(Regional_LN 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 39 arm-level results and 7 clinical features across 112 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 | GENDER |
DISTANT METASTASIS |
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(1p12) | 32 (29%) | 80 |
0.157 (1.00) |
0.862 (1.00) |
0.822 (1.00) |
0.516 (1.00) |
0.476 (1.00) |
0.483 (1.00) |
|
Amp Peak 2(1q44) | 54 (48%) | 58 |
0.116 (1.00) |
0.72 (1.00) |
1 (1.00) |
0.87 (1.00) |
0.169 (1.00) |
0.182 (1.00) |
|
Amp Peak 3(3p13) | 24 (21%) | 88 |
0.165 (1.00) |
0.127 (1.00) |
0.466 (1.00) |
1 (1.00) |
0.758 (1.00) |
0.86 (1.00) |
|
Amp Peak 4(5p15 33) | 32 (29%) | 80 |
0.212 (1.00) |
0.92 (1.00) |
0.658 (1.00) |
0.682 (1.00) |
0.189 (1.00) |
0.334 (1.00) |
|
Amp Peak 5(5q35 3) | 13 (12%) | 99 |
0.458 (1.00) |
0.0514 (1.00) |
0.54 (1.00) |
0.425 (1.00) |
0.751 (1.00) |
0.829 (1.00) |
|
Amp Peak 6(6p25 1) | 61 (54%) | 51 |
0.192 (1.00) |
0.00486 (1.00) |
0.152 (1.00) |
1 (1.00) |
0.238 (1.00) |
0.795 (1.00) |
|
Amp Peak 7(6q12) | 23 (21%) | 89 |
0.628 (1.00) |
0.604 (1.00) |
0.322 (1.00) |
1 (1.00) |
0.0317 (1.00) |
0.373 (1.00) |
|
Amp Peak 8(7p22 1) | 60 (54%) | 52 |
0.683 (1.00) |
0.86 (1.00) |
1 (1.00) |
1 (1.00) |
0.408 (1.00) |
0.386 (1.00) |
|
Amp Peak 9(7q34) | 62 (55%) | 50 |
0.61 (1.00) |
0.906 (1.00) |
0.544 (1.00) |
1 (1.00) |
0.442 (1.00) |
0.145 (1.00) |
|
Amp Peak 10(8q11 21) | 41 (37%) | 71 |
0.598 (1.00) |
0.0311 (1.00) |
1 (1.00) |
0.608 (1.00) |
0.715 (1.00) |
0.847 (1.00) |
|
Amp Peak 11(8q24 21) | 50 (45%) | 62 |
0.53 (1.00) |
0.122 (1.00) |
1 (1.00) |
0.409 (1.00) |
0.839 (1.00) |
0.968 (1.00) |
|
Amp Peak 12(9p24 1) | 5 (4%) | 107 |
0.00411 (0.961) |
0.858 (1.00) |
1 (1.00) |
1 (1.00) |
0.548 (1.00) |
0.596 (1.00) |
|
Amp Peak 13(11q13 3) | 19 (17%) | 93 |
0.709 (1.00) |
0.491 (1.00) |
0.787 (1.00) |
1 (1.00) |
0.949 (1.00) |
0.659 (1.00) |
|
Amp Peak 14(12q14 1) | 20 (18%) | 92 |
0.338 (1.00) |
0.371 (1.00) |
0.791 (1.00) |
1 (1.00) |
0.661 (1.00) |
0.183 (1.00) |
|
Amp Peak 15(15q26 2) | 43 (38%) | 69 |
0.698 (1.00) |
0.453 (1.00) |
0.676 (1.00) |
1 (1.00) |
0.529 (1.00) |
0.319 (1.00) |
|
Amp Peak 16(17q25 3) | 44 (39%) | 68 |
0.54 (1.00) |
0.0191 (1.00) |
0.836 (1.00) |
1 (1.00) |
0.73 (1.00) |
0.453 (1.00) |
|
Amp Peak 17(19p13 2) | 19 (17%) | 93 |
0.588 (1.00) |
0.543 (1.00) |
0.417 (1.00) |
0.362 (1.00) |
0.817 (1.00) |
0.218 (1.00) |
|
Amp Peak 18(22q13 2) | 48 (43%) | 64 |
0.697 (1.00) |
0.599 (1.00) |
1 (1.00) |
0.704 (1.00) |
0.379 (1.00) |
0.727 (1.00) |
|
Del Peak 1(1p36 31) | 27 (24%) | 85 |
0.959 (1.00) |
0.458 (1.00) |
0.481 (1.00) |
1 (1.00) |
0.49 (1.00) |
0.434 (1.00) |
|
Del Peak 2(1p21 3) | 30 (27%) | 82 |
0.136 (1.00) |
0.0661 (1.00) |
1 (1.00) |
0.698 (1.00) |
0.368 (1.00) |
0.638 (1.00) |
|
Del Peak 3(2q37 3) | 21 (19%) | 91 |
