This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 61 arm-level events and 8 molecular subtypes across 66 patients, 55 significant findings detected with P value < 0.05 and Q value < 0.25.
-
4p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
4q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
11p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
11q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
16p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
16q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
1p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
1q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
2p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
2q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
6p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
6q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
8p loss cnv correlated to 'CN_CNMF'.
-
8q loss cnv correlated to 'CN_CNMF'.
-
10p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
10q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
13q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
17p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
17q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
1q loss | 52 (79%) | 14 |
0.474 (1.00) |
1e-05 (0.00488) |
7e-05 (0.0317) |
5e-05 (0.0228) |
0.231 (1.00) |
0.00051 (0.221) |
0.176 (1.00) |
0.00402 (1.00) |
2p loss | 46 (70%) | 20 |
0.0888 (1.00) |
1e-05 (0.00488) |
1e-05 (0.00488) |
1e-05 (0.00488) |
0.0815 (1.00) |
1e-05 (0.00488) |
0.0306 (1.00) |
0.00073 (0.314) |
2q loss | 46 (70%) | 20 |
0.0888 (1.00) |
1e-05 (0.00488) |
1e-05 (0.00488) |
1e-05 (0.00488) |
0.0814 (1.00) |
1e-05 (0.00488) |
0.0306 (1.00) |
0.00062 (0.268) |
6p loss | 51 (77%) | 15 |
0.332 (1.00) |
0.00014 (0.0626) |
3e-05 (0.0138) |
1e-05 (0.00488) |
0.352 (1.00) |
0.00118 (0.5) |
0.176 (1.00) |
0.0004 (0.175) |
6q loss | 51 (77%) | 15 |
0.331 (1.00) |
0.00016 (0.071) |
3e-05 (0.0138) |
1e-05 (0.00488) |
0.351 (1.00) |
0.00104 (0.444) |
0.176 (1.00) |
0.00032 (0.14) |
10p loss | 48 (73%) | 18 |
0.343 (1.00) |
0.00029 (0.128) |
7e-05 (0.0317) |
1e-05 (0.00488) |
0.276 (1.00) |
0.00014 (0.0626) |
0.759 (1.00) |
0.0101 (1.00) |
10q loss | 49 (74%) | 17 |
0.247 (1.00) |
0.00031 (0.136) |
2e-05 (0.00934) |
1e-05 (0.00488) |
0.225 (1.00) |
0.0002 (0.0886) |
0.538 (1.00) |
0.00338 (1.00) |
17p loss | 50 (76%) | 16 |
0.298 (1.00) |
1e-05 (0.00488) |
1e-05 (0.00488) |
1e-05 (0.00488) |
0.0518 (1.00) |
