This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 79 arm-level results and 13 clinical features across 389 patients, 3 significant findings detected with Q value < 0.25.
-
Amp Peak 18(11q13.3) cnv correlated to 'AGE'.
-
Del Peak 23(10p15.3) cnv correlated to 'GENDER'.
-
Del Peak 42(19p13.2) cnv correlated to 'GENDER'.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | YEAROFTOBACCOSMOKINGONSET |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
COMPLETENESS OF RESECTION |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | Chi-square test | Fisher's exact test | t-test | t-test | Chi-square test | Chi-square test | Fisher's exact test | t-test | Chi-square test | |
Amp Peak 18(11q13 3) | 0 (0%) | 252 |
0.945 (1.00) |
4.09e-05 (0.0387) |
0.201 (1.00) |
0.579 (1.00) |
0.357 (1.00) |
1 (1.00) |
0.775 (1.00) |
0.255 (1.00) |
0.651 (1.00) |
0.513 (1.00) |
0.301 (1.00) |
0.615 (1.00) |
|
Del Peak 23(10p15 3) | 0 (0%) | 299 |
0.0541 (1.00) |
0.465 (1.00) |
0.000101 (0.0956) |
0.816 (1.00) |
0.438 (1.00) |
0.388 (1.00) |
0.691 (1.00) |
0.731 (1.00) |
0.705 (1.00) |
0.696 (1.00) |
0.966 (1.00) |
0.245 (1.00) |
|
Del Peak 42(19p13 2) | 0 (0%) | 181 |
0.291 (1.00) |
0.0328 (1.00) |
0.000154 (0.146) |
0.876 (1.00) |
0.55 (1.00) |
0.812 (1.00) |
0.845 (1.00) |
0.303 (1.00) |
0.0848 (1.00) |
0.165 (1.00) |
0.539 (1.00) |
0.0506 (1.00) |
|
Amp Peak 1(1p34 3) | 0 (0%) | 283 |
0.995 (1.00) |
0.0221 (1.00) |
0.819 (1.00) |
0.401 (1.00) |
0.666 (1.00) |
1 (1.00) |
0.987 (1.00) |
0.999 (1.00) |
0.815 (1.00) |
0.491 (1.00) |
0.294 (1.00) |
0.922 (1.00) |
|
Amp Peak 2(1p22 3) | 0 (0%) | 285 |
0.979 (1.00) |
0.00157 (1.00) |
0.909 (1.00) |
0.648 (1.00) |
0.188 (1.00) |
1 (1.00) |
0.653 (1.00) |
0.581 (1.00) |
0.819 (1.00) |
0.144 (1.00) |
0.616 (1.00) |
0.821 (1.00) |
|
Amp Peak 3(1q21 3) | 0 (0%) | 108 |
0.529 (1.00) |
0.121 (1.00) |
0.0228 (1.00) |
0.302 (1.00) |
0.00973 (1.00) |
0.42 (1.00) |
0.449 (1.00) |
0.206 (1.00) |
0.592 (1.00) |
0.798 (1.00) |
0.438 (1.00) |
0.44 (1.00) |
|
Amp Peak 4(3q26 2) | 0 (0%) | 258 |
0.852 (1.00) |
0.349 (1.00) |
0.668 (1.00) |
0.781 (1.00) |
0.697 (1.00) |
1 (1.00) |
0.0804 (1.00) |
0.0634 (1.00) |
0.505 (1.00) |
0.449 (1.00) |
0.429 (1.00) |
0.614 (1.00) |
|
Amp Peak 5(4q12) | 0 (0%) | 313 |
0.448 (1.00) |
0.0162 (1.00) |
0.609 (1.00) |
0.994 (1.00) |
0.372 (1.00) |
0.544 (1.00) |
