This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 9 genes and 8 molecular subtypes across 111 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.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
MET | 9 (8%) | 102 |
1 (1.00) |
0.346 (1.00) |
0.502 (1.00) |
0.773 (1.00) |
0.752 (1.00) |
0.0974 (1.00) |
0.0934 (1.00) |
|
IL32 | 4 (4%) | 107 |
0.2 (1.00) |
0.0522 (1.00) |
0.649 (1.00) |
0.603 (1.00) |
0.129 (1.00) |
0.803 (1.00) |
||
CDC27 | 4 (4%) | 107 |
0.785 (1.00) |
0.571 (1.00) |
0.84 (1.00) |
1 (1.00) |
0.334 (1.00) |
0.381 (1.00) |
||
NF2 | 7 (6%) | 104 |
0.0754 (1.00) |
0.0298 (1.00) |
0.23 (1.00) |
0.104 (1.00) |
0.789 (1.00) |
1 (1.00) |
||
SFRS2IP | 5 (5%) | 106 |
0.659 (1.00) |
0.507 (1.00) |
0.116 (1.00) |
0.681 (1.00) |
0.389 (1.00) |
0.923 (1.00) |
||
PPARGC1B | 3 (3%) | 108 |
0.2 (1.00) |
0.194 (1.00) |
0.189 (1.00) |
0.0601 (1.00) |
||||
LGI4 | 4 (4%) | 107 |
0.441 (1.00) |
0.688 (1.00) |
0.686 (1.00) |
1 (1.00) |
0.0436 (1.00) |
0.24 (1.00) |
||
RPTN | 3 (3%) | 108 |
0.2 (1.00) |
0.121 (1.00) |
0.522 (1.00) |
0.0436 (1.00) |
||||
BHMT | 4 (4%) | 107 |
0.457 (1.00) |
0.571 (1.00) |
0.769 (1.00) |
0.323 (1.00) |
0.69 (1.00) |
0.803 (1.00) |
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Mutation data file = KIRP-TP.mutsig.cluster.txt
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Molecular subtypes file = KIRP-TP.transferedmergedcluster.txt
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Number of patients = 111
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Number of significantly mutated genes = 9
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Number of Molecular subtypes = 8
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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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.