This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between subtypes identified by 74 different clustering approaches and 12 clinical features across 125 patients, 8 significant findings detected with Q value < 0.25.
-
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 correlate to 'NUMBER.OF.LYMPH.NODES'.
-
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 correlate to 'NUMBER.OF.LYMPH.NODES'.
-
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 correlate to 'NUMBER.OF.LYMPH.NODES'.
-
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 correlate to 'NUMBER.OF.LYMPH.NODES'.
-
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 correlate to 'Time to Death'.
-
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 correlate to 'NUMBER.OF.LYMPH.NODES'.
-
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 '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 '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 correlate to 'KARNOFSKY.PERFORMANCE.SCORE'.
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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 '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 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
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 '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 |
KARNOFSKY PERFORMANCE SCORE |
NUMBERPACKYEARSSMOKED | STOPPEDSMOKINGYEAR | TOBACCOSMOKINGHISTORYINDICATOR |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
Statistical Tests | logrank test | t-test | Fisher's exact test | t-test | t-test | t-test | t-test | Chi-square test | Chi-square test | t-test | t-test | Chi-square test |
1p gain |
0.119 (1.00) |
0.545 (1.00) |
0.52 (1.00) |
0.494 (1.00) |
0.494 (1.00) |
0.887 (1.00) |
0.865 (1.00) |
0.678 (1.00) |
0.0183 (1.00) |
0.675 (1.00) |
0.546 (1.00) |
|
1q gain |
0.0469 (1.00) |
0.0293 (1.00) |
0.809 (1.00) |
0.257 (1.00) |
0.543 (1.00) |
0.299 (1.00) |
0.531 (1.00) |
0.41 (1.00) |
0.286 (1.00) |
0.994 (1.00) |
0.408 (1.00) |
|
2p gain |
0.408 (1.00) |
0.872 (1.00) |
0.000345 (0.268) |
0.257 (1.00) |
0.811 (1.00) |
0.00925 (1.00) |
0.669 (1.00) |
0.834 (1.00) |
0.367 (1.00) |
0.517 (1.00) |
0.431 (1.00) |
|
2q gain |
0.606 (1.00) |
0.554 (1.00) |
0.697 (1.00) |
0.257 (1.00) |
0.524 (1.00) |
0.00199 (1.00) |
0.381 (1.00) |
0.316 (1.00) |
0.193 (1.00) |
0.319 (1.00) |
0.0451 (1.00) |
|
3p gain |
0.402 (1.00) |
0.182 (1.00) |
0.46 (1.00) |
0.869 (1.00) |
0.975 (1.00) |
0.644 (1.00) |
0.904 (1.00) |
0.552 (1.00) |
0.0696 (1.00) |
0.273 (1.00) |
0.156 (1.00) |
|
3q gain |
0.117 (1.00) |
0.575 (1.00) |
0.124 (1.00) |
0.665 (1.00) |
0.809 (1.00) |
0.931 (1.00) |
0.796 (1.00) |
0.555 (1.00) |
0.0758 (1.00) |
0.26 (1.00) |
0.202 (1.00) |
|
4p gain |
0.0779 (1.00) |
0.858 (1.00) |
0.68 (1.00) |
0.312 (1.00) |
0.962 (1.00) |
0.604 (1.00) |
0.232 (1.00) |
0.41 (1.00) |
0.000235 (0.183) |
0.431 (1.00) |
||
4q gain |
0.296 (1.00) |
0.499 (1.00) |
1 (1.00) |
0.249 (1.00) |
