This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 28 genes and 10 molecular subtypes across 293 patients, 10 significant findings detected with P value < 0.05 and Q value < 0.25.
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PBRM1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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BAP1 mutation correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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SETD2 mutation correlated to 'METHLYATION_CNMF'.
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MTOR mutation correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.
Clinical Features |
MRNA CNMF |
MRNA 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 | 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 | |
PBRM1 | 107 (37%) | 186 |
0.0211 (1.00) |
0.0735 (1.00) |
0.000201 (0.0448) |
0.000645 (0.143) |
0.00738 (1.00) |
0.799 (1.00) |
0.000649 (0.143) |
0.0822 (1.00) |
0.0456 (1.00) |
0.000141 (0.0318) |
BAP1 | 27 (9%) | 266 |
0.0212 (1.00) |
0.0111 (1.00) |
0.0883 (1.00) |
0.00376 (0.82) |
0.0259 (1.00) |
0.774 (1.00) |
0.00145 (0.317) |
3.76e-08 (8.61e-06) |
0.000192 (0.043) |
9.92e-07 (0.000226) |
MTOR | 24 (8%) | 269 |
0.631 (1.00) |
0.043 (1.00) |
8.32e-05 (0.0188) |
0.000582 (0.129) |
0.707 (1.00) |
0.323 (1.00) |
0.358 (1.00) |
0.544 (1.00) |
||
SETD2 | 34 (12%) | 259 |
0.747 (1.00) |
1 (1.00) |
0.0992 (1.00) |
8e-05 (0.0182) |
0.249 (1.00) |
0.21 (1.00) |
0.338 (1.00) |
0.655 (1.00) |
0.0978 (1.00) |
0.465 (1.00) |
VHL | 138 (47%) | 155 |
0.0307 (1.00) |
0.0514 (1.00) |
0.582 (1.00) |
0.397 (1.00) |
0.885 (1.00) |
0.307 (1.00) |
0.00744 (1.00) |
0.0654 (1.00) |
0.311 (1.00) |
0.156 (1.00) |
SV2C | 3 (1%) | 290 |
0.169 (1.00) |
0.0102 (1.00) |
0.54 (1.00) |
0.79 (1.00) |
0.236 (1.00) |
0.0191 (1.00) |
||||
KDM5C | 18 (6%) | 275 |
0.351 (1.00) |
0.261 (1.00) |
0.71 (1.00) |
0.0388 (1.00) |
0.105 (1.00) |
0.671 (1.00) |
0.0516 (1.00) |
0.684 (1.00) |
||
TP53 | 6 (2%) | 287 |
0.875 (1.00) |
0.535 (1.00) |
0.506 (1.00) |
0.427 (1.00) |
0.481 (1.00) |
0.245 (1.00) |
0.868 (1.00) |
0.0787 (1.00) |
||
PTEN | 9 (3%) | 284 |
0.163 (1.00) |
0.665 (1.00) |
1 (1.00) |
0.317 (1.00) |
0.0869 (1.00) |
0.606 (1.00) |
0.00835 (1.00) |
0.0437 (1.00) |
0.412 (1.00) |
0.661 (1.00) |
EBPL | 6 (2%) | 287 |
0.769 (1.00) |
0.797 (1.00) |
0.477 (1.00) |
0.414 (1.00) |
0.318 (1.00) |
0.174 (1.00) |
0.2 (1.00) |
0.313 (1.00) |
||
PIK3CA | 10 (3%) | 283 |
0.319 (1.00) |
0.205 (1.00) |
0.445 (1.00) |
1 (1.00) |
0.914 (1.00) |
0.586 (1.00) |
0.84 (1.00) |
0.404 (1.00) |
||
TSPAN19 | 4 (1%) | 289 |
0.473 (1.00) |
0.06 (1.00) |
0.248 (1.00) |
0.391 (1.00) |
0.454 (1.00) |
0.274 (1.00) |
0.0583 (1.00) |
|||
NBPF10 | 19 (6%) | 274 |
0.537 (1.00) |
0.602 (1.00) |
0.594 (1.00) |
0.872 (1.00) |
0.0897 (1.00) |
0.45 (1.00) |
0.35 (1.00) |
0.0484 (1.00) |
0.647 (1.00) |
0.921 (1.00) |
TOR1A | 3 (1%) | 290 |
0.464 (1.00) |
0.828 (1.00) |
0.225 (1.00) |
0.563 (1.00) |
1 (1.00) |
0.8 (1.00) |
1 (1.00) |
|||
MUC4 | 41 (14%) | 252 |
0.786 (1.00) |
0.892 (1.00) |
0.0839 (1.00) |
0.044 (1.00) |
0.0467 (1.00) |
0.543 (1.00) |
0.0476 (1.00) |
0.114 (1.00) |
0.0889 (1.00) |
0.0622 (1.00) |
UQCRFS1 | 3 (1%) | 290 |
0.253 (1.00) |
0.293 (1.00) |
0.341 (1.00) |
0.322 (1.00) |
0.617 (1.00) |
|||||
WDR52 | 9 (3%) | 284 |
0.283 (1.00) |
0.482 (1.00) |
0.576 (1.00) |
1 (1.00) |
0.448 (1.00) |
0.506 (1.00) |
0.623 (1.00) |
0.233 (1.00) |
||
BAGE2 | 4 (1%) | 289 |
0.816 (1.00) |
0.117 (1.00) |
0.635 (1.00) |
0.0749 (1.00) |
0.171 (1.00) |
0.0914 (1.00) |
0.0473 (1.00) |
0.00644 (1.00) |
||
CNTNAP4 | 9 (3%) | 284 |
0.758 (1.00) |
0.369 (1.00) |
0.0932 (1.00) |
