Correlation between copy number variations of arm-level result and molecular subtypes
Uterine Carcinosarcoma (Primary solid tumor)
02 April 2015
|
analyses__2015_04_02
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
(2015):
Correlation between copy number variations of arm-level result and molecular subtypes.
Broad Institute of MIT and Harvard.
doi:10.7908/C1RB73QN
Overview
Introduction
This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Summary
Testing the association between copy number variation 79 arm-level events and 10 molecular subtypes across 56 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.
-
4q loss cnv correlated to 'MIRSEQ_CNMF'.
-
9p loss cnv correlated to 'RPPA_CHIERARCHICAL'.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 2 significant findings detected.
|
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
| nCNV (%) | nWild-Type | 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 | Fisher's exact test | Fisher's exact test | |
| 4q loss | 33 (59%) | 23 |
0.19 (0.773) |
0.0185 (0.513) |
0.232 (0.778) |
0.0901 (0.705) |
0.00461 (0.376) |
0.0394 (0.618) |
0.00018 (0.142) |
0.248 (0.792) |
0.0203 (0.513) |
0.136 (0.74) |
| 9p loss | 34 (61%) | 22 |
0.298 (0.808) |
0.00782 (0.405) |
1 (1.00) |
0.00048 (0.19) |
0.675 (0.998) |
0.136 (0.74) |
0.862 (1.00) |
0.289 (0.808) |
1 (1.00) |
0.0593 (0.668) |
| 1p gain | 24 (43%) | 32 |
0.202 (0.773) |
0.754 (0.998) |
0.767 (0.998) |
0.695 (0.998) |
0.82 (1.00) |
0.9 (1.00) |
0.527 (0.965) |
0.281 (0.808) |
0.608 (0.974) |
0.567 (0.971) |
| 1q gain | 31 (55%) | 25 |
0.439 (0.928) |
0.768 (0.998) |
0.774 (0.998) |
0.589 (0.971) |
0.761 (0.998) |
0.618 (0.976) |
0.706 (0.998) |
0.456 (0.94) |
0.884 (1.00) |
0.813 (1.00) |
| 2p gain | 23 (41%) | 33 |
0.888 (1.00) |
0.00735 (0.405) |
1 (1.00) |
0.0345 (0.618) |
0.0195 (0.513) |
0.0555 (0.637) |
0.494 (0.958) |
0.0724 (0.68) |
0.102 (0.729) |
0.135 (0.74) |
| 2q gain | 21 (38%) | 35 |
0.37 (0.875) |
0.0191 (0.513) |
0.551 (0.971) |
0.316 (0.825) |
0.0122 (0.472) |
0.113 (0.729) |
0.622 (0.976) |
0.0493 (0.618) |
0.195 (0.773) |
0.111 (0.729) |
| 3p gain | 12 (21%) | 44 |
0.211 (0.773) |
0.261 (0.805) |
0.0864 (0.705) |
0.21 (0.773) |
0.433 (0.926) |
0.2 (0.773) |
0.861 (1.00) |
0.264 (0.808) |
0.452 (0.94) |
0.552 (0.971) |
| 3q gain | 23 (41%) | 33 |
0.101 (0.729) |
0.0479 (0.618) |
0.149 (0.753) |
0.565 (0.971) |
0.197 (0.773) |
0.12 (0.729) |
0.491 (0.958) |