0.888 (1.00) |
0.929 (1.00) |
0.69 (1.00) |
0.532 (1.00) |
||||
5p gain |
0.53 (1.00) |
0.329 (1.00) |
0.509 (1.00) |
0.0924 (1.00) |
0.586 (1.00) |
0.726 (1.00) |
0.41 (1.00) |
0.976 (1.00) |
0.00362 (1.00) |
0.0654 (1.00) |
0.367 (1.00) |
|
5q gain |
0.519 (1.00) |
0.438 (1.00) |
0.556 (1.00) |
0.36 (1.00) |
0.877 (1.00) |
0.768 (1.00) |
0.762 (1.00) |
0.708 (1.00) |
0.11 (1.00) |
0.000136 (0.105) |
0.0207 (1.00) |
|
6p gain |
0.225 (1.00) |
0.401 (1.00) |
1 (1.00) |
0.45 (1.00) |
0.896 (1.00) |
0.162 (1.00) |
0.392 (1.00) |
0.865 (1.00) |
0.579 (1.00) |
0.00805 (1.00) |
0.824 (1.00) |
|
6q gain |
0.237 (1.00) |
0.621 (1.00) |
0.572 (1.00) |
0.689 (1.00) |
0.553 (1.00) |
0.0696 (1.00) |
0.78 (1.00) |
0.15 (1.00) |
0.00748 (1.00) |
0.618 (1.00) |
||
7p gain |
0.386 (1.00) |
0.523 (1.00) |
0.509 (1.00) |
0.141 (1.00) |
0.777 (1.00) |
0.794 (1.00) |
0.199 (1.00) |
0.425 (1.00) |
0.197 (1.00) |
0.688 (1.00) |
0.332 (1.00) |
|
7q gain |
0.66 (1.00) |
0.599 (1.00) |
0.042 (1.00) |
0.212 (1.00) |
0.353 (1.00) |
0.867 (1.00) |
0.482 (1.00) |
0.357 (1.00) |
0.0661 (1.00) |
0.822 (1.00) |
0.37 (1.00) |
|
8p gain |
0.957 (1.00) |
0.201 (1.00) |
0.759 (1.00) |
0.821 (1.00) |
0.17 (1.00) |
0.0522 (1.00) |
0.134 (1.00) |
0.738 (1.00) |
0.618 (1.00) |
0.00174 (1.00) |
0.662 (1.00) |
|
8q gain |
0.846 (1.00) |
0.444 (1.00) |
1 (1.00) |
0.315 (1.00) |
0.422 (1.00) |
0.477 (1.00) |
0.884 (1.00) |
0.454 (1.00) |
0.835 (1.00) |
0.0211 (1.00) |
0.209 (1.00) |
|
9p gain |
0.0295 (1.00) |
0.0278 (1.00) |
0.181 (1.00) |
0.842 (1.00) |
0.0398 (1.00) |
0.699 (1.00) |
0.092 (1.00) |
0.347 (1.00) |
0.657 (1.00) |
0.00175 (1.00) |
0.0197 (1.00) |
|
9q gain |
0.0699 (1.00) |
0.279 (1.00) |
0.479 (1.00) |
0.786 (1.00) |
0.0462 (1.00) |
0.257 (1.00) |
0.787 (1.00) |
0.258 (1.00) |
0.168 (1.00) |
4.93e-06 (0.00386) |
0.000507 (0.393) |
|
10p gain |
0.68 (1.00) |
0.99 (1.00) |
1 (1.00) |
0.593 (1.00) |
0.602 (1.00) |
0.26 (1.00) |
0.81 (1.00) |
0.419 (1.00) |
0.395 (1.00) |
0.747 (1.00) |
0.0927 (1.00) |
|
10q gain |
0.425 (1.00) |
0.118 (1.00) |
1 (1.00) |
0.631 (1.00) |
0.37 (1.00) |
0.842 (1.00) |
0.326 (1.00) |
0.204 (1.00) |
0.54 (1.00) |
0.328 (1.00) |
||
11p gain |
0.0696 (1.00) |
0.118 (1.00) |
0.339 (1.00) |
0.0875 (1.00) |
0.563 (1.00) |
0.0741 (1.00) |
0.213 (1.00) |
0.767 (1.00) |
0.301 (1.00) |
0.0955 (1.00) |
0.674 (1.00) |
|
11q gain |
0.199 (1.00) |
0.523 (1.00) |
0.339 (1.00) |
0.624 (1.00) |
0.571 (1.00) |
0.443 (1.00) |
0.599 (1.00) |
0.859 (1.00) |
0.342 (1.00) |
0.34 (1.00) |
0.82 (1.00) |
|
12p gain |
0.849 (1.00) |
0.771 (1.00) |
0.794 (1.00) |
0.465 (1.00) |
0.902 (1.00) |
0.511 (1.00) |
0.487 (1.00) |
0.609 (1.00) |
0.953 (1.00) |
0.0202 (1.00) |
0.11 (1.00) |
|
12q gain |
0.3 (1.00) |
0.502 (1.00) |
0.235 (1.00) |
0.347 (1.00) |
0.66 (1.00) |
0.421 (1.00) |
0.89 (1.00) |
0.331 (1.00) |
0.827 (1.00) |
0.0775 (1.00) |
0.0235 (1.00) |
|
13q gain |
0.482 (1.00) |
0.669 (1.00) |
1 (1.00) |
0.64 (1.00) |
