Correlation between gene mutation status and selected clinical features
Adrenocortical Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1R78CX0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1R78CX0
Overview
Introduction

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

Summary

Testing the association between mutation status of 125 genes and 7 clinical features across 56 patients, 2 significant findings detected with Q value < 0.25.

  • NEFH 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 125 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 		AGE 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
NEFH 5 (9%) 51 0.000236
(0.2) 		0.307
(1.00) 		0.652
(1.00) 		0.2
(1.00) 		0.465
(1.00) 		1
(1.00) 		0.145
(1.00)
PTX4 3 (5%) 53 0.000239
(0.203) 		0.267
(1.00) 		0.0263
(1.00) 		0.0725
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ZFPM1 23 (41%) 33 0.175
(1.00) 		0.434
(1.00) 		0.256
(1.00) 		0.949
(1.00) 		0.683
(1.00) 		0.777
(1.00) 		1
(1.00)
LACTB 17 (30%) 39 0.651
(1.00) 		0.695
(1.00) 		0.176
(1.00) 		0.0765
(1.00) 		1
(1.00) 		0.543
(1.00) 		0.646
(1.00)
CCDC102A 16 (29%) 40 0.193
(1.00) 		0.31
(1.00) 		0.138
(1.00) 		0.249
(1.00) 		0.161
(1.00) 		1
(1.00) 		0.639
(1.00)
ZNF517 11 (20%) 45 0.621
(1.00) 		0.117
(1.00) 		0.766
(1.00) 		0.736
(1.00) 		1
(1.00) 		0.732
(1.00) 		0.545
(1.00)
TOR3A 11 (20%) 45 0.575
(1.00) 		0.613
(1.00) 		0.192
(1.00) 		0.182
(1.00) 		0.581
(1.00) 		0.481
(1.00) 		1
(1.00)
USP42 13 (23%) 43 0.355
(1.00) 		0.281
(1.00) 		0.554
(1.00) 		0.811
(1.00) 		0.627
(1.00) 		1
(1.00) 		1
(1.00)
CLDN23 10 (18%) 46 0.992
(1.00) 		0.814
(1.00) 		0.588
(1.00) 		0.656
(1.00) 		0.315
(1.00) 		0.467
(1.00) 		0.545
(1.00)
TP53 11 (20%) 45 0.0356
(1.00) 		0.628
(1.00) 		0.159
(1.00) 		0.406
(1.00) 		1
(1.00) 		0.481
(1.00) 		0.574
(1.00)
KCNK17 8 (14%) 48 0.293
(1.00) 		0.888
(1.00) 		0.892
(1.00) 		0.416
(1.00) 		0.582
(1.00) 		0.423
(1.00) 		0.145
(1.00)
LZTR1 4 (7%) 52 0.159
(1.00) 		0.484
(1.00) 		0.878
(1.00) 		0.882
(1.00) 		0.391
(1.00) 		0.598
(1.00) 		1
(1.00)
APOE 5 (9%) 51 0.676
(1.00) 		0.139
(1.00) 		1
(1.00) 		0.883
(1.00) 		1
(1.00) 		0.324
(1.00)
CCDC105 6 (11%) 50 0.499
(1.00) 		0.361
(1.00) 		0.437
(1.00) 		0.13
(1.00) 		0.532
(1.00) 		0.0857
(1.00) 		1
