This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between subtypes identified by 80 different clustering approaches and 9 clinical features across 846 patients, one significant finding detected with Q value < 0.25.
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2 subtypes identified in current cancer cohort by '1p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '1q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '2p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '2q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '3p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '3q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '4p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '4q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '5p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '5q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '6p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '6q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '7p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '7q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '8p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '8q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '9p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '9q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '10p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '10q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '11p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '11q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '12p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '12q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '13q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '14q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '15q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '16p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '16q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '17p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '17q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '18p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '18q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '19p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '19q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '20p gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '20q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '21q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '22q gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Xq gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '1p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '1q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '2p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '2q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '3p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '3q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '4p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '4q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '5p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '5q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '6p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '6q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '7p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '7q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '8p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '8q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '9p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '9q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '10p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '10q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '11p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '11q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '12p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '12q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '13q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '14q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '15q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '16p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '16q loss mutation analysis'. These subtypes correlate to 'AGE'.
-
2 subtypes identified in current cancer cohort by '17p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '17q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '18p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '18q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '19p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '19q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '20p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '20q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '21q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '22q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Xq loss mutation analysis'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
RADIATIONS RADIATION REGIMENINDICATION |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
Statistical Tests | logrank test | t-test | Fisher's exact test | Fisher's exact test | Chi-square test | Chi-square test | t-test | t-test | Chi-square test |
1p gain |
0.193 (1.00) |
0.478 (1.00) |
1 (1.00) |
0.0124 (1.00) |
0.82 (1.00) |
0.514 (1.00) |
0.604 (1.00) |
0.888 (1.00) |
|
1q gain |
0.0749 (1.00) |
0.259 (1.00) |
1 (1.00) |
0.376 (1.00) |
0.609 (1.00) |
0.686 (1.00) |
0.51 (1.00) |
0.436 (1.00) |
|
2p gain |
0.781 (1.00) |
0.683 (1.00) |
1 (1.00) |
0.228 (1.00) |
0.534 (1.00) |
0.905 (1.00) |
0.418 (1.00) |
0.308 (1.00) |
|
2q gain |
0.972 (1.00) |
0.958 (1.00) |
1 (1.00) |
0.00801 (1.00) |
0.678 (1.00) |
0.659 (1.00) |
0.278 (1.00) |
0.788 (1.00) |
|
3p gain |
0.846 (1.00) |
0.0588 (1.00) |
1 (1.00) |
0.866 (1.00) |
0.605 (1.00) |
0.683 (1.00) |
0.529 (1.00) |
0.178 (1.00) |
|
3q gain |
0.317 (1.00) |
0.719 (1.00) |
0.608 (1.00) |
0.899 (1.00) |
0.547 (1.00) |
0.562 (1.00) |
0.152 (1.00) |
0.23 (1.00) |
|
4p gain |
0.0672 (1.00) |
0.487 (1.00) |
1 (1.00) |
0.509 (1.00) |
0.329 (1.00) |
0.783 (1.00) |
0.821 (1.00) |
0.0052 (1.00) |
|
4q gain |
0.0252 (1.00) |
0.359 (1.00) |
1 (1.00) |
1 (1.00) |
0.344 (1.00) |
0.755 (1.00) |
0.661 (1.00) |
0.00824 (1.00) |
|
5p gain |
0.106 (1.00) |
0.0511 (1.00) |
0.681 (1.00) |
0.1 (1.00) |
0.697 (1.00) |
0.21 (1.00) |
0.365 (1.00) |
0.783 (1.00) |
|
5q gain |
0.331 (1.00) |
0.00258 (1.00) |
1 (1.00) |
0.166 (1.00) |
0.32 (1.00) |
0.789 (1.00) |
0.816 (1.00) |
0.914 (1.00) |
|
6p gain |
0.86 (1.00) |
0.199 (1.00) |
1 (1.00) |
0.0105 (1.00) |
0.518 (1.00) |
0.91 (1.00) |
0.661 (1.00) |
0.777 (1.00) |
|
6q gain |
0.265 (1.00) |
0.059 (1.00) |
0.468 (1.00) |
0.521 (1.00) |
0.54 (1.00) |
0.498 (1.00) |
0.904 (1.00) |
0.87 (1.00) |
|
7p gain |
0.847 (1.00) |
0.0899 (1.00) |
0.0113 (1.00) |
0.027 (1.00) |
0.507 (1.00) |
0.307 (1.00) |
0.403 (1.00) |
0.824 (1.00) |
|
7q gain |
0.508 (1.00) |
0.572 (1.00) |
0.0935 (1.00) |
0.0158 (1.00) |
0.957 (1.00) |
0.395 (1.00) |
0.452 (1.00) |
