This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 84 arm-level results and 14 clinical features across 325 patients, one significant finding detected with Q value < 0.25.
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Del Peak 39(17p11.2) cnv correlated to 'NUMBERPACKYEARSSMOKED'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 84 arm-level results and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET |
COMPLETENESS OF RESECTION |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | Fisher's exact test | t-test | Fisher's exact test | |
Del Peak 39(17p11 2) | 0 (0%) | 157 |
0.382 (1.00) |
0.29 (1.00) |
0.373 (1.00) |
0.138 (1.00) |
0.383 (1.00) |
0.681 (1.00) |
0.398 (1.00) |
0.831 (1.00) |
1 (1.00) |
0.0626 (1.00) |
8.1e-05 (0.0952) |
0.128 (1.00) |
0.0773 (1.00) |
0.233 (1.00) |
Amp Peak 1(1p34 2) | 0 (0%) | 269 |
0.336 (1.00) |
0.68 (1.00) |
0.0289 (1.00) |
0.939 (1.00) |
0.0731 (1.00) |
0.287 (1.00) |
0.432 (1.00) |
0.174 (1.00) |
0.1 (1.00) |
1 (1.00) |
0.15 (1.00) |
0.976 (1.00) |
0.57 (1.00) |
1 (1.00) |
Amp Peak 2(1q21 2) | 0 (0%) | 150 |
0.059 (1.00) |
0.639 (1.00) |
1 (1.00) |
0.718 (1.00) |
0.212 (1.00) |
0.138 (1.00) |
0.764 (1.00) |
0.336 (1.00) |
0.518 (1.00) |
0.555 (1.00) |
0.642 (1.00) |
0.477 (1.00) |
0.469 (1.00) |
0.595 (1.00) |
Amp Peak 3(2p16 1) | 0 (0%) | 147 |
0.905 (1.00) |
0.658 (1.00) |
0.201 (1.00) |
0.496 (1.00) |
0.2 (1.00) |
0.0409 (1.00) |
0.0142 (1.00) |
0.377 (1.00) |
0.419 (1.00) |
0.76 (1.00) |
0.107 (1.00) |
0.936 (1.00) |
0.0895 (1.00) |
0.427 (1.00) |
Amp Peak 4(2q31 2) | 0 (0%) | 212 |
0.778 (1.00) |
0.461 (1.00) |
0.142 (1.00) |
0.856 (1.00) |
0.205 (1.00) |
0.912 (1.00) |
0.858 (1.00) |
0.828 (1.00) |
0.969 (1.00) |
0.341 (1.00) |
0.439 (1.00) |
0.451 (1.00) |
0.159 (1.00) |
0.0911 (1.00) |
Amp Peak 5(3p11 1) | 0 (0%) | 259 |
0.82 (1.00) |
0.323 (1.00) |
0.752 (1.00) |
0.835 (1.00) |
0.918 (1.00) |
0.471 (1.00) |
0.529 (1.00) |
0.433 (1.00) |
0.397 (1.00) |
0.0504 (1.00) |
0.928 (1.00) |
0.569 (1.00) |
0.98 (1.00) |
0.276 (1.00) |
Amp Peak 6(3q26 33) | 0 (0%) | 28 |
0.00633 (1.00) |
0.642 (1.00) |
0.255 (1.00) |
0.859 (1.00) |
0.0219 (1.00) |
0.826 (1.00) |
0.497 (1.00) |
1 (1.00) |
0.351 (1.00) |
0.608 (1.00) |
0.68 (1.00) |
0.476 (1.00) |
0.992 (1.00) |
0.848 (1.00) |
Amp Peak 7(4q12) | 0 (0%) | 247 |
0.235 (1.00) |
0.185 (1.00) |
1 (1.00) |
0.32 (1.00) |
0.677 (1.00) |
0.528 (1.00) |
0.515 (1.00) |
0.486 (1.00) |
0.157 (1.00) |
1 (1.00) |
0.457 (1.00) |
0.804 (1.00) |
0.0746 (1.00) |
0.419 (1.00) |
Amp Peak 8(5p15 33) | 0 (0%) | 67 |
0.675 (1.00) |
0.983 (1.00) |
0.637 (1.00) |
0.925 (1.00) |
0.324 (1.00) |
0.617 (1.00) |
0.00811 (1.00) |
0.281 (1.00) |
0.643 (1.00) |
1 (1.00) |
0.693 (1.00) |
0.0728 (1.00) |
