 		0.644
(1.00) 		0.852
(1.00) 		1
(1.00) 		1
(1.00) 		0.438
(1.00) 		1
(1.00)
CCDC150 4 (6%) 58 0.0832
(1.00) 		0.456
(1.00) 		0.0337
(0.956) 		0.105
(1.00) 		0.351
(1.00) 		1
(1.00) 		0.101
(1.00)
TAF5 4 (6%) 58 0.382
(1.00) 		0.596
(1.00) 		0.32
(1.00) 		0.844
(1.00) 		0.351
(1.00) 		1
(1.00) 		0.374
(1.00)
GARS 19 (31%) 43 0.0285
(0.956) 		0.225
(1.00) 		0.00878
(0.858) 		0.0066
(0.858) 		0.658
(1.00) 		1
(1.00) 		0.644
(1.00)
MUC5B 22 (35%) 40 0.958
(1.00) 		0.581
(1.00) 		0.734
(1.00) 		0.803
(1.00) 		0.412
(1.00) 		1
(1.00) 		1
(1.00)
KIAA1984 4 (6%) 58 0.861
(1.00) 		0.657
(1.00) 		0.833
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.124
(1.00) 		0.511
(1.00)
SRPX 3 (5%) 59 0.928
(1.00) 		0.922
(1.00) 		0.833
(1.00) 		0.624
(1.00) 		0.275
(1.00) 		0.546
(1.00) 		0.511
(1.00)
TNIP2 5 (8%) 57 0.555
(1.00) 		0.605
(1.00) 		0.0865
(1.00) 		0.641
(1.00) 		0.0463
(0.956) 		1
(1.00) 		1
(1.00)
IDUA 8 (13%) 54 0.145
(1.00) 		0.204
(1.00) 		0.109
(1.00) 		0.232
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
RNF39 5 (8%) 57 0.738
(1.00) 		0.776
(1.00) 		0.322
(1.00) 		0.84
(1.00) 		0.351
(1.00) 		1
(1.00) 		0.374
(1.00)
PABPC1 4 (6%) 58 0.646
(1.00) 		0.398
(1.00) 		1
(1.00) 		1
(1.00) 		0.351
(1.00) 		0.61
(1.00) 		0.559
(1.00)
SCRT1 3 (5%) 59 0.0357
(0.956) 		0.225
(1.00) 		0.834
(1.00) 		0.332
(1.00) 		0.275
(1.00) 		0.546
(1.00) 		1
(1.00)
MAP1S 5 (8%) 57 0.688
(1.00) 		0.401
(1.00) 		0.388
(1.00) 		1
(1.00) 		0.421
(1.00) 		0.337
(1.00) 		1
(1.00)
NF1 7 (11%) 55 0.297
(1.00) 		0.681
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.00642
(0.858) 		0.511
(1.00)
AKAP2 4 (6%) 58 0.73
(1.00) 		0.586
(1.00) 		0.32
(1.00) 		0.737
(1.00) 		1
(1.00) 		0.124
(1.00)
NOTCH2 5 (8%) 57 0.474
(1.00) 		0.766
(1.00) 		0.686
(1.00) 		0.465
(1.00) 		0.351
(1.00) 		1
(1.00) 		1
(1.00)
FANK1 4 (6%) 58 0.696
(1.00) 		0.218
(1.00) 		0.062
(1.00) 		0.0853
(1.00) 		0.351
(1.00) 		0.287
(1.00) 		0.559
(1.00)
NEFH 6 (10%) 56 0.21
(1.00) 		0.536
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.484
(1.00) 		1
(1.00) 		0.18
(1.00)
NPTX1 3 (5%) 59 0.979
(1.00) 		0.896
(1.00) 		0.245
(1.00) 		0.244
(1.00) 		1
(1.00) 		0.285
(1.00) 		1
(1.00)
KBTBD13 9 (15%) 53 0.427
(1.00) 		0.497
(1.00) 		0.0883
(1.00) 		0.112
(1.00) 		0.218
(1.00) 		0.14
(1.00) 		1
(1.00)
RASIP1 6 (10%) 56 0.106
(1.00) 		0.99
(1.00) 		0.638
(1.00) 		0.479
(1.00) 		0.484
(1.00) 		0.409
(1.00) 		1
(1.00)
AR 4 (6%) 58 0.141
(1.00) 		0.785
(1.00) 		0.319
(1.00) 		0.155
(1.00) 		0.351
(1.00) 		1
(1.00) 		1
(1.00)
KNDC1 9 (15%) 53 0.169
(1.00) 		0.912
(1.00) 		0.129
(1.00) 		0.068
(1.00) 		1
(1.00) 		0.14
(1.00) 		1
(1.00)
SEZ6L2 8 (13%) 54 0.577
(1.00) 		0.883
(1.00) 		0.851
(1.00) 		0.615
