This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 75 arm-level results and 11 clinical features across 187 patients, no significant finding detected with Q value < 0.25.
-
No arm-level cnvs related to clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | t-test | t-test | Chi-square test | |
Amp Peak 1(1p36 22) | 0 (0%) | 161 |
0.288 (1.00) |
0.673 (1.00) |
0.0301 (1.00) |
0.607 (1.00) |
1 (1.00) |
0.637 (1.00) |
0.69 (1.00) |
0.486 (1.00) |
0.429 (1.00) |
0.671 (1.00) |
|
Amp Peak 2(1q21 3) | 0 (0%) | 123 |
0.801 (1.00) |
0.332 (1.00) |
0.755 (1.00) |
0.171 (1.00) |
0.00695 (1.00) |
0.183 (1.00) |
0.178 (1.00) |
0.212 (1.00) |
0.0991 (1.00) |
0.363 (1.00) |
|
Amp Peak 3(1q42 3) | 0 (0%) | 123 |
0.696 (1.00) |
0.791 (1.00) |
0.875 (1.00) |
0.0347 (1.00) |
0.233 (1.00) |
0.438 (1.00) |
0.451 (1.00) |
0.943 (1.00) |
0.329 (1.00) |
0.667 (1.00) |
|
Amp Peak 4(3q27 1) | 0 (0%) | 127 |
0.63 (1.00) |
0.7 (1.00) |
0.199 (1.00) |
0.322 (1.00) |
1 (1.00) |
0.12 (1.00) |
0.612 (1.00) |
0.905 (1.00) |
0.933 (1.00) |
0.699 (1.00) |
|
Amp Peak 5(5p13 1) | 0 (0%) | 133 |
0.619 (1.00) |
0.187 (1.00) |
0.326 (1.00) |
0.452 (1.00) |
0.414 (1.00) |
0.587 (1.00) |
0.116 (1.00) |
0.534 (1.00) |
0.235 (1.00) |
0.0086 (1.00) |
|
Amp Peak 6(6p21 1) | 0 (0%) | 132 |
0.0123 (1.00) |
0.1 (1.00) |
0.511 (1.00) |
0.0744 (1.00) |
0.198 (1.00) |
0.114 (1.00) |
0.551 (1.00) |
0.165 (1.00) |
0.0586 (1.00) |
0.271 (1.00) |
|
Amp Peak 7(6q12) | 0 (0%) | 145 |
0.89 (1.00) |
0.889 (1.00) |
0.859 (1.00) |
0.206 (1.00) |
0.189 (1.00) |
0.785 (1.00) |
0.749 (1.00) |
0.4 (1.00) |
0.235 (1.00) |
0.823 (1.00) |
|
Amp Peak 8(6q21) | 0 (0%) | 152 |
0.895 (1.00) |
0.677 (1.00) |
1 (1.00) |
0.0888 (1.00) |
0.123 (1.00) |
0.531 (1.00) |
0.338 (1.00) |
0.264 (1.00) |
0.233 (1.00) |
0.625 (1.00) |
|
Amp Peak 9(7p22 3) | 0 (0%) | 91 |
0.441 (1.00) |
0.0155 (1.00) |
0.23 (1.00) |
0.226 (1.00) |
0.715 (1.00) |
0.535 (1.00) |
0.863 (1.00) |
0.817 (1.00) |
0.301 (1.00) |
0.45 (1.00) |
|
Amp Peak 10(7p11 2) | 0 (0%) | 98 |
0.604 (1.00) |
0.0841 (1.00) |
0.295 (1.00) |
0.312 (1.00) |
0.448 (1.00) |
0.376 (1.00) |
0.955 (1.00) |
0.658 (1.00) |
0.998 (1.00) |
0.117 (1.00) |
|
Amp Peak 11(7q21 2) | 0 (0%) | 98 |
0.95 (1.00) |
0.125 (1.00) |
0.0995 (1.00) |
0.9 (1.00) |
1 (1.00) |
0.226 (1.00) |
0.366 (1.00) |
0.429 (1.00) |
0.226 (1.00) |
0.554 (1.00) |
|
Amp Peak 12(8p23 1) | 0 (0%) | 114 |
0.96 (1.00) |
0.274 (1.00) |
0.171 (1.00) |
0.57 (1.00) |