0.936 (1.00) |
|
8p gain |
0.974 (1.00) |
0.116 (1.00) |
0.681 (1.00) |
1 (1.00) |
0.785 (1.00) |
0.81 (1.00) |
0.828 (1.00) |
0.88 (1.00) |
|
8q gain |
0.898 (1.00) |
0.0142 (1.00) |
0.503 (1.00) |
0.143 (1.00) |
0.486 (1.00) |
0.16 (1.00) |
0.761 (1.00) |
0.668 (1.00) |
|
9p gain |
0.503 (1.00) |
0.524 (1.00) |
1 (1.00) |
0.365 (1.00) |
0.835 (1.00) |
0.141 (1.00) |
0.3 (1.00) |
0.161 (1.00) |
|
9q gain |
0.434 (1.00) |
0.31 (1.00) |
1 (1.00) |
0.184 (1.00) |
0.963 (1.00) |
0.381 (1.00) |
0.433 (1.00) |
0.729 (1.00) |
|
10p gain |
0.768 (1.00) |
0.615 (1.00) |
0.612 (1.00) |
0.277 (1.00) |
0.0893 (1.00) |
0.571 (1.00) |
0.139 (1.00) |
0.0105 (1.00) |
|
10q gain |
0.788 (1.00) |
0.337 (1.00) |
1 (1.00) |
0.211 (1.00) |
0.981 (1.00) |
0.902 (1.00) |
0.948 (1.00) |
0.86 (1.00) |
|
11p gain |
0.615 (1.00) |
0.769 (1.00) |
0.503 (1.00) |
0.545 (1.00) |
0.978 (1.00) |
0.67 (1.00) |
0.421 (1.00) |
0.0709 (1.00) |
|
11q gain |
0.0483 (1.00) |
0.811 (1.00) |
1 (1.00) |
0.591 (1.00) |
0.737 (1.00) |
0.254 (1.00) |
0.946 (1.00) |
0.0373 (1.00) |
|
12p gain |
0.664 (1.00) |
0.363 (1.00) |
0.0196 (1.00) |
0.28 (1.00) |
0.586 (1.00) |
0.768 (1.00) |
0.74 (1.00) |
0.931 (1.00) |
|
12q gain |
0.105 (1.00) |
0.0812 (1.00) |
0.0495 (1.00) |
0.282 (1.00) |
0.166 (1.00) |
0.846 (1.00) |
0.833 (1.00) |
0.951 (1.00) |
|
13q gain |
0.803 (1.00) |
0.941 (1.00) |
1 (1.00) |
0.591 (1.00) |
0.192 (1.00) |
0.842 (1.00) |
0.0792 (1.00) |
0.959 (1.00) |
|
14q gain |
0.256 (1.00) |
0.552 (1.00) |
1 (1.00) |
0.325 (1.00) |
0.96 (1.00) |
0.359 (1.00) |
0.0368 (1.00) |
0.0914 (1.00) |
|
15q gain |
0.609 (1.00) |
0.76 (1.00) |
0.39 (1.00) |
0.283 (1.00) |
0.925 (1.00) |
0.926 (1.00) |
0.643 (1.00) |
0.879 (1.00) |
|
16p gain |
0.606 (1.00) |
0.0532 (1.00) |
1 (1.00) |
0.369 (1.00) |
0.798 (1.00) |
0.102 (1.00) |
0.104 (1.00) |
0.248 (1.00) |
|
16q gain |
0.0455 (1.00) |
0.807 (1.00) |
0.437 (1.00) |
1 (1.00) |
0.043 (1.00) |
0.629 (1.00) |
0.994 (1.00) |
0.0277 (1.00) |
|
17p gain |
0.643 (1.00) |
0.45 (1.00) |
0.00944 (1.00) |
0.859 (1.00) |
0.925 (1.00) |
0.884 (1.00) |
0.412 (1.00) |
0.756 (1.00) |
|
17q gain |
0.796 (1.00) |
0.664 (1.00) |
0.0274 (1.00) |
0.908 (1.00) |
0.186 (1.00) |
0.727 (1.00) |
0.573 (1.00) |
0.63 (1.00) |
|
18p gain |
0.12 (1.00) |
0.0422 (1.00) |
0.607 (1.00) |
0.078 (1.00) |
0.514 (1.00) |
0.642 (1.00) |
0.817 (1.00) |
0.571 (1.00) |
|
18q gain |
0.137 (1.00) |
0.475 (1.00) |
0.553 (1.00) |
0.195 (1.00) |
0.377 (1.00) |
0.909 (1.00) |
0.977 (1.00) |
0.42 (1.00) |
|
19p gain |
0.0949 (1.00) |
0.262 (1.00) |
0.155 (1.00) |
0.101 (1.00) |
0.179 (1.00) |
0.868 (1.00) |
0.359 (1.00) |
0.733 (1.00) |
|
19q gain |
0.0129 (1.00) |
0.674 (1.00) |
0.214 (1.00) |
0.587 (1.00) |
0.0655 (1.00) |
0.0736 (1.00) |
0.355 (1.00) |
0.862 (1.00) |
|
20p gain |
0.0451 (1.00) |
0.126 (1.00) |
0.0692 (1.00) |
0.59 (1.00) |
0.162 (1.00) |
0.287 (1.00) |
0.0325 (1.00) |
0.298 (1.00) |
|
20q gain |
0.14 (1.00) |
0.55 (1.00) |
0.149 (1.00) |
0.436 (1.00) |
0.322 (1.00) |
0.338 (1.00) |
0.0194 (1.00) |
0.128 (1.00) |
|
21q gain |
0.0414 (1.00) |
0.0359 (1.00) |
1 (1.00) |
0.044 (1.00) |
0.702 (1.00) |
0.15 (1.00) |
0.0283 (1.00) |
0.151 (1.00) |
|
22q gain |
0.805 (1.00) |
0.351 (1.00) |
1 (1.00) |
0.703 (1.00) |
0.814 (1.00) |
0.182 (1.00) |
0.706 (1.00) |
0.145 (1.00) |
|
Xq gain |
0.119 (1.00) |
0.112 (1.00) |
1 (1.00) |
0.288 (1.00) |
0.0408 (1.00) |
0.0129 (1.00) |
0.622 (1.00) |
0.152 (1.00) |
|
1p loss |
0.192 (1.00) |
0.0151 (1.00) |
1 (1.00) |