0.638 (1.00) |
0.555 (1.00) |
Amp Peak 9(5p12) | 0 (0%) | 109 |
0.764 (1.00) |
0.0982 (1.00) |
0.687 (1.00) |
0.752 (1.00) |
0.337 (1.00) |
0.125 (1.00) |
0.638 (1.00) |
0.65 (1.00) |
0.785 (1.00) |
0.757 (1.00) |
0.956 (1.00) |
0.32 (1.00) |
0.943 (1.00) |
0.694 (1.00) |
Amp Peak 10(6p12 1) | 0 (0%) | 219 |
0.752 (1.00) |
0.729 (1.00) |
0.892 (1.00) |
0.799 (1.00) |
0.288 (1.00) |
0.233 (1.00) |
0.416 (1.00) |
0.0986 (1.00) |
0.568 (1.00) |
0.347 (1.00) |
0.361 (1.00) |
0.951 (1.00) |
0.376 (1.00) |
0.715 (1.00) |
Amp Peak 11(6q12) | 0 (0%) | 228 |
0.495 (1.00) |
0.343 (1.00) |
0.678 (1.00) |
0.411 (1.00) |
0.204 (1.00) |
0.447 (1.00) |
0.144 (1.00) |
0.483 (1.00) |
0.369 (1.00) |
0.314 (1.00) |
0.137 (1.00) |
0.888 (1.00) |
0.0967 (1.00) |
0.787 (1.00) |
Amp Peak 12(7p11 2) | 0 (0%) | 161 |
0.13 (1.00) |
0.341 (1.00) |
0.373 (1.00) |
0.542 (1.00) |
0.372 (1.00) |
0.0365 (1.00) |
0.165 (1.00) |
0.451 (1.00) |
0.11 (1.00) |
0.769 (1.00) |
0.143 (1.00) |
0.22 (1.00) |
0.402 (1.00) |
0.547 (1.00) |
Amp Peak 13(7q21 2) | 0 (0%) | 148 |
0.345 (1.00) |
0.529 (1.00) |
0.126 (1.00) |
0.0155 (1.00) |
0.517 (1.00) |
0.558 (1.00) |
0.0532 (1.00) |
0.504 (1.00) |
0.295 (1.00) |
0.237 (1.00) |
0.681 (1.00) |
0.389 (1.00) |
0.746 (1.00) |
0.45 (1.00) |
Amp Peak 14(8p11 23) | 0 (0%) | 166 |
0.0841 (1.00) |
0.521 (1.00) |
0.0572 (1.00) |
0.0599 (1.00) |
0.546 (1.00) |
0.46 (1.00) |
1 (1.00) |
0.372 (1.00) |
0.237 (1.00) |
0.766 (1.00) |
0.818 (1.00) |
0.499 (1.00) |
0.35 (1.00) |
0.00228 (1.00) |
Amp Peak 15(8q24 21) | 0 (0%) | 95 |
0.661 (1.00) |
0.782 (1.00) |
0.485 (1.00) |
0.496 (1.00) |
0.404 (1.00) |
0.0338 (1.00) |
0.0885 (1.00) |
0.0941 (1.00) |
0.203 (1.00) |
1 (1.00) |
0.817 (1.00) |
0.398 (1.00) |
0.884 (1.00) |
0.0507 (1.00) |
Amp Peak 16(9p24 1) | 0 (0%) | 264 |
0.358 (1.00) |
0.712 (1.00) |
0.629 (1.00) |
0.303 (1.00) |
0.0193 (1.00) |
0.383 (1.00) |
0.636 (1.00) |
0.9 (1.00) |
0.452 (1.00) |
0.229 (1.00) |
0.499 (1.00) |
0.866 (1.00) |
0.538 (1.00) |
0.801 (1.00) |
Amp Peak 17(9p13 3) | 0 (0%) | 238 |
0.146 (1.00) |
0.45 (1.00) |
0.473 (1.00) |
0.146 (1.00) |
0.144 (1.00) |
0.786 (1.00) |
0.697 (1.00) |
0.412 (1.00) |
0.941 (1.00) |
0.734 (1.00) |
0.413 (1.00) |
0.318 (1.00) |
0.637 (1.00) |
0.163 (1.00) |
Amp Peak 18(11q13 3) | 0 (0%) | 206 |
0.435 (1.00) |
0.538 (1.00) |
0.598 (1.00) |
0.154 (1.00) |
0.543 (1.00) |
0.108 (1.00) |
0.723 (1.00) |
0.74 (1.00) |
0.671 (1.00) |
0.34 (1.00) |
0.592 (1.00) |
0.709 (1.00) |
0.18 (1.00) |
0.9 (1.00) |
Amp Peak 19(12p13 33) | 0 (0%) | 160 |
0.906 (1.00) |
0.44 (1.00) |
0.0223 (1.00) |
0.315 (1.00) |
0.534 (1.00) |
0.261 (1.00) |
0.37 (1.00) |
0.333 (1.00) |
0.556 (1.00) |
0.373 (1.00) |
0.666 (1.00) |
0.385 (1.00) |
0.49 (1.00) |
0.86 (1.00) |
