Correlation between copy number variation genes (focal events) and selected clinical features
Rectum Adenocarcinoma (Primary solid tumor)
17 October 2014
|
analyses__2014_10_17
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
(2014):
Correlation between copy number variation genes (focal events) and selected clinical features.
Broad Institute of MIT and Harvard.
doi:10.7908/C1JS9PCK
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 59 focal events and 12 clinical features across 165 patients, no significant finding detected with Q value < 0.25.
-
No focal 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 59 focal events and 12 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 |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
RACE | ||
| nCNV (%) | nWild-Type | logrank test | Wilcoxon-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 | Wilcoxon-test | Fisher's exact test | |
| amp 1q21 3 | 48 (29%) | 117 |
0.708 (1.00) |
0.646 (1.00) |
0.878 (1.00) |
0.104 (1.00) |
0.47 (1.00) |
0.0978 (1.00) |
0.734 (1.00) |
1 (1.00) |
0.06 (1.00) |
0.582 (1.00) |
0.507 (1.00) |
0.172 (1.00) |
| amp 1q32 2 | 48 (29%) | 117 |
0.549 (1.00) |
0.976 (1.00) |
0.756 (1.00) |
0.0235 (1.00) |
0.278 (1.00) |
0.344 (1.00) |
1 (1.00) |
1 (1.00) |
0.358 (1.00) |
0.573 (1.00) |
0.126 (1.00) |
0.119 (1.00) |
| amp 5q22 3 | 20 (12%) | 145 |
0.172 (1.00) |
0.298 (1.00) |
0.677 (1.00) |
0.885 (1.00) |
0.853 (1.00) |
0.75 (1.00) |
0.637 (1.00) |
0.374 (1.00) |
1 (1.00) |
0.84 (1.00) |
0.737 (1.00) |
1 (1.00) |
| amp 6p21 1 | 54 (33%) | 111 |
0.759 (1.00) |
0.861 (1.00) |
0.143 (1.00) |
0.416 (1.00) |
0.00655 (1.00) |
0.00894 (1.00) |
0.406 (1.00) |
0.062 (1.00) |
0.0903 (1.00) |
0.174 (1.00) |
0.0117 (1.00) |
0.18 (1.00) |
| amp 8p11 23 | 53 (32%) | 112 |
0.0273 (1.00) |
0.355 (1.00) |
0.131 (1.00) |
0.221 (1.00) |
0.323 (1.00) |
0.304 (1.00) |
0.0941 (1.00) |
0.222 (1.00) |
1 (1.00) |
0.00948 (1.00) |
0.147 (1.00) |
1 (1.00) |
| amp 8p11 21 | 70 (42%) | 95 |
0.169 (1.00) |
0.664 (1.00) |
0.143 (1.00) |
0.412 (1.00) |
0.673 (1.00) |
0.191 (1.00) |
0.753 (1.00) |
0.156 (1.00) |
0.243 (1.00) |
0.0012 (0.844) |
0.346 (1.00) |
0.825 (1.00) |
| amp 8q24 21 | 109 (66%) | 56 |
0.168 (1.00) |
0.343 (1.00) |
0.168 (1.00) |
0.496 (1.00) |
0.624 (1.00) |
0.539 (1.00) |
0.743 (1.00) |
