Correlation between copy number variations of arm-level result and selected clinical features
Esophageal Carcinoma (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 variations of arm-level result and selected clinical features.
Broad Institute of MIT and Harvard.
doi:10.7908/C1KW5DWT
Overview
Introduction
This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Summary
Testing the association between copy number variation 80 arm-level events and 9 clinical features across 150 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 80 arm-level events and 9 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 | NUMBERPACKYEARSSMOKED | 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 | Wilcoxon-test | Fisher's exact test | |
| 1p gain | 26 (17%) | 124 |
0.955 (1.00) |
0.0661 (1.00) |
0.183 (1.00) |
0.423 (1.00) |
0.631 (1.00) |
0.646 (1.00) |
1 (1.00) |
0.588 (1.00) |
0.485 (1.00) |
| 1q gain | 47 (31%) | 103 |
0.413 (1.00) |
0.156 (1.00) |
0.954 (1.00) |
0.465 (1.00) |
0.818 (1.00) |
0.481 (1.00) |
0.217 (1.00) |
0.55 (1.00) |
0.661 (1.00) |
| 2p gain | 47 (31%) | 103 |
0.0694 (1.00) |
0.0189 (1.00) |
0.635 (1.00) |
0.648 (1.00) |
0.897 (1.00) |
0.242 (1.00) |
0.217 (1.00) |
0.0721 (1.00) |
0.0165 (1.00) |
| 2q gain | 35 (23%) | 115 |
0.482 (1.00) |
0.0739 (1.00) |
0.697 (1.00) |
0.881 (1.00) |
0.957 (1.00) |
0.563 (1.00) |
0.407 (1.00) |
0.514 (1.00) |
0.298 (1.00) |
| 3p gain | 22 (15%) | 128 |
0.89 (1.00) |
0.229 (1.00) |
0.177 (1.00) |
0.649 (1.00) |
0.324 (1.00) |
0.26 (1.00) |
0.74 (1.00) |
0.153 (1.00) |
0.586 (1.00) |
| 3q gain | 63 (42%) | 87 |
0.936 (1.00) |
0.000789 (0.568) |
0.881 (1.00) |
0.196 (1.00) |
0.829 (1.00) |
0.879 (1.00) |
0.478 (1.00) |
0.413 (1.00) |
0.443 (1.00) |
| 4p gain | 12 (8%) | 138 |
0.0876 (1.00) |
0.528 (1.00) |
0.876 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.449 (1.00) |
0.592 (1.00) |
| 4q gain | 13 (9%) | 137 |
0.215 (1.00) |
0.44 (1.00) |
1 (1.00) |
0.491 (1.00) |
0.94 (1.00) |
0.566 (1.00) |
0.695 (1.00) |
0.601 (1.00) |
0.182 (1.00) |
| 5p gain | 60 (40%) | 90 |
0.383 (1.00) |
0.772 (1.00) |
0.123 (1.00) |
0.354 (1.00) |
0.168 (1.00) |
0.43 (1.00) |
0.236 (1.00) |
0.989 (1.00) |
1 (1.00) |
| 5q gain | 18 (12%) | 132 |
0.649 (1.00) |
0.436 (1.00) |
0.204 (1.00) |
0.639 (1.00) |
0.00996 (1.00) |
0.389 (1.00) |
0.72 (1.00) |
0.339 (1.00) |