(1.00)
RINL 7 (12%) 49 0.373
(1.00) 		0.766
(1.00) 		0.602
(1.00) 		0.537
(1.00) 		1
(1.00) 		1
(1.00) 		0.253
(1.00)
MAL2 9 (16%) 47 0.342
(1.00) 		0.215
(1.00) 		0.771
(1.00) 		0.289
(1.00) 		0.267
(1.00) 		0.0212
(1.00) 		0.29
(1.00)
LRIG1 14 (25%) 42 0.566
(1.00) 		0.712
(1.00) 		0.723
(1.00) 		0.898
(1.00) 		0.15
(1.00) 		0.338
(1.00) 		0.639
(1.00)
C19ORF10 6 (11%) 50 0.236
(1.00) 		0.194
(1.00) 		0.111
(1.00) 		0.42
(1.00) 		0.532
(1.00) 		0.652
(1.00) 		1
(1.00)
C10ORF95 6 (11%) 50 0.559
(1.00) 		0.842
(1.00) 		0.382
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.551
(1.00)
SYT8 5 (9%) 51 0.394
(1.00) 		0.537
(1.00) 		0.382
(1.00) 		1
(1.00) 		1
(1.00) 		0.652
(1.00) 		1
(1.00)
IDUA 8 (14%) 48 0.424
(1.00) 		0.153
(1.00) 		0.207
(1.00) 		0.502
(1.00) 		0.582
(1.00) 		1
(1.00) 		0.551
(1.00)
HHIPL1 6 (11%) 50 0.291
(1.00) 		0.333
(1.00) 		0.576
(1.00) 		0.681
(1.00) 		0.532
(1.00) 		0.397
(1.00) 		1
(1.00)
ASPDH 8 (14%) 48 0.803
(1.00) 		0.861
(1.00) 		0.00714
(1.00) 		0.532
(1.00) 		0.131
(1.00) 		0.703
(1.00) 		1
(1.00)
C1ORF106 8 (14%) 48 0.222
(1.00) 		0.504
(1.00) 		0.389
(1.00) 		0.249
(1.00) 		0.219
(1.00) 		0.243
(1.00) 		0.545
(1.00)
THEM4 4 (7%) 52 0.342
(1.00) 		0.445
(1.00) 		0.459
(1.00) 		0.299
(1.00) 		0.308
(1.00) 		1
(1.00) 		1
(1.00)
CTNNB1 6 (11%) 50 0.468
(1.00) 		0.0803
(1.00) 		0.71
(1.00) 		0.926
(1.00) 		0.131
(1.00) 		0.0857
(1.00) 		0.551
(1.00)
GDF1 4 (7%) 52 0.136
(1.00) 		0.874
(1.00) 		0.333
(1.00) 		0.585
(1.00) 		1
(1.00) 		0.598
(1.00) 		1
(1.00)
TSC22D2 8 (14%) 48 0.115
(1.00) 		0.504
(1.00) 		0.573
(1.00) 		0.3
(1.00) 		0.582
(1.00) 		0.703
(1.00) 		1
(1.00)
ZAR1 11 (20%) 45 0.528
(1.00) 		0.543
(1.00) 		0.531
(1.00) 		0.248
(1.00) 		0.592
(1.00) 		0.0769
(1.00) 		0.545
(1.00)
RGS9BP 7 (12%) 49 0.849
(1.00) 		0.664
(1.00) 		0.936
(1.00) 		0.0312
(1.00) 		0.532
(1.00) 		0.679
(1.00) 		0.444
(1.00)
OPRD1 11 (20%) 45 0.767
(1.00) 		0.265
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.299
(1.00) 		1
(1.00)
C16ORF3 5 (9%) 51 0.329
(1.00) 		0.829
(1.00) 		0.569
(1.00) 		0.615
(1.00) 		0.465
(1.00) 		0.155
(1.00) 		1
(1.00)
FPGS 5 (9%) 51 0.786
(1.00) 		0.256
(1.00) 		0.567
(1.00) 		0.618
(1.00) 		0.465
(1.00) 		1
(1.00) 		0.551
(1.00)
PLIN5 5 (9%) 51 0.39