0.0328 (1.00) |
0.665 (1.00) |
0.408 (1.00) |
0.706 (1.00) |
0.327 (1.00) |
| amp 10q22 2 | 11 (7%) | 154 |
0.449 (1.00) |
0.702 (1.00) |
0.848 (1.00) |
0.934 (1.00) |
0.915 (1.00) |
0.737 (1.00) |
0.756 (1.00) |
0.585 (1.00) |
0.343 (1.00) |
1 (1.00) |
0.619 (1.00) |
1 (1.00) |
| amp 11p15 5 | 45 (27%) | 120 |
0.326 (1.00) |
0.913 (1.00) |
0.616 (1.00) |
0.964 (1.00) |
0.189 (1.00) |
0.799 (1.00) |
1 (1.00) |
0.114 (1.00) |
0.665 (1.00) |
1 (1.00) |
0.208 (1.00) |
0.102 (1.00) |
| amp 11q13 3 | 28 (17%) | 137 |
0.628 (1.00) |
0.0462 (1.00) |
0.678 (1.00) |
0.606 (1.00) |
0.355 (1.00) |
0.357 (1.00) |
1 (1.00) |
0.468 (1.00) |
0.591 (1.00) |
0.26 (1.00) |
0.297 (1.00) |
0.00503 (1.00) |
| amp 12p13 33 | 41 (25%) | 124 |
0.806 (1.00) |
0.256 (1.00) |
0.781 (1.00) |
0.383 (1.00) |
0.601 (1.00) |
0.0963 (1.00) |
0.588 (1.00) |
0.305 (1.00) |
0.163 (1.00) |
0.503 (1.00) |
0.62 (1.00) |
0.108 (1.00) |
| amp 12p12 1 | 40 (24%) | 125 |
0.73 (1.00) |
0.289 (1.00) |
0.6 (1.00) |
0.327 (1.00) |
0.597 (1.00) |
0.0763 (1.00) |
0.716 (1.00) |
0.183 (1.00) |
0.154 (1.00) |
0.324 (1.00) |
0.605 (1.00) |
0.0927 (1.00) |
| amp 13q12 13 | 126 (76%) | 39 |
0.0887 (1.00) |
0.188 (1.00) |
0.0698 (1.00) |
0.0645 (1.00) |
0.0116 (1.00) |
0.318 (1.00) |
0.717 (1.00) |
0.00229 (1.00) |
0.627 (1.00) |
1 (1.00) |
0.0076 (1.00) |
0.121 (1.00) |
| amp 13q12 2 | 125 (76%) | 40 |
0.263 (1.00) |
0.0964 (1.00) |
0.0895 (1.00) |
0.0643 (1.00) |
0.0181 (1.00) |
0.362 (1.00) |
0.368 (1.00) |
0.00279 (1.00) |
0.633 (1.00) |
1 (1.00) |
0.0076 (1.00) |
0.154 (1.00) |
| amp 13q22 1 | 120 (73%) | 45 |
0.755 (1.00) |
0.663 (1.00) |
0.857 (1.00) |
0.194 (1.00) |
0.154 (1.00) |
0.304 (1.00) |
0.485 (1.00) |
0.00113 (0.798) |
0.665 (1.00) |
0.625 (1.00) |
0.0581 (1.00) |
0.476 (1.00) |
| amp 15q26 1 | 13 (8%) | 152 |
0.969 (1.00) |
0.818 (1.00) |
0.446 (1.00) |
0.461 (1.00) |
0.271 (1.00) |
0.541 (1.00) |
0.263 (1.00) |
0.288 (1.00) |
0.072 (1.00) |
0.342 (1.00) |
0.378 (1.00) |
1 (1.00) |
| amp 16p11 2 | 47 (28%) | 118 |
0.61 (1.00) |
0.673 (1.00) |
0.082 (1.00) |
0.608 (1.00) |
0.0773 (1.00) |
0.0822 (1.00) |
0.607 (1.00) |
0.0109 (1.00) |
0.354 (1.00) |
0.0395 (1.00) |
0.144 (1.00) |
0.0979 (1.00) |
| amp 17q12 | 46 (28%) | 119 |
0.155 (1.00) |
0.33 (1.00) |
0.67 (1.00) |
0.85 (1.00) |
0.271 (1.00) |
0.432 (1.00) |
