(All_Samples 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 9 clinical features across 202 patients, no significant finding detected with Q value < 0.25.
-
No arm-level cnvs related to clinical features.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
GENDER |
RADIATIONS RADIATION REGIMENINDICATION |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Chi-square test | t-test | Chi-square test | |
Amp Peak 1(1p12) | 59 (29%) | 143 |
0.0199 (1.00) |
0.996 (1.00) |
0.773 (1.00) |
0.526 (1.00) |
0.205 (1.00) |
0.768 (1.00) |
0.604 (1.00) |
0.287 (1.00) |
|
Amp Peak 2(1q44) | 106 (52%) | 96 |
0.0925 (1.00) |
0.827 (1.00) |
0.288 (1.00) |
0.248 (1.00) |
0.605 (1.00) |
0.727 (1.00) |
0.407 (1.00) |
0.528 (1.00) |
|
Amp Peak 3(3p13) | 47 (23%) | 155 |
0.181 (1.00) |
0.0984 (1.00) |
0.224 (1.00) |
0.0855 (1.00) |
0.55 (1.00) |
0.702 (1.00) |
0.552 (1.00) |
0.197 (1.00) |
|
Amp Peak 4(4q12) | 33 (16%) | 169 |
0.418 (1.00) |
0.372 (1.00) |
0.0901 (1.00) |
0.56 (1.00) |
1 (1.00) |
0.341 (1.00) |
0.812 (1.00) |
0.864 (1.00) |
|
Amp Peak 5(5p15 33) | 53 (26%) | 149 |
0.0788 (1.00) |
0.487 (1.00) |
0.725 (1.00) |
1 (1.00) |
1 (1.00) |
0.538 (1.00) |
0.177 (1.00) |
0.615 (1.00) |
|
Amp Peak 6(5q35 3) | 24 (12%) | 178 |
0.426 (1.00) |
0.168 (1.00) |
0.153 (1.00) |
0.187 (1.00) |
1 (1.00) |
0.0783 (1.00) |
0.976 (1.00) |
0.504 (1.00) |
|
Amp Peak 7(6p25 1) | 113 (56%) | 89 |
0.0877 (1.00) |
0.033 (1.00) |
0.13 (1.00) |
0.885 (1.00) |
0.584 (1.00) |
0.423 (1.00) |
0.0912 (1.00) |
0.55 (1.00) |
|
Amp Peak 8(6q12) | 39 (19%) | 163 |
0.414 (1.00) |
0.727 (1.00) |
0.0619 (1.00) |
0.585 (1.00) |
0.476 (1.00) |
0.74 (1.00) |
0.399 (1.00) |
0.104 (1.00) |
|
Amp Peak 9(7p22 3) | 111 (55%) | 91 |
0.738 (1.00) |
0.834 (1.00) |
0.726 (1.00) |
0.662 (1.00) |
0.59 (1.00) |
0.46 (1.00) |
0.768 (1.00) |
0.386 (1.00) |
|
Amp Peak 10(7q34) | 118 (58%) | 84 |
0.86 (1.00) |
0.369 (1.00) |
0.651 (1.00) |
0.661 (1.00) |
0.572 (1.00) |
0.558 (1.00) |
0.432 (1.00) |
0.0331 (1.00) |
|
Amp Peak 11(8q11 22) | 83 (41%) | 119 |
0.272 (1.00) |
0.0888 (1.00) |
0.434 (1.00) |
0.557 (1.00) |
1 (1.00) |
0.1 (1.00) |
0.776 (1.00) |
0.689 (1.00) |
|
Amp Peak 12(8q24 3) | 97 (48%) | 105 |
0.335 (1.00) |