(1.00) 		0.509
(1.00) 		0.92
(1.00) 		1
(1.00) 		0.465
(1.00) 		0.652
(1.00) 		0.444
(1.00)
IRX3 4 (7%) 52 0.874
(1.00) 		0.166
(1.00) 		0.281
(1.00) 		0.457
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
TRIOBP 10 (18%) 46 0.431
(1.00) 		0.856
(1.00) 		0.881
(1.00) 		1
(1.00) 		0.0732
(1.00) 		0.139
(1.00) 		0.639
(1.00)
KRTAP4-5 4 (7%) 52 0.185
(1.00) 		0.787
(1.00) 		0.534
(1.00) 		0.261
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ATXN1 9 (16%) 47 0.822
(1.00) 		0.299
(1.00) 		0.908
(1.00) 		0.507
(1.00) 		1
(1.00) 		0.146
(1.00) 		1
(1.00)
ZNF628 6 (11%) 50 0.241
(1.00) 		0.404
(1.00) 		0.51
(1.00) 		0.391
(1.00) 		1
(1.00) 		1
(1.00) 		0.444
(1.00)
WDR34 5 (9%) 51 0.497
(1.00) 		0.625
(1.00) 		1
(1.00) 		0.883
(1.00) 		1
(1.00) 		0.0406
(1.00) 		1
(1.00)
BTBD11 5 (9%) 51 0.539
(1.00) 		0.635
(1.00) 		0.0108
(1.00) 		0.13
(1.00) 		0.465
(1.00) 		0.652
(1.00) 		1
(1.00)
GARS 17 (30%) 39 0.1
(1.00) 		0.196
(1.00) 		0.0174
(1.00) 		0.0161
(1.00) 		0.655
(1.00) 		0.763
(1.00) 		0.639
(1.00)
ZNF598 10 (18%) 46 0.3
(1.00) 		0.0689
(1.00) 		0.55
(1.00) 		0.893
(1.00) 		0.574
(1.00) 		0.0223
(1.00) 		0.253
(1.00)
BHLHE22 5 (9%) 51 0.259
(1.00) 		0.852
(1.00) 		0.655
(1.00) 		1
(1.00) 		0.0925
(1.00) 		0.652
(1.00) 		0.253
(1.00)
PTPLA 3 (5%) 53 0.7
(1.00) 		1
(1.00) 		0.533
(1.00) 		0.486
(1.00) 		1
(1.00) 		0.263
(1.00) 		0.444
(1.00)
CD320 4 (7%) 52 0.951
(1.00) 		0.332
(1.00) 		0.225
(1.00) 		0.574
(1.00) 		1
(1.00) 		1
(1.00) 		0.145
(1.00)
KIAA1984 3 (5%) 53 0.919
(1.00) 		0.308
(1.00) 		1
(1.00) 		0.263
(1.00) 		0.444
(1.00)
TPO 10 (18%) 46 0.416
(1.00) 		0.889
(1.00) 		0.794
(1.00) 		0.946
(1.00) 		0.0732
(1.00) 		0.72
(1.00) 		1
(1.00)
AATK 5 (9%) 51 0.502
(1.00) 		0.0771
(1.00) 		0.608
(1.00) 		0.682
(1.00) 		0.465
(1.00) 		0.652
(1.00) 		1
(1.00)
PANK2 4 (7%) 52 0.00214
(1.00) 		0.408
(1.00) 		0.879
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.108
(1.00) 		1
(1.00)
SNED1 6 (11%) 50 0.716
(1.00) 		0.771
(1.00) 		0.208
(1.00) 		0.267
(1.00) 		0.131
(1.00) 		0.652
(1.00) 		0.551
(1.00)
CCDC150 4 (7%) 52 0.135
(1.00) 		0.504
(1.00) 		0.0857
(1.00) 		0.179
(1.00) 		0.391
(1.00) 		1
(1.00) 		0.145
(1.00)
ERCC2 10 (18%) 46 0.596
(1.00) 		0.949
(1.00) 		0.69
(1.00) 		0.492
(1.00) 		0.315
(1.00) 		1