0.299 (1.00) |
0.35 (1.00) |
0.187 (1.00) |
0.136 (1.00) |
0.97 (1.00) |
0.0737 (1.00) |
| amp 17q24 1 | 39 (24%) | 126 |
0.317 (1.00) |
0.25 (1.00) |
0.37 (1.00) |
0.266 (1.00) |
0.264 (1.00) |
0.223 (1.00) |
1 (1.00) |
0.0392 (1.00) |
0.337 (1.00) |
0.199 (1.00) |
0.756 (1.00) |
0.731 (1.00) |
| amp 19p13 2 | 36 (22%) | 129 |
0.397 (1.00) |
0.887 (1.00) |
0.296 (1.00) |
0.216 (1.00) |
0.68 (1.00) |
0.549 (1.00) |
0.706 (1.00) |
0.0412 (1.00) |
0.341 (1.00) |
0.721 (1.00) |
0.488 (1.00) |
0.0183 (1.00) |
| amp 20q11 21 | 146 (88%) | 19 |
0.358 (1.00) |
0.0825 (1.00) |
0.22 (1.00) |
0.56 (1.00) |
0.0989 (1.00) |
0.575 (1.00) |
1 (1.00) |
0.000663 (0.467) |
0.526 (1.00) |
0.71 (1.00) |
0.156 (1.00) |
0.0979 (1.00) |
| amp 20q11 23 | 147 (89%) | 18 |
0.367 (1.00) |
0.169 (1.00) |
0.273 (1.00) |
0.593 (1.00) |
0.0372 (1.00) |
0.453 (1.00) |
1 (1.00) |
0.000447 (0.316) |
0.506 (1.00) |
0.709 (1.00) |
0.156 (1.00) |
0.0851 (1.00) |
| amp 20q13 31 | 148 (90%) | 17 |
0.387 (1.00) |
0.26 (1.00) |
0.31 (1.00) |
0.609 (1.00) |
0.063 (1.00) |
0.485 (1.00) |
0.799 (1.00) |
0.000447 (0.316) |
0.485 (1.00) |
0.591 (1.00) |
0.221 (1.00) |
0.117 (1.00) |
| amp xp22 2 | 32 (19%) | 133 |
0.573 (1.00) |
0.895 (1.00) |
0.0296 (1.00) |
0.858 (1.00) |
0.537 (1.00) |
0.379 (1.00) |
0.238 (1.00) |
0.469 (1.00) |
0.598 (1.00) |
0.32 (1.00) |
0.782 (1.00) |
0.0589 (1.00) |
| del 1p36 11 | 75 (45%) | 90 |
0.781 (1.00) |
0.615 (1.00) |
0.688 (1.00) |
0.107 (1.00) |
0.329 (1.00) |
0.462 (1.00) |
0.877 (1.00) |
0.566 (1.00) |
1 (1.00) |
0.711 (1.00) |
0.0557 (1.00) |
0.00833 (1.00) |
| del 1p33 | 53 (32%) | 112 |
0.535 (1.00) |
0.51 (1.00) |
0.919 (1.00) |
0.532 (1.00) |
0.411 (1.00) |
0.809 (1.00) |
0.868 (1.00) |
0.0643 (1.00) |
0.387 (1.00) |
0.855 (1.00) |
0.491 (1.00) |
0.0183 (1.00) |
| del 1p13 2 | 54 (33%) | 111 |
0.503 (1.00) |
0.644 (1.00) |
0.161 (1.00) |
0.214 (1.00) |
0.816 (1.00) |
0.471 (1.00) |
1 (1.00) |
0.227 (1.00) |
0.394 (1.00) |
0.954 (1.00) |
0.315 (1.00) |
0.193 (1.00) |
| del 2p12 | 13 (8%) | 152 |
0.768 (1.00) |
0.0264 (1.00) |
0.822 (1.00) |
1 (1.00) |
0.438 (1.00) |
0.238 (1.00) |
0.577 (1.00) |
1 (1.00) |
0.394 (1.00) |
1 (1.00) |
0.766 (1.00) |
1 (1.00) |
| del 3p14 2 | 31 (19%) | 134 |
0.206 (1.00) |
0.573 (1.00) |
0.156 (1.00) |
0.251 (1.00) |
0.777 (1.00) |
