This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 9 genes and 6 molecular subtypes across 39 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
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No gene mutations related to molecuar subtypes.
Table 1. Get Full Table Overview of the association between mutation status of 9 genes and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
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nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
PIK3CA | 9 (23%) | 30 |
0.098 (1.00) |
0.358 (1.00) |
0.387 (1.00) |
0.734 (1.00) |
0.88 (1.00) |
0.669 (1.00) |
TMCC1 | 4 (10%) | 35 |
1 (1.00) |
0.489 (1.00) |
0.0537 (1.00) |
0.628 (1.00) |
0.556 (1.00) |
|
PRG4 | 5 (13%) | 34 |
0.294 (1.00) |
0.83 (1.00) |
0.0205 (1.00) |
0.1 (1.00) |
0.252 (1.00) |
0.302 (1.00) |
CDC27 | 5 (13%) | 34 |
0.397 (1.00) |
0.221 (1.00) |
0.128 (1.00) |
0.0681 (1.00) |
0.456 (1.00) |
0.302 (1.00) |
NFE2L2 | 6 (15%) | 33 |
0.714 (1.00) |
0.506 (1.00) |
0.584 (1.00) |
0.23 (1.00) |
0.195 (1.00) |
0.308 (1.00) |
MAPK1 | 3 (8%) | 36 |
0.141 (1.00) |
1 (1.00) |
0.398 (1.00) |
0.68 (1.00) |
0.0885 (1.00) |
0.556 (1.00) |
SSX7 | 3 (8%) | 36 |
0.762 (1.00) |
0.24 (1.00) |
0.0517 (1.00) |
0.803 (1.00) |
0.556 (1.00) |
|
UGT3A2 | 3 (8%) | 36 |
0.762 (1.00) |
0.0166 (0.83) |
0.0517 (1.00) |
0.55 (1.00) |
0.556 (1.00) |
|
PRB2 | 4 (10%) | 35 |
1 (1.00) |
0.489 (1.00) |
0.0537 (1.00) |
0.628 (1.00) |
0.556 (1.00) |
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Mutation data file = CESC-TP.mutsig.cluster.txt
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Molecular subtypes file = CESC-TP.transferedmergedcluster.txt
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Number of patients = 39
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Number of significantly mutated genes = 9
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Number of Molecular subtypes = 6
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Exclude genes that fewer than K tumors have mutations, K = 3
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.