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 9 clinical features across 161 patients, 6 significant findings 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 '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 '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 correlate to 'GENDER'.
-
2 subtypes identified in current cancer cohort by '20q gain mutation analysis'. These subtypes correlate to 'GENDER'.
-
2 subtypes identified in current cancer cohort by '22q gain mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by '1p loss mutation analysis'. These subtypes correlate to 'PATHOLOGICSPREAD(M)' and 'TUMOR.STAGE'.
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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 correlate to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
-
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 do not correlate to any clinical features.
-
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.
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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 |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
Statistical Tests | logrank test | t-test | Fisher's exact test | Chi-square test | Chi-square test | Chi-square test | Chi-square test | Chi-square test | Fisher's exact test |
1p gain |
0.212 (1.00) |
0.403 (1.00) |
0.712 (1.00) |
0.969 (1.00) |
0.74 (1.00) |
0.454 (1.00) |
0.959 (1.00) |
1 (1.00) |
|
1q gain |
0.77 (1.00) |
0.521 (1.00) |
0.22 (1.00) |
0.3 (1.00) |
0.505 (1.00) |
0.253 (1.00) |
0.6 (1.00) |
0.341 (1.00) |
0.106 (1.00) |
2p gain |
0.692 (1.00) |
0.292 (1.00) |
0.741 (1.00) |
0.586 (1.00) |
0.275 (1.00) |
0.224 (1.00) |
0.662 (1.00) |
0.0587 (1.00) |
1 (1.00) |
2q gain |
0.406 (1.00) |
0.588 (1.00) |
0.527 (1.00) |
0.605 (1.00) |
0.508 (1.00) |
0.224 (1.00) |
0.935 (1.00) |
0.251 (1.00) |
1 (1.00) |
3p gain |
0.543 (1.00) |
0.648 (1.00) |
0.862 (1.00) |
0.885 (1.00) |
0.289 (1.00) |
0.637 (1.00) |
0.622 (1.00) |
1 (1.00) |
|
3q gain |
0.377 (1.00) |
0.0273 (1.00) |
0.0157 (1.00) |
0.484 (1.00) |
0.891 (1.00) |
0.76 (1.00) |
0.411 (1.00) |
0.987 (1.00) |
1 (1.00) |
4p gain |
0.159 (1.00) |
0.273 (1.00) |
0.0296 (1.00) |
0.806 (1.00) |
0.715 (1.00) |
0.321 (1.00) |
1 (1.00) |
||
5p gain |
0.975 (1.00) |
0.763 (1.00) |
0.19 (1.00) |
0.494 (1.00) |
0.743 (1.00) |
0.663 (1.00) |
0.268 (1.00) |
0.118 (1.00) |
0.184 (1.00) |
5q gain |
0.137 (1.00) |
0.792 (1.00) |
0.403 (1.00) |
0.0419 (1.00) |
0.856 (1.00) |
0.717 (1.00) |
0.504 (1.00) |
0.679 (1.00) |
1 (1.00) |
6p gain |
0.788 (1.00) |
0.838 (1.00) |
0.758 (1.00) |
0.799 (1.00) |
0.232 (1.00) |
0.627 (1.00) |
0.617 (1.00) |
0.387 (1.00) |
1 (1.00) |
6q gain |
0.35 (1.00) |
0.891 (1.00) |
1 (1.00) |
0.78 (1.00) |
0.363 (1.00) |
0.655 (1.00) |
0.31 (1.00) |
0.694 (1.00) |
1 (1.00) |
7p gain |
0.524 (1.00) |
0.0136 (1.00) |
0.117 (1.00) |
0.319 (1.00) |
0.475 (1.00) |
0.543 (1.00) |
0.677 (1.00) |
0.167 (1.00) |