0.79 (1.00) |
0.23 (1.00) |
0.646 (1.00) |
0.374 (1.00) |
0.54 (1.00) |
0.126 (1.00) |
|
Amp Peak 6(5p15 33) | 0 (0%) | 136 |
0.256 (1.00) |
0.00291 (1.00) |
0.166 (1.00) |
0.0273 (1.00) |
0.0158 (1.00) |
0.618 (1.00) |
0.00897 (1.00) |
0.291 (1.00) |
0.769 (1.00) |
0.583 (1.00) |
0.289 (1.00) |
0.595 (1.00) |
|
Amp Peak 7(5p13 1) | 0 (0%) | 159 |
0.085 (1.00) |
0.00248 (1.00) |
0.148 (1.00) |
0.929 (1.00) |
0.0566 (1.00) |
1 (1.00) |
0.011 (1.00) |
0.372 (1.00) |
0.626 (1.00) |
0.379 (1.00) |
0.0849 (1.00) |
0.0875 (1.00) |
|
Amp Peak 8(5q35 1) | 0 (0%) | 299 |
0.134 (1.00) |
0.177 (1.00) |
0.0158 (1.00) |
0.994 (1.00) |
0.737 (1.00) |
1 (1.00) |
0.454 (1.00) |
0.112 (1.00) |
0.685 (1.00) |
0.786 (1.00) |
0.674 (1.00) |
0.19 (1.00) |
|
Amp Peak 9(6p21 1) | 0 (0%) | 244 |
0.617 (1.00) |
0.291 (1.00) |
0.833 (1.00) |
0.877 (1.00) |
0.532 (1.00) |
0.463 (1.00) |
0.817 (1.00) |
0.524 (1.00) |
0.324 (1.00) |
0.57 (1.00) |
0.183 (1.00) |
0.708 (1.00) |
|
Amp Peak 10(7p21 1) | 0 (0%) | 172 |
0.801 (1.00) |
0.569 (1.00) |
0.413 (1.00) |
0.966 (1.00) |
0.269 (1.00) |
0.341 (1.00) |
0.289 (1.00) |
0.958 (1.00) |
0.245 (1.00) |
0.111 (1.00) |
0.252 (1.00) |
0.969 (1.00) |
|
Amp Peak 11(7p11 2) | 0 (0%) | 180 |
0.148 (1.00) |
0.241 (1.00) |
0.36 (1.00) |
0.755 (1.00) |
0.314 (1.00) |
0.811 (1.00) |
0.159 (1.00) |
0.358 (1.00) |
0.306 (1.00) |
0.0225 (1.00) |
0.802 (1.00) |
0.725 (1.00) |
|
Amp Peak 12(7q31 2) | 0 (0%) | 226 |
0.706 (1.00) |
0.0214 (1.00) |
0.837 (1.00) |
0.35 (1.00) |
0.224 (1.00) |
0.328 (1.00) |
0.338 (1.00) |
0.879 (1.00) |
0.576 (1.00) |
0.22 (1.00) |
0.381 (1.00) |
0.382 (1.00) |
|
Amp Peak 13(8p11 23) | 0 (0%) | 283 |
0.933 (1.00) |
0.0076 (1.00) |
0.109 (1.00) |
0.119 (1.00) |
0.224 (1.00) |
0.59 (1.00) |
0.777 (1.00) |
0.228 (1.00) |
0.971 (1.00) |
0.806 (1.00) |
0.942 (1.00) |
0.997 (1.00) |
|
Amp Peak 14(8p11 21) | 0 (0%) | 256 |
0.471 (1.00) |
0.0596 (1.00) |
0.0013 (1.00) |
0.972 (1.00) |
0.0152 (1.00) |
0.8 (1.00) |
0.762 (1.00) |
0.773 (1.00) |
0.474 (1.00) |
0.543 (1.00) |
0.976 (1.00) |
0.677 (1.00) |
|
Amp Peak 15(8q11 1) | 0 (0%) | 208 |
0.918 (1.00) |
0.0115 (1.00) |
0.222 (1.00) |
0.997 (1.00) |
0.0374 (1.00) |
1 (1.00) |
0.88 (1.00) |
0.0931 (1.00) |
0.644 (1.00) |
0.303 (1.00) |
0.694 (1.00) |
0.54 (1.00) |
|
Amp Peak 16(8q24 21) | 0 (0%) | 141 |
0.471 (1.00) |
0.0889 (1.00) |
0.916 (1.00) |