0.513 (1.00) |
0.815 (1.00) |
0.625 (1.00) |
0.908 (1.00) |
1 (1.00) |
||
CR1 | 10 (3%) | 283 |
1 (1.00) |
0.279 (1.00) |
0.178 (1.00) |
0.497 (1.00) |
0.0978 (1.00) |
0.483 (1.00) |
0.602 (1.00) |
0.574 (1.00) |
||
STAG2 | 9 (3%) | 284 |
0.0789 (1.00) |
0.0119 (1.00) |
0.468 (1.00) |
0.412 (1.00) |
0.355 (1.00) |
0.13 (1.00) |
0.0785 (1.00) |
0.0676 (1.00) |
||
MSN | 4 (1%) | 289 |
0.581 (1.00) |
0.444 (1.00) |
0.794 (1.00) |
0.533 (1.00) |
0.284 (1.00) |
0.17 (1.00) |
0.352 (1.00) |
0.665 (1.00) |
||
ABCB1 | 8 (3%) | 285 |
0.333 (1.00) |
0.608 (1.00) |
0.0733 (1.00) |
0.0793 (1.00) |
0.265 (1.00) |
0.161 (1.00) |
0.268 (1.00) |
0.0892 (1.00) |
||
ADCY8 | 5 (2%) | 288 |
0.527 (1.00) |
0.106 (1.00) |
0.953 (1.00) |
1 (1.00) |
0.848 (1.00) |
1 (1.00) |
0.621 (1.00) |
0.358 (1.00) |
||
NPNT | 6 (2%) | 287 |
0.667 (1.00) |
0.502 (1.00) |
0.18 (1.00) |
1 (1.00) |
0.333 (1.00) |
0.382 (1.00) |
0.581 (1.00) |
0.756 (1.00) |
||
OR5H1 | 3 (1%) | 290 |
1 (1.00) |
0.258 (1.00) |
0.0476 (1.00) |
0.768 (1.00) |
0.721 (1.00) |
0.602 (1.00) |
0.101 (1.00) |
|||
SPAM1 | 5 (2%) | 288 |
0.386 (1.00) |
0.44 (1.00) |
0.277 (1.00) |
0.116 (1.00) |
0.11 (1.00) |
0.196 (1.00) |
0.478 (1.00) |
|||
TPTE2 | 7 (2%) | 286 |
0.549 (1.00) |
0.63 (1.00) |
0.609 (1.00) |
0.694 (1.00) |
0.876 (1.00) |
0.873 (1.00) |
0.157 (1.00) |
0.608 (1.00) |
P value = 0.000201 (Fisher's exact test), Q value = 0.045
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 73 | 130 | 89 |
PBRM1 MUTATED | 36 | 53 | 18 |
PBRM1 WILD-TYPE | 37 | 77 | 71 |
P value = 0.000645 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 71 | 84 | 44 |
PBRM1 MUTATED | 36 | 31 | 7 |
PBRM1 WILD-TYPE | 35 | 53 | 37 |
P value = 0.000649 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 124 | 110 | 46 |
PBRM1 MUTATED | 58 | 34 | 8 |
PBRM1 WILD-TYPE | 66 | 76 | 38 |
P value = 0.000141 (Fisher's exact test), Q value = 0.032
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 85 | 189 |
PBRM1 MUTATED | 2 | 18 | 84 |
PBRM1 WILD-TYPE | 12 | 67 | 105 |
P value = 3.76e-08 (Fisher's exact test), Q value = 8.6e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 31 | 132 | 117 |
BAP1 MUTATED | 1 | 1 | 25 |
BAP1 WILD-TYPE | 30 | 131 | 92 |
P value = 0.000192 (Fisher's exact test), Q value = 0.043
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 64 | 128 | 96 |
BAP1 MUTATED | 7 | 3 | 17 |
BAP1 WILD-TYPE | 57 | 125 | 79 |
P value = 9.92e-07 (Fisher's exact test), Q value = 0.00023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 85 | 189 |
BAP1 MUTATED | 5 | 16 | 6 |
BAP1 WILD-TYPE | 9 | 69 | 183 |
P value = 8e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 71 | 84 | 44 |
SETD2 MUTATED | 18 | 8 | 0 |
SETD2 WILD-TYPE | 53 | 76 | 44 |
P value = 8.32e-05 (Chi-square test), Q value = 0.019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 66 | 52 | 60 | 46 | 24 | 26 |
MTOR MUTATED | 5 | 1 | 7 | 1 | 0 | 8 |
MTOR WILD-TYPE | 61 | 51 | 53 | 45 | 24 | 18 |
P value = 0.000582 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 117 | 105 | 52 |
MTOR MUTATED | 2 | 11 | 9 |
MTOR WILD-TYPE | 115 | 94 | 43 |
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Mutation data file = KIRC-TP.mutsig.cluster.txt
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Molecular subtypes file = KIRC-TP.transferedmergedcluster.txt
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Number of patients = 293
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Number of significantly mutated genes = 28
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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 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.