0.303 (1.00) |
| 6p gain | 34 (23%) | 116 |
0.803 (1.00) |
0.183 (1.00) |
0.295 (1.00) |
0.697 (1.00) |
0.982 (1.00) |
0.165 (1.00) |
0.785 (1.00) |
1 (1.00) |
0.886 (1.00) |
| 6q gain | 28 (19%) | 122 |
0.669 (1.00) |
0.146 (1.00) |
0.116 (1.00) |
0.266 (1.00) |
0.561 (1.00) |
0.124 (1.00) |
0.368 (1.00) |
0.747 (1.00) |
1 (1.00) |
| 7p gain | 90 (60%) | 60 |
0.273 (1.00) |
0.373 (1.00) |
0.316 (1.00) |
0.0213 (1.00) |
0.248 (1.00) |
0.193 (1.00) |
0.0967 (1.00) |
0.339 (1.00) |
0.668 (1.00) |
| 7q gain | 72 (48%) | 78 |
0.897 (1.00) |
0.82 (1.00) |
0.533 (1.00) |
0.0617 (1.00) |
0.725 (1.00) |
0.104 (1.00) |
0.0191 (1.00) |
0.616 (1.00) |
0.583 (1.00) |
| 8p gain | 56 (37%) | 94 |
0.184 (1.00) |
0.932 (1.00) |
0.754 (1.00) |
0.35 (1.00) |
0.419 (1.00) |
0.242 (1.00) |
0.63 (1.00) |
0.442 (1.00) |
0.671 (1.00) |
| 8q gain | 81 (54%) | 69 |
0.503 (1.00) |
0.895 (1.00) |
0.224 (1.00) |
0.0385 (1.00) |
0.135 (1.00) |
0.385 (1.00) |
0.638 (1.00) |
0.43 (1.00) |
0.463 (1.00) |
| 9p gain | 12 (8%) | 138 |
0.432 (1.00) |
0.521 (1.00) |
0.943 (1.00) |
0.489 (1.00) |
0.138 (1.00) |
1 (1.00) |
1 (1.00) |
0.362 (1.00) |
0.274 (1.00) |
| 9q gain | 23 (15%) | 127 |
0.191 (1.00) |
0.451 (1.00) |
0.431 (1.00) |
0.169 (1.00) |
0.206 (1.00) |
0.892 (1.00) |
0.201 (1.00) |
0.161 (1.00) |
0.0454 (1.00) |
| 10p gain | 31 (21%) | 119 |
0.376 (1.00) |
0.757 (1.00) |
0.0573 (1.00) |
0.37 (1.00) |
0.364 (1.00) |
0.0379 (1.00) |
0.248 (1.00) |
0.826 (1.00) |
1 (1.00) |
| 10q gain | 24 (16%) | 126 |
0.831 (1.00) |
0.562 (1.00) |
0.0412 (1.00) |
0.299 (1.00) |
0.129 (1.00) |
0.0743 (1.00) |
0.2 (1.00) |
0.169 (1.00) |
0.597 (1.00) |
| 11p gain | 33 (22%) | 117 |
0.552 (1.00) |
0.371 (1.00) |
0.595 (1.00) |
0.176 (1.00) |
0.212 (1.00) |
0.239 (1.00) |
0.782 (1.00) |
0.0463 (1.00) |
0.617 (1.00) |
| 11q gain | 25 (17%) | 125 |
0.672 (1.00) |
0.0689 (1.00) |
0.683 (1.00) |
0.077 (1.00) |
0.0551 (1.00) |
0.602 (1.00) |
1 (1.00) |
0.296 (1.00) |
0.869 (1.00) |
| 12p gain | 46 (31%) | 104 |
0.361 (1.00) |
0.153 (1.00) |
0.17 (1.00) |
0.0995 (1.00) |
0.784 (1.00) |
0.055 (1.00) |
0.124 (1.00) |
0.281 (1.00) |
0.0181 (1.00) |
| 12q gain | 30 (20%) | 120 |
0.666 (1.00) |
0.466 (1.00) |
0.0434 (1.00) |
0.372 (1.00) |
0.31 (1.00) |
0.127 (1.00) |
0.25 (1.00) |
0.031 (1.00) |
0.156 (1.00) |
| 13q gain | 37 (25%) | 113 |
0.59 (1.00) |
