Correlation between copy number variation genes (focal) and selected clinical features
Stomach Adenocarcinoma (Primary solid tumor)
21 April 2013
|
analyses__2013_04_21
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team
(Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as
Broad Institute TCGA Genome Data Analysis Center
(2013):
Stomach Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes (focal) and selected clinical features.
Broad Institute of MIT and Harvard.
doi:10.7908/C1MP518F
Overview
Introduction
This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Summary
Testing the association between copy number variation 75 arm-level results and 11 clinical features across 180 patients, no significant finding detected with Q value < 0.25.
-
No arm-level cnvs related to clinical features.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between significant copy number variation of 75 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.
|
Clinical Features |
Time to Death |
AGE | GENDER |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
||
| nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | |
| Amp Peak 1(1p36 22) | 0 (0%) | 154 |
0.387 (1.00) |
0.576 (1.00) |
0.0289 (1.00) |
0.178 (1.00) |
0.642 (1.00) |
0.428 (1.00) |
0.436 (1.00) |
0.128 (1.00) |
0.546 (1.00) |
0.545 (1.00) |
0.388 (1.00) |
| Amp Peak 2(1q21 3) | 0 (0%) | 120 |
0.82 (1.00) |
0.253 (1.00) |
0.75 (1.00) |
0.429 (1.00) |
0.934 (1.00) |
0.474 (1.00) |
1 (1.00) |
0.882 (1.00) |
0.043 (1.00) |
0.521 (1.00) |
0.0953 (1.00) |
| Amp Peak 3(1q42 3) | 0 (0%) | 119 |
0.663 (1.00) |
0.838 (1.00) |
0.748 (1.00) |
0.0754 (1.00) |
0.811 (1.00) |
0.736 (1.00) |
0.909 (1.00) |
0.568 (1.00) |
0.338 (1.00) |
0.92 (1.00) |
0.314 (1.00) |
| Amp Peak 4(3q27 1) | 0 (0%) | 122 |
0.558 (1.00) |
0.714 (1.00) |
0.195 (1.00) |
0.0654 (1.00) |
0.129 (1.00) |
0.459 (1.00) |
0.909 (1.00) |
0.387 (1.00) |
1 (1.00) |
0.771 (1.00) |
0.585 (1.00) |
| Amp Peak 5(5p13 1) | 0 (0%) | 126 |
0.586 (1.00) |
0.264 (1.00) |
0.25 (1.00) |
0.217 (1.00) |
0.387 (1.00) |
0.192 (1.00) |
0.741 (1.00) |
0.0686 (1.00) |
0.16 (1.00) |
0.447 (1.00) |
0.332 (1.00) |
| Amp Peak 6(6p21 1) | 0 (0%) | 127 |
0.00992 (1.00) |
0.166 (1.00) |
0.507 (1.00) |
0.307 (1.00) |
0.523 (1.00) |
0.388 (1.00) |
0.0483 (1.00) |
0.189 (1.00) |
0.153 (1.00) |
0.169 (1.00) |
0.272 (1.00) |
| Amp Peak 7(6q12) | 0 (0%) | 140 |
0.71 (1.00) |
0.928 (1.00) |
0.718 (1.00) |
0.636 (1.00) |
