This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 62 arm-level results and 11 clinical features across 131 patients, one significant finding detected with Q value < 0.25.
-
Amp Peak 8(4q13.3) cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 62 arm-level results and 11 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 |
NUMBERPACKYEARSSMOKED | TOBACCOSMOKINGHISTORYINDICATOR |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | t-test | t-test | Fisher's exact test | Chi-square test | t-test | t-test | Fisher's exact test | |
Amp Peak 8(4q13 3) | 0 (0%) | 114 |
0.522 (1.00) |
0.112 (1.00) |
0.0363 (1.00) |
7.05e-05 (0.0437) |
0.886 (1.00) |
0.714 (1.00) |
1 (1.00) |
0.727 (1.00) |
0.902 (1.00) |
0.622 (1.00) |
|
Amp Peak 1(1p34 2) | 0 (0%) | 90 |
0.762 (1.00) |
0.246 (1.00) |
0.518 (1.00) |
0.193 (1.00) |
0.237 (1.00) |
0.825 (1.00) |
1 (1.00) |
0.593 (1.00) |
0.463 (1.00) |
0.583 (1.00) |
|
Amp Peak 2(1p22 3) | 0 (0%) | 92 |
0.38 (1.00) |
0.174 (1.00) |
0.827 (1.00) |
0.671 (1.00) |
0.0722 (1.00) |
0.316 (1.00) |
0.297 (1.00) |
0.316 (1.00) |
0.184 (1.00) |
0.308 (1.00) |
|
Amp Peak 3(1q21 3) | 0 (0%) | 63 |
0.432 (1.00) |
0.401 (1.00) |
0.691 (1.00) |
0.366 (1.00) |
0.0467 (1.00) |
0.673 (1.00) |
0.508 (1.00) |
0.131 (1.00) |
0.0852 (1.00) |
0.135 (1.00) |
|
Amp Peak 4(1q23 3) | 0 (0%) | 59 |
0.638 (1.00) |
0.42 (1.00) |
0.423 (1.00) |
0.301 (1.00) |
0.242 (1.00) |
0.333 (1.00) |
0.314 (1.00) |
0.155 (1.00) |
0.0745 (1.00) |
0.0809 (1.00) |
|
Amp Peak 5(3p25 2) | 0 (0%) | 68 |
0.0544 (1.00) |
0.491 (1.00) |
0.026 (1.00) |
0.0947 (1.00) |
0.921 (1.00) |
0.0413 (1.00) |
0.816 (1.00) |
0.777 (1.00) |
0.401 (1.00) |
0.532 (1.00) |
|
Amp Peak 6(3q26 32) | 0 (0%) | 56 |
0.0481 (1.00) |
0.624 (1.00) |
0.839 (1.00) |
0.751 (1.00) |
0.871 (1.00) |
0.533 (1.00) |
0.847 (1.00) |
0.417 (1.00) |
0.921 (1.00) |
0.271 (1.00) |
|
Amp Peak 7(4p16 3) | 0 (0%) | 104 |
0.0532 (1.00) |
0.61 (1.00) |
0.0805 (1.00) |
0.391 (1.00) |
0.444 (1.00) |
0.422 (1.00) |
0.0427 (1.00) |
0.174 (1.00) |
0.953 (1.00) |
0.0295 (1.00) |
|
Amp Peak 9(5p15 1) | 0 (0%) | 67 |
0.753 (1.00) |
0.398 (1.00) |
0.232 (1.00) |
0.595 (1.00) |
0.365 (1.00) |
0.273 (1.00) |
0.247 (1.00) |
0.0269 (1.00) |
0.088 (1.00) |
0.596 (1.00) |
|
Amp Peak 10(6p22 3) | 0 (0%) | 76 |
0.302 (1.00) |
0.367 (1.00) |
0.686 (1.00) |
0.703 (1.00) |
0.644 (1.00) |
0.451 (1.00) |
0.649 (1.00) |
0.865 (1.00) |
0.0136 (1.00) |
0.522 (1.00) |
|
Amp Peak 11(6q12) | 0 (0%) | 109 |
0.409 (1.00) |
0.101 (1.00) |
0.28 (1.00) |
0.256 (1.00) |
0.126 (1.00) |
0.963 (1.00) |