0.189 (0.773) |
0.0746 (0.68) |
0.219 (0.773) |
| 4p gain | 9 (16%) | 47 |
0.732 (0.998) |
0.7 (0.998) |
0.217 (0.773) |
0.0271 (0.573) |
0.823 (1.00) |
0.867 (1.00) |
0.776 (0.998) |
0.326 (0.843) |
0.261 (0.805) |
0.369 (0.875) |
| 4q gain | 3 (5%) | 53 |
1 (1.00) |
0.257 (0.805) |
1 (1.00) |
0.514 (0.965) |
0.794 (1.00) |
0.673 (0.998) |
0.565 (0.971) |
0.6 (0.971) |
0.695 (0.998) |
|
| 5p gain | 23 (41%) | 33 |
0.0458 (0.618) |
0.377 (0.875) |
0.0157 (0.513) |
0.198 (0.773) |
0.454 (0.94) |
0.245 (0.788) |
0.742 (0.998) |
0.0277 (0.573) |
0.602 (0.971) |
0.148 (0.753) |
| 5q gain | 8 (14%) | 48 |
0.508 (0.965) |
0.565 (0.971) |
0.158 (0.759) |
0.208 (0.773) |
0.309 (0.817) |
0.249 (0.792) |
0.0802 (0.68) |
0.153 (0.753) |
0.13 (0.736) |
0.193 (0.773) |
| 6p gain | 30 (54%) | 26 |
0.196 (0.773) |
0.524 (0.965) |
0.77 (0.998) |
0.525 (0.965) |
0.601 (0.971) |
0.413 (0.922) |
1 (1.00) |
0.476 (0.944) |
0.735 (0.998) |
0.323 (0.837) |
| 6q gain | 27 (48%) | 29 |
0.209 (0.773) |
0.208 (0.773) |
1 (1.00) |
0.619 (0.976) |
0.223 (0.773) |
0.165 (0.773) |
1 (1.00) |
0.189 (0.773) |
0.65 (0.994) |
0.138 (0.74) |
| 7p gain | 21 (38%) | 35 |
0.198 (0.773) |
0.554 (0.971) |
0.222 (0.773) |
0.295 (0.808) |
0.152 (0.753) |
0.282 (0.808) |
0.588 (0.971) |
0.129 (0.736) |
0.33 (0.843) |
0.121 (0.729) |
| 7q gain | 17 (30%) | 39 |
0.587 (0.971) |
0.841 (1.00) |
0.52 (0.965) |
0.871 (1.00) |
0.342 (0.861) |
0.809 (1.00) |
0.745 (0.998) |
0.166 (0.773) |
1 (1.00) |
0.154 (0.753) |
| 8p gain | 19 (34%) | 37 |
0.188 (0.773) |
0.744 (0.998) |
0.758 (0.998) |
0.28 (0.808) |
0.444 (0.935) |
0.873 (1.00) |
0.97 (1.00) |
0.558 (0.971) |
0.662 (0.998) |
0.596 (0.971) |
| 8q gain | 30 (54%) | 26 |
0.0146 (0.501) |
0.198 (0.773) |
0.772 (0.998) |
0.593 (0.971) |
0.0487 (0.618) |
0.505 (0.964) |
0.218 (0.773) |
0.329 (0.843) |
0.0657 (0.668) |
0.122 (0.729) |
| 9p gain | 6 (11%) | 50 |
0.349 (0.863) |
0.703 (0.998) |
0.311 (0.817) |
0.122 (0.729) |
0.936 (1.00) |
0.664 (0.998) |
0.832 (1.00) |
0.803 (1.00) |
0.862 (1.00) |
1 (1.00) |
| 10p gain | 21 (38%) | 35 |
0.331 (0.844) |
0.0205 (0.513) |
0.0434 (0.618) |
0.299 (0.808) |
0.0403 (0.618) |
0.12 (0.729) |
0.323 (0.837) |
0.105 (0.729) |
0.676 (0.998) |
0.2 (0.773) |
| 10q gain | 17 (30%) | 39 |
0.872 (1.00) |
0.337 (0.854) |
0.122 (0.729) |
0.464 (0.944) |
0.555 (0.971) |
0.0463 (0.618) |
0.223 (0.773) |
0.185 (0.773) |
0.383 (0.875) |
0.0719 (0.68) |