0.112 (1.00) |
0.608 (1.00) |
0.665 (1.00) |
0.359 (1.00) |
0.871 (1.00) |
0.723 (1.00) |
|
Amp Peak 13(8q24 21) | 0 (0%) | 58 |
0.597 (1.00) |
0.0645 (1.00) |
0.872 (1.00) |
0.0271 (1.00) |
1 (1.00) |
0.601 (1.00) |
0.465 (1.00) |
0.63 (1.00) |
0.331 (1.00) |
0.67 (1.00) |
|
Amp Peak 14(9p24 1) | 0 (0%) | 157 |
0.84 (1.00) |
0.782 (1.00) |
0.684 (1.00) |
0.396 (1.00) |
0.0834 (1.00) |
0.567 (1.00) |
0.534 (1.00) |
0.887 (1.00) |
0.17 (1.00) |
0.626 (1.00) |
|
Amp Peak 15(9q34 3) | 0 (0%) | 139 |
0.259 (1.00) |
0.141 (1.00) |
1 (1.00) |
0.00223 (1.00) |
0.375 (1.00) |
0.608 (1.00) |
0.859 (1.00) |
0.818 (1.00) |
0.269 (1.00) |
0.61 (1.00) |
|
Amp Peak 16(10q22 2) | 0 (0%) | 152 |
0.311 (1.00) |
0.296 (1.00) |
0.85 (1.00) |
0.967 (1.00) |
0.617 (1.00) |
1 (1.00) |
0.47 (1.00) |
0.383 (1.00) |
0.976 (1.00) |
0.686 (1.00) |
|
Amp Peak 17(10q26 13) | 0 (0%) | 143 |
0.401 (1.00) |
0.645 (1.00) |
0.597 (1.00) |
0.734 (1.00) |
0.668 (1.00) |
0.744 (1.00) |
0.979 (1.00) |
0.825 (1.00) |
0.947 (1.00) |
0.486 (1.00) |
|
Amp Peak 18(11p13) | 0 (0%) | 151 |
0.704 (1.00) |
0.504 (1.00) |
1 (1.00) |
0.901 (1.00) |
0.622 (1.00) |
0.262 (1.00) |
0.105 (1.00) |
0.94 (1.00) |
0.254 (1.00) |
0.0127 (1.00) |
|
Amp Peak 19(11q13 3) | 0 (0%) | 149 |
0.181 (1.00) |
0.177 (1.00) |
0.353 (1.00) |
0.407 (1.00) |
0.632 (1.00) |
0.479 (1.00) |
0.51 (1.00) |
0.914 (1.00) |
0.48 (1.00) |
0.0695 (1.00) |
|
Amp Peak 20(12p12 1) | 0 (0%) | 142 |
0.781 (1.00) |
0.697 (1.00) |
0.387 (1.00) |
0.22 (1.00) |
0.675 (1.00) |
0.622 (1.00) |
0.0174 (1.00) |
0.119 (1.00) |
0.0556 (1.00) |
0.159 (1.00) |
|
Amp Peak 21(12q15) | 0 (0%) | 141 |
0.562 (1.00) |
0.883 (1.00) |
0.862 (1.00) |
0.739 (1.00) |
0.366 (1.00) |
0.629 (1.00) |
0.373 (1.00) |
0.491 (1.00) |
0.321 (1.00) |
0.793 (1.00) |
|
Amp Peak 22(13q12 3) | 0 (0%) | 111 |
0.446 (1.00) |
0.935 (1.00) |
0.172 (1.00) |
0.816 (1.00) |
1 (1.00) |
0.661 (1.00) |
0.145 (1.00) |
0.783 (1.00) |
0.0266 (1.00) |
0.65 (1.00) |
|
Amp Peak 23(13q22 1) | 0 (0%) | 105 |
0.96 (1.00) |
0.976 (1.00) |
0.036 (1.00) |
0.454 (1.00) |
0.47 (1.00) |
0.308 (1.00) |
0.874 (1.00) |
0.819 (1.00) |
0.918 (1.00) |
0.687 (1.00) |
|
Amp Peak 24(15q26 1) | 0 (0%) | 140 |
0.425 (1.00) |
0.343 (1.00) |
0.167 (1.00) |
0.561 (1.00) |
1 (1.00) |
0.376 (1.00) |
0.303 (1.00) |
0.393 (1.00) |
0.248 (1.00) |
0.851 (1.00) |
|
Amp Peak 25(17q12) | 0 (0%) | 127 |
0.941 (1.00) |
0.531 (1.00) |
0.336 (1.00) |
0.15 (1.00) |
0.682 (1.00) |