Amp Peak 20(12q15) | 0 (0%) | 202 |
0.597 (1.00) |
0.684 (1.00) |
0.0355 (1.00) |
0.932 (1.00) |
0.537 (1.00) |
0.604 (1.00) |
0.719 (1.00) |
0.704 (1.00) |
0.426 (1.00) |
0.544 (1.00) |
0.93 (1.00) |
0.777 (1.00) |
0.766 (1.00) |
0.688 (1.00) |
Amp Peak 21(13q34) | 0 (0%) | 268 |
0.206 (1.00) |
0.0898 (1.00) |
0.0932 (1.00) |
0.272 (1.00) |
0.0115 (1.00) |
0.0476 (1.00) |
0.255 (1.00) |
0.834 (1.00) |
0.613 (1.00) |
1 (1.00) |
0.059 (1.00) |
0.357 (1.00) |
0.104 (1.00) |
0.2 (1.00) |
Amp Peak 22(14q13 3) | 0 (0%) | 224 |
0.213 (1.00) |
0.000711 (0.835) |
0.891 (1.00) |
0.727 (1.00) |
0.398 (1.00) |
0.103 (1.00) |
0.373 (1.00) |
0.166 (1.00) |
0.137 (1.00) |
1 (1.00) |
0.371 (1.00) |
0.0626 (1.00) |
0.53 (1.00) |
0.353 (1.00) |
Amp Peak 23(15q26 3) | 0 (0%) | 209 |
0.92 (1.00) |
0.2 (1.00) |
0.235 (1.00) |
0.694 (1.00) |
0.546 (1.00) |
0.264 (1.00) |
0.662 (1.00) |
0.26 (1.00) |
0.787 (1.00) |
0.752 (1.00) |
0.395 (1.00) |
0.00963 (1.00) |
0.87 (1.00) |
0.882 (1.00) |
Amp Peak 24(17q25 1) | 0 (0%) | 170 |
0.988 (1.00) |
0.531 (1.00) |
0.0158 (1.00) |
0.701 (1.00) |
0.559 (1.00) |
0.163 (1.00) |
0.0603 (1.00) |
1 (1.00) |
0.32 (1.00) |
0.125 (1.00) |
0.888 (1.00) |
0.217 (1.00) |
0.0222 (1.00) |
0.0551 (1.00) |
Amp Peak 25(18p11 32) | 0 (0%) | 213 |
0.319 (1.00) |
0.235 (1.00) |
0.0831 (1.00) |
0.784 (1.00) |
0.333 (1.00) |
0.609 (1.00) |
0.61 (1.00) |
0.632 (1.00) |
0.73 (1.00) |
0.522 (1.00) |
0.451 (1.00) |
0.066 (1.00) |
0.57 (1.00) |
0.433 (1.00) |
Amp Peak 26(18q11 2) | 0 (0%) | 217 |
0.874 (1.00) |
0.981 (1.00) |
0.787 (1.00) |
0.582 (1.00) |
0.508 (1.00) |
0.253 (1.00) |
0.329 (1.00) |
0.786 (1.00) |
0.449 (1.00) |
1 (1.00) |
0.421 (1.00) |
0.483 (1.00) |
0.442 (1.00) |
0.774 (1.00) |
Amp Peak 27(19q12) | 0 (0%) | 189 |
0.177 (1.00) |
0.425 (1.00) |
0.898 (1.00) |
0.401 (1.00) |
0.25 (1.00) |
0.524 (1.00) |
0.0434 (1.00) |
0.719 (1.00) |
0.575 (1.00) |
0.0577 (1.00) |
0.507 (1.00) |
0.994 (1.00) |
0.118 (1.00) |
1 (1.00) |
Amp Peak 28(19q13 2) | 0 (0%) | 185 |
0.542 (1.00) |
0.26 (1.00) |
0.522 (1.00) |
0.19 (1.00) |
0.334 (1.00) |
0.447 (1.00) |
0.456 (1.00) |
0.886 (1.00) |
0.871 (1.00) |
0.54 (1.00) |
0.00706 (1.00) |
0.66 (1.00) |
0.00803 (1.00) |
0.61 (1.00) |
Amp Peak 29(20p12 2) | 0 (0%) | 146 |
0.334 (1.00) |
0.332 (1.00) |
0.097 (1.00) |
0.399 (1.00) |
0.232 (1.00) |
0.608 (1.00) |
0.482 (1.00) |
0.629 (1.00) |
0.723 (1.00) |
0.76 (1.00) |
0.651 (1.00) |
0.703 (1.00) |
0.658 (1.00) |
0.871 (1.00) |
Amp Peak 30(20q11 21) | 0 (0%) | 132 |
0.406 (1.00) |
0.176 (1.00) |
0.00432 (1.00) |
0.851 (1.00) |
0.171 (1.00) |
0.64 (1.00) |
0.0367 (1.00) |
0.247 (1.00) |
0.817 (1.00) |
0.535 (1.00) |
0.296 (1.00) |
0.195 (1.00) |
0.0895 (1.00) |
0.923 (1.00) |