| 11p gain | 5 (9%) | 51 |
0.722 (0.998) |
0.445 (0.936) |
0.644 (0.993) |
0.924 (1.00) |
0.268 (0.808) |
0.851 (1.00) |
0.49 (0.958) |
0.116 (0.729) |
0.518 (0.965) |
0.0923 (0.708) |
| 11q gain | 7 (12%) | 49 |
0.684 (0.998) |
0.387 (0.879) |
0.684 (0.998) |
0.717 (0.998) |
0.226 (0.773) |
0.382 (0.875) |
0.753 (0.998) |
0.0348 (0.618) |
0.58 (0.971) |
0.0294 (0.576) |
| 12p gain | 22 (39%) | 34 |
0.262 (0.805) |
0.00415 (0.376) |
0.374 (0.875) |
0.595 (0.971) |
0.374 (0.875) |
0.0418 (0.618) |
0.81 (1.00) |
0.977 (1.00) |
0.532 (0.965) |
0.627 (0.976) |
| 12q gain | 11 (20%) | 45 |
0.54 (0.971) |
0.533 (0.965) |
0.475 (0.944) |
0.856 (1.00) |
0.803 (1.00) |
0.523 (0.965) |
1 (1.00) |
0.297 (0.808) |
0.912 (1.00) |
0.268 (0.808) |
| 13q gain | 15 (27%) | 41 |
0.649 (0.993) |
0.0704 (0.68) |
0.0999 (0.729) |
0.542 (0.971) |
0.0222 (0.515) |
0.0245 (0.553) |
0.225 (0.773) |
0.0465 (0.618) |
0.01 (0.434) |
0.142 (0.746) |
| 14q gain | 7 (12%) | 49 |
0.609 (0.974) |
0.577 (0.971) |
0.117 (0.729) |
0.0489 (0.618) |
0.257 (0.805) |
0.261 (0.805) |
0.207 (0.773) |
0.733 (0.998) |
0.226 (0.773) |
0.477 (0.944) |
| 15q gain | 4 (7%) | 52 |
0.188 (0.773) |
0.257 (0.805) |
0.311 (0.817) |
0.581 (0.971) |
0.576 (0.971) |
0.329 (0.843) |
0.756 (0.998) |
0.35 (0.863) |
0.422 (0.923) |
0.355 (0.864) |
| 16p gain | 10 (18%) | 46 |
0.108 (0.729) |
0.279 (0.808) |
1 (1.00) |
0.827 (1.00) |
0.195 (0.773) |
0.277 (0.808) |
1 (1.00) |
0.483 (0.948) |
0.903 (1.00) |
0.407 (0.912) |
| 16q gain | 6 (11%) | 50 |
0.17 (0.773) |
0.847 (1.00) |
1 (1.00) |
0.924 (1.00) |
0.544 (0.971) |
0.969 (1.00) |
0.771 (0.998) |
0.925 (1.00) |
0.479 (0.944) |
0.868 (1.00) |
| 17p gain | 9 (16%) | 47 |
0.386 (0.878) |
0.896 (1.00) |
0.437 (0.926) |
0.827 (1.00) |
0.567 (0.971) |
0.559 (0.971) |
0.283 (0.808) |
0.0606 (0.668) |
0.128 (0.736) |
0.173 (0.773) |
| 17q gain | 18 (32%) | 38 |
0.422 (0.923) |
0.27 (0.808) |
0.758 (0.998) |
0.801 (1.00) |
0.698 (0.998) |
0.514 (0.965) |
0.392 (0.887) |
0.303 (0.808) |
0.76 (0.998) |
0.43 (0.926) |
| 18p gain | 18 (32%) | 38 |
0.68 (0.998) |
0.0491 (0.618) |
0.355 (0.864) |
0.785 (1.00) |
0.0933 (0.709) |
0.345 (0.862) |
0.145 (0.753) |
0.202 (0.773) |
0.407 (0.912) |
0.433 (0.926) |
| 18q gain | 14 (25%) | 42 |
0.685 (0.998) |
0.0808 (0.68) |
0.475 (0.944) |
0.592 (0.971) |
0.153 (0.753) |
0.242 (0.788) |
0.203 (0.773) |
0.088 (0.705) |
0.14 (0.743) |
0.169 (0.773) |
| 19p gain | 24 (43%) | 32 |
