Rectum Adenocarcinoma: Correlation between copy number variation genes (focal) and selected clinical features
(primary solid tumor cohort)
(primary solid tumor cohort)
Maintained by TCGA GDAC Team
(Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 62 arm-level results and 11 clinical features across 162 patients, 2 significant findings detected with Q value < 0.25.
-
Del Peak 6(3q26.31) cnv correlated to 'Time to Death'.
-
Del Peak 30(18q21.2) cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
Results
Overview of the results
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, 2 significant findings 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 | Fisher's exact 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 | |
| Del Peak 6(3q26 31) | 17 (10%) | 145 |
8.16e-05 (0.0556) |
0.705 (1.00) |
0.0036 (1.00) |
0.0303 (1.00) |
0.216 (1.00) |
0.573 (1.00) |
0.2 (1.00) |
0.00346 (1.00) |
0.121 (1.00) |
0.0387 (1.00) |
0.251 (1.00) |
| Del Peak 30(18q21 2) | 143 (88%) | 19 |
0.653 (1.00) |
0.443 (1.00) |
1 (1.00) |
1 (1.00) |
0.00589 (1.00) |
0.0568 (1.00) |
0.208 (1.00) |
0.0231 (1.00) |
1 (1.00) |
0.673 (1.00) |
0.000153 (0.104) |
| Amp Peak 1(1q21 3) | 48 (30%) | 114 |
0.538 (1.00) |
0.951 (1.00) |
0.863 (1.00) |
1 (1.00) |
0.121 (1.00) |
0.441 (1.00) |
0.106 (1.00) |
0.835 (1.00) |
0.0639 (1.00) |
0.691 (1.00) |
0.227 (1.00) |
| Amp Peak 2(1q32 2) | 48 (30%) | 114 |
0.0492 (1.00) |
0.645 (1.00) |
1 (1.00) |
1 (1.00) |
0.0297 (1.00) |
0.264 (1.00) |
0.357 (1.00) |
0.604 (1.00) |
0.362 (1.00) |
0.64 (1.00) |
0.0174 (1.00) |
| Amp Peak 3(5q22 3) | 19 (12%) | 143 |
0.529 (1.00) |
0.383 (1.00) |
0.81 (1.00) |
0.37 (1.00) |
0.881 (1.00) |
0.772 (1.00) |
0.743 (1.00) |
0.784 (1.00) |
1 (1.00) |
0.806 (1.00) |
0.372 (1.00) |
| Amp Peak 4(6p21 1) | 52 (32%) | 110 |
0.178 (1.00) |
0.528 (1.00) |
0.4 (1.00) |
0.0626 (1.00) |
0.428 (1.00) |
0.00855 (1.00) |
0.00762 (1.00) |
0.0299 (1.00) |
0.0844 (1.00) |
0.0957 (1.00) |
0.0836 (1.00) |
| Amp Peak 5(8p11 23) | 52 (32%) | 110 |
0.0852 (1.00) |
0.264 (1.00) |
0.0635 (1.00) |
0.222 (1.00) |
0.216 (1.00) |
0.457 (1.00) |
0.305 (1.00) |
0.223 (1.00) |
1 (1.00) |
0.0229 (1.00) |
0.289 (1.00) |
| Amp Peak 6(8p11 21) | 69 (43%) | 93 |
0.478 (1.00) |
0.541 (1.00) |
0.637 (1.00) |
0.154 (1.00) |
0.408 (1.00) |
0.814 (1.00) |
0.191 (1.00) |
0.074 (1.00) |
0.241 (1.00) |
0.00288 (1.00) |
0.574 (1.00) |
| Amp Peak 7(8q24 21) | 107 (66%) | 55 |
0.693 (1.00) |
0.228 (1.00) |