0.641 (1.00) |
7q gain |
0.735 (1.00) |
0.00432 (1.00) |
0.37 (1.00) |
0.446 (1.00) |
0.224 (1.00) |
0.619 (1.00) |
0.24 (1.00) |
0.136 (1.00) |
1 (1.00) |
8p gain |
0.599 (1.00) |
0.0443 (1.00) |
0.386 (1.00) |
0.487 (1.00) |
0.0986 (1.00) |
0.581 (1.00) |
0.0778 (1.00) |
0.589 (1.00) |
0.174 (1.00) |
8q gain |
0.302 (1.00) |
0.03 (1.00) |
0.421 (1.00) |
0.635 (1.00) |
0.013 (1.00) |
0.181 (1.00) |
0.16 (1.00) |
0.249 (1.00) |
0.651 (1.00) |
9p gain |
0.844 (1.00) |
0.319 (1.00) |
0.353 (1.00) |
0.708 (1.00) |
0.0257 (1.00) |
0.147 (1.00) |
0.617 (1.00) |
0.0091 (1.00) |
0.301 (1.00) |
9q gain |
0.856 (1.00) |
0.188 (1.00) |
0.595 (1.00) |
0.942 (1.00) |
0.111 (1.00) |
0.168 (1.00) |
0.962 (1.00) |
0.124 (1.00) |
0.391 (1.00) |
10p gain |
0.976 (1.00) |
0.34 (1.00) |
0.362 (1.00) |
0.315 (1.00) |
0.446 (1.00) |
0.789 (1.00) |
0.528 (1.00) |
0.0423 (1.00) |
1 (1.00) |
10q gain |
0.634 (1.00) |
0.987 (1.00) |
0.741 (1.00) |
0.646 (1.00) |
0.842 (1.00) |
0.655 (1.00) |
0.916 (1.00) |
0.767 (1.00) |
1 (1.00) |
11p gain |
0.572 (1.00) |
0.648 (1.00) |
0.676 (1.00) |
0.395 (1.00) |
0.171 (1.00) |
0.637 (1.00) |
0.245 (1.00) |
1 (1.00) |
|
11q gain |
0.24 (1.00) |
0.77 (1.00) |
1 (1.00) |
0.802 (1.00) |
0.831 (1.00) |
0.672 (1.00) |
0.397 (1.00) |
0.731 (1.00) |
1 (1.00) |
12p gain |
0.726 (1.00) |
0.273 (1.00) |
0.105 (1.00) |
0.998 (1.00) |
0.303 (1.00) |
0.68 (1.00) |
0.266 (1.00) |
0.639 (1.00) |
1 (1.00) |
12q gain |
0.669 (1.00) |
0.0563 (1.00) |
0.741 (1.00) |
0.309 (1.00) |
0.842 (1.00) |
0.122 (1.00) |
0.916 (1.00) |
0.613 (1.00) |
0.277 (1.00) |
13q gain |
0.331 (1.00) |
0.731 (1.00) |
0.222 (1.00) |
0.501 (1.00) |
0.674 (1.00) |
0.432 (1.00) |
0.445 (1.00) |
0.714 (1.00) |
1 (1.00) |
15q gain |
0.178 (1.00) |
0.414 (1.00) |
0.243 (1.00) |
0.364 (1.00) |
0.451 (1.00) |
0.111 (1.00) |
0.75 (1.00) |
0.476 (1.00) |
1 (1.00) |
16p gain |
0.575 (1.00) |
0.614 (1.00) |
0.763 (1.00) |
0.61 (1.00) |
0.317 (1.00) |
0.0657 (1.00) |
0.279 (1.00) |
0.0137 (1.00) |
0.325 (1.00) |
16q gain |
0.671 (1.00) |
0.864 (1.00) |
1 (1.00) |
0.862 (1.00) |
0.0368 (1.00) |
0.297 (1.00) |
0.329 (1.00) |
0.0152 (1.00) |
1 (1.00) |
17p gain |
0.16 (1.00) |
0.55 (1.00) |
1 (1.00) |
0.805 (1.00) |
0.877 (1.00) |
0.0378 (1.00) |
0.00821 (1.00) |
0.197 (1.00) |
1 (1.00) |
17q gain |
0.174 (1.00) |
0.666 (1.00) |
0.741 (1.00) |
0.879 (1.00) |
0.79 (1.00) |
0.125 (1.00) |
0.0043 (1.00) |
0.216 (1.00) |
1 (1.00) |
18p gain |
0.61 (1.00) |
0.564 (1.00) |
1 (1.00) |
0.813 (1.00) |
0.879 (1.00) |
0.116 (1.00) |
0.868 (1.00) |
0.604 (1.00) |
0.347 (1.00) |
18q gain |
0.598 (1.00) |
0.619 (1.00) |
0.441 (1.00) |
0.313 (1.00) |
0.61 (1.00) |
0.84 (1.00) |
0.21 (1.00) |
0.822 (1.00) |
1 (1.00) |
19p gain |
0.965 (1.00) |
0.429 (1.00) |
0.0155 (1.00) |
0.536 (1.00) |
0.718 (1.00) |
0.123 (1.00) |
0.00967 (1.00) |
0.0316 (1.00) |
1 (1.00) |
19q gain |
0.309 (1.00) |
0.214 (1.00) |
0.121 (1.00) |
0.509 (1.00) |