Amp Peak 31(22q11 21) | 0 (0%) | 163 |
0.841 (1.00) |
0.265 (1.00) |
0.446 (1.00) |
0.803 (1.00) |
0.156 (1.00) |
0.492 (1.00) |
0.106 (1.00) |
0.159 (1.00) |
0.0368 (1.00) |
0.542 (1.00) |
0.813 (1.00) |
0.85 (1.00) |
0.178 (1.00) |
0.0525 (1.00) |
Amp Peak 32(Xq28) | 0 (0%) | 242 |
0.267 (1.00) |
0.436 (1.00) |
0.562 (1.00) |
0.187 (1.00) |
0.457 (1.00) |
0.00183 (1.00) |
0.573 (1.00) |
1 (1.00) |
0.556 (1.00) |
0.736 (1.00) |
0.369 (1.00) |
0.424 (1.00) |
0.0553 (1.00) |
0.299 (1.00) |
Del Peak 1(1p36 22) | 0 (0%) | 182 |
0.677 (1.00) |
0.294 (1.00) |
0.0153 (1.00) |
0.757 (1.00) |
0.426 (1.00) |
0.738 (1.00) |
0.626 (1.00) |
0.269 (1.00) |
0.971 (1.00) |
0.545 (1.00) |
0.386 (1.00) |
0.323 (1.00) |
0.159 (1.00) |
1 (1.00) |
Del Peak 2(1p13 2) | 0 (0%) | 180 |
0.799 (1.00) |
0.09 (1.00) |
0.204 (1.00) |
0.509 (1.00) |
0.581 (1.00) |
0.264 (1.00) |
0.715 (1.00) |
0.166 (1.00) |
0.927 (1.00) |
0.357 (1.00) |
0.593 (1.00) |
0.0807 (1.00) |
0.0268 (1.00) |
1 (1.00) |
Del Peak 3(2p25 3) | 0 (0%) | 295 |
0.383 (1.00) |
0.0327 (1.00) |
0.378 (1.00) |
0.882 (1.00) |
0.0295 (1.00) |
0.0795 (1.00) |
0.159 (1.00) |
0.38 (1.00) |
0.0441 (1.00) |
1 (1.00) |
0.117 (1.00) |
0.575 (1.00) |
0.495 (1.00) |
0.781 (1.00) |
Del Peak 4(2q22 1) | 0 (0%) | 238 |
0.956 (1.00) |
0.00218 (1.00) |
0.252 (1.00) |
0.308 (1.00) |
0.0779 (1.00) |
0.628 (1.00) |
0.035 (1.00) |
0.858 (1.00) |
0.0678 (1.00) |
0.3 (1.00) |
0.821 (1.00) |
0.245 (1.00) |
0.00163 (1.00) |
0.371 (1.00) |
Del Peak 5(2q36 2) | 0 (0%) | 221 |
0.239 (1.00) |
0.00547 (1.00) |
0.413 (1.00) |
0.601 (1.00) |
0.54 (1.00) |
0.925 (1.00) |
0.395 (1.00) |
1 (1.00) |
0.63 (1.00) |
0.338 (1.00) |
0.243 (1.00) |
0.0919 (1.00) |
0.00489 (1.00) |
0.933 (1.00) |
Del Peak 6(3p25 3) | 0 (0%) | 66 |
0.372 (1.00) |
0.361 (1.00) |
0.637 (1.00) |
0.395 (1.00) |
0.332 (1.00) |
0.261 (1.00) |
0.186 (1.00) |
0.687 (1.00) |
0.0463 (1.00) |
0.701 (1.00) |
0.913 (1.00) |
0.549 (1.00) |
0.34 (1.00) |
0.735 (1.00) |
Del Peak 7(3p13) | 0 (0%) | 46 |
0.601 (1.00) |
0.244 (1.00) |
1 (1.00) |
0.12 (1.00) |
0.171 (1.00) |
0.0507 (1.00) |
0.831 (1.00) |
0.254 (1.00) |
0.00474 (1.00) |
0.375 (1.00) |
0.974 (1.00) |
0.39 (1.00) |
0.581 (1.00) |
0.167 (1.00) |
Del Peak 8(3p12 3) | 0 (0%) | 53 |
0.275 (1.00) |
0.156 (1.00) |
0.864 (1.00) |
0.197 (1.00) |
0.236 (1.00) |
0.00567 (1.00) |
0.246 (1.00) |
0.436 (1.00) |
0.0963 (1.00) |
1 (1.00) |
0.732 (1.00) |
0.463 (1.00) |
0.6 (1.00) |
0.337 (1.00) |
Del Peak 9(3q11 1) | 0 (0%) | 275 |
0.0466 (1.00) |
0.356 (1.00) |
0.725 (1.00) |
0.14 (1.00) |
0.128 (1.00) |
0.505 (1.00) |
0.318 (1.00) |
0.189 (1.00) |
0.17 (1.00) |
1 (1.00) |
0.302 (1.00) |
0.132 (1.00) |
0.432 (1.00) |
0.472 (1.00) |
Del Peak 10(4p15 2) | 0 (0%) | 128 |
0.129 (1.00) |