0.819 (1.00) |
0.873 (1.00) |
0.557 (1.00) |
0.954 (1.00) |
0.308 (1.00) |
0.373 (1.00) |
0.118 (1.00) |
| Amp Peak 8(6q21) | 0 (0%) | 147 |
0.781 (1.00) |
0.859 (1.00) |
0.845 (1.00) |
0.313 (1.00) |
0.774 (1.00) |
0.833 (1.00) |
0.835 (1.00) |
0.791 (1.00) |
0.227 (1.00) |
0.278 (1.00) |
0.276 (1.00) |
| Amp Peak 9(7p22 3) | 0 (0%) | 88 |
0.642 (1.00) |
0.00906 (1.00) |
0.171 (1.00) |
0.25 (1.00) |
0.83 (1.00) |
0.836 (1.00) |
0.471 (1.00) |
0.636 (1.00) |
0.677 (1.00) |
0.827 (1.00) |
0.294 (1.00) |
| Amp Peak 10(7p11 2) | 0 (0%) | 95 |
0.838 (1.00) |
0.0524 (1.00) |
0.286 (1.00) |
0.567 (1.00) |
0.412 (1.00) |
0.969 (1.00) |
0.418 (1.00) |
0.39 (1.00) |
0.372 (1.00) |
0.682 (1.00) |
0.868 (1.00) |
| Amp Peak 11(7q21 2) | 0 (0%) | 94 |
0.774 (1.00) |
0.0807 (1.00) |
0.0674 (1.00) |
0.729 (1.00) |
0.82 (1.00) |
0.439 (1.00) |
0.138 (1.00) |
0.376 (1.00) |
1 (1.00) |
0.571 (1.00) |
0.294 (1.00) |
| Amp Peak 12(8p23 1) | 0 (0%) | 110 |
0.862 (1.00) |
0.287 (1.00) |
0.123 (1.00) |
0.885 (1.00) |
0.871 (1.00) |
0.974 (1.00) |
0.478 (1.00) |
0.521 (1.00) |
0.0759 (1.00) |
0.354 (1.00) |
0.47 (1.00) |
| Amp Peak 13(8q24 21) | 0 (0%) | 56 |
0.487 (1.00) |
0.0442 (1.00) |
1 (1.00) |
0.0556 (1.00) |
0.678 (1.00) |
0.79 (1.00) |
0.479 (1.00) |
0.472 (1.00) |
0.647 (1.00) |
0.522 (1.00) |
0.554 (1.00) |
| Amp Peak 14(9p24 1) | 0 (0%) | 150 |
0.684 (1.00) |
0.691 (1.00) |
0.688 (1.00) |
0.575 (1.00) |
0.399 (1.00) |
0.272 (1.00) |
1 (1.00) |
0.0899 (1.00) |
0.194 (1.00) |
0.802 (1.00) |
0.813 (1.00) |
| Amp Peak 15(9q34 3) | 0 (0%) | 134 |
0.233 (1.00) |
0.121 (1.00) |
0.863 (1.00) |
0.102 (1.00) |
0.819 (1.00) |
0.388 (1.00) |
0.544 (1.00) |
0.306 (1.00) |
0.106 (1.00) |
0.876 (1.00) |
0.933 (1.00) |
| Amp Peak 16(10q22 2) | 0 (0%) | 146 |
0.187 (1.00) |
0.347 (1.00) |
0.849 (1.00) |
0.182 (1.00) |
0.841 (1.00) |
0.733 (1.00) |
1 (1.00) |
0.748 (1.00) |
0.239 (1.00) |
0.505 (1.00) |
0.587 (1.00) |
| Amp Peak 17(10q26 13) | 0 (0%) | 137 |
0.264 (1.00) |
0.589 (1.00) |
0.593 (1.00) |
0.77 (1.00) |
1 (1.00) |
0.883 (1.00) |
0.607 (1.00) |
0.773 (1.00) |
0.594 (1.00) |
0.901 (1.00) |
0.898 (1.00) |
| Amp Peak 18(11p13) | 0 (0%) | 145 |
0.851 (1.00) |
0.635 (1.00) |
1 (1.00) |
0.332 (1.00) |
0.212 (1.00) |
0.0658 (1.00) |
0.895 (1.00) |
0.279 (1.00) |
1 (1.00) |
0.855 (1.00) |
0.117 (1.00) |
| Amp Peak 19(11q13 3) | 0 (0%) | 143 |
0.0828 (1.00) |
0.249 (1.00) |
0.349 (1.00) |
0.131 (1.00) |
0.353 (1.00) |
0.557 (1.00) |
0.907 (1.00) |
