This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 75 arm-level events and 9 clinical features across 78 patients, 8 significant findings detected with Q value < 0.25.
-
19q gain cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
-
2p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
7q loss cnv correlated to 'Time to Death'.
-
8q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
14q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
16p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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16q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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19q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 75 arm-level events and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 8 significant findings detected.
Clinical Features |
Time to Death |
AGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED |
NUMBER OF LYMPH NODES |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | t-test | t-test | |
19q gain | 17 (22%) | 61 |
0.015 (1.00) |
0.395 (1.00) |
1 (1.00) |
0.356 (1.00) |
0.611 (1.00) |
0.781 (1.00) |
6.08e-05 (0.0375) |
0.935 (1.00) |
0.283 (1.00) |
2p loss | 4 (5%) | 74 |
0.384 (1.00) |
0.773 (1.00) |
1 (1.00) |
0.309 (1.00) |
1 (1.00) |
0.0646 (1.00) |
0.525 (1.00) |
0.000271 (0.166) |
|
7q loss | 10 (13%) | 68 |
3.87e-05 (0.0239) |
0.231 (1.00) |
0.257 (1.00) |
0.0471 (1.00) |
0.154 (1.00) |
0.96 (1.00) |
0.00943 (1.00) |
0.722 (1.00) |
0.0505 (1.00) |
8q loss | 5 (6%) | 73 |
0.985 (1.00) |
0.183 (1.00) |
0.588 (1.00) |
0.309 (1.00) |
0.365 (1.00) |
0.914 (1.00) |
1 (1.00) |
0.000274 (0.167) |
|
14q loss | 5 (6%) | 73 |
0.712 (1.00) |
0.656 (1.00) |
0.652 (1.00) |
1 (1.00) |
0.693 (1.00) |
0.914 (1.00) |
0.583 (1.00) |
0.000271 (0.166) |
|
16p loss | 6 (8%) | 72 |
0.936 (1.00) |
0.23 (1.00) |
0.17 (1.00) |
0.313 (1.00) |
0.264 (1.00) |
0.0125 (1.00) |
0.582 (1.00) |
0.000271 (0.166) |
|
16q loss | 9 (12%) | 69 |
0.652 (1.00) |
0.104 (1.00) |
0.422 (1.00) |
0.0949 (1.00) |
0.764 (1.00) |
0.00122 (0.739) |
0.342 (1.00) |
0.000261 (0.161) |
|
19q loss | 4 (5%) | 74 |
0.282 (1.00) |
0.919 (1.00) |
0.546 (1.00) |
0.549 (1.00) |
1 (1.00) |
0.943 (1.00) |
0.525 (1.00) |
0.000274 (0.167) |
|
1p gain | 23 (29%) | 55 |
0.202 (1.00) |
0.793 (1.00) |
0.596 (1.00) |
1 (1.00) |
1 (1.00) |
0.516 (1.00) |
0.745 (1.00) |
0.497 (1.00) |
0.702 (1.00) |
1q gain | 34 (44%) | 44 |
0.155 (1.00) |
0.652 (1.00) |
0.133 (1.00) |
1 (1.00) |
0.903 (1.00) |
0.475 (1.00) |
0.221 (1.00) |