(1.00) 		1
(1.00)
RREB1 4 (7%) 52 0.354
(1.00) 		0.874
(1.00) 		0.73
(1.00) 		0.175
(1.00) 		0.0586
(1.00) 		0.598
(1.00) 		0.25
(1.00)
RNF39 5 (9%) 51 0.842
(1.00) 		0.73
(1.00) 		0.73
(1.00) 		0.882
(1.00) 		0.391
(1.00) 		1
(1.00) 		0.444
(1.00)
SEMA5B 6 (11%) 50 0.915
(1.00) 		0.624
(1.00) 		0.575
(1.00) 		0.685
(1.00) 		0.532
(1.00) 		0.165
(1.00) 		1
(1.00)
TAF5 3 (5%) 53 0.333
(1.00) 		0.927
(1.00) 		0.394
(1.00) 		0.808
(1.00) 		0.308
(1.00) 		0.544
(1.00) 		0.25
(1.00)
SARM1 6 (11%) 50 0.101
(1.00) 		0.937
(1.00) 		0.242
(1.00) 		0.2
(1.00) 		1
(1.00) 		0.397
(1.00) 		0.145
(1.00)
PRSS27 3 (5%) 53 0.134
(1.00) 		0.344
(1.00) 		0.617
(1.00) 		0.809
(1.00) 		1
(1.00) 		0.263
(1.00) 		0.0556
(1.00)
TMEM189 3 (5%) 53 0.392
(1.00) 		1
(1.00) 		1
(1.00) 		0.444
(1.00)
NOXA1 4 (7%) 52 0.803
(1.00) 		0.714
(1.00) 		0.878
(1.00) 		0.884
(1.00) 		0.391
(1.00) 		0.288
(1.00) 		1
(1.00)
LRP11 4 (7%) 52 0.154
(1.00) 		0.0747
(1.00) 		0.849
(1.00) 		1
(1.00) 		1
(1.00) 		0.598
(1.00) 		1
(1.00)
RNF149 3 (5%) 53 0.226
(1.00) 		0.126
(1.00) 		0.279
(1.00) 		0.299
(1.00) 		1
(1.00) 		0.544
(1.00) 		1
(1.00)
DMKN 3 (5%) 53 0.163
(1.00) 		0.326
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
FANK1 3 (5%) 53 0.822
(1.00) 		0.353
(1.00) 		0.00829
(1.00) 		0.0514
(1.00) 		0.308
(1.00) 		0.544
(1.00) 		0.551
(1.00)
MUC5B 19 (34%) 37 0.991
(1.00) 		0.924
(1.00) 		0.862
(1.00) 		0.919
(1.00) 		0.651
(1.00) 		0.772
(1.00) 		0.674
(1.00)
GLTPD2 6 (11%) 50 0.494
(1.00) 		0.0736
(1.00) 		0.769
(1.00) 		0.832
(1.00) 		1
(1.00) 		0.397
(1.00) 		0.25
(1.00)
MEN1 5 (9%) 51 0.116
(1.00) 		0.615
(1.00) 		0.0859
(1.00) 		0.217
(1.00) 		0.391
(1.00) 		1
(1.00) 		1
(1.00)
SRPX 3 (5%) 53 0.792
(1.00) 		0.884
(1.00) 		1
(1.00) 		0.39
(1.00) 		0.308
(1.00) 		0.544
(1.00) 		1
(1.00)
MAP1S 5 (9%) 51 0.724
(1.00) 		0.35
(1.00) 		0.381
(1.00) 		0.684
(1.00) 		0.465
(1.00) 		0.324
(1.00) 		1
(1.00)
SCRT1 3 (5%) 53 0.0355
(1.00) 		0.184
(1.00) 		1
(1.00) 		0.807
(1.00) 		0.308
(1.00) 		0.544
(1.00) 		1
(1.00)
OBSCN 18 (32%) 38 0.64
(1.00) 		0.118
(1.00) 		0.314
(1.00) 		0.893
(1.00) 		0.0756
(1.00) 		0.56
(1.00) 		1
(1.00)
IER5 3 (5%) 53 0.501
(1.00) 		0.135
(1.00) 		0.0723
(1.00) 		0.308
(1.00) 		0.544
(1.00) 		1
(1.00)
TNIP2 5 (9%) 51 0.134
