This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 4 genes and 8 molecular subtypes across 112 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 |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE 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 | Fisher's exact test | Fisher's exact test | |
CDC27 | 4 (4%) | 108 |
0.517 (1.00) |
0.555 (1.00) |
1 (1.00) |
1 (1.00) |
0.469 (1.00) |
0.355 (1.00) |
1 (1.00) |
1 (1.00) |
IL32 | 4 (4%) | 108 |
1 (1.00) |
0.299 (1.00) |
0.589 (1.00) |
0.311 (1.00) |
0.83 (1.00) |
|||
NF2 | 7 (6%) | 105 |
0.0123 (0.307) |
0.0669 (1.00) |
0.234 (1.00) |
0.261 (1.00) |
0.53 (1.00) |
0.787 (1.00) |
1 (1.00) |
1 (1.00) |
PPARGC1B | 3 (3%) | 109 |
0.0703 (1.00) |
0.197 (1.00) |
0.304 (1.00) |
0.38 (1.00) |
0.0114 (0.297) |
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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 = 112
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Number of significantly mutated genes = 4
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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 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.