This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 8 genes and 10 clinical features across 179 patients, 2 significant findings detected with Q value < 0.25.
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NF1 mutation correlated to 'YEARS_TO_BIRTH'.
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RET mutation correlated to 'RACE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
TUMOR TISSUE SITE |
GENDER |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
NUMBER OF LYMPH NODES |
RACE | ETHNICITY | ||
nMutated (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
NF1 | 15 (8%) | 164 |
0.574 (1.00) |
0.0017 (0.136) |
0.478 (1.00) |
1 (1.00) |
1 (1.00) |
0.94 (1.00) |
0.753 (1.00) |
0.552 (1.00) |
0.281 (1.00) |
|
RET | 6 (3%) | 173 |
0.71 (1.00) |
0.458 (1.00) |
0.593 (1.00) |
0.698 (1.00) |
1 (1.00) |
1 (1.00) |
0.00576 (0.23) |
1 (1.00) |
||
HRAS | 18 (10%) | 161 |
0.435 (1.00) |
0.169 (1.00) |
0.204 (1.00) |
0.804 (1.00) |
1 (1.00) |
0.35 (1.00) |
0.475 (1.00) |
0.0984 (0.875) |
1 (1.00) |
|
EPAS1 | 8 (4%) | 171 |
0.488 (1.00) |
0.955 (1.00) |
0.0352 (0.705) |
0.469 (1.00) |
0.209 (1.00) |
0.0615 (0.828) |
0.0121 (0.323) |
0.152 (1.00) |
1 (1.00) |
|
NUDT11 | 5 (3%) | 174 |
0.645 (1.00) |
0.186 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.619 (1.00) |
0.185 (1.00) |
1 (1.00) |
||
SHROOM4 | 3 (2%) | 176 |
0.757 (1.00) |
0.229 (1.00) |
0.448 (1.00) |
0.581 (1.00) |
1 (1.00) |
0.228 (1.00) |
1 (1.00) |
0.0689 (0.828) |
||
AMMECR1 | 3 (2%) | 176 |
0.804 (1.00) |
0.301 (1.00) |
0.0828 (0.828) |
1 (1.00) |
1 (1.00) |
0.078 (0.828) |
0.399 (1.00) |
1 (1.00) |
||
GPR128 | 4 (2%) | 175 |
0.724 (1.00) |
0.907 (1.00) |
1 (1.00) |
0.633 (1.00) |
1 (1.00) |
1 (1.00) |
0.49 (1.00) |
1 (1.00) |
P value = 0.0017 (Wilcoxon-test), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 179 | 47.3 (15.1) |
NF1 MUTATED | 15 | 59.4 (13.4) |
NF1 WILD-TYPE | 164 | 46.2 (14.8) |
P value = 0.00576 (Fisher's exact test), Q value = 0.23
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 6 | 20 | 148 |
RET MUTATED | 1 | 1 | 1 | 3 |
RET WILD-TYPE | 0 | 5 | 19 | 145 |
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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/PCPG-TP/22569699/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/22506925/PCPG-TP.merged_data.txt
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Number of patients = 179
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Number of significantly mutated genes = 8
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Number of selected clinical features = 10
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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.