0.352 (1.00) |
0.0158 (1.00) |
0.702 (1.00) |
0.314 (1.00) |
0.118 (1.00) |
0.621 (1.00) |
0.0679 (1.00) |
| del 3q26 31 | 18 (11%) | 147 |
0.332 (1.00) |
0.404 (1.00) |
0.0833 (1.00) |
0.722 (1.00) |
0.352 (1.00) |
0.082 (1.00) |
0.0437 (1.00) |
0.0043 (1.00) |
0.506 (1.00) |
0.26 (1.00) |
0.156 (1.00) |
0.129 (1.00) |
| del 4p13 | 60 (36%) | 105 |
0.223 (1.00) |
0.704 (1.00) |
0.796 (1.00) |
0.771 (1.00) |
0.351 (1.00) |
1 (1.00) |
0.147 (1.00) |
0.377 (1.00) |
0.00196 (1.00) |
0.654 (1.00) |
0.297 (1.00) |
0.781 (1.00) |
| del 4q22 1 | 73 (44%) | 92 |
0.144 (1.00) |
0.46 (1.00) |
0.484 (1.00) |
0.431 (1.00) |
0.595 (1.00) |
0.89 (1.00) |
0.16 (1.00) |
0.395 (1.00) |
0.0886 (1.00) |
0.494 (1.00) |
0.302 (1.00) |
1 (1.00) |
| del 4q35 1 | 72 (44%) | 93 |
0.484 (1.00) |
0.779 (1.00) |
0.373 (1.00) |
0.538 (1.00) |
0.385 (1.00) |
1 (1.00) |
0.348 (1.00) |
0.156 (1.00) |
0.0868 (1.00) |
0.365 (1.00) |
0.251 (1.00) |
0.427 (1.00) |
| del 5q12 1 | 53 (32%) | 112 |
0.799 (1.00) |
0.555 (1.00) |
0.739 (1.00) |
0.928 (1.00) |
0.975 (1.00) |
0.49 (1.00) |
0.407 (1.00) |
0.224 (1.00) |
0.0135 (1.00) |
0.906 (1.00) |
0.962 (1.00) |
0.178 (1.00) |
| del 5q22 2 | 59 (36%) | 106 |
0.706 (1.00) |
0.366 (1.00) |
0.656 (1.00) |
0.464 (1.00) |
0.571 (1.00) |
0.961 (1.00) |
0.416 (1.00) |
0.135 (1.00) |
0.0225 (1.00) |
0.881 (1.00) |
0.67 (1.00) |
0.0227 (1.00) |
| del 6p25 3 | 24 (15%) | 141 |
0.613 (1.00) |
0.346 (1.00) |
0.356 (1.00) |
0.232 (1.00) |
0.407 (1.00) |
0.664 (1.00) |
0.665 (1.00) |
0.383 (1.00) |
0.211 (1.00) |
0.691 (1.00) |
0.283 (1.00) |
0.12 (1.00) |
| del 6q26 | 30 (18%) | 135 |
0.484 (1.00) |
0.963 (1.00) |
0.46 (1.00) |
0.405 (1.00) |
0.104 (1.00) |
0.623 (1.00) |
0.157 (1.00) |
0.0125 (1.00) |
0.299 (1.00) |
0.62 (1.00) |
0.557 (1.00) |
0.135 (1.00) |
| del 7q31 1 | 4 (2%) | 161 |
0.679 (1.00) |
0.215 (1.00) |
0.917 (1.00) |
1 (1.00) |
0.532 (1.00) |
1 (1.00) |
1 (1.00) |
0.291 (1.00) |
1 (1.00) |
1 (1.00) |
0.695 (1.00) |
|
| del 8p23 2 | 100 (61%) | 65 |
0.462 (1.00) |
0.26 (1.00) |
0.409 (1.00) |
0.202 (1.00) |
0.537 (1.00) |
0.73 (1.00) |
1 (1.00) |
0.769 (1.00) |
0.405 (1.00) |
0.297 (1.00) |
0.229 (1.00) |
1 (1.00) |
| del 8p11 21 | 45 (27%) | 120 |
0.747 (1.00) |
0.503 (1.00) |
0.241 (1.00) |
0.897 (1.00) |
0.918 (1.00) |
0.661 (1.00) |
0.162 (1.00) |
0.75 (1.00) |