0.868 (1.00) |
0.0326 (1.00) |
0.49 (1.00) |
0.671 (1.00) |
0.533 (1.00) |
0.284 (1.00) |
0.665 (1.00) |
0.372 (1.00) |
0.763 (1.00) |
| Amp Peak 8(10q22 2) | 11 (7%) | 151 |
0.306 (1.00) |
0.686 (1.00) |
0.551 (1.00) |
0.592 (1.00) |
0.935 (1.00) |
0.914 (1.00) |
0.743 (1.00) |
0.969 (1.00) |
0.349 (1.00) |
1 (1.00) |
0.939 (1.00) |
| Amp Peak 9(11p15 5) | 43 (27%) | 119 |
0.607 (1.00) |
0.969 (1.00) |
1 (1.00) |
0.188 (1.00) |
0.907 (1.00) |
0.195 (1.00) |
0.803 (1.00) |
0.258 (1.00) |
0.656 (1.00) |
0.938 (1.00) |
0.685 (1.00) |
| Amp Peak 10(11q13 3) | 26 (16%) | 136 |
0.456 (1.00) |
0.0577 (1.00) |
1 (1.00) |
0.697 (1.00) |
0.494 (1.00) |
0.361 (1.00) |
0.288 (1.00) |
0.104 (1.00) |
0.591 (1.00) |
0.66 (1.00) |
0.0272 (1.00) |
| Amp Peak 11(12p13 33) | 41 (25%) | 121 |
0.984 (1.00) |
0.246 (1.00) |
0.589 (1.00) |
0.308 (1.00) |
0.418 (1.00) |
0.546 (1.00) |
0.105 (1.00) |
0.633 (1.00) |
0.171 (1.00) |
0.274 (1.00) |
0.339 (1.00) |
| Amp Peak 12(12p12 1) | 40 (25%) | 122 |
0.702 (1.00) |
0.334 (1.00) |
0.716 (1.00) |
0.191 (1.00) |
0.373 (1.00) |
0.516 (1.00) |
0.0872 (1.00) |
0.446 (1.00) |
0.161 (1.00) |
0.219 (1.00) |
0.102 (1.00) |
| Amp Peak 13(13q12 13) | 121 (75%) | 41 |
0.0417 (1.00) |
0.113 (1.00) |
0.718 (1.00) |
0.00387 (1.00) |
0.068 (1.00) |
0.0187 (1.00) |
0.254 (1.00) |
0.258 (1.00) |
0.171 (1.00) |
1 (1.00) |
0.524 (1.00) |
| Amp Peak 14(13q12 2) | 120 (74%) | 42 |
0.052 (1.00) |
0.0514 (1.00) |
0.369 (1.00) |
0.00467 (1.00) |
0.0663 (1.00) |
0.027 (1.00) |
0.306 (1.00) |
0.307 (1.00) |
0.181 (1.00) |
1 (1.00) |
0.524 (1.00) |
| Amp Peak 15(13q22 1) | 117 (72%) | 45 |
0.202 (1.00) |
0.337 (1.00) |
0.482 (1.00) |
0.00132 (0.894) |
0.202 (1.00) |
0.139 (1.00) |
0.289 (1.00) |
0.433 (1.00) |
0.67 (1.00) |
0.801 (1.00) |
0.861 (1.00) |
| Amp Peak 16(15q26 1) | 15 (9%) | 147 |
0.854 (1.00) |
0.944 (1.00) |
0.106 (1.00) |
0.362 (1.00) |
0.221 (1.00) |
0.423 (1.00) |
0.446 (1.00) |
0.572 (1.00) |
0.0967 (1.00) |
0.375 (1.00) |
0.487 (1.00) |
| Amp Peak 17(16p11 2) | 45 (28%) | 117 |
0.183 (1.00) |
0.323 (1.00) |
0.862 (1.00) |
0.0205 (1.00) |
0.607 (1.00) |
0.146 (1.00) |
0.0837 (1.00) |
0.371 (1.00) |
0.67 (1.00) |
0.0597 (1.00) |
0.907 (1.00) |
| Amp Peak 18(17q12) | 43 (27%) | 119 |
0.653 (1.00) |
0.676 (1.00) |
0.215 (1.00) |
0.517 (1.00) |
0.725 (1.00) |
0.364 (1.00) |
0.335 (1.00) |
0.429 (1.00) |
0.343 (1.00) |
0.173 (1.00) |
0.31 (1.00) |
| Amp Peak 19(17q24 1) | 37 (23%) | 125 |
0.659 (1.00) |