0.116 (0.729) |
0.181 (0.773) |
1 (1.00) |
0.726 (0.998) |
0.271 (0.808) |
0.369 (0.875) |
0.535 (0.968) |
0.228 (0.774) |
0.416 (0.923) |
0.518 (0.965) |
| 19q gain | 28 (50%) | 28 |
0.124 (0.729) |
0.0766 (0.68) |
1 (1.00) |
0.874 (1.00) |
0.376 (0.875) |
0.396 (0.894) |
0.93 (1.00) |
0.899 (1.00) |
0.884 (1.00) |
0.937 (1.00) |
| 20p gain | 37 (66%) | 19 |
0.287 (0.808) |
0.503 (0.964) |
1 (1.00) |
0.597 (0.971) |
0.923 (1.00) |
0.76 (0.998) |
0.874 (1.00) |
0.698 (0.998) |
0.221 (0.773) |
0.467 (0.944) |
| 20q gain | 44 (79%) | 12 |
0.0515 (0.636) |
0.919 (1.00) |
1 (1.00) |
0.953 (1.00) |
0.969 (1.00) |
0.997 (1.00) |
0.59 (0.971) |
0.574 (0.971) |
0.215 (0.773) |
0.68 (0.998) |
| 21q gain | 18 (32%) | 38 |
0.0719 (0.68) |
0.379 (0.875) |
0.758 (0.998) |
0.787 (1.00) |
0.902 (1.00) |
0.892 (1.00) |
0.915 (1.00) |
0.572 (0.971) |
1 (1.00) |
0.948 (1.00) |
| 22q gain | 8 (14%) | 48 |
0.711 (0.998) |
0.96 (1.00) |
0.311 (0.817) |
0.302 (0.808) |
0.804 (1.00) |
0.926 (1.00) |
0.887 (1.00) |
0.944 (1.00) |
1 (1.00) |
1 (1.00) |
| xp gain | 18 (32%) | 38 |
0.938 (1.00) |
0.0101 (0.434) |
0.533 (0.965) |
0.479 (0.944) |
0.0193 (0.513) |
0.245 (0.788) |
0.798 (1.00) |
0.56 (0.971) |
0.202 (0.773) |
0.433 (0.926) |
| xq gain | 15 (27%) | 41 |
0.695 (0.998) |
0.362 (0.867) |
0.342 (0.861) |
0.764 (0.998) |
0.764 (0.998) |
0.716 (0.998) |
0.869 (1.00) |
0.292 (0.808) |
1 (1.00) |
0.0898 (0.705) |
| 1p loss | 9 (16%) | 47 |
0.594 (0.971) |
0.603 (0.971) |
0.437 (0.926) |
0.628 (0.976) |
0.921 (1.00) |
0.119 (0.729) |
0.11 (0.729) |
0.0299 (0.576) |
0.0555 (0.637) |
0.0468 (0.618) |
| 1q loss | 9 (16%) | 47 |
0.483 (0.948) |
0.518 (0.965) |
0.437 (0.926) |
0.3 (0.808) |
0.515 (0.965) |
0.0787 (0.68) |
0.422 (0.923) |
0.153 (0.753) |
0.21 (0.773) |
0.144 (0.753) |
| 3p loss | 20 (36%) | 36 |
0.0104 (0.434) |
0.423 (0.923) |
1 (1.00) |
0.712 (0.998) |
0.0486 (0.618) |
0.228 (0.774) |
0.376 (0.875) |
0.929 (1.00) |
0.421 (0.923) |
0.43 (0.926) |
| 3q loss | 14 (25%) | 42 |
0.139 (0.74) |
0.461 (0.944) |
0.744 (0.998) |
0.795 (1.00) |
0.137 (0.74) |
0.604 (0.971) |
0.526 (0.965) |
0.879 (1.00) |
0.382 (0.875) |
1 (1.00) |
| 4p loss | 31 (55%) | 25 |
0.0648 (0.668) |
0.064 (0.668) |
1 (1.00) |
0.0809 (0.68) |
0.257 (0.805) |
0.203 (0.773) |
0.0372 (0.618) |
0.715 (0.998) |
0.148 (0.753) |
0.448 (0.938) |
| 5p loss | 9 (16%) | 47 |
0.903 (1.00) |
0.477 (0.944) |
0.00562 (0.376) |
0.0609 (0.668) |