9e-05 (0.0405) |
0.0491 (1.00) |
0.00211 (0.88) |
17q loss | 50 (76%) | 16 |
0.298 (1.00) |
1e-05 (0.00488) |
1e-05 (0.00488) |
1e-05 (0.00488) |
0.0514 (1.00) |
0.0001 (0.0448) |
0.0491 (1.00) |
0.00212 (0.882) |
1p loss | 53 (80%) | 13 |
0.672 (1.00) |
2e-05 (0.00934) |
0.00048 (0.209) |
0.00033 (0.145) |
0.162 (1.00) |
0.0013 (0.55) |
0.176 (1.00) |
0.00411 (1.00) |
4p gain | 24 (36%) | 42 |
0.0554 (1.00) |
1 (1.00) |
2e-05 (0.00934) |
6e-05 (0.0272) |
0.769 (1.00) |
0.00903 (1.00) |
0.0349 (1.00) |
0.0173 (1.00) |
4q gain | 24 (36%) | 42 |
0.0556 (1.00) |
1 (1.00) |
2e-05 (0.00934) |
5e-05 (0.0228) |
0.772 (1.00) |
0.00908 (1.00) |
0.0349 (1.00) |
0.0173 (1.00) |
11p gain | 15 (23%) | 51 |
0.28 (1.00) |
0.676 (1.00) |
3e-05 (0.0138) |
0.00023 (0.102) |
0.871 (1.00) |
0.0279 (1.00) |
0.197 (1.00) |
0.0789 (1.00) |
11q gain | 15 (23%) | 51 |
0.281 (1.00) |
0.679 (1.00) |
1e-05 (0.00488) |
5e-05 (0.0228) |
0.618 (1.00) |
0.0193 (1.00) |
0.197 (1.00) |
0.104 (1.00) |
16p gain | 21 (32%) | 45 |
0.107 (1.00) |
1 (1.00) |
2e-05 (0.00934) |
8e-05 (0.0361) |
0.159 (1.00) |
0.00541 (1.00) |
0.0312 (1.00) |
0.0074 (1.00) |
16q gain | 21 (32%) | 45 |
0.106 (1.00) |
1 (1.00) |
2e-05 (0.00934) |
9e-05 (0.0405) |
0.162 (1.00) |
0.00531 (1.00) |
0.0312 (1.00) |
0.00714 (1.00) |
13q loss | 43 (65%) | 23 |
0.261 (1.00) |
0.00049 (0.213) |
0.00331 (1.00) |
0.00015 (0.0667) |
0.85 (1.00) |
0.196 (1.00) |
0.541 (1.00) |
0.00599 (1.00) |
8p loss | 9 (14%) | 57 |
1e-05 (0.00488) |
0.0838 (1.00) |
0.0547 (1.00) |
0.0387 (1.00) |
0.15 (1.00) |
0.467 (1.00) |
0.142 (1.00) |
0.32 (1.00) |
8q loss | 8 (12%) | 58 |
2e-05 (0.00934) |
0.0446 (1.00) |
0.134 (1.00) |
0.0718 (1.00) |
0.29 (1.00) |
0.529 (1.00) |
0.142 (1.00) |
0.32 (1.00) |
3p gain | 8 (12%) | 58 |
0.272 (1.00) |
0.53 (1.00) |
0.951 (1.00) |
0.647 (1.00) |
0.516 (1.00) |
0.691 (1.00) |
0.669 (1.00) |
0.6 (1.00) |
3q gain | 8 (12%) | 58 |
0.27 (1.00) |
0.53 (1.00) |
0.952 (1.00) |
0.648 (1.00) |
0.515 (1.00) |
0.69 (1.00) |
0.669 (1.00) |
0.602 (1.00) |
5p gain | 8 (12%) | 58 |
0.424 (1.00) |
0.681 (1.00) |
0.448 (1.00) |
0.443 (1.00) |
0.367 (1.00) |
0.0584 (1.00) |
1 (1.00) |
0.126 (1.00) |
5q gain | 8 (12%) | 58 |
0.424 (1.00) |
0.683 (1.00) |
0.449 (1.00) |
0.445 (1.00) |
0.362 (1.00) |
0.0602 (1.00) |
1 (1.00) |
0.127 (1.00) |
7p gain | 24 (36%) | 42 |
0.15 (1.00) |
1 (1.00) |
0.0159 (1.00) |
0.0609 (1.00) |
0.899 (1.00) |
0.117 (1.00) |
0.766 (1.00) |
0.0991 (1.00) |
7q gain | 24 (36%) | 42 |
0.152 (1.00) |