0.358 (1.00) |
0.145 (1.00) |
0.232 (1.00) |
0.015 (1.00) |
0.432 (1.00) |
20p gain |
0.0693 (1.00) |
0.207 (1.00) |
0.000128 (0.083) |
0.685 (1.00) |
0.0673 (1.00) |
0.702 (1.00) |
0.138 (1.00) |
0.179 (1.00) |
0.651 (1.00) |
20q gain |
0.0524 (1.00) |
0.134 (1.00) |
0.00037 (0.24) |
0.399 (1.00) |
0.00151 (0.974) |
0.265 (1.00) |
0.0558 (1.00) |
0.186 (1.00) |
0.665 (1.00) |
22q gain |
0.765 (1.00) |
0.266 (1.00) |
1 (1.00) |
0.927 (1.00) |
0.708 (1.00) |
0.37 (1.00) |
0.715 (1.00) |
0.321 (1.00) |
1 (1.00) |
1p loss |
0.00489 (1.00) |
0.688 (1.00) |
0.222 (1.00) |
0.885 (1.00) |
0.345 (1.00) |
0.245 (1.00) |
7.97e-08 (5.2e-05) |
0.000121 (0.0786) |
1 (1.00) |
2p loss |
0.566 (1.00) |
0.708 (1.00) |
0.361 (1.00) |
0.168 (1.00) |
0.358 (1.00) |
0.0909 (1.00) |
|||
2q loss |
0.867 (1.00) |
1 (1.00) |
0.308 (1.00) |
0.468 (1.00) |
0.0819 (1.00) |
0.202 (1.00) |
0.213 (1.00) |
0.12 (1.00) |
|
3p loss |
0.633 (1.00) |
0.561 (1.00) |
1 (1.00) |
0.865 (1.00) |
0.616 (1.00) |
0.655 (1.00) |
0.662 (1.00) |
0.71 (1.00) |
1 (1.00) |
3q loss |
0.727 (1.00) |
0.639 (1.00) |
0.403 (1.00) |
0.852 (1.00) |
0.914 (1.00) |
0.717 (1.00) |
0.504 (1.00) |
0.722 (1.00) |
1 (1.00) |
4p loss |
0.704 (1.00) |
0.129 (1.00) |
0.824 (1.00) |
0.0812 (1.00) |
0.0416 (1.00) |
0.981 (1.00) |
0.487 (1.00) |
0.0792 (1.00) |
0.161 (1.00) |
4q loss |
0.748 (1.00) |
0.338 (1.00) |
0.466 (1.00) |
0.0279 (1.00) |
0.0164 (1.00) |
0.825 (1.00) |
0.92 (1.00) |
0.345 (1.00) |
0.117 (1.00) |
5p loss |
0.415 (1.00) |
0.607 (1.00) |
1 (1.00) |
0.022 (1.00) |
0.532 (1.00) |
0.367 (1.00) |
0.448 (1.00) |
0.29 (1.00) |
1 (1.00) |
5q loss |
0.12 (1.00) |
0.5 (1.00) |
0.286 (1.00) |
0.000403 (0.26) |
0.0509 (1.00) |
0.831 (1.00) |
0.163 (1.00) |
0.241 (1.00) |
0.391 (1.00) |
6p loss |
0.958 (1.00) |
0.0474 (1.00) |
0.715 (1.00) |
0.0136 (1.00) |
0.11 (1.00) |
0.109 (1.00) |
0.795 (1.00) |
0.259 (1.00) |
1 (1.00) |
6q loss |
0.611 (1.00) |
0.218 (1.00) |
0.763 (1.00) |
0.191 (1.00) |
0.223 (1.00) |
0.393 (1.00) |
0.933 (1.00) |
0.0693 (1.00) |
1 (1.00) |
7p loss |
0.213 (1.00) |
0.192 (1.00) |
0.273 (1.00) |
0.721 (1.00) |
0.0476 (1.00) |
0.0911 (1.00) |
0.715 (1.00) |
0.624 (1.00) |
1 (1.00) |
7q loss |
0.208 (1.00) |
0.14 (1.00) |
0.0819 (1.00) |
0.454 (1.00) |
0.297 (1.00) |
0.424 (1.00) |
0.567 (1.00) |
0.924 (1.00) |
1 (1.00) |
8p loss |
0.27 (1.00) |
0.439 (1.00) |
0.741 (1.00) |
0.0385 (1.00) |
0.529 (1.00) |
0.286 (1.00) |
0.916 (1.00) |
0.645 (1.00) |
1 (1.00) |
8q loss |
0.607 (1.00) |
1 (1.00) |
0.00448 (1.00) |
0.715 (1.00) |
1 (1.00) |
||||
9p loss |
0.0551 (1.00) |
0.513 (1.00) |
0.663 (1.00) |
0.414 (1.00) |
0.036 (1.00) |
0.377 (1.00) |
0.805 (1.00) |
0.584 (1.00) |
0.591 (1.00) |
9q loss |
0.199 (1.00) |
0.368 (1.00) |
1 (1.00) |
0.675 (1.00) |
0.12 (1.00) |
0.322 (1.00) |
0.935 (1.00) |
0.923 (1.00) |
0.301 (1.00) |
10p loss |
0.203 (1.00) |
0.355 (1.00) |
0.318 (1.00) |
0.0191 (1.00) |
0.0433 (1.00) |
