Correlation between copy number variations of arm-level result and selected clinical features
Pancreatic Adenocarcinoma (Primary solid tumor)
15 July 2014
|
analyses__2014_07_15
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/C16T0KDM
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 72 arm-level events and 12 clinical features across 86 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 72 arm-level 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 |
NUMBERPACKYEARSSMOKED |
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 | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | |
| 1p gain | 7 (8%) | 79 |
0.45 (1.00) |
0.788 (1.00) |
0.362 (1.00) |
1 (1.00) |
1 (1.00) |
0.31 (1.00) |
0.71 (1.00) |
0.334 (1.00) |
1 (1.00) |
0.521 (1.00) |
1 (1.00) |
|
| 1q gain | 22 (26%) | 64 |
0.194 (1.00) |
0.526 (1.00) |
0.202 (1.00) |
0.674 (1.00) |
0.398 (1.00) |
0.273 (1.00) |
0.326 (1.00) |
0.729 (1.00) |
0.255 (1.00) |
1 (1.00) |
0.935 (1.00) |
1 (1.00) |
| 2p gain | 7 (8%) | 79 |
0.378 (1.00) |
0.641 (1.00) |
0.856 (1.00) |
1 (1.00) |
1 (1.00) |
0.103 (1.00) |
0.26 (1.00) |
1 (1.00) |
0.375 (1.00) |
0.496 (1.00) |
0.615 (1.00) |
1 (1.00) |
| 2q gain | 8 (9%) | 78 |
0.373 (1.00) |
0.384 (1.00) |
0.885 (1.00) |
1 (1.00) |
1 (1.00) |
0.372 (1.00) |
0.152 (1.00) |
0.687 (1.00) |
0.375 (1.00) |
0.752 (1.00) |
0.819 (1.00) |
1 (1.00) |
| 3p gain | 5 (6%) | 81 |
0.975 (1.00) |
0.789 (1.00) |
0.467 (1.00) |
0.394 (1.00) |
0.593 (1.00) |
0.333 (1.00) |
0.197 (1.00) |
1 (1.00) |
0.707 (1.00) |
0.656 (1.00) |
1 (1.00) |
|
| 3q gain | 8 (9%) | 78 |
0.99 (1.00) |
0.766 (1.00) |
0.0761 (1.00) |
0.16 (1.00) |
0.0991 (1.00) |
0.127 (1.00) |
0.152 (1.00) |
1 (1.00) |
0.447 (1.00) |
0.982 (1.00) |
1 (1.00) |
|
| 4p gain | 3 (3%) | 83 |
0.897 (1.00) |
1 (1.00) |
1 (1.00) |
0.571 (1.00) |
0.319 (1.00) |
1 (1.00) |
1 (1.00) |
0.592 (1.00) |
0.646 (1.00) |
1 (1.00) |
||
| 4q gain | 3 (3%) | 83 |
0.897 (1.00) |
1 (1.00) |
1 (1.00) |
0.571 (1.00) |
0.316 (1.00) |
1 (1.00) |
1 (1.00) |
0.595 (1.00) |
0.646 (1.00) |
1 (1.00) |
||
| 5p gain | 12 (14%) | 74 |
0.716 (1.00) |
0.0886 (1.00) |
0.761 (1.00) |
0.309 (1.00) |
0.48 (1.00) |
1 (1.00) |
0.545 (1.00) |
1 (1.00) |
0.133 (1.00) |
0.282 (1.00) |
0.974 (1.00) |
1 (1.00) |
| 5q gain | 9 (10%) | 77 |
0.601 (1.00) |
0.23 (1.00) |
0.772 (1.00) |
0.196 (1.00) |
0.683 (1.00) |
1 (1.00) |
1 (1.00) |
0.709 (1.00) |
0.259 (1.00) |
0.611 (1.00) |
0.902 (1.00) |
0.578 (1.00) |
| 7p gain | 25 (29%) | 61 |
