This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 17 genes and 9 clinical features across 247 patients, one significant finding detected with Q value < 0.25.
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TP53 mutation correlated to 'HISTOLOGICAL_TYPE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
TUMOR TISSUE SITE |
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 | |
TP53 | 85 (34%) | 162 |
0.748 (1.00) |
0.268 (1.00) |
0.157 (1.00) |
0.592 (1.00) |
1 (1.00) |
1e-05 (0.00153) |
0.739 (1.00) |
0.745 (1.00) |
0.176 (1.00) |
RB1 | 24 (10%) | 223 |
0.935 (1.00) |
0.965 (1.00) |
0.914 (1.00) |
0.203 (1.00) |
0.0959 (1.00) |
0.038 (0.831) |
0.609 (1.00) |
1 (1.00) |
1 (1.00) |
ATRX | 36 (15%) | 211 |
0.226 (1.00) |
0.00621 (0.475) |
0.874 (1.00) |
0.592 (1.00) |
0.317 (1.00) |
0.226 (1.00) |
0.816 (1.00) |
0.573 (1.00) |
1 (1.00) |
NUMBL | 8 (3%) | 239 |
0.82 (1.00) |
0.0505 (0.966) |
0.968 (1.00) |
1 (1.00) |
0.442 (1.00) |
0.468 (1.00) |
0.225 (1.00) |
1 (1.00) |
1 (1.00) |
MSH3 | 7 (3%) | 240 |
0.527 (1.00) |
0.637 (1.00) |
0.646 (1.00) |
0.127 (1.00) |
1 (1.00) |
0.731 (1.00) |
0.88 (1.00) |
1 (1.00) |
0.131 (1.00) |
LTBP3 | 5 (2%) | 242 |
0.552 (1.00) |
0.71 (1.00) |
0.37 (1.00) |
0.664 (1.00) |
0.325 (1.00) |
0.676 (1.00) |
0.476 (1.00) |
0.397 (1.00) |
1 (1.00) |
EOMES | 5 (2%) | 242 |
0.672 (1.00) |
0.77 (1.00) |
0.114 (1.00) |
0.664 (1.00) |
0.0274 (0.831) |
0.101 (1.00) |
1 (1.00) |
0.398 (1.00) |
1 (1.00) |
PTEN | 7 (3%) | 240 |
0.673 (1.00) |
0.293 (1.00) |
0.0201 (0.767) |
1 (1.00) |
0.364 (1.00) |
0.826 (1.00) |
0.522 (1.00) |
1 (1.00) |
1 (1.00) |
KRTAP5-5 | 7 (3%) | 240 |
0.94 (1.00) |
0.146 (1.00) |
0.703 (1.00) |
0.456 (1.00) |
0.423 (1.00) |
0.385 (1.00) |
0.0983 (1.00) |
1 (1.00) |
0.152 (1.00) |
CABLES1 | 3 (1%) | 244 |
0.536 (1.00) |
0.848 (1.00) |
0.397 (1.00) |
0.597 (1.00) |
1 (1.00) |
1 (1.00) |
0.707 (1.00) |
1 (1.00) |
1 (1.00) |
TRAF7 | 4 (2%) | 243 |
0.711 (1.00) |
0.848 (1.00) |
0.416 (1.00) |
0.338 (1.00) |
1 (1.00) |
0.345 (1.00) |
0.61 (1.00) |
1 (1.00) |
1 (1.00) |
LOR | 6 (2%) | 241 |
0.758 (1.00) |
0.848 (1.00) |
0.294 (1.00) |
0.419 (1.00) |
0.673 (1.00) |
0.192 (1.00) |
0.411 (1.00) |
1 (1.00) |
1 (1.00) |
R3HDM1 | 4 (2%) | 243 |
0.948 (1.00) |
0.207 (1.00) |
0.126 (1.00) |
1 (1.00) |
0.583 (1.00) |
0.638 (1.00) |
0.478 (1.00) |
1 (1.00) |
1 (1.00) |
NF1 | 9 (4%) | 238 |
0.517 (1.00) |
0.268 (1.00) |
0.194 (1.00) |
0.736 (1.00) |
0.456 (1.00) |
0.0372 (0.831) |
0.118 (1.00) |
1 (1.00) |
1 (1.00) |
COL4A3 | 4 (2%) | 243 |
0.14 (1.00) |
0.542 (1.00) |
0.176 (1.00) |
1 (1.00) |
0.323 (1.00) |
0.17 (1.00) |
0.118 (1.00) |
1 (1.00) |
1 (1.00) |
MEGF9 | 3 (1%) | 244 |
0.225 (1.00) |
0.292 (1.00) |
0.0143 (0.728) |
0.597 (1.00) |
1 (1.00) |
0.473 (1.00) |
0.36 (1.00) |
1 (1.00) |
1 (1.00) |
SCAP | 3 (1%) | 244 |
0.505 (1.00) |
0.36 (1.00) |
0.296 (1.00) |
0.0969 (1.00) |
0.557 (1.00) |
0.894 (1.00) |
0.358 (1.00) |
1 (1.00) |
1 (1.00) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0015
nPatients | DEDIFFERENTIATED LIPOSARCOMA | DESMOID TUMOR | GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS | LEIOMYOSARCOMA (LMS) | MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) | MYXOFIBROSARCOMA | PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA | SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED | SYNOVIAL SARCOMA - BIPHASIC | SYNOVIAL SARCOMA - MONOPHASIC | UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS) |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 56 | 2 | 1 | 98 | 8 | 22 | 29 | 2 | 2 | 6 | 21 |
TP53 MUTATED | 5 | 0 | 0 | 50 | 1 | 8 | 12 | 0 | 0 | 0 | 9 |
TP53 WILD-TYPE | 51 | 2 | 1 | 48 | 7 | 14 | 17 | 2 | 2 | 6 | 12 |
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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/SARC-TP/22573934/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SARC-TP/22507207/SARC-TP.merged_data.txt
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Number of patients = 247
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Number of significantly mutated genes = 17
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Number of selected clinical features = 9
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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.