0.496 (1.00) |
0.574 (1.00) |
0.0806 (1.00) |
0.176 (1.00) |
|
Amp Peak 12(6q21) | 0 (0%) | 116 |
0.878 (1.00) |
0.384 (1.00) |
1 (1.00) |
0.364 (1.00) |
0.299 (1.00) |
0.808 (1.00) |
0.483 (1.00) |
0.882 (1.00) |
0.903 (1.00) |
1 (1.00) |
|
Amp Peak 13(7p11 2) | 0 (0%) | 61 |
0.623 (1.00) |
0.058 (1.00) |
1 (1.00) |
0.688 (1.00) |
0.424 (1.00) |
0.527 (1.00) |
0.168 (1.00) |
0.826 (1.00) |
0.29 (1.00) |
0.623 (1.00) |
|
Amp Peak 14(8p11 23) | 0 (0%) | 86 |
0.66 (1.00) |
0.897 (1.00) |
0.674 (1.00) |
0.866 (1.00) |
0.201 (1.00) |
0.7 (1.00) |
1 (1.00) |
0.844 (1.00) |
0.908 (1.00) |
0.735 (1.00) |
|
Amp Peak 15(8p11 21) | 0 (0%) | 86 |
0.0139 (1.00) |
0.499 (1.00) |
0.205 (1.00) |
0.425 (1.00) |
0.0946 (1.00) |
0.166 (1.00) |
0.485 (1.00) |
0.82 (1.00) |
0.779 (1.00) |
0.506 (1.00) |
|
Amp Peak 16(8q22 3) | 0 (0%) | 49 |
0.241 (1.00) |
0.968 (1.00) |
0.0629 (1.00) |
0.563 (1.00) |
0.233 (1.00) |
0.59 (1.00) |
0.0878 (1.00) |
0.413 (1.00) |
0.095 (1.00) |
0.602 (1.00) |
|
Amp Peak 17(8q24 21) | 0 (0%) | 51 |
0.135 (1.00) |
0.709 (1.00) |
0.101 (1.00) |
0.595 (1.00) |
0.765 (1.00) |
0.823 (1.00) |
0.211 (1.00) |
0.731 (1.00) |
0.117 (1.00) |
0.151 (1.00) |
|
Amp Peak 18(10p15 1) | 0 (0%) | 75 |
0.629 (1.00) |
0.0715 (1.00) |
1 (1.00) |
0.687 (1.00) |
0.7 (1.00) |
0.112 (1.00) |
0.4 (1.00) |
0.182 (1.00) |
0.539 (1.00) |
0.88 (1.00) |
|
Amp Peak 19(11q13 3) | 0 (0%) | 80 |
0.843 (1.00) |
0.345 (1.00) |
0.682 (1.00) |
0.578 (1.00) |
0.445 (1.00) |
0.417 (1.00) |
0.0464 (1.00) |
0.155 (1.00) |
0.353 (1.00) |
0.608 (1.00) |
|
Amp Peak 20(12q15) | 0 (0%) | 87 |
0.721 (1.00) |
0.971 (1.00) |
0.677 (1.00) |
0.592 (1.00) |
0.0724 (1.00) |
0.491 (1.00) |
0.231 (1.00) |
0.23 (1.00) |
0.501 (1.00) |
0.0146 (1.00) |
|
Amp Peak 21(13q34) | 0 (0%) | 82 |
0.789 (1.00) |
0.548 (1.00) |
0.837 (1.00) |
0.654 (1.00) |
0.126 (1.00) |
0.0142 (1.00) |
1 (1.00) |
0.587 (1.00) |
0.554 (1.00) |
0.196 (1.00) |
|
Amp Peak 22(16p12 1) | 0 (0%) | 96 |
0.564 (1.00) |
0.655 (1.00) |
1 (1.00) |
0.375 (1.00) |
0.991 (1.00) |
0.737 (1.00) |
1 (1.00) |
0.353 (1.00) |
0.99 (1.00) |
0.15 (1.00) |
|
Amp Peak 23(17q11 2) | 0 (0%) | 69 |
0.747 (1.00) |
0.396 (1.00) |
0.842 (1.00) |
0.0164 (1.00) |
0.967 (1.00) |
0.924 (1.00) |
0.00971 (1.00) |
0.223 (1.00) |
0.68 (1.00) |
0.103 (1.00) |
|
Amp Peak 24(17q12) | 0 (0%) | 75 |
0.281 (1.00) |
0.512 (1.00) |
1 (1.00) |
0.0578 (1.00) |
0.156 (1.00) |
0.176 (1.00) |
0.027 (1.00) |
0.57 (1.00) |
0.871 (1.00) |
0.312 (1.00) |
|
Amp Peak 25(19q12) | 0 (0%) | 73 |
0.16 (1.00) |
0.421 (1.00) |
0.842 (1.00) |