0.104 (1.00) |
0.664 (1.00) |
0.981 (1.00) |
0.196 (1.00) |
0.426 (1.00) |
0.899 (1.00) |
0.724 (1.00) |
|
14q gain |
0.896 (1.00) |
0.68 (1.00) |
0.479 (1.00) |
0.471 (1.00) |
0.271 (1.00) |
0.531 (1.00) |
0.322 (1.00) |
0.513 (1.00) |
0.444 (1.00) |
9.18e-05 (0.0715) |
0.577 (1.00) |
|
15q gain |
0.113 (1.00) |
0.809 (1.00) |
1 (1.00) |
0.494 (1.00) |
0.236 (1.00) |
0.566 (1.00) |
0.939 (1.00) |
0.951 (1.00) |
||||
16p gain |
8.9e-05 (0.0695) |
0.493 (1.00) |
0.453 (1.00) |
0.616 (1.00) |
0.189 (1.00) |
0.902 (1.00) |
0.409 (1.00) |
0.117 (1.00) |
0.796 (1.00) |
0.0652 (1.00) |
0.9 (1.00) |
|
16q gain |
0.00253 (1.00) |
0.351 (1.00) |
0.0799 (1.00) |
0.468 (1.00) |
0.382 (1.00) |
0.994 (1.00) |
0.376 (1.00) |
0.429 (1.00) |
0.638 (1.00) |
0.0508 (1.00) |
0.754 (1.00) |
|
17p gain |
0.473 (1.00) |
0.998 (1.00) |
0.434 (1.00) |
0.744 (1.00) |
0.615 (1.00) |
0.978 (1.00) |
0.302 (1.00) |
0.289 (1.00) |
5.22e-06 (0.00408) |
0.00107 (0.824) |
||
17q gain |
0.562 (1.00) |
0.985 (1.00) |
1 (1.00) |
0.0421 (1.00) |
0.483 (1.00) |
0.538 (1.00) |
0.117 (1.00) |
0.228 (1.00) |
0.0668 (1.00) |
0.965 (1.00) |
0.0457 (1.00) |
|
18p gain |
0.691 (1.00) |
0.666 (1.00) |
0.596 (1.00) |
0.469 (1.00) |
0.342 (1.00) |
0.376 (1.00) |
0.0561 (1.00) |
0.261 (1.00) |
0.419 (1.00) |
0.683 (1.00) |
0.431 (1.00) |
|
18q gain |
0.0396 (1.00) |
0.825 (1.00) |
1 (1.00) |
0.739 (1.00) |
0.531 (1.00) |
0.213 (1.00) |
0.203 (1.00) |
0.876 (1.00) |
0.258 (1.00) |
0.824 (1.00) |
||
19p gain |
0.892 (1.00) |
0.929 (1.00) |
1 (1.00) |
0.136 (1.00) |
0.581 (1.00) |
0.56 (1.00) |
0.529 (1.00) |
0.787 (1.00) |
0.775 (1.00) |
0.0606 (1.00) |
0.662 (1.00) |
|
19q gain |
0.211 (1.00) |
0.976 (1.00) |
0.309 (1.00) |
0.226 (1.00) |
0.368 (1.00) |
0.628 (1.00) |
0.539 (1.00) |
0.855 (1.00) |
0.853 (1.00) |
0.712 (1.00) |
0.639 (1.00) |
|
20p gain |
0.426 (1.00) |
0.979 (1.00) |
0.211 (1.00) |
0.753 (1.00) |
0.255 (1.00) |
0.193 (1.00) |
0.646 (1.00) |
0.261 (1.00) |
0.695 (1.00) |
0.445 (1.00) |
0.591 (1.00) |
|
20q gain |
0.693 (1.00) |
0.407 (1.00) |
1 (1.00) |
0.632 (1.00) |
0.0908 (1.00) |
0.185 (1.00) |
0.0882 (1.00) |
0.881 (1.00) |
0.936 (1.00) |
0.367 (1.00) |
0.559 (1.00) |
|
21q gain |
0.298 (1.00) |
0.353 (1.00) |
1 (1.00) |
0.907 (1.00) |
0.541 (1.00) |
0.765 (1.00) |
0.711 (1.00) |
0.775 (1.00) |
0.211 (1.00) |
0.826 (1.00) |
0.0293 (1.00) |
|
22q gain |
0.0684 (1.00) |
0.573 (1.00) |
0.726 (1.00) |
0.606 (1.00) |
0.412 (1.00) |
0.211 (1.00) |
0.00778 (1.00) |
0.737 (1.00) |
0.295 (1.00) |
0.52 (1.00) |
0.808 (1.00) |
|
Xq gain |
0.415 (1.00) |
0.785 (1.00) |
0.654 (1.00) |
0.567 (1.00) |
0.824 (1.00) |
0.0625 (1.00) |
0.13 (1.00) |
0.705 (1.00) |
0.674 (1.00) |
|||
2p loss |
0.624 (1.00) |
0.68 (1.00) |
0.674 (1.00) |
0.904 (1.00) |
0.215 (1.00) |
0.912 (1.00) |
0.556 (1.00) |
0.738 (1.00) |
0.343 (1.00) |
0.392 (1.00) |
||
2q loss |
0.033 (1.00) |
0.608 (1.00) |
0.757 (1.00) |
0.492 (1.00) |
0.208 (1.00) |
0.923 (1.00) |