0.885 (1.00) |
0.136 (0.74) |
1 (1.00) |
0.298 (0.808) |
1 (1.00) |
0.418 (0.923) |
| 5q loss | 18 (32%) | 38 |
0.771 (0.998) |
0.307 (0.816) |
0.547 (0.971) |
0.0785 (0.68) |
0.267 (0.808) |
0.234 (0.783) |
0.362 (0.867) |
0.946 (1.00) |
0.356 (0.864) |
0.947 (1.00) |
| 6p loss | 5 (9%) | 51 |
0.424 (0.923) |
0.955 (1.00) |
0.579 (0.971) |
0.749 (0.998) |
0.755 (0.998) |
0.957 (1.00) |
0.543 (0.971) |
0.909 (1.00) |
1 (1.00) |
1 (1.00) |
| 6q loss | 7 (12%) | 49 |
0.064 (0.668) |
0.7 (0.998) |
0.644 (0.993) |
0.167 (0.773) |
0.639 (0.99) |
0.9 (1.00) |
0.706 (0.998) |
0.619 (0.976) |
0.673 (0.998) |
0.614 (0.976) |
| 7p loss | 13 (23%) | 43 |
1 (1.00) |
0.666 (0.998) |
1 (1.00) |
0.287 (0.808) |
0.735 (0.998) |
0.5 (0.961) |
0.314 (0.822) |
0.455 (0.94) |
0.775 (0.998) |
0.598 (0.971) |
| 7q loss | 13 (23%) | 43 |
0.121 (0.729) |
0.854 (1.00) |
0.734 (0.998) |
0.495 (0.958) |
0.92 (1.00) |
0.822 (1.00) |
0.714 (0.998) |
0.221 (0.773) |
1 (1.00) |
0.529 (0.965) |
| 8p loss | 23 (41%) | 33 |
0.285 (0.808) |
0.981 (1.00) |
0.775 (0.998) |
0.272 (0.808) |
0.826 (1.00) |
0.745 (0.998) |
0.689 (0.998) |
0.514 (0.965) |
0.605 (0.971) |
0.579 (0.971) |
| 8q loss | 9 (16%) | 47 |
1 (1.00) |
0.757 (0.998) |
0.436 (0.926) |
0.689 (0.998) |
0.294 (0.808) |
0.715 (0.998) |
0.95 (1.00) |
0.757 (0.998) |
0.262 (0.805) |
0.671 (0.998) |
| 9q loss | 39 (70%) | 17 |
0.189 (0.773) |
0.00147 (0.29) |
1 (1.00) |
0.0213 (0.513) |
0.496 (0.958) |
0.0381 (0.618) |
0.664 (0.998) |
0.117 (0.729) |
1 (1.00) |
0.161 (0.771) |
| 10p loss | 23 (41%) | 33 |
0.624 (0.976) |
0.0134 (0.483) |
0.245 (0.788) |
0.721 (0.998) |
0.0283 (0.573) |
0.185 (0.773) |
0.243 (0.788) |
0.79 (1.00) |
0.88 (1.00) |
0.894 (1.00) |
| 10q loss | 21 (38%) | 35 |
0.886 (1.00) |
0.3 (0.808) |
0.138 (0.74) |
0.781 (1.00) |
0.176 (0.773) |
0.171 (0.773) |
0.123 (0.729) |
0.473 (0.944) |
0.398 (0.895) |
0.737 (0.998) |
| 11p loss | 26 (46%) | 30 |
1 (1.00) |
0.00402 (0.376) |
0.774 (0.998) |
0.855 (1.00) |
0.378 (0.875) |
0.516 (0.965) |
0.269 (0.808) |
0.58 (0.971) |
0.51 (0.965) |
0.362 (0.867) |
| 11q loss | 24 (43%) | 32 |
0.626 (0.976) |
0.0082 (0.405) |
0.775 (0.998) |
0.806 (1.00) |
0.804 (1.00) |
0.895 (1.00) |
0.294 (0.808) |
0.588 (0.971) |
0.225 (0.773) |
0.185 (0.773) |
| 12p loss | 13 (23%) | 43 |
0.302 (0.808) |
0.275 (0.808) |
0.181 (0.773) |
0.741 (0.998) |
0.579 (0.971) |
0.734 (0.998) |
0.55 (0.971) |
0.58 (0.971) |