1 (1.00) |
0.0166 (1.00) |
0.0618 (1.00) |
0.901 (1.00) |
0.119 (1.00) |
0.766 (1.00) |
0.0995 (1.00) |
8p gain | 17 (26%) | 49 |
0.413 (1.00) |
0.417 (1.00) |
0.0036 (1.00) |
0.0317 (1.00) |
0.464 (1.00) |
0.101 (1.00) |
1 (1.00) |
0.0292 (1.00) |
8q gain | 18 (27%) | 48 |
0.343 (1.00) |
0.377 (1.00) |
0.00108 (0.459) |
0.00964 (1.00) |
0.696 (1.00) |
0.0878 (1.00) |
0.751 (1.00) |
0.0424 (1.00) |
9p gain | 10 (15%) | 56 |
1 (1.00) |
1 (1.00) |
0.723 (1.00) |
0.813 (1.00) |
0.833 (1.00) |
0.602 (1.00) |
1 (1.00) |
0.265 (1.00) |
9q gain | 10 (15%) | 56 |
1 (1.00) |
1 (1.00) |
0.723 (1.00) |
0.813 (1.00) |
0.831 (1.00) |
0.599 (1.00) |
1 (1.00) |
0.262 (1.00) |
10p gain | 4 (6%) | 62 |
0.441 (1.00) |
0.162 (1.00) |
0.517 (1.00) |
0.204 (1.00) |
1 (1.00) |
0.167 (1.00) |
1 (1.00) |
0.458 (1.00) |
12p gain | 19 (29%) | 47 |
0.481 (1.00) |
0.767 (1.00) |
0.0797 (1.00) |
0.158 (1.00) |
1 (1.00) |
0.0667 (1.00) |
0.213 (1.00) |
0.156 (1.00) |
12q gain | 20 (30%) | 46 |
0.444 (1.00) |
0.595 (1.00) |
0.145 (1.00) |
0.0824 (1.00) |
0.943 (1.00) |
0.0323 (1.00) |
0.235 (1.00) |
0.132 (1.00) |
14q gain | 21 (32%) | 45 |
0.106 (1.00) |
0.829 (1.00) |
0.00087 (0.373) |
0.00514 (1.00) |
0.427 (1.00) |
0.0566 (1.00) |
0.0312 (1.00) |
0.0773 (1.00) |
15q gain | 21 (32%) | 45 |
0.106 (1.00) |
0.83 (1.00) |
0.00171 (0.718) |
0.0621 (1.00) |
0.757 (1.00) |
0.215 (1.00) |
0.762 (1.00) |
0.473 (1.00) |
18p gain | 17 (26%) | 49 |
0.518 (1.00) |
0.805 (1.00) |
0.00194 (0.811) |
0.013 (1.00) |
0.937 (1.00) |
0.0495 (1.00) |
0.341 (1.00) |
0.0472 (1.00) |
18q gain | 16 (24%) | 50 |
0.64 (1.00) |
0.926 (1.00) |
0.001 (0.428) |
0.0189 (1.00) |
0.821 (1.00) |
0.0519 (1.00) |
0.119 (1.00) |
0.0623 (1.00) |
19p gain | 19 (29%) | 47 |
0.483 (1.00) |
0.273 (1.00) |
0.0215 (1.00) |
0.00799 (1.00) |
0.66 (1.00) |
0.039 (1.00) |
1 (1.00) |
0.708 (1.00) |
19q gain | 17 (26%) | 49 |
0.518 (1.00) |
0.31 (1.00) |
0.00137 (0.578) |
0.00166 (0.699) |
0.411 (1.00) |
0.0475 (1.00) |
1 (1.00) |
0.655 (1.00) |
20p gain | 20 (30%) | 46 |
0.216 (1.00) |
0.595 (1.00) |
0.0296 (1.00) |
0.0317 (1.00) |
0.708 (1.00) |
0.0305 (1.00) |
0.535 (1.00) |
0.182 (1.00) |
20q gain | 21 (32%) | 45 |
0.227 (1.00) |
0.386 (1.00) |
0.0675 (1.00) |
0.0168 (1.00) |
0.677 (1.00) |
0.0369 (1.00) |
0.762 (1.00) |
0.0991 (1.00) |
21q gain | 4 (6%) | 62 |
0.438 (1.00) |
0.163 (1.00) |
0.513 (1.00) |
0.106 (1.00) |
0.674 (1.00) |
0.165 (1.00) |
1 (1.00) |
0.41 (1.00) |
22q gain | 19 (29%) | 47 |