0.485 (1.00) |
0.435 (1.00) |
0.52 (1.00) |
0.579 (1.00) |
0.675 (1.00) |
0.799 (1.00) |
0.913 (1.00) |
0.785 (1.00) |
0.537 (1.00) |
0.893 (1.00) |
0.29 (1.00) |
0.743 (1.00) |
0.477 (1.00) |
Del Peak 11(4q22 1) | 0 (0%) | 141 |
0.0233 (1.00) |
0.361 (1.00) |
0.248 (1.00) |
0.742 (1.00) |
0.496 (1.00) |
0.432 (1.00) |
0.279 (1.00) |
0.437 (1.00) |
0.0962 (1.00) |
0.122 (1.00) |
0.188 (1.00) |
0.442 (1.00) |
0.507 (1.00) |
0.448 (1.00) |
Del Peak 12(4q32 3) | 0 (0%) | 119 |
0.2 (1.00) |
0.416 (1.00) |
0.291 (1.00) |
0.922 (1.00) |
0.382 (1.00) |
0.19 (1.00) |
0.124 (1.00) |
0.595 (1.00) |
0.0628 (1.00) |
0.752 (1.00) |
0.0099 (1.00) |
0.16 (1.00) |
0.89 (1.00) |
0.748 (1.00) |
Del Peak 13(4q35 2) | 0 (0%) | 116 |
0.659 (1.00) |
0.923 (1.00) |
0.895 (1.00) |
0.7 (1.00) |
0.362 (1.00) |
0.25 (1.00) |
0.0969 (1.00) |
0.752 (1.00) |
0.0781 (1.00) |
0.752 (1.00) |
0.0197 (1.00) |
0.114 (1.00) |
0.49 (1.00) |
0.704 (1.00) |
Del Peak 14(5q11 2) | 0 (0%) | 86 |
0.428 (1.00) |
0.0961 (1.00) |
0.252 (1.00) |
0.928 (1.00) |
0.202 (1.00) |
0.724 (1.00) |
0.332 (1.00) |
0.407 (1.00) |
0.391 (1.00) |
0.3 (1.00) |
0.419 (1.00) |
0.137 (1.00) |
0.228 (1.00) |
0.125 (1.00) |
Del Peak 15(5q31 1) | 0 (0%) | 77 |
0.322 (1.00) |
0.651 (1.00) |
0.657 (1.00) |
0.494 (1.00) |
0.257 (1.00) |
0.975 (1.00) |
0.47 (1.00) |
0.661 (1.00) |
0.262 (1.00) |
0.469 (1.00) |
0.611 (1.00) |
0.0665 (1.00) |
0.139 (1.00) |
0.155 (1.00) |
Del Peak 16(6p25 3) | 0 (0%) | 240 |
0.111 (1.00) |
0.713 (1.00) |
0.06 (1.00) |
0.524 (1.00) |
0.469 (1.00) |
0.85 (1.00) |
0.547 (1.00) |
0.638 (1.00) |
0.186 (1.00) |
0.734 (1.00) |
0.94 (1.00) |
0.648 (1.00) |
0.78 (1.00) |
0.055 (1.00) |
Del Peak 17(6q22 31) | 0 (0%) | 245 |
0.861 (1.00) |
0.976 (1.00) |
0.376 (1.00) |
0.244 (1.00) |
0.437 (1.00) |
0.42 (1.00) |
0.705 (1.00) |
0.751 (1.00) |
0.497 (1.00) |
0.735 (1.00) |
0.559 (1.00) |
0.633 (1.00) |
0.127 (1.00) |
0.339 (1.00) |
Del Peak 18(6q26) | 0 (0%) | 236 |
0.254 (1.00) |
0.352 (1.00) |
0.478 (1.00) |
0.156 (1.00) |
0.491 (1.00) |
0.8 (1.00) |
0.83 (1.00) |
0.202 (1.00) |
0.849 (1.00) |
0.501 (1.00) |
0.649 (1.00) |
0.108 (1.00) |
0.557 (1.00) |
0.752 (1.00) |
Del Peak 19(7q11 22) | 0 (0%) | 294 |
0.331 (1.00) |
0.635 (1.00) |
0.666 (1.00) |
0.588 (1.00) |
0.974 (1.00) |
0.876 (1.00) |
0.625 (1.00) |
0.679 (1.00) |
0.447 (1.00) |
0.283 (1.00) |
0.865 (1.00) |
0.354 (1.00) |
0.76 (1.00) |
0.503 (1.00) |
Del Peak 20(7q36 3) | 0 (0%) | 257 |
0.512 (1.00) |
0.0945 (1.00) |
0.436 (1.00) |
0.234 (1.00) |
0.903 (1.00) |
0.782 (1.00) |
0.291 (1.00) |
0.654 (1.00) |
0.296 (1.00) |
0.705 (1.00) |
0.407 (1.00) |
0.494 (1.00) |
0.0377 (1.00) |
0.651 (1.00) |
Del Peak 21(8p23 2) | 0 (0%) | 100 |
0.923 (1.00) |
0.0345 (1.00) |
1 (1.00) |