0.844 (1.00) |
0.0106 (1.00) |
1 (1.00) |
0.584 (1.00) |
0.999 (1.00) |
0.919 (1.00) |
0.43 (1.00) |
0.529 (1.00) |
0.756 (1.00) |
|
Amp Peak 17(10p15 1) | 0 (0%) | 280 |
0.0712 (1.00) |
0.497 (1.00) |
0.00662 (1.00) |
0.436 (1.00) |
0.281 (1.00) |
0.0304 (1.00) |
0.00151 (1.00) |
0.979 (1.00) |
0.954 (1.00) |
0.0431 (1.00) |
0.371 (1.00) |
0.552 (1.00) |
|
Amp Peak 19(12p12 1) | 0 (0%) | 256 |
0.0759 (1.00) |
0.372 (1.00) |
1 (1.00) |
0.879 (1.00) |
0.466 (1.00) |
0.8 (1.00) |
0.966 (1.00) |
0.236 (1.00) |
0.739 (1.00) |
0.529 (1.00) |
0.0302 (1.00) |
0.646 (1.00) |
|
Amp Peak 20(12q14 1) | 0 (0%) | 267 |
0.144 (1.00) |
0.0466 (1.00) |
0.381 (1.00) |
0.625 (1.00) |
0.421 (1.00) |
0.603 (1.00) |
0.465 (1.00) |
0.000645 (0.607) |
0.411 (1.00) |
0.813 (1.00) |
0.269 (1.00) |
0.882 (1.00) |
|
Amp Peak 21(12q15) | 0 (0%) | 263 |
0.304 (1.00) |
0.327 (1.00) |
0.514 (1.00) |
0.305 (1.00) |
0.494 (1.00) |
0.608 (1.00) |
0.335 (1.00) |
0.0027 (1.00) |
0.643 (1.00) |
0.797 (1.00) |
0.283 (1.00) |
0.743 (1.00) |
|
Amp Peak 22(13q33 3) | 0 (0%) | 324 |
0.47 (1.00) |
0.654 (1.00) |
0.221 (1.00) |
0.872 (1.00) |
0.518 (1.00) |
0.374 (1.00) |
0.941 (1.00) |
0.15 (1.00) |
0.313 (1.00) |
0.574 (1.00) |
0.28 (1.00) |
||
Amp Peak 23(14q13 3) | 0 (0%) | 221 |
0.538 (1.00) |
0.47 (1.00) |
0.758 (1.00) |
0.495 (1.00) |
0.271 (1.00) |
0.47 (1.00) |
0.564 (1.00) |
0.165 (1.00) |
0.0804 (1.00) |
0.567 (1.00) |
0.855 (1.00) |
0.751 (1.00) |
|
Amp Peak 24(16p11 2) | 0 (0%) | 260 |
0.684 (1.00) |
0.148 (1.00) |
0.519 (1.00) |
0.929 (1.00) |
0.526 (1.00) |
0.799 (1.00) |
0.0964 (1.00) |
0.833 (1.00) |
0.586 (1.00) |
0.484 (1.00) |
0.419 (1.00) |
0.836 (1.00) |
|
Amp Peak 25(17q12) | 0 (0%) | 217 |
0.987 (1.00) |
0.629 (1.00) |
0.682 (1.00) |
0.0892 (1.00) |
0.366 (1.00) |
0.341 (1.00) |
0.00331 (1.00) |
0.76 (1.00) |
0.524 (1.00) |
0.611 (1.00) |
0.00711 (1.00) |
0.598 (1.00) |
|
Amp Peak 26(17q23 1) | 0 (0%) | 200 |
0.492 (1.00) |
0.145 (1.00) |
0.541 (1.00) |
0.532 (1.00) |
0.112 (1.00) |
1 (1.00) |
0.0256 (1.00) |
0.209 (1.00) |
0.62 (1.00) |
0.446 (1.00) |
0.0276 (1.00) |
0.697 (1.00) |
|
Amp Peak 27(18q11 2) | 0 (0%) | 307 |
0.858 (1.00) |
0.357 (1.00) |
0.134 (1.00) |
0.855 (1.00) |
0.0835 (1.00) |
0.385 (1.00) |
0.503 (1.00) |
0.89 (1.00) |
0.432 (1.00) |
0.612 (1.00) |
0.35 (1.00) |
0.311 (1.00) |
|
Amp Peak 28(19q12) | 0 (0%) | 278 |
