This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 20 genes and 12 clinical features across 194 patients, 10 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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ARID1A mutation correlated to 'Time to Death'.
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BAP1 mutation correlated to 'GENDER'.
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ALB mutation correlated to 'RACE'.
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IL6ST mutation correlated to 'Time to Death'.
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HIST1H1C mutation correlated to 'PATHOLOGY_T_STAGE'.
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 | 61 (31%) | 133 |
0.0849 (0.719) |
0.087 (0.719) |
0.396 (1.00) |
0.179 (0.86) |
0.559 (1.00) |
0.308 (1.00) |
0.00202 (0.114) |
1 (1.00) |
0.693 (1.00) |
0.96 (1.00) |
5e-05 (0.006) |
0.179 (0.86) |
RB1 | 15 (8%) | 179 |
0.608 (1.00) |
0.00267 (0.114) |
0.455 (1.00) |
0.178 (0.86) |
1 (1.00) |
1 (1.00) |
0.404 (1.00) |
1 (1.00) |
1 (1.00) |
0.528 (1.00) |
0.00687 (0.206) |
0.358 (1.00) |
CTNNB1 | 50 (26%) | 144 |
0.981 (1.00) |
0.208 (0.887) |
0.75 (1.00) |
0.598 (1.00) |
0.161 (0.86) |
1 (1.00) |
3.08e-05 (0.006) |
0.173 (0.86) |
0.681 (1.00) |
0.117 (0.799) |
0.293 (1.00) |
1 (1.00) |
ARID1A | 17 (9%) | 177 |
0.00957 (0.23) |
0.198 (0.887) |
0.189 (0.872) |
0.633 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.22 (0.9) |
1 (1.00) |
0.297 (1.00) |
0.415 (1.00) |
1 (1.00) |
BAP1 | 11 (6%) | 183 |
0.237 (0.912) |
0.712 (1.00) |
0.0478 (0.603) |
0.072 (0.709) |
0.181 (0.86) |
0.227 (0.9) |
0.000161 (0.0129) |
1 (1.00) |
1 (1.00) |
0.642 (1.00) |
0.898 (1.00) |
1 (1.00) |
ALB | 18 (9%) | 176 |
0.541 (1.00) |
0.028 (0.517) |
0.241 (0.912) |
0.113 (0.799) |
0.243 (0.912) |
1 (1.00) |
0.0356 (0.57) |
1 (1.00) |
1 (1.00) |
0.403 (1.00) |
0.00863 (0.23) |
1 (1.00) |
IL6ST | 7 (4%) | 187 |
0.00285 (0.114) |
0.17 (0.86) |
0.954 (1.00) |
0.867 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.115 (0.799) |
1 (1.00) |
0.687 (1.00) |
0.824 (1.00) |
1 (1.00) |
HIST1H1C | 5 (3%) | 189 |
0.171 (0.86) |
0.88 (1.00) |
0.0434 (0.603) |
0.00484 (0.166) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0991 (0.743) |
0.318 (1.00) |
0.0226 (0.452) |
1 (1.00) |
AXIN1 | 9 (5%) | 185 |
0.0321 (0.551) |
0.799 (1.00) |
0.0929 (0.719) |
0.63 (1.00) |
1 (1.00) |
0.18 (0.86) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.296 (1.00) |
1 (1.00) |
0.206 (0.887) |
TSC2 | 9 (5%) | 185 |
0.989 (1.00) |
0.515 (1.00) |
0.179 (0.86) |
0.0768 (0.709) |
1 (1.00) |
1 (1.00) |
0.723 (1.00) |
1 (1.00) |
1 (1.00) |
0.549 (1.00) |
0.211 (0.887) |
0.183 (0.86) |
APOB | 24 (12%) | 170 |
0.768 (1.00) |
0.543 (1.00) |
0.0615 (0.671) |
0.776 (1.00) |
0.375 (1.00) |
0.413 (1.00) |
0.503 (1.00) |
1 (1.00) |
1 (1.00) |
0.683 (1.00) |
0.0765 (0.709) |
1 (1.00) |
PTEN | 7 (4%) | 187 |
0.341 (1.00) |
0.26 (0.945) |
0.85 (1.00) |
0.759 (1.00) |
1 (1.00) |
1 (1.00) |
0.425 (1.00) |
1 (1.00) |
1 (1.00) |
0.2 (0.887) |
0.457 (1.00) |
0.158 (0.86) |
EEF1A1 | 5 (3%) | 189 |
0.0392 (0.588) |
0.326 (1.00) |
0.669 (1.00) |
0.386 (1.00) |
1 (1.00) |
1 (1.00) |
0.163 (0.86) |
1 (1.00) |
1 (1.00) |
0.561 (1.00) |
0.178 (0.86) |
1 (1.00) |
KIF19 | 10 (5%) | 184 |
0.0916 (0.719) |
0.0452 (0.603) |
0.918 (1.00) |
0.64 (1.00) |
1 (1.00) |
1 (1.00) |