0.423 (1.00) |
1 (1.00) |
0.0401 (1.00) |
0.258 (1.00) |
0.266 (1.00) |
0.192 (1.00) |
0.204 (1.00) |
0.338 (1.00) |
0.221 (1.00) |
0.206 (1.00) |
| Amp Peak 20(19p13 2) | 32 (20%) | 130 |
0.0245 (1.00) |
0.451 (1.00) |
0.693 (1.00) |
0.0717 (1.00) |
0.228 (1.00) |
0.545 (1.00) |
0.578 (1.00) |
0.709 (1.00) |
0.599 (1.00) |
0.511 (1.00) |
0.554 (1.00) |
| Amp Peak 21(20q11 21) | 143 (88%) | 19 |
0.209 (1.00) |
0.099 (1.00) |
1 (1.00) |
0.000738 (0.499) |
0.55 (1.00) |
0.0956 (1.00) |
0.547 (1.00) |
0.0969 (1.00) |
0.533 (1.00) |
0.581 (1.00) |
0.486 (1.00) |
| Amp Peak 22(20q11 23) | 144 (89%) | 18 |
0.211 (1.00) |
0.179 (1.00) |
1 (1.00) |
0.000498 (0.338) |
0.603 (1.00) |
0.0293 (1.00) |
0.433 (1.00) |
0.0857 (1.00) |
0.513 (1.00) |
0.581 (1.00) |
0.486 (1.00) |
| Amp Peak 23(20q13 31) | 145 (90%) | 17 |
0.217 (1.00) |
0.239 (1.00) |
0.8 (1.00) |
0.000498 (0.338) |
0.614 (1.00) |
0.0489 (1.00) |
0.493 (1.00) |
0.139 (1.00) |
0.492 (1.00) |
0.55 (1.00) |
0.446 (1.00) |
| Amp Peak 24(Xp22 2) | 33 (20%) | 129 |
0.945 (1.00) |
0.427 (1.00) |
0.0771 (1.00) |
0.303 (1.00) |
0.699 (1.00) |
0.654 (1.00) |
0.465 (1.00) |
0.598 (1.00) |
0.348 (1.00) |
0.273 (1.00) |
0.43 (1.00) |
| Amp Peak 25(Xq27 3) | 38 (23%) | 124 |
0.459 (1.00) |
0.225 (1.00) |
0.356 (1.00) |
0.3 (1.00) |
0.35 (1.00) |
0.743 (1.00) |
0.667 (1.00) |
0.645 (1.00) |
0.337 (1.00) |
0.685 (1.00) |
0.806 (1.00) |
| Del Peak 1(1p36 11) | 71 (44%) | 91 |
0.939 (1.00) |
0.617 (1.00) |
0.751 (1.00) |
0.56 (1.00) |
0.102 (1.00) |
0.215 (1.00) |
0.393 (1.00) |
0.643 (1.00) |
1 (1.00) |
0.327 (1.00) |
0.0468 (1.00) |
| Del Peak 2(1p33) | 49 (30%) | 113 |
0.522 (1.00) |
0.652 (1.00) |
1 (1.00) |
0.11 (1.00) |
0.528 (1.00) |
0.229 (1.00) |
0.76 (1.00) |
0.637 (1.00) |
0.368 (1.00) |
0.547 (1.00) |
0.649 (1.00) |
| Del Peak 3(1p13 2) | 51 (31%) | 111 |
0.944 (1.00) |
0.646 (1.00) |
0.735 (1.00) |
0.347 (1.00) |
0.147 (1.00) |
0.779 (1.00) |
0.499 (1.00) |
0.182 (1.00) |
0.38 (1.00) |
0.688 (1.00) |
0.245 (1.00) |
| Del Peak 4(2p12) | 17 (10%) | 145 |
0.498 (1.00) |
0.175 (1.00) |
0.8 (1.00) |
1 (1.00) |
0.364 (1.00) |
0.653 (1.00) |
0.285 (1.00) |
0.252 (1.00) |
0.492 (1.00) |
1 (1.00) |
0.471 (1.00) |
| Del Peak 5(3p14 2) | 29 (18%) | 133 |
0.052 (1.00) |
0.811 (1.00) |
0.013 (1.00) |
0.456 (1.00) |
0.196 (1.00) |
0.943 (1.00) |
0.285 (1.00) |
0.0402 (1.00) |
0.292 (1.00) |
0.0853 (1.00) |
0.367 (1.00) |
| Del Peak 7(4p13) | 58 (36%) | 104 |
0.215 (1.00) |
0.877 (1.00) |