0.131 (1.00) |
0.242 (1.00) |
0.299 (1.00) |
0.216 (1.00) |
0.00545 (1.00) |
0.138 (1.00) |
1 (1.00) |
0.178 (1.00) |
0.0151 (1.00) |
0.747 (1.00) |
0.379 (1.00) |
Del Peak 22(9p23) | 0 (0%) | 118 |
0.706 (1.00) |
0.185 (1.00) |
0.0853 (1.00) |
0.582 (1.00) |
0.242 (1.00) |
0.348 (1.00) |
0.533 (1.00) |
0.886 (1.00) |
0.513 (1.00) |
1 (1.00) |
0.518 (1.00) |
0.28 (1.00) |
0.348 (1.00) |
0.832 (1.00) |
Del Peak 23(9p21 3) | 0 (0%) | 83 |
0.702 (1.00) |
0.231 (1.00) |
0.0577 (1.00) |
0.314 (1.00) |
0.0396 (1.00) |
0.515 (1.00) |
0.271 (1.00) |
0.906 (1.00) |
0.573 (1.00) |
0.481 (1.00) |
0.375 (1.00) |
0.192 (1.00) |
0.22 (1.00) |
1 (1.00) |
Del Peak 24(9q21 11) | 0 (0%) | 169 |
0.888 (1.00) |
0.00437 (1.00) |
0.128 (1.00) |
0.938 (1.00) |
0.556 (1.00) |
0.447 (1.00) |
0.758 (1.00) |
0.0862 (1.00) |
0.827 (1.00) |
0.223 (1.00) |
0.466 (1.00) |
0.0266 (1.00) |
0.106 (1.00) |
0.955 (1.00) |
Del Peak 25(10p15 3) | 0 (0%) | 177 |
0.243 (1.00) |
0.874 (1.00) |
0.251 (1.00) |
0.774 (1.00) |
0.31 (1.00) |
0.975 (1.00) |
0.901 (1.00) |
0.207 (1.00) |
0.361 (1.00) |
0.556 (1.00) |
0.131 (1.00) |
0.427 (1.00) |
0.731 (1.00) |
0.864 (1.00) |
Del Peak 26(10p15 1) | 0 (0%) | 186 |
0.197 (1.00) |
0.703 (1.00) |
0.441 (1.00) |
0.502 (1.00) |
0.489 (1.00) |
0.973 (1.00) |
0.778 (1.00) |
0.18 (1.00) |
0.373 (1.00) |
0.539 (1.00) |
0.132 (1.00) |
0.524 (1.00) |
0.628 (1.00) |
0.908 (1.00) |
Del Peak 27(10q23 31) | 0 (0%) | 160 |
0.263 (1.00) |
0.485 (1.00) |
0.205 (1.00) |
0.787 (1.00) |
0.542 (1.00) |
0.488 (1.00) |
0.553 (1.00) |
0.133 (1.00) |
0.066 (1.00) |
0.373 (1.00) |
0.817 (1.00) |
0.371 (1.00) |
0.638 (1.00) |
0.37 (1.00) |
Del Peak 28(11p15 5) | 0 (0%) | 169 |
0.192 (1.00) |
0.9 (1.00) |
0.252 (1.00) |
0.277 (1.00) |
0.502 (1.00) |
0.101 (1.00) |
0.611 (1.00) |
0.108 (1.00) |
0.133 (1.00) |
0.364 (1.00) |
0.693 (1.00) |
0.0415 (1.00) |
0.618 (1.00) |
0.827 (1.00) |
Del Peak 29(11q22 1) | 0 (0%) | 230 |
0.779 (1.00) |
0.352 (1.00) |
0.163 (1.00) |
0.694 (1.00) |
0.421 (1.00) |
0.771 (1.00) |
0.0941 (1.00) |
0.802 (1.00) |
0.914 (1.00) |
0.737 (1.00) |
0.871 (1.00) |
0.937 (1.00) |
0.681 (1.00) |
0.821 (1.00) |
Del Peak 30(11q25) | 0 (0%) | 202 |
0.629 (1.00) |
0.794 (1.00) |
0.294 (1.00) |
0.632 (1.00) |
0.408 (1.00) |
0.62 (1.00) |
0.146 (1.00) |
0.581 (1.00) |
0.858 (1.00) |
0.753 (1.00) |
0.822 (1.00) |
0.938 (1.00) |
0.778 (1.00) |
0.685 (1.00) |
Del Peak 31(12q24 31) | 0 (0%) | 271 |
0.0695 (1.00) |
0.259 (1.00) |
0.233 (1.00) |
0.548 (1.00) |
0.39 (1.00) |
0.227 (1.00) |
0.58 (1.00) |
1 (1.00) |
0.324 (1.00) |
0.699 (1.00) |
0.381 (1.00) |
0.797 (1.00) |
0.448 (1.00) |
0.73 (1.00) |
Del Peak 32(13q12 11) | 0 (0%) | 106 |
0.3 (1.00) |
0.883 (1.00) |
1 (1.00) |
0.723 (1.00) |
0.497 (1.00) |