0.301 (1.00) |
0.311 (1.00) |
0.546 (1.00) |
0.428 (1.00) |
0.783 (1.00) |
1 (1.00) |
0.813 (1.00) |
0.86 (1.00) |
0.00934 (1.00) |
0.00092 (0.757) |
0.663 (1.00) |
0.303 (1.00) |
| 7q gain | 22 (26%) | 64 |
0.442 (1.00) |
0.37 (1.00) |
0.87 (1.00) |
0.674 (1.00) |
1 (1.00) |
0.914 (1.00) |
1 (1.00) |
1 (1.00) |
0.0418 (1.00) |
0.00041 (0.338) |
0.254 (1.00) |
0.129 (1.00) |
| 8p gain | 12 (14%) | 74 |
0.744 (1.00) |
0.896 (1.00) |
0.626 (1.00) |
1 (1.00) |
0.48 (1.00) |
0.715 (1.00) |
1 (1.00) |
0.744 (1.00) |
0.262 (1.00) |
0.595 (1.00) |
0.692 (1.00) |
|
| 8q gain | 21 (24%) | 65 |
0.549 (1.00) |
0.216 (1.00) |
0.985 (1.00) |
1 (1.00) |
0.771 (1.00) |
0.203 (1.00) |
0.804 (1.00) |
0.255 (1.00) |
0.544 (1.00) |
0.0872 (1.00) |
0.482 (1.00) |
0.463 (1.00) |
| 9q gain | 3 (3%) | 83 |
0.225 (1.00) |
0.65 (1.00) |
1 (1.00) |
1 (1.00) |
0.656 (1.00) |
0.612 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
| 10p gain | 4 (5%) | 82 |
0.73 (1.00) |
0.853 (1.00) |
0.517 (1.00) |
1 (1.00) |
0.254 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.643 (1.00) |
0.736 (1.00) |
0.00109 (0.896) |
|
| 10q gain | 6 (7%) | 80 |
0.814 (1.00) |
0.346 (1.00) |
0.238 (1.00) |
1 (1.00) |
0.634 (1.00) |
0.156 (1.00) |
0.428 (1.00) |
1 (1.00) |
0.497 (1.00) |
0.896 (1.00) |
0.00888 (1.00) |
|
| 11p gain | 10 (12%) | 76 |
0.601 (1.00) |
0.309 (1.00) |
0.437 (1.00) |
0.588 (1.00) |
0.254 (1.00) |
0.375 (1.00) |
0.191 (1.00) |
0.236 (1.00) |
0.0859 (1.00) |
0.589 (1.00) |
1 (1.00) |
|
| 11q gain | 8 (9%) | 78 |
0.797 (1.00) |
0.608 (1.00) |
0.631 (1.00) |
1 (1.00) |
0.402 (1.00) |
0.373 (1.00) |
0.479 (1.00) |
1 (1.00) |
0.387 (1.00) |
0.963 (1.00) |
1 (1.00) |
|
| 12p gain | 8 (9%) | 78 |
0.908 (1.00) |
0.368 (1.00) |
0.551 (1.00) |
0.16 (1.00) |
0.673 (1.00) |
0.787 (1.00) |
0.152 (1.00) |
0.688 (1.00) |
0.285 (1.00) |
0.0532 (1.00) |
1 (1.00) |
|
| 12q gain | 6 (7%) | 80 |
0.891 (1.00) |
0.819 (1.00) |
0.824 (1.00) |
1 (1.00) |
0.329 (1.00) |
0.739 (1.00) |
0.106 (1.00) |
0.577 (1.00) |
0.0629 (1.00) |
0.0196 (1.00) |
1 (1.00) |
|
| 13q gain | 8 (9%) | 78 |
0.124 (1.00) |
0.818 (1.00) |
0.729 (1.00) |
0.558 (1.00) |
0.191 (1.00) |
0.453 (1.00) |
1 (1.00) |
0.275 (1.00) |
0.254 (1.00) |
0.144 (1.00) |
1 (1.00) |
|
| 14q gain | 12 (14%) | 74 |
0.659 (1.00) |
0.965 (1.00) |
0.733 (1.00) |
0.593 (1.00) |
0.722 (1.00) |
0.511 (1.00) |
0.545 (1.00) |
0.745 (1.00) |
0.0245 (1.00) |
0.259 (1.00) |
0.249 (1.00) |
0.692 (1.00) |