0.487 (1.00) |
0.377 (1.00) |
0.0436 (1.00) |
0.0229 (1.00) |
0.00254 (1.00) |
|
1q loss |
0.987 (1.00) |
0.64 (1.00) |
1 (1.00) |
1 (1.00) |
0.836 (1.00) |
0.932 (1.00) |
0.73 (1.00) |
0.976 (1.00) |
|
2p loss |
0.654 (1.00) |
0.275 (1.00) |
1 (1.00) |
0.145 (1.00) |
0.213 (1.00) |
0.504 (1.00) |
0.363 (1.00) |
0.218 (1.00) |
|
2q loss |
0.513 (1.00) |
0.467 (1.00) |
0.611 (1.00) |
0.226 (1.00) |
0.142 (1.00) |
0.49 (1.00) |
0.333 (1.00) |
0.0824 (1.00) |
|
3p loss |
0.0422 (1.00) |
0.0409 (1.00) |
0.609 (1.00) |
0.51 (1.00) |
0.581 (1.00) |
0.999 (1.00) |
0.421 (1.00) |
0.797 (1.00) |
|
3q loss |
0.267 (1.00) |
0.0688 (1.00) |
1 (1.00) |
0.0684 (1.00) |
0.368 (1.00) |
0.644 (1.00) |
0.672 (1.00) |
0.765 (1.00) |
|
4p loss |
0.454 (1.00) |
0.248 (1.00) |
1 (1.00) |
0.235 (1.00) |
0.817 (1.00) |
0.326 (1.00) |
0.492 (1.00) |
0.682 (1.00) |
|
4q loss |
0.479 (1.00) |
0.945 (1.00) |
0.373 (1.00) |
0.343 (1.00) |
0.854 (1.00) |
0.113 (1.00) |
0.953 (1.00) |
0.625 (1.00) |
|
5p loss |
0.14 (1.00) |
0.119 (1.00) |
0.526 (1.00) |
1 (1.00) |
0.657 (1.00) |
0.157 (1.00) |
0.772 (1.00) |
0.14 (1.00) |
|
5q loss |
0.413 (1.00) |
0.153 (1.00) |
0.621 (1.00) |
0.643 (1.00) |
0.784 (1.00) |
0.152 (1.00) |
0.106 (1.00) |
0.17 (1.00) |
|
6p loss |
0.311 (1.00) |
0.179 (1.00) |
0.611 (1.00) |
0.273 (1.00) |
0.183 (1.00) |
0.695 (1.00) |
0.955 (1.00) |
0.972 (1.00) |
|
6q loss |
0.861 (1.00) |
0.00927 (1.00) |
0.221 (1.00) |
0.0643 (1.00) |
0.598 (1.00) |
0.889 (1.00) |
0.688 (1.00) |
0.827 (1.00) |
|
7p loss |
0.525 (1.00) |
0.405 (1.00) |
1 (1.00) |
0.292 (1.00) |
0.702 (1.00) |
0.673 (1.00) |
0.591 (1.00) |
0.0251 (1.00) |
|
7q loss |
0.134 (1.00) |
0.268 (1.00) |
1 (1.00) |
0.545 (1.00) |
0.0873 (1.00) |
0.968 (1.00) |
0.272 (1.00) |
0.0648 (1.00) |
|
8p loss |
0.022 (1.00) |
0.36 (1.00) |
1 (1.00) |
0.795 (1.00) |
0.722 (1.00) |
0.459 (1.00) |
0.252 (1.00) |
0.767 (1.00) |
|
8q loss |
0.00364 (1.00) |
0.597 (1.00) |
1 (1.00) |
0.717 (1.00) |
0.301 (1.00) |
0.567 (1.00) |
0.452 (1.00) |
0.655 (1.00) |
|
9p loss |
0.0258 (1.00) |
0.979 (1.00) |
0.414 (1.00) |
0.625 (1.00) |
0.221 (1.00) |
0.153 (1.00) |
0.633 (1.00) |
0.0968 (1.00) |
|
9q loss |
0.0198 (1.00) |
0.512 (1.00) |
0.172 (1.00) |
0.914 (1.00) |
0.402 (1.00) |
0.202 (1.00) |
0.978 (1.00) |
0.283 (1.00) |
|
10p loss |
0.0628 (1.00) |
0.226 (1.00) |
1 (1.00) |
0.556 (1.00) |
0.0276 (1.00) |
0.507 (1.00) |
0.621 (1.00) |
0.311 (1.00) |
|
10q loss |
0.00325 (1.00) |
0.51 (1.00) |
0.611 (1.00) |
0.466 (1.00) |
0.184 (1.00) |
0.312 (1.00) |
0.765 (1.00) |
0.695 (1.00) |
|
11p loss |
0.0209 (1.00) |
0.584 (1.00) |
0.37 (1.00) |
0.52 (1.00) |
0.91 (1.00) |
0.259 (1.00) |
0.0575 (1.00) |
0.18 (1.00) |
|
11q loss |
0.17 (1.00) |
0.78 (1.00) |
0.0562 (1.00) |
0.521 (1.00) |
0.701 (1.00) |
0.25 (1.00) |
0.184 (1.00) |
0.0972 (1.00) |
|
12p loss |
0.0969 (1.00) |
0.969 (1.00) |
0.509 (1.00) |
0.544 (1.00) |
0.665 (1.00) |
0.514 (1.00) |
0.871 (1.00) |
0.486 (1.00) |
|
12q loss |
0.229 (1.00) |
0.201 (1.00) |
1 (1.00) |
0.731 (1.00) |
0.769 (1.00) |
0.723 (1.00) |
0.603 (1.00) |
0.138 (1.00) |
|
13q loss |
0.0807 (1.00) |
0.157 (1.00) |
0.464 (1.00) |
0.93 (1.00) |
0.499 (1.00) |
0.273 (1.00) |
0.639 (1.00) |
0.864 (1.00) |
|
14q loss |
0.00773 (1.00) |
0.233 (1.00) |
0.371 (1.00) |
0.734 (1.00) |
0.371 (1.00) |
0.0637 (1.00) |
0.921 (1.00) |
0.812 (1.00) |
|
15q loss |
0.221 (1.00) |
0.16 (1.00) |
0.376 (1.00) |
0.404 (1.00) |
0.333 (1.00) |
0.582 (1.00) |
0.439 (1.00) |
0.496 (1.00) |
|
16p loss |