0.328 (1.00) |
0.718 (1.00) |
0.204 (1.00) |
0.193 (1.00) |
1 (1.00) |
0.637 (1.00) |
0.129 (1.00) |
0.105 (1.00) |
0.882 (1.00) |
Del Peak 33(13q14 2) | 0 (0%) | 99 |
0.937 (1.00) |
0.433 (1.00) |
0.0974 (1.00) |
0.549 (1.00) |
0.234 (1.00) |
0.215 (1.00) |
0.794 (1.00) |
0.146 (1.00) |
0.159 (1.00) |
1 (1.00) |
0.438 (1.00) |
0.0354 (1.00) |
0.487 (1.00) |
0.869 (1.00) |
Del Peak 34(14q11 2) | 0 (0%) | 205 |
0.174 (1.00) |
0.468 (1.00) |
0.792 (1.00) |
0.522 (1.00) |
0.56 (1.00) |
0.263 (1.00) |
0.925 (1.00) |
0.174 (1.00) |
0.241 (1.00) |
1 (1.00) |
0.943 (1.00) |
0.105 (1.00) |
0.344 (1.00) |
0.958 (1.00) |
Del Peak 35(15q12) | 0 (0%) | 214 |
0.546 (1.00) |
0.0995 (1.00) |
0.141 (1.00) |
0.487 (1.00) |
0.547 (1.00) |
0.437 (1.00) |
0.101 (1.00) |
0.531 (1.00) |
0.124 (1.00) |
0.52 (1.00) |
0.258 (1.00) |
0.795 (1.00) |
0.411 (1.00) |
0.388 (1.00) |
Del Peak 36(15q21 1) | 0 (0%) | 221 |
0.665 (1.00) |
0.223 (1.00) |
0.344 (1.00) |
0.205 (1.00) |
0.393 (1.00) |
0.296 (1.00) |
0.0124 (1.00) |
0.299 (1.00) |
0.019 (1.00) |
0.338 (1.00) |
0.426 (1.00) |
0.536 (1.00) |
0.671 (1.00) |
0.574 (1.00) |
Del Peak 37(16p13 3) | 0 (0%) | 211 |
0.0987 (1.00) |
0.248 (1.00) |
0.505 (1.00) |
0.691 (1.00) |
0.0757 (1.00) |
0.442 (1.00) |
0.425 (1.00) |
0.819 (1.00) |
0.977 (1.00) |
0.753 (1.00) |
0.174 (1.00) |
0.0899 (1.00) |
0.222 (1.00) |
0.388 (1.00) |
Del Peak 38(16q23 1) | 0 (0%) | 199 |
0.178 (1.00) |
0.47 (1.00) |
0.151 (1.00) |
0.833 (1.00) |
0.743 (1.00) |
0.538 (1.00) |
0.724 (1.00) |
0.0549 (1.00) |
0.325 (1.00) |
0.755 (1.00) |
0.146 (1.00) |
0.141 (1.00) |
0.395 (1.00) |
0.452 (1.00) |
Del Peak 40(17q11 2) | 0 (0%) | 246 |
0.964 (1.00) |
0.456 (1.00) |
0.459 (1.00) |
0.23 (1.00) |
0.387 (1.00) |
0.547 (1.00) |
0.0387 (1.00) |
0.622 (1.00) |
0.0885 (1.00) |
1 (1.00) |
0.116 (1.00) |
0.816 (1.00) |
0.56 (1.00) |
0.903 (1.00) |
Del Peak 41(17q25 3) | 0 (0%) | 260 |
0.442 (1.00) |
0.594 (1.00) |
0.751 (1.00) |
0.262 (1.00) |
0.899 (1.00) |
0.568 (1.00) |
0.567 (1.00) |
0.0958 (1.00) |
0.855 (1.00) |
0.465 (1.00) |
0.985 (1.00) |
0.854 (1.00) |
0.164 (1.00) |
0.921 (1.00) |
Del Peak 42(18q23) | 0 (0%) | 175 |
0.364 (1.00) |
0.04 (1.00) |
0.0411 (1.00) |
0.456 (1.00) |
0.212 (1.00) |
0.52 (1.00) |
0.71 (1.00) |
1 (1.00) |
0.961 (1.00) |
1 (1.00) |
0.986 (1.00) |
0.495 (1.00) |
0.205 (1.00) |
0.375 (1.00) |
Del Peak 43(19p13 3) | 0 (0%) | 177 |
0.356 (1.00) |
0.652 (1.00) |
0.372 (1.00) |
0.0679 (1.00) |
0.517 (1.00) |
0.962 (1.00) |
0.085 (1.00) |
0.377 (1.00) |
0.205 (1.00) |
0.76 (1.00) |
0.145 (1.00) |
0.723 (1.00) |
0.211 (1.00) |
0.852 (1.00) |
Del Peak 44(19q13 33) | 0 (0%) | 239 |
0.366 (1.00) |
0.0326 (1.00) |
0.313 (1.00) |
0.206 (1.00) |
0.343 (1.00) |
1 (1.00) |
0.369 (1.00) |