0.577 (1.00) |
0.186 (1.00) |
0.0682 (1.00) |
0.177 (1.00) |
0.00528 (1.00) |
1 (1.00) |
0.182 (1.00) |
0.146 (1.00) |
| 14q gain | 38 (25%) | 112 |
0.133 (1.00) |
0.363 (1.00) |
0.987 (1.00) |
0.0119 (1.00) |
0.376 (1.00) |
0.844 (1.00) |
0.00207 (1.00) |
0.946 (1.00) |
0.134 (1.00) |
| 15q gain | 24 (16%) | 126 |
0.667 (1.00) |
0.804 (1.00) |
0.572 (1.00) |
0.896 (1.00) |
1 (1.00) |
0.695 (1.00) |
0.53 (1.00) |
0.0554 (1.00) |
0.846 (1.00) |
| 16p gain | 32 (21%) | 118 |
0.978 (1.00) |
0.878 (1.00) |
0.383 (1.00) |
0.132 (1.00) |
0.183 (1.00) |
0.71 (1.00) |
0.00765 (1.00) |
0.573 (1.00) |
0.0237 (1.00) |
| 16q gain | 28 (19%) | 122 |
0.356 (1.00) |
0.604 (1.00) |
0.197 (1.00) |
0.194 (1.00) |
0.332 (1.00) |
0.451 (1.00) |
0.0141 (1.00) |
0.818 (1.00) |
0.0187 (1.00) |
| 17p gain | 24 (16%) | 126 |
0.962 (1.00) |
0.29 (1.00) |
0.906 (1.00) |
0.504 (1.00) |
0.539 (1.00) |
0.497 (1.00) |
0.2 (1.00) |
0.509 (1.00) |
0.311 (1.00) |
| 17q gain | 36 (24%) | 114 |
0.617 (1.00) |
0.721 (1.00) |
0.46 (1.00) |
0.404 (1.00) |
0.209 (1.00) |
0.338 (1.00) |
0.107 (1.00) |
0.158 (1.00) |
0.107 (1.00) |
| 18p gain | 41 (27%) | 109 |
0.175 (1.00) |
0.311 (1.00) |
0.502 (1.00) |
0.986 (1.00) |
0.4 (1.00) |
1 (1.00) |
0.0634 (1.00) |
0.836 (1.00) |
0.297 (1.00) |
| 18q gain | 22 (15%) | 128 |
0.153 (1.00) |
0.512 (1.00) |
0.155 (1.00) |
0.503 (1.00) |
0.69 (1.00) |
1 (1.00) |
0.74 (1.00) |
0.582 (1.00) |
0.831 (1.00) |
| 19p gain | 21 (14%) | 129 |
0.923 (1.00) |
0.584 (1.00) |
0.96 (1.00) |
0.577 (1.00) |
0.016 (1.00) |
0.171 (1.00) |
0.0453 (1.00) |
0.979 (1.00) |
0.337 (1.00) |
| 19q gain | 31 (21%) | 119 |
0.904 (1.00) |
0.305 (1.00) |
0.59 (1.00) |
0.865 (1.00) |
0.261 (1.00) |
0.372 (1.00) |
0.0775 (1.00) |
0.52 (1.00) |
0.209 (1.00) |
| 20p gain | 88 (59%) | 62 |
0.371 (1.00) |
0.253 (1.00) |
0.848 (1.00) |
0.521 (1.00) |
0.514 (1.00) |
0.537 (1.00) |
0.34 (1.00) |
0.832 (1.00) |
0.322 (1.00) |
| 20q gain | 97 (65%) | 53 |
0.53 (1.00) |
0.426 (1.00) |
0.912 (1.00) |
0.0143 (1.00) |
0.184 (1.00) |
0.552 (1.00) |
0.225 (1.00) |
0.885 (1.00) |
0.0974 (1.00) |
| 21q gain | 14 (9%) | 136 |
0.33 (1.00) |
0.737 (1.00) |
0.762 (1.00) |
0.485 (1.00) |
0.943 (1.00) |
1 (1.00) |
0.693 (1.00) |
0.127 (1.00) |
0.0672 (1.00) |
| 22q gain | 23 (15%) | 127 |
0.458 (1.00) |
0.0722 (1.00) |
0.645 (1.00) |
0.12 (1.00) |
0.0188 (1.00) |
