This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between subtypes identified by 58 different clustering approaches and 8 clinical features across 103 patients, 8 significant findings detected with Q value < 0.25.
-
2 subtypes identified in current cancer cohort by '1q gain mutation analysis'. These subtypes correlate to 'Time to Death'.
-
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 correlate to 'PATHOLOGICSPREAD(M)'.
-
2 subtypes identified in current cancer cohort by '6q gain mutation analysis'. These subtypes correlate to 'Time to Death' and 'PATHOLOGICSPREAD(M)'.
-
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 '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 '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 '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 correlate to 'PATHOLOGY.T'.
-
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 '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 'Xq gain mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '1p loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '1q loss mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by '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 correlate to 'Time to Death'.
-
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 correlate to 'Time to Death'.
-
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 '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 '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 '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 correlate to 'Time to Death'.
-
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 '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 |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
Statistical Tests | logrank test | t-test | Fisher's exact test | t-test | Chi-square test | Chi-square test | Chi-square test | Chi-square test |
1q gain |
9.91e-05 (0.04) |
0.793 (1.00) |
0.265 (1.00) |
0.00155 (0.614) |
0.884 (1.00) |
0.0333 (1.00) |
0.00501 (1.00) |
|
2p gain |
0.191 (1.00) |
0.348 (1.00) |
0.742 (1.00) |
0.54 (1.00) |
0.833 (1.00) |
0.361 (1.00) |
0.0389 (1.00) |
0.0553 (1.00) |
2q gain |
0.35 (1.00) |
0.859 (1.00) |
0.751 (1.00) |
0.5 (1.00) |
0.948 (1.00) |
0.0575 (1.00) |
0.0698 (1.00) |
0.0103 (1.00) |
3p gain |
0.414 (1.00) |
0.937 (1.00) |
0.0822 (1.00) |
0.088 (1.00) |
0.0237 (1.00) |
0.806 (1.00) |
0.496 (1.00) |
0.278 (1.00) |
3q gain |
0.288 (1.00) |
0.877 (1.00) |
0.0507 (1.00) |
0.208 (1.00) |
0.0514 (1.00) |
0.661 (1.00) |
0.464 (1.00) |
0.394 (1.00) |
4p gain |
0.0702 (1.00) |
0.0414 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.426 (1.00) |
0.0291 (1.00) |
0.00894 (1.00) |
|
4q gain |
0.694 (1.00) |
0.0406 (1.00) |
1 (1.00) |
0.51 (1.00) |
||||
5p gain |
0.76 (1.00) |
0.377 (1.00) |
0.723 (1.00) |
0.395 (1.00) |
0.11 (1.00) |
0.731 (1.00) |
0.589 (1.00) |
0.182 (1.00) |
5q gain |
0.31 (1.00) |
0.603 (1.00) |
0.723 (1.00) |
0.395 (1.00) |
0.394 (1.00) |
0.731 (1.00) |
0.714 (1.00) |
0.405 (1.00) |
6p gain |
0.0755 (1.00) |
0.361 (1.00) |
0.303 (1.00) |
0.147 (1.00) |
0.368 (1.00) |
0.000177 (0.0713) |
0.0459 (1.00) |
|
6q gain |
5.18e-06 (0.0021) |
0.258 (1.00) |
0.549 (1.00) |
0.379 (1.00) |
8.32e-06 (0.00336) |
0.00894 (1.00) |
||
7p gain |
0.0708 (1.00) |
0.918 (1.00) |
0.0592 (1.00) |
0.2 (1.00) |