0.848 (1.00) |
0.424 (1.00) |
2p gain | 11 (14%) | 67 |
0.312 (1.00) |
0.15 (1.00) |
0.454 (1.00) |
0.437 (1.00) |
0.782 (1.00) |
0.835 (1.00) |
0.38 (1.00) |
0.42 (1.00) |
|
2q gain | 6 (8%) | 72 |
0.254 (1.00) |
0.269 (1.00) |
0.652 (1.00) |
0.155 (1.00) |
1 (1.00) |
0.964 (1.00) |
1 (1.00) |
0.25 (1.00) |
|
3p gain | 12 (15%) | 66 |
0.313 (1.00) |
0.892 (1.00) |
0.736 (1.00) |
0.286 (1.00) |
0.809 (1.00) |
0.108 (1.00) |
1 (1.00) |
0.224 (1.00) |
|
3q gain | 46 (59%) | 32 |
0.48 (1.00) |
0.858 (1.00) |
0.799 (1.00) |
0.191 (1.00) |
0.271 (1.00) |
0.00809 (1.00) |
0.219 (1.00) |
0.751 (1.00) |
0.0892 (1.00) |
4p gain | 3 (4%) | 75 |
0.177 (1.00) |
0.3 (1.00) |
0.967 (1.00) |
1 (1.00) |
|||||
5p gain | 24 (31%) | 54 |
0.701 (1.00) |
0.707 (1.00) |
0.58 (1.00) |
1 (1.00) |
0.72 (1.00) |
0.178 (1.00) |
0.744 (1.00) |
0.681 (1.00) |
0.577 (1.00) |
5q gain | 9 (12%) | 69 |
0.24 (1.00) |
0.609 (1.00) |
1 (1.00) |
1 (1.00) |
0.567 (1.00) |
0.763 (1.00) |
1 (1.00) |
0.529 (1.00) |
0.727 (1.00) |
6p gain | 15 (19%) | 63 |
0.888 (1.00) |
0.362 (1.00) |
1 (1.00) |
0.741 (1.00) |
0.708 (1.00) |
0.272 (1.00) |
0.707 (1.00) |
0.86 (1.00) |
0.0168 (1.00) |
6q gain | 6 (8%) | 72 |
0.916 (1.00) |
0.598 (1.00) |
1 (1.00) |
0.661 (1.00) |
0.171 (1.00) |
0.881 (1.00) |
1 (1.00) |
0.118 (1.00) |
|
7p gain | 7 (9%) | 71 |
0.174 (1.00) |
0.431 (1.00) |
0.319 (1.00) |
0.632 (1.00) |
0.716 (1.00) |
0.972 (1.00) |
0.33 (1.00) |
0.3 (1.00) |
|
7q gain | 8 (10%) | 70 |
0.582 (1.00) |
0.307 (1.00) |
1 (1.00) |
1 (1.00) |
0.756 (1.00) |
0.805 (1.00) |
0.0232 (1.00) |
0.568 (1.00) |
|
8p gain | 13 (17%) | 65 |
0.258 (1.00) |
0.242 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.878 (1.00) |
0.446 (1.00) |
0.593 (1.00) |
0.895 (1.00) |
8q gain | 22 (28%) | 56 |
0.64 (1.00) |
0.145 (1.00) |
1 (1.00) |
1 (1.00) |
0.898 (1.00) |
0.781 (1.00) |
0.749 (1.00) |
0.39 (1.00) |
0.909 (1.00) |
9p gain | 8 (10%) | 70 |
0.501 (1.00) |
0.559 (1.00) |
0.257 (1.00) |
0.689 (1.00) |
1 (1.00) |
0.973 (1.00) |
1 (1.00) |
0.727 (1.00) |
|
9q gain | 10 (13%) | 68 |
0.495 (1.00) |
0.863 (1.00) |
0.454 (1.00) |
1 (1.00) |
1 (1.00) |
0.96 (1.00) |
1 (1.00) |
0.727 (1.00) |
|
10p gain | 5 (6%) | 73 |
0.596 (1.00) |
0.347 (1.00) |
0.17 (1.00) |
0.155 (1.00) |
1 (1.00) |
0.914 (1.00) |
0.583 (1.00) |
0.253 (1.00) |
|
11p gain | 3 (4%) | 75 |
0.0823 (1.00) |
0.513 (1.00) |
0.754 (1.00) |
1 (1.00) |
|||||
12p gain | 10 (13%) | 68 |
0.928 (1.00) |
0.082 (1.00) |
0.273 (1.00) |
1 (1.00) |
0.614 (1.00) |
0.96 (1.00) |
0.357 (1.00) |