0.456 (1.00) |
0.31 (1.00) |
0.406 (1.00) |
0.0315 (1.00) |
10q loss |
0.263 (1.00) |
0.676 (1.00) |
0.741 (1.00) |
0.0248 (1.00) |
0.262 (1.00) |
0.57 (1.00) |
0.351 (1.00) |
0.256 (1.00) |
0.253 (1.00) |
11p loss |
0.347 (1.00) |
0.237 (1.00) |
0.548 (1.00) |
0.297 (1.00) |
0.216 (1.00) |
0.815 (1.00) |
0.031 (1.00) |
0.489 (1.00) |
1 (1.00) |
11q loss |
0.356 (1.00) |
0.466 (1.00) |
0.315 (1.00) |
0.469 (1.00) |
0.312 (1.00) |
0.74 (1.00) |
0.425 (1.00) |
0.478 (1.00) |
1 (1.00) |
12p loss |
0.174 (1.00) |
0.705 (1.00) |
0.527 (1.00) |
0.361 (1.00) |
0.0877 (1.00) |
0.000375 (0.243) |
0.467 (1.00) |
0.000212 (0.138) |
0.301 (1.00) |
12q loss |
0.335 (1.00) |
0.21 (1.00) |
0.0819 (1.00) |
0.705 (1.00) |
0.226 (1.00) |
0.0432 (1.00) |
0.504 (1.00) |
0.11 (1.00) |
1 (1.00) |
13q loss |
0.866 (1.00) |
1 (1.00) |
0.325 (1.00) |
0.657 (1.00) |
0.527 (1.00) |
0.7 (1.00) |
0.445 (1.00) |
0.148 (1.00) |
|
14q loss |
0.208 (1.00) |
0.0776 (1.00) |
1 (1.00) |
0.905 (1.00) |
0.754 (1.00) |
0.462 (1.00) |
0.489 (1.00) |
0.73 (1.00) |
1 (1.00) |
15q loss |
0.58 (1.00) |
0.328 (1.00) |
1 (1.00) |
0.117 (1.00) |
0.0818 (1.00) |
0.452 (1.00) |
0.916 (1.00) |
0.573 (1.00) |
0.0315 (1.00) |
16p loss |
0.606 (1.00) |
0.396 (1.00) |
0.0853 (1.00) |
0.386 (1.00) |
0.269 (1.00) |
0.697 (1.00) |
0.702 (1.00) |
0.869 (1.00) |
1 (1.00) |
16q loss |
0.539 (1.00) |
0.941 (1.00) |
0.406 (1.00) |
0.464 (1.00) |
0.233 (1.00) |
0.296 (1.00) |
0.882 (1.00) |
0.808 (1.00) |
0.369 (1.00) |
17p loss |
0.463 (1.00) |
0.351 (1.00) |
0.547 (1.00) |
0.022 (1.00) |
0.0733 (1.00) |
0.292 (1.00) |
0.959 (1.00) |
0.45 (1.00) |
0.0541 (1.00) |
17q loss |
0.858 (1.00) |
0.667 (1.00) |
0.487 (1.00) |
0.0316 (1.00) |
0.873 (1.00) |
0.393 (1.00) |
0.457 (1.00) |
0.457 (1.00) |
0.253 (1.00) |
18p loss |
0.278 (1.00) |
0.872 (1.00) |
1 (1.00) |
0.952 (1.00) |
0.448 (1.00) |
0.339 (1.00) |
0.791 (1.00) |
0.44 (1.00) |
1 (1.00) |
18q loss |
0.213 (1.00) |
0.46 (1.00) |
0.505 (1.00) |
0.836 (1.00) |
0.453 (1.00) |
0.231 (1.00) |
0.245 (1.00) |
0.398 (1.00) |
1 (1.00) |
19p loss |
0.671 (1.00) |
0.905 (1.00) |
0.283 (1.00) |
0.544 (1.00) |
0.652 (1.00) |
0.346 (1.00) |
0.52 (1.00) |
0.541 (1.00) |
1 (1.00) |
19q loss |
0.879 (1.00) |
0.182 (1.00) |
0.364 (1.00) |
0.559 (1.00) |
0.562 (1.00) |
0.25 (1.00) |
0.539 (1.00) |
0.177 (1.00) |
1 (1.00) |
20p loss |
0.286 (1.00) |
0.873 (1.00) |
0.304 (1.00) |
0.862 (1.00) |
0.318 (1.00) |
0.707 (1.00) |
0.0424 (1.00) |
0.348 (1.00) |
1 (1.00) |
21q loss |
0.996 (1.00) |
0.668 (1.00) |
1 (1.00) |
0.647 (1.00) |
0.342 (1.00) |
0.968 (1.00) |
0.884 (1.00) |
0.722 (1.00) |
1 (1.00) |
22q loss |
0.655 (1.00) |
0.465 (1.00) |
1 (1.00) |
0.208 (1.00) |
0.549 (1.00) |
0.7 (1.00) |
0.82 (1.00) |
0.611 (1.00) |
0.525 (1.00) |
Xq loss |
0.139 (1.00) |
0.289 (1.00) |
0.702 (1.00) |
0.207 (1.00) |
0.0906 (1.00) |
0.37 (1.00) |
0.448 (1.00) |
0.222 (1.00) |
0.202 (1.00) |
Cluster Labels | 1P GAIN MUTATED | 1P GAIN WILD-TYPE |