0.868 (1.00) |
0.451 (1.00) |
0.0243 (1.00) |
0.252 (1.00) |
0.577 (1.00) |
0.299 (1.00) |
0.08 (1.00) |
0.201 (1.00) |
0.939 (1.00) |
0.193 (1.00) |
0.783 (1.00) |
0.765 (1.00) |
|
Amp Peak 29(20p11 21) | 0 (0%) | 244 |
0.784 (1.00) |
0.879 (1.00) |
0.916 (1.00) |
0.196 (1.00) |
0.216 (1.00) |
0.217 (1.00) |
0.582 (1.00) |
0.355 (1.00) |
0.39 (1.00) |
0.119 (1.00) |
0.525 (1.00) |
0.037 (1.00) |
|
Amp Peak 30(20q13 33) | 0 (0%) | 202 |
0.247 (1.00) |
0.237 (1.00) |
0.919 (1.00) |
0.304 (1.00) |
0.0417 (1.00) |
0.233 (1.00) |
0.602 (1.00) |
0.398 (1.00) |
0.216 (1.00) |
0.814 (1.00) |
0.804 (1.00) |
0.23 (1.00) |
|
Amp Peak 31(22q11 22) | 0 (0%) | 323 |
0.481 (1.00) |
0.967 (1.00) |
0.418 (1.00) |
0.255 (1.00) |
1 (1.00) |
0.402 (1.00) |
0.594 (1.00) |
0.151 (1.00) |
0.477 (1.00) |
0.952 (1.00) |
0.0836 (1.00) |
||
Amp Peak 32(Xq28) | 0 (0%) | 261 |
0.2 (1.00) |
0.213 (1.00) |
0.129 (1.00) |
0.334 (1.00) |
0.346 (1.00) |
0.309 (1.00) |
0.586 (1.00) |
0.831 (1.00) |
0.471 (1.00) |
0.494 (1.00) |
0.952 (1.00) |
0.979 (1.00) |
|
Del Peak 1(1p36 13) | 0 (0%) | 300 |
0.129 (1.00) |
0.366 (1.00) |
0.0526 (1.00) |
0.427 (1.00) |
0.547 (1.00) |
1 (1.00) |
0.549 (1.00) |
0.894 (1.00) |
0.619 (1.00) |
0.132 (1.00) |
0.192 (1.00) |
0.209 (1.00) |
|
Del Peak 2(1p13 2) | 0 (0%) | 274 |
0.989 (1.00) |
0.478 (1.00) |
0.824 (1.00) |
0.783 (1.00) |
0.879 (1.00) |
1 (1.00) |
0.838 (1.00) |
0.902 (1.00) |
0.36 (1.00) |
0.517 (1.00) |
0.436 (1.00) |
0.307 (1.00) |
|
Del Peak 3(2q22 1) | 0 (0%) | 346 |
0.727 (1.00) |
0.641 (1.00) |
1 (1.00) |
0.939 (1.00) |
0.238 (1.00) |
1 (1.00) |
0.0521 (1.00) |
0.651 (1.00) |
0.525 (1.00) |
0.7 (1.00) |
0.76 (1.00) |
0.707 (1.00) |
|
Del Peak 4(2q37 3) | 0 (0%) | 331 |
0.267 (1.00) |
0.906 (1.00) |
0.0648 (1.00) |
0.548 (1.00) |
0.114 (1.00) |
0.088 (1.00) |
0.777 (1.00) |
0.522 (1.00) |
0.363 (1.00) |
0.298 (1.00) |
0.829 (1.00) |
0.0969 (1.00) |
|
Del Peak 5(3p21 31) | 0 (0%) | 202 |
0.505 (1.00) |
0.367 (1.00) |
1 (1.00) |
0.068 (1.00) |
0.718 (1.00) |
0.476 (1.00) |
0.761 (1.00) |
0.000275 (0.259) |
0.464 (1.00) |
0.0758 (1.00) |
0.928 (1.00) |
0.578 (1.00) |
|
Del Peak 6(3q11 1) | 0 (0%) | 276 |
0.392 (1.00) |
0.27 (1.00) |
0.737 (1.00) |
0.0885 (1.00) |
0.966 (1.00) |
1 (1.00) |
0.254 (1.00) |
0.099 (1.00) |
0.946 (1.00) |
0.389 (1.00) |
0.774 (1.00) |
0.565 (1.00) |
|
Del Peak 7(3q29) | 0 (0%) | 280 |