0.499 (1.00) |
0.161 (0.86) |
1 (1.00) |
0.596 (1.00) |
0.506 (1.00) |
1 (1.00) |
THADA | 6 (3%) | 188 |
0.695 (1.00) |
0.0584 (0.667) |
0.919 (1.00) |
0.53 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.12 (0.799) |
0.0928 (0.719) |
0.303 (1.00) |
1 (1.00) |
PRKDC | 11 (6%) | 183 |
0.0169 (0.369) |
0.987 (1.00) |
0.434 (1.00) |
0.328 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
HNF1A | 8 (4%) | 186 |
0.674 (1.00) |
0.403 (1.00) |
0.229 (0.9) |
0.281 (0.993) |
1 (1.00) |
1 (1.00) |
0.458 (1.00) |
1 (1.00) |
1 (1.00) |
0.247 (0.913) |
0.689 (1.00) |
1 (1.00) |
F5 | 4 (2%) | 190 |
0.844 (1.00) |
0.225 (0.9) |
0.624 (1.00) |
0.443 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0503 (0.603) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
GNAS | 7 (4%) | 187 |
0.266 (0.951) |
0.975 (1.00) |
0.686 (1.00) |
0.316 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.689 (1.00) |
1 (1.00) |
MLL4 | 10 (5%) | 184 |
0.986 (1.00) |
0.935 (1.00) |
0.976 (1.00) |
0.956 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0721 (0.709) |
1 (1.00) |
P value = 0.00202 (Fisher's exact test), Q value = 0.11
nPatients | FEMALE | MALE |
---|---|---|
ALL | 69 | 125 |
TP53 MUTATED | 12 | 49 |
TP53 WILD-TYPE | 57 | 76 |
P value = 5e-05 (Fisher's exact test), Q value = 0.006
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 54 | 14 | 117 |
TP53 MUTATED | 1 | 23 | 10 | 25 |
TP53 WILD-TYPE | 0 | 31 | 4 | 92 |
P value = 3.08e-05 (Fisher's exact test), Q value = 0.006
nPatients | FEMALE | MALE |
---|---|---|
ALL | 69 | 125 |
CTNNB1 MUTATED | 6 | 44 |
CTNNB1 WILD-TYPE | 63 | 81 |
P value = 0.00267 (Wilcoxon-test), Q value = 0.11
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) |
P value = 0.00687 (Fisher's exact test), Q value = 0.21
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 |
P value = 0.00957 (logrank test), Q value = 0.23
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 192 | 88 | 0.0 - 114.3 (19.3) |
ARID1A MUTATED | 16 | 11 | 0.3 - 60.9 (13.6) |
ARID1A WILD-TYPE | 176 | 77 | 0.0 - 114.3 (19.6) |
P value = 0.000161 (Fisher's exact test), Q value = 0.013
nPatients | FEMALE | MALE |
---|---|---|
ALL | 69 | 125 |
BAP1 MUTATED | 10 | 1 |
BAP1 WILD-TYPE | 59 | 124 |
P value = 0.00863 (Fisher's exact test), Q value = 0.23
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 |
P value = 0.00285 (logrank test), Q value = 0.11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 192 | 88 | 0.0 - 114.3 (19.3) |
IL6ST MUTATED | 7 | 0 | 7.2 - 113.0 (56.2) |
IL6ST WILD-TYPE | 185 | 88 | 0.0 - 114.3 (19.0) |
P value = 0.00484 (Fisher's exact test), Q value = 0.17
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 79 | 50 | 52 | 11 |
HIST1H1C MUTATED | 0 | 4 | 0 | 1 |
HIST1H1C WILD-TYPE | 79 | 46 | 52 | 10 |
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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/19897751/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/19775332/LIHC-TP.merged_data.txt
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Number of patients = 194
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Number of significantly mutated genes = 20
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Number of selected clinical features = 12
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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.