0.00623 (1.00) |
0.823 (1.00) |
0.0011 (0.828) |
0.711 (1.00) |
0.868 (1.00) |
|
Amp Peak 26(18q11 2) | 0 (0%) | 128 |
0.043 (1.00) |
0.364 (1.00) |
0.629 (1.00) |
0.173 (1.00) |
0.033 (1.00) |
0.857 (1.00) |
0.136 (1.00) |
0.052 (1.00) |
0.0296 (1.00) |
0.238 (1.00) |
|
Amp Peak 27(19q12) | 0 (0%) | 131 |
0.0902 (1.00) |
0.266 (1.00) |
0.745 (1.00) |
0.315 (1.00) |
0.0261 (1.00) |
0.3 (1.00) |
0.523 (1.00) |
0.183 (1.00) |
0.0813 (1.00) |
0.26 (1.00) |
|
Amp Peak 28(20q13 2) | 0 (0%) | 60 |
0.222 (1.00) |
0.431 (1.00) |
0.0168 (1.00) |
0.015 (1.00) |
1 (1.00) |
0.752 (1.00) |
0.293 (1.00) |
0.36 (1.00) |
0.0741 (1.00) |
0.287 (1.00) |
|
Amp Peak 29(Xq27 3) | 0 (0%) | 150 |
0.617 (1.00) |
0.0414 (1.00) |
0.852 (1.00) |
0.523 (1.00) |
1 (1.00) |
0.937 (1.00) |
0.529 (1.00) |
0.73 (1.00) |
0.761 (1.00) |
0.351 (1.00) |
|
Del Peak 1(1p36 11) | 0 (0%) | 138 |
0.914 (1.00) |
0.524 (1.00) |
0.311 (1.00) |
0.291 (1.00) |
0.0783 (1.00) |
0.758 (1.00) |
0.259 (1.00) |
0.0174 (1.00) |
0.288 (1.00) |
0.709 (1.00) |
|
Del Peak 2(1p13 2) | 0 (0%) | 151 |
0.354 (1.00) |
0.931 (1.00) |
0.849 (1.00) |
0.212 (1.00) |
0.622 (1.00) |
0.619 (1.00) |
0.596 (1.00) |
0.406 (1.00) |
0.739 (1.00) |
0.563 (1.00) |
|
Del Peak 3(1q44) | 0 (0%) | 175 |
0.0323 (1.00) |
0.0333 (1.00) |
0.768 (1.00) |
0.782 (1.00) |
1 (1.00) |
0.393 (1.00) |
0.609 (1.00) |
0.18 (1.00) |
0.238 (1.00) |
0.681 (1.00) |
|
Del Peak 4(2q32 1) | 0 (0%) | 164 |
0.172 (1.00) |
0.891 (1.00) |
0.82 (1.00) |
0.0792 (1.00) |
1 (1.00) |
0.907 (1.00) |
0.257 (1.00) |
0.715 (1.00) |
0.138 (1.00) |
0.0285 (1.00) |
|
Del Peak 5(2q37 2) | 0 (0%) | 162 |
0.897 (1.00) |
0.0847 (1.00) |
0.187 (1.00) |
0.0382 (1.00) |
1 (1.00) |
0.688 (1.00) |
0.255 (1.00) |
0.0341 (1.00) |
0.347 (1.00) |
0.297 (1.00) |
|
Del Peak 6(3p26 1) | 0 (0%) | 129 |
0.866 (1.00) |
0.332 (1.00) |
0.63 (1.00) |
0.612 (1.00) |
1 (1.00) |
0.528 (1.00) |
0.0652 (1.00) |
0.337 (1.00) |
0.779 (1.00) |
0.286 (1.00) |
|
Del Peak 7(3p14 2) | 0 (0%) | 120 |
0.574 (1.00) |
0.959 (1.00) |
0.435 (1.00) |
0.0959 (1.00) |
0.702 (1.00) |
0.585 (1.00) |
0.235 (1.00) |
0.0132 (1.00) |
0.651 (1.00) |
0.283 (1.00) |
|
Del Peak 8(3q26 31) | 0 (0%) | 166 |
0.984 (1.00) |
0.641 (1.00) |
1 (1.00) |
0.436 (1.00) |
0.572 (1.00) |
0.133 (1.00) |
0.446 (1.00) |
0.738 (1.00) |
0.328 (1.00) |
0.422 (1.00) |
|
Del Peak 9(4p16 3) | 0 (0%) | 120 |
0.559 (1.00) |
0.871 (1.00) |
0.535 (1.00) |
0.239 (1.00) |
0.702 (1.00) |
0.176 (1.00) |