0.378 (1.00) |
1 (1.00) |
0.83 (1.00) |
0.587 (1.00) |
| Amp Peak 20(12p12 1) | 0 (0%) | 136 |
0.932 (1.00) |
0.862 (1.00) |
0.382 (1.00) |
0.406 (1.00) |
0.0163 (1.00) |
0.0122 (1.00) |
0.357 (1.00) |
0.00251 (1.00) |
0.337 (1.00) |
0.175 (1.00) |
0.0167 (1.00) |
| Amp Peak 21(12q15) | 0 (0%) | 136 |
0.691 (1.00) |
0.695 (1.00) |
0.861 (1.00) |
0.515 (1.00) |
0.287 (1.00) |
0.231 (1.00) |
0.369 (1.00) |
0.287 (1.00) |
0.597 (1.00) |
0.448 (1.00) |
0.103 (1.00) |
| Amp Peak 22(13q12 3) | 0 (0%) | 109 |
0.228 (1.00) |
0.907 (1.00) |
0.213 (1.00) |
0.335 (1.00) |
0.421 (1.00) |
0.0284 (1.00) |
0.699 (1.00) |
0.111 (1.00) |
1 (1.00) |
0.769 (1.00) |
0.0329 (1.00) |
| Amp Peak 23(13q22 1) | 0 (0%) | 103 |
0.653 (1.00) |
0.839 (1.00) |
0.0456 (1.00) |
0.503 (1.00) |
0.645 (1.00) |
0.723 (1.00) |
0.353 (1.00) |
0.0609 (1.00) |
1 (1.00) |
0.752 (1.00) |
0.691 (1.00) |
| Amp Peak 24(15q26 1) | 0 (0%) | 134 |
0.549 (1.00) |
0.291 (1.00) |
0.163 (1.00) |
0.232 (1.00) |
0.539 (1.00) |
0.266 (1.00) |
0.595 (1.00) |
0.519 (1.00) |
0.603 (1.00) |
0.515 (1.00) |
0.135 (1.00) |
| Amp Peak 25(17q12) | 0 (0%) | 124 |
0.699 (1.00) |
0.353 (1.00) |
0.325 (1.00) |
0.0602 (1.00) |
0.239 (1.00) |
0.49 (1.00) |
0.0122 (1.00) |
0.436 (1.00) |
0.647 (1.00) |
0.00238 (1.00) |
0.349 (1.00) |
| Amp Peak 26(18q11 2) | 0 (0%) | 123 |
0.0826 (1.00) |
0.514 (1.00) |
0.625 (1.00) |
0.214 (1.00) |
0.266 (1.00) |
0.0691 (1.00) |
0.7 (1.00) |
0.178 (1.00) |
0.328 (1.00) |
0.0552 (1.00) |
0.0921 (1.00) |
| Amp Peak 27(19q12) | 0 (0%) | 126 |
0.124 (1.00) |
0.265 (1.00) |
1 (1.00) |
0.177 (1.00) |
0.44 (1.00) |
0.249 (1.00) |
0.7 (1.00) |
0.457 (1.00) |
0.0289 (1.00) |
0.216 (1.00) |
0.0384 (1.00) |
| Amp Peak 28(20q13 2) | 0 (0%) | 59 |
0.15 (1.00) |
0.356 (1.00) |
0.0229 (1.00) |
0.126 (1.00) |
0.532 (1.00) |
0.193 (1.00) |
0.776 (1.00) |
0.116 (1.00) |
0.663 (1.00) |
0.444 (1.00) |
0.0202 (1.00) |
| Amp Peak 29(Xq27 3) | 0 (0%) | 143 |
0.814 (1.00) |
0.0612 (1.00) |
1 (1.00) |
0.723 (1.00) |
0.375 (1.00) |
0.773 (1.00) |
0.849 (1.00) |
0.327 (1.00) |
1 (1.00) |
0.522 (1.00) |
0.731 (1.00) |
| Del Peak 1(1p36 11) | 0 (0%) | 134 |
0.675 (1.00) |
0.522 (1.00) |
0.486 (1.00) |
0.391 (1.00) |
0.333 (1.00) |
0.897 (1.00) |
0.695 (1.00) |
0.865 (1.00) |
0.603 (1.00) |
0.0834 (1.00) |
0.584 (1.00) |
| Del Peak 2(1p13 2) | 0 (0%) | 146 |
0.289 (1.00) |
0.967 (1.00) |
0.849 (1.00) |
0.272 (1.00) |
0.906 (1.00) |
0.873 (1.00) |
0.671 (1.00) |
