This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 15 genes and 8 clinical features across 417 patients, 4 significant findings detected with Q value < 0.25.
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BAP1 mutation correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'GENDER'.
Table 1. Get Full Table Overview of the association between mutation status of 15 genes and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 4 significant findings detected.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
||
nMutated (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | |
BAP1 | 42 (10%) | 375 |
0.00143 (0.149) |
0.385 (1.00) |
0.000107 (0.0115) |
0.000185 (0.0196) |
0.681 (1.00) |
0.0126 (1.00) |
0.000954 (0.1) |
|
TPSD1 | 4 (1%) | 413 |
0.454 (1.00) |
0.691 (1.00) |
0.326 (1.00) |
0.225 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
NEFH | 12 (3%) | 405 |
0.707 (1.00) |
0.287 (1.00) |
0.486 (1.00) |
0.372 (1.00) |
1 (1.00) |
0.419 (1.00) |
0.553 (1.00) |
|
VHL | 218 (52%) | 199 |
0.802 (1.00) |
0.346 (1.00) |
0.0852 (1.00) |
0.163 (1.00) |
0.768 (1.00) |
0.112 (1.00) |
0.918 (1.00) |
0.272 (1.00) |
SETD2 | 48 (12%) | 369 |
0.246 (1.00) |
0.146 (1.00) |
0.118 (1.00) |
0.0941 (1.00) |
0.367 (1.00) |
0.207 (1.00) |
0.148 (1.00) |
|
PBRM1 | 137 (33%) | 280 |
0.421 (1.00) |
0.39 (1.00) |
0.969 (1.00) |
0.217 (1.00) |
0.515 (1.00) |
1 (1.00) |
0.229 (1.00) |
0.387 (1.00) |
KDM5C | 27 (6%) | 390 |
0.0591 (1.00) |
0.0684 (1.00) |
0.916 (1.00) |
0.924 (1.00) |
1 (1.00) |
1 (1.00) |
0.00612 (0.63) |
|
PTEN | 18 (4%) | 399 |
0.347 (1.00) |
0.653 (1.00) |
0.0477 (1.00) |
0.244 (1.00) |
0.11 (1.00) |
0.329 (1.00) |
0.129 (1.00) |
0.357 (1.00) |
TSPAN19 | 5 (1%) | 412 |
0.641 (1.00) |
0.278 (1.00) |
0.476 (1.00) |
0.7 (1.00) |
1 (1.00) |
0.585 (1.00) |
0.661 (1.00) |
|
TCEB1 | 3 (1%) | 414 |
0.278 (1.00) |
0.246 (1.00) |
0.586 (1.00) |
0.383 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
FAM22F | 4 (1%) | 413 |
0.772 (1.00) |
0.746 (1.00) |
0.168 (1.00) |
1 (1.00) |
1 (1.00) |
0.123 (1.00) |
0.614 (1.00) |
|
C15ORF40 | 3 (1%) | 414 |
0.797 (1.00) |
0.283 (1.00) |
0.586 (1.00) |
0.383 (1.00) |
1 (1.00) |
1 (1.00) |
||
PLA2G4E | 8 (2%) | 409 |
0.413 (1.00) |
0.282 (1.00) |
0.434 (1.00) |
0.811 (1.00) |
1 (1.00) |
0.365 (1.00) |
0.135 (1.00) |
|
UQCRFS1 | 3 (1%) | 414 |
0.233 (1.00) |
0.55 (1.00) |
0.0367 (1.00) |
0.0797 (1.00) |
1 (1.00) |
1 (1.00) |
0.281 (1.00) |
|
GPRIN1 | 8 (2%) | 409 |
0.786 (1.00) |
0.828 (1.00) |
0.136 (1.00) |
0.646 (1.00) |
1 (1.00) |
0.122 (1.00) |
0.135 (1.00) |
P value = 0.00143 (logrank test), Q value = 0.15
Table S1. Gene #6: 'BAP1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 416 | 141 | 0.1 - 120.6 (37.0) |
BAP1 MUTATED | 42 | 24 | 0.1 - 93.3 (28.3) |
BAP1 WILD-TYPE | 374 | 117 | 0.1 - 120.6 (37.2) |
Figure S1. Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D6V1.png)
P value = 0.000107 (Fisher's exact test), Q value = 0.011
Table S2. Gene #6: 'BAP1 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 197 | 40 | 113 | 67 |
BAP1 MUTATED | 7 | 7 | 16 | 12 |
BAP1 WILD-TYPE | 190 | 33 | 97 | 55 |
Figure S2. Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'
![](D6V3.png)
P value = 0.000185 (Fisher's exact test), Q value = 0.02
Table S3. Gene #6: 'BAP1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 202 | 49 | 160 | 6 |
BAP1 MUTATED | 8 | 10 | 24 | 0 |
BAP1 WILD-TYPE | 194 | 39 | 136 | 6 |
Figure S3. Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
![](D6V4.png)
P value = 0.000954 (Fisher's exact test), Q value = 0.1
Table S4. Gene #6: 'BAP1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 146 | 271 |
BAP1 MUTATED | 25 | 17 |
BAP1 WILD-TYPE | 121 | 254 |
Figure S4. Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
![](D6V7.png)
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Mutation data file = KIRC-TP.mutsig.cluster.txt
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Clinical data file = KIRC-TP.clin.merged.picked.txt
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Number of patients = 417
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Number of significantly mutated genes = 15
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Number of selected clinical features = 8
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Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.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.