0.0025 (0.985) |
0.437 (1.00) |
0.112 (1.00) |
0.00142 (0.566) |
7q gain |
0.0708 (1.00) |
0.918 (1.00) |
0.137 (1.00) |
0.2 (1.00) |
0.00651 (1.00) |
0.437 (1.00) |
0.134 (1.00) |
0.00399 (1.00) |
8p gain |
0.576 (1.00) |
0.243 (1.00) |
0.654 (1.00) |
0.0512 (1.00) |
0.661 (1.00) |
0.557 (1.00) |
0.183 (1.00) |
|
8q gain |
0.00501 (1.00) |
0.627 (1.00) |
0.677 (1.00) |
0.00519 (1.00) |
0.152 (1.00) |
0.523 (1.00) |
0.0059 (1.00) |
|
10p gain |
0.488 (1.00) |
0.804 (1.00) |
1 (1.00) |
0.747 (1.00) |
0.894 (1.00) |
|||
10q gain |
0.488 (1.00) |
0.804 (1.00) |
0.549 (1.00) |
0.355 (1.00) |
||||
12p gain |
0.991 (1.00) |
0.677 (1.00) |
0.037 (1.00) |
0.26 (1.00) |
0.958 (1.00) |
0.451 (1.00) |
0.284 (1.00) |
0.348 (1.00) |
12q gain |
0.991 (1.00) |
0.677 (1.00) |
0.037 (1.00) |
0.26 (1.00) |
0.958 (1.00) |
0.451 (1.00) |
0.284 (1.00) |
0.348 (1.00) |
13q gain |
0.717 (1.00) |
0.231 (1.00) |
0.742 (1.00) |
0.208 (1.00) |
0.504 (1.00) |
0.714 (1.00) |
0.481 (1.00) |
|
16p gain |
0.537 (1.00) |
0.459 (1.00) |
0.0108 (1.00) |
0.531 (1.00) |
0.942 (1.00) |
0.286 (1.00) |
0.614 (1.00) |
0.769 (1.00) |
16q gain |
0.103 (1.00) |
0.573 (1.00) |
0.032 (1.00) |
0.264 (1.00) |
0.714 (1.00) |
0.187 (1.00) |
0.208 (1.00) |
0.739 (1.00) |
17p gain |
0.222 (1.00) |
0.0472 (1.00) |
0.0208 (1.00) |
0.201 (1.00) |
0.000449 (0.179) |
0.177 (1.00) |
0.0403 (1.00) |
0.000843 (0.336) |
17q gain |
0.768 (1.00) |
0.0952 (1.00) |
0.281 (1.00) |
0.556 (1.00) |
0.122 (1.00) |
0.178 (1.00) |
0.098 (1.00) |
0.189 (1.00) |
18p gain |
0.195 (1.00) |
0.592 (1.00) |
0.661 (1.00) |
0.54 (1.00) |
0.933 (1.00) |
0.277 (1.00) |
0.742 (1.00) |
|
18q gain |
0.609 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.659 (1.00) |
0.894 (1.00) |
0.814 (1.00) |
||
20p gain |
0.439 (1.00) |
0.018 (1.00) |
0.819 (1.00) |
0.639 (1.00) |
0.266 (1.00) |
0.905 (1.00) |
0.368 (1.00) |
0.515 (1.00) |
20q gain |
0.439 (1.00) |
0.0434 (1.00) |
0.652 (1.00) |
0.639 (1.00) |
0.381 (1.00) |
0.905 (1.00) |
0.73 (1.00) |
0.718 (1.00) |
Xq gain |
0.416 (1.00) |
0.359 (1.00) |
0.0956 (1.00) |
0.596 (1.00) |
0.549 (1.00) |
0.494 (1.00) |
||
1p loss |
0.721 (1.00) |
0.421 (1.00) |
1 (1.00) |
0.349 (1.00) |
0.887 (1.00) |
0.729 (1.00) |
0.512 (1.00) |
|
1q loss |
0.646 (1.00) |
0.819 (1.00) |
1 (1.00) |
0.349 (1.00) |
0.73 (1.00) |
0.523 (1.00) |
0.65 (1.00) |
|
3p loss |
0.211 (1.00) |
0.0512 (1.00) |
0.661 (1.00) |
0.108 (1.00) |
0.43 (1.00) |
0.441 (1.00) |
0.214 (1.00) |
|
3q loss |
2.89e-06 (0.00117) |
0.324 (1.00) |
1 (1.00) |
0.0325 (1.00) |
0.368 (1.00) |
0.0864 (1.00) |
0.115 (1.00) |
|
4p loss |
0.131 (1.00) |
0.13 (1.00) |
0.0126 (1.00) |
0.118 (1.00) |
0.591 (1.00) |
0.627 (1.00) |
0.0531 (1.00) |
|
4q loss |
0.699 (1.00) |
0.475 (1.00) |
0.107 (1.00) |
0.462 (1.00) |
0.806 (1.00) |
0.627 (1.00) |
0.268 (1.00) |
|
5p loss |
0.000217 (0.087) |
0.0657 (1.00) |
0.0956 (1.00) |
0.00988 (1.00) |
0.103 (1.00) |
0.549 (1.00) |
0.115 (1.00) |
|
5q loss |
0.0275 (1.00) |
0.229 (1.00) |
0.0956 (1.00) |
0.147 (1.00) |
0.549 (1.00) |
0.39 (1.00) |
||
6p loss |
0.0312 (1.00) |
0.989 (1.00) |
0.463 (1.00) |
0.26 (1.00) |
0.183 (1.00) |
0.292 (1.00) |
0.777 (1.00) |
0.316 (1.00) |
6q loss |
0.279 (1.00) |
0.367 (1.00) |
0.0713 (1.00) |
0.392 (1.00) |
0.0861 (1.00) |
0.301 (1.00) |
0.397 (1.00) |
0.46 (1.00) |
8p loss |