0.714 (1.00) |
0.717 (1.00) |
0.8 (1.00) |
0.546 (1.00) |
0.863 (1.00) |
0.0294 (1.00) |
|
Del Peak 4(3p24 3) | 17 (15%) | 95 |
0.513 (1.00) |
0.485 (1.00) |
0.158 (1.00) |
1 (1.00) |
0.16 (1.00) |
0.0398 (1.00) |
|
Del Peak 5(4q34 3) | 23 (21%) | 89 |
0.981 (1.00) |
0.391 (1.00) |
0.207 (1.00) |
0.0961 (1.00) |
0.827 (1.00) |
0.585 (1.00) |
|
Del Peak 6(5q31 3) | 45 (40%) | 67 |
0.446 (1.00) |
0.832 (1.00) |
0.836 (1.00) |
0.236 (1.00) |
0.435 (1.00) |
0.373 (1.00) |
|
Del Peak 7(6q25 3) | 67 (60%) | 45 |
0.701 (1.00) |
0.151 (1.00) |
0.684 (1.00) |
1 (1.00) |
0.385 (1.00) |
0.833 (1.00) |
|
Del Peak 8(6q26) | 63 (56%) | 49 |
0.988 (1.00) |
0.149 (1.00) |
0.413 (1.00) |
1 (1.00) |
0.344 (1.00) |
0.888 (1.00) |
|
Del Peak 9(8p23 3) | 29 (26%) | 83 |
0.594 (1.00) |
0.833 (1.00) |
0.485 (1.00) |
0.251 (1.00) |
0.41 (1.00) |
0.794 (1.00) |
|
Del Peak 10(9p23) | 75 (67%) | 37 |
0.557 (1.00) |
0.529 (1.00) |
0.289 (1.00) |
0.622 (1.00) |
0.443 (1.00) |
0.818 (1.00) |
|
Del Peak 11(9p21 3) | 86 (77%) | 26 |
0.161 (1.00) |
0.322 (1.00) |
0.055 (1.00) |
1 (1.00) |
0.242 (1.00) |
0.682 (1.00) |
|
Del Peak 12(10p15 3) | 55 (49%) | 57 |
0.324 (1.00) |
0.486 (1.00) |
0.309 (1.00) |
0.87 (1.00) |
0.326 (1.00) |
0.812 (1.00) |
|
Del Peak 13(10q23 31) | 64 (57%) | 48 |
0.757 (1.00) |
0.131 (1.00) |
0.0146 (1.00) |
0.405 (1.00) |
0.47 (1.00) |
0.856 (1.00) |
|
Del Peak 14(11q23 1) | 61 (54%) | 51 |
0.147 (1.00) |
0.575 (1.00) |
1 (1.00) |
0.422 (1.00) |
0.132 (1.00) |
0.374 (1.00) |
|
Del Peak 15(12q24 33) | 21 (19%) | 91 |
0.755 (1.00) |
0.245 (1.00) |
0.296 (1.00) |
0.344 (1.00) |
0.139 (1.00) |
0.906 (1.00) |
|
Del Peak 16(13q34) | 31 (28%) | 81 |
0.298 (1.00) |
0.986 (1.00) |
0.501 (1.00) |
0.037 (1.00) |
0.775 (1.00) |
0.182 (1.00) |
|
Del Peak 17(15q13 3) | 25 (22%) | 87 |
0.349 (1.00) |
0.817 (1.00) |
0.144 (1.00) |
0.628 (1.00) |
0.805 (1.00) |
0.351 (1.00) |
|
Del Peak 18(15q15 3) | 26 (23%) | 86 |
0.0206 (1.00) |
0.47 (1.00) |
0.0897 (1.00) |
0.218 (1.00) |
0.838 (1.00) |
0.194 (1.00) |
|
Del Peak 19(16p13 3) | 22 (20%) | 90 |
0.363 (1.00) |
0.115 (1.00) |
0.31 (1.00) |
1 (1.00) |
0.107 (1.00) |
0.426 (1.00) |
|
Del Peak 20(16q12 1) | 38 (34%) | 74 |
0.357 (1.00) |
0.754 (1.00) |
0.67 (1.00) |
1 (1.00) |
0.75 (1.00) |
0.234 (1.00) |
|
Del Peak 21(16q24 2) | 43 (38%) | 69 |
0.0526 (1.00) |
0.271 (1.00) |
0.148 (1.00) |
1 (1.00) |
0.119 (1.00) |
0.0156 (1.00) |
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Mutation data file = all_lesions.conf_99.cnv.cluster.txt
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Clinical data file = SKCM-Regional_LN.clin.merged.picked.txt
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Number of patients = 112
-
Number of significantly arm-level cnvs = 39
-
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.