0.322 (1.00) |
0.703 (1.00) |
12q gain | 10 (13%) | 68 |
0.94 (1.00) |
0.123 (1.00) |
0.716 (1.00) |
1 (1.00) |
1 (1.00) |
0.72 (1.00) |
0.357 (1.00) |
0.703 (1.00) |
|
13q gain | 3 (4%) | 75 |
0.865 (1.00) |
0.866 (1.00) |
1 (1.00) |
1 (1.00) |
0.586 (1.00) |
0.754 (1.00) |
1 (1.00) |
||
14q gain | 9 (12%) | 69 |
0.758 (1.00) |
0.857 (1.00) |
0.673 (1.00) |
0.421 (1.00) |
1 (1.00) |
0.763 (1.00) |
1 (1.00) |
0.87 (1.00) |
|
15q gain | 10 (13%) | 68 |
0.0395 (1.00) |
0.671 (1.00) |
0.1 (1.00) |
0.689 (1.00) |
0.764 (1.00) |
0.72 (1.00) |
0.67 (1.00) |
0.128 (1.00) |
0.284 (1.00) |
16p gain | 9 (12%) | 69 |
0.615 (1.00) |
0.692 (1.00) |
0.133 (1.00) |
0.437 (1.00) |
1 (1.00) |
0.968 (1.00) |
0.64 (1.00) |
0.42 (1.00) |
|
16q gain | 8 (10%) | 70 |
0.651 (1.00) |
0.535 (1.00) |
0.1 (1.00) |
0.689 (1.00) |
0.764 (1.00) |
0.973 (1.00) |
0.614 (1.00) |
0.645 (1.00) |
|
17p gain | 4 (5%) | 74 |
0.195 (1.00) |
0.972 (1.00) |
0.093 (1.00) |
0.0776 (1.00) |
1 (1.00) |
0.885 (1.00) |
0.127 (1.00) |
0.355 (1.00) |
|
17q gain | 8 (10%) | 70 |
0.51 (1.00) |
0.143 (1.00) |
0.00104 (0.635) |
0.229 (1.00) |
0.764 (1.00) |
0.973 (1.00) |
0.614 (1.00) |
0.535 (1.00) |
|
18p gain | 6 (8%) | 72 |
0.36 (1.00) |
0.0443 (1.00) |
0.0779 (1.00) |
1 (1.00) |
1 (1.00) |
0.881 (1.00) |
0.26 (1.00) |
0.467 (1.00) |
|
18q gain | 4 (5%) | 74 |
0.606 (1.00) |
0.182 (1.00) |
0.093 (1.00) |
0.578 (1.00) |
1 (1.00) |
0.943 (1.00) |
0.127 (1.00) |
0.882 (1.00) |
|
19p gain | 10 (13%) | 68 |
0.688 (1.00) |
0.337 (1.00) |
0.716 (1.00) |
0.154 (1.00) |
1 (1.00) |
0.96 (1.00) |
0.00943 (1.00) |
0.565 (1.00) |
|
20p gain | 21 (27%) | 57 |
0.145 (1.00) |
0.796 (1.00) |
0.562 (1.00) |
0.143 (1.00) |
0.23 (1.00) |
0.45 (1.00) |
0.74 (1.00) |
0.478 (1.00) |
0.321 (1.00) |
20q gain | 26 (33%) | 52 |
0.572 (1.00) |
0.401 (1.00) |
0.289 (1.00) |
0.575 (1.00) |
0.645 (1.00) |
0.357 (1.00) |
0.751 (1.00) |
0.654 (1.00) |
0.965 (1.00) |
21q gain | 9 (12%) | 69 |
0.0525 (1.00) |
0.0805 (1.00) |
0.673 (1.00) |
0.421 (1.00) |
1 (1.00) |
0.763 (1.00) |
0.167 (1.00) |
0.467 (1.00) |
|
22q gain | 10 (13%) | 68 |
0.337 (1.00) |
0.0385 (1.00) |
0.133 (1.00) |
0.437 (1.00) |
0.782 (1.00) |
0.96 (1.00) |
0.67 (1.00) |
0.489 (1.00) |
|
xq gain | 7 (9%) | 71 |
0.995 (1.00) |
0.682 (1.00) |
0.418 (1.00) |
1 (1.00) |
0.756 (1.00) |
0.972 (1.00) |
0.33 (1.00) |
0.568 (1.00) |
|
1p loss | 3 (4%) | 75 |
0.797 (1.00) |
0.513 (1.00) |
0.967 (1.00) |
0.0704 (1.00) |
|||||
1q loss | 3 (4%) | 75 |
0.183 (1.00) |
0.587 (1.00) |
0.546 (1.00) |
0.212 (1.00) |
