This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between subtypes identified by 75 different clustering approaches and 9 clinical features across 162 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 '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.
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2 subtypes identified in current cancer cohort by '20q gain mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
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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.
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2 subtypes identified in current cancer cohort by 'Xq 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 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 '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 '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 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.
-
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 | Fisher's exact test | Chi-square test | Chi-square test | Chi-square test | Chi-square test | Fisher's exact test |
1p gain |
0.0152 (1.00) |
0.859 (1.00) |
0.332 (1.00) |
0.296 (1.00) |
0.0234 (1.00) |
0.019 (1.00) |
0.745 (1.00) |
0.574 (1.00) |
1 (1.00) |
1q gain |
0.417 (1.00) |
0.383 (1.00) |
0.53 (1.00) |
0.233 (1.00) |
0.00138 (0.922) |
0.112 (1.00) |
0.844 (1.00) |
0.743 (1.00) |
1 (1.00) |
2p gain |
0.284 (1.00) |
0.451 (1.00) |
0.0073 (1.00) |
0.221 (1.00) |
0.473 (1.00) |
0.271 (1.00) |
0.33 (1.00) |
0.662 (1.00) |
1 (1.00) |
2q gain |
0.153 (1.00) |
0.443 (1.00) |
0.0174 (1.00) |
0.218 (1.00) |
0.189 (1.00) |
0.0712 (1.00) |
0.759 (1.00) |
0.676 (1.00) |
1 (1.00) |
3p gain |
0.814 (1.00) |
0.748 (1.00) |
1 (1.00) |
0.363 (1.00) |
0.731 (1.00) |
0.217 (1.00) |
0.121 (1.00) |
0.263 (1.00) |
0.121 (1.00) |
3q gain |
0.506 (1.00) |
0.668 (1.00) |
0.27 (1.00) |
0.218 (1.00) |
0.551 (1.00) |
0.308 (1.00) |
0.146 (1.00) |
0.411 (1.00) |
0.203 (1.00) |
4p gain |
0.574 (1.00) |
0.233 (1.00) |
0.626 (1.00) |
1 (1.00) |
0.376 (1.00) |
0.533 (1.00) |
0.522 (1.00) |
0.223 (1.00) |
1 (1.00) |
4q gain |
0.354 (1.00) |
0.251 (1.00) |
1 (1.00) |
0.692 (1.00) |
0.297 (1.00) |
0.758 (1.00) |
0.764 (1.00) |
1 (1.00) |
|
5p gain |
0.854 (1.00) |
0.0481 (1.00) |
0.638 (1.00) |
0.221 (1.00) |
0.831 (1.00) |
0.651 (1.00) |
0.406 (1.00) |
0.518 (1.00) |
0.552 (1.00) |
5q gain |
0.462 (1.00) |
0.0508 (1.00) |
1 (1.00) |
0.601 (1.00) |
0.839 (1.00) |
0.815 (1.00) |
0.225 (1.00) |
0.28 (1.00) |
1 (1.00) |
6p gain |
0.858 (1.00) |
0.947 (1.00) |
0.834 (1.00) |
0.127 (1.00) |
0.897 (1.00) |
0.504 (1.00) |
0.408 (1.00) |
0.527 (1.00) |
0.0587 (1.00) |
6q gain |
0.228 (1.00) |
0.356 (1.00) |
1 (1.00) |
0.128 (1.00) |
0.598 (1.00) |
0.319 (1.00) |
0.166 (1.00) |
0.159 (1.00) |
0.262 (1.00) |
7p gain |
0.338 (1.00) |