0.0996 (1.00) |
0.38 (1.00) |
0.748 (1.00) |
0.327 (1.00) |
0.961 (1.00) |
0.673 (1.00) |
0.00177 (1.00) |
0.399 (1.00) |
0.675 (1.00) |
| Del Peak 8(4q22 1) | 72 (44%) | 90 |
0.107 (1.00) |
0.378 (1.00) |
0.153 (1.00) |
0.393 (1.00) |
0.287 (1.00) |
0.714 (1.00) |
0.857 (1.00) |
0.622 (1.00) |
0.0892 (1.00) |
0.215 (1.00) |
0.078 (1.00) |
| Del Peak 9(4q35 1) | 72 (44%) | 90 |
0.294 (1.00) |
0.645 (1.00) |
0.428 (1.00) |
0.15 (1.00) |
0.445 (1.00) |
0.56 (1.00) |
0.957 (1.00) |
0.791 (1.00) |
0.0892 (1.00) |
0.118 (1.00) |
0.306 (1.00) |
| Del Peak 10(5q11 2) | 49 (30%) | 113 |
0.708 (1.00) |
0.836 (1.00) |
0.233 (1.00) |
0.347 (1.00) |
0.927 (1.00) |
0.871 (1.00) |
0.336 (1.00) |
0.253 (1.00) |
0.01 (1.00) |
0.888 (1.00) |
0.708 (1.00) |
| Del Peak 11(5q22 2) | 55 (34%) | 107 |
0.58 (1.00) |
0.56 (1.00) |
0.405 (1.00) |
0.222 (1.00) |
0.495 (1.00) |
0.423 (1.00) |
0.903 (1.00) |
0.565 (1.00) |
0.0176 (1.00) |
1 (1.00) |
0.374 (1.00) |
| Del Peak 12(6p25 3) | 24 (15%) | 138 |
0.409 (1.00) |
0.391 (1.00) |
0.825 (1.00) |
0.386 (1.00) |
0.213 (1.00) |
0.38 (1.00) |
0.67 (1.00) |
0.08 (1.00) |
0.217 (1.00) |
0.66 (1.00) |
0.979 (1.00) |
| Del Peak 13(6q26) | 30 (19%) | 132 |
0.4 (1.00) |
0.852 (1.00) |
0.158 (1.00) |
0.0138 (1.00) |
0.392 (1.00) |
0.0813 (1.00) |
0.677 (1.00) |
0.533 (1.00) |
0.308 (1.00) |
0.588 (1.00) |
0.217 (1.00) |
| Del Peak 14(7q31 1) | 4 (2%) | 158 |
0.174 (1.00) |
1 (1.00) |
0.296 (1.00) |
1 (1.00) |
0.528 (1.00) |
1 (1.00) |
0.919 (1.00) |
1 (1.00) |
1 (1.00) |
0.548 (1.00) |
|
| Del Peak 15(8p23 2) | 100 (62%) | 62 |
0.71 (1.00) |
0.494 (1.00) |
0.872 (1.00) |
0.564 (1.00) |
0.201 (1.00) |
0.537 (1.00) |
0.799 (1.00) |
0.79 (1.00) |
0.0831 (1.00) |
0.386 (1.00) |
0.112 (1.00) |
| Del Peak 16(8p11 21) | 24 (15%) | 138 |
0.847 (1.00) |
0.184 (1.00) |
0.506 (1.00) |
1 (1.00) |
0.755 (1.00) |
0.812 (1.00) |
0.0829 (1.00) |
0.328 (1.00) |
0.217 (1.00) |
0.742 (1.00) |
0.123 (1.00) |
| Del Peak 17(10q21 1) | 37 (23%) | 125 |
0.498 (1.00) |
0.261 (1.00) |
0.574 (1.00) |
0.179 (1.00) |
0.828 (1.00) |
0.568 (1.00) |
0.107 (1.00) |
0.197 (1.00) |
0.0249 (1.00) |
0.109 (1.00) |
0.806 (1.00) |
| Del Peak 18(10q25 2) | 47 (29%) | 115 |
0.422 (1.00) |
0.369 (1.00) |
0.864 (1.00) |
0.0535 (1.00) |
0.148 (1.00) |
0.904 (1.00) |
0.563 (1.00) |
0.298 (1.00) |
0.00819 (1.00) |
0.204 (1.00) |
0.914 (1.00) |
| Del Peak 19(11q22 3) | 37 (23%) | 125 |
0.298 (1.00) |
0.453 (1.00) |
0.71 (1.00) |
0.0322 (1.00) |