0.688 (1.00) |
0.973 (1.00) |
0.101 (1.00) |
1 (1.00) |
0.839 (1.00) |
0.772 (1.00) |
0.501 (1.00) |
0.86 (1.00) |
|
16q loss |
0.017 (1.00) |
0.000325 (0.208) |
1 (1.00) |
0.418 (1.00) |
0.492 (1.00) |
0.5 (1.00) |
0.0329 (1.00) |
0.811 (1.00) |
|
17p loss |
0.335 (1.00) |
0.0212 (1.00) |
0.742 (1.00) |
0.104 (1.00) |
0.445 (1.00) |
0.503 (1.00) |
0.349 (1.00) |
0.352 (1.00) |
|
17q loss |
0.604 (1.00) |
0.246 (1.00) |
0.368 (1.00) |
1 (1.00) |
0.846 (1.00) |
0.291 (1.00) |
0.262 (1.00) |
0.971 (1.00) |
|
18p loss |
0.00615 (1.00) |
0.00117 (0.744) |
1 (1.00) |
0.613 (1.00) |
0.546 (1.00) |
0.514 (1.00) |
0.299 (1.00) |
0.405 (1.00) |
|
18q loss |
0.0406 (1.00) |
0.00125 (0.799) |
1 (1.00) |
0.613 (1.00) |
0.411 (1.00) |
0.486 (1.00) |
0.17 (1.00) |
0.0722 (1.00) |
|
19p loss |
0.534 (1.00) |
0.439 (1.00) |
1 (1.00) |
0.224 (1.00) |
0.498 (1.00) |
0.225 (1.00) |
0.538 (1.00) |
0.286 (1.00) |
|
19q loss |
0.633 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.609 (1.00) |
0.657 (1.00) |
0.234 (1.00) |
0.837 (1.00) |
0.0514 (1.00) |
|
20p loss |
0.00361 (1.00) |
0.809 (1.00) |
0.43 (1.00) |
1 (1.00) |
0.546 (1.00) |
0.141 (1.00) |
0.34 (1.00) |
0.251 (1.00) |
|
20q loss |
0.578 (1.00) |
0.854 (1.00) |
1 (1.00) |
0.36 (1.00) |
0.669 (1.00) |
0.454 (1.00) |
0.735 (1.00) |
0.609 (1.00) |
|
21q loss |
0.987 (1.00) |
0.716 (1.00) |
0.611 (1.00) |
0.79 (1.00) |
0.142 (1.00) |
0.576 (1.00) |
0.409 (1.00) |
0.00585 (1.00) |
|
22q loss |
0.121 (1.00) |
0.778 (1.00) |
0.173 (1.00) |
0.0891 (1.00) |
0.912 (1.00) |
0.0696 (1.00) |
0.0958 (1.00) |
0.773 (1.00) |
|
Xq loss |
0.0544 (1.00) |
0.553 (1.00) |
0.0375 (1.00) |
0.392 (1.00) |
0.643 (1.00) |
0.992 (1.00) |
0.39 (1.00) |
0.00108 (0.69) |
Cluster Labels | 1P GAIN MUTATED | 1P GAIN WILD-TYPE |
---|---|---|
Number of samples | 88 | 758 |
Cluster Labels | 1Q GAIN MUTATED | 1Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 452 | 394 |
Cluster Labels | 2P GAIN MUTATED | 2P GAIN WILD-TYPE |
---|---|---|
Number of samples | 48 | 798 |
Cluster Labels | 2Q GAIN MUTATED | 2Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 25 | 821 |
Cluster Labels | 3P GAIN MUTATED | 3P GAIN WILD-TYPE |
---|---|---|
Number of samples | 51 | 795 |
Cluster Labels | 3Q GAIN MUTATED | 3Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 95 | 751 |
Cluster Labels | 4P GAIN MUTATED | 4P GAIN WILD-TYPE |
---|---|---|
Number of samples | 29 | 817 |
Cluster Labels | 4Q GAIN MUTATED | 4Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 27 | 819 |
Cluster Labels | 5P GAIN MUTATED | 5P GAIN WILD-TYPE |
---|---|---|
Number of samples | 160 | 686 |
Cluster Labels | 5Q GAIN MUTATED | 5Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 97 | 749 |
Cluster Labels | 6P GAIN MUTATED | 6P GAIN WILD-TYPE |
---|---|---|
Number of samples | 94 | 752 |
Cluster Labels | 6Q GAIN MUTATED | 6Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 57 | 789 |
Cluster Labels | 7P GAIN MUTATED | 7P GAIN WILD-TYPE |
---|---|---|
Number of samples | 150 | 696 |
Cluster Labels | 7Q GAIN MUTATED | 7Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 107 | 739 |
Cluster Labels | 8P GAIN MUTATED | 8P GAIN WILD-TYPE |
---|---|---|
Number of samples | 160 | 686 |
Cluster Labels | 8Q GAIN MUTATED | 8Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 355 | 491 |
Cluster Labels | 9P GAIN MUTATED | 9P GAIN WILD-TYPE |
---|---|---|
Number of samples | 65 | 781 |
Cluster Labels | 9Q GAIN MUTATED | 9Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 53 | 793 |