0.498 (1.00) |
0.34 (1.00) |
0.644 (1.00) |
0.491 (1.00) |
0.57 (1.00) |
0.154 (1.00) |
0.516 (1.00) |
|
Amp Peak 26(19q13 43) | 0 (0%) | 75 |
0.088 (1.00) |
0.5 (1.00) |
0.839 (1.00) |
0.479 (1.00) |
0.626 (1.00) |
0.787 (1.00) |
0.702 (1.00) |
0.343 (1.00) |
0.0772 (1.00) |
0.516 (1.00) |
|
Amp Peak 27(20q11 21) | 0 (0%) | 39 |
0.793 (1.00) |
0.406 (1.00) |
1 (1.00) |
0.61 (1.00) |
0.0297 (1.00) |
0.707 (1.00) |
0.576 (1.00) |
0.341 (1.00) |
0.622 (1.00) |
0.571 (1.00) |
|
Amp Peak 28(22q11 23) | 0 (0%) | 99 |
0.113 (1.00) |
0.397 (1.00) |
0.169 (1.00) |
0.684 (1.00) |
0.379 (1.00) |
0.482 (1.00) |
0.503 (1.00) |
0.764 (1.00) |
0.747 (1.00) |
0.796 (1.00) |
|
Del Peak 1(1p36 11) | 0 (0%) | 108 |
0.134 (1.00) |
0.144 (1.00) |
1 (1.00) |
0.942 (1.00) |
0.679 (1.00) |
0.761 (1.00) |
1 (1.00) |
0.00706 (1.00) |
0.38 (1.00) |
0.282 (1.00) |
|
Del Peak 2(1q32 1) | 0 (0%) | 106 |
0.663 (1.00) |
0.119 (1.00) |
0.0382 (1.00) |
0.666 (1.00) |
0.00608 (1.00) |
0.575 (1.00) |
0.487 (1.00) |
0.0544 (1.00) |
0.304 (1.00) |
0.333 (1.00) |
|
Del Peak 3(2q22 1) | 0 (0%) | 91 |
0.204 (1.00) |
0.681 (1.00) |
0.125 (1.00) |
0.534 (1.00) |
0.992 (1.00) |
0.292 (1.00) |
0.42 (1.00) |
0.61 (1.00) |
0.624 (1.00) |
0.268 (1.00) |
|
Del Peak 4(2q34) | 0 (0%) | 76 |
0.232 (1.00) |
0.293 (1.00) |
0.839 (1.00) |
0.632 (1.00) |
0.565 (1.00) |
0.396 (1.00) |
0.424 (1.00) |
0.522 (1.00) |
0.439 (1.00) |
0.937 (1.00) |
|
Del Peak 5(2q37 1) | 0 (0%) | 64 |
0.355 (1.00) |
0.602 (1.00) |
0.0694 (1.00) |
0.433 (1.00) |
0.297 (1.00) |
0.163 (1.00) |
0.168 (1.00) |
0.882 (1.00) |
0.952 (1.00) |
0.769 (1.00) |
|
Del Peak 6(3p21 31) | 0 (0%) | 89 |
0.76 (1.00) |
0.673 (1.00) |
0.667 (1.00) |
0.63 (1.00) |
0.684 (1.00) |
0.233 (1.00) |
1 (1.00) |
0.414 (1.00) |
0.257 (1.00) |
0.0274 (1.00) |
|
Del Peak 7(3p14 2) | 0 (0%) | 88 |
0.543 (1.00) |
0.392 (1.00) |
0.67 (1.00) |
0.63 (1.00) |
0.48 (1.00) |
0.548 (1.00) |
0.573 (1.00) |
0.439 (1.00) |
0.0772 (1.00) |
0.139 (1.00) |
|
Del Peak 8(3p12 3) | 0 (0%) | 94 |
0.798 (1.00) |
0.0607 (1.00) |
0.505 (1.00) |
0.105 (1.00) |
0.993 (1.00) |
0.377 (1.00) |
0.39 (1.00) |
0.763 (1.00) |
0.234 (1.00) |
0.302 (1.00) |
|
Del Peak 9(4q22 1) | 0 (0%) | 79 |
0.825 (1.00) |
0.121 (1.00) |
0.304 (1.00) |
0.861 (1.00) |
1 (1.00) |
0.0216 (1.00) |
0.389 (1.00) |
0.739 (1.00) |
0.171 (1.00) |
1 (1.00) |
|
Del Peak 10(4q34 2) | 0 (0%) | 72 |
0.338 (1.00) |
0.0777 (1.00) |
0.84 (1.00) |
0.631 (1.00) |
0.476 (1.00) |
0.377 (1.00) |
0.762 (1.00) |
0.601 (1.00) |
0.486 (1.00) |
0.364 (1.00) |
|
Del Peak 11(5q11 2) | 0 (0%) | 63 |