(1.00) 		1
(1.00) 		1
(1.00) 		0.306
(1.00)
VARS 6 (10%) 56 0.967
(1.00) 		0.84
(1.00) 		0.316
(1.00) 		0.233
(1.00) 		1
(1.00) 		0.174
(1.00) 		0.0211
(0.956)
NMU 5 (8%) 57 0.45
(1.00) 		0.272
(1.00) 		1
(1.00) 		0.896
(1.00) 		0.421
(1.00) 		0.151
(1.00) 		0.511
(1.00)
TMEM189 3 (5%) 59 0.207
(1.00) 		0.441
(1.00) 		1
(1.00) 		1
(1.00) 		0.374
(1.00)
ADAD2 4 (6%) 58 0.985
(1.00) 		0.626
(1.00) 		0.836
(1.00) 		1
(1.00) 		1
(1.00) 		0.124
(1.00) 		1
(1.00)
PLEC 13 (21%) 49 0.784
(1.00) 		0.568
(1.00) 		0.82
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.112
(1.00) 		0.644
(1.00)
RGMB 6 (10%) 56 0.823
(1.00) 		0.73
(1.00) 		1
(1.00) 		0.707
(1.00) 		0.484
(1.00) 		1
(1.00) 		0.306
(1.00)
CLIC6 5 (8%) 57 0.338
(1.00) 		0.345
(1.00) 		0.472
(1.00) 		0.707
(1.00) 		1
(1.00) 		0.647
(1.00) 		1
(1.00)
ZNF814 3 (5%) 59 0.196
(1.00) 		0.743
(1.00) 		0.0256
(0.956) 		0.0636
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
DSPP 9 (15%) 53 0.933
(1.00) 		0.412
(1.00) 		0.691
(1.00) 		1
(1.00) 		0.218
(1.00) 		0.471
(1.00) 		1
(1.00)
AMDHD1 10 (16%) 52 0.547
(1.00) 		0.0434
(0.956) 		0.825
(1.00) 		1
(1.00) 		0.578
(1.00) 		0.307
(1.00) 		0.511
(1.00)
CRIPAK 10 (16%) 52 0.648
(1.00) 		0.116
(1.00) 		0.0963
(1.00) 		0.325
(1.00) 		0.577
(1.00) 		1
(1.00) 		1
(1.00)
NOM1 6 (10%) 56 0.923
(1.00) 		0.625
(1.00) 		0.208
(1.00) 		0.258
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
MAP7 3 (5%) 59 0.947
(1.00) 		0.73
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
LRP11 6 (10%) 56 0.649
(1.00) 		0.497
(1.00) 		0.754
(1.00) 		1
(1.00) 		1
(1.00) 		0.657
(1.00) 		0.559
(1.00)
PDCD6 3 (5%) 59 0.929
(1.00) 		0.0879
(1.00) 		0.0103
(0.858) 		0.00482
(0.858) 		0.275
(1.00) 		1
(1.00) 		0.206
(1.00)
SHOX2 3 (5%) 59 0.224
(1.00) 		0.896
(1.00) 		1
(1.00) 		0.784
(1.00) 		0.275
(1.00) 		1
(1.00) 		1
(1.00)
UQCRFS1 5 (8%) 57 0.199
(1.00) 		0.0493
(0.956) 		0.0361
(0.956) 		0.0207
(0.956) 		0.421
(1.00) 		1
(1.00) 		0.18
(1.00)
CTBP2 3 (5%) 59 0.918
(1.00) 		0.244
(1.00) 		0.388
(1.00) 		0.16
(1.00) 		1
(1.00) 		1
(1.00) 		0.511
(1.00)
PRKAR1A 6 (10%) 56 0.784
(1.00) 		0.83
(1.00) 		0.0608
(1.00) 		0.0624
(1.00) 		0.484
(1.00) 		0.0808
(1.00) 		0.374
(1.00)
JMJD4 3 (5%) 59 0.858
(1.00) 		0.844
(1.00) 		1
(1.00) 		0.626
(1.00) 		1
(1.00) 		0.285
(1.00) 		0.374
(1.00)
HSD17B1 4 (6%) 58 0.624
(1.00) 		0.596
(1.00) 		0.186
(1.00) 		0.229
(1.00) 		1
(1.00) 		1
(1.00) 		0.374
(1.00)
COQ2 5 (8%) 57 0.884
(1.00) 		0.124
(1.00) 		0.47
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.647
(1.00) 		1
(1.00)
FEZ2 3 (5%) 59 0.743
(1.00) 		0.491
(1.00) 		0.833
(1.00) 		0.784
(1.00) 		0.275
(1.00) 		1
(1.00) 		1
(1.00)
DLEU7 3 (5%) 59 0.398
(1.00) 		0.611
