(metastatic tumor 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 51 arm-level results and 7 clinical features across 158 patients, no significant finding detected with Q value < 0.25.
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No arm-level cnvs related to clinical features.
Table 1. Get Full Table Overview of the association between significant copy number variation of 51 arm-level results and 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.
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 | Chi-square test | Chi-square test | t-test | Chi-square test | |
Amp Peak 1(1p12) | 47 (30%) | 111 |
0.00815 (1.00) |
0.676 (1.00) |
0.476 (1.00) |
0.77 (1.00) |
0.306 (1.00) |
0.17 (1.00) |
|
Amp Peak 2(1q21 3) | 83 (53%) | 75 |
0.803 (1.00) |
0.854 (1.00) |
0.872 (1.00) |
0.31 (1.00) |
0.207 (1.00) |
0.839 (1.00) |
|
Amp Peak 3(1q44) | 85 (54%) | 73 |
0.137 (1.00) |
0.943 (1.00) |
0.627 (1.00) |
0.325 (1.00) |
0.305 (1.00) |
0.606 (1.00) |
|
Amp Peak 4(3p13) | 35 (22%) | 123 |
0.149 (1.00) |
0.0223 (1.00) |
0.24 (1.00) |
0.629 (1.00) |
0.984 (1.00) |
0.228 (1.00) |
|
Amp Peak 5(4q12) | 30 (19%) | 128 |
0.443 (1.00) |
0.237 (1.00) |
0.679 (1.00) |
0.652 (1.00) |
0.862 (1.00) |
0.888 (1.00) |
|
Amp Peak 6(5p15 33) | 43 (27%) | 115 |
0.0763 (1.00) |
0.554 (1.00) |
1 (1.00) |
0.209 (1.00) |
0.567 (1.00) |
0.228 (1.00) |
|
Amp Peak 7(5q35 3) | 20 (13%) | 138 |
0.555 (1.00) |
0.269 (1.00) |
0.332 (1.00) |
0.0208 (1.00) |
0.589 (1.00) |
0.538 (1.00) |
|
Amp Peak 8(6p25 1) | 95 (60%) | 63 |
0.0231 (1.00) |
0.1 (1.00) |
0.869 (1.00) |
0.467 (1.00) |
0.0753 (1.00) |
0.557 (1.00) |
|
Amp Peak 9(6q12) | 34 (22%) | 124 |
0.422 (1.00) |
0.957 (1.00) |
1 (1.00) |
0.768 (1.00) |
0.291 (1.00) |
0.387 (1.00) |
|
Amp Peak 10(7p22 3) | 88 (56%) | 70 |
0.504 (1.00) |
0.668 (1.00) |
0.256 (1.00) |
0.19 (1.00) |
0.423 (1.00) |
0.176 (1.00) |
|
Amp Peak 11(7q34) | 90 (57%) | 68 |
0.775 (1.00) |
0.196 (1.00) |
0.624 (1.00) |
0.23 (1.00) |
0.335 (1.00) |
0.0264 (1.00) |
|
Amp Peak 12(8q11 21) | 64 (41%) | 94 |
0.653 (1.00) |
0.0604 (1.00) |
0.511 (1.00) |
0.175 (1.00) |
0.946 (1.00) |
0.86 (1.00) |
|
Amp Peak 13(8q24 21) | 75 (47%) | 83 |
0.651 (1.00) |
0.0959 (1.00) |
0.514 (1.00) |
0.294 (1.00) |
0.988 (1.00) |
0.915 (1.00) |
|
Amp Peak 14(9p24 1) | 12 (8%) | 146 |
0.592 (1.00) |
0.636 (1.00) |
0.541 (1.00) |
0.0345 (1.00) |
0.558 (1.00) |
0.0566 (1.00) |
|
Amp Peak 15(11q13 3) | 23 (15%) | 135 |
0.513 (1.00) |
0.727 (1.00) |
0.069 (1.00) |
0.875 (1.00) |
0.409 (1.00) |
0.442 (1.00) |
|
Amp Peak 16(11q13 4) | 23 (15%) | 135 |
0.669 (1.00) |
0.845 (1.00) |
0.069 (1.00) |