0.998 (1.00) |
0.358 (1.00) |
0.652 (1.00) |
0.404 (1.00) |
0.808 (1.00) |
0.115 (1.00) |
0.22 (1.00) |
0.43 (1.00) |
0.804 (1.00) |
0.252 (1.00) |
0.339 (1.00) |
0.492 (1.00) |
|
Del Peak 8(4p16 3) | 0 (0%) | 295 |
0.172 (1.00) |
0.0453 (1.00) |
0.813 (1.00) |
0.598 (1.00) |
0.448 (1.00) |
1 (1.00) |
0.0859 (1.00) |
0.0531 (1.00) |
0.947 (1.00) |
0.0241 (1.00) |
0.843 (1.00) |
0.526 (1.00) |
|
Del Peak 9(4q22 1) | 0 (0%) | 269 |
0.508 (1.00) |
0.506 (1.00) |
0.661 (1.00) |
0.174 (1.00) |
0.195 (1.00) |
0.443 (1.00) |
0.346 (1.00) |
0.168 (1.00) |
0.758 (1.00) |
0.0339 (1.00) |
0.367 (1.00) |
0.349 (1.00) |
|
Del Peak 10(4q35 1) | 0 (0%) | 246 |
0.896 (1.00) |
0.213 (1.00) |
0.115 (1.00) |
0.212 (1.00) |
0.185 (1.00) |
0.316 (1.00) |
0.355 (1.00) |
0.104 (1.00) |
0.263 (1.00) |
0.113 (1.00) |
0.879 (1.00) |
0.727 (1.00) |
|
Del Peak 11(5q11 2) | 0 (0%) | 251 |
0.255 (1.00) |
0.0187 (1.00) |
0.75 (1.00) |
0.528 (1.00) |
0.138 (1.00) |
0.617 (1.00) |
0.0302 (1.00) |
0.279 (1.00) |
0.373 (1.00) |
0.0565 (1.00) |
0.54 (1.00) |
0.592 (1.00) |
|
Del Peak 12(5q31 1) | 0 (0%) | 228 |
0.312 (1.00) |
0.000946 (0.886) |
0.409 (1.00) |
0.528 (1.00) |
0.476 (1.00) |
0.81 (1.00) |
0.0339 (1.00) |
0.0348 (1.00) |
0.716 (1.00) |
0.531 (1.00) |
0.592 (1.00) |
0.494 (1.00) |
|
Del Peak 13(6q12) | 0 (0%) | 248 |
0.44 (1.00) |
0.327 (1.00) |
0.752 (1.00) |
0.174 (1.00) |
0.142 (1.00) |
0.462 (1.00) |
0.0113 (1.00) |
0.0885 (1.00) |
0.603 (1.00) |
0.13 (1.00) |
0.315 (1.00) |
0.132 (1.00) |
|
Del Peak 14(6q22 31) | 0 (0%) | 195 |
0.958 (1.00) |
0.155 (1.00) |
0.542 (1.00) |
0.174 (1.00) |
0.88 (1.00) |
0.81 (1.00) |
0.0394 (1.00) |
0.227 (1.00) |
0.558 (1.00) |
0.385 (1.00) |
0.697 (1.00) |
0.695 (1.00) |
|
Del Peak 15(6q26) | 0 (0%) | 193 |
0.674 (1.00) |
0.137 (1.00) |
0.542 (1.00) |
0.252 (1.00) |
0.807 (1.00) |
1 (1.00) |
0.285 (1.00) |
0.24 (1.00) |
0.177 (1.00) |
0.245 (1.00) |
0.672 (1.00) |
0.636 (1.00) |
|
Del Peak 16(8p23 2) | 0 (0%) | 202 |
0.711 (1.00) |
0.262 (1.00) |
0.187 (1.00) |
0.0429 (1.00) |
0.00943 (1.00) |
1 (1.00) |
0.51 (1.00) |
0.265 (1.00) |
0.42 (1.00) |
0.795 (1.00) |
0.865 (1.00) |
0.548 (1.00) |
|
Del Peak 17(8p12) | 0 (0%) | 221 |
0.681 (1.00) |
0.631 (1.00) |
0.182 (1.00) |
0.211 (1.00) |
0.0143 (1.00) |
0.226 (1.00) |
0.518 (1.00) |
0.78 (1.00) |
0.252 (1.00) |
0.331 (1.00) |
0.317 (1.00) |