0.924 (1.00) |
0.751 (1.00) |
0.158 (1.00) |
0.262 (1.00) |
0.665 (1.00) |
|
3p loss |
0.991 (1.00) |
0.694 (1.00) |
0.242 (1.00) |
0.429 (1.00) |
0.76 (1.00) |
0.053 (1.00) |
0.792 (1.00) |
0.598 (1.00) |
0.876 (1.00) |
0.94 (1.00) |
||
4p loss |
0.576 (1.00) |
0.912 (1.00) |
1 (1.00) |
0.0948 (1.00) |
0.535 (1.00) |
0.621 (1.00) |
0.919 (1.00) |
0.153 (1.00) |
0.0254 (1.00) |
0.266 (1.00) |
0.246 (1.00) |
|
4q loss |
0.782 (1.00) |
0.841 (1.00) |
0.794 (1.00) |
0.0948 (1.00) |
0.944 (1.00) |
0.401 (1.00) |
0.862 (1.00) |
0.195 (1.00) |
0.794 (1.00) |
0.74 (1.00) |
0.323 (1.00) |
|
5p loss |
0.335 (1.00) |
0.287 (1.00) |
0.299 (1.00) |
0.0998 (1.00) |
0.944 (1.00) |
0.212 (1.00) |
0.139 (1.00) |
0.737 (1.00) |
0.969 (1.00) |
0.77 (1.00) |
0.132 (1.00) |
|
5q loss |
0.806 (1.00) |
0.242 (1.00) |
0.813 (1.00) |
0.666 (1.00) |
0.256 (1.00) |
0.298 (1.00) |
0.127 (1.00) |
0.141 (1.00) |
0.359 (1.00) |
0.426 (1.00) |
0.284 (1.00) |
|
6p loss |
0.984 (1.00) |
0.515 (1.00) |
0.539 (1.00) |
6.63e-05 (0.0518) |
0.737 (1.00) |
0.927 (1.00) |
0.494 (1.00) |
0.496 (1.00) |
0.0282 (1.00) |
0.358 (1.00) |
0.0341 (1.00) |
|
6q loss |
0.351 (1.00) |
0.798 (1.00) |
0.62 (1.00) |
0.242 (1.00) |
0.2 (1.00) |
0.21 (1.00) |
0.0557 (1.00) |
0.171 (1.00) |
0.108 (1.00) |
0.245 (1.00) |
0.0165 (1.00) |
|
8p loss |
0.303 (1.00) |
0.671 (1.00) |
0.395 (1.00) |
0.29 (1.00) |
0.37 (1.00) |
0.35 (1.00) |
0.883 (1.00) |
0.0125 (1.00) |
0.22 (1.00) |
0.49 (1.00) |
0.104 (1.00) |
|
8q loss |
0.519 (1.00) |
0.08 (1.00) |
0.607 (1.00) |
0.851 (1.00) |
0.54 (1.00) |
0.716 (1.00) |
0.0827 (1.00) |
0.791 (1.00) |
0.25 (1.00) |
0.394 (1.00) |
||
9p loss |
0.812 (1.00) |
0.425 (1.00) |
0.27 (1.00) |
0.743 (1.00) |
0.193 (1.00) |
0.382 (1.00) |
0.139 (1.00) |
0.24 (1.00) |
0.669 (1.00) |
0.928 (1.00) |
0.67 (1.00) |
|
9q loss |
0.678 (1.00) |
0.767 (1.00) |
0.178 (1.00) |
0.651 (1.00) |
0.129 (1.00) |
0.481 (1.00) |
0.393 (1.00) |
0.623 (1.00) |
0.615 (1.00) |
0.0646 (1.00) |
0.639 (1.00) |
|
10p loss |
0.564 (1.00) |
0.987 (1.00) |
1 (1.00) |
0.0186 (1.00) |
0.648 (1.00) |
0.771 (1.00) |
0.00691 (1.00) |
0.513 (1.00) |
0.696 (1.00) |
0.031 (1.00) |
0.914 (1.00) |
|
10q loss |
0.52 (1.00) |
0.0266 (1.00) |
0.805 (1.00) |
0.134 (1.00) |
0.612 (1.00) |
0.817 (1.00) |
0.141 (1.00) |
0.959 (1.00) |
0.773 (1.00) |
0.812 (1.00) |
0.791 (1.00) |
|
11p loss |
0.457 (1.00) |
0.127 (1.00) |
0.668 (1.00) |
0.0359 (1.00) |
0.697 (1.00) |
0.818 (1.00) |
0.586 (1.00) |
0.0294 (1.00) |
0.85 (1.00) |
0.276 (1.00) |
0.108 (1.00) |
|
11q loss |
0.895 (1.00) |
0.715 (1.00) |
0.645 (1.00) |
0.708 (1.00) |
0.216 (1.00) |
0.663 (1.00) |
0.455 (1.00) |
0.269 (1.00) |
0.286 (1.00) |
0.15 (1.00) |
0.669 (1.00) |
|
12p loss |
0.997 (1.00) |
0.321 (1.00) |
0.324 (1.00) |
0.783 (1.00) |
0.18 (1.00) |
0.916 (1.00) |
0.791 (1.00) |
0.861 (1.00) |
0.908 (1.00) |
|||
12q loss |
0.127 (1.00) |
0.804 (1.00) |
0.68 (1.00) |
0.528 (1.00) |
0.956 (1.00) |
0.884 (1.00) |
0.975 (1.00) |