0.547 (1.00) |
0.258 (1.00) |
0.648 (1.00) |
|
Amp Peak 17(12q14 1) | 25 (16%) | 133 |
0.978 (1.00) |
0.869 (1.00) |
1 (1.00) |
0.62 (1.00) |
0.295 (1.00) |
0.0566 (1.00) |
|
Amp Peak 18(12q15) | 20 (13%) | 138 |
0.53 (1.00) |
0.479 (1.00) |
0.628 (1.00) |
0.898 (1.00) |
0.101 (1.00) |
0.0881 (1.00) |
|
Amp Peak 19(15q24 3) | 50 (32%) | 108 |
0.697 (1.00) |
0.364 (1.00) |
0.863 (1.00) |
0.293 (1.00) |
0.413 (1.00) |
0.341 (1.00) |
|
Amp Peak 20(17q25 3) | 61 (39%) | 97 |
0.412 (1.00) |
0.0269 (1.00) |
0.132 (1.00) |
0.556 (1.00) |
0.717 (1.00) |
0.781 (1.00) |
|
Amp Peak 21(19p13 2) | 31 (20%) | 127 |
0.83 (1.00) |
0.626 (1.00) |
0.686 (1.00) |
0.00176 (0.539) |
0.608 (1.00) |
0.197 (1.00) |
|
Amp Peak 22(20q13 2) | 82 (52%) | 76 |
0.537 (1.00) |
0.1 (1.00) |
0.194 (1.00) |
0.139 (1.00) |
0.758 (1.00) |
0.181 (1.00) |
|
Amp Peak 23(22q13 2) | 74 (47%) | 84 |
0.673 (1.00) |
0.95 (1.00) |
0.519 (1.00) |
0.866 (1.00) |
0.303 (1.00) |
0.451 (1.00) |
|
Amp Peak 24(Xq28) | 28 (18%) | 130 |
0.99 (1.00) |
0.52 (1.00) |
0.0933 (1.00) |
0.643 (1.00) |
0.893 (1.00) |
0.582 (1.00) |
|
Del Peak 1(1p36 31) | 42 (27%) | 116 |
0.621 (1.00) |
0.573 (1.00) |
0.363 (1.00) |
0.12 (1.00) |
0.684 (1.00) |
0.838 (1.00) |
|
Del Peak 2(1p22 1) | 41 (26%) | 117 |
0.033 (1.00) |
0.00578 (1.00) |
0.853 (1.00) |
0.11 (1.00) |
0.689 (1.00) |
0.369 (1.00) |
|
Del Peak 3(2q37 3) | 41 (26%) | 117 |
0.348 (1.00) |
0.823 (1.00) |
0.353 (1.00) |
0.0219 (1.00) |
0.578 (1.00) |
0.391 (1.00) |
|
Del Peak 4(3q23) | 23 (15%) | 135 |
0.633 (1.00) |
0.151 (1.00) |
0.176 (1.00) |
0.00481 (1.00) |
0.71 (1.00) |
0.135 (1.00) |
|
Del Peak 5(4q22 1) | 31 (20%) | 127 |
0.182 (1.00) |
0.00699 (1.00) |
0.0642 (1.00) |
0.216 (1.00) |
0.441 (1.00) |
0.219 (1.00) |
|
Del Peak 6(4q34 3) | 41 (26%) | 117 |
0.344 (1.00) |
0.136 (1.00) |
0.0152 (1.00) |
0.306 (1.00) |
0.762 (1.00) |
0.0759 (1.00) |
|
Del Peak 7(5q11 2) | 48 (30%) | 110 |
0.178 (1.00) |
0.771 (1.00) |
0.725 (1.00) |
0.42 (1.00) |
0.609 (1.00) |
0.466 (1.00) |
|
Del Peak 8(5q31 3) | 62 (39%) | 96 |
0.0858 (1.00) |
0.527 (1.00) |
0.868 (1.00) |
0.556 (1.00) |
0.616 (1.00) |
0.837 (1.00) |
|
Del Peak 9(6q26) | 96 (61%) | 62 |
0.647 (1.00) |
0.427 (1.00) |
0.739 (1.00) |
0.71 (1.00) |
0.251 (1.00) |
0.819 (1.00) |
|
Del Peak 10(8p23 3) | 38 (24%) | 120 |
0.926 (1.00) |
0.0257 (1.00) |
0.182 (1.00) |
0.216 (1.00) |
0.422 (1.00) |
0.122 (1.00) |
|
Del Peak 11(9p23) | 111 (70%) | 47 |
0.985 (1.00) |
0.659 (1.00) |
0.476 (1.00) |
0.0929 (1.00) |
0.347 (1.00) |
0.5 (1.00) |
|
Del Peak 12(9p21 3) | 126 (80%) | 32 |
0.384 (1.00) |
0.706 (1.00) |
0.32 (1.00) |