0.735 (1.00) |
0.0156 (1.00) |
0.232 (1.00) |
0.338 (1.00) |
0.372 (1.00) |
0.734 (1.00) |
0.68 (1.00) |
0.0577 (1.00) |
0.262 (1.00) |
0.0266 (1.00) |
|
Del Peak 12(5q35 1) | 0 (0%) | 65 |
0.509 (1.00) |
0.0914 (1.00) |
0.0724 (1.00) |
0.24 (1.00) |
0.506 (1.00) |
0.998 (1.00) |
0.446 (1.00) |
0.0839 (1.00) |
0.171 (1.00) |
0.0125 (1.00) |
|
Del Peak 13(6p25 3) | 0 (0%) | 95 |
0.14 (1.00) |
0.825 (1.00) |
0.259 (1.00) |
0.154 (1.00) |
0.354 (1.00) |
0.635 (1.00) |
0.238 (1.00) |
0.0888 (1.00) |
0.0729 (1.00) |
0.224 (1.00) |
|
Del Peak 14(6q21) | 0 (0%) | 76 |
0.107 (1.00) |
0.175 (1.00) |
0.839 (1.00) |
0.966 (1.00) |
0.826 (1.00) |
0.798 (1.00) |
0.779 (1.00) |
0.00186 (1.00) |
0.0031 (1.00) |
0.00253 (1.00) |
|
Del Peak 15(8p23 1) | 0 (0%) | 57 |
0.559 (1.00) |
0.349 (1.00) |
0.0697 (1.00) |
0.907 (1.00) |
0.661 (1.00) |
0.938 (1.00) |
0.476 (1.00) |
0.682 (1.00) |
0.481 (1.00) |
0.506 (1.00) |
|
Del Peak 16(9p23) | 0 (0%) | 73 |
0.651 (1.00) |
0.788 (1.00) |
0.549 (1.00) |
0.753 (1.00) |
0.661 (1.00) |
0.652 (1.00) |
0.789 (1.00) |
0.86 (1.00) |
0.57 (1.00) |
1 (1.00) |
|
Del Peak 17(9p21 3) | 0 (0%) | 55 |
0.334 (1.00) |
0.771 (1.00) |
0.419 (1.00) |
0.975 (1.00) |
0.214 (1.00) |
0.728 (1.00) |
0.789 (1.00) |
0.272 (1.00) |
0.533 (1.00) |
0.43 (1.00) |
|
Del Peak 18(10p12 1) | 0 (0%) | 104 |
0.966 (1.00) |
0.176 (1.00) |
1 (1.00) |
0.635 (1.00) |
0.932 (1.00) |
0.345 (1.00) |
0.597 (1.00) |
0.944 (1.00) |
0.328 (1.00) |
1 (1.00) |
|
Del Peak 19(10q23 31) | 0 (0%) | 74 |
0.688 (1.00) |
0.00687 (1.00) |
1 (1.00) |
0.0916 (1.00) |
0.606 (1.00) |
0.719 (1.00) |
0.5 (1.00) |
0.275 (1.00) |
0.186 (1.00) |
0.443 (1.00) |
|
Del Peak 20(11p15 5) | 0 (0%) | 65 |
0.409 (1.00) |
0.00881 (1.00) |
0.842 (1.00) |
0.00871 (1.00) |
0.869 (1.00) |
0.272 (1.00) |
1 (1.00) |
0.36 (1.00) |
0.182 (1.00) |
0.773 (1.00) |
|
Del Peak 21(11q25) | 0 (0%) | 89 |
0.538 (1.00) |
0.537 (1.00) |
1 (1.00) |
0.966 (1.00) |
0.256 (1.00) |
0.718 (1.00) |
0.699 (1.00) |
0.698 (1.00) |
0.0475 (1.00) |
0.85 (1.00) |
|
Del Peak 22(13q14 2) | 0 (0%) | 80 |
0.353 (1.00) |
0.0997 (1.00) |
0.303 (1.00) |
0.753 (1.00) |
0.696 (1.00) |
0.0343 (1.00) |
0.731 (1.00) |
0.895 (1.00) |
0.221 (1.00) |
0.344 (1.00) |
|
Del Peak 23(14q12) | 0 (0%) | 94 |
0.378 (1.00) |
0.258 (1.00) |
0.181 (1.00) |
0.487 (1.00) |
0.0496 (1.00) |
0.428 (1.00) |
0.801 (1.00) |
0.12 (1.00) |
0.16 (1.00) |
0.151 (1.00) |
|
Del Peak 24(14q32 31) | 0 (0%) | 93 |
0.676 (1.00) |
0.113 (1.00) |
0.0478 (1.00) |
0.312 (1.00) |
0.55 (1.00) |
0.707 (1.00) |