0.509 (1.00) |
0.131 (1.00) |
0.668 (1.00) |
0.241 (1.00) |
|
Del Peak 10(4q22 1) | 0 (0%) | 108 |
0.538 (1.00) |
0.323 (1.00) |
0.763 (1.00) |
0.288 (1.00) |
0.135 (1.00) |
0.817 (1.00) |
0.405 (1.00) |
0.124 (1.00) |
0.126 (1.00) |
0.435 (1.00) |
|
Del Peak 11(4q34 3) | 0 (0%) | 111 |
0.98 (1.00) |
0.183 (1.00) |
0.879 (1.00) |
0.173 (1.00) |
0.122 (1.00) |
0.809 (1.00) |
0.661 (1.00) |
0.0949 (1.00) |
0.777 (1.00) |
0.0218 (1.00) |
|
Del Peak 12(5q11 2) | 0 (0%) | 127 |
0.465 (1.00) |
0.237 (1.00) |
0.748 (1.00) |
0.0141 (1.00) |
0.214 (1.00) |
0.357 (1.00) |
0.536 (1.00) |
0.0592 (1.00) |
0.99 (1.00) |
0.513 (1.00) |
|
Del Peak 13(5q23 2) | 0 (0%) | 136 |
0.184 (1.00) |
0.927 (1.00) |
0.239 (1.00) |
0.074 (1.00) |
0.393 (1.00) |
0.307 (1.00) |
0.337 (1.00) |
0.166 (1.00) |
0.381 (1.00) |
0.255 (1.00) |
|
Del Peak 14(6p25 3) | 0 (0%) | 145 |
0.188 (1.00) |
0.988 (1.00) |
0.373 (1.00) |
0.206 (1.00) |
1 (1.00) |
0.112 (1.00) |
0.367 (1.00) |
0.294 (1.00) |
0.689 (1.00) |
0.772 (1.00) |
|
Del Peak 15(6q26) | 0 (0%) | 142 |
0.677 (1.00) |
0.917 (1.00) |
0.863 (1.00) |
0.272 (1.00) |
0.362 (1.00) |
0.554 (1.00) |
0.537 (1.00) |
0.0207 (1.00) |
0.116 (1.00) |
0.62 (1.00) |
|
Del Peak 16(7q31 1) | 0 (0%) | 166 |
0.056 (1.00) |
0.298 (1.00) |
0.158 (1.00) |
0.194 (1.00) |
0.572 (1.00) |
0.724 (1.00) |
0.0326 (1.00) |
0.961 (1.00) |
0.623 (1.00) |
0.709 (1.00) |
|
Del Peak 17(7q36 3) | 0 (0%) | 154 |
0.199 (1.00) |
0.745 (1.00) |
0.557 (1.00) |
0.495 (1.00) |
0.106 (1.00) |
0.641 (1.00) |
0.00671 (1.00) |
0.917 (1.00) |
0.156 (1.00) |
0.441 (1.00) |
|
Del Peak 18(8p23 2) | 0 (0%) | 134 |
0.801 (1.00) |
0.127 (1.00) |
0.409 (1.00) |
0.583 (1.00) |
1 (1.00) |
0.786 (1.00) |
0.597 (1.00) |
0.114 (1.00) |
0.0954 (1.00) |
0.0545 (1.00) |
|
Del Peak 19(9p23) | 0 (0%) | 106 |
0.0109 (1.00) |
0.378 (1.00) |
0.881 (1.00) |
0.214 (1.00) |
0.469 (1.00) |
0.594 (1.00) |
0.154 (1.00) |
0.662 (1.00) |
0.0735 (1.00) |
0.0288 (1.00) |
|
Del Peak 20(9p21 3) | 0 (0%) | 112 |
0.144 (1.00) |
0.481 (1.00) |
0.76 (1.00) |
0.178 (1.00) |
0.441 (1.00) |
0.526 (1.00) |
0.277 (1.00) |
0.36 (1.00) |
0.5 (1.00) |
0.733 (1.00) |
|
Del Peak 21(9q21 11) | 0 (0%) | 143 |
0.187 (1.00) |
0.446 (1.00) |
0.484 (1.00) |
0.367 (1.00) |
0.668 (1.00) |
0.147 (1.00) |
0.915 (1.00) |
0.706 (1.00) |
0.994 (1.00) |
0.101 (1.00) |
|
Del Peak 22(10p15 1) | 0 (0%) | 162 |
0.189 (1.00) |
0.27 (1.00) |
1 (1.00) |
0.192 (1.00) |
1 (1.00) |
0.625 (1.00) |