(1.00) 		0.666
(1.00) 		0.2
(1.00) 		0.669
(1.00) 		0.0586
(1.00) 		1
(1.00) 		0.551
(1.00)
NOTCH2 5 (9%) 51 0.937
(1.00) 		0.874
(1.00) 		0.881
(1.00) 		0.883
(1.00) 		0.391
(1.00) 		1
(1.00) 		1
(1.00)
RASIP1 7 (12%) 49 0.0225
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.321
(1.00) 		1
(1.00) 		0.403
(1.00) 		1
(1.00)
NMU 4 (7%) 52 0.134
(1.00) 		0.39
(1.00) 		1
(1.00) 		0.884
(1.00) 		0.391
(1.00) 		0.288
(1.00) 		0.444
(1.00)
VARS 6 (11%) 50 0.821
(1.00) 		0.926
(1.00) 		0.292
(1.00) 		0.365
(1.00) 		1
(1.00) 		0.165
(1.00) 		0.0376
(1.00)
HSD17B1 4 (7%) 52 0.657
(1.00) 		0.524
(1.00) 		0.322
(1.00) 		0.458
(1.00) 		1
(1.00) 		1
(1.00) 		0.444
(1.00)
COQ2 4 (7%) 52 0.628
(1.00) 		0.34
(1.00) 		0.417
(1.00) 		0.667
(1.00) 		1
(1.00) 		1
(1.00)
KNDC1 9 (16%) 47 0.628
(1.00) 		0.982
(1.00) 		0.136
(1.00) 		0.196
(1.00) 		1
(1.00) 		0.146
(1.00) 		0.551
(1.00)
AR 4 (7%) 52 0.105
(1.00) 		0.714
(1.00) 		0.728
(1.00) 		0.215
(1.00) 		0.391
(1.00) 		1
(1.00) 		1
(1.00)
KCTD3 3 (5%) 53 0.536
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
KRTAP5-5 3 (5%) 53 0.00164
(1.00) 		0.402
(1.00) 		0.394
(1.00) 		0.809
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
AKAP2 4 (7%) 52 0.874
(1.00) 		0.545
(1.00) 		0.368
(1.00) 		0.882
(1.00) 		1
(1.00) 		0.108
(1.00)
KBTBD13 9 (16%) 47 0.423
(1.00) 		0.569
(1.00) 		0.165
(1.00) 		0.132
(1.00) 		0.267
(1.00) 		0.146
(1.00) 		1
(1.00)
SPIRE2 3 (5%) 53 0.871
(1.00) 		0.0806
(1.00) 		0.533
(1.00) 		0.223
(1.00) 		1
(1.00) 		0.544
(1.00) 		0.25
(1.00)
NPTX1 3 (5%) 53 0.961
(1.00) 		0.827
(1.00) 		0.459
(1.00) 		0.486
(1.00) 		1
(1.00) 		0.263
(1.00) 		1
(1.00)
ADAD2 3 (5%) 53 0.848
(1.00) 		0.942
(1.00) 		1
(1.00) 		0.263
(1.00)
SEZ6L2 5 (9%) 51 0.815
(1.00) 		0.537
(1.00) 		0.14
(1.00) 		0.249
(1.00) 		0.465
(1.00) 		0.652
(1.00) 		0.551
(1.00)
AMDHD1 10 (18%) 46 0.935
(1.00) 		0.0239
(1.00) 		0.694
(1.00) 		0.946
(1.00) 		0.574
(1.00) 		0.281
(1.00) 		1
(1.00)
GLTSCR2 4 (7%) 52 0.644
(1.00) 		0.209
(1.00) 		1
(1.00) 		1
(1.00) 		0.391
(1.00) 		0.108
(1.00) 		1
(1.00)
PLEC 10 (18%) 46 0.332
(1.00) 		0.386
(1.00) 		0.451
(1.00) 		0.585
(1.00) 		1
(1.00) 		0.139
(1.00) 		1
(1.00)
MAP7 3 (5%) 53 0.91
(1.00) 		0.785
(1.00) 		0.851
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