0.948 (1.00) |
1 (1.00) |
0.447 (1.00) |
0.288 (1.00) |
| Del Peak 3(1q44) | 0 (0%) | 168 |
0.029 (1.00) |
0.0381 (1.00) |
0.765 (1.00) |
0.627 (1.00) |
0.419 (1.00) |
0.506 (1.00) |
0.546 (1.00) |
0.857 (1.00) |
1 (1.00) |
0.161 (1.00) |
0.457 (1.00) |
| Del Peak 4(2q32 1) | 0 (0%) | 159 |
0.336 (1.00) |
0.817 (1.00) |
1 (1.00) |
0.0482 (1.00) |
0.519 (1.00) |
0.126 (1.00) |
1 (1.00) |
0.71 (1.00) |
0.466 (1.00) |
0.378 (1.00) |
0.405 (1.00) |
| Del Peak 5(2q37 2) | 0 (0%) | 155 |
0.515 (1.00) |
0.106 (1.00) |
0.195 (1.00) |
0.0289 (1.00) |
0.826 (1.00) |
0.348 (1.00) |
0.787 (1.00) |
0.581 (1.00) |
0.531 (1.00) |
0.0288 (1.00) |
0.194 (1.00) |
| Del Peak 6(3p26 1) | 0 (0%) | 126 |
0.705 (1.00) |
0.301 (1.00) |
0.622 (1.00) |
0.749 (1.00) |
0.588 (1.00) |
0.285 (1.00) |
0.927 (1.00) |
0.762 (1.00) |
1 (1.00) |
0.201 (1.00) |
0.81 (1.00) |
| Del Peak 7(3p14 2) | 0 (0%) | 116 |
0.972 (1.00) |
0.827 (1.00) |
0.341 (1.00) |
0.195 (1.00) |
0.321 (1.00) |
0.673 (1.00) |
0.327 (1.00) |
0.191 (1.00) |
1 (1.00) |
0.00571 (1.00) |
0.624 (1.00) |
| Del Peak 8(3q26 31) | 0 (0%) | 160 |
0.884 (1.00) |
0.539 (1.00) |
1 (1.00) |
0.449 (1.00) |
0.682 (1.00) |
0.284 (1.00) |
0.111 (1.00) |
0.799 (1.00) |
0.449 (1.00) |
0.653 (1.00) |
0.0605 (1.00) |
| Del Peak 9(4p16 3) | 0 (0%) | 117 |
0.296 (1.00) |
0.855 (1.00) |
0.526 (1.00) |
0.527 (1.00) |
0.673 (1.00) |
0.852 (1.00) |
0.169 (1.00) |
0.881 (1.00) |
1 (1.00) |
0.138 (1.00) |
0.524 (1.00) |
| Del Peak 10(4q22 1) | 0 (0%) | 105 |
0.315 (1.00) |
0.277 (1.00) |
0.76 (1.00) |
0.13 (1.00) |
0.187 (1.00) |
0.183 (1.00) |
1 (1.00) |
0.422 (1.00) |
0.162 (1.00) |
0.325 (1.00) |
0.235 (1.00) |
| Del Peak 11(4q34 3) | 0 (0%) | 107 |
0.623 (1.00) |
0.21 (1.00) |
1 (1.00) |
0.124 (1.00) |
0.226 (1.00) |
0.308 (1.00) |
0.534 (1.00) |
0.099 (1.00) |
0.397 (1.00) |
0.184 (1.00) |
0.659 (1.00) |
| Del Peak 12(5q11 2) | 0 (0%) | 124 |
0.456 (1.00) |
0.168 (1.00) |
0.743 (1.00) |
0.00417 (1.00) |
0.107 (1.00) |
0.771 (1.00) |
0.112 (1.00) |
0.432 (1.00) |
0.647 (1.00) |
0.199 (1.00) |
0.691 (1.00) |
| Del Peak 13(5q23 2) | 0 (0%) | 133 |
0.188 (1.00) |
0.906 (1.00) |
0.227 (1.00) |
0.108 (1.00) |
0.395 (1.00) |
0.441 (1.00) |
0.0926 (1.00) |
0.143 (1.00) |
1 (1.00) |
0.343 (1.00) |
0.197 (1.00) |
| Del Peak 14(6p25 3) | 0 (0%) | 139 |
0.263 (1.00) |
0.916 (1.00) |
0.369 (1.00) |
0.0147 (1.00) |
0.467 (1.00) |
0.444 (1.00) |
0.424 (1.00) |
1 (1.00) |
1 (1.00) |
0.386 (1.00) |
0.187 (1.00) |