1 (1.00) |
0.967 (1.00) |
0.00376 (1.00) |
0.454 (1.00) |
|
2q loss | 9 (12%) | 69 |
0.894 (1.00) |
0.372 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.376 (1.00) |
0.167 (1.00) |
0.526 (1.00) |
|
3p loss | 19 (24%) | 59 |
0.404 (1.00) |
0.425 (1.00) |
0.554 (1.00) |
0.0138 (1.00) |
0.868 (1.00) |
0.335 (1.00) |
0.0726 (1.00) |
0.748 (1.00) |
0.26 (1.00) |
4p loss | 31 (40%) | 47 |
0.619 (1.00) |
0.207 (1.00) |
0.798 (1.00) |
0.292 (1.00) |
0.665 (1.00) |
0.0528 (1.00) |
0.12 (1.00) |
0.972 (1.00) |
0.352 (1.00) |
4q loss | 14 (18%) | 64 |
0.0415 (1.00) |
0.307 (1.00) |
0.324 (1.00) |
0.0494 (1.00) |
1 (1.00) |
0.541 (1.00) |
0.0499 (1.00) |
0.784 (1.00) |
0.131 (1.00) |
5p loss | 3 (4%) | 75 |
0.000892 (0.543) |
0.409 (1.00) |
0.546 (1.00) |
0.0243 (1.00) |
1 (1.00) |
0.967 (1.00) |
0.0704 (1.00) |
0.131 (1.00) |
|
5q loss | 15 (19%) | 63 |
0.0227 (1.00) |
0.123 (1.00) |
0.525 (1.00) |
0.745 (1.00) |
0.561 (1.00) |
0.497 (1.00) |
0.262 (1.00) |
0.759 (1.00) |
0.666 (1.00) |
6p loss | 7 (9%) | 71 |
0.871 (1.00) |
0.0878 (1.00) |
1 (1.00) |
0.0617 (1.00) |
1 (1.00) |
0.972 (1.00) |
0.594 (1.00) |
0.238 (1.00) |
0.363 (1.00) |
6q loss | 14 (18%) | 64 |
0.245 (1.00) |
0.155 (1.00) |
1 (1.00) |
0.489 (1.00) |
0.321 (1.00) |
0.554 (1.00) |
0.443 (1.00) |
0.0491 (1.00) |
0.568 (1.00) |
7p loss | 6 (8%) | 72 |
0.513 (1.00) |
0.886 (1.00) |
1 (1.00) |
0.355 (1.00) |
0.716 (1.00) |
0.881 (1.00) |
0.00612 (1.00) |
0.902 (1.00) |
0.32 (1.00) |
8p loss | 22 (28%) | 56 |
0.246 (1.00) |
0.833 (1.00) |
0.562 (1.00) |
1 (1.00) |
0.881 (1.00) |
0.121 (1.00) |
1 (1.00) |
0.104 (1.00) |
0.73 (1.00) |
9p loss | 15 (19%) | 63 |
0.0459 (1.00) |
0.966 (1.00) |
0.529 (1.00) |
1 (1.00) |
1 (1.00) |
0.438 (1.00) |
1 (1.00) |
0.736 (1.00) |
0.63 (1.00) |
9q loss | 10 (13%) | 68 |
0.391 (1.00) |
0.24 (1.00) |
0.485 (1.00) |
0.714 (1.00) |
0.804 (1.00) |
0.0311 (1.00) |
0.67 (1.00) |
0.772 (1.00) |
|
10p loss | 14 (18%) | 64 |
0.0869 (1.00) |
0.347 (1.00) |
0.312 (1.00) |
0.0746 (1.00) |
0.42 (1.00) |
0.887 (1.00) |
0.235 (1.00) |
0.953 (1.00) |
0.144 (1.00) |
10q loss | 17 (22%) | 61 |
0.0265 (1.00) |
0.395 (1.00) |
0.537 (1.00) |
0.00892 (1.00) |
0.248 (1.00) |
0.879 (1.00) |
0.143 (1.00) |
0.442 (1.00) |
0.0303 (1.00) |
11p loss | 23 (29%) | 55 |
0.911 (1.00) |
0.738 (1.00) |
0.289 (1.00) |
0.575 (1.00) |
1 (1.00) |
0.113 (1.00) |
0.745 (1.00) |
0.328 (1.00) |
0.179 (1.00) |
11q loss | 32 (41%) | 46 |
0.923 (1.00) |
0.053 (1.00) |
0.311 (1.00) |
0.789 (1.00) |
0.812 (1.00) |
0.33 (1.00) |
1 (1.00) |