(1.00) 		0.834
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
RNF135 3 (5%) 59 0.224
(1.00) 		0.831
(1.00) 		0.576
(1.00) 		0.784
(1.00) 		1
(1.00) 		1
(1.00) 		0.511
(1.00)
SPIRE2 3 (5%) 59 0.945
(1.00) 		0.0637
(1.00) 		0.388
(1.00) 		0.16
(1.00) 		1
(1.00) 		0.546
(1.00) 		0.206
(1.00)
KRTAP5-5 3 (5%) 59 0.324
(1.00) 		0.0661
(1.00) 		0.833
(1.00) 		1
(1.00) 		1
(1.00) 		0.285
(1.00) 		1
(1.00)
SGK223 3 (5%) 59 0.737
(1.00) 		0.46
(1.00) 		0.469
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.546
(1.00) 		0.374
(1.00)
C9ORF66 5 (8%) 57 0.233
(1.00) 		0.359
(1.00) 		0.426
(1.00) 		0.561
(1.00) 		1
(1.00) 		0.337
(1.00) 		0.0374
(0.956)
AQP7 3 (5%) 59 0.737
(1.00) 		0.0435
(0.956) 		0.574
(1.00) 		0.784
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ADAMTS7 4 (6%) 58 0.169
(1.00) 		0.129
(1.00) 		0.23
(1.00) 		0.385
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PCDHB13 5 (8%) 57 0.696
(1.00) 		0.127
(1.00) 		0.347
(1.00) 		0.206
(1.00) 		1
(1.00) 		1
(1.00) 		0.101
(1.00)
CSGALNACT2 3 (5%) 59 0.866
(1.00) 		0.706
(1.00) 		0.831
(1.00) 		1
(1.00) 		1
(1.00) 		0.546
(1.00) 		1
(1.00)
HLA-A 3 (5%) 59 0.321
(1.00) 		0.225
(1.00) 		1
(1.00) 		0.625
(1.00) 		1
(1.00) 		0.285
(1.00) 		0.206
(1.00)
MTFMT 3 (5%) 59 0.893
(1.00) 		0.577
(1.00) 		0.833
(1.00) 		1
(1.00) 		1
(1.00) 		0.0407
(0.956) 		1
(1.00)
NLRP5 4 (6%) 58 0.97
(1.00) 		0.053
(0.981) 		0.478
(1.00) 		0.189
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
KCNJ11 4 (6%) 58 0.485
(1.00) 		0.414
(1.00) 		0.0346
(0.956) 		0.736
(1.00) 		0.0463
(0.956) 		0.61
(1.00) 		1
(1.00)
'IER5 MUTATION STATUS' versus 'Time to Death'

P value = 0.000211 (logrank test), Q value = 0.088

Table S1.  Gene #82: 'IER5 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 62 22 0.0 - 153.6 (41.0)
IER5 MUTATED 3 3 0.0 - 32.7 (18.1)
IER5 WILD-TYPE 59 19 4.1 - 153.6 (43.3)

Figure S1.  Get High-res Image Gene #82: 'IER5 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PTX4 MUTATION STATUS' versus 'Time to Death'

P value = 0.000151 (logrank test), Q value = 0.088

Table S2.  Gene #95: 'PTX4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 62 22 0.0 - 153.6 (41.0)
PTX4 MUTATED 3 3 5.2 - 30.3 (18.1)
PTX4 WILD-TYPE 59 19 0.0 - 153.6 (43.3)

Figure S2.  Get High-res Image Gene #95: 'PTX4 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/ACC-TP/15172905/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/15074660/ACC-TP.merged_data.txt

  • Number of patients = 62

  • Number of significantly mutated genes = 119

  • Number of selected clinical features = 7

  • 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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