| Del Peak 15(6q26) | 0 (0%) | 137 |
0.509 (1.00) |
0.985 (1.00) |
1 (1.00) |
0.62 (1.00) |
0.943 (1.00) |
0.237 (1.00) |
0.851 (1.00) |
0.336 (1.00) |
0.594 (1.00) |
0.108 (1.00) |
0.171 (1.00) |
| Del Peak 16(7q31 1) | 0 (0%) | 159 |
0.0662 (1.00) |
0.352 (1.00) |
0.154 (1.00) |
0.228 (1.00) |
0.812 (1.00) |
0.00382 (1.00) |
0.876 (1.00) |
0.435 (1.00) |
1 (1.00) |
0.925 (1.00) |
0.604 (1.00) |
| Del Peak 17(7q36 3) | 0 (0%) | 147 |
0.212 (1.00) |
0.634 (1.00) |
0.436 (1.00) |
0.0792 (1.00) |
0.531 (1.00) |
0.0066 (1.00) |
0.515 (1.00) |
0.0143 (1.00) |
1 (1.00) |
0.874 (1.00) |
0.0833 (1.00) |
| Del Peak 18(8p23 2) | 0 (0%) | 128 |
0.784 (1.00) |
0.11 (1.00) |
0.403 (1.00) |
0.347 (1.00) |
0.819 (1.00) |
0.195 (1.00) |
0.929 (1.00) |
0.364 (1.00) |
1 (1.00) |
0.0551 (1.00) |
0.0634 (1.00) |
| Del Peak 19(9p23) | 0 (0%) | 104 |
0.0205 (1.00) |
0.314 (1.00) |
0.879 (1.00) |
0.19 (1.00) |
0.694 (1.00) |
0.139 (1.00) |
0.1 (1.00) |
0.00474 (1.00) |
0.651 (1.00) |
0.686 (1.00) |
0.0155 (1.00) |
| Del Peak 20(9p21 3) | 0 (0%) | 109 |
0.245 (1.00) |
0.407 (1.00) |
1 (1.00) |
0.322 (1.00) |
0.586 (1.00) |
0.535 (1.00) |
0.478 (1.00) |
0.706 (1.00) |
0.384 (1.00) |
0.397 (1.00) |
0.249 (1.00) |
| Del Peak 21(9q21 11) | 0 (0%) | 140 |
0.253 (1.00) |
0.605 (1.00) |
0.855 (1.00) |
0.202 (1.00) |
0.629 (1.00) |
0.957 (1.00) |
0.0745 (1.00) |
0.0826 (1.00) |
0.308 (1.00) |
0.78 (1.00) |
0.555 (1.00) |
| Del Peak 22(10p15 1) | 0 (0%) | 156 |
0.213 (1.00) |
0.346 (1.00) |
1 (1.00) |
0.225 (1.00) |
0.671 (1.00) |
0.123 (1.00) |
0.527 (1.00) |
0.897 (1.00) |
0.515 (1.00) |
0.46 (1.00) |
0.562 (1.00) |
| Del Peak 23(10q22 3) | 0 (0%) | 152 |
0.676 (1.00) |
0.057 (1.00) |
1 (1.00) |
0.669 (1.00) |
0.107 (1.00) |
0.427 (1.00) |
0.479 (1.00) |
0.925 (1.00) |
0.575 (1.00) |
0.942 (1.00) |
0.388 (1.00) |
| Del Peak 24(10q23 31) | 0 (0%) | 138 |
0.257 (1.00) |
0.117 (1.00) |
0.858 (1.00) |
0.524 (1.00) |
0.0154 (1.00) |
0.818 (1.00) |
0.679 (1.00) |
0.629 (1.00) |
1 (1.00) |
1 (1.00) |
0.313 (1.00) |
| Del Peak 25(11p15 4) | 0 (0%) | 138 |
0.368 (1.00) |
0.684 (1.00) |
0.591 (1.00) |
0.0067 (1.00) |
0.228 (1.00) |
0.421 (1.00) |
0.796 (1.00) |
1 (1.00) |
0.332 (1.00) |
0.165 (1.00) |
0.0912 (1.00) |
| Del Peak 26(11q23 2) | 0 (0%) | 136 |
0.184 (1.00) |
0.409 (1.00) |
0.382 (1.00) |
0.378 (1.00) |
0.853 (1.00) |
0.813 (1.00) |
0.601 (1.00) |
0.788 (1.00) |
0.597 (1.00) |
0.405 (1.00) |
0.102 (1.00) |
| Del Peak 27(12p13 31) | 0 (0%) | 151 |