0.0987 (1.00) |
0.866 (1.00) |
0.561 (1.00) |
0.247 (1.00) |
0.142 (1.00) |
0.707 (1.00) |
0.901 (1.00) |
|
Amp Peak 13(9p24 1) | 14 (7%) | 188 |
0.432 (1.00) |
0.97 (1.00) |
0.0707 (1.00) |
0.777 (1.00) |
0.195 (1.00) |
0.0541 (1.00) |
0.33 (1.00) |
0.132 (1.00) |
|
Amp Peak 14(11q13 3) | 30 (15%) | 172 |
0.423 (1.00) |
0.207 (1.00) |
0.208 (1.00) |
0.417 (1.00) |
1 (1.00) |
0.806 (1.00) |
0.496 (1.00) |
0.73 (1.00) |
|
Amp Peak 15(11q13 4) | 29 (14%) | 173 |
0.704 (1.00) |
0.618 (1.00) |
0.23 (1.00) |
0.536 (1.00) |
1 (1.00) |
0.497 (1.00) |
0.244 (1.00) |
0.768 (1.00) |
|
Amp Peak 16(12q15) | 26 (13%) | 176 |
0.909 (1.00) |
0.459 (1.00) |
0.278 (1.00) |
0.388 (1.00) |
0.34 (1.00) |
0.842 (1.00) |
0.104 (1.00) |
0.186 (1.00) |
|
Amp Peak 17(13q31 3) | 53 (26%) | 149 |
0.59 (1.00) |
0.474 (1.00) |
0.0302 (1.00) |
1 (1.00) |
0.568 (1.00) |
0.551 (1.00) |
0.533 (1.00) |
0.935 (1.00) |
|
Amp Peak 18(15q24 3) | 60 (30%) | 142 |
0.304 (1.00) |
0.336 (1.00) |
0.00615 (1.00) |
1 (1.00) |
0.556 (1.00) |
0.505 (1.00) |
0.274 (1.00) |
0.0118 (1.00) |
|
Amp Peak 19(17q25 3) | 70 (35%) | 132 |
0.408 (1.00) |
0.0264 (1.00) |
0.155 (1.00) |
0.361 (1.00) |
0.553 (1.00) |
0.699 (1.00) |
0.623 (1.00) |
0.85 (1.00) |
|
Amp Peak 20(19p13 2) | 38 (19%) | 164 |
0.381 (1.00) |
0.769 (1.00) |
0.421 (1.00) |
0.46 (1.00) |
0.467 (1.00) |
0.000983 (0.401) |
0.789 (1.00) |
0.28 (1.00) |
|
Amp Peak 21(20q13 2) | 102 (50%) | 100 |
0.227 (1.00) |
0.273 (1.00) |
0.361 (1.00) |
0.562 (1.00) |
0.619 (1.00) |
0.137 (1.00) |
0.914 (1.00) |
0.237 (1.00) |
|
Amp Peak 22(22q13 2) | 88 (44%) | 114 |
0.366 (1.00) |
0.805 (1.00) |
0.493 (1.00) |
0.464 (1.00) |
1 (1.00) |
0.993 (1.00) |
0.242 (1.00) |
0.842 (1.00) |
|
Del Peak 1(1p36 31) | 54 (27%) | 148 |
0.667 (1.00) |
0.899 (1.00) |
0.719 (1.00) |
0.253 (1.00) |
0.566 (1.00) |
0.0941 (1.00) |
0.391 (1.00) |
0.92 (1.00) |
|
Del Peak 2(1p22 1) | 53 (26%) | 149 |
0.0835 (1.00) |
0.0171 (1.00) |
0.501 (1.00) |
0.743 (1.00) |
0.568 (1.00) |
0.0889 (1.00) |
0.114 (1.00) |
0.148 (1.00) |
|
Del Peak 3(2q37 3) | 48 (24%) | 154 |
0.283 (1.00) |
0.492 (1.00) |
0.119 (1.00) |
0.609 (1.00) |
0.559 (1.00) |
0.0385 (1.00) |
0.774 (1.00) |
0.418 (1.00) |
|