Cluster Labels | 10P GAIN MUTATED | 10P GAIN WILD-TYPE |
---|---|---|
Number of samples | 106 | 740 |
Cluster Labels | 10Q GAIN MUTATED | 10Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 44 | 802 |
Cluster Labels | 11P GAIN MUTATED | 11P GAIN WILD-TYPE |
---|---|---|
Number of samples | 63 | 783 |
Cluster Labels | 11Q GAIN MUTATED | 11Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 44 | 802 |
Cluster Labels | 12P GAIN MUTATED | 12P GAIN WILD-TYPE |
---|---|---|
Number of samples | 109 | 737 |
Cluster Labels | 12Q GAIN MUTATED | 12Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 83 | 763 |
Cluster Labels | 13Q GAIN MUTATED | 13Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 44 | 802 |
Cluster Labels | 14Q GAIN MUTATED | 14Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 76 | 770 |
Cluster Labels | 15Q GAIN MUTATED | 15Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 45 | 801 |
Cluster Labels | 16P GAIN MUTATED | 16P GAIN WILD-TYPE |
---|---|---|
Number of samples | 234 | 612 |
Cluster Labels | 16Q GAIN MUTATED | 16Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 52 | 794 |
Cluster Labels | 17P GAIN MUTATED | 17P GAIN WILD-TYPE |
---|---|---|
Number of samples | 45 | 801 |
Cluster Labels | 17Q GAIN MUTATED | 17Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 120 | 726 |
Cluster Labels | 18P GAIN MUTATED | 18P GAIN WILD-TYPE |
---|---|---|
Number of samples | 83 | 763 |
Cluster Labels | 18Q GAIN MUTATED | 18Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 72 | 774 |
Cluster Labels | 19P GAIN MUTATED | 19P GAIN WILD-TYPE |
---|---|---|
Number of samples | 67 | 779 |
Cluster Labels | 19Q GAIN MUTATED | 19Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 82 | 764 |
Cluster Labels | 20P GAIN MUTATED | 20P GAIN WILD-TYPE |
---|---|---|
Number of samples | 232 | 614 |
Cluster Labels | 20Q GAIN MUTATED | 20Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 266 | 580 |
Cluster Labels | 21Q GAIN MUTATED | 21Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 98 | 748 |
Cluster Labels | 22Q GAIN MUTATED | 22Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 39 | 807 |
Cluster Labels | XQ GAIN MUTATED | XQ GAIN WILD-TYPE |
---|---|---|
Number of samples | 20 | 826 |
Cluster Labels | 1P LOSS MUTATED | 1P LOSS WILD-TYPE |
---|---|---|
Number of samples | 117 | 729 |
Cluster Labels | 1Q LOSS MUTATED | 1Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 20 | 826 |
Cluster Labels | 2P LOSS MUTATED | 2P LOSS WILD-TYPE |
---|---|---|
Number of samples | 70 | 776 |
Cluster Labels | 2Q LOSS MUTATED | 2Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 84 | 762 |
Cluster Labels | 3P LOSS MUTATED | 3P LOSS WILD-TYPE |
---|---|---|
Number of samples | 88 | 758 |
Cluster Labels | 3Q LOSS MUTATED | 3Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 44 | 802 |
Cluster Labels | 4P LOSS MUTATED | 4P LOSS WILD-TYPE |
---|---|---|
Number of samples | 176 | 670 |
Cluster Labels | 4Q LOSS MUTATED | 4Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 148 | 698 |
Cluster Labels | 5P LOSS MUTATED | 5P LOSS WILD-TYPE |
---|---|---|
Number of samples | 67 | 779 |
Cluster Labels | 5Q LOSS MUTATED | 5Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 118 | 728 |
Cluster Labels | 6P LOSS MUTATED | 6P LOSS WILD-TYPE |
---|---|---|
Number of samples | 105 | 741 |
Cluster Labels | 6Q LOSS MUTATED | 6Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 160 | 686 |