0.479 (1.00) |
0.601 (1.00) |
12p loss | 12 (15%) | 66 |
0.367 (1.00) |
0.218 (1.00) |
0.485 (1.00) |
0.712 (1.00) |
0.804 (1.00) |
0.93 (1.00) |
0.2 (1.00) |
0.604 (1.00) |
0.772 (1.00) |
13q loss | 20 (26%) | 58 |
0.0699 (1.00) |
0.72 (1.00) |
0.562 (1.00) |
0.143 (1.00) |
0.881 (1.00) |
0.299 (1.00) |
1 (1.00) |
0.715 (1.00) |
0.281 (1.00) |
15q loss | 7 (9%) | 71 |
0.717 (1.00) |
0.436 (1.00) |
1 (1.00) |
0.666 (1.00) |
1 (1.00) |
0.276 (1.00) |
1 (1.00) |
0.93 (1.00) |
|
17p loss | 20 (26%) | 58 |
0.235 (1.00) |
0.74 (1.00) |
0.771 (1.00) |
1 (1.00) |
0.249 (1.00) |
0.299 (1.00) |
1 (1.00) |
0.506 (1.00) |
0.606 (1.00) |
17q loss | 5 (6%) | 73 |
0.412 (1.00) |
0.788 (1.00) |
0.299 (1.00) |
1 (1.00) |
0.365 (1.00) |
0.914 (1.00) |
1 (1.00) |
0.248 (1.00) |
|
18p loss | 12 (15%) | 66 |
0.34 (1.00) |
0.0306 (1.00) |
0.0927 (1.00) |
0.485 (1.00) |
1 (1.00) |
0.57 (1.00) |
0.107 (1.00) |
0.0285 (1.00) |
0.652 (1.00) |
18q loss | 18 (23%) | 60 |
0.886 (1.00) |
0.378 (1.00) |
0.239 (1.00) |
0.121 (1.00) |
0.749 (1.00) |
0.214 (1.00) |
0.483 (1.00) |
0.282 (1.00) |
0.284 (1.00) |
19p loss | 13 (17%) | 65 |
0.3 (1.00) |
0.0967 (1.00) |
0.709 (1.00) |
0.261 (1.00) |
0.804 (1.00) |
0.586 (1.00) |
0.446 (1.00) |
0.2 (1.00) |
|
20p loss | 7 (9%) | 71 |
0.826 (1.00) |
0.822 (1.00) |
0.657 (1.00) |
1 (1.00) |
1 (1.00) |
0.547 (1.00) |
0.594 (1.00) |
0.187 (1.00) |
0.467 (1.00) |
20q loss | 3 (4%) | 75 |
0.0259 (1.00) |
0.513 (1.00) |
0.754 (1.00) |
1 (1.00) |
|||||
21q loss | 10 (13%) | 68 |
0.36 (1.00) |
0.274 (1.00) |
0.716 (1.00) |
1 (1.00) |
1 (1.00) |
0.72 (1.00) |
0.67 (1.00) |
0.54 (1.00) |
|
22q loss | 11 (14%) | 67 |
0.573 (1.00) |
0.236 (1.00) |
0.709 (1.00) |
0.714 (1.00) |
0.804 (1.00) |
0.0715 (1.00) |
0.38 (1.00) |
0.526 (1.00) |
|
xq loss | 15 (19%) | 63 |
0.0051 (1.00) |
0.699 (1.00) |
0.529 (1.00) |
0.511 (1.00) |
0.825 (1.00) |
0.852 (1.00) |
0.262 (1.00) |
0.411 (1.00) |
0.327 (1.00) |
P value = 6.08e-05 (Fisher's exact test), Q value = 0.037
Table S1. Gene #32: '19q gain' versus Clinical Feature #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 13 | 65 |
19Q GAIN MUTATED | 9 | 8 |
19Q GAIN WILD-TYPE | 4 | 57 |
Figure S1. Get High-res Image Gene #32: '19q gain' versus Clinical Feature #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000271 (t-test), Q value = 0.17
Table S2. Gene #40: '2p loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 64 | 0.6 (1.3) |
2P LOSS MUTATED | 4 | 0.0 (0.0) |
2P LOSS WILD-TYPE | 60 | 0.7 (1.3) |