DSPP 9 (16%) 47 0.793
(1.00) 		0.337
(1.00) 		0.952
(1.00) 		0.945
(1.00) 		0.267
(1.00) 		0.703
(1.00) 		0.639
(1.00)
CRIPAK 8 (14%) 48 0.905
(1.00) 		0.325
(1.00) 		0.101
(1.00) 		0.299
(1.00) 		0.574
(1.00) 		0.703
(1.00) 		1
(1.00)
PRKAR1A 6 (11%) 50 0.633
(1.00) 		0.926
(1.00) 		0.206
(1.00) 		0.153
(1.00) 		0.532
(1.00) 		0.0857
(1.00) 		0.444
(1.00)
CYP4A22 3 (5%) 53 0.0575
(1.00) 		0.445
(1.00) 		0.392
(1.00) 		0.806
(1.00) 		1
(1.00) 		1
(1.00) 		0.444
(1.00)
NOM1 5 (9%) 51 0.657
(1.00) 		0.829
(1.00) 		0.167
(1.00) 		0.222
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
C12ORF65 3 (5%) 53 0.000684
(0.58) 		0.251
(1.00) 		0.135
(1.00) 		0.0701
(1.00) 		0.308
(1.00) 		0.544
(1.00) 		1
(1.00)
HLA-B 6 (11%) 50 0.11
(1.00) 		0.947
(1.00) 		0.92
(1.00) 		1
(1.00) 		0.465
(1.00) 		0.165
(1.00) 		1
(1.00)
CSGALNACT2 3 (5%) 53 0.746
(1.00) 		0.799
(1.00) 		0.726
(1.00) 		1
(1.00) 		1
(1.00) 		0.544
(1.00) 		1
(1.00)
UQCRFS1 5 (9%) 51 0.296
(1.00) 		0.0541
(1.00) 		0.0979
(1.00) 		0.0473
(1.00) 		0.465
(1.00) 		1
(1.00) 		0.253
(1.00)
PDCD6 3 (5%) 53 0.963
(1.00) 		0.101
(1.00) 		0.00862
(1.00) 		0.00676
(1.00) 		0.308
(1.00) 		1
(1.00) 		0.25
(1.00)
POLRMT 4 (7%) 52 0.156
(1.00) 		0.911
(1.00) 		0.252
(1.00) 		0.35
(1.00) 		1
(1.00) 		0.598
(1.00)
NF1 7 (12%) 49 0.286
(1.00) 		0.629
(1.00) 		0.658
(1.00) 		0.801
(1.00) 		1
(1.00) 		0.00455
(1.00) 		1
(1.00)
ADAMTS7 4 (7%) 52 0.168
(1.00) 		0.101
(1.00) 		0.254
(1.00) 		0.351
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
CLIC6 4 (7%) 52 0.43
(1.00) 		0.691
(1.00) 		0.421
(1.00) 		0.667
(1.00) 		1
(1.00) 		0.288
(1.00) 		1
(1.00)
EMR2 4 (7%) 52 0.853
(1.00) 		0.0371
(1.00) 		0.723
(1.00) 		1
(1.00) 		1
(1.00) 		0.108
(1.00) 		1
(1.00)
PCDHB13 4 (7%) 52 0.667
(1.00) 		0.0343
(1.00) 		0.199
(1.00) 		0.0959
(1.00) 		1
(1.00) 		0.598
(1.00) 		0.0556
(1.00)
HLA-A 3 (5%) 53 0.315
(1.00) 		0.244
(1.00) 		0.851
(1.00) 		0.392
(1.00) 		1
(1.00) 		0.263
(1.00) 		0.25
(1.00)
ASB16 4 (7%) 52 0.612
(1.00) 		0.436
(1.00) 		1
(1.00) 		0.883
(1.00) 		1
(1.00) 		1
(1.00)
GPRIN2 7 (12%) 49 0.988
(1.00) 		0.647
(1.00) 		0.795
(1.00) 		0.684
(1.00) 		0.582
(1.00) 		1
(1.00) 		1
(1.00)
HNRNPCL1 3 (5%) 53 0.649
(1.00) 		1
(1.00) 		0.81