1 (1.00) |
0.22 (0.773) |
| 12q loss | 14 (25%) | 42 |
0.428 (0.926) |
0.881 (1.00) |
0.505 (0.964) |
0.125 (0.734) |
0.82 (1.00) |
0.915 (1.00) |
0.964 (1.00) |
0.907 (1.00) |
0.921 (1.00) |
0.603 (0.971) |
| 13q loss | 26 (46%) | 30 |
0.416 (0.923) |
0.00114 (0.29) |
0.239 (0.786) |
0.148 (0.753) |
0.0557 (0.637) |
0.0279 (0.573) |
0.354 (0.864) |
0.121 (0.729) |
0.0393 (0.618) |
0.195 (0.773) |
| 14q loss | 27 (48%) | 29 |
0.943 (1.00) |
0.0906 (0.705) |
0.561 (0.971) |
0.118 (0.729) |
0.122 (0.729) |
0.123 (0.729) |
0.617 (0.976) |
0.898 (1.00) |
0.939 (1.00) |
0.936 (1.00) |
| 15q loss | 32 (57%) | 24 |
0.00619 (0.376) |
0.713 (0.998) |
0.772 (0.998) |
0.0534 (0.637) |
0.929 (1.00) |
0.981 (1.00) |
0.93 (1.00) |
0.978 (1.00) |
1 (1.00) |
0.895 (1.00) |
| 16p loss | 32 (57%) | 24 |
0.244 (0.788) |
0.494 (0.958) |
1 (1.00) |
0.0881 (0.705) |
0.347 (0.862) |
0.0998 (0.729) |
0.811 (1.00) |
0.913 (1.00) |
0.471 (0.944) |
0.897 (1.00) |
| 16q loss | 37 (66%) | 19 |
0.777 (0.998) |
0.794 (1.00) |
1 (1.00) |
0.129 (0.736) |
0.452 (0.94) |
0.091 (0.705) |
0.686 (0.998) |
0.923 (1.00) |
0.139 (0.74) |
0.857 (1.00) |
| 17p loss | 34 (61%) | 22 |
0.548 (0.971) |
0.285 (0.808) |
0.0434 (0.618) |
0.273 (0.808) |
0.98 (1.00) |
0.758 (0.998) |
0.805 (1.00) |
0.891 (1.00) |
0.238 (0.786) |
0.887 (1.00) |
| 17q loss | 17 (30%) | 39 |
0.162 (0.772) |
0.358 (0.865) |
0.528 (0.965) |
0.627 (0.976) |
0.715 (0.998) |
0.383 (0.875) |
0.969 (1.00) |
0.212 (0.773) |
0.93 (1.00) |
0.278 (0.808) |
| 18p loss | 18 (32%) | 38 |
0.0318 (0.598) |
0.0166 (0.513) |
0.355 (0.864) |
0.286 (0.808) |
0.0547 (0.637) |
0.0903 (0.705) |
0.0669 (0.669) |
0.0792 (0.68) |
0.0617 (0.668) |
0.0471 (0.618) |
| 18q loss | 20 (36%) | 36 |
0.116 (0.729) |
0.0713 (0.68) |
0.366 (0.873) |
0.295 (0.808) |
0.185 (0.773) |
0.119 (0.729) |
0.0126 (0.472) |
0.00571 (0.376) |
0.006 (0.376) |
0.00231 (0.365) |
| 19p loss | 15 (27%) | 41 |
0.563 (0.971) |
0.465 (0.944) |
0.3 (0.808) |
0.471 (0.944) |
0.203 (0.773) |
0.357 (0.864) |
0.346 (0.862) |
0.716 (0.998) |
0.212 (0.773) |
0.704 (0.998) |
| 19q loss | 13 (23%) | 43 |
0.733 (0.998) |
0.152 (0.753) |
0.475 (0.944) |
0.818 (1.00) |
0.944 (1.00) |
0.616 (0.976) |
0.23 (0.776) |
0.875 (1.00) |
0.235 (0.783) |
1 (1.00) |
| 20p loss | 7 (12%) | 49 |
0.537 (0.969) |
0.208 (0.773) |
1 (1.00) |
0.00315 (0.376) |
0.0808 (0.68) |
0.0737 (0.68) |
0.618 (0.976) |
0.693 (0.998) |
0.577 (0.971) |