0.89 (1.00) |
0.743 (1.00) |
0.693 (1.00) |
0.00136 (0.978) |
| xq gain | 28 (19%) | 122 |
0.722 (1.00) |
0.883 (1.00) |
0.798 (1.00) |
0.231 (1.00) |
0.269 (1.00) |
0.0861 (1.00) |
0.127 (1.00) |
0.584 (1.00) |
0.108 (1.00) |
| 1p loss | 31 (21%) | 119 |
0.941 (1.00) |
0.634 (1.00) |
0.11 (1.00) |
1 (1.00) |
0.624 (1.00) |
0.0924 (1.00) |
0.772 (1.00) |
0.341 (1.00) |
0.17 (1.00) |
| 1q loss | 17 (11%) | 133 |
0.0599 (1.00) |
0.232 (1.00) |
0.0365 (1.00) |
0.656 (1.00) |
0.212 (1.00) |
0.00957 (1.00) |
0.709 (1.00) |
0.68 (1.00) |
0.477 (1.00) |
| 2p loss | 8 (5%) | 142 |
0.0373 (1.00) |
0.0893 (1.00) |
0.437 (1.00) |
0.299 (1.00) |
0.679 (1.00) |
0.705 (1.00) |
0.311 (1.00) |
0.957 (1.00) |
1 (1.00) |
| 2q loss | 15 (10%) | 135 |
0.951 (1.00) |
0.307 (1.00) |
0.873 (1.00) |
0.561 (1.00) |
0.578 (1.00) |
0.445 (1.00) |
0.443 (1.00) |
0.451 (1.00) |
0.812 (1.00) |
| 3p loss | 74 (49%) | 76 |
0.542 (1.00) |
0.195 (1.00) |
0.411 (1.00) |
0.836 (1.00) |
0.156 (1.00) |
0.218 (1.00) |
0.246 (1.00) |
0.465 (1.00) |
0.00417 (1.00) |
| 3q loss | 23 (15%) | 127 |
0.235 (1.00) |
0.196 (1.00) |
0.365 (1.00) |
0.53 (1.00) |
0.246 (1.00) |
0.0795 (1.00) |
1 (1.00) |
0.562 (1.00) |
0.399 (1.00) |
| 4p loss | 85 (57%) | 65 |
0.0433 (1.00) |
0.214 (1.00) |
0.49 (1.00) |
0.252 (1.00) |
0.132 (1.00) |
0.0078 (1.00) |
0.813 (1.00) |
0.138 (1.00) |
0.0329 (1.00) |
| 4q loss | 74 (49%) | 76 |
0.149 (1.00) |
0.186 (1.00) |
0.35 (1.00) |
0.578 (1.00) |
0.416 (1.00) |
0.739 (1.00) |
0.348 (1.00) |
0.768 (1.00) |
0.228 (1.00) |
| 5p loss | 38 (25%) | 112 |
0.404 (1.00) |
0.426 (1.00) |
0.00728 (1.00) |
0.0435 (1.00) |
0.654 (1.00) |
0.533 (1.00) |
1 (1.00) |
0.723 (1.00) |
0.897 (1.00) |
| 5q loss | 67 (45%) | 83 |
0.353 (1.00) |
0.982 (1.00) |
0.0917 (1.00) |
0.196 (1.00) |
0.584 (1.00) |
0.226 (1.00) |
0.816 (1.00) |
0.573 (1.00) |
0.622 (1.00) |
| 6p loss | 29 (19%) | 121 |
0.156 (1.00) |
0.125 (1.00) |
0.787 (1.00) |
0.419 (1.00) |
0.0634 (1.00) |
0.286 (1.00) |
0.559 (1.00) |
0.821 (1.00) |
0.134 (1.00) |
| 6q loss | 30 (20%) | 120 |
0.0984 (1.00) |
0.328 (1.00) |
0.671 (1.00) |
0.255 (1.00) |
0.18 (1.00) |
0.284 (1.00) |
0.572 (1.00) |
0.826 (1.00) |
0.22 (1.00) |
| 7p loss | 12 (8%) | 138 |
0.779 (1.00) |
0.95 (1.00) |
0.952 (1.00) |
0.446 (1.00) |
0.896 (1.00) |
0.586 (1.00) |
0.376 (1.00) |
0.0256 (1.00) |