Del Peak 4(3p26 1) | 30 (15%) | 172 |
0.822 (1.00) |
0.205 (1.00) |
0.7 (1.00) |
0.839 (1.00) |
0.384 (1.00) |
0.753 (1.00) |
0.429 (1.00) |
0.0269 (1.00) |
|
Del Peak 5(3q23) | 25 (12%) | 177 |
0.411 (1.00) |
0.188 (1.00) |
0.4 (1.00) |
0.513 (1.00) |
0.329 (1.00) |
0.29 (1.00) |
0.486 (1.00) |
0.488 (1.00) |
|
Del Peak 6(4p16 3) | 41 (20%) | 161 |
0.97 (1.00) |
0.414 (1.00) |
0.0469 (1.00) |
0.21 (1.00) |
0.496 (1.00) |
0.573 (1.00) |
0.655 (1.00) |
0.818 (1.00) |
|
Del Peak 7(4q34 3) | 53 (26%) | 149 |
0.219 (1.00) |
0.392 (1.00) |
0.205 (1.00) |
0.0128 (1.00) |
0.568 (1.00) |
0.0993 (1.00) |
0.471 (1.00) |
0.254 (1.00) |
|
Del Peak 8(5q11 2) | 60 (30%) | 142 |
0.277 (1.00) |
0.125 (1.00) |
0.41 (1.00) |
0.751 (1.00) |
0.556 (1.00) |
0.0889 (1.00) |
0.346 (1.00) |
0.478 (1.00) |
|
Del Peak 9(5q31 3) | 78 (39%) | 124 |
0.104 (1.00) |
0.552 (1.00) |
0.64 (1.00) |
0.882 (1.00) |
1 (1.00) |
0.236 (1.00) |
0.2 (1.00) |
0.738 (1.00) |
|
Del Peak 10(6q16 3) | 112 (55%) | 90 |
0.572 (1.00) |
0.159 (1.00) |
0.0275 (1.00) |
0.884 (1.00) |
0.0868 (1.00) |
0.688 (1.00) |
0.226 (1.00) |
0.971 (1.00) |
|
Del Peak 11(6q26) | 117 (58%) | 85 |
0.983 (1.00) |
0.278 (1.00) |
0.29 (1.00) |
0.659 (1.00) |
0.073 (1.00) |
0.678 (1.00) |
0.118 (1.00) |
0.792 (1.00) |
|
Del Peak 12(6q27) | 116 (57%) | 86 |
0.835 (1.00) |
0.244 (1.00) |
0.456 (1.00) |
0.557 (1.00) |
0.0756 (1.00) |
0.681 (1.00) |
0.114 (1.00) |
0.712 (1.00) |
|
Del Peak 13(8p23 3) | 51 (25%) | 151 |
0.897 (1.00) |
0.137 (1.00) |
0.159 (1.00) |
0.183 (1.00) |
0.573 (1.00) |
0.551 (1.00) |
0.297 (1.00) |
0.662 (1.00) |
|
Del Peak 14(9p23) | 141 (70%) | 61 |
0.493 (1.00) |
0.566 (1.00) |
0.543 (1.00) |
0.268 (1.00) |
0.0266 (1.00) |
0.161 (1.00) |
0.316 (1.00) |
0.291 (1.00) |
|
Del Peak 15(9p21 3) | 160 (79%) | 42 |
0.141 (1.00) |
0.223 (1.00) |
0.409 (1.00) |
0.107 (1.00) |
0.11 (1.00) |
0.571 (1.00) |
0.497 (1.00) |
0.657 (1.00) |
|
Del Peak 16(10p15 3) | 109 (54%) | 93 |
0.309 (1.00) |
0.0823 (1.00) |
0.162 (1.00) |
0.308 (1.00) |
0.596 (1.00) |
0.629 (1.00) |
0.59 (1.00) |
0.827 (1.00) |
|
Del Peak 17(10q23 31) | 126 (62%) | 76 |
0.484 (1.00) |
0.0144 (1.00) |
0.139 (1.00) |
0.011 (1.00) |
0.558 (1.00) |
0.822 (1.00) |
0.7 (1.00) |