0.363 (1.00) |
0.874 (1.00) |
0.00225 (1.00) |
0.18 (1.00) |
0.102 (1.00) |
0.768 (1.00) |
0.291 (1.00) |
1 (1.00) |
7q gain |
0.425 (1.00) |
0.351 (1.00) |
1 (1.00) |
0.00232 (1.00) |
0.48 (1.00) |
0.0419 (1.00) |
0.462 (1.00) |
0.0213 (1.00) |
1 (1.00) |
8p gain |
0.361 (1.00) |
0.15 (1.00) |
0.834 (1.00) |
1 (1.00) |
0.725 (1.00) |
0.598 (1.00) |
0.769 (1.00) |
0.295 (1.00) |
0.591 (1.00) |
8q gain |
0.0685 (1.00) |
0.525 (1.00) |
1 (1.00) |
0.145 (1.00) |
0.751 (1.00) |
0.229 (1.00) |
0.108 (1.00) |
0.443 (1.00) |
0.228 (1.00) |
9p gain |
0.827 (1.00) |
0.296 (1.00) |
0.706 (1.00) |
1 (1.00) |
0.319 (1.00) |
0.533 (1.00) |
0.437 (1.00) |
0.379 (1.00) |
0.342 (1.00) |
9q gain |
0.358 (1.00) |
0.0862 (1.00) |
0.831 (1.00) |
1 (1.00) |
0.372 (1.00) |
0.851 (1.00) |
0.751 (1.00) |
0.266 (1.00) |
0.591 (1.00) |
10p gain |
0.993 (1.00) |
0.988 (1.00) |
0.471 (1.00) |
1 (1.00) |
0.608 (1.00) |
0.363 (1.00) |
0.667 (1.00) |
0.94 (1.00) |
1 (1.00) |
10q gain |
0.332 (1.00) |
0.171 (1.00) |
0.0416 (1.00) |
1 (1.00) |
0.581 (1.00) |
0.296 (1.00) |
0.858 (1.00) |
0.53 (1.00) |
1 (1.00) |
11p gain |
0.459 (1.00) |
0.195 (1.00) |
0.249 (1.00) |
0.218 (1.00) |
0.258 (1.00) |
0.861 (1.00) |
0.256 (1.00) |
0.446 (1.00) |
1 (1.00) |
11q gain |
0.937 (1.00) |
0.0317 (1.00) |
0.8 (1.00) |
0.363 (1.00) |
0.207 (1.00) |
0.499 (1.00) |
0.153 (1.00) |
0.0955 (1.00) |
1 (1.00) |
12p gain |
0.999 (1.00) |
0.0797 (1.00) |
1 (1.00) |
1 (1.00) |
0.199 (1.00) |
0.391 (1.00) |
0.522 (1.00) |
0.757 (1.00) |
0.277 (1.00) |
12q gain |
0.507 (1.00) |
0.0205 (1.00) |
0.328 (1.00) |
1 (1.00) |
0.423 (1.00) |
0.832 (1.00) |
0.905 (1.00) |
0.719 (1.00) |
1 (1.00) |
13q gain |
0.0286 (1.00) |
0.489 (1.00) |
0.871 (1.00) |
0.000377 (0.252) |
0.253 (1.00) |
0.0343 (1.00) |
0.185 (1.00) |
0.186 (1.00) |
0.671 (1.00) |
14q gain |
0.345 (1.00) |
0.447 (1.00) |
0.0416 (1.00) |
1 (1.00) |
0.581 (1.00) |
0.1 (1.00) |
0.522 (1.00) |
0.691 (1.00) |
0.141 (1.00) |
16p gain |
0.229 (1.00) |
0.636 (1.00) |
0.539 (1.00) |
0.129 (1.00) |
0.709 (1.00) |
0.532 (1.00) |
0.485 (1.00) |
0.514 (1.00) |
0.292 (1.00) |
16q gain |
0.871 (1.00) |
0.596 (1.00) |
1 (1.00) |
0.0747 (1.00) |
0.794 (1.00) |
0.241 (1.00) |
0.169 (1.00) |
0.365 (1.00) |
0.308 (1.00) |
17p gain |
0.257 (1.00) |
0.593 (1.00) |
1 (1.00) |
0.0595 (1.00) |
0.111 (1.00) |
0.758 (1.00) |
0.602 (1.00) |
1 (1.00) |
|
17q gain |
0.652 (1.00) |
0.469 (1.00) |
0.621 (1.00) |
0.365 (1.00) |
0.689 (1.00) |
0.139 (1.00) |
0.397 (1.00) |
0.757 (1.00) |
1 (1.00) |
18p gain |
0.964 (1.00) |
0.622 (1.00) |
1 (1.00) |
0.463 (1.00) |
0.271 (1.00) |
0.262 (1.00) |
0.238 (1.00) |
0.492 (1.00) |
0.236 (1.00) |
18q gain |
0.747 (1.00) |
0.626 (1.00) |
1 (1.00) |
0.0234 (1.00) |
0.0967 (1.00) |
0.0133 (1.00) |
0.142 (1.00) |
0.141 (1.00) |
|
19p gain |