---|---|---|
Number of samples | 6 | 155 |
Cluster Labels | 1Q GAIN MUTATED | 1Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 19 | 142 |
Cluster Labels | 2P GAIN MUTATED | 2P GAIN WILD-TYPE |
---|---|---|
Number of samples | 10 | 151 |
Cluster Labels | 2Q GAIN MUTATED | 2Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 11 | 150 |
Cluster Labels | 3P GAIN MUTATED | 3P GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 157 |
Cluster Labels | 3Q GAIN MUTATED | 3Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 13 | 148 |
Cluster Labels | 4P GAIN MUTATED | 4P GAIN WILD-TYPE |
---|---|---|
Number of samples | 3 | 158 |
Cluster Labels | 5P GAIN MUTATED | 5P GAIN WILD-TYPE |
---|---|---|
Number of samples | 26 | 135 |
Cluster Labels | 5Q GAIN MUTATED | 5Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 6 | 155 |
Cluster Labels | 6P GAIN MUTATED | 6P GAIN WILD-TYPE |
---|---|---|
Number of samples | 11 | 150 |
Cluster Labels | 6Q GAIN MUTATED | 6Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 10 | 151 |
Cluster Labels | 7P GAIN MUTATED | 7P GAIN WILD-TYPE |
---|---|---|
Number of samples | 49 | 112 |
Cluster Labels | 7Q GAIN MUTATED | 7Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 44 | 117 |
Cluster Labels | 8P GAIN MUTATED | 8P GAIN WILD-TYPE |
---|---|---|
Number of samples | 50 | 111 |
Cluster Labels | 8Q GAIN MUTATED | 8Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 68 | 93 |
Cluster Labels | 9P GAIN MUTATED | 9P GAIN WILD-TYPE |
---|---|---|
Number of samples | 11 | 150 |
Cluster Labels | 9Q GAIN MUTATED | 9Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 15 | 146 |
Cluster Labels | 10P GAIN MUTATED | 10P GAIN WILD-TYPE |
---|---|---|
Number of samples | 23 | 138 |
Cluster Labels | 10Q GAIN MUTATED | 10Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 10 | 151 |
Cluster Labels | 11P GAIN MUTATED | 11P GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 157 |
Cluster Labels | 11Q GAIN MUTATED | 11Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 8 | 153 |
Cluster Labels | 12P GAIN MUTATED | 12P GAIN WILD-TYPE |
---|---|---|
Number of samples | 15 | 146 |
Cluster Labels | 12Q GAIN MUTATED | 12Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 10 | 151 |
Cluster Labels | 13Q GAIN MUTATED | 13Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 30 | 131 |
Cluster Labels | 15Q GAIN MUTATED | 15Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 7 | 154 |
Cluster Labels | 16P GAIN MUTATED | 16P GAIN WILD-TYPE |
---|---|---|
Number of samples | 12 | 149 |
Cluster Labels | 16Q GAIN MUTATED | 16Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 8 | 153 |
Cluster Labels | 17P GAIN MUTATED | 17P GAIN WILD-TYPE |
---|---|---|
Number of samples | 6 | 155 |
Cluster Labels | 17Q GAIN MUTATED | 17Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 9 | 152 |
Cluster Labels | 18P GAIN MUTATED | 18P GAIN WILD-TYPE |