0.716 (1.00) |
|
Del Peak 18(10q26 3) | 126 (62%) | 76 |
0.251 (1.00) |
0.00185 (0.751) |
0.0213 (1.00) |
0.011 (1.00) |
0.558 (1.00) |
0.335 (1.00) |
0.917 (1.00) |
0.874 (1.00) |
|
Del Peak 19(11q23 3) | 115 (57%) | 87 |
0.179 (1.00) |
0.493 (1.00) |
0.115 (1.00) |
0.465 (1.00) |
0.0783 (1.00) |
0.994 (1.00) |
0.00813 (1.00) |
0.27 (1.00) |
|
Del Peak 20(12q24 33) | 47 (23%) | 155 |
0.451 (1.00) |
0.927 (1.00) |
0.228 (1.00) |
0.492 (1.00) |
0.55 (1.00) |
0.689 (1.00) |
0.472 (1.00) |
0.717 (1.00) |
|
Del Peak 21(13q34) | 47 (23%) | 155 |
0.311 (1.00) |
0.496 (1.00) |
0.14 (1.00) |
0.394 (1.00) |
0.55 (1.00) |
0.0288 (1.00) |
0.0514 (1.00) |
0.0729 (1.00) |
|
Del Peak 22(14q32 2) | 66 (33%) | 136 |
0.491 (1.00) |
0.883 (1.00) |
0.54 (1.00) |
1 (1.00) |
0.552 (1.00) |
0.442 (1.00) |
0.793 (1.00) |
0.062 (1.00) |
|
Del Peak 23(15q13 3) | 45 (22%) | 157 |
0.652 (1.00) |
0.481 (1.00) |
0.857 (1.00) |
0.489 (1.00) |
1 (1.00) |
0.512 (1.00) |
0.685 (1.00) |
0.821 (1.00) |
|
Del Peak 24(15q15 1) | 48 (24%) | 154 |
0.405 (1.00) |
0.693 (1.00) |
0.96 (1.00) |
0.232 (1.00) |
1 (1.00) |
0.538 (1.00) |
0.939 (1.00) |
0.561 (1.00) |
|
Del Peak 25(16p13 3) | 35 (17%) | 167 |
0.689 (1.00) |
0.159 (1.00) |
0.68 (1.00) |
0.0836 (1.00) |
1 (1.00) |
0.753 (1.00) |
0.214 (1.00) |
0.789 (1.00) |
|
Del Peak 26(16q12 1) | 66 (33%) | 136 |
0.423 (1.00) |
0.723 (1.00) |
0.554 (1.00) |
0.355 (1.00) |
0.552 (1.00) |
0.564 (1.00) |
0.613 (1.00) |
0.629 (1.00) |
|
Del Peak 27(16q24 3) | 71 (35%) | 131 |
0.137 (1.00) |
0.385 (1.00) |
0.709 (1.00) |
0.362 (1.00) |
0.553 (1.00) |
0.536 (1.00) |
0.124 (1.00) |
0.387 (1.00) |
|
Del Peak 28(19p13 3) | 61 (30%) | 141 |
0.657 (1.00) |
0.869 (1.00) |
0.361 (1.00) |
0.531 (1.00) |
1 (1.00) |
0.457 (1.00) |
0.818 (1.00) |
0.755 (1.00) |
|
Del Peak 29(22q12 1) | 28 (14%) | 174 |
0.72 (1.00) |
0.706 (1.00) |
0.883 (1.00) |
0.837 (1.00) |
1 (1.00) |
0.523 (1.00) |
0.913 (1.00) |
0.509 (1.00) |
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = SKCM-All_Samples.clin.merged.picked.txt
-
Number of patients = 202
-
Number of significantly arm-level cnvs = 51
-
Number of selected clinical features = 9
-
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.