| 15q gain | 5 (6%) | 81 |
0.0159 (1.00) |
0.791 (1.00) |
1 (1.00) |
0.326 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.707 (1.00) |
0.127 (1.00) |
1 (1.00) |
||
| 16p gain | 11 (13%) | 75 |
0.519 (1.00) |
0.178 (1.00) |
0.563 (1.00) |
0.271 (1.00) |
0.453 (1.00) |
0.467 (1.00) |
0.346 (1.00) |
1 (1.00) |
0.0137 (1.00) |
0.0572 (1.00) |
0.609 (1.00) |
0.623 (1.00) |
| 16q gain | 12 (14%) | 74 |
0.474 (1.00) |
0.195 (1.00) |
0.707 (1.00) |
0.309 (1.00) |
0.48 (1.00) |
0.433 (1.00) |
0.545 (1.00) |
1 (1.00) |
0.0137 (1.00) |
0.0912 (1.00) |
0.985 (1.00) |
0.664 (1.00) |
| 17q gain | 5 (6%) | 81 |
0.509 (1.00) |
0.883 (1.00) |
0.618 (1.00) |
1 (1.00) |
0.593 (1.00) |
0.73 (1.00) |
1 (1.00) |
1 (1.00) |
0.642 (1.00) |
0.704 (1.00) |
0.341 (1.00) |
|
| 18p gain | 12 (14%) | 74 |
0.284 (1.00) |
0.267 (1.00) |
0.708 (1.00) |
1 (1.00) |
0.48 (1.00) |
0.127 (1.00) |
0.223 (1.00) |
0.201 (1.00) |
0.0636 (1.00) |
0.454 (1.00) |
0.221 (1.00) |
0.696 (1.00) |
| 18q gain | 4 (5%) | 82 |
0.746 (1.00) |
0.272 (1.00) |
0.517 (1.00) |
1 (1.00) |
0.254 (1.00) |
1 (1.00) |
0.0527 (1.00) |
0.177 (1.00) |
1 (1.00) |
0.246 (1.00) |
1 (1.00) |
|
| 19p gain | 4 (5%) | 82 |
0.646 (1.00) |
0.782 (1.00) |
1 (1.00) |
1 (1.00) |
0.568 (1.00) |
0.445 (1.00) |
0.355 (1.00) |
1 (1.00) |
0.308 (1.00) |
0.0767 (1.00) |
1 (1.00) |
|
| 19q gain | 9 (10%) | 77 |
0.696 (1.00) |
0.916 (1.00) |
0.325 (1.00) |
0.592 (1.00) |
0.441 (1.00) |
0.814 (1.00) |
0.308 (1.00) |
0.71 (1.00) |
0.0498 (1.00) |
0.447 (1.00) |
0.00984 (1.00) |
0.622 (1.00) |
| 20p gain | 19 (22%) | 67 |
0.337 (1.00) |
0.261 (1.00) |
0.73 (1.00) |
0.367 (1.00) |
1 (1.00) |
0.338 (1.00) |
0.197 (1.00) |
0.363 (1.00) |
0.253 (1.00) |
0.578 (1.00) |
0.983 (1.00) |
1 (1.00) |
| 20q gain | 22 (26%) | 64 |
0.304 (1.00) |
0.339 (1.00) |
0.758 (1.00) |
0.416 (1.00) |
1 (1.00) |
0.752 (1.00) |
0.326 (1.00) |
0.424 (1.00) |
0.0761 (1.00) |
0.224 (1.00) |
0.819 (1.00) |
1 (1.00) |
| 22q gain | 4 (5%) | 82 |
0.645 (1.00) |
0.75 (1.00) |
0.754 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.616 (1.00) |
1 (1.00) |
1 (1.00) |
0.405 (1.00) |
0.341 (1.00) |
|
| xq gain | 4 (5%) | 82 |
0.704 (1.00) |
0.237 (1.00) |
1 (1.00) |
1 (1.00) |
0.667 (1.00) |
1 (1.00) |
1 (1.00) |
0.402 (1.00) |
0.992 (1.00) |
1 (1.00) |
||
| 1p loss | 16 (19%) | 70 |
0.0182 (1.00) |
0.337 (1.00) |
0.826 (1.00) |
1 (1.00) |
0.753 (1.00) |
0.388 (1.00) |
0.274 (1.00) |
0.241 (1.00) |
0.058 (1.00) |
1 (1.00) |
0.182 (1.00) |