0.859 (1.00) |
0.365 (1.00) |
0.473 (1.00) |
0.221 (1.00) |
0.196 (1.00) |
0.827 (1.00) |
0.235 (1.00) |
0.389 (1.00) |
1 (1.00) |
19q gain |
0.827 (1.00) |
0.645 (1.00) |
0.27 (1.00) |
0.218 (1.00) |
0.228 (1.00) |
0.931 (1.00) |
0.137 (1.00) |
0.316 (1.00) |
0.595 (1.00) |
20p gain |
0.874 (1.00) |
0.962 (1.00) |
0.2 (1.00) |
0.00182 (1.00) |
0.975 (1.00) |
0.206 (1.00) |
0.614 (1.00) |
0.522 (1.00) |
0.692 (1.00) |
20q gain |
0.0358 (1.00) |
0.13 (1.00) |
0.686 (1.00) |
2.52e-05 (0.0168) |
0.373 (1.00) |
0.175 (1.00) |
0.285 (1.00) |
0.168 (1.00) |
0.308 (1.00) |
21q gain |
0.829 (1.00) |
0.0302 (1.00) |
0.703 (1.00) |
1 (1.00) |
0.693 (1.00) |
0.952 (1.00) |
0.578 (1.00) |
0.65 (1.00) |
1 (1.00) |
22q gain |
0.0152 (1.00) |
0.781 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.834 (1.00) |
0.316 (1.00) |
0.888 (1.00) |
0.4 (1.00) |
1 (1.00) |
Xq gain |
0.808 (1.00) |
0.718 (1.00) |
1 (1.00) |
0.463 (1.00) |
0.0481 (1.00) |
0.238 (1.00) |
0.578 (1.00) |
0.113 (1.00) |
1 (1.00) |
1p loss |
0.806 (1.00) |
0.388 (1.00) |
0.105 (1.00) |
0.221 (1.00) |
0.451 (1.00) |
0.44 (1.00) |
0.905 (1.00) |
0.595 (1.00) |
0.571 (1.00) |
1q loss |
0.789 (1.00) |
0.629 (1.00) |
0.455 (1.00) |
1 (1.00) |
0.693 (1.00) |
0.0303 (1.00) |
0.883 (1.00) |
0.113 (1.00) |
0.236 (1.00) |
2p loss |
0.611 (1.00) |
0.0489 (1.00) |
0.661 (1.00) |
0.296 (1.00) |
0.834 (1.00) |
0.911 (1.00) |
0.888 (1.00) |
0.943 (1.00) |
1 (1.00) |
3p loss |
0.849 (1.00) |
0.91 (1.00) |
0.292 (1.00) |
0.106 (1.00) |
0.26 (1.00) |
0.703 (1.00) |
0.135 (1.00) |
0.492 (1.00) |
0.266 (1.00) |
3q loss |
0.877 (1.00) |
0.766 (1.00) |
0.626 (1.00) |
0.00175 (1.00) |
0.581 (1.00) |
0.966 (1.00) |
0.758 (1.00) |
0.691 (1.00) |
0.141 (1.00) |
4p loss |
0.276 (1.00) |
0.132 (1.00) |
0.581 (1.00) |
0.304 (1.00) |
0.351 (1.00) |
0.442 (1.00) |
0.854 (1.00) |
0.701 (1.00) |
0.151 (1.00) |
4q loss |
0.109 (1.00) |
0.306 (1.00) |
0.301 (1.00) |
0.188 (1.00) |
0.279 (1.00) |
0.705 (1.00) |
0.839 (1.00) |
0.878 (1.00) |
0.353 (1.00) |
5p loss |
0.153 (1.00) |
0.788 (1.00) |
0.114 (1.00) |
0.601 (1.00) |
0.565 (1.00) |
0.352 (1.00) |
0.726 (1.00) |
0.85 (1.00) |
0.349 (1.00) |
5q loss |
0.58 (1.00) |
0.6 (1.00) |
0.27 (1.00) |
0.695 (1.00) |
0.457 (1.00) |
0.733 (1.00) |
0.512 (1.00) |
0.469 (1.00) |
0.00392 (1.00) |
6p loss |
0.102 (1.00) |
0.504 (1.00) |
1 (1.00) |
0.106 (1.00) |
0.608 (1.00) |
0.188 (1.00) |
0.82 (1.00) |
0.297 (1.00) |
1 (1.00) |
6q loss |
0.657 (1.00) |
0.434 (1.00) |
0.577 (1.00) |
0.0643 (1.00) |
0.385 (1.00) |
0.181 (1.00) |
0.819 (1.00) |
0.331 (1.00) |
1 (1.00) |
8p loss |
0.268 (1.00) |
0.555 (1.00) |
0.623 (1.00) |
1 (1.00) |
0.931 (1.00) |
0.927 (1.00) |
0.351 (1.00) |
0.771 (1.00) |
0.183 (1.00) |
8q loss |
0.679 (1.00) |
1 (1.00) |
1 (1.00) |
0.173 (1.00) |
0.68 (1.00) |
0.758 (1.00) |