0.976 (1.00) |
|
Del Peak 18(8p11 21) | 0 (0%) | 304 |
0.505 (1.00) |
0.927 (1.00) |
0.00946 (1.00) |
0.125 (1.00) |
0.0663 (1.00) |
0.774 (1.00) |
0.519 (1.00) |
0.347 (1.00) |
0.772 (1.00) |
0.522 (1.00) |
0.0965 (1.00) |
0.658 (1.00) |
|
Del Peak 19(8q11 21) | 0 (0%) | 343 |
0.595 (1.00) |
0.111 (1.00) |
0.212 (1.00) |
0.00461 (1.00) |
0.0636 (1.00) |
0.708 (1.00) |
0.906 (1.00) |
0.139 (1.00) |
0.962 (1.00) |
0.0666 (1.00) |
0.211 (1.00) |
0.658 (1.00) |
|
Del Peak 20(9p23) | 0 (0%) | 181 |
0.09 (1.00) |
0.23 (1.00) |
0.476 (1.00) |
0.559 (1.00) |
0.708 (1.00) |
0.631 (1.00) |
0.874 (1.00) |
0.452 (1.00) |
0.545 (1.00) |
0.0446 (1.00) |
0.973 (1.00) |
0.613 (1.00) |
|
Del Peak 21(9p21 3) | 0 (0%) | 175 |
0.455 (1.00) |
0.111 (1.00) |
0.0665 (1.00) |
0.755 (1.00) |
0.539 (1.00) |
0.809 (1.00) |
0.416 (1.00) |
0.34 (1.00) |
0.423 (1.00) |
0.0141 (1.00) |
0.965 (1.00) |
0.439 (1.00) |
|
Del Peak 22(9q21 11) | 0 (0%) | 199 |
0.349 (1.00) |
0.949 (1.00) |
0.919 (1.00) |
0.841 (1.00) |
0.0366 (1.00) |
0.229 (1.00) |
0.0625 (1.00) |
0.391 (1.00) |
0.774 (1.00) |
0.338 (1.00) |
0.351 (1.00) |
0.961 (1.00) |
|
Del Peak 24(10q26 3) | 0 (0%) | 285 |
0.669 (1.00) |
0.568 (1.00) |
0.0857 (1.00) |
0.261 (1.00) |
0.683 (1.00) |
0.174 (1.00) |
0.0138 (1.00) |
0.161 (1.00) |
0.965 (1.00) |
0.616 (1.00) |
0.401 (1.00) |
0.637 (1.00) |
|
Del Peak 25(11p15 5) | 0 (0%) | 286 |
0.433 (1.00) |
0.0739 (1.00) |
0.0835 (1.00) |
0.369 (1.00) |
0.184 (1.00) |
0.791 (1.00) |
0.164 (1.00) |
0.096 (1.00) |
0.103 (1.00) |
0.858 (1.00) |
0.97 (1.00) |
0.788 (1.00) |
|
Del Peak 26(11q25) | 0 (0%) | 306 |
0.214 (1.00) |
0.627 (1.00) |
0.138 (1.00) |
0.507 (1.00) |
0.924 (1.00) |
0.774 (1.00) |
0.279 (1.00) |
0.267 (1.00) |
0.581 (1.00) |
0.361 (1.00) |
0.567 (1.00) |
0.878 (1.00) |
|
Del Peak 27(12p13 2) | 0 (0%) | 278 |
0.33 (1.00) |
0.905 (1.00) |
0.00104 (0.975) |
0.893 (1.00) |
0.788 (1.00) |
0.113 (1.00) |
0.0257 (1.00) |
0.194 (1.00) |
0.192 (1.00) |
0.724 (1.00) |
0.319 (1.00) |
0.248 (1.00) |
|
Del Peak 28(12q12) | 0 (0%) | 314 |
0.234 (1.00) |
0.0913 (1.00) |
0.122 (1.00) |
0.794 (1.00) |
0.686 (1.00) |
0.217 (1.00) |
0.0702 (1.00) |
0.736 (1.00) |
0.149 (1.00) |
0.652 (1.00) |
0.292 (1.00) |
0.529 (1.00) |
|
Del Peak 29(12q24 33) | 0 (0%) | 296 |
0.493 (1.00) |
0.98 (1.00) |
0.0433 (1.00) |
0.374 (1.00) |
0.415 (1.00) |
0.086 (1.00) |