0.665 (1.00) |
0.57 (1.00) |
0.583 (1.00) |
1 (1.00) |
| del 10q21 1 | 41 (25%) | 124 |
0.98 (1.00) |
0.578 (1.00) |
0.613 (1.00) |
0.714 (1.00) |
0.812 (1.00) |
0.357 (1.00) |
0.588 (1.00) |
0.0929 (1.00) |
0.163 (1.00) |
0.746 (1.00) |
0.719 (1.00) |
0.693 (1.00) |
| del 10q25 2 | 48 (29%) | 117 |
0.223 (1.00) |
0.455 (1.00) |
0.611 (1.00) |
0.162 (1.00) |
0.678 (1.00) |
0.386 (1.00) |
0.864 (1.00) |
0.0542 (1.00) |
0.06 (1.00) |
0.287 (1.00) |
0.964 (1.00) |
1 (1.00) |
| del 11q22 3 | 38 (23%) | 127 |
0.456 (1.00) |
0.862 (1.00) |
0.357 (1.00) |
0.453 (1.00) |
0.939 (1.00) |
0.0524 (1.00) |
0.584 (1.00) |
0.0341 (1.00) |
0.136 (1.00) |
0.179 (1.00) |
0.978 (1.00) |
0.0883 (1.00) |
| del 12p13 1 | 33 (20%) | 132 |
0.118 (1.00) |
0.977 (1.00) |
0.366 (1.00) |
0.935 (1.00) |
0.126 (1.00) |
0.261 (1.00) |
0.846 (1.00) |
0.465 (1.00) |
1 (1.00) |
0.594 (1.00) |
0.654 (1.00) |
1 (1.00) |
| del 12q22 | 26 (16%) | 139 |
0.509 (1.00) |
0.215 (1.00) |
0.13 (1.00) |
0.847 (1.00) |
1 (1.00) |
0.779 (1.00) |
1 (1.00) |
0.694 (1.00) |
0.24 (1.00) |
0.427 (1.00) |
1 (1.00) |
0.661 (1.00) |
| del 14q11 2 | 70 (42%) | 95 |
0.916 (1.00) |
0.541 (1.00) |
0.582 (1.00) |
0.647 (1.00) |
0.391 (1.00) |
0.694 (1.00) |
0.753 (1.00) |
0.0431 (1.00) |
0.403 (1.00) |
0.092 (1.00) |
0.717 (1.00) |
0.41 (1.00) |
| del 14q31 1 | 72 (44%) | 93 |
0.941 (1.00) |
0.962 (1.00) |
0.257 (1.00) |
0.187 (1.00) |
0.0825 (1.00) |
0.592 (1.00) |
0.531 (1.00) |
0.00712 (1.00) |
0.697 (1.00) |
0.431 (1.00) |
0.73 (1.00) |
0.406 (1.00) |
| del 15q21 1 | 79 (48%) | 86 |
0.395 (1.00) |
0.876 (1.00) |
0.455 (1.00) |
0.393 (1.00) |
0.52 (1.00) |
0.768 (1.00) |
0.211 (1.00) |
1 (1.00) |
0.428 (1.00) |
0.819 (1.00) |
0.116 (1.00) |
0.419 (1.00) |
| del 15q22 33 | 77 (47%) | 88 |
0.989 (1.00) |
0.941 (1.00) |
0.149 (1.00) |
0.029 (1.00) |
0.273 (1.00) |
0.756 (1.00) |
0.531 (1.00) |
1 (1.00) |
0.0985 (1.00) |
0.602 (1.00) |
0.0461 (1.00) |
1 (1.00) |
| del 16p13 3 | 13 (8%) | 152 |
0.292 (1.00) |
0.699 (1.00) |
0.146 (1.00) |
0.75 (1.00) |
0.182 (1.00) |
0.793 (1.00) |
1 (1.00) |
0.255 (1.00) |
1 (1.00) |
1 (1.00) |
0.953 (1.00) |
1 (1.00) |
| del 16q23 1 | 23 (14%) | 142 |
0.385 (1.00) |
0.498 (1.00) |
0.0303 (1.00) |
0.599 (1.00) |
0.0182 (1.00) |
0.788 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.308 (1.00) |
