This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 15 genes and 10 molecular subtypes across 283 patients, 17 significant findings detected with P value < 0.05 and Q value < 0.25.
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EGFR mutation correlated to 'CN_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.
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IDH1 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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TP53 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'CN_CNMF', and 'MRNASEQ_CNMF'.
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NF1 mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
MIR CNMF |
MIR CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
||
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 | Fisher's exact test | Fisher's exact test | |
IDH1 | 14 (5%) | 269 |
9.13e-05 (0.0121) |
8.2e-07 (0.000114) |
0.000237 (0.0311) |
3.9e-05 (0.00531) |
7.61e-05 (0.0102) |
0.00151 (0.189) |
0.00352 (0.423) |
0.0203 (1.00) |
0.000712 (0.0912) |
0.00263 (0.319) |
TP53 | 79 (28%) | 204 |
0.000661 (0.0853) |
0.000459 (0.0597) |
0.00139 (0.176) |
0.025 (1.00) |
0.000122 (0.0161) |
0.00837 (0.962) |
0.0384 (1.00) |
0.00968 (1.00) |
0.00184 (0.227) |
0.0375 (1.00) |
EGFR | 74 (26%) | 209 |
0.00703 (0.815) |
0.0309 (1.00) |
0.369 (1.00) |
0.184 (1.00) |
8.23e-07 (0.000114) |
0.00564 (0.672) |
6.37e-05 (0.0086) |
1.46e-06 (2e-04) |
0.0413 (1.00) |
0.357 (1.00) |
NF1 | 29 (10%) | 254 |
0.0811 (1.00) |
0.0533 (1.00) |
0.0866 (1.00) |
0.423 (1.00) |
0.00123 (0.156) |
0.00167 (0.207) |
0.23 (1.00) |
0.12 (1.00) |
0.566 (1.00) |
0.915 (1.00) |
PIK3R1 | 32 (11%) | 251 |
0.751 (1.00) |
0.681 (1.00) |
0.445 (1.00) |
0.314 (1.00) |
0.115 (1.00) |
0.407 (1.00) |
0.988 (1.00) |
0.273 (1.00) |
0.406 (1.00) |
0.649 (1.00) |
BRAF | 6 (2%) | 277 |
0.768 (1.00) |
0.352 (1.00) |
0.619 (1.00) |
0.0919 (1.00) |
0.585 (1.00) |
1 (1.00) |
0.0781 (1.00) |
0.791 (1.00) |
1 (1.00) |
|
PTEN | 87 (31%) | 196 |
0.116 (1.00) |
0.426 (1.00) |
0.0461 (1.00) |
0.859 (1.00) |
0.599 (1.00) |
0.917 (1.00) |
0.378 (1.00) |
0.389 (1.00) |
0.27 (1.00) |
0.196 (1.00) |
PIK3CA | 30 (11%) | 253 |
0.725 (1.00) |
0.631 (1.00) |
0.537 (1.00) |
0.649 (1.00) |
0.5 (1.00) |
0.916 (1.00) |
0.754 (1.00) |
0.281 (1.00) |
0.262 (1.00) |
0.838 (1.00) |
RB1 | 25 (9%) | 258 |
0.015 (1.00) |
0.00648 (0.765) |
0.0558 (1.00) |
0.343 (1.00) |
0.065 (1.00) |
0.0709 (1.00) |
0.493 (1.00) |
0.691 (1.00) |
0.0434 (1.00) |
0.0407 (1.00) |
PRB2 | 6 (2%) | 277 |
0.642 (1.00) |
0.373 (1.00) |
0.478 (1.00) |
0.624 (1.00) |
0.771 (1.00) |
|||||
STAG2 | 12 (4%) | 271 |
0.392 (1.00) |
0.132 (1.00) |
0.306 (1.00) |
0.0194 (1.00) |
0.756 (1.00) |
0.752 (1.00) |
0.00694 (0.812) |
0.184 (1.00) |
0.479 (1.00) |
0.771 (1.00) |
CDC27 | 6 (2%) | 277 |
0.351 (1.00) |
0.373 (1.00) |
0.757 (1.00) |
0.373 (1.00) |
0.448 (1.00) |
0.227 (1.00) |
0.278 (1.00) |
0.325 (1.00) |
||
WNT2 | 5 (2%) | 278 |
0.151 (1.00) |
0.00235 (0.286) |
1 (1.00) |
0.784 (1.00) |
1 (1.00) |
0.0416 (1.00) |
0.423 (1.00) |
|||
TPTE2 | 8 (3%) | 275 |
0.46 (1.00) |
1 (1.00) |
0.36 (1.00) |
0.244 (1.00) |
0.306 (1.00) |
0.438 (1.00) |
0.624 (1.00) |
0.409 (1.00) |
0.376 (1.00) |
0.741 (1.00) |
GABRA6 | 11 (4%) | 272 |
0.111 (1.00) |
0.56 (1.00) |
0.51 (1.00) |
0.555 (1.00) |
0.365 (1.00) |
0.67 (1.00) |
0.318 (1.00) |
0.474 (1.00) |
0.124 (1.00) |
1 (1.00) |