0.772 (1.00) |
| 7q loss | 19 (13%) | 131 |
0.843 (1.00) |
0.224 (1.00) |
0.509 (1.00) |
0.00731 (1.00) |
0.589 (1.00) |
0.304 (1.00) |
0.732 (1.00) |
0.19 (1.00) |
1 (1.00) |
| 8p loss | 52 (35%) | 98 |
0.857 (1.00) |
0.651 (1.00) |
0.317 (1.00) |
0.947 (1.00) |
0.116 (1.00) |
0.286 (1.00) |
1 (1.00) |
0.584 (1.00) |
0.658 (1.00) |
| 8q loss | 20 (13%) | 130 |
0.197 (1.00) |
0.738 (1.00) |
0.26 (1.00) |
0.514 (1.00) |
0.694 (1.00) |
0.461 (1.00) |
1 (1.00) |
0.48 (1.00) |
0.173 (1.00) |
| 9p loss | 82 (55%) | 68 |
0.761 (1.00) |
0.393 (1.00) |
0.933 (1.00) |
0.355 (1.00) |
0.518 (1.00) |
0.958 (1.00) |
0.155 (1.00) |
0.51 (1.00) |
0.051 (1.00) |
| 9q loss | 51 (34%) | 99 |
0.599 (1.00) |
0.409 (1.00) |
0.166 (1.00) |
0.381 (1.00) |
0.867 (1.00) |
0.534 (1.00) |
0.331 (1.00) |
0.164 (1.00) |
0.28 (1.00) |
| 10p loss | 35 (23%) | 115 |
0.46 (1.00) |
0.814 (1.00) |
0.813 (1.00) |
0.108 (1.00) |
0.0335 (1.00) |
0.432 (1.00) |
0.269 (1.00) |
0.967 (1.00) |
0.128 (1.00) |
| 10q loss | 37 (25%) | 113 |
0.564 (1.00) |
0.448 (1.00) |
0.541 (1.00) |
0.0824 (1.00) |
0.858 (1.00) |
0.0167 (1.00) |
0.785 (1.00) |
0.666 (1.00) |
0.0014 (1.00) |
| 11p loss | 39 (26%) | 111 |
0.672 (1.00) |
0.298 (1.00) |
0.0911 (1.00) |
0.797 (1.00) |
0.165 (1.00) |
0.638 (1.00) |
0.594 (1.00) |
0.337 (1.00) |
0.667 (1.00) |
| 11q loss | 43 (29%) | 107 |
0.0732 (1.00) |
0.789 (1.00) |
0.116 (1.00) |
0.986 (1.00) |
0.0756 (1.00) |
0.614 (1.00) |
1 (1.00) |
0.944 (1.00) |
0.51 (1.00) |
| 12p loss | 30 (20%) | 120 |
0.789 (1.00) |
0.749 (1.00) |
0.698 (1.00) |
0.726 (1.00) |
0.501 (1.00) |
0.39 (1.00) |
0.375 (1.00) |
0.236 (1.00) |
0.0697 (1.00) |
| 12q loss | 25 (17%) | 125 |
0.698 (1.00) |
0.872 (1.00) |
0.00986 (1.00) |
0.172 (1.00) |
0.621 (1.00) |
0.283 (1.00) |
0.0514 (1.00) |
0.121 (1.00) |
0.00511 (1.00) |
| 13q loss | 53 (35%) | 97 |
0.493 (1.00) |
0.133 (1.00) |
0.57 (1.00) |
0.414 (1.00) |
0.406 (1.00) |
0.0432 (1.00) |
0.138 (1.00) |
0.822 (1.00) |
0.00733 (1.00) |
| 14q loss | 39 (26%) | 111 |
0.708 (1.00) |
0.379 (1.00) |
0.243 (1.00) |
0.462 (1.00) |
0.305 (1.00) |
0.364 (1.00) |
0.427 (1.00) |
0.45 (1.00) |
0.336 (1.00) |
| 15q loss | 45 (30%) | 105 |
0.324 (1.00) |
0.374 (1.00) |
0.164 (1.00) |
0.263 (1.00) |
0.561 (1.00) |
0.00533 (1.00) |
1 (1.00) |
0.772 (1.00) |
0.41 (1.00) |
| 16p loss | 45 (30%) | 105 |
0.762 (1.00) |