0.748 (1.00) |
0.401 (1.00) |
0.0309 (1.00) |
0.355 (1.00) |
0.894 (1.00) |
0.282 (1.00) |
||
9p loss |
0.0576 (1.00) |
0.527 (1.00) |
0.0168 (1.00) |
0.424 (1.00) |
0.0944 (1.00) |
0.884 (1.00) |
0.744 (1.00) |
0.3 (1.00) |
9q loss |
0.0985 (1.00) |
0.5 (1.00) |
0.0506 (1.00) |
0.424 (1.00) |
0.0645 (1.00) |
0.884 (1.00) |
0.838 (1.00) |
0.421 (1.00) |
10p loss |
0.129 (1.00) |
0.949 (1.00) |
0.654 (1.00) |
0.737 (1.00) |
0.136 (1.00) |
0.717 (1.00) |
||
10q loss |
0.0067 (1.00) |
0.739 (1.00) |
1 (1.00) |
0.312 (1.00) |
0.368 (1.00) |
0.297 (1.00) |
0.631 (1.00) |
|
11p loss |
0.00515 (1.00) |
0.0523 (1.00) |
0.709 (1.00) |
0.425 (1.00) |
0.627 (1.00) |
0.244 (1.00) |
||
11q loss |
0.0224 (1.00) |
0.0682 (1.00) |
1 (1.00) |
0.0479 (1.00) |
0.661 (1.00) |
0.714 (1.00) |
0.144 (1.00) |
|
13q loss |
0.025 (1.00) |
0.424 (1.00) |
0.00451 (1.00) |
0.241 (1.00) |
0.667 (1.00) |
0.423 (1.00) |
0.439 (1.00) |
|
14q loss |
0.974 (1.00) |
0.341 (1.00) |
0.58 (1.00) |
0.396 (1.00) |
0.789 (1.00) |
0.387 (1.00) |
0.471 (1.00) |
0.332 (1.00) |
15q loss |
0.0655 (1.00) |
0.362 (1.00) |
0.723 (1.00) |
0.654 (1.00) |
0.0861 (1.00) |
0.667 (1.00) |
0.699 (1.00) |
0.124 (1.00) |
16q loss |
0.0309 (1.00) |
0.379 (1.00) |
0.549 (1.00) |
0.494 (1.00) |
||||
17p loss |
2.02e-07 (8.22e-05) |
0.488 (1.00) |
0.0354 (1.00) |
0.238 (1.00) |
0.426 (1.00) |
0.125 (1.00) |
0.0615 (1.00) |
|
18p loss |
0.00216 (0.856) |
0.85 (1.00) |
1 (1.00) |
0.349 (1.00) |
0.108 (1.00) |
0.43 (1.00) |
0.905 (1.00) |
0.291 (1.00) |
18q loss |
0.00216 (0.856) |
0.85 (1.00) |
0.771 (1.00) |
0.349 (1.00) |
0.0503 (1.00) |
0.43 (1.00) |
0.945 (1.00) |
0.131 (1.00) |
19p loss |
0.646 (1.00) |
0.585 (1.00) |
1 (1.00) |
0.747 (1.00) |
0.549 (1.00) |
0.282 (1.00) |
||
19q loss |
0.748 (1.00) |
0.88 (1.00) |
1 (1.00) |
0.51 (1.00) |
||||
21q loss |
0.151 (1.00) |
0.438 (1.00) |
0.324 (1.00) |
0.549 (1.00) |
0.806 (1.00) |
0.688 (1.00) |
0.124 (1.00) |
|
22q loss |
0.704 (1.00) |
0.748 (1.00) |
0.172 (1.00) |
0.457 (1.00) |
0.19 (1.00) |
0.691 (1.00) |
0.306 (1.00) |
0.353 (1.00) |
Xq loss |
0.748 (1.00) |
0.921 (1.00) |
1 (1.00) |
0.797 (1.00) |
0.88 (1.00) |
Cluster Labels | 1Q GAIN MUTATED | 1Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 8 | 95 |
P value = 9.91e-05 (logrank test), Q value = 0.04
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 96 | 14 | 0.0 - 182.7 (13.7) |
1Q GAIN MUTATED | 7 | 2 | 0.7 - 25.4 (7.6) |
1Q GAIN WILD-TYPE | 89 | 12 | 0.0 - 182.7 (14.6) |
Cluster Labels | 2P GAIN MUTATED | 2P GAIN WILD-TYPE |
---|---|---|
Number of samples | 11 | 92 |
Cluster Labels | 2Q GAIN MUTATED | 2Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 13 | 90 |
Cluster Labels | 3P GAIN MUTATED | 3P GAIN WILD-TYPE |
---|---|---|
Number of samples | 24 | 79 |
Cluster Labels | 3Q GAIN MUTATED | 3Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 26 | 77 |
Cluster Labels | 4P GAIN MUTATED | 4P GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 99 |
Cluster Labels | 4Q GAIN MUTATED | 4Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 3 | 100 |
Cluster Labels | 5P GAIN MUTATED | 5P GAIN WILD-TYPE |
---|---|---|
Number of samples | 10 | 93 |
Cluster Labels | 5Q GAIN MUTATED | 5Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 10 | 93 |