Cluster Labels | 7P LOSS MUTATED | 7P LOSS WILD-TYPE |
---|---|---|
Number of samples | 46 | 800 |
Cluster Labels | 7Q LOSS MUTATED | 7Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 63 | 783 |
Cluster Labels | 8P LOSS MUTATED | 8P LOSS WILD-TYPE |
---|---|---|
Number of samples | 264 | 582 |
Cluster Labels | 8Q LOSS MUTATED | 8Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 44 | 802 |
Cluster Labels | 9P LOSS MUTATED | 9P LOSS WILD-TYPE |
---|---|---|
Number of samples | 182 | 664 |
Cluster Labels | 9Q LOSS MUTATED | 9Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 139 | 707 |
Cluster Labels | 10P LOSS MUTATED | 10P LOSS WILD-TYPE |
---|---|---|
Number of samples | 68 | 778 |
Cluster Labels | 10Q LOSS MUTATED | 10Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 105 | 741 |
Cluster Labels | 11P LOSS MUTATED | 11P LOSS WILD-TYPE |
---|---|---|
Number of samples | 142 | 704 |
Cluster Labels | 11Q LOSS MUTATED | 11Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 220 | 626 |
Cluster Labels | 12P LOSS MUTATED | 12P LOSS WILD-TYPE |
---|---|---|
Number of samples | 64 | 782 |
Cluster Labels | 12Q LOSS MUTATED | 12Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 49 | 797 |
Cluster Labels | 13Q LOSS MUTATED | 13Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 254 | 592 |
Cluster Labels | 14Q LOSS MUTATED | 14Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 124 | 722 |
Cluster Labels | 15Q LOSS MUTATED | 15Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 153 | 693 |
Cluster Labels | 16P LOSS MUTATED | 16P LOSS WILD-TYPE |
---|---|---|
Number of samples | 52 | 794 |
Cluster Labels | 16Q LOSS MUTATED | 16Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 371 | 475 |
P value = 0.000325 (t-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 845 | 58.5 (13.2) |
16Q LOSS MUTATED | 371 | 60.4 (12.8) |
16Q LOSS WILD-TYPE | 474 | 57.1 (13.4) |
Cluster Labels | 17P LOSS MUTATED | 17P LOSS WILD-TYPE |
---|---|---|
Number of samples | 353 | 493 |
Cluster Labels | 17Q LOSS MUTATED | 17Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 135 | 711 |
Cluster Labels | 18P LOSS MUTATED | 18P LOSS WILD-TYPE |
---|---|---|
Number of samples | 166 | 680 |
Cluster Labels | 18Q LOSS MUTATED | 18Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 166 | 680 |
Cluster Labels | 19P LOSS MUTATED | 19P LOSS WILD-TYPE |
---|---|---|
Number of samples | 64 | 782 |
Cluster Labels | 19Q LOSS MUTATED | 19Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 50 | 796 |
Cluster Labels | 20P LOSS MUTATED | 20P LOSS WILD-TYPE |
---|---|---|
Number of samples | 51 | 795 |
Cluster Labels | 20Q LOSS MUTATED | 20Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 27 | 819 |
Cluster Labels | 21Q LOSS MUTATED | 21Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 84 | 762 |
Cluster Labels | 22Q LOSS MUTATED | 22Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 285 | 561 |
Cluster Labels | XQ LOSS MUTATED | XQ LOSS WILD-TYPE |
---|---|---|
Number of samples | 30 | 816 |
-
Cluster data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = BRCA-TP.clin.merged.picked.txt
-
Number of patients = 846
-
Number of clustering approaches = 80
-
Number of selected clinical features = 9
-
Exclude small clusters that include fewer than K patients, 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 two tumor subtypes using 't.test' function in R
For binary clinical features, 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.