0.108 (1.00) |
1 (1.00) |
|
9p loss |
0.0169 (1.00) |
0.122 (1.00) |
1 (1.00) |
1 (1.00) |
0.46 (1.00) |
0.898 (1.00) |
0.171 (1.00) |
0.285 (1.00) |
1 (1.00) |
9q loss |
0.00797 (1.00) |
0.677 (1.00) |
1 (1.00) |
0.592 (1.00) |
0.175 (1.00) |
0.6 (1.00) |
0.726 (1.00) |
0.752 (1.00) |
1 (1.00) |
10p loss |
0.221 (1.00) |
0.00571 (1.00) |
1 (1.00) |
0.0377 (1.00) |
0.34 (1.00) |
0.39 (1.00) |
0.675 (1.00) |
0.959 (1.00) |
0.492 (1.00) |
10q loss |
0.534 (1.00) |
0.0482 (1.00) |
0.491 (1.00) |
0.0773 (1.00) |
0.708 (1.00) |
0.836 (1.00) |
0.504 (1.00) |
0.743 (1.00) |
0.571 (1.00) |
11p loss |
0.464 (1.00) |
0.578 (1.00) |
0.626 (1.00) |
0.046 (1.00) |
0.508 (1.00) |
0.632 (1.00) |
0.56 (1.00) |
0.0593 (1.00) |
0.533 (1.00) |
11q loss |
0.353 (1.00) |
0.656 (1.00) |
0.508 (1.00) |
0.0137 (1.00) |
0.381 (1.00) |
0.741 (1.00) |
0.403 (1.00) |
0.276 (1.00) |
0.0379 (1.00) |
12p loss |
0.177 (1.00) |
0.642 (1.00) |
0.0397 (1.00) |
0.601 (1.00) |
0.305 (1.00) |
0.393 (1.00) |
0.491 (1.00) |
0.388 (1.00) |
1 (1.00) |
12q loss |
0.0971 (1.00) |
0.466 (1.00) |
1 (1.00) |
1 (1.00) |
0.683 (1.00) |
0.258 (1.00) |
0.215 (1.00) |
0.617 (1.00) |
1 (1.00) |
13q loss |
0.98 (1.00) |
1 (1.00) |
0.357 (1.00) |
0.554 (1.00) |
0.279 (1.00) |
0.00134 (0.891) |
0.471 (1.00) |
1 (1.00) |
|
14q loss |
0.635 (1.00) |
0.881 (1.00) |
0.735 (1.00) |
0.00981 (1.00) |
0.225 (1.00) |
0.24 (1.00) |
0.425 (1.00) |
0.463 (1.00) |
1 (1.00) |
15q loss |
0.0719 (1.00) |
0.415 (1.00) |
0.511 (1.00) |
1 (1.00) |
0.171 (1.00) |
0.764 (1.00) |
0.763 (1.00) |
0.173 (1.00) |
0.668 (1.00) |
16p loss |
0.238 (1.00) |
0.413 (1.00) |
0.357 (1.00) |
0.396 (1.00) |
0.226 (1.00) |
0.883 (1.00) |
0.0407 (1.00) |
1 (1.00) |
|
16q loss |
0.877 (1.00) |
0.532 (1.00) |
1 (1.00) |
0.553 (1.00) |
0.885 (1.00) |
0.122 (1.00) |
0.96 (1.00) |
0.426 (1.00) |
0.322 (1.00) |
17p loss |
0.44 (1.00) |
0.0299 (1.00) |
0.527 (1.00) |
0.572 (1.00) |
0.126 (1.00) |
0.745 (1.00) |
0.372 (1.00) |
0.285 (1.00) |
0.691 (1.00) |
17q loss |
0.465 (1.00) |
0.864 (1.00) |
0.788 (1.00) |
1 (1.00) |
0.638 (1.00) |
0.766 (1.00) |
0.974 (1.00) |
0.992 (1.00) |
0.0967 (1.00) |
18p loss |
0.65 (1.00) |
0.0737 (1.00) |
0.863 (1.00) |
0.00925 (1.00) |
0.00702 (1.00) |
0.453 (1.00) |
0.266 (1.00) |
0.581 (1.00) |
1 (1.00) |
18q loss |
0.407 (1.00) |
0.0453 (1.00) |
0.448 (1.00) |
0.482 (1.00) |
0.0037 (1.00) |
0.45 (1.00) |
0.539 (1.00) |
0.232 (1.00) |
0.615 (1.00) |
19p loss |
0.0864 (1.00) |
0.794 (1.00) |
0.703 (1.00) |
1 (1.00) |
0.863 (1.00) |
0.671 (1.00) |
0.858 (1.00) |
0.584 (1.00) |
1 (1.00) |
19q loss |
0.0462 (1.00) |
0.403 (1.00) |
1 (1.00) |
1 (1.00) |
0.505 (1.00) |
0.561 (1.00) |
0.532 (1.00) |
0.106 (1.00) |
1 (1.00) |
20p loss |
1 (1.00) |
0.689 (1.00) |
0.803 (1.00) |
0.636 (1.00) |
0.717 (1.00) |
0.92 (1.00) |
0.909 (1.00) |