0.863 (1.00) |
0.231 (1.00) |
0.518 (1.00) |
0.929 (1.00) |
|
13q loss |
0.798 (1.00) |
0.62 (1.00) |
0.151 (1.00) |
0.0159 (1.00) |
0.595 (1.00) |
0.642 (1.00) |
0.0718 (1.00) |
0.603 (1.00) |
0.797 (1.00) |
0.562 (1.00) |
0.678 (1.00) |
|
14q loss |
0.254 (1.00) |
0.452 (1.00) |
0.397 (1.00) |
0.772 (1.00) |
0.0488 (1.00) |
0.0573 (1.00) |
0.715 (1.00) |
0.389 (1.00) |
0.589 (1.00) |
0.609 (1.00) |
0.0503 (1.00) |
|
15q loss |
0.419 (1.00) |
0.752 (1.00) |
0.539 (1.00) |
0.763 (1.00) |
0.767 (1.00) |
0.842 (1.00) |
0.207 (1.00) |
0.0612 (1.00) |
0.954 (1.00) |
0.928 (1.00) |
0.721 (1.00) |
|
16p loss |
0.41 (1.00) |
0.237 (1.00) |
0.111 (1.00) |
0.0945 (1.00) |
0.546 (1.00) |
0.864 (1.00) |
0.00476 (1.00) |
0.738 (1.00) |
0.594 (1.00) |
0.996 (1.00) |
0.875 (1.00) |
|
16q loss |
0.793 (1.00) |
0.361 (1.00) |
0.35 (1.00) |
0.191 (1.00) |
0.825 (1.00) |
0.234 (1.00) |
8.95e-05 (0.0698) |
0.611 (1.00) |
0.0667 (1.00) |
0.349 (1.00) |
0.665 (1.00) |
|
17p loss |
0.259 (1.00) |
0.823 (1.00) |
0.826 (1.00) |
0.856 (1.00) |
0.246 (1.00) |
0.916 (1.00) |
0.602 (1.00) |
0.528 (1.00) |
0.566 (1.00) |
0.674 (1.00) |
0.741 (1.00) |
|
17q loss |
0.821 (1.00) |
0.428 (1.00) |
1 (1.00) |
0.77 (1.00) |
0.565 (1.00) |
0.96 (1.00) |
0.916 (1.00) |
0.0346 (1.00) |
0.49 (1.00) |
|||
18p loss |
0.131 (1.00) |
0.0381 (1.00) |
0.58 (1.00) |
0.295 (1.00) |
0.588 (1.00) |
0.373 (1.00) |
0.993 (1.00) |
0.52 (1.00) |
0.681 (1.00) |
0.829 (1.00) |
0.605 (1.00) |
|
18q loss |
0.0276 (1.00) |
0.0314 (1.00) |
0.178 (1.00) |
0.57 (1.00) |
0.748 (1.00) |
0.23 (1.00) |
0.332 (1.00) |
0.681 (1.00) |
0.865 (1.00) |
0.847 (1.00) |
0.152 (1.00) |
|
19p loss |
0.382 (1.00) |
0.995 (1.00) |
1 (1.00) |
0.848 (1.00) |
0.213 (1.00) |
0.322 (1.00) |
0.000687 (0.532) |
0.0296 (1.00) |
0.267 (1.00) |
0.021 (1.00) |
||
19q loss |
0.00162 (1.00) |
0.867 (1.00) |
0.565 (1.00) |
0.39 (1.00) |
0.574 (1.00) |
0.686 (1.00) |
0.698 (1.00) |
0.642 (1.00) |
||||
20p loss |
0.876 (1.00) |
0.235 (1.00) |
1 (1.00) |
0.0367 (1.00) |
0.109 (1.00) |
0.659 (1.00) |
0.78 (1.00) |
0.875 (1.00) |
0.73 (1.00) |
0.618 (1.00) |
||
21q loss |
0.94 (1.00) |
0.0244 (1.00) |
1 (1.00) |
0.383 (1.00) |
0.808 (1.00) |
0.275 (1.00) |
0.93 (1.00) |
0.551 (1.00) |
0.192 (1.00) |
0.709 (1.00) |
0.518 (1.00) |
|
22q loss |
0.172 (1.00) |
0.64 (1.00) |
0.61 (1.00) |
0.187 (1.00) |
0.802 (1.00) |
0.983 (1.00) |
0.0686 (1.00) |
0.131 (1.00) |
0.204 (1.00) |
0.537 (1.00) |
0.562 (1.00) |
|
Xq loss |
0.738 (1.00) |
1 (1.00) |
0.956 (1.00) |
0.929 (1.00) |
0.00632 (1.00) |
0.0583 (1.00) |
Cluster Labels | 1P GAIN MUTATED | 1P GAIN WILD-TYPE |
---|---|---|
Number of samples | 14 | 111 |
Cluster Labels | 1Q GAIN MUTATED | 1Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 28 | 97 |
Cluster Labels | 2P GAIN MUTATED | 2P GAIN WILD-TYPE |
---|---|---|
Number of samples | 22 | 103 |
Cluster Labels | 2Q GAIN MUTATED | 2Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 9 | 116 |
