Correlation between gene mutation status and selected clinical features
Rectum Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
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/C1B27TQV
Overview
Introduction

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

Summary

Testing the association between mutation status of 40 genes and 11 clinical features across 122 patients, no significant finding detected with Q value < 0.25.

  • No gene mutations related to clinical features.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 40 genes and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding 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
NUMBER
OF
LYMPH
NODES
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 Wilcoxon-test
APC 108 (89%) 14 0.305
(1.00)
0.778
(1.00)
0.0546
(1.00)
0.0483
(1.00)
0.629
(1.00)
0.455
(1.00)
0.573
(1.00)
0.703
(1.00)
0.101
(1.00)
0.467
(1.00)
0.878
(1.00)
CRIPAK 11 (9%) 111 0.272
(1.00)
0.183
(1.00)
0.163
(1.00)
0.943
(1.00)
0.117
(1.00)
1
(1.00)
0.22
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.677
(1.00)
TP53 91 (75%) 31 0.022
(1.00)
0.376
(1.00)
0.283
(1.00)
0.0209
(1.00)
0.624
(1.00)
0.764
(1.00)
0.412
(1.00)
0.758
(1.00)
0.0513
(1.00)
0.36
(1.00)
0.408
(1.00)
NRAS 11 (9%) 111 0.499
(1.00)
0.241
(1.00)
0.972
(1.00)
0.072
(1.00)
0.291
(1.00)
1
(1.00)
1
(1.00)
0.681
(1.00)
0.595
(1.00)
0.781
(1.00)
0.163
(1.00)
FMN2 14 (11%) 108 0.819
(1.00)
0.685
(1.00)
0.526
(1.00)
0.522
(1.00)
0.508
(1.00)
1
(1.00)
0.399
(1.00)
0.65
(1.00)
1
(1.00)
0.00774
(1.00)
0.0546
(1.00)
SHROOM4 7 (6%) 115 0.257
(1.00)
0.412
(1.00)
0.806
(1.00)
0.236
(1.00)
1
(1.00)
0.587
(1.00)
0.242
(1.00)
0.6
(1.00)
1
(1.00)
0.433
(1.00)
0.735
(1.00)
RPTN 5 (4%) 117 0.0586
(1.00)
0.245
(1.00)
0.314
(1.00)
0.574
(1.00)
0.143
(1.00)
1
(1.00)
0.174
(1.00)
1
(1.00)
1
(1.00)
0.249
(1.00)
0.225
(1.00)
ARID1A 11 (9%) 111 0.909
(1.00)
0.886
(1.00)
0.0879
(1.00)
0.239
(1.00)
0.911
(1.00)
0.654
(1.00)
0.541
(1.00)
0.274
(1.00)
0.597
(1.00)
1
(1.00)
0.692
(1.00)
CDH1 12 (10%) 110 0.399
(1.00)
0.51
(1.00)
0.385
(1.00)
0.279
(1.00)
0.407
(1.00)
0.188
(1.00)
0.544
(1.00)
1
(1.00)
0.596
(1.00)
0.208
(1.00)
0.181
(1.00)
RBM10 6 (5%) 116 0.228
(1.00)
0.111
(1.00)
0.653
(1.00)
0.85
(1.00)
0.0614
(1.00)
0.172
(1.00)
1
(1.00)
0.585
(1.00)
0.425
(1.00)
0.619
(1.00)
0.294
(1.00)
HAUS6 5 (4%) 117 0.411
(1.00)
0.684
(1.00)
1
(1.00)
0.0777
(1.00)
0.831
(1.00)
1
(1.00)
0.174
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.0611
(1.00)
CTNNB1 19 (16%) 103 0.867
(1.00)
0.37
(1.00)
0.228
(1.00)
0.855
(1.00)
0.428
(1.00)
0.458
(1.00)
0.131
(1.00)
0.0652
(1.00)
1
(1.00)
0.464
(1.00)
0.166
(1.00)
GABRP 4 (3%) 118 0.291
(1.00)
0.666
(1.00)
0.0827
(1.00)
0.072
(1.00)
0.378
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.152
(1.00)
PON3 4 (3%) 118 1
(1.00)
0.284
(1.00)
0.133
(1.00)
1
(1.00)
0.63
(1.00)
0.0231
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
RLIM 4 (3%) 118 0.51
(1.00)
0.167
(1.00)
0.511
(1.00)
1
(1.00)
0.814
(1.00)
0.498
(1.00)
0.626
(1.00)
0.316
(1.00)
1
(1.00)
0.726
(1.00)
SMAD2 6 (5%) 116 0.252
(1.00)
0.794
(1.00)
0.922
(1.00)
0.852
(1.00)
0.526
(1.00)
1
(1.00)
1
(1.00)
0.583
(1.00)
1
(1.00)
0.147
(1.00)
0.13
(1.00)
TCF7L2 12 (10%) 110 0.845
(1.00)
0.294
(1.00)
0.361
(1.00)
0.903
(1.00)
0.044
(1.00)
0.0676
(1.00)
0.222
(1.00)
1
(1.00)
0.597
(1.00)
1
(1.00)
0.231
(1.00)
OXSM 4 (3%) 118 0.588
(1.00)
0.404
(1.00)
0.754
(1.00)
0.312
(1.00)
0.377
(1.00)
1
(1.00)
1
(1.00)
0.537
(1.00)
0.306
(1.00)
0.0154
(1.00)
PCBP1 5 (4%) 117 0.244
(1.00)
0.281
(1.00)
0.343
(1.00)
0.574
(1.00)
0.829
(1.00)
0.579
(1.00)
0.377
(1.00)
0.203
(1.00)
1
(1.00)
1
(1.00)
0.322
(1.00)
KRAS 63 (52%) 59 0.256
(1.00)
0.745
(1.00)
0.722
(1.00)
0.519
(1.00)
0.939
(1.00)
0.794
(1.00)
0.589
(1.00)
0.587
(1.00)
0.743
(1.00)
0.609
(1.00)
0.99
(1.00)
FLT1 8 (7%) 114 0.965
(1.00)
0.979
(1.00)
0.787
(1.00)
0.428
(1.00)
1
(1.00)
0.587
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.74
(1.00)
SLC12A6 6 (5%) 116 0.989
(1.00)
0.582
(1.00)
0.282
(1.00)
0.158
(1.00)
0.154
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.0392
(1.00)
AKAP9 7 (6%) 115 0.216
(1.00)
0.969
(1.00)
0.347
(1.00)
0.0765
(1.00)
0.265
(1.00)
1
(1.00)
1
(1.00)
0.585
(1.00)
0.368
(1.00)
0.375
(1.00)
0.349
(1.00)
VCX2 5 (4%) 117 0.0356
(1.00)
0.141
(1.00)
0.439
(1.00)
0.69
(1.00)
0.293
(1.00)
0.0628
(1.00)
0.657
(1.00)
1
(1.00)
1
(1.00)
0.937
(1.00)
ELF3 4 (3%) 118 0.719
(1.00)
0.165
(1.00)
0.845
(1.00)
0.238
(1.00)
0.499
(1.00)
1
(1.00)
0.626
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.676
(1.00)
PIK3CA 36 (30%) 86 0.0716
(1.00)
0.297
(1.00)
0.582
(1.00)
0.355
(1.00)
0.889
(1.00)
1
(1.00)
0.234
(1.00)
0.136
(1.00)
0.486
(1.00)
0.0482
(1.00)
0.986
(1.00)
BRAF 13 (11%) 109 0.852
(1.00)
0.669
(1.00)
0.217
(1.00)
0.718
(1.00)
0.781
(1.00)
0.687
(1.00)
0.564
(1.00)
1
(1.00)
0.311
(1.00)
0.429
(1.00)
0.962
(1.00)
KIAA1804 10 (8%) 112 0.312
(1.00)
0.163
(1.00)
0.918
(1.00)
0.874
(1.00)
1
(1.00)
1
(1.00)
0.753
(1.00)
0.6
(1.00)
1
(1.00)
1
(1.00)
0.578
(1.00)
ERBB2 9 (7%) 113 0.629
(1.00)
0.81
(1.00)
0.734
(1.00)
0.205
(1.00)
0.691
(1.00)
1
(1.00)
0.183
(1.00)
0.35
(1.00)
1
(1.00)
1
(1.00)
0.248
(1.00)
CDKL5 4 (3%) 118 0.926
(1.00)
0.29
(1.00)
0.598
(1.00)
0.116
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.318
(1.00)
ZNF354C 5 (4%) 117 0.95
(1.00)
0.118
(1.00)
0.859
(1.00)
0.574
(1.00)
1
(1.00)
0.579
(1.00)
0.377
(1.00)
0.583
(1.00)
1
(1.00)
1
(1.00)
0.884
(1.00)
LIG1 4 (3%) 118 0.519
(1.00)
0.989
(1.00)
0.492
(1.00)
0.0943
(1.00)
1
(1.00)
1
(1.00)
0.326
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.494
(1.00)
IQCD 3 (2%) 119 0.699
(1.00)
0.286
(1.00)
0.221
(1.00)
0.192
(1.00)
0.134
(1.00)
1
(1.00)
0.251
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.121
(1.00)
ZBED4 4 (3%) 118 0.287
(1.00)
0.442
(1.00)
0.756
(1.00)
1
(1.00)
0.375
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.0958
(1.00)
GMCL1 4 (3%) 118 0.928
(1.00)
0.0109
(1.00)
0.877
(1.00)
1
(1.00)
0.814
(1.00)
1
(1.00)
0.626
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.585
(1.00)
CIR1 3 (2%) 119 0.901
(1.00)
0.141
(1.00)
0.754
(1.00)
0.13
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.504
(1.00)
AGL 4 (3%) 118 0.47
(1.00)
0.238
(1.00)
0.975
(1.00)
1
(1.00)
0.629
(1.00)
0.498
(1.00)
0.626
(1.00)
0.537
(1.00)
1
(1.00)
0.473
(1.00)
0.778
(1.00)
FAM123B 10 (8%) 112 0.331
(1.00)
0.959
(1.00)
0.488
(1.00)
0.501
(1.00)
0.71
(1.00)
0.146
(1.00)
1
(1.00)
0.585
(1.00)
0.597
(1.00)
0.265
(1.00)
0.548
(1.00)
VANGL1 3 (2%) 119 0.755
(1.00)
0.96
(1.00)
0.911
(1.00)
0.72
(1.00)
1
(1.00)
0.402
(1.00)
0.588
(1.00)
1
(1.00)
1
(1.00)
0.382
(1.00)
0.761
(1.00)
CREBBP 10 (8%) 112 0.332
(1.00)
0.0638
(1.00)
0.626
(1.00)
1
(1.00)
0.901
(1.00)
0.108
(1.00)
0.112
(1.00)
0.35
(1.00)
0.597
(1.00)
0.38
(1.00)
0.926
(1.00)
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/READ-TP/22571878/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/READ-TP/22507018/READ-TP.merged_data.txt

  • Number of patients = 122

  • Number of significantly mutated genes = 40

  • Number of selected clinical features = 11

  • 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)