0.356 (1.00) |
0.161 (1.00) |
0.257 (1.00) |
0.794 (1.00) |
0.774 (1.00) |
0.271 (1.00) |
|
Del Peak 30(13q12 11) | 0 (0%) | 174 |
0.311 (1.00) |
0.0902 (1.00) |
0.0106 (1.00) |
0.0264 (1.00) |
0.0467 (1.00) |
0.0868 (1.00) |
0.000707 (0.665) |
0.185 (1.00) |
0.578 (1.00) |
0.797 (1.00) |
0.928 (1.00) |
0.678 (1.00) |
|
Del Peak 31(13q12 13) | 0 (0%) | 172 |
0.39 (1.00) |
0.194 (1.00) |
0.0518 (1.00) |
0.0422 (1.00) |
0.0182 (1.00) |
0.026 (1.00) |
0.00769 (1.00) |
0.16 (1.00) |
0.467 (1.00) |
0.742 (1.00) |
0.926 (1.00) |
0.74 (1.00) |
|
Del Peak 32(13q14 2) | 0 (0%) | 181 |
0.673 (1.00) |
0.103 (1.00) |
0.61 (1.00) |
0.7 (1.00) |
0.169 (1.00) |
0.475 (1.00) |
0.155 (1.00) |
0.167 (1.00) |
0.451 (1.00) |
0.762 (1.00) |
0.913 (1.00) |
1 (1.00) |
|
Del Peak 33(13q34) | 0 (0%) | 214 |
0.777 (1.00) |
0.0819 (1.00) |
0.759 (1.00) |
0.627 (1.00) |
0.334 (1.00) |
0.343 (1.00) |
0.154 (1.00) |
0.227 (1.00) |
0.185 (1.00) |
0.707 (1.00) |
0.357 (1.00) |
0.765 (1.00) |
|
Del Peak 34(14q32 33) | 0 (0%) | 270 |
0.29 (1.00) |
0.715 (1.00) |
1 (1.00) |
0.698 (1.00) |
0.355 (1.00) |
0.797 (1.00) |
0.284 (1.00) |
0.0601 (1.00) |
0.747 (1.00) |
0.547 (1.00) |
0.0755 (1.00) |
0.486 (1.00) |
|
Del Peak 35(15q11 2) | 0 (0%) | 188 |
0.303 (1.00) |
0.0156 (1.00) |
0.186 (1.00) |
0.261 (1.00) |
0.0318 (1.00) |
0.147 (1.00) |
0.933 (1.00) |
0.164 (1.00) |
0.816 (1.00) |
0.728 (1.00) |
0.647 (1.00) |
0.323 (1.00) |
|
Del Peak 36(16q23 1) | 0 (0%) | 257 |
0.973 (1.00) |
0.578 (1.00) |
0.915 (1.00) |
0.553 (1.00) |
0.764 (1.00) |
1 (1.00) |
0.65 (1.00) |
0.704 (1.00) |
0.741 (1.00) |
0.247 (1.00) |
0.806 (1.00) |
0.884 (1.00) |
|
Del Peak 37(17p13 3) | 0 (0%) | 178 |
0.624 (1.00) |
0.0603 (1.00) |
0.0837 (1.00) |
0.831 (1.00) |
0.0286 (1.00) |
0.471 (1.00) |
0.862 (1.00) |
0.0135 (1.00) |
0.701 (1.00) |
0.585 (1.00) |
0.345 (1.00) |
0.823 (1.00) |
|
Del Peak 38(17p11 2) | 0 (0%) | 213 |
0.195 (1.00) |
0.0664 (1.00) |
0.0835 (1.00) |
0.147 (1.00) |
0.201 (1.00) |
0.15 (1.00) |
0.779 (1.00) |
0.0967 (1.00) |
0.254 (1.00) |
0.578 (1.00) |
0.276 (1.00) |
0.49 (1.00) |
|
Del Peak 39(18q21 32) | 0 (0%) | 192 |
0.117 (1.00) |
0.269 (1.00) |
0.155 (1.00) |
0.348 (1.00) |
0.444 (1.00) |
0.343 (1.00) |
0.849 (1.00) |
0.136 (1.00) |
0.199 (1.00) |
0.343 (1.00) |
0.0304 (1.00) |
0.045 (1.00) |
|
Del Peak 40(18q23) | 0 (0%) | 198 |
0.182 (1.00) |