0.316 (1.00) |
1 (1.00) |
21q loss |
0.162 (1.00) |
0.807 (1.00) |
0.476 (1.00) |
0.517 (1.00) |
0.306 (1.00) |
0.0648 (1.00) |
0.833 (1.00) |
0.152 (1.00) |
0.656 (1.00) |
22q loss |
0.0236 (1.00) |
0.284 (1.00) |
0.475 (1.00) |
0.745 (1.00) |
0.523 (1.00) |
0.0874 (1.00) |
0.584 (1.00) |
0.237 (1.00) |
0.181 (1.00) |
Xq loss |
0.518 (1.00) |
0.0974 (1.00) |
0.689 (1.00) |
1 (1.00) |
0.636 (1.00) |
0.277 (1.00) |
0.398 (1.00) |
0.285 (1.00) |
1 (1.00) |
Cluster Labels | 1P GAIN MUTATED | 1P GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 158 |
Cluster Labels | 1Q GAIN MUTATED | 1Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 27 | 135 |
Cluster Labels | 2P GAIN MUTATED | 2P GAIN WILD-TYPE |
---|---|---|
Number of samples | 20 | 142 |
Cluster Labels | 2Q GAIN MUTATED | 2Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 21 | 141 |
Cluster Labels | 3P GAIN MUTATED | 3P GAIN WILD-TYPE |
---|---|---|
Number of samples | 17 | 145 |
Cluster Labels | 3Q GAIN MUTATED | 3Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 23 | 139 |
Cluster Labels | 4P GAIN MUTATED | 4P GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 158 |
Cluster Labels | 4Q GAIN MUTATED | 4Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 3 | 159 |
Cluster Labels | 5P GAIN MUTATED | 5P GAIN WILD-TYPE |
---|---|---|
Number of samples | 20 | 142 |
Cluster Labels | 5Q GAIN MUTATED | 5Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 12 | 150 |
Cluster Labels | 6P GAIN MUTATED | 6P GAIN WILD-TYPE |
---|---|---|
Number of samples | 27 | 135 |
Cluster Labels | 6Q GAIN MUTATED | 6Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 27 | 135 |
Cluster Labels | 7P GAIN MUTATED | 7P GAIN WILD-TYPE |
---|---|---|
Number of samples | 90 | 72 |
Cluster Labels | 7Q GAIN MUTATED | 7Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 79 | 83 |
Cluster Labels | 8P GAIN MUTATED | 8P GAIN WILD-TYPE |
---|---|---|
Number of samples | 27 | 135 |
Cluster Labels | 8Q GAIN MUTATED | 8Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 72 | 90 |
Cluster Labels | 9P GAIN MUTATED | 9P GAIN WILD-TYPE |
---|---|---|
Number of samples | 35 | 127 |
Cluster Labels | 9Q GAIN MUTATED | 9Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 26 | 136 |
Cluster Labels | 10P GAIN MUTATED | 10P GAIN WILD-TYPE |
---|---|---|
Number of samples | 8 | 154 |
Cluster Labels | 10Q GAIN MUTATED | 10Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 158 |
Cluster Labels | 11P GAIN MUTATED | 11P GAIN WILD-TYPE |
---|---|---|
Number of samples | 21 | 141 |
Cluster Labels | 11Q GAIN MUTATED | 11Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 17 | 145 |
Cluster Labels | 12P GAIN MUTATED | 12P GAIN WILD-TYPE |
---|---|---|
Number of samples | 28 | 134 |