0.635 (1.00) |
0.941 (1.00) |
0.0617 (1.00) |
0.272 (1.00) |
0.133 (1.00) |
0.164 (1.00) |
0.225 (1.00) |
| Del Peak 20(12p13 1) | 33 (20%) | 129 |
0.0863 (1.00) |
0.894 (1.00) |
0.845 (1.00) |
0.465 (1.00) |
0.891 (1.00) |
0.136 (1.00) |
0.28 (1.00) |
0.754 (1.00) |
1 (1.00) |
0.568 (1.00) |
0.488 (1.00) |
| Del Peak 21(12q21 33) | 28 (17%) | 134 |
0.626 (1.00) |
0.292 (1.00) |
1 (1.00) |
0.469 (1.00) |
0.697 (1.00) |
0.851 (1.00) |
0.677 (1.00) |
0.254 (1.00) |
0.277 (1.00) |
0.314 (1.00) |
0.707 (1.00) |
| Del Peak 22(14q11 2) | 67 (41%) | 95 |
0.23 (1.00) |
0.427 (1.00) |
0.427 (1.00) |
0.0746 (1.00) |
0.617 (1.00) |
0.291 (1.00) |
0.724 (1.00) |
0.334 (1.00) |
0.232 (1.00) |
0.101 (1.00) |
0.501 (1.00) |
| Del Peak 23(14q31 1) | 69 (43%) | 93 |
0.607 (1.00) |
0.84 (1.00) |
0.27 (1.00) |
0.00787 (1.00) |
0.16 (1.00) |
0.0566 (1.00) |
0.606 (1.00) |
0.265 (1.00) |
1 (1.00) |
0.436 (1.00) |
0.518 (1.00) |
| Del Peak 24(15q22 33) | 75 (46%) | 87 |
0.558 (1.00) |
0.86 (1.00) |
0.344 (1.00) |
1 (1.00) |
0.0115 (1.00) |
0.262 (1.00) |
0.741 (1.00) |
0.0732 (1.00) |
0.0966 (1.00) |
0.575 (1.00) |
0.0338 (1.00) |
| Del Peak 25(16p13 3) | 13 (8%) | 149 |
0.00338 (1.00) |
0.433 (1.00) |
1 (1.00) |
0.263 (1.00) |
0.788 (1.00) |
0.181 (1.00) |
0.797 (1.00) |
0.135 (1.00) |
1 (1.00) |
1 (1.00) |
0.309 (1.00) |
| Del Peak 26(16q23 1) | 23 (14%) | 139 |
0.925 (1.00) |
0.585 (1.00) |
0.826 (1.00) |
1 (1.00) |
0.606 (1.00) |
0.0144 (1.00) |
0.841 (1.00) |
0.327 (1.00) |
1 (1.00) |
1 (1.00) |
0.072 (1.00) |
| Del Peak 27(17p12) | 110 (68%) | 52 |
0.4 (1.00) |
0.0943 (1.00) |
0.866 (1.00) |
0.122 (1.00) |
0.0153 (1.00) |
0.893 (1.00) |
0.88 (1.00) |
0.211 (1.00) |
1 (1.00) |
0.854 (1.00) |
0.73 (1.00) |
| Del Peak 28(17p11 2) | 102 (63%) | 60 |
0.775 (1.00) |
0.201 (1.00) |
0.514 (1.00) |
0.0783 (1.00) |
0.0832 (1.00) |
0.693 (1.00) |
0.357 (1.00) |
0.598 (1.00) |
0.671 (1.00) |
0.862 (1.00) |
0.689 (1.00) |
| Del Peak 29(17q25 3) | 24 (15%) | 138 |
0.103 (1.00) |
0.696 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.366 (1.00) |
0.828 (1.00) |
0.13 (1.00) |
0.369 (1.00) |
0.217 (1.00) |
0.102 (1.00) |
0.627 (1.00) |
| Del Peak 31(18q22 1) | 138 (85%) | 24 |
0.653 (1.00) |
0.227 (1.00) |
0.825 (1.00) |
0.397 (1.00) |
0.0492 (1.00) |
0.337 (1.00) |
0.567 (1.00) |
0.126 (1.00) |
0.593 (1.00) |
0.585 (1.00) |
0.00206 (1.00) |
| Del Peak 32(19p13 3) | 38 (23%) | 124 |
0.816 (1.00) |
0.795 (1.00) |
1 (1.00) |
0.734 (1.00) |
0.297 (1.00) |