0.674 (1.00) |
0.432 (1.00) |
0.714 (1.00) |
|
Del Peak 13(10p15 3) | 82 (52%) | 76 |
0.361 (1.00) |
0.232 (1.00) |
0.416 (1.00) |
0.277 (1.00) |
0.555 (1.00) |
0.98 (1.00) |
|
Del Peak 14(10q23 31) | 96 (61%) | 62 |
0.502 (1.00) |
0.0907 (1.00) |
0.0193 (1.00) |
0.69 (1.00) |
0.747 (1.00) |
0.619 (1.00) |
|
Del Peak 15(10q26 3) | 96 (61%) | 62 |
0.267 (1.00) |
0.0143 (1.00) |
0.0193 (1.00) |
0.285 (1.00) |
0.858 (1.00) |
0.782 (1.00) |
|
Del Peak 16(11q23 3) | 93 (59%) | 65 |
0.374 (1.00) |
0.574 (1.00) |
0.508 (1.00) |
0.673 (1.00) |
0.00751 (1.00) |
0.171 (1.00) |
|
Del Peak 17(12p13 31) | 21 (13%) | 137 |
0.351 (1.00) |
0.34 (1.00) |
0.474 (1.00) |
0.547 (1.00) |
0.243 (1.00) |
0.653 (1.00) |
|
Del Peak 18(12q23 3) | 37 (23%) | 121 |
0.407 (1.00) |
0.428 (1.00) |
0.57 (1.00) |
0.216 (1.00) |
0.216 (1.00) |
0.956 (1.00) |
|
Del Peak 19(12q24 33) | 37 (23%) | 121 |
0.514 (1.00) |
0.852 (1.00) |
0.344 (1.00) |
0.629 (1.00) |
0.206 (1.00) |
0.758 (1.00) |
|
Del Peak 20(13q34) | 39 (25%) | 119 |
0.258 (1.00) |
0.682 (1.00) |
0.707 (1.00) |
0.0375 (1.00) |
0.102 (1.00) |
0.138 (1.00) |
|
Del Peak 21(14q32 2) | 51 (32%) | 107 |
0.764 (1.00) |
0.536 (1.00) |
0.384 (1.00) |
0.209 (1.00) |
0.47 (1.00) |
0.333 (1.00) |
|
Del Peak 22(15q13 3) | 39 (25%) | 119 |
0.374 (1.00) |
0.875 (1.00) |
0.573 (1.00) |
0.272 (1.00) |
0.655 (1.00) |
0.802 (1.00) |
|
Del Peak 23(15q15 3) | 38 (24%) | 120 |
0.201 (1.00) |
0.912 (1.00) |
0.257 (1.00) |
0.259 (1.00) |
0.837 (1.00) |
0.756 (1.00) |
|
Del Peak 24(16p13 3) | 29 (18%) | 129 |
0.893 (1.00) |
0.273 (1.00) |
0.0603 (1.00) |
0.811 (1.00) |
0.44 (1.00) |
0.824 (1.00) |
|
Del Peak 25(16q12 1) | 54 (34%) | 104 |
0.176 (1.00) |
0.885 (1.00) |
0.23 (1.00) |
0.373 (1.00) |
0.844 (1.00) |
0.324 (1.00) |
|
Del Peak 26(16q24 3) | 56 (35%) | 102 |
0.0649 (1.00) |
0.697 (1.00) |
0.178 (1.00) |
0.378 (1.00) |
0.258 (1.00) |
0.262 (1.00) |
|
Del Peak 27(19p13 3) | 47 (30%) | 111 |
0.715 (1.00) |
0.906 (1.00) |
0.378 (1.00) |
0.069 (1.00) |
0.761 (1.00) |
0.349 (1.00) |
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Mutation data file = all_lesions.conf_99.cnv.cluster.txt
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Clinical data file = SKCM-TM.clin.merged.picked.txt
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Number of patients = 158
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Number of significantly arm-level cnvs = 51
-
Number of selected clinical features = 7
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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 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.