This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 8 genes and 12 molecular subtypes across 316 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
-
No gene mutations related to molecuar subtypes.
Table 1. Get Full Table Overview of the association between mutation status of 8 genes and 12 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 |
MRNA CNMF |
MRNA CHIERARCHICAL |
MIR CNMF |
MIR CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nMutated (%) | nWild-Type | Fisher's exact test | 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
TP53 | 276 (87%) | 40 |
0.667 (1.00) |
0.366 (1.00) |
0.502 (1.00) |
0.367 (1.00) |
0.716 (1.00) |
0.702 (1.00) |
0.411 (1.00) |
0.313 (1.00) |
0.779 (1.00) |
0.898 (1.00) |
0.326 (1.00) |
0.186 (1.00) |
SRC | 4 (1%) | 312 |
0.836 (1.00) |
0.683 (1.00) |
0.566 (1.00) |
0.16 (1.00) |
0.127 (1.00) |
0.462 (1.00) |
0.483 (1.00) |
0.325 (1.00) |
||||
TBP | 4 (1%) | 312 |
1 (1.00) |
1 (1.00) |
0.692 (1.00) |
0.596 (1.00) |
0.0357 (1.00) |
0.0184 (1.00) |
0.131 (1.00) |
0.872 (1.00) |
1 (1.00) |
1 (1.00) |
0.689 (1.00) |
1 (1.00) |
RB1 | 9 (3%) | 307 |
0.758 (1.00) |
0.118 (1.00) |
0.402 (1.00) |
0.712 (1.00) |
0.776 (1.00) |
0.199 (1.00) |
0.892 (1.00) |
0.818 (1.00) |
0.358 (1.00) |
0.557 (1.00) |
||
GABRA6 | 6 (2%) | 310 |
0.882 (1.00) |
0.77 (1.00) |
1 (1.00) |
0.72 (1.00) |
0.29 (1.00) |
0.212 (1.00) |
0.398 (1.00) |
1 (1.00) |
0.791 (1.00) |
0.78 (1.00) |
1 (1.00) |
1 (1.00) |
BRCA1 | 12 (4%) | 304 |
0.173 (1.00) |
0.814 (1.00) |
0.256 (1.00) |
0.172 (1.00) |
0.506 (1.00) |
0.298 (1.00) |
0.488 (1.00) |
0.184 (1.00) |
1 (1.00) |
0.893 (1.00) |
0.718 (1.00) |
0.784 (1.00) |
CSMD3 | 18 (6%) | 298 |
0.341 (1.00) |
0.712 (1.00) |
0.24 (1.00) |
0.296 (1.00) |
0.516 (1.00) |
0.0567 (1.00) |
0.0457 (1.00) |
0.616 (1.00) |
0.786 (1.00) |
0.704 (1.00) |
0.183 (1.00) |
0.849 (1.00) |
NF1 | 14 (4%) | 302 |
0.425 (1.00) |
0.45 (1.00) |
0.836 (1.00) |
0.468 (1.00) |
0.7 (1.00) |
0.188 (1.00) |
0.112 (1.00) |
0.0351 (1.00) |
0.434 (1.00) |
0.145 (1.00) |
0.736 (1.00) |
1 (1.00) |
-
Mutation data file = OV-TP.mutsig.cluster.txt
-
Molecular subtypes file = OV-TP.transferedmergedcluster.txt
-
Number of patients = 316
-
Number of significantly mutated genes = 8
-
Number of Molecular subtypes = 12
-
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.