0.359 (1.00) |
0.177 (1.00) |
0.68 (1.00) |
0.286 (1.00) |
0.761 (1.00) |
0.806 (1.00) |
0.803 (1.00) |
0.253 (1.00) |
0.589 (1.00) |
0.133 (1.00) |
0.496 (1.00) |
| Del Peak 28(13q12 11) | 0 (0%) | 152 |
0.634 (1.00) |
0.504 (1.00) |
0.407 (1.00) |
0.901 (1.00) |
0.459 (1.00) |
0.891 (1.00) |
0.394 (1.00) |
0.925 (1.00) |
0.00216 (1.00) |
0.246 (1.00) |
0.203 (1.00) |
| Del Peak 29(14q21 1) | 0 (0%) | 137 |
0.491 (1.00) |
0.405 (1.00) |
0.593 (1.00) |
0.425 (1.00) |
0.0626 (1.00) |
0.223 (1.00) |
0.607 (1.00) |
0.229 (1.00) |
0.594 (1.00) |
0.88 (1.00) |
0.859 (1.00) |
| Del Peak 30(14q32 33) | 0 (0%) | 129 |
0.137 (1.00) |
0.417 (1.00) |
1 (1.00) |
0.256 (1.00) |
0.415 (1.00) |
0.095 (1.00) |
0.0201 (1.00) |
0.0692 (1.00) |
0.139 (1.00) |
0.111 (1.00) |
0.734 (1.00) |
| Del Peak 31(15q15 1) | 0 (0%) | 134 |
0.333 (1.00) |
0.883 (1.00) |
0.486 (1.00) |
0.0204 (1.00) |
0.156 (1.00) |
0.00271 (1.00) |
0.275 (1.00) |
0.126 (1.00) |
0.106 (1.00) |
0.273 (1.00) |
0.113 (1.00) |
| Del Peak 32(16p13 3) | 0 (0%) | 152 |
0.55 (1.00) |
0.146 (1.00) |
0.0944 (1.00) |
0.0338 (1.00) |
0.647 (1.00) |
0.886 (1.00) |
0.33 (1.00) |
0.957 (1.00) |
0.575 (1.00) |
0.0852 (1.00) |
0.786 (1.00) |
| Del Peak 33(16q23 1) | 0 (0%) | 114 |
0.0936 (1.00) |
0.906 (1.00) |
0.0578 (1.00) |
0.191 (1.00) |
0.463 (1.00) |
0.202 (1.00) |
0.0737 (1.00) |
0.149 (1.00) |
0.358 (1.00) |
0.119 (1.00) |
0.0456 (1.00) |
| Del Peak 34(17p12) | 0 (0%) | 111 |
0.0276 (1.00) |
0.922 (1.00) |
0.642 (1.00) |
0.0571 (1.00) |
0.0296 (1.00) |
0.292 (1.00) |
0.449 (1.00) |
0.374 (1.00) |
0.072 (1.00) |
0.0463 (1.00) |
0.88 (1.00) |
| Del Peak 35(17q24 3) | 0 (0%) | 150 |
0.434 (1.00) |
0.0803 (1.00) |
0.839 (1.00) |
0.256 (1.00) |
0.851 (1.00) |
0.0382 (1.00) |
0.591 (1.00) |
0.718 (1.00) |
0.592 (1.00) |
0.395 (1.00) |
0.235 (1.00) |
| Del Peak 36(18q21 2) | 0 (0%) | 106 |
0.208 (1.00) |
0.873 (1.00) |
0.878 (1.00) |
0.697 (1.00) |
0.17 (1.00) |
0.00695 (1.00) |
0.773 (1.00) |
0.121 (1.00) |
1 (1.00) |
0.0706 (1.00) |
0.00102 (0.84) |
| Del Peak 37(19p13 3) | 0 (0%) | 120 |
0.205 (1.00) |
0.72 (1.00) |
0.0251 (1.00) |
0.65 (1.00) |
0.625 (1.00) |
0.563 (1.00) |
0.729 (1.00) |
0.878 (1.00) |
0.043 (1.00) |
0.83 (1.00) |
0.239 (1.00) |
| Del Peak 38(19q13 11) | 0 (0%) | 153 |
0.519 (1.00) |
0.16 (1.00) |
1 (1.00) |
0.076 (1.00) |
0.775 (1.00) |
0.202 (1.00) |
0.559 (1.00) |
0.871 (1.00) |
0.561 (1.00) |
0.578 (1.00) |
0.436 (1.00) |