Figure S2. Get High-res Image Gene #40: '2p loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

P value = 3.87e-05 (logrank test), Q value = 0.024
Table S3. Gene #50: '7q loss' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 76 | 11 | 0.0 - 177.0 (6.0) |
7Q LOSS MUTATED | 10 | 5 | 1.0 - 40.9 (13.0) |
7Q LOSS WILD-TYPE | 66 | 6 | 0.0 - 177.0 (5.9) |
Figure S3. Get High-res Image Gene #50: '7q loss' versus Clinical Feature #1: 'Time to Death'

P value = 0.000274 (t-test), Q value = 0.17
Table S4. Gene #52: '8q loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 64 | 0.6 (1.3) |
8Q LOSS MUTATED | 3 | 0.0 (0.0) |
8Q LOSS WILD-TYPE | 61 | 0.6 (1.3) |
Figure S4. Get High-res Image Gene #52: '8q loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

P value = 0.000271 (t-test), Q value = 0.17
Table S5. Gene #61: '14q loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 64 | 0.6 (1.3) |
14Q LOSS MUTATED | 4 | 0.0 (0.0) |
14Q LOSS WILD-TYPE | 60 | 0.7 (1.3) |
Figure S5. Get High-res Image Gene #61: '14q loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

P value = 0.000271 (t-test), Q value = 0.17
Table S6. Gene #63: '16p loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 64 | 0.6 (1.3) |
16P LOSS MUTATED | 4 | 0.0 (0.0) |
16P LOSS WILD-TYPE | 60 | 0.7 (1.3) |
Figure S6. Get High-res Image Gene #63: '16p loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

P value = 0.000261 (t-test), Q value = 0.16
Table S7. Gene #64: '16q loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 64 | 0.6 (1.3) |
16Q LOSS MUTATED | 7 | 0.0 (0.0) |
16Q LOSS WILD-TYPE | 57 | 0.7 (1.3) |
Figure S7. Get High-res Image Gene #64: '16q loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

P value = 0.000274 (t-test), Q value = 0.17
Table S8. Gene #70: '19q loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 64 | 0.6 (1.3) |
19Q LOSS MUTATED | 3 | 0.0 (0.0) |
19Q LOSS WILD-TYPE | 61 | 0.6 (1.3) |
Figure S8. Get High-res Image Gene #70: '19q loss' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = CESC-TP.merged_data.txt
-
Number of patients = 78
-
Number of significantly arm-level cnvs = 75
-
Number of selected clinical features = 9
-
Exclude regions that fewer than K tumors have mutations, K = 3
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
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
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
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
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.
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.