0.648 (1.00) |
| del 17p11 2 | 113 (68%) | 52 |
0.612 (1.00) |
0.0672 (1.00) |
0.707 (1.00) |
0.0158 (1.00) |
0.854 (1.00) |
0.935 (1.00) |
0.614 (1.00) |
0.118 (1.00) |
1 (1.00) |
0.909 (1.00) |
0.815 (1.00) |
0.58 (1.00) |
| del 18q21 2 | 145 (88%) | 20 |
0.705 (1.00) |
0.418 (1.00) |
0.107 (1.00) |
0.00774 (1.00) |
0.107 (1.00) |
0.193 (1.00) |
1 (1.00) |
0.656 (1.00) |
1 (1.00) |
0.557 (1.00) |
0.0368 (1.00) |
1 (1.00) |
| del 18q22 1 | 141 (85%) | 24 |
0.73 (1.00) |
0.361 (1.00) |
0.0962 (1.00) |
0.0426 (1.00) |
0.355 (1.00) |
0.562 (1.00) |
0.665 (1.00) |
0.393 (1.00) |
0.594 (1.00) |
0.773 (1.00) |
0.128 (1.00) |
0.164 (1.00) |
| del 19p13 3 | 37 (22%) | 128 |
0.198 (1.00) |
0.848 (1.00) |
0.805 (1.00) |
0.361 (1.00) |
0.658 (1.00) |
0.234 (1.00) |
0.713 (1.00) |
0.3 (1.00) |
1 (1.00) |
0.856 (1.00) |
0.465 (1.00) |
0.258 (1.00) |
| del 20p12 1 | 49 (30%) | 116 |
0.00913 (1.00) |
0.612 (1.00) |
0.285 (1.00) |
0.954 (1.00) |
0.707 (1.00) |
0.765 (1.00) |
0.495 (1.00) |
0.535 (1.00) |
0.181 (1.00) |
0.689 (1.00) |
0.234 (1.00) |
0.109 (1.00) |
| del 21q11 2 | 73 (44%) | 92 |
0.681 (1.00) |
0.59 (1.00) |
0.495 (1.00) |
0.088 (1.00) |
0.384 (1.00) |
0.755 (1.00) |
0.64 (1.00) |
0.152 (1.00) |
1 (1.00) |
0.291 (1.00) |
0.443 (1.00) |
1 (1.00) |
| del 22q13 31 | 68 (41%) | 97 |
0.0786 (1.00) |
0.096 (1.00) |
0.324 (1.00) |
0.262 (1.00) |
0.0119 (1.00) |
0.237 (1.00) |
0.527 (1.00) |
0.562 (1.00) |
0.691 (1.00) |
0.517 (1.00) |
0.148 (1.00) |
1 (1.00) |
| del xp22 33 | 34 (21%) | 131 |
0.696 (1.00) |
0.609 (1.00) |
0.959 (1.00) |
0.714 (1.00) |
0.844 (1.00) |
0.598 (1.00) |
0.7 (1.00) |
0.719 (1.00) |
1 (1.00) |
0.848 (1.00) |
0.484 (1.00) |
1 (1.00) |
Methods & Data
Input
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = READ-TP.merged_data.txt
-
Number of patients = 165
-
Number of significantly focal cnvs = 59
-
Number of selected clinical features = 12
-
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
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
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.
References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] 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)
[3] 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 © 2015
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.