0.315 (1.00) |
0.963 (1.00) |
0.696 (1.00) |
0.496 (1.00) |
|
Del Peak 25(15q13 1) | 0 (0%) | 82 |
0.205 (1.00) |
0.123 (1.00) |
0.407 (1.00) |
0.285 (1.00) |
0.62 (1.00) |
0.602 (1.00) |
0.129 (1.00) |
0.779 (1.00) |
0.452 (1.00) |
0.846 (1.00) |
|
Del Peak 26(16p13 3) | 0 (0%) | 83 |
0.487 (1.00) |
0.258 (1.00) |
0.682 (1.00) |
0.862 (1.00) |
0.627 (1.00) |
0.368 (1.00) |
0.731 (1.00) |
0.759 (1.00) |
0.688 (1.00) |
0.276 (1.00) |
|
Del Peak 27(16q23 1) | 0 (0%) | 94 |
0.213 (1.00) |
0.847 (1.00) |
0.658 (1.00) |
0.127 (1.00) |
0.823 (1.00) |
0.111 (1.00) |
0.341 (1.00) |
0.265 (1.00) |
0.213 (1.00) |
0.322 (1.00) |
|
Del Peak 28(17p12) | 0 (0%) | 63 |
0.124 (1.00) |
0.478 (1.00) |
0.426 (1.00) |
0.827 (1.00) |
0.969 (1.00) |
0.689 (1.00) |
0.385 (1.00) |
0.166 (1.00) |
0.522 (1.00) |
0.0627 (1.00) |
|
Del Peak 29(18q23) | 0 (0%) | 74 |
0.215 (1.00) |
0.088 (1.00) |
0.841 (1.00) |
0.125 (1.00) |
0.406 (1.00) |
0.525 (1.00) |
0.664 (1.00) |
0.992 (1.00) |
0.457 (1.00) |
0.937 (1.00) |
|
Del Peak 30(19p13 3) | 0 (0%) | 80 |
0.609 (1.00) |
0.622 (1.00) |
1 (1.00) |
0.206 (1.00) |
0.187 (1.00) |
0.523 (1.00) |
0.15 (1.00) |
0.455 (1.00) |
0.544 (1.00) |
0.518 (1.00) |
|
Del Peak 31(22q13 32) | 0 (0%) | 78 |
0.912 (1.00) |
0.35 (1.00) |
0.839 (1.00) |
0.0926 (1.00) |
0.868 (1.00) |
0.745 (1.00) |
0.0882 (1.00) |
0.926 (1.00) |
0.429 (1.00) |
0.522 (1.00) |
|
Del Peak 32(Xp11 3) | 0 (0%) | 94 |
0.824 (1.00) |
0.17 (1.00) |
0.374 (1.00) |
0.785 (1.00) |
0.18 (1.00) |
0.704 (1.00) |
0.868 (1.00) |
0.179 (1.00) |
0.96 (1.00) |
0.0712 (1.00) |
|
Del Peak 33(Xq21 33) | 0 (0%) | 100 |
0.446 (1.00) |
0.888 (1.00) |
1 (1.00) |
0.508 (1.00) |
0.634 (1.00) |
0.241 (1.00) |
0.286 (1.00) |
0.613 (1.00) |
0.929 (1.00) |
0.75 (1.00) |
|
Del Peak 34(Xq23) | 0 (0%) | 101 |
0.423 (1.00) |
0.607 (1.00) |
1 (1.00) |
0.845 (1.00) |
0.835 (1.00) |
0.363 (1.00) |
0.758 (1.00) |
0.9 (1.00) |
0.941 (1.00) |
0.868 (1.00) |
P value = 7.05e-05 (t-test), Q value = 0.044
Table S1. Gene #8: 'Amp Peak 8(4q13.3)' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 37 | 78.1 (16.3) |
AMP PEAK 8(4Q13.3) CNV | 3 | 90.0 (0.0) |
AMP PEAK 8(4Q13.3) WILD-TYPE | 34 | 77.1 (16.6) |
Figure S1. Get High-res Image Gene #8: 'Amp Peak 8(4q13.3)' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D8V4.png)
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = BLCA-TP.clin.merged.picked.txt
-
Number of patients = 131
-
Number of significantly arm-level cnvs = 62
-
Number of selected clinical features = 11
-
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.