Cluster Labels | 12Q GAIN MUTATED | 12Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 19 | 143 |
Cluster Labels | 13Q GAIN MUTATED | 13Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 102 | 60 |
Cluster Labels | 14Q GAIN MUTATED | 14Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 158 |
Cluster Labels | 16P GAIN MUTATED | 16P GAIN WILD-TYPE |
---|---|---|
Number of samples | 29 | 133 |
Cluster Labels | 16Q GAIN MUTATED | 16Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 30 | 132 |
Cluster Labels | 17P GAIN MUTATED | 17P GAIN WILD-TYPE |
---|---|---|
Number of samples | 3 | 159 |
Cluster Labels | 17Q GAIN MUTATED | 17Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 18 | 144 |
Cluster Labels | 18P GAIN MUTATED | 18P GAIN WILD-TYPE |
---|---|---|
Number of samples | 7 | 155 |
Cluster Labels | 18Q GAIN MUTATED | 18Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 158 |
Cluster Labels | 19P GAIN MUTATED | 19P GAIN WILD-TYPE |
---|---|---|
Number of samples | 20 | 142 |
Cluster Labels | 19Q GAIN MUTATED | 19Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 23 | 139 |
Cluster Labels | 20P GAIN MUTATED | 20P GAIN WILD-TYPE |
---|---|---|
Number of samples | 95 | 67 |
Cluster Labels | 20Q GAIN MUTATED | 20Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 132 | 30 |
P value = 2.52e-05 (Fisher's exact test), Q value = 0.017
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 143 | 13 |
20Q GAIN MUTATED | 124 | 4 |
20Q GAIN WILD-TYPE | 19 | 9 |
Cluster Labels | 21Q GAIN MUTATED | 21Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 7 | 155 |
Cluster Labels | 22Q GAIN MUTATED | 22Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 5 | 157 |
Cluster Labels | XQ GAIN MUTATED | XQ GAIN WILD-TYPE |
---|---|---|
Number of samples | 7 | 155 |
Cluster Labels | 1P LOSS MUTATED | 1P LOSS WILD-TYPE |
---|---|---|
Number of samples | 21 | 141 |
Cluster Labels | 1Q LOSS MUTATED | 1Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 7 | 155 |
Cluster Labels | 2P LOSS MUTATED | 2P LOSS WILD-TYPE |
---|---|---|
Number of samples | 5 | 157 |
Cluster Labels | 3P LOSS MUTATED | 3P LOSS WILD-TYPE |
---|---|---|
Number of samples | 8 | 154 |
Cluster Labels | 3Q LOSS MUTATED | 3Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 4 | 158 |
Cluster Labels | 4P LOSS MUTATED | 4P LOSS WILD-TYPE |
---|---|---|
Number of samples | 39 | 123 |
Cluster Labels | 4Q LOSS MUTATED | 4Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 46 | 116 |
Cluster Labels | 5P LOSS MUTATED | 5P LOSS WILD-TYPE |
---|---|---|
Number of samples | 11 | 151 |
Cluster Labels | 5Q LOSS MUTATED | 5Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 23 | 139 |
Cluster Labels | 6P LOSS MUTATED | 6P LOSS WILD-TYPE |
---|---|---|
Number of samples | 8 | 154 |
Cluster Labels | 6Q LOSS MUTATED | 6Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 14 | 148 |
