(NRAS_Hotspot_Mutants cohort)
This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 33 arm-level results and 7 clinical features across 45 patients, no significant finding detected with Q value < 0.25.
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No arm-level cnvs related to clinical features.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
GENDER |
LYMPH NODE METASTASIS |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Chi-square test | t-test | Chi-square test | |
Amp Peak 1(1p13 2) | 13 (29%) | 32 |
0.00482 (0.955) |
0.532 (1.00) |
0.9 (1.00) |
1 (1.00) |
0.676 (1.00) |
0.682 (1.00) |
|
Amp Peak 2(1q31 2) | 28 (62%) | 17 |
0.568 (1.00) |
0.322 (1.00) |
1 (1.00) |
0.541 (1.00) |
0.347 (1.00) |
0.599 (1.00) |
|
Amp Peak 3(1q44) | 27 (60%) | 18 |
0.446 (1.00) |
0.132 (1.00) |
0.912 (1.00) |
1 (1.00) |
0.3 (1.00) |
0.853 (1.00) |
|
Amp Peak 4(5p15 33) | 7 (16%) | 38 |
0.849 (1.00) |
0.667 (1.00) |
0.162 (1.00) |
1 (1.00) |
0.0145 (1.00) |
0.0149 (1.00) |
|
Amp Peak 5(6p25 1) | 33 (73%) | 12 |
0.809 (1.00) |
0.307 (1.00) |
1 (1.00) |
0.491 (1.00) |
0.709 (1.00) |
0.46 (1.00) |
|
Amp Peak 6(7p21 3) | 18 (40%) | 27 |
0.86 (1.00) |
0.0377 (1.00) |
0.755 (1.00) |
0.354 (1.00) |
0.479 (1.00) |
0.205 (1.00) |
|
Amp Peak 7(11q14 1) | 8 (18%) | 37 |
0.212 (1.00) |
0.203 (1.00) |
0.743 (1.00) |
0.691 (1.00) |
0.598 (1.00) |
0.157 (1.00) |
|
Amp Peak 8(12q15) | 6 (13%) | 39 |
0.564 (1.00) |
0.963 (1.00) |
1 (1.00) |
0.166 (1.00) |
0.0552 (1.00) |
0.11 (1.00) |
|
Amp Peak 9(15q26 1) | 16 (36%) | 29 |
0.368 (1.00) |
0.487 (1.00) |
0.826 (1.00) |
0.518 (1.00) |
0.0576 (1.00) |
0.611 (1.00) |
|
Amp Peak 10(17q25 3) | 18 (40%) | 27 |
0.52 (1.00) |
0.764 (1.00) |
0.687 (1.00) |
0.758 (1.00) |
0.0383 (1.00) |
0.117 (1.00) |
|
Amp Peak 11(20q13 2) | 21 (47%) | 24 |
0.604 (1.00) |
0.983 (1.00) |
0.172 (1.00) |
0.765 (1.00) |
0.796 (1.00) |
0.451 (1.00) |
|
Amp Peak 12(22q13 2) | 19 (42%) | 26 |
0.909 (1.00) |
0.623 (1.00) |
0.572 (1.00) |
1 (1.00) |
0.392 (1.00) |
0.172 (1.00) |
|
Del Peak 1(1p36 13) | 10 (22%) | 35 |
0.78 (1.00) |
0.351 (1.00) |
0.459 (1.00) |
0.455 (1.00) |
0.312 (1.00) |
0.819 (1.00) |
|
Del Peak 2(4q34 3) | 11 (24%) | 34 |
0.529 (1.00) |
0.154 (1.00) |
0.286 (1.00) |
0.00852 (1.00) |
0.246 (1.00) |
0.15 (1.00) |
|
Del Peak 3(5q31 1) | 19 (42%) | 26 |
0.911 (1.00) |
0.439 (1.00) |
0.912 (1.00) |
0.212 (1.00) |
0.549 (1.00) |
0.496 (1.00) |
|
Del Peak 4(5q31 1) | 19 (42%) | 26 |
0.911 (1.00) |
0.439 (1.00) |
0.912 (1.00) |
0.212 (1.00) |
0.549 (1.00) |
0.496 (1.00) |
|
Del Peak 5(6q16 3) | 31 (69%) | 14 |
0.368 (1.00) |