---|---|---|
Number of samples | 13 | 148 |
Cluster Labels | 18Q GAIN MUTATED | 18Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 7 | 154 |
Cluster Labels | 19P GAIN MUTATED | 19P GAIN WILD-TYPE |
---|---|---|
Number of samples | 10 | 151 |
Cluster Labels | 19Q GAIN MUTATED | 19Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 17 | 144 |
Cluster Labels | 20P GAIN MUTATED | 20P GAIN WILD-TYPE |
---|---|---|
Number of samples | 61 | 100 |
P value = 0.000128 (Fisher's exact test), Q value = 0.083
nPatients | FEMALE | MALE |
---|---|---|
ALL | 65 | 96 |
20P GAIN MUTATED | 13 | 48 |
20P GAIN WILD-TYPE | 52 | 48 |
Cluster Labels | 20Q GAIN MUTATED | 20Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 75 | 86 |
P value = 0.00037 (Fisher's exact test), Q value = 0.24
nPatients | FEMALE | MALE |
---|---|---|
ALL | 65 | 96 |
20Q GAIN MUTATED | 19 | 56 |
20Q GAIN WILD-TYPE | 46 | 40 |
Cluster Labels | 22Q GAIN MUTATED | 22Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 3 | 158 |
Cluster Labels | 1P LOSS MUTATED | 1P LOSS WILD-TYPE |
---|---|---|
Number of samples | 6 | 155 |
P value = 7.97e-08 (Chi-square test), Q value = 5.2e-05
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 132 | 18 | 11 |
1P LOSS MUTATED | 1 | 5 | 0 |
1P LOSS WILD-TYPE | 131 | 13 | 11 |
P value = 0.000121 (Chi-square test), Q value = 0.079
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 25 | 43 | 48 | 29 |
1P LOSS MUTATED | 0 | 0 | 0 | 5 |
1P LOSS WILD-TYPE | 25 | 43 | 48 | 24 |
Cluster Labels | 2P LOSS MUTATED | 2P LOSS WILD-TYPE |
---|---|---|
Number of samples | 3 | 158 |
Cluster Labels | 2Q LOSS MUTATED | 2Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 4 | 157 |
Cluster Labels | 3P LOSS MUTATED | 3P LOSS WILD-TYPE |
---|---|---|
Number of samples | 10 | 151 |
Cluster Labels | 3Q LOSS MUTATED | 3Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 6 | 155 |
Cluster Labels | 4P LOSS MUTATED | 4P LOSS WILD-TYPE |
---|---|---|
Number of samples | 24 | 137 |
Cluster Labels | 4Q LOSS MUTATED | 4Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 20 | 141 |
Cluster Labels | 5P LOSS MUTATED | 5P LOSS WILD-TYPE |
---|---|---|
Number of samples | 7 | 154 |
Cluster Labels | 5Q LOSS MUTATED | 5Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 15 | 146 |
Cluster Labels | 6P LOSS MUTATED | 6P LOSS WILD-TYPE |
---|---|---|
Number of samples | 8 | 153 |
Cluster Labels | 6Q LOSS MUTATED | 6Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 12 | 149 |
Cluster Labels | 7P LOSS MUTATED | 7P LOSS WILD-TYPE |
---|---|---|
Number of samples | 3 | 158 |
Cluster Labels | 7Q LOSS MUTATED | 7Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 5 | 156 |
Cluster Labels | 8P LOSS MUTATED | 8P LOSS WILD-TYPE |
---|---|---|
Number of samples | 10 | 151 |
Cluster Labels | 8Q LOSS MUTATED | 8Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 3 | 158 |
Cluster Labels | 9P LOSS MUTATED | 9P LOSS WILD-TYPE |