P value = 8.23e-07 (Fisher's exact test), Q value = 0.00011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 87 | 78 | 108 |
EGFR MUTATED | 16 | 9 | 47 |
EGFR WILD-TYPE | 71 | 69 | 61 |
P value = 6.37e-05 (Fisher's exact test), Q value = 0.0086
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 41 | 38 | 31 | 33 |
EGFR MUTATED | 13 | 5 | 16 | 2 |
EGFR WILD-TYPE | 28 | 33 | 15 | 31 |
P value = 1.46e-06 (Fisher's exact test), Q value = 2e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 47 | 28 | 68 |
EGFR MUTATED | 24 | 6 | 6 |
EGFR WILD-TYPE | 23 | 22 | 62 |
P value = 9.13e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 43 | 74 | 54 |
IDH1 MUTATED | 1 | 3 | 0 | 9 |
IDH1 WILD-TYPE | 68 | 40 | 74 | 45 |
P value = 8.2e-07 (Fisher's exact test), Q value = 0.00011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 54 | 82 | 104 |
IDH1 MUTATED | 0 | 13 | 0 |
IDH1 WILD-TYPE | 54 | 69 | 104 |
P value = 0.000237 (Fisher's exact test), Q value = 0.031
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 56 | 71 | 31 | 44 |
IDH1 MUTATED | 0 | 10 | 0 | 0 |
IDH1 WILD-TYPE | 56 | 61 | 31 | 44 |
P value = 3.9e-05 (Fisher's exact test), Q value = 0.0053
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 81 | 68 | 53 |
IDH1 MUTATED | 1 | 0 | 9 |
IDH1 WILD-TYPE | 80 | 68 | 44 |
P value = 7.61e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 87 | 78 | 108 |
IDH1 MUTATED | 3 | 10 | 0 |
IDH1 WILD-TYPE | 84 | 68 | 108 |
P value = 0.00151 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 28 | 16 | 26 |
IDH1 MUTATED | 0 | 0 | 0 | 5 |
IDH1 WILD-TYPE | 38 | 28 | 16 | 21 |
P value = 0.000712 (Fisher's exact test), Q value = 0.091
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 62 | 35 |
IDH1 MUTATED | 7 | 0 | 1 |
IDH1 WILD-TYPE | 37 | 62 | 34 |
P value = 0.000661 (Fisher's exact test), Q value = 0.085
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 69 | 43 | 74 | 54 |
TP53 MUTATED | 16 | 19 | 11 | 22 |
TP53 WILD-TYPE | 53 | 24 | 63 | 32 |
P value = 0.000459 (Fisher's exact test), Q value = 0.06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 54 | 82 | 104 |
TP53 MUTATED | 7 | 35 | 26 |
TP53 WILD-TYPE | 47 | 47 | 78 |
P value = 0.00139 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 56 | 71 | 31 | 44 |
TP53 MUTATED | 8 | 32 | 7 | 15 |
TP53 WILD-TYPE | 48 | 39 | 24 | 29 |
P value = 0.000122 (Fisher's exact test), Q value = 0.016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 87 | 78 | 108 |
TP53 MUTATED | 35 | 27 | 16 |
TP53 WILD-TYPE | 52 | 51 | 92 |
P value = 0.00184 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 62 | 35 |
TP53 MUTATED | 23 | 13 | 8 |
TP53 WILD-TYPE | 21 | 49 | 27 |
P value = 0.00123 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 87 | 78 | 108 |
NF1 MUTATED | 4 | 17 | 8 |
NF1 WILD-TYPE | 83 | 61 | 100 |
P value = 0.00167 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 28 | 16 | 26 |
NF1 MUTATED | 11 | 1 | 0 | 1 |
NF1 WILD-TYPE | 27 | 27 | 16 | 25 |
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Mutation data file = GBM-TP.mutsig.cluster.txt
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Molecular subtypes file = GBM-TP.transferedmergedcluster.txt
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Number of patients = 283
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Number of significantly mutated genes = 15
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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 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.