This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between 'TP53 MUTATION ANALYSIS' and 10 molecular subtypes across 28 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 |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nMutated (%) | nWild-Type | Chi-square 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 | Fisher's exact test | Fisher's exact test | |
TP53 | 11 (39%) | 17 |
0.746 (1.00) |
0.787 (1.00) |
0.112 (0.909) |
0.292 (1.00) |
0.0271 (0.271) |
0.874 (1.00) |
0.883 (1.00) |
0.101 (0.909) |
0.715 (1.00) |
0.577 (1.00) |
P value = 0.746 (Chi-square test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|
ALL | 3 | 11 | 3 | 4 | 4 | 1 |
TP53 MUTATED | 1 | 3 | 1 | 2 | 2 | 1 |
TP53 WILD-TYPE | 2 | 8 | 2 | 2 | 2 | 0 |
P value = 0.787 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 6 | 12 | 10 |
TP53 MUTATED | 3 | 5 | 3 |
TP53 WILD-TYPE | 3 | 7 | 7 |
P value = 0.112 (Chi-square test), Q value = 0.91
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 6 | 5 | 11 | 1 | 2 |
TP53 MUTATED | 1 | 1 | 8 | 0 | 1 |
TP53 WILD-TYPE | 5 | 4 | 3 | 1 | 1 |
P value = 0.292 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 10 | 1 | 7 | 7 |
TP53 MUTATED | 3 | 0 | 5 | 3 |
TP53 WILD-TYPE | 7 | 1 | 2 | 4 |
P value = 0.0271 (Fisher's exact test), Q value = 0.27
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 5 | 11 | 4 | 8 |
TP53 MUTATED | 2 | 6 | 3 | 0 |
TP53 WILD-TYPE | 3 | 5 | 1 | 8 |
P value = 0.874 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 10 | 5 | 13 |
TP53 MUTATED | 3 | 2 | 6 |
TP53 WILD-TYPE | 7 | 3 | 7 |
P value = 0.883 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 7 | 8 | 13 |
TP53 MUTATED | 2 | 3 | 6 |
TP53 WILD-TYPE | 5 | 5 | 7 |
P value = 0.101 (Fisher's exact test), Q value = 0.91
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 20 | 2 | 6 |
TP53 MUTATED | 8 | 2 | 1 |
TP53 WILD-TYPE | 12 | 0 | 5 |
P value = 0.715 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 9 | 5 | 7 |
TP53 MUTATED | 2 | 5 | 2 | 2 |
TP53 WILD-TYPE | 5 | 4 | 3 | 5 |
P value = 0.577 (Fisher's exact test), Q value = 1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 6 | 5 | 6 |
TP53 MUTATED | 5 | 2 | 3 | 1 |
TP53 WILD-TYPE | 6 | 4 | 2 | 5 |
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Mutation data file = transformed.cor.cli.txt
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Molecular subtypes file = BLCA-TP.transferedmergedcluster.txt
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Number of patients = 28
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Number of significantly mutated genes = 1: 'TP53 MUTATION ANALYSIS'
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Number of Molecular subtypes = 10
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Exclude genes that fewer than K tumors have mutations, K = 3
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 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.