(primary solid tumor cohort)
This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 47 genes and 10 clinical features across 116 patients, 6 significant findings detected with Q value < 0.25.
-
HLA-B mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
POTEG mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
TPTE mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
CPS1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
INO80E mutation correlated to 'PATHOLOGY.T'.
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UPF3A mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
Clinical Features |
Time to Death |
AGE | GENDER |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
||
nMutated (%) | nWild-Type | logrank test | t-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 | t-test | |
HLA-B | 9 (8%) | 107 |
0.963 (1.00) |
0.717 (1.00) |
0.028 (1.00) |
0.556 (1.00) |
0.126 (1.00) |
0.111 (1.00) |
0.329 (1.00) |
0.303 (1.00) |
0.916 (1.00) |
1.71e-07 (7.78e-05) |
POTEG | 6 (5%) | 110 |
0.221 (1.00) |
0.0101 (1.00) |
0.68 (1.00) |
0.568 (1.00) |
0.643 (1.00) |
0.683 (1.00) |
1 (1.00) |
0.806 (1.00) |
0.309 (1.00) |
3.6e-05 (0.0163) |
TPTE | 14 (12%) | 102 |
0.382 (1.00) |
0.92 (1.00) |
0.401 (1.00) |
0.00396 (1.00) |
0.283 (1.00) |
0.263 (1.00) |
0.505 (1.00) |
0.974 (1.00) |
0.58 (1.00) |
2.59e-06 (0.00118) |
CPS1 | 13 (11%) | 103 |
0.862 (1.00) |
0.922 (1.00) |
0.24 (1.00) |
0.471 (1.00) |
0.608 (1.00) |
0.526 (1.00) |
0.202 (1.00) |
0.943 (1.00) |
0.233 (1.00) |
3.12e-07 (0.000142) |
INO80E | 5 (4%) | 111 |
0.936 (1.00) |
0.0798 (1.00) |
0.805 (1.00) |
0.000484 (0.218) |
0.913 (1.00) |
0.554 (1.00) |
0.0587 (1.00) |
0.0932 (1.00) |
0.537 (1.00) |
|
UPF3A | 6 (5%) | 110 |
0.647 (1.00) |
0.253 (1.00) |
0.68 (1.00) |
0.86 (1.00) |
0.00203 (0.906) |
0.789 (1.00) |
0.21 (1.00) |
0.244 (1.00) |
0.511 (1.00) |
3.6e-05 (0.0163) |
CBWD1 | 14 (12%) | 102 |
0.303 (1.00) |
0.0229 (1.00) |
0.243 (1.00) |
0.312 (1.00) |
0.000583 (0.262) |
0.692 (1.00) |
0.505 (1.00) |
0.264 (1.00) |
0.541 (1.00) |
0.036 (1.00) |
KRAS | 14 (12%) | 102 |
0.353 (1.00) |
0.496 (1.00) |
0.243 (1.00) |
0.701 (1.00) |
0.8 (1.00) |
0.348 (1.00) |
0.623 (1.00) |
0.41 (1.00) |
0.0502 (1.00) |
0.147 (1.00) |
PGM5 | 16 (14%) | 100 |
0.962 (1.00) |
0.00184 (0.821) |
0.0138 (1.00) |
0.495 (1.00) |
0.00445 (1.00) |
0.898 (1.00) |
0.555 (1.00) |
0.381 (1.00) |
0.45 (1.00) |
0.773 (1.00) |
RPL22 | 9 (8%) | 107 |
0.478 (1.00) |
0.0449 (1.00) |
0.48 (1.00) |
0.591 (1.00) |
0.0528 (1.00) |
0.303 (1.00) |
0.000925 (0.415) |
0.099 (1.00) |