0.485 (1.00) |
1 (1.00) |
1 (1.00) |
0.17 (1.00) |
0.258 (1.00) |
|
Del Peak 6(6q22 31) | 31 (69%) | 14 |
0.729 (1.00) |
0.417 (1.00) |
0.815 (1.00) |
0.738 (1.00) |
0.17 (1.00) |
0.0797 (1.00) |
|
Del Peak 7(6q26) | 32 (71%) | 13 |
0.98 (1.00) |
0.269 (1.00) |
0.9 (1.00) |
0.743 (1.00) |
0.204 (1.00) |
0.0376 (1.00) |
|
Del Peak 8(7q31 1) | 8 (18%) | 37 |
0.915 (1.00) |
0.276 (1.00) |
0.0127 (1.00) |
0.226 (1.00) |
0.891 (1.00) |
0.424 (1.00) |
|
Del Peak 9(9p23) | 34 (76%) | 11 |
0.438 (1.00) |
0.228 (1.00) |
0.154 (1.00) |
0.279 (1.00) |
0.517 (1.00) |
0.67 (1.00) |
|
Del Peak 10(9p21 3) | 38 (84%) | 7 |
0.738 (1.00) |
0.872 (1.00) |
0.125 (1.00) |
0.0398 (1.00) |
0.782 (1.00) |
0.546 (1.00) |
|
Del Peak 11(10p15 3) | 24 (53%) | 21 |
0.18 (1.00) |
0.145 (1.00) |
0.0576 (1.00) |
0.212 (1.00) |
0.0382 (1.00) |
0.553 (1.00) |
|
Del Peak 12(10q23 31) | 25 (56%) | 20 |
0.593 (1.00) |
0.573 (1.00) |
0.0066 (1.00) |
0.0661 (1.00) |
0.0438 (1.00) |
0.76 (1.00) |
|
Del Peak 13(11q24 2) | 31 (69%) | 14 |
0.534 (1.00) |
0.262 (1.00) |
0.0896 (1.00) |
1 (1.00) |
0.578 (1.00) |
0.448 (1.00) |
|
Del Peak 14(12p12 3) | 7 (16%) | 38 |
0.293 (1.00) |
0.0293 (1.00) |
0.248 (1.00) |
0.686 (1.00) |
0.199 (1.00) |
0.241 (1.00) |
|
Del Peak 15(12q23 3) | 13 (29%) | 32 |
0.914 (1.00) |
0.328 (1.00) |
0.579 (1.00) |
0.494 (1.00) |
0.24 (1.00) |
0.331 (1.00) |
|
Del Peak 16(13q14 2) | 6 (13%) | 39 |
0.508 (1.00) |
0.296 (1.00) |
0.397 (1.00) |
1 (1.00) |
0.0234 (1.00) |
0.441 (1.00) |
|
Del Peak 17(14q31 3) | 19 (42%) | 26 |
0.401 (1.00) |
0.23 (1.00) |
0.912 (1.00) |
0.757 (1.00) |
0.549 (1.00) |
0.583 (1.00) |
|
Del Peak 18(15q13 3) | 13 (29%) | 32 |
0.384 (1.00) |
0.598 (1.00) |
0.579 (1.00) |
1 (1.00) |
0.247 (1.00) |
0.715 (1.00) |
|
Del Peak 19(16p13 3) | 8 (18%) | 37 |
0.963 (1.00) |
0.84 (1.00) |
0.356 (1.00) |
0.427 (1.00) |
0.355 (1.00) |
0.243 (1.00) |
|
Del Peak 20(16q23 3) | 14 (31%) | 31 |
0.124 (1.00) |
0.539 (1.00) |
0.815 (1.00) |
1 (1.00) |
0.135 (1.00) |
0.448 (1.00) |
|
Del Peak 21(21q11 2) | 10 (22%) | 35 |
0.682 (1.00) |
0.424 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.132 (1.00) |
0.332 (1.00) |
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Mutation data file = all_lesions.conf_99.cnv.cluster.txt
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Clinical data file = SKCM-NRAS_Hotspot_Mutants.clin.merged.picked.txt
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Number of patients = 45
-
Number of significantly arm-level cnvs = 33
-
Number of selected clinical features = 7
-
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.