Cluster Labels | 3P GAIN MUTATED | 3P GAIN WILD-TYPE |
---|---|---|
Number of samples | 27 | 98 |
Cluster Labels | 3Q GAIN MUTATED | 3Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 36 | 89 |
Cluster Labels | 4P GAIN MUTATED | 4P GAIN WILD-TYPE |
---|---|---|
Number of samples | 8 | 117 |
P value = 0.000235 (t-test), Q value = 0.18
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 94 | 1.9 (3.8) |
4P GAIN MUTATED | 5 | 0.2 (0.4) |
4P GAIN WILD-TYPE | 89 | 2.0 (3.9) |
Cluster Labels | 4Q GAIN MUTATED | 4Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 3 | 122 |
Cluster Labels | 5P GAIN MUTATED | 5P GAIN WILD-TYPE |
---|---|---|
Number of samples | 37 | 88 |
Cluster Labels | 5Q GAIN MUTATED | 5Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 17 | 108 |
P value = 0.000136 (t-test), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 94 | 1.9 (3.8) |
5Q GAIN MUTATED | 11 | 0.3 (0.5) |
5Q GAIN WILD-TYPE | 83 | 2.1 (4.0) |
Cluster Labels | 6P GAIN MUTATED | 6P GAIN WILD-TYPE |
---|---|---|
Number of samples | 7 | 118 |
Cluster Labels | 6Q GAIN MUTATED | 6Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 121 |
Cluster Labels | 7P GAIN MUTATED | 7P GAIN WILD-TYPE |
---|---|---|
Number of samples | 36 | 89 |
Cluster Labels | 7Q GAIN MUTATED | 7Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 35 | 90 |
Cluster Labels | 8P GAIN MUTATED | 8P GAIN WILD-TYPE |
---|---|---|
Number of samples | 14 | 111 |
Cluster Labels | 8Q GAIN MUTATED | 8Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 34 | 91 |
Cluster Labels | 9P GAIN MUTATED | 9P GAIN WILD-TYPE |
---|---|---|
Number of samples | 13 | 112 |
Cluster Labels | 9Q GAIN MUTATED | 9Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 11 | 114 |
P value = 4.93e-06 (t-test), Q value = 0.0039
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 94 | 1.9 (3.8) |
9Q GAIN MUTATED | 9 | 0.0 (0.0) |
9Q GAIN WILD-TYPE | 85 | 2.1 (4.0) |
Cluster Labels | 10P GAIN MUTATED | 10P GAIN WILD-TYPE |
---|---|---|
Number of samples | 25 | 100 |
Cluster Labels | 10Q GAIN MUTATED | 10Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 7 | 118 |
Cluster Labels | 11P GAIN MUTATED | 11P GAIN WILD-TYPE |
---|---|---|
Number of samples | 6 | 119 |
Cluster Labels | 11Q GAIN MUTATED | 11Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 6 | 119 |
Cluster Labels | 12P GAIN MUTATED | 12P GAIN WILD-TYPE |
---|---|---|
Number of samples | 22 | 103 |
Cluster Labels | 12Q GAIN MUTATED | 12Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 17 | 108 |
Cluster Labels | 13Q GAIN MUTATED | 13Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 21 | 104 |
Cluster Labels | 14Q GAIN MUTATED | 14Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 11 | 114 |
P value = 9.18e-05 (t-test), Q value = 0.072
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 94 | 1.9 (3.8) |
14Q GAIN MUTATED | 6 | 0.2 (0.4) |
14Q GAIN WILD-TYPE | 88 | 2.0 (3.9) |
