This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 16 genes and 13 clinical features across 178 patients, one significant finding detected with Q value < 0.25.
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ASCL4 mutation correlated to 'NUMBERPACKYEARSSMOKED'.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | YEAROFTOBACCOSMOKINGONSET |
COMPLETENESS OF RESECTION |
||
nMutated (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | Fisher's exact test | Fisher's exact test | t-test | t-test | Fisher's exact test | |
ASCL4 | 6 (3%) | 172 |
0.96 (1.00) |
0.318 (1.00) |
0.634 (1.00) |
0.858 (1.00) |
0.13 (1.00) |
1 (1.00) |
0.655 (1.00) |
1 (1.00) |
1 (1.00) |
8.63e-07 (0.000174) |
0.193 (1.00) |
0.152 (1.00) |
|
CDKN2A | 26 (15%) | 152 |
0.27 (1.00) |
0.679 (1.00) |
0.919 (1.00) |
0.433 (1.00) |
0.472 (1.00) |
0.746 (1.00) |
0.812 (1.00) |
0.937 (1.00) |
0.618 (1.00) |
0.471 (1.00) |
0.378 (1.00) |
0.638 (1.00) |
0.877 (1.00) |
TP53 | 141 (79%) | 37 |
0.0797 (1.00) |
0.772 (1.00) |
0.897 (1.00) |
0.221 (1.00) |
0.546 (1.00) |
0.126 (1.00) |
1 (1.00) |
0.134 (1.00) |
0.671 (1.00) |
0.582 (1.00) |
0.316 (1.00) |
0.915 (1.00) |
0.378 (1.00) |
NFE2L2 | 27 (15%) | 151 |
0.673 (1.00) |
0.788 (1.00) |
0.7 (1.00) |
0.529 (1.00) |
0.831 (1.00) |
0.267 (1.00) |
0.161 (1.00) |
0.925 (1.00) |
0.633 (1.00) |
1 (1.00) |
0.0966 (1.00) |
0.88 (1.00) |
0.497 (1.00) |
PIK3CA | 27 (15%) | 151 |
0.143 (1.00) |
0.355 (1.00) |
0.0275 (1.00) |
0.156 (1.00) |
0.671 (1.00) |
0.393 (1.00) |
0.161 (1.00) |
0.482 (1.00) |
1 (1.00) |
1 (1.00) |
0.148 (1.00) |
0.967 (1.00) |
1 (1.00) |
PTEN | 14 (8%) | 164 |
0.0571 (1.00) |
0.822 (1.00) |
0.322 (1.00) |
0.612 (1.00) |
0.295 (1.00) |
0.0371 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.585 (1.00) |
0.797 (1.00) |
0.294 (1.00) |
|
KEAP1 | 22 (12%) | 156 |
0.385 (1.00) |
0.769 (1.00) |
0.945 (1.00) |
0.522 (1.00) |
0.882 (1.00) |
1 (1.00) |
0.8 (1.00) |
0.388 (1.00) |
0.226 (1.00) |
1 (1.00) |
0.727 (1.00) |
0.502 (1.00) |
0.838 (1.00) |
CSMD3 | 81 (46%) | 97 |
0.11 (1.00) |
0.482 (1.00) |
0.0953 (1.00) |
0.388 (1.00) |
0.115 (1.00) |
0.0611 (1.00) |
0.495 (1.00) |
0.679 (1.00) |
0.816 (1.00) |
1 (1.00) |
0.573 (1.00) |
0.64 (1.00) |
0.723 (1.00) |
MLL2 | 36 (20%) | 142 |
0.0465 (1.00) |
0.945 (1.00) |
0.958 (1.00) |
0.673 (1.00) |
0.772 (1.00) |
0.799 (1.00) |
1 (1.00) |
0.868 (1.00) |
0.669 (1.00) |
0.584 (1.00) |
0.262 (1.00) |
0.999 (1.00) |
0.651 (1.00) |
FBXW7 | 11 (6%) | 167 |
0.125 (1.00) |
0.996 (1.00) |
0.132 (1.00) |
0.899 (1.00) |
0.297 (1.00) |
1 (1.00) |
0.292 (1.00) |
0.00639 (1.00) |
0.322 (1.00) |
1 (1.00) |
0.508 (1.00) |
0.00663 (1.00) |
0.691 (1.00) |
RB1 | 12 (7%) | 166 |
0.979 (1.00) |
0.481 (1.00) |
0.918 (1.00) |
0.863 (1.00) |
0.321 (1.00) |
1 (1.00) |
0.306 (1.00) |
0.0539 (1.00) |
1 (1.00) |
0.206 (1.00) |
0.233 (1.00) |
0.263 (1.00) |
|
HS6ST1 | 5 (3%) | 173 |
0.447 (1.00) |
0.907 (1.00) |
0.754 (1.00) |
0.499 (1.00) |
0.658 (1.00) |
1 (1.00) |
1 (1.00) |
0.159 (1.00) |
1 (1.00) |
0.176 (1.00) |
0.0959 (1.00) |
1 (1.00) |
|
ZNF567 | 3 (2%) | 175 |
0.713 (1.00) |
0.268 (1.00) |
0.00346 (0.692) |
0.466 (1.00) |
0.00209 (0.42) |
1 (1.00) |
0.171 (1.00) |
1 (1.00) |
1 (1.00) |
0.608 (1.00) |
1 (1.00) |
||
ELTD1 | 18 (10%) | 160 |
0.497 (1.00) |
0.416 (1.00) |
0.0964 (1.00) |
0.0796 (1.00) |
0.703 (1.00) |
0.635 (1.00) |
0.0452 (1.00) |
0.684 (1.00) |
0.478 (1.00) |
1 (1.00) |
0.306 (1.00) |
0.683 (1.00) |
0.581 (1.00) |
OR2G6 | 16 (9%) | 162 |
0.395 (1.00) |
0.583 (1.00) |
0.908 (1.00) |
0.961 (1.00) |
1 (1.00) |
1 (1.00) |
0.244 (1.00) |
0.746 (1.00) |
0.092 (1.00) |
1 (1.00) |
0.31 (1.00) |
0.884 (1.00) |
0.137 (1.00) |
NOTCH1 | 14 (8%) | 164 |
0.388 (1.00) |
0.989 (1.00) |
0.309 (1.00) |
0.039 (1.00) |
0.439 (1.00) |
1 (1.00) |
0.527 (1.00) |
0.00631 (1.00) |
1 (1.00) |
1 (1.00) |
0.683 (1.00) |
0.278 (1.00) |
0.769 (1.00) |
P value = 8.63e-07 (t-test), Q value = 0.00017
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 147 | 52.4 (31.3) |
ASCL4 MUTATED | 4 | 23.8 (4.8) |
ASCL4 WILD-TYPE | 143 | 53.2 (31.3) |
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Mutation data file = LUSC-TP.mutsig.cluster.txt
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Clinical data file = LUSC-TP.clin.merged.picked.txt
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Number of patients = 178
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Number of significantly mutated genes = 16
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Number of selected clinical features = 13
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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 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 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.