0.562 (1.00) |
0.251 (1.00) |
0.736 (1.00) |
1 (1.00) |
0.778 (1.00) |
0.693 (1.00) |
| Del Peak 33(20p12 1) | 60 (37%) | 102 |
0.131 (1.00) |
0.23 (1.00) |
0.257 (1.00) |
1 (1.00) |
0.85 (1.00) |
0.88 (1.00) |
0.473 (1.00) |
0.839 (1.00) |
0.0855 (1.00) |
0.466 (1.00) |
0.557 (1.00) |
| Del Peak 34(20p12 1) | 60 (37%) | 102 |
0.131 (1.00) |
0.23 (1.00) |
0.257 (1.00) |
1 (1.00) |
0.85 (1.00) |
0.88 (1.00) |
0.473 (1.00) |
0.839 (1.00) |
0.0855 (1.00) |
0.466 (1.00) |
0.557 (1.00) |
| Del Peak 35(21q11 2) | 70 (43%) | 92 |
0.996 (1.00) |
0.454 (1.00) |
0.633 (1.00) |
0.24 (1.00) |
0.139 (1.00) |
0.322 (1.00) |
0.764 (1.00) |
0.594 (1.00) |
1 (1.00) |
0.501 (1.00) |
0.295 (1.00) |
| Del Peak 36(22q13 31) | 66 (41%) | 96 |
0.0572 (1.00) |
0.255 (1.00) |
0.339 (1.00) |
0.563 (1.00) |
0.28 (1.00) |
0.00822 (1.00) |
0.207 (1.00) |
0.331 (1.00) |
0.688 (1.00) |
0.246 (1.00) |
0.425 (1.00) |
| Del Peak 37(Xp22 33) | 33 (20%) | 129 |
0.626 (1.00) |
0.681 (1.00) |
0.845 (1.00) |
0.716 (1.00) |
0.699 (1.00) |
0.856 (1.00) |
0.596 (1.00) |
0.894 (1.00) |
1 (1.00) |
0.682 (1.00) |
0.787 (1.00) |
'Del Peak 6(3q26.31) mutation analysis' versus 'Time to Death'
P value = 8.16e-05 (logrank test), Q value = 0.056
Table S1. Gene #31: 'Del Peak 6(3q26.31) mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 125 | 11 | 0.2 - 121.1 (6.3) |
| DEL PEAK 6(3Q26.31) MUTATED | 15 | 3 | 0.2 - 38.9 (2.8) |
| DEL PEAK 6(3Q26.31) WILD-TYPE | 110 | 8 | 0.4 - 121.1 (7.0) |
Figure S1. Get High-res Image Gene #31: 'Del Peak 6(3q26.31) mutation analysis' versus Clinical Feature #1: 'Time to Death'
'Del Peak 30(18q21.2) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'
P value = 0.000153 (t-test), Q value = 0.1
Table S2. Gene #55: 'Del Peak 30(18q21.2) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 149 | 2.7 (5.4) |
| DEL PEAK 30(18Q21.2) MUTATED | 130 | 2.9 (5.7) |
| DEL PEAK 30(18Q21.2) WILD-TYPE | 19 | 0.6 (1.4) |
Figure S2. Get High-res Image Gene #55: 'Del Peak 30(18q21.2) mutation analysis' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'
Methods & Data
Input
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = READ-TP.clin.merged.picked.txt
-
Number of patients = 162
-
Number of significantly arm-level cnvs = 62
-
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
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] 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.
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