---|---|---|
Number of samples | 26 | 135 |
Cluster Labels | 9Q LOSS MUTATED | 9Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 11 | 150 |
Cluster Labels | 10P LOSS MUTATED | 10P LOSS WILD-TYPE |
---|---|---|
Number of samples | 10 | 151 |
Cluster Labels | 10Q LOSS MUTATED | 10Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 9 | 152 |
Cluster Labels | 11P LOSS MUTATED | 11P LOSS WILD-TYPE |
---|---|---|
Number of samples | 12 | 149 |
Cluster Labels | 11Q LOSS MUTATED | 11Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 9 | 152 |
Cluster Labels | 12P LOSS MUTATED | 12P LOSS WILD-TYPE |
---|---|---|
Number of samples | 11 | 150 |
P value = 0.000375 (Chi-square test), Q value = 0.24
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 50 | 57 | 24 | 19 |
12P LOSS MUTATED | 10 | 0 | 0 | 1 |
12P LOSS WILD-TYPE | 40 | 57 | 24 | 18 |
P value = 0.000212 (Chi-square test), Q value = 0.14
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 25 | 43 | 48 | 29 |
12P LOSS MUTATED | 7 | 3 | 0 | 1 |
12P LOSS WILD-TYPE | 18 | 40 | 48 | 28 |
Cluster Labels | 12Q LOSS MUTATED | 12Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 6 | 155 |
Cluster Labels | 13Q LOSS MUTATED | 13Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 5 | 156 |
Cluster Labels | 14Q LOSS MUTATED | 14Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 10 | 151 |
Cluster Labels | 15Q LOSS MUTATED | 15Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 10 | 151 |
Cluster Labels | 16P LOSS MUTATED | 16P LOSS WILD-TYPE |
---|---|---|
Number of samples | 9 | 152 |
Cluster Labels | 16Q LOSS MUTATED | 16Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 14 | 147 |
Cluster Labels | 17P LOSS MUTATED | 17P LOSS WILD-TYPE |
---|---|---|
Number of samples | 32 | 129 |
Cluster Labels | 17Q LOSS MUTATED | 17Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 9 | 152 |
Cluster Labels | 18P LOSS MUTATED | 18P LOSS WILD-TYPE |
---|---|---|
Number of samples | 12 | 149 |
Cluster Labels | 18Q LOSS MUTATED | 18Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 24 | 137 |
Cluster Labels | 19P LOSS MUTATED | 19P LOSS WILD-TYPE |
---|---|---|
Number of samples | 16 | 145 |
Cluster Labels | 19Q LOSS MUTATED | 19Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 12 | 149 |
Cluster Labels | 20P LOSS MUTATED | 20P LOSS WILD-TYPE |
---|---|---|
Number of samples | 4 | 157 |
Cluster Labels | 21Q LOSS MUTATED | 21Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 29 | 132 |
Cluster Labels | 22Q LOSS MUTATED | 22Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 22 | 139 |
Cluster Labels | XQ LOSS MUTATED | XQ LOSS WILD-TYPE |
---|---|---|
Number of samples | 7 | 154 |
-
Cluster data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = STAD-TP.clin.merged.picked.txt
-
Number of patients = 161
-
Number of clustering approaches = 74
-
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.