Cluster Labels | 15Q GAIN MUTATED | 15Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 121 |
Cluster Labels | 16P GAIN MUTATED | 16P GAIN WILD-TYPE |
---|---|---|
Number of samples | 10 | 115 |
P value = 8.9e-05 (logrank test), Q value = 0.069
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 118 | 31 | 0.1 - 131.2 (6.9) |
16P GAIN MUTATED | 10 | 5 | 0.8 - 9.7 (4.5) |
16P GAIN WILD-TYPE | 108 | 26 | 0.1 - 131.2 (7.0) |
Cluster Labels | 16Q GAIN MUTATED | 16Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 12 | 113 |
Cluster Labels | 17P GAIN MUTATED | 17P GAIN WILD-TYPE |
---|---|---|
Number of samples | 8 | 117 |
P value = 5.22e-06 (t-test), Q value = 0.0041
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 94 | 1.9 (3.8) |
17P GAIN MUTATED | 5 | 0.0 (0.0) |
17P GAIN WILD-TYPE | 89 | 2.0 (3.9) |
Cluster Labels | 17Q GAIN MUTATED | 17Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 22 | 103 |
Cluster Labels | 18P GAIN MUTATED | 18P GAIN WILD-TYPE |
---|---|---|
Number of samples | 22 | 103 |
Cluster Labels | 18Q GAIN MUTATED | 18Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 7 | 118 |
Cluster Labels | 19P GAIN MUTATED | 19P GAIN WILD-TYPE |
---|---|---|
Number of samples | 13 | 112 |
Cluster Labels | 19Q GAIN MUTATED | 19Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 25 | 100 |
Cluster Labels | 20P GAIN MUTATED | 20P GAIN WILD-TYPE |
---|---|---|
Number of samples | 48 | 77 |
Cluster Labels | 20Q GAIN MUTATED | 20Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 50 | 75 |
Cluster Labels | 21Q GAIN MUTATED | 21Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 23 | 102 |
Cluster Labels | 22Q GAIN MUTATED | 22Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 11 | 114 |
Cluster Labels | XQ GAIN MUTATED | XQ GAIN WILD-TYPE |
---|---|---|
Number of samples | 6 | 119 |
Cluster Labels | 2P LOSS MUTATED | 2P LOSS WILD-TYPE |
---|---|---|
Number of samples | 7 | 118 |
Cluster Labels | 2Q LOSS MUTATED | 2Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 15 | 110 |
Cluster Labels | 3P LOSS MUTATED | 3P LOSS WILD-TYPE |
---|---|---|
Number of samples | 9 | 116 |
Cluster Labels | 4P LOSS MUTATED | 4P LOSS WILD-TYPE |
---|---|---|
Number of samples | 24 | 101 |
Cluster Labels | 4Q LOSS MUTATED | 4Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 22 | 103 |
Cluster Labels | 5P LOSS MUTATED | 5P LOSS WILD-TYPE |
---|---|---|
Number of samples | 12 | 113 |
Cluster Labels | 5Q LOSS MUTATED | 5Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 30 | 95 |
Cluster Labels | 6P LOSS MUTATED | 6P LOSS WILD-TYPE |
---|---|---|
Number of samples | 15 | 110 |
P value = 6.63e-05 (t-test), Q value = 0.052
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 37 | 78.1 (16.3) |
6P LOSS MUTATED | 4 | 90.0 (0.0) |
6P LOSS WILD-TYPE | 33 | 76.7 (16.7) |
Cluster Labels | 6Q LOSS MUTATED | 6Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 26 | 99 |
Cluster Labels | 8P LOSS MUTATED | 8P LOSS WILD-TYPE |