Cluster Labels | 6P GAIN MUTATED | 6P GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 99 |
P value = 0.000177 (Chi-square test), Q value = 0.071
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 54 | 5 | 35 |
6P GAIN MUTATED | 2 | 2 | 0 |
6P GAIN WILD-TYPE | 52 | 3 | 35 |
Cluster Labels | 6Q GAIN MUTATED | 6Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 3 | 100 |
P value = 5.18e-06 (logrank test), Q value = 0.0021
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 96 | 14 | 0.0 - 182.7 (13.7) |
6Q GAIN MUTATED | 3 | 2 | 7.9 - 13.6 (9.6) |
6Q GAIN WILD-TYPE | 93 | 12 | 0.0 - 182.7 (14.1) |
P value = 8.32e-06 (Chi-square test), Q value = 0.0034
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 54 | 5 | 35 |
6Q GAIN MUTATED | 1 | 2 | 0 |
6Q GAIN WILD-TYPE | 53 | 3 | 35 |
Cluster Labels | 7P GAIN MUTATED | 7P GAIN WILD-TYPE |
---|---|---|
Number of samples | 55 | 48 |
Cluster Labels | 7Q GAIN MUTATED | 7Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 56 | 47 |
Cluster Labels | 8P GAIN MUTATED | 8P GAIN WILD-TYPE |
---|---|---|
Number of samples | 5 | 98 |
Cluster Labels | 8Q GAIN MUTATED | 8Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 7 | 96 |
Cluster Labels | 10P GAIN MUTATED | 10P GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 99 |
Cluster Labels | 10Q GAIN MUTATED | 10Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 3 | 100 |
Cluster Labels | 12P GAIN MUTATED | 12P GAIN WILD-TYPE |
---|---|---|
Number of samples | 31 | 72 |
Cluster Labels | 12Q GAIN MUTATED | 12Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 31 | 72 |
Cluster Labels | 13Q GAIN MUTATED | 13Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 11 | 92 |
Cluster Labels | 16P GAIN MUTATED | 16P GAIN WILD-TYPE |
---|---|---|
Number of samples | 44 | 59 |
Cluster Labels | 16Q GAIN MUTATED | 16Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 41 | 62 |
Cluster Labels | 17P GAIN MUTATED | 17P GAIN WILD-TYPE |
---|---|---|
Number of samples | 52 | 51 |
P value = 0.000449 (Chi-square test), Q value = 0.18
nPatients | T1 | T2 | T3+T4 |
---|---|---|---|
ALL | 58 | 13 | 32 |
17P GAIN MUTATED | 36 | 9 | 7 |
17P GAIN WILD-TYPE | 22 | 4 | 25 |
Cluster Labels | 17Q GAIN MUTATED | 17Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 62 | 41 |
Cluster Labels | 18P GAIN MUTATED | 18P GAIN WILD-TYPE |
---|---|---|
Number of samples | 6 | 97 |
Cluster Labels | 18Q GAIN MUTATED | 18Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 99 |
Cluster Labels | 20P GAIN MUTATED | 20P GAIN WILD-TYPE |
---|---|---|
Number of samples | 31 | 72 |
Cluster Labels | 20Q GAIN MUTATED | 20Q GAIN WILD-TYPE |
---|---|---|
Number of samples | 32 | 71 |
Cluster Labels | XQ GAIN MUTATED | XQ GAIN WILD-TYPE |
---|---|---|
Number of samples | 4 | 99 |
Cluster Labels | 1P LOSS MUTATED | 1P LOSS WILD-TYPE |
---|---|---|
Number of samples | 11 | 92 |
Cluster Labels | 1Q LOSS MUTATED | 1Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 6 | 97 |
Cluster Labels | 3P LOSS MUTATED | 3P LOSS WILD-TYPE |
---|---|---|
Number of samples | 6 | 97 |
Cluster Labels | 3Q LOSS MUTATED | 3Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 3 | 100 |
P value = 2.89e-06 (logrank test), Q value = 0.0012
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 96 | 14 | 0.0 - 182.7 (13.7) |