0.0988 (1.00) |
0.287 (1.00) |
0.93 (1.00) |
0.0864 (1.00) |
|
Del Peak 23(10q22 3) | 0 (0%) | 157 |
0.911 (1.00) |
0.0599 (1.00) |
0.84 (1.00) |
0.266 (1.00) |
0.312 (1.00) |
0.62 (1.00) |
0.257 (1.00) |
0.822 (1.00) |
0.538 (1.00) |
0.571 (1.00) |
|
Del Peak 24(10q23 31) | 0 (0%) | 142 |
0.253 (1.00) |
0.125 (1.00) |
0.604 (1.00) |
0.322 (1.00) |
0.675 (1.00) |
0.705 (1.00) |
0.469 (1.00) |
0.874 (1.00) |
0.589 (1.00) |
0.17 (1.00) |
|
Del Peak 25(11p15 4) | 0 (0%) | 144 |
0.59 (1.00) |
0.63 (1.00) |
0.595 (1.00) |
0.00912 (1.00) |
0.2 (1.00) |
1 (1.00) |
0.652 (1.00) |
0.0976 (1.00) |
0.286 (1.00) |
0.779 (1.00) |
|
Del Peak 26(11q23 2) | 0 (0%) | 142 |
0.269 (1.00) |
0.363 (1.00) |
0.387 (1.00) |
0.389 (1.00) |
0.675 (1.00) |
0.0297 (1.00) |
0.513 (1.00) |
0.282 (1.00) |
0.414 (1.00) |
0.891 (1.00) |
|
Del Peak 27(12p13 31) | 0 (0%) | 156 |
0.452 (1.00) |
0.176 (1.00) |
0.841 (1.00) |
0.186 (1.00) |
0.0907 (1.00) |
0.422 (1.00) |
0.809 (1.00) |
0.344 (1.00) |
0.889 (1.00) |
0.27 (1.00) |
|
Del Peak 28(13q12 11) | 0 (0%) | 159 |
0.546 (1.00) |
0.599 (1.00) |
0.53 (1.00) |
0.529 (1.00) |
0.0104 (1.00) |
0.714 (1.00) |
0.933 (1.00) |
0.435 (1.00) |
0.387 (1.00) |
0.448 (1.00) |
|
Del Peak 29(14q21 1) | 0 (0%) | 142 |
0.293 (1.00) |
0.455 (1.00) |
0.726 (1.00) |
0.537 (1.00) |
0.675 (1.00) |
0.0369 (1.00) |
0.559 (1.00) |
0.965 (1.00) |
0.973 (1.00) |
0.342 (1.00) |
|
Del Peak 30(14q32 33) | 0 (0%) | 133 |
0.318 (1.00) |
0.375 (1.00) |
1 (1.00) |
0.884 (1.00) |
0.414 (1.00) |
0.0333 (1.00) |
0.369 (1.00) |
0.0949 (1.00) |
0.46 (1.00) |
0.196 (1.00) |
|
Del Peak 31(15q15 1) | 0 (0%) | 136 |
0.587 (1.00) |
0.975 (1.00) |
0.401 (1.00) |
0.00157 (1.00) |
0.017 (1.00) |
0.151 (1.00) |
0.107 (1.00) |
0.0711 (1.00) |
0.105 (1.00) |
0.42 (1.00) |
|
Del Peak 32(16p13 3) | 0 (0%) | 158 |
0.463 (1.00) |
0.139 (1.00) |
0.0972 (1.00) |
0.0368 (1.00) |
0.297 (1.00) |
0.923 (1.00) |
0.293 (1.00) |
0.035 (1.00) |
0.953 (1.00) |
0.838 (1.00) |
|
Del Peak 33(16q23 1) | 0 (0%) | 119 |
0.0934 (1.00) |
0.881 (1.00) |
0.0444 (1.00) |
0.0687 (1.00) |
0.101 (1.00) |
0.338 (1.00) |
0.386 (1.00) |
0.12 (1.00) |
0.0853 (1.00) |
0.275 (1.00) |
|
Del Peak 34(17p12) | 0 (0%) | 114 |
0.0573 (1.00) |
0.661 (1.00) |
0.759 (1.00) |
0.0325 (1.00) |
0.112 (1.00) |
0.235 (1.00) |
0.428 (1.00) |
0.0464 (1.00) |
0.645 (1.00) |
0.323 (1.00) |
|
Del Peak 35(17q24 3) | 0 (0%) | 157 |
0.22 (1.00) |
0.0557 (1.00) |
0.84 (1.00) |
0.191 (1.00) |