| Del Peak 39(20p12 1) | 0 (0%) | 151 |
0.0967 (1.00) |
0.806 (1.00) |
0.839 (1.00) |
0.833 (1.00) |
0.326 (1.00) |
0.839 (1.00) |
0.265 (1.00) |
0.92 (1.00) |
0.184 (1.00) |
0.971 (1.00) |
0.303 (1.00) |
| Del Peak 40(20p12 1) | 0 (0%) | 151 |
0.0967 (1.00) |
0.806 (1.00) |
0.839 (1.00) |
0.833 (1.00) |
0.326 (1.00) |
0.839 (1.00) |
0.265 (1.00) |
0.92 (1.00) |
0.184 (1.00) |
0.971 (1.00) |
0.303 (1.00) |
| Del Peak 41(21q11 2) | 0 (0%) | 118 |
0.651 (1.00) |
0.124 (1.00) |
0.202 (1.00) |
0.175 (1.00) |
0.263 (1.00) |
0.633 (1.00) |
0.646 (1.00) |
0.814 (1.00) |
1 (1.00) |
0.387 (1.00) |
0.622 (1.00) |
| Del Peak 42(21q22 13) | 0 (0%) | 112 |
0.9 (1.00) |
0.252 (1.00) |
1 (1.00) |
0.248 (1.00) |
0.22 (1.00) |
0.212 (1.00) |
0.901 (1.00) |
0.604 (1.00) |
0.651 (1.00) |
0.306 (1.00) |
0.285 (1.00) |
| Del Peak 43(22q13 31) | 0 (0%) | 121 |
0.578 (1.00) |
0.329 (1.00) |
0.517 (1.00) |
0.0833 (1.00) |
0.371 (1.00) |
0.439 (1.00) |
1 (1.00) |
0.961 (1.00) |
0.332 (1.00) |
0.456 (1.00) |
0.374 (1.00) |
| Del Peak 44(Xp22 2) | 0 (0%) | 148 |
0.436 (1.00) |
0.887 (1.00) |
0.843 (1.00) |
0.034 (1.00) |
0.36 (1.00) |
0.616 (1.00) |
0.548 (1.00) |
0.917 (1.00) |
1 (1.00) |
0.617 (1.00) |
0.53 (1.00) |
| Del Peak 45(Xp21 1) | 0 (0%) | 148 |
0.488 (1.00) |
0.647 (1.00) |
0.165 (1.00) |
0.0751 (1.00) |
0.851 (1.00) |
0.166 (1.00) |
0.371 (1.00) |
0.737 (1.00) |
0.588 (1.00) |
0.0302 (1.00) |
0.0992 (1.00) |
| Del Peak 46(Xq21 33) | 0 (0%) | 157 |
0.255 (1.00) |
0.732 (1.00) |
1 (1.00) |
0.563 (1.00) |
0.425 (1.00) |
0.333 (1.00) |
0.475 (1.00) |
0.211 (1.00) |
0.499 (1.00) |
0.259 (1.00) |
0.65 (1.00) |
Methods & Data
Input
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = STAD-TP.clin.merged.picked.txt
-
Number of patients = 180
-
Number of significantly arm-level cnvs = 75
-
Number of selected clinical features = 11
-
Exclude genes that fewer than K tumors have mutations, K = 3
Survival analysis
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
Student's t-test analysis
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
Fisher's exact test
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
Chi-square test
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
Q value calculation
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.
Download Results
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.
References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2013
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.