0.0981 (1.00) |
0.154 (1.00) |
0.367 (1.00) |
0.288 (1.00) |
0.471 (1.00) |
0.683 (1.00) |
0.0405 (1.00) |
0.475 (1.00) |
0.223 (1.00) |
0.0311 (1.00) |
0.0196 (1.00) |
|
Del Peak 41(19p13 3) | 0 (0%) | 174 |
0.0638 (1.00) |
0.155 (1.00) |
0.000736 (0.691) |
0.763 (1.00) |
0.348 (1.00) |
1 (1.00) |
0.749 (1.00) |
0.182 (1.00) |
0.286 (1.00) |
0.371 (1.00) |
0.278 (1.00) |
0.0486 (1.00) |
|
Del Peak 43(19q13 33) | 0 (0%) | 246 |
0.0398 (1.00) |
0.339 (1.00) |
0.462 (1.00) |
0.409 (1.00) |
0.326 (1.00) |
1 (1.00) |
0.947 (1.00) |
0.652 (1.00) |
0.211 (1.00) |
0.893 (1.00) |
0.225 (1.00) |
0.549 (1.00) |
|
Del Peak 44(20q13 12) | 0 (0%) | 323 |
0.373 (1.00) |
0.956 (1.00) |
0.176 (1.00) |
0.178 (1.00) |
0.749 (1.00) |
0.136 (1.00) |
0.139 (1.00) |
0.0967 (1.00) |
0.244 (1.00) |
0.756 (1.00) |
0.0394 (1.00) |
||
Del Peak 45(21q11 2) | 0 (0%) | 257 |
0.601 (1.00) |
0.362 (1.00) |
0.454 (1.00) |
0.707 (1.00) |
0.381 (1.00) |
0.621 (1.00) |
0.182 (1.00) |
0.0538 (1.00) |
0.921 (1.00) |
0.965 (1.00) |
0.82 (1.00) |
0.421 (1.00) |
|
Del Peak 46(22q13 32) | 0 (0%) | 202 |
0.46 (1.00) |
0.000871 (0.817) |
0.0667 (1.00) |
0.58 (1.00) |
0.184 (1.00) |
0.233 (1.00) |
0.82 (1.00) |
0.00358 (1.00) |
0.256 (1.00) |
0.805 (1.00) |
0.554 (1.00) |
0.287 (1.00) |
|
Del Peak 47(Xp22 2) | 0 (0%) | 276 |
0.367 (1.00) |
0.193 (1.00) |
0.0436 (1.00) |
0.833 (1.00) |
0.521 (1.00) |
0.605 (1.00) |
0.683 (1.00) |
0.0771 (1.00) |
0.927 (1.00) |
0.651 (1.00) |
0.815 (1.00) |
0.667 (1.00) |
P value = 4.09e-05 (t-test), Q value = 0.039
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 358 | 65.2 (9.8) |
AMP PEAK 18(11Q13.3) CNV | 128 | 62.4 (9.8) |
AMP PEAK 18(11Q13.3) WILD-TYPE | 230 | 66.8 (9.5) |
P value = 0.000101 (Fisher's exact test), Q value = 0.096
nPatients | FEMALE | MALE |
---|---|---|
ALL | 211 | 178 |
DEL PEAK 23(10P15.3) CNV | 65 | 25 |
DEL PEAK 23(10P15.3) WILD-TYPE | 146 | 153 |
P value = 0.000154 (Fisher's exact test), Q value = 0.15
nPatients | FEMALE | MALE |
---|---|---|
ALL | 211 | 178 |
DEL PEAK 42(19P13.2) CNV | 94 | 114 |
DEL PEAK 42(19P13.2) WILD-TYPE | 117 | 64 |
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = LUAD-TP.clin.merged.picked.txt
-
Number of patients = 389
-
Number of significantly arm-level cnvs = 79
-
Number of selected clinical features = 13
-
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.