0.194 (1.00) |
| 1q loss | 5 (6%) | 81 |
0.0386 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.728 (1.00) |
0.197 (1.00) |
1 (1.00) |
0.705 (1.00) |
0.827 (1.00) |
0.408 (1.00) |
||
| 2p loss | 7 (8%) | 79 |
0.413 (1.00) |
0.641 (1.00) |
0.857 (1.00) |
1 (1.00) |
1 (1.00) |
0.776 (1.00) |
0.71 (1.00) |
0.131 (1.00) |
0.164 (1.00) |
0.39 (1.00) |
0.0725 (1.00) |
|
| 2q loss | 3 (3%) | 83 |
0.199 (1.00) |
0.646 (1.00) |
1 (1.00) |
1 (1.00) |
0.658 (1.00) |
0.612 (1.00) |
0.123 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
| 3p loss | 16 (19%) | 70 |
0.435 (1.00) |
0.331 (1.00) |
1 (1.00) |
0.639 (1.00) |
1 (1.00) |
1 (1.00) |
0.274 (1.00) |
1 (1.00) |
0.0498 (1.00) |
0.284 (1.00) |
0.201 (1.00) |
0.544 (1.00) |
| 3q loss | 13 (15%) | 73 |
0.442 (1.00) |
0.947 (1.00) |
0.958 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.377 (1.00) |
1 (1.00) |
0.0167 (1.00) |
0.597 (1.00) |
0.413 (1.00) |
0.0714 (1.00) |
| 4p loss | 11 (13%) | 75 |
0.564 (1.00) |
0.393 (1.00) |
0.566 (1.00) |
1 (1.00) |
0.703 (1.00) |
0.132 (1.00) |
0.0246 (1.00) |
0.266 (1.00) |
0.513 (1.00) |
0.551 (1.00) |
0.808 (1.00) |
0.171 (1.00) |
| 4q loss | 11 (13%) | 75 |
0.55 (1.00) |
0.426 (1.00) |
0.563 (1.00) |
1 (1.00) |
0.703 (1.00) |
0.467 (1.00) |
0.00313 (1.00) |
0.267 (1.00) |
0.335 (1.00) |
0.55 (1.00) |
0.787 (1.00) |
0.172 (1.00) |
| 5p loss | 4 (5%) | 82 |
0.519 (1.00) |
0.926 (1.00) |
1 (1.00) |
1 (1.00) |
0.568 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.744 (1.00) |
1 (1.00) |
|
| 5q loss | 7 (8%) | 79 |
0.807 (1.00) |
0.262 (1.00) |
0.753 (1.00) |
1 (1.00) |
0.185 (1.00) |
1 (1.00) |
0.26 (1.00) |
0.635 (1.00) |
0.0438 (1.00) |
0.0649 (1.00) |
0.197 (1.00) |
1 (1.00) |
| 6p loss | 31 (36%) | 55 |
0.0529 (1.00) |
0.168 (1.00) |
0.789 (1.00) |
0.705 (1.00) |
0.799 (1.00) |
0.665 (1.00) |
0.116 (1.00) |
0.752 (1.00) |
0.315 (1.00) |
0.94 (1.00) |
0.69 (1.00) |
0.842 (1.00) |
| 6q loss | 40 (47%) | 46 |
0.0897 (1.00) |
0.325 (1.00) |
0.703 (1.00) |
0.275 (1.00) |
0.621 (1.00) |
0.488 (1.00) |
1 (1.00) |
0.883 (1.00) |
0.34 (1.00) |
0.855 (1.00) |
0.89 (1.00) |
0.511 (1.00) |
| 8p loss | 16 (19%) | 70 |
0.396 (1.00) |
0.491 (1.00) |
0.653 (1.00) |
1 (1.00) |
0.51 (1.00) |
0.681 (1.00) |
0.274 (1.00) |
0.108 (1.00) |
0.411 (1.00) |
0.154 (1.00) |
0.217 (1.00) |
0.387 (1.00) |
| 8q loss | 7 (8%) | 79 |
0.552 (1.00) |
0.339 (1.00) |
0.138 (1.00) |
1 (1.00) |
0.157 (1.00) |
0.562 (1.00) |
0.26 (1.00) |
0.0106 (1.00) |