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
BTNL9 3 (5%) 53 0.755
(1.00) 		0.757
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
KCNJ11 4 (7%) 52 0.496
(1.00) 		0.474
(1.00) 		0.0851
(1.00) 		0.882
(1.00) 		0.0586
(1.00) 		0.598
(1.00) 		1
(1.00)
LRRC4B 6 (11%) 50 0.263
(1.00) 		0.701
(1.00) 		0.39
(1.00) 		1
(1.00) 		0.131
(1.00) 		0.652
(1.00) 		0.545
(1.00)
OPLAH 3 (5%) 53 0.174
(1.00) 		0.308
(1.00) 		0.178
(1.00) 		0.148
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
MADCAM1 3 (5%) 53 0.514
(1.00) 		0.434
(1.00) 		0.179
(1.00) 		0.145
(1.00) 		0.308
(1.00) 		0.544
(1.00) 		0.444
(1.00)
MSH3 3 (5%) 53 0.0412
(1.00) 		0.623
(1.00) 		0.0729
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.544
(1.00) 		1
(1.00)
UTS2R 3 (5%) 53 0.453
(1.00) 		0.326
(1.00) 		0.337
(1.00) 		0.584
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SMG1 3 (5%) 53 0.767
(1.00) 		0.771
(1.00) 		0.136
(1.00) 		0.807
(1.00) 		0.308
(1.00) 		1
(1.00) 		0.551
(1.00)
FEZ2 3 (5%) 53 0.722
(1.00) 		0.445
(1.00) 		0.722
(1.00) 		0.582
(1.00) 		0.308
(1.00) 		1
(1.00) 		0.551
(1.00)
GLI3 5 (9%) 51 0.288
(1.00) 		0.92
(1.00) 		0.0416
(1.00) 		0.0233
(1.00) 		1
(1.00) 		0.652
(1.00) 		1
(1.00)
NOL9 3 (5%) 53 0.878
(1.00) 		0.0608
(1.00) 		1
(1.00) 		0.263
(1.00)
'NEFH MUTATION STATUS' versus 'Time to Death'

P value = 0.000236 (logrank test), Q value = 0.2

Table S1.  Gene #89: 'NEFH MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 55 20 4.1 - 153.6 (36.3)
NEFH MUTATED 5 4 4.9 - 32.7 (15.4)
NEFH WILD-TYPE 50 16 4.1 - 153.6 (40.0)

Figure S1.  Get High-res Image Gene #89: 'NEFH MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PTX4 MUTATION STATUS' versus 'Time to Death'

P value = 0.000239 (logrank test), Q value = 0.2

Table S2.  Gene #104: 'PTX4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 55 20 4.1 - 153.6 (36.3)
PTX4 MUTATED 3 3 5.2 - 30.3 (18.1)
PTX4 WILD-TYPE 52 17 4.1 - 153.6 (39.5)

Figure S2.  Get High-res Image Gene #104: 'PTX4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Clinical data file = ACC-TP.merged_data.txt

  • Number of patients = 56

  • Number of significantly mutated genes = 125

  • 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)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle