This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 18 genes and 11 clinical features across 194 patients, 9 significant findings detected with Q value < 0.25.
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TP53 mutation correlated to 'GENDER' and 'RACE'.
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CTNNB1 mutation correlated to 'GENDER'.
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RB1 mutation correlated to 'YEARS_TO_BIRTH' and 'RACE'.
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BAP1 mutation correlated to 'GENDER'.
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IL6ST mutation correlated to 'Time to Death'.
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ALB mutation correlated to 'RACE'.
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HIST1H1C mutation correlated to 'PATHOLOGY_T_STAGE'.
Table 1. Get Full Table Overview of the association between mutation status of 18 genes and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 9 significant findings detected.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
COMPLETENESS OF RESECTION |
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 | |
TP53 | 61 (31%) | 133 |
0.338 (0.985) |
0.087 (0.749) |
0.136 (0.887) |
0.0549 (0.561) |
0.559 (1.00) |
0.308 (0.962) |
0.000623 (0.0308) |
0.694 (1.00) |
0.961 (1.00) |
0.00014 (0.0139) |
1 (1.00) |
RB1 | 15 (8%) | 179 |
0.89 (1.00) |
0.00267 (0.106) |
0.454 (1.00) |
0.18 (0.887) |
1 (1.00) |
1 (1.00) |
0.404 (1.00) |
1 (1.00) |
0.528 (1.00) |
0.00706 (0.175) |
0.358 (1.00) |
CTNNB1 | 50 (26%) | 144 |
0.99 (1.00) |
0.208 (0.887) |
0.75 (1.00) |
0.598 (1.00) |
0.161 (0.887) |
1 (1.00) |
3.08e-05 (0.0061) |
0.683 (1.00) |
0.117 (0.86) |
0.287 (0.962) |
1 (1.00) |
BAP1 | 10 (5%) | 184 |
0.185 (0.887) |
0.804 (1.00) |
0.0476 (0.555) |
0.036 (0.509) |
0.181 (0.887) |
0.227 (0.892) |
0.000452 (0.0298) |
1 (1.00) |
0.596 (1.00) |
1 (1.00) |
1 (1.00) |
IL6ST | 7 (4%) | 187 |
0.0045 (0.133) |
0.17 (0.887) |
0.953 (1.00) |
0.866 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.685 (1.00) |
0.825 (1.00) |
1 (1.00) |
ALB | 18 (9%) | 176 |
0.504 (1.00) |
0.028 (0.462) |
0.241 (0.904) |
0.112 (0.856) |
0.243 (0.904) |
1 (1.00) |
0.0356 (0.509) |
1 (1.00) |
0.405 (1.00) |
0.00847 (0.186) |
1 (1.00) |
HIST1H1C | 5 (3%) | 189 |
0.219 (0.892) |
0.88 (1.00) |
0.0445 (0.555) |
0.00469 (0.133) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.101 (0.799) |
0.32 (0.962) |
0.022 (0.436) |
1 (1.00) |
AXIN1 | 9 (5%) | 185 |
0.141 (0.887) |
0.799 (1.00) |
0.0942 (0.777) |
0.631 (1.00) |
1 (1.00) |
0.18 (0.887) |
1 (1.00) |
1 (1.00) |
0.297 (0.962) |
1 (1.00) |
0.206 (0.887) |
TSC2 | 9 (5%) | 185 |
0.771 (1.00) |
0.515 (1.00) |
0.177 (0.887) |
0.0765 (0.689) |
1 (1.00) |
1 (1.00) |
0.723 (1.00) |
1 (1.00) |
0.547 (1.00) |
0.211 (0.887) |
0.183 (0.887) |
ARID1A | 16 (8%) | 178 |
0.0567 (0.561) |
0.295 (0.962) |
0.188 (0.887) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.313 (0.962) |
0.467 (1.00) |
1 (1.00) |
HNF1A | 8 (4%) | 186 |
0.482 (1.00) |
0.403 (1.00) |
0.23 (0.892) |
0.281 (0.962) |
1 (1.00) |
1 (1.00) |
0.458 (1.00) |
1 (1.00) |
0.247 (0.904) |
0.687 (1.00) |
1 (1.00) |
APOB | 23 (12%) | 171 |
0.695 (1.00) |
0.325 (0.962) |
0.21 (0.887) |
0.846 (1.00) |
1 (1.00) |
0.413 (1.00) |
0.487 (1.00) |
1 (1.00) |
0.741 (1.00) |
0.0541 (0.561) |
1 (1.00) |
EEF1A1 | 5 (3%) | 189 |
0.0277 (0.462) |
0.326 (0.962) |
0.667 (1.00) |
0.385 (1.00) |
1 (1.00) |
1 (1.00) |
0.163 (0.887) |
1 (1.00) |
0.559 (1.00) |
0.179 (0.887) |
1 (1.00) |
KIF19 | 10 (5%) | 184 |
0.0702 (0.662) |
0.0452 (0.555) |
0.919 (1.00) |
0.637 (1.00) |
1 (1.00) |
1 (1.00) |
0.499 (1.00) |
1 (1.00) |
0.597 (1.00) |
0.507 (1.00) |
1 (1.00) |
GNAS | 7 (4%) | 187 |
0.158 (0.887) |
0.975 (1.00) |
0.684 (1.00) |
0.314 (0.962) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.693 (1.00) |
1 (1.00) |
F5 | 4 (2%) | 190 |
0.473 (1.00) |
0.225 (0.892) |
0.62 (1.00) |
0.446 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
PTEN | 7 (4%) | 187 |
0.566 (1.00) |
0.26 (0.936) |
0.85 (1.00) |
0.761 (1.00) |
1 (1.00) |
1 (1.00) |
0.425 (1.00) |
1 (1.00) |
0.202 (0.887) |
0.458 (1.00) |
0.158 (0.887) |
DLK2 | 4 (2%) | 190 |
0.37 (1.00) |
0.733 (1.00) |
0.475 (1.00) |
0.301 (0.962) |
1 (1.00) |
1 (1.00) |
0.299 (0.962) |
1 (1.00) |
1 (1.00) |
0.355 (1.00) |
1 (1.00) |
P value = 0.000623 (Fisher's exact test), Q value = 0.031
Table S1. Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 69 | 125 |
TP53 MUTATED | 11 | 50 |
TP53 WILD-TYPE | 58 | 75 |
Figure S1. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
![](D1V7.png)
P value = 0.00014 (Fisher's exact test), Q value = 0.014
Table S2. Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 54 | 14 | 117 |
TP53 MUTATED | 1 | 22 | 10 | 26 |
TP53 WILD-TYPE | 0 | 32 | 4 | 91 |
Figure S2. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'RACE'
![](D1V10.png)
P value = 3.08e-05 (Fisher's exact test), Q value = 0.0061
Table S3. Gene #2: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 69 | 125 |
CTNNB1 MUTATED | 6 | 44 |
CTNNB1 WILD-TYPE | 63 | 81 |
Figure S3. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
![](D2V7.png)
P value = 0.00267 (Wilcoxon-test), Q value = 0.11
Table S4. Gene #3: 'RB1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 192 | 60.1 (13.9) |
RB1 MUTATED | 15 | 51.8 (11.3) |
RB1 WILD-TYPE | 177 | 60.8 (13.9) |
Figure S4. Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D3V2.png)
P value = 0.00706 (Fisher's exact test), Q value = 0.17
Table S5. Gene #3: 'RB1 MUTATION STATUS' versus Clinical Feature #10: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 54 | 14 | 117 |
RB1 MUTATED | 0 | 10 | 1 | 4 |
RB1 WILD-TYPE | 1 | 44 | 13 | 113 |
Figure S5. Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Clinical Feature #10: 'RACE'
![](D3V10.png)
P value = 0.000452 (Fisher's exact test), Q value = 0.03
Table S6. Gene #5: 'BAP1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 69 | 125 |
BAP1 MUTATED | 9 | 1 |
BAP1 WILD-TYPE | 60 | 124 |
Figure S6. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
![](D5V7.png)
P value = 0.0045 (logrank test), Q value = 0.13
Table S7. Gene #8: 'IL6ST MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 178 | 75 | 0.0 - 114.3 (18.6) |
IL6ST MUTATED | 6 | 0 | 13.4 - 113.0 (66.0) |
IL6ST WILD-TYPE | 172 | 75 | 0.0 - 114.3 (18.2) |
Figure S7. Get High-res Image Gene #8: 'IL6ST MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D8V1.png)
P value = 0.00847 (Fisher's exact test), Q value = 0.19
Table S8. Gene #9: 'ALB MUTATION STATUS' versus Clinical Feature #10: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 54 | 14 | 117 |
ALB MUTATED | 1 | 1 | 1 | 15 |
ALB WILD-TYPE | 0 | 53 | 13 | 102 |
Figure S8. Get High-res Image Gene #9: 'ALB MUTATION STATUS' versus Clinical Feature #10: 'RACE'
![](D9V10.png)
P value = 0.00469 (Fisher's exact test), Q value = 0.13
Table S9. Gene #17: 'HIST1H1C MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 79 | 50 | 52 | 11 |
HIST1H1C MUTATED | 0 | 4 | 0 | 1 |
HIST1H1C WILD-TYPE | 79 | 46 | 52 | 10 |
Figure S9. Get High-res Image Gene #17: 'HIST1H1C MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D17V4.png)
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Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
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Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/15165528/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/15082975/LIHC-TP.merged_data.txt
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Number of patients = 194
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Number of significantly mutated genes = 18
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Number of selected clinical features = 11
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Exclude genes that fewer than K tumors have mutations, K = 3
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
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
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.
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.