0.107 (1.00) |
0.00755 (1.00) |
TP53 | 52 (45%) | 64 |
0.0826 (1.00) |
0.519 (1.00) |
0.345 (1.00) |
0.0205 (1.00) |
0.754 (1.00) |
0.975 (1.00) |
0.123 (1.00) |
0.747 (1.00) |
0.376 (1.00) |
0.888 (1.00) |
TRIM48 | 10 (9%) | 106 |
0.322 (1.00) |
0.157 (1.00) |
0.191 (1.00) |
0.448 (1.00) |
0.0924 (1.00) |
0.698 (1.00) |
0.0506 (1.00) |
0.241 (1.00) |
0.0335 (1.00) |
0.022 (1.00) |
XPOT | 6 (5%) | 110 |
0.238 (1.00) |
0.68 (1.00) |
0.812 (1.00) |
1 (1.00) |
0.646 (1.00) |
0.114 (1.00) |
0.489 (1.00) |
0.25 (1.00) |
||
PIK3CA | 24 (21%) | 92 |
0.407 (1.00) |
0.457 (1.00) |
0.253 (1.00) |
0.789 (1.00) |
0.669 (1.00) |
0.655 (1.00) |
1 (1.00) |
0.375 (1.00) |
0.324 (1.00) |
0.544 (1.00) |
ACVR2A | 13 (11%) | 103 |
0.00155 (0.693) |
0.218 (1.00) |
0.131 (1.00) |
0.263 (1.00) |
0.128 (1.00) |
0.881 (1.00) |
0.371 (1.00) |
0.414 (1.00) |
0.342 (1.00) |
0.012 (1.00) |
RHOA | 7 (6%) | 109 |
0.0968 (1.00) |
0.0615 (1.00) |
0.701 (1.00) |
0.451 (1.00) |
0.559 (1.00) |
0.765 (1.00) |
0.681 (1.00) |
0.157 (1.00) |
1 (1.00) |
0.679 (1.00) |
ARID1A | 22 (19%) | 94 |
0.225 (1.00) |
0.814 (1.00) |
0.0525 (1.00) |
0.298 (1.00) |
0.114 (1.00) |
0.422 (1.00) |
0.0193 (1.00) |
0.168 (1.00) |
0.0325 (1.00) |
0.77 (1.00) |
OR8H3 | 10 (9%) | 106 |
0.626 (1.00) |
0.424 (1.00) |
0.738 (1.00) |
0.0783 (1.00) |
0.774 (1.00) |
0.113 (1.00) |
0.724 (1.00) |
0.688 (1.00) |
0.0919 (1.00) |
0.444 (1.00) |
EDNRB | 12 (10%) | 104 |
0.877 (1.00) |
0.831 (1.00) |
0.537 (1.00) |
0.365 (1.00) |
0.233 (1.00) |
0.339 (1.00) |
0.451 (1.00) |
0.885 (1.00) |
0.283 (1.00) |
0.786 (1.00) |
ZNF804B | 18 (16%) | 98 |
0.909 (1.00) |
0.267 (1.00) |
0.61 (1.00) |
0.416 (1.00) |
1 (1.00) |
0.13 (1.00) |
0.382 (1.00) |
0.0243 (1.00) |
0.694 (1.00) |
0.985 (1.00) |
IRF2 | 8 (7%) | 108 |
0.74 (1.00) |
0.234 (1.00) |
0.0568 (1.00) |
0.762 (1.00) |
0.0166 (1.00) |
0.873 (1.00) |
0.288 (1.00) |
0.928 (1.00) |
0.0937 (1.00) |
0.135 (1.00) |
IAPP | 4 (3%) | 112 |
0.485 (1.00) |
1 (1.00) |
0.937 (1.00) |
1 (1.00) |
0.897 (1.00) |
0.189 (1.00) |
0.107 (1.00) |
0.647 (1.00) |
0.0298 (1.00) |
|
PCDH15 | 22 (19%) | 94 |
0.855 (1.00) |
0.534 (1.00) |
0.63 (1.00) |
0.878 (1.00) |
0.407 (1.00) |
0.757 (1.00) |
0.649 (1.00) |
0.222 (1.00) |
0.921 (1.00) |
0.39 (1.00) |
SPRYD5 | 8 (7%) | 108 |
0.143 (1.00) |
0.135 (1.00) |
1 (1.00) |
0.904 (1.00) |
0.0528 (1.00) |
0.765 (1.00) |
0.103 (1.00) |
0.0411 (1.00) |
0.538 (1.00) |
0.492 (1.00) |
TUSC3 | 9 (8%) | 107 |
0.76 (1.00) |
0.28 (1.00) |
1 (1.00) |
0.783 (1.00) |
0.46 (1.00) |
0.488 (1.00) |
0.329 (1.00) |
0.551 (1.00) |