Cluster Labels | 8P LOSS MUTATED | 8P LOSS WILD-TYPE |
---|---|---|
Number of samples | 56 | 106 |
Cluster Labels | 8Q LOSS MUTATED | 8Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 3 | 159 |
Cluster Labels | 9P LOSS MUTATED | 9P LOSS WILD-TYPE |
---|---|---|
Number of samples | 12 | 150 |
Cluster Labels | 9Q LOSS MUTATED | 9Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 11 | 151 |
Cluster Labels | 10P LOSS MUTATED | 10P LOSS WILD-TYPE |
---|---|---|
Number of samples | 17 | 145 |
Cluster Labels | 10Q LOSS MUTATED | 10Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 21 | 141 |
Cluster Labels | 11P LOSS MUTATED | 11P LOSS WILD-TYPE |
---|---|---|
Number of samples | 19 | 143 |
Cluster Labels | 11Q LOSS MUTATED | 11Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 23 | 139 |
Cluster Labels | 12P LOSS MUTATED | 12P LOSS WILD-TYPE |
---|---|---|
Number of samples | 12 | 150 |
Cluster Labels | 12Q LOSS MUTATED | 12Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 8 | 154 |
Cluster Labels | 13Q LOSS MUTATED | 13Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 5 | 157 |
Cluster Labels | 14Q LOSS MUTATED | 14Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 51 | 111 |
Cluster Labels | 15Q LOSS MUTATED | 15Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 58 | 104 |
Cluster Labels | 16P LOSS MUTATED | 16P LOSS WILD-TYPE |
---|---|---|
Number of samples | 6 | 156 |
Cluster Labels | 16Q LOSS MUTATED | 16Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 10 | 152 |
Cluster Labels | 17P LOSS MUTATED | 17P LOSS WILD-TYPE |
---|---|---|
Number of samples | 89 | 73 |
Cluster Labels | 17Q LOSS MUTATED | 17Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 15 | 147 |
Cluster Labels | 18P LOSS MUTATED | 18P LOSS WILD-TYPE |
---|---|---|
Number of samples | 114 | 48 |
Cluster Labels | 18Q LOSS MUTATED | 18Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 126 | 36 |
Cluster Labels | 19P LOSS MUTATED | 19P LOSS WILD-TYPE |
---|---|---|
Number of samples | 7 | 155 |
Cluster Labels | 19Q LOSS MUTATED | 19Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 7 | 155 |
Cluster Labels | 20P LOSS MUTATED | 20P LOSS WILD-TYPE |
---|---|---|
Number of samples | 18 | 144 |
Cluster Labels | 21Q LOSS MUTATED | 21Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 43 | 119 |
Cluster Labels | 22Q LOSS MUTATED | 22Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 42 | 120 |
Cluster Labels | XQ LOSS MUTATED | XQ LOSS WILD-TYPE |
---|---|---|
Number of samples | 6 | 156 |
-
Cluster data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = READ-TP.clin.merged.picked.txt
-
Number of patients = 162
-
Number of clustering approaches = 75
-
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.