0.692 (0.998) |
| 20q loss | 4 (7%) | 52 |
0.372 (0.875) |
0.602 (0.971) |
0.579 (0.971) |
0.192 (0.773) |
0.118 (0.729) |
0.475 (0.944) |
1 (1.00) |
0.886 (1.00) |
0.666 (0.998) |
0.789 (1.00) |
| 21q loss | 17 (30%) | 39 |
0.671 (0.998) |
0.182 (0.773) |
1 (1.00) |
0.333 (0.846) |
0.63 (0.979) |
0.747 (0.998) |
0.682 (0.998) |
0.972 (1.00) |
0.932 (1.00) |
0.942 (1.00) |
| 22q loss | 33 (59%) | 23 |
0.178 (0.773) |
0.971 (1.00) |
0.0659 (0.668) |
0.0214 (0.513) |
0.963 (1.00) |
0.902 (1.00) |
0.711 (0.998) |
0.29 (0.808) |
0.469 (0.944) |
0.758 (0.998) |
| xp loss | 15 (27%) | 41 |
0.649 (0.993) |
0.837 (1.00) |
0.752 (0.998) |
0.345 (0.862) |
0.928 (1.00) |
0.928 (1.00) |
0.449 (0.938) |
0.646 (0.993) |
0.5 (0.961) |
0.76 (0.998) |
| xq loss | 18 (32%) | 38 |
0.768 (0.998) |
0.158 (0.759) |
0.758 (0.998) |
0.216 (0.773) |
0.237 (0.786) |
0.621 (0.976) |
0.457 (0.941) |
0.646 (0.993) |
0.531 (0.965) |
0.709 (0.998) |
'4q loss' versus 'MIRSEQ_CNMF'
P value = 0.00018 (Fisher's exact test), Q value = 0.14
Table S1. Gene #46: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 10 | 22 | 4 | 19 |
| 4Q LOSS MUTATED | 10 | 16 | 0 | 7 |
| 4Q LOSS WILD-TYPE | 0 | 6 | 4 | 12 |
Figure S1. Get High-res Image Gene #46: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
'9p loss' versus 'RPPA_CHIERARCHICAL'
P value = 0.00048 (Fisher's exact test), Q value = 0.19
Table S2. Gene #55: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
|---|---|---|---|---|---|---|---|
| ALL | 8 | 8 | 7 | 7 | 7 | 5 | 5 |
| 9P LOSS MUTATED | 8 | 6 | 7 | 1 | 4 | 2 | 1 |
| 9P LOSS WILD-TYPE | 0 | 2 | 0 | 6 | 3 | 3 | 4 |
Figure S2. Get High-res Image Gene #55: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
Methods & Data
Input
-
Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCS-TP/15107631/transformed.cor.cli.txt
-
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/15115115/UCS-TP.transferedmergedcluster.txt
-
Number of patients = 56
-
Number of significantly arm-level cnvs = 79
-
Number of molecular subtypes = 10
-
Exclude genes that fewer than K tumors have mutations, K = 3
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] 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)
[2] 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)
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Broad Institute TCGA GDAC as part of the TCGA Research Network.
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