0.632 (1.00) |
0.222 (1.00) |
FGF22 | 3 (3%) | 113 |
0.0539 (1.00) |
0.562 (1.00) |
0.712 (1.00) |
0.381 (1.00) |
0.382 (1.00) |
|||||
PTH2 | 3 (3%) | 113 |
0.782 (1.00) |
0.562 (1.00) |
0.775 (1.00) |
0.78 (1.00) |
0.377 (1.00) |
1 (1.00) |
0.687 (1.00) |
0.737 (1.00) |
0.273 (1.00) |
|
C17ORF63 | 3 (3%) | 113 |
0.524 (1.00) |
0.562 (1.00) |
0.836 (1.00) |
0.121 (1.00) |
0.437 (1.00) |
1 (1.00) |
0.532 (1.00) |
1 (1.00) |
||
SMAD4 | 7 (6%) | 109 |
0.103 (1.00) |
0.051 (1.00) |
0.701 (1.00) |
0.663 (1.00) |
0.9 (1.00) |
1 (1.00) |
0.153 (1.00) |
1 (1.00) |
0.0935 (1.00) |
0.0418 (1.00) |
RNF43 | 13 (11%) | 103 |
0.0257 (1.00) |
0.0612 (1.00) |
0.368 (1.00) |
0.151 (1.00) |
0.062 (1.00) |
0.881 (1.00) |
0.484 (1.00) |
0.185 (1.00) |
0.233 (1.00) |
0.14 (1.00) |
WBSCR17 | 12 (10%) | 104 |
0.116 (1.00) |
0.185 (1.00) |
0.537 (1.00) |
0.281 (1.00) |
0.419 (1.00) |
0.965 (1.00) |
0.333 (1.00) |
0.835 (1.00) |
0.893 (1.00) |
0.00345 (1.00) |
PHF2 | 12 (10%) | 104 |
0.905 (1.00) |
0.017 (1.00) |
0.537 (1.00) |
0.403 (1.00) |
0.0106 (1.00) |
0.6 (1.00) |
0.00397 (1.00) |
0.118 (1.00) |
0.308 (1.00) |
0.00906 (1.00) |
CDH1 | 11 (9%) | 105 |
0.516 (1.00) |
0.137 (1.00) |
0.751 (1.00) |
0.116 (1.00) |
0.565 (1.00) |
0.79 (1.00) |
1 (1.00) |
0.134 (1.00) |
0.309 (1.00) |
0.565 (1.00) |
ELF3 | 5 (4%) | 111 |
0.541 (1.00) |
0.701 (1.00) |
0.384 (1.00) |
0.402 (1.00) |
0.366 (1.00) |
0.623 (1.00) |
1 (1.00) |
0.928 (1.00) |
1 (1.00) |
0.0887 (1.00) |
PARK2 | 9 (8%) | 107 |
0.73 (1.00) |
0.00874 (1.00) |
1 (1.00) |
0.109 (1.00) |
0.292 (1.00) |
0.351 (1.00) |
0.329 (1.00) |
0.199 (1.00) |
0.916 (1.00) |
0.00642 (1.00) |
LARP4B | 5 (4%) | 111 |
0.541 (1.00) |
0.445 (1.00) |
0.384 (1.00) |
0.402 (1.00) |
0.0286 (1.00) |
0.897 (1.00) |
1 (1.00) |
0.489 (1.00) |
0.836 (1.00) |
0.221 (1.00) |
OR6K3 | 6 (5%) | 110 |
0.63 (1.00) |
0.436 (1.00) |
0.212 (1.00) |
0.153 (1.00) |
0.322 (1.00) |
1 (1.00) |
0.309 (1.00) |
0.147 (1.00) |
0.36 (1.00) |
0.874 (1.00) |
TM7SF4 | 7 (6%) | 109 |
0.915 (1.00) |
0.553 (1.00) |
0.701 (1.00) |
0.855 (1.00) |
0.619 (1.00) |
0.847 (1.00) |
1 (1.00) |
0.676 (1.00) |
1 (1.00) |
0.281 (1.00) |
C7ORF63 | 5 (4%) | 111 |
0.471 (1.00) |
0.42 (1.00) |
0.0798 (1.00) |
0.322 (1.00) |
0.0223 (1.00) |
0.646 (1.00) |
0.155 (1.00) |
0.587 (1.00) |
0.0773 (1.00) |
|
KDM4B | 10 (9%) | 106 |
0.81 (1.00) |
0.0778 (1.00) |
0.0136 (1.00) |
0.435 (1.00) |
0.126 (1.00) |
0.847 (1.00) |
0.369 (1.00) |
0.512 (1.00) |
0.189 (1.00) |
0.316 (1.00) |
KIAA0748 | 7 (6%) | 109 |
0.337 (1.00) |
0.375 (1.00) |
1 (1.00) |
0.735 (1.00) |