0.638 (1.00) |
0.859 (1.00) |
0.49 (1.00) |
0.0449 (1.00) |
0.526 (1.00) |
0.00152 (1.00) |
0.186 (1.00) |
Del Peak 45(21q21 1) | 0 (0%) | 168 |
0.301 (1.00) |
0.455 (1.00) |
0.076 (1.00) |
0.858 (1.00) |
0.532 (1.00) |
0.647 (1.00) |
0.607 (1.00) |
0.926 (1.00) |
0.793 (1.00) |
0.544 (1.00) |
0.937 (1.00) |
0.246 (1.00) |
0.652 (1.00) |
0.814 (1.00) |
Del Peak 46(21q22 3) | 0 (0%) | 140 |
0.81 (1.00) |
0.408 (1.00) |
0.0102 (1.00) |
0.821 (1.00) |
0.406 (1.00) |
0.782 (1.00) |
0.738 (1.00) |
0.575 (1.00) |
0.195 (1.00) |
1 (1.00) |
0.906 (1.00) |
0.0423 (1.00) |
0.618 (1.00) |
0.825 (1.00) |
Del Peak 47(22q11 21) | 0 (0%) | 269 |
0.911 (1.00) |
0.109 (1.00) |
0.614 (1.00) |
0.976 (1.00) |
0.261 (1.00) |
0.87 (1.00) |
0.255 (1.00) |
0.16 (1.00) |
0.155 (1.00) |
0.41 (1.00) |
0.927 (1.00) |
0.899 (1.00) |
0.44 (1.00) |
0.223 (1.00) |
Del Peak 48(22q13 32) | 0 (0%) | 249 |
0.256 (1.00) |
0.0201 (1.00) |
0.295 (1.00) |
0.274 (1.00) |
0.021 (1.00) |
0.855 (1.00) |
0.0623 (1.00) |
0.245 (1.00) |
0.408 (1.00) |
0.723 (1.00) |
0.545 (1.00) |
0.911 (1.00) |
0.373 (1.00) |
0.822 (1.00) |
Del Peak 49(Xp22 2) | 0 (0%) | 225 |
0.373 (1.00) |
0.242 (1.00) |
0.27 (1.00) |
0.091 (1.00) |
0.683 (1.00) |
0.535 (1.00) |
0.0502 (1.00) |
0.753 (1.00) |
0.409 (1.00) |
0.743 (1.00) |
0.685 (1.00) |
0.439 (1.00) |
0.0188 (1.00) |
0.772 (1.00) |
Del Peak 50(Xp21 1) | 0 (0%) | 224 |
0.298 (1.00) |
0.728 (1.00) |
0.217 (1.00) |
0.0206 (1.00) |
0.398 (1.00) |
0.125 (1.00) |
0.038 (1.00) |
0.753 (1.00) |
0.872 (1.00) |
1 (1.00) |
0.769 (1.00) |
0.476 (1.00) |
0.077 (1.00) |
0.407 (1.00) |
Del Peak 51(Xp11 3) | 0 (0%) | 225 |
0.819 (1.00) |
0.501 (1.00) |
0.408 (1.00) |
0.0064 (1.00) |
0.532 (1.00) |
0.197 (1.00) |
0.138 (1.00) |
0.761 (1.00) |
0.924 (1.00) |
1 (1.00) |
0.821 (1.00) |
0.254 (1.00) |
0.0538 (1.00) |
0.621 (1.00) |
Del Peak 52(Xq22 3) | 0 (0%) | 245 |
0.8 (1.00) |
0.625 (1.00) |
0.304 (1.00) |
0.268 (1.00) |
0.437 (1.00) |
0.738 (1.00) |
0.252 (1.00) |
0.578 (1.00) |
0.763 (1.00) |
0.735 (1.00) |
0.119 (1.00) |
0.615 (1.00) |
0.292 (1.00) |
0.115 (1.00) |
P value = 8.1e-05 (t-test), Q value = 0.095
Table S1. Gene #71: 'Del Peak 39(17p11.2)' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 274 | 52.5 (32.6) |
DEL PEAK 39(17P11.2) CNV | 149 | 59.3 (37.4) |
DEL PEAK 39(17P11.2) WILD-TYPE | 125 | 44.4 (23.5) |
Figure S1. Get High-res Image Gene #71: 'Del Peak 39(17p11.2)' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
![](D71V11.png)
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = LUSC-TP.clin.merged.picked.txt
-
Number of patients = 325
-
Number of significantly arm-level cnvs = 84
-
Number of selected clinical features = 14
-
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.