1 (1.00) |
0.208 (1.00) |
0.18 (1.00) |
0.0725 (1.00) |
| 9p loss | 36 (42%) | 50 |
0.654 (1.00) |
0.652 (1.00) |
0.119 (1.00) |
0.459 (1.00) |
0.447 (1.00) |
0.254 (1.00) |
0.282 (1.00) |
0.254 (1.00) |
0.0604 (1.00) |
0.23 (1.00) |
0.226 (1.00) |
0.843 (1.00) |
| 9q loss | 23 (27%) | 63 |
0.798 (1.00) |
0.922 (1.00) |
0.429 (1.00) |
1 (1.00) |
1 (1.00) |
0.617 (1.00) |
0.63 (1.00) |
0.857 (1.00) |
0.0468 (1.00) |
0.259 (1.00) |
0.371 (1.00) |
0.792 (1.00) |
| 10p loss | 15 (17%) | 71 |
0.687 (1.00) |
0.356 (1.00) |
0.343 (1.00) |
0.14 (1.00) |
0.753 (1.00) |
0.22 (1.00) |
0.402 (1.00) |
0.796 (1.00) |
0.578 (1.00) |
0.547 (1.00) |
0.374 (1.00) |
0.713 (1.00) |
| 10q loss | 15 (17%) | 71 |
0.599 (1.00) |
0.557 (1.00) |
1 (1.00) |
0.624 (1.00) |
0.753 (1.00) |
0.668 (1.00) |
0.402 (1.00) |
0.495 (1.00) |
0.226 (1.00) |
0.545 (1.00) |
0.165 (1.00) |
0.716 (1.00) |
| 11p loss | 6 (7%) | 80 |
0.653 (1.00) |
0.2 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.285 (1.00) |
1 (1.00) |
1 (1.00) |
0.499 (1.00) |
0.269 (1.00) |
0.0525 (1.00) |
|
| 11q loss | 8 (9%) | 78 |
0.472 (1.00) |
0.475 (1.00) |
0.886 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.479 (1.00) |
0.0751 (1.00) |
0.339 (1.00) |
0.487 (1.00) |
0.578 (1.00) |
|
| 12p loss | 8 (9%) | 78 |
0.771 (1.00) |
0.48 (1.00) |
0.26 (1.00) |
1 (1.00) |
0.357 (1.00) |
0.0399 (1.00) |
0.479 (1.00) |
0.39 (1.00) |
0.375 (1.00) |
0.21 (1.00) |
0.661 (1.00) |
0.0325 (1.00) |
| 12q loss | 10 (12%) | 76 |
0.715 (1.00) |
0.571 (1.00) |
0.47 (1.00) |
0.233 (1.00) |
0.683 (1.00) |
0.0686 (1.00) |
1 (1.00) |
0.239 (1.00) |
0.592 (1.00) |
0.507 (1.00) |
0.954 (1.00) |
0.00195 (1.00) |
| 13q loss | 13 (15%) | 73 |
0.0958 (1.00) |
0.538 (1.00) |
0.304 (1.00) |
0.601 (1.00) |
0.171 (1.00) |
0.175 (1.00) |
0.377 (1.00) |
0.761 (1.00) |
0.0926 (1.00) |
0.0168 (1.00) |
0.107 (1.00) |
0.469 (1.00) |
| 14q loss | 6 (7%) | 80 |
0.609 (1.00) |
0.905 (1.00) |
0.343 (1.00) |
0.454 (1.00) |
0.593 (1.00) |
1 (1.00) |
1 (1.00) |
0.281 (1.00) |
0.747 (1.00) |
0.496 (1.00) |
0.333 (1.00) |
0.0137 (1.00) |
| 15q loss | 13 (15%) | 73 |
0.996 (1.00) |
0.971 (1.00) |
0.111 (1.00) |
1 (1.00) |
0.16 (1.00) |
0.175 (1.00) |
0.139 (1.00) |
0.0817 (1.00) |
0.0671 (1.00) |
0.431 (1.00) |
0.202 (1.00) |
0.173 (1.00) |
| 16p loss | 3 (3%) | 83 |
0.906 (1.00) |
1 (1.00) |
1 (1.00) |
0.571 (1.00) |
1 (1.00) |
0.612 (1.00) |
0.344 (1.00) |
0.277 (1.00) |
1 (1.00) |
|||
| 17p loss | 32 (37%) | 54 |
0.369 (1.00) |
