This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 13 genes and 6 molecular subtypes across 83 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 13 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 | |
NKX3-1 | 5 (6%) | 78 |
0.177 (1.00) |
0.366 (1.00) |
0.845 (1.00) |
0.583 (1.00) |
0.0691 (1.00) |
0.18 (1.00) |
TP53 | 5 (6%) | 78 |
0.00583 (0.455) |
0.366 (1.00) |
0.21 (1.00) |
0.117 (1.00) |
0.547 (1.00) |
0.18 (1.00) |
FRG1 | 4 (5%) | 79 |
0.255 (1.00) |
0.57 (1.00) |
0.363 (1.00) |
0.668 (1.00) |
0.357 (1.00) |
1 (1.00) |
SPOP | 4 (5%) | 79 |
0.0148 (1.00) |
0.0695 (1.00) |
0.0596 (1.00) |
0.00937 (0.712) |
0.788 (1.00) |
0.79 (1.00) |
YBX1 | 3 (4%) | 80 |
0.701 (1.00) |
0.225 (1.00) |
1 (1.00) |
0.295 (1.00) |
0.511 (1.00) |
0.687 (1.00) |
CCNF | 3 (4%) | 80 |
1 (1.00) |
0.796 (1.00) |
0.471 (1.00) |
0.436 (1.00) |
1 (1.00) |
0.687 (1.00) |
CLSTN1 | 3 (4%) | 80 |
1 (1.00) |
0.441 (1.00) |
0.618 (1.00) |
1 (1.00) |
0.738 (1.00) |
1 (1.00) |
PRR21 | 4 (5%) | 79 |
0.701 (1.00) |
0.459 (1.00) |
1 (1.00) |
1 (1.00) |
0.185 (1.00) |
0.229 (1.00) |
AGT | 3 (4%) | 80 |
0.701 (1.00) |
1 (1.00) |
1 (1.00) |
0.771 (1.00) |
0.511 (1.00) |
0.235 (1.00) |
CTNNB1 | 3 (4%) | 80 |
1 (1.00) |
0.603 (1.00) |
0.471 (1.00) |
0.436 (1.00) |
0.356 (1.00) |
0.00646 (0.497) |
DUSP27 | 3 (4%) | 80 |
0.513 (1.00) |
0.441 (1.00) |
0.618 (1.00) |
0.583 (1.00) |
0.738 (1.00) |
0.687 (1.00) |
OR4D5 | 3 (4%) | 80 |
0.224 (1.00) |
1 (1.00) |
1 (1.00) |
0.771 (1.00) |
1 (1.00) |
0.687 (1.00) |
OR6N1 | 3 (4%) | 80 |
0.364 (1.00) |
1 (1.00) |
1 (1.00) |
0.771 (1.00) |
0.173 (1.00) |
0.687 (1.00) |
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Mutation data file = PRAD-TP.mutsig.cluster.txt
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Molecular subtypes file = PRAD-TP.transferedmergedcluster.txt
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Number of patients = 83
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Number of significantly mutated genes = 13
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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.