3Q LOSS MUTATED | 3 | 2 | 3.7 - 21.6 (8.8) |
3Q LOSS WILD-TYPE | 93 | 12 | 0.0 - 182.7 (13.7) |
Cluster Labels | 4P LOSS MUTATED | 4P LOSS WILD-TYPE |
---|---|---|
Number of samples | 8 | 95 |
Cluster Labels | 4Q LOSS MUTATED | 4Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 8 | 95 |
Cluster Labels | 5P LOSS MUTATED | 5P LOSS WILD-TYPE |
---|---|---|
Number of samples | 4 | 99 |
P value = 0.000217 (logrank test), Q value = 0.087
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 96 | 14 | 0.0 - 182.7 (13.7) |
5P LOSS MUTATED | 4 | 2 | 0.0 - 22.9 (7.4) |
5P LOSS WILD-TYPE | 92 | 12 | 0.0 - 182.7 (13.9) |
Cluster Labels | 5Q LOSS MUTATED | 5Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 4 | 99 |
Cluster Labels | 6P LOSS MUTATED | 6P LOSS WILD-TYPE |
---|---|---|
Number of samples | 9 | 94 |
Cluster Labels | 6Q LOSS MUTATED | 6Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 10 | 93 |
Cluster Labels | 8P LOSS MUTATED | 8P LOSS WILD-TYPE |
---|---|---|
Number of samples | 3 | 100 |
Cluster Labels | 9P LOSS MUTATED | 9P LOSS WILD-TYPE |
---|---|---|
Number of samples | 12 | 91 |
Cluster Labels | 9Q LOSS MUTATED | 9Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 12 | 91 |
Cluster Labels | 10P LOSS MUTATED | 10P LOSS WILD-TYPE |
---|---|---|
Number of samples | 5 | 98 |
Cluster Labels | 10Q LOSS MUTATED | 10Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 5 | 98 |
Cluster Labels | 11P LOSS MUTATED | 11P LOSS WILD-TYPE |
---|---|---|
Number of samples | 8 | 95 |
Cluster Labels | 11Q LOSS MUTATED | 11Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 9 | 94 |
Cluster Labels | 13Q LOSS MUTATED | 13Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 9 | 94 |
Cluster Labels | 14Q LOSS MUTATED | 14Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 18 | 85 |
Cluster Labels | 15Q LOSS MUTATED | 15Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 10 | 93 |
Cluster Labels | 16Q LOSS MUTATED | 16Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 3 | 100 |
Cluster Labels | 17P LOSS MUTATED | 17P LOSS WILD-TYPE |
---|---|---|
Number of samples | 5 | 98 |
P value = 2.02e-07 (logrank test), Q value = 8.2e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 96 | 14 | 0.0 - 182.7 (13.7) |
17P LOSS MUTATED | 4 | 2 | 0.2 - 11.1 (5.2) |
17P LOSS WILD-TYPE | 92 | 12 | 0.0 - 182.7 (14.4) |
Cluster Labels | 18P LOSS MUTATED | 18P LOSS WILD-TYPE |
---|---|---|
Number of samples | 15 | 88 |
Cluster Labels | 18Q LOSS MUTATED | 18Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 16 | 87 |
Cluster Labels | 19P LOSS MUTATED | 19P LOSS WILD-TYPE |
---|---|---|
Number of samples | 4 | 99 |
Cluster Labels | 19Q LOSS MUTATED | 19Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 3 | 100 |
Cluster Labels | 21Q LOSS MUTATED | 21Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 11 | 92 |
Cluster Labels | 22Q LOSS MUTATED | 22Q LOSS WILD-TYPE |
---|---|---|
Number of samples | 19 | 84 |
Cluster Labels | XQ LOSS MUTATED | XQ LOSS WILD-TYPE |
---|---|---|
Number of samples | 3 | 100 |
-
Cluster data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = KIRP-TP.clin.merged.picked.txt
-
Number of patients = 103
-
Number of clustering approaches = 58
-
Number of selected clinical features = 8
-
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.