0.809 (1.00) |
0.402 (1.00) |
0.249 (1.00) |
0.796 (1.00) |
0.715 (1.00) |
0.826 (1.00) |
0.59 (1.00) |
0.0319 (1.00) |
0.00646 (1.00) |
0.723 (1.00) |
1 (1.00) |
| 17q loss | 12 (14%) | 74 |
0.54 (1.00) |
0.852 (1.00) |
0.792 (1.00) |
0.593 (1.00) |
1 (1.00) |
0.431 (1.00) |
0.223 (1.00) |
0.532 (1.00) |
0.0976 (1.00) |
0.391 (1.00) |
0.305 (1.00) |
|
| 18p loss | 29 (34%) | 57 |
0.965 (1.00) |
0.12 (1.00) |
0.0759 (1.00) |
0.434 (1.00) |
0.293 (1.00) |
0.265 (1.00) |
1 (1.00) |
0.663 (1.00) |
0.0505 (1.00) |
0.392 (1.00) |
0.333 (1.00) |
0.696 (1.00) |
| 18q loss | 46 (53%) | 40 |
0.859 (1.00) |
0.9 (1.00) |
0.223 (1.00) |
0.719 (1.00) |
1 (1.00) |
0.138 (1.00) |
0.666 (1.00) |
0.688 (1.00) |
0.832 (1.00) |
0.0211 (1.00) |
0.652 (1.00) |
0.372 (1.00) |
| 19p loss | 11 (13%) | 75 |
0.715 (1.00) |
0.445 (1.00) |
0.724 (1.00) |
0.589 (1.00) |
0.724 (1.00) |
0.469 (1.00) |
1 (1.00) |
0.266 (1.00) |
1 (1.00) |
0.104 (1.00) |
0.0926 (1.00) |
1 (1.00) |
| 19q loss | 8 (9%) | 78 |
0.422 (1.00) |
0.322 (1.00) |
0.677 (1.00) |
1 (1.00) |
1 (1.00) |
0.23 (1.00) |
1 (1.00) |
0.385 (1.00) |
0.117 (1.00) |
0.572 (1.00) |
1 (1.00) |
|
| 20p loss | 9 (10%) | 77 |
0.595 (1.00) |
0.893 (1.00) |
1 (1.00) |
1 (1.00) |
0.441 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.748 (1.00) |
0.0858 (1.00) |
0.442 (1.00) |
0.174 (1.00) |
| 20q loss | 3 (3%) | 83 |
0.39 (1.00) |
0.648 (1.00) |
1 (1.00) |
1 (1.00) |
0.317 (1.00) |
0.612 (1.00) |
0.126 (1.00) |
0.312 (1.00) |
0.717 (1.00) |
0.272 (1.00) |
||
| 21q loss | 29 (34%) | 57 |
0.154 (1.00) |
0.701 (1.00) |
0.248 (1.00) |
0.257 (1.00) |
0.116 (1.00) |
0.186 (1.00) |
0.652 (1.00) |
0.746 (1.00) |
0.918 (1.00) |
0.249 (1.00) |
0.0112 (1.00) |
0.583 (1.00) |
| 22q loss | 20 (23%) | 66 |
0.399 (1.00) |
0.471 (1.00) |
0.912 (1.00) |
0.675 (1.00) |
0.771 (1.00) |
0.823 (1.00) |
0.0414 (1.00) |
0.714 (1.00) |
0.315 (1.00) |
0.808 (1.00) |
0.637 (1.00) |
0.617 (1.00) |
| xq loss | 7 (8%) | 79 |
0.744 (1.00) |
0.794 (1.00) |
0.855 (1.00) |
1 (1.00) |
1 (1.00) |
0.43 (1.00) |
0.71 (1.00) |
0.333 (1.00) |
0.642 (1.00) |
0.747 (1.00) |
0.575 (1.00) |
0.0733 (1.00) |
Methods & Data
Input
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = PAAD-TP.merged_data.txt
-
Number of patients = 86
-
Number of significantly arm-level cnvs = 72
-
Number of selected clinical features = 12
-
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 © 2014
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.