0.923 (1.00) |
0.63 (1.00) |
0.105 (1.00) |
0.405 (1.00) |
0.539 (1.00) |
0.798 (1.00) |
0.702 (1.00) |
0.279 (1.00) |
| 16q loss | 44 (29%) | 106 |
0.733 (1.00) |
0.619 (1.00) |
0.74 (1.00) |
0.342 (1.00) |
0.666 (1.00) |
0.378 (1.00) |
0.438 (1.00) |
0.6 (1.00) |
0.281 (1.00) |
| 17p loss | 58 (39%) | 92 |
0.837 (1.00) |
0.0614 (1.00) |
0.599 (1.00) |
0.206 (1.00) |
0.859 (1.00) |
0.782 (1.00) |
1 (1.00) |
0.608 (1.00) |
0.276 (1.00) |
| 17q loss | 17 (11%) | 133 |
0.211 (1.00) |
0.661 (1.00) |
0.814 (1.00) |
0.879 (1.00) |
1 (1.00) |
0.833 (1.00) |
0.709 (1.00) |
0.4 (1.00) |
1 (1.00) |
| 18p loss | 62 (41%) | 88 |
0.797 (1.00) |
0.117 (1.00) |
0.482 (1.00) |
0.101 (1.00) |
0.232 (1.00) |
0.198 (1.00) |
0.34 (1.00) |
0.0793 (1.00) |
0.116 (1.00) |
| 18q loss | 84 (56%) | 66 |
0.653 (1.00) |
0.26 (1.00) |
0.502 (1.00) |
0.205 (1.00) |
0.228 (1.00) |
0.261 (1.00) |
0.64 (1.00) |
0.232 (1.00) |
0.924 (1.00) |
| 19p loss | 54 (36%) | 96 |
0.967 (1.00) |
0.635 (1.00) |
0.443 (1.00) |
0.351 (1.00) |
0.112 (1.00) |
0.296 (1.00) |
1 (1.00) |
0.0389 (1.00) |
0.233 (1.00) |
| 19q loss | 41 (27%) | 109 |
0.914 (1.00) |
0.262 (1.00) |
0.96 (1.00) |
0.565 (1.00) |
0.407 (1.00) |
1 (1.00) |
1 (1.00) |
0.163 (1.00) |
0.033 (1.00) |
| 20p loss | 17 (11%) | 133 |
0.0297 (1.00) |
0.774 (1.00) |
0.935 (1.00) |
0.62 (1.00) |
0.93 (1.00) |
1 (1.00) |
1 (1.00) |
0.892 (1.00) |
0.318 (1.00) |
| 20q loss | 6 (4%) | 144 |
0.25 (1.00) |
0.733 (1.00) |
0.425 (1.00) |
0.11 (1.00) |
0.219 (1.00) |
0.352 (1.00) |
1 (1.00) |
0.639 (1.00) |
0.653 (1.00) |
| 21q loss | 85 (57%) | 65 |
0.225 (1.00) |
0.374 (1.00) |
0.353 (1.00) |
0.65 (1.00) |
0.901 (1.00) |
1 (1.00) |
0.161 (1.00) |
0.00763 (1.00) |
0.0997 (1.00) |
| 22q loss | 64 (43%) | 86 |
0.369 (1.00) |
0.567 (1.00) |
0.0383 (1.00) |
0.0573 (1.00) |
0.0763 (1.00) |
0.0156 (1.00) |
0.641 (1.00) |
0.737 (1.00) |
0.557 (1.00) |
| xq loss | 37 (25%) | 113 |
0.952 (1.00) |
0.995 (1.00) |
0.569 (1.00) |
0.629 (1.00) |
0.588 (1.00) |
0.589 (1.00) |
0.286 (1.00) |
0.0128 (1.00) |
0.11 (1.00) |
Methods & Data
Input
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = ESCA-TP.merged_data.txt
-
Number of patients = 150
-
Number of significantly arm-level cnvs = 80
-
Number of selected clinical features = 9
-
Exclude regions 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.