0.699 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.199 (1.00) |
1 (1.00) |
0.807 (1.00) |
OR8B4 | 3 (3%) | 113 |
0.541 (1.00) |
0.782 (1.00) |
0.562 (1.00) |
0.389 (1.00) |
0.357 (1.00) |
0.082 (1.00) |
1 (1.00) |
0.292 (1.00) |
0.737 (1.00) |
0.948 (1.00) |
POM121L12 | 7 (6%) | 109 |
0.943 (1.00) |
0.449 (1.00) |
1 (1.00) |
0.568 (1.00) |
0.106 (1.00) |
0.769 (1.00) |
0.153 (1.00) |
0.38 (1.00) |
0.429 (1.00) |
0.663 (1.00) |
RASA1 | 9 (8%) | 107 |
0.307 (1.00) |
0.0831 (1.00) |
0.739 (1.00) |
0.216 (1.00) |
0.0242 (1.00) |
0.698 (1.00) |
0.0915 (1.00) |
0.547 (1.00) |
0.216 (1.00) |
0.222 (1.00) |
SLITRK6 | 10 (9%) | 106 |
0.231 (1.00) |
0.693 (1.00) |
0.738 (1.00) |
0.742 (1.00) |
0.925 (1.00) |
0.619 (1.00) |
0.26 (1.00) |
0.327 (1.00) |
0.41 (1.00) |
0.143 (1.00) |
TP53TG5 | 4 (3%) | 112 |
0.739 (1.00) |
0.758 (1.00) |
1 (1.00) |
0.048 (1.00) |
0.0655 (1.00) |
0.404 (1.00) |
1 (1.00) |
0.489 (1.00) |
0.785 (1.00) |
|
LHCGR | 7 (6%) | 109 |
0.863 (1.00) |
0.369 (1.00) |
1 (1.00) |
0.808 (1.00) |
0.0805 (1.00) |
0.442 (1.00) |
0.249 (1.00) |
0.928 (1.00) |
0.174 (1.00) |
0.47 (1.00) |
P value = 1.71e-07 (t-test), Q value = 7.8e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 71 | 4.5 (6.3) |
HLA-B MUTATED | 7 | 0.1 (0.4) |
HLA-B WILD-TYPE | 64 | 5.0 (6.5) |
P value = 3.6e-05 (t-test), Q value = 0.016
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 71 | 4.5 (6.3) |
POTEG MUTATED | 5 | 0.8 (0.8) |
POTEG WILD-TYPE | 66 | 4.8 (6.5) |
P value = 2.59e-06 (t-test), Q value = 0.0012
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 71 | 4.5 (6.3) |
TPTE MUTATED | 8 | 0.6 (0.5) |
TPTE WILD-TYPE | 63 | 5.0 (6.6) |
P value = 3.12e-07 (t-test), Q value = 0.00014
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 71 | 4.5 (6.3) |
CPS1 MUTATED | 8 | 0.2 (0.5) |
CPS1 WILD-TYPE | 63 | 5.0 (6.5) |
P value = 0.000484 (Fisher's exact test), Q value = 0.22
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 4 | 46 | 41 | 15 |
INO80E MUTATED | 0 | 0 | 0 | 4 |
INO80E WILD-TYPE | 4 | 46 | 41 | 11 |
P value = 3.6e-05 (t-test), Q value = 0.016
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 71 | 4.5 (6.3) |
UPF3A MUTATED | 5 | 0.8 (0.8) |
UPF3A WILD-TYPE | 66 | 4.8 (6.5) |
-
Mutation data file = STAD-TP.mutsig.cluster.txt
-
Clinical data file = STAD-TP.clin.merged.picked.txt
-
Number of patients = 116
-
Number of significantly mutated genes = 47
-
Number of selected clinical features = 10
-
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 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.