0.6 (1.00) |
0.269 (1.00) |
0.0926 (1.00) |
0.394 (1.00) |
0.247 (1.00) |
0.3 (1.00) |
|
Del Peak 36(18q21 2) | 0 (0%) | 108 |
0.209 (1.00) |
0.838 (1.00) |
0.88 (1.00) |
0.787 (1.00) |
1 (1.00) |
0.348 (1.00) |
0.0623 (1.00) |
0.0213 (1.00) |
0.00146 (1.00) |
0.303 (1.00) |
|
Del Peak 37(19p13 3) | 0 (0%) | 126 |
0.404 (1.00) |
0.708 (1.00) |
0.0787 (1.00) |
0.458 (1.00) |
0.00525 (1.00) |
0.378 (1.00) |
0.913 (1.00) |
0.808 (1.00) |
0.498 (1.00) |
0.443 (1.00) |
|
Del Peak 38(19q13 11) | 0 (0%) | 160 |
0.215 (1.00) |
0.126 (1.00) |
0.835 (1.00) |
0.0253 (1.00) |
0.267 (1.00) |
0.917 (1.00) |
0.67 (1.00) |
0.494 (1.00) |
0.477 (1.00) |
0.694 (1.00) |
|
Del Peak 39(20p12 1) | 0 (0%) | 156 |
0.144 (1.00) |
0.903 (1.00) |
0.692 (1.00) |
0.423 (1.00) |
0.328 (1.00) |
0.856 (1.00) |
0.669 (1.00) |
0.871 (1.00) |
0.452 (1.00) |
0.64 (1.00) |
|
Del Peak 40(20p12 1) | 0 (0%) | 156 |
0.144 (1.00) |
0.903 (1.00) |
0.692 (1.00) |
0.423 (1.00) |
0.328 (1.00) |
0.856 (1.00) |
0.669 (1.00) |
0.871 (1.00) |
0.452 (1.00) |
0.64 (1.00) |
|
Del Peak 41(21q11 2) | 0 (0%) | 121 |
0.796 (1.00) |
0.139 (1.00) |
0.211 (1.00) |
0.143 (1.00) |
0.245 (1.00) |
0.664 (1.00) |
0.693 (1.00) |
0.36 (1.00) |
0.728 (1.00) |
0.497 (1.00) |
|
Del Peak 42(21q22 13) | 0 (0%) | 115 |
0.999 (1.00) |
0.375 (1.00) |
1 (1.00) |
0.228 (1.00) |
1 (1.00) |
0.6 (1.00) |
0.302 (1.00) |
0.591 (1.00) |
0.153 (1.00) |
0.189 (1.00) |
|
Del Peak 43(22q13 31) | 0 (0%) | 125 |
0.796 (1.00) |
0.444 (1.00) |
0.427 (1.00) |
0.0209 (1.00) |
0.0412 (1.00) |
0.848 (1.00) |
0.883 (1.00) |
0.438 (1.00) |
0.407 (1.00) |
0.395 (1.00) |
|
Del Peak 44(Xp22 2) | 0 (0%) | 152 |
0.584 (1.00) |
0.775 (1.00) |
0.85 (1.00) |
0.0322 (1.00) |
0.617 (1.00) |
0.57 (1.00) |
0.721 (1.00) |
0.321 (1.00) |
0.37 (1.00) |
0.805 (1.00) |
|
Del Peak 45(Xp21 1) | 0 (0%) | 153 |
0.668 (1.00) |
0.583 (1.00) |
0.121 (1.00) |
0.0514 (1.00) |
0.613 (1.00) |
0.601 (1.00) |
0.165 (1.00) |
0.00246 (1.00) |
0.0666 (1.00) |
0.745 (1.00) |
|
Del Peak 46(Xq21 33) | 0 (0%) | 163 |
0.637 (1.00) |
0.721 (1.00) |
1 (1.00) |
0.477 (1.00) |
1 (1.00) |
0.682 (1.00) |
0.802 (1.00) |
0.155 (1.00) |
0.681 (1.00) |
0.268 (1.00) |
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
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Clinical data file = STAD-TP.clin.merged.picked.txt
-
Number of patients = 187
-
Number of significantly arm-level cnvs = 75
-
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.