---|---|---|
Number of samples | 43 | 82 |
Cluster Labels | 8Q LOSS MUTATED | 8Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 5 | 120 |
Cluster Labels | 9P LOSS MUTATED | 9P LOSS WILD-TYPE |
---|---|---|
Number of samples | 38 | 87 |
Cluster Labels | 9Q LOSS MUTATED | 9Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 36 | 89 |
Cluster Labels | 10P LOSS MUTATED | 10P LOSS WILD-TYPE |
---|---|---|
Number of samples | 17 | 108 |
Cluster Labels | 10Q LOSS MUTATED | 10Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 25 | 100 |
Cluster Labels | 11P LOSS MUTATED | 11P LOSS WILD-TYPE |
---|---|---|
Number of samples | 41 | 84 |
Cluster Labels | 11Q LOSS MUTATED | 11Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 31 | 94 |
Cluster Labels | 12P LOSS MUTATED | 12P LOSS WILD-TYPE |
---|---|---|
Number of samples | 5 | 120 |
Cluster Labels | 12Q LOSS MUTATED | 12Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 8 | 117 |
Cluster Labels | 13Q LOSS MUTATED | 13Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 18 | 107 |
Cluster Labels | 14Q LOSS MUTATED | 14Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 19 | 106 |
Cluster Labels | 15Q LOSS MUTATED | 15Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 15 | 110 |
Cluster Labels | 16P LOSS MUTATED | 16P LOSS WILD-TYPE |
---|---|---|
Number of samples | 14 | 111 |
Cluster Labels | 16Q LOSS MUTATED | 16Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 15 | 110 |
P value = 8.95e-05 (t-test), Q value = 0.07
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 119 | 2.6 (1.1) |
16Q LOSS MUTATED | 15 | 3.4 (0.6) |
16Q LOSS WILD-TYPE | 104 | 2.5 (1.2) |
Cluster Labels | 17P LOSS MUTATED | 17P LOSS WILD-TYPE |
---|---|---|
Number of samples | 36 | 89 |
Cluster Labels | 17Q LOSS MUTATED | 17Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 5 | 120 |
Cluster Labels | 18P LOSS MUTATED | 18P LOSS WILD-TYPE |
---|---|---|
Number of samples | 19 | 106 |
Cluster Labels | 18Q LOSS MUTATED | 18Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 34 | 91 |
Cluster Labels | 19P LOSS MUTATED | 19P LOSS WILD-TYPE |
---|---|---|
Number of samples | 8 | 117 |
Cluster Labels | 19Q LOSS MUTATED | 19Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 3 | 122 |
Cluster Labels | 20P LOSS MUTATED | 20P LOSS WILD-TYPE |
---|---|---|
Number of samples | 4 | 121 |
Cluster Labels | 21Q LOSS MUTATED | 21Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 14 | 111 |
Cluster Labels | 22Q LOSS MUTATED | 22Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 23 | 102 |
Cluster Labels | XQ LOSS MUTATED | XQ LOSS WILD-TYPE |
---|---|---|
Number of samples | 3 | 122 |
-
Cluster data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = BLCA-TP.clin.merged.picked.txt
-
Number of patients = 125
-
Number of clustering approaches = 74
-
Number of selected clinical features = 12
-
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.