0.901 (1.00) |
0.712 (1.00) |
0.07 (1.00) |
0.361 (1.00) |
0.552 (1.00) |
0.0233 (1.00) |
1 (1.00) |
0.00935 (1.00) |
xq gain | 6 (9%) | 60 |
1 (1.00) |
0.722 (1.00) |
0.00676 (1.00) |
0.121 (1.00) |
0.264 (1.00) |
0.118 (1.00) |
0.142 (1.00) |
0.0714 (1.00) |
3p loss | 9 (14%) | 57 |
0.0362 (1.00) |
0.895 (1.00) |
0.0645 (1.00) |
0.00299 (1.00) |
0.903 (1.00) |
0.2 (1.00) |
0.381 (1.00) |
0.845 (1.00) |
3q loss | 8 (12%) | 58 |
0.0207 (1.00) |
0.367 (1.00) |
0.0243 (1.00) |
0.00187 (0.784) |
0.571 (1.00) |
0.182 (1.00) |
0.142 (1.00) |
0.689 (1.00) |
5p loss | 10 (15%) | 56 |
0.0984 (1.00) |
0.253 (1.00) |
0.00066 (0.284) |
0.0193 (1.00) |
0.425 (1.00) |
0.0147 (1.00) |
0.451 (1.00) |
0.344 (1.00) |
5q loss | 10 (15%) | 56 |
0.0991 (1.00) |
0.253 (1.00) |
0.00063 (0.272) |
0.0191 (1.00) |
0.425 (1.00) |
0.0144 (1.00) |
0.451 (1.00) |
0.345 (1.00) |
9p loss | 10 (15%) | 56 |
1 (1.00) |
0.904 (1.00) |
0.0644 (1.00) |
0.0163 (1.00) |
0.909 (1.00) |
0.603 (1.00) |
0.695 (1.00) |
0.891 (1.00) |
9q loss | 10 (15%) | 56 |
1 (1.00) |
0.903 (1.00) |
0.0637 (1.00) |
0.0168 (1.00) |
0.912 (1.00) |
0.601 (1.00) |
0.695 (1.00) |
0.89 (1.00) |
11p loss | 7 (11%) | 59 |
0.631 (1.00) |
0.575 (1.00) |
0.109 (1.00) |
0.317 (1.00) |
0.205 (1.00) |
0.937 (1.00) |
0.381 (1.00) |
0.579 (1.00) |
11q loss | 7 (11%) | 59 |
0.628 (1.00) |
0.573 (1.00) |
0.109 (1.00) |
0.317 (1.00) |
0.204 (1.00) |
0.937 (1.00) |
0.381 (1.00) |
0.575 (1.00) |
16p loss | 4 (6%) | 62 |
0.683 (1.00) |
0.521 (1.00) |
0.023 (1.00) |
0.0366 (1.00) |
0.676 (1.00) |
0.0875 (1.00) |
0.286 (1.00) |
0.985 (1.00) |
16q loss | 5 (8%) | 61 |
0.721 (1.00) |
0.387 (1.00) |
0.00596 (1.00) |
0.00666 (1.00) |
0.427 (1.00) |
0.0497 (1.00) |
0.0724 (1.00) |
0.688 (1.00) |
18p loss | 8 (12%) | 58 |
0.677 (1.00) |
0.0964 (1.00) |
0.315 (1.00) |
0.212 (1.00) |
0.72 (1.00) |
0.949 (1.00) |
0.669 (1.00) |
0.771 (1.00) |
18q loss | 10 (15%) | 56 |
0.622 (1.00) |
0.0799 (1.00) |
0.443 (1.00) |
0.281 (1.00) |
0.572 (1.00) |
0.864 (1.00) |
0.695 (1.00) |
0.512 (1.00) |
19q loss | 3 (5%) | 63 |
0.644 (1.00) |
0.765 (1.00) |
0.767 (1.00) |
0.823 (1.00) |
0.516 (1.00) |
0.864 (1.00) |
1 (1.00) |
0.821 (1.00) |
20p loss | 4 (6%) | 62 |
0.3 (1.00) |
0.807 (1.00) |
0.211 (1.00) |
0.215 (1.00) |
0.451 (1.00) |
0.659 (1.00) |
0.286 (1.00) |
0.551 (1.00) |
20q loss | 3 (5%) | 63 |
1 (1.00) |
0.416 (1.00) |
0.226 (1.00) |
0.0581 (1.00) |
0.295 (1.00) |
0.826 (1.00) |
0.056 (1.00) |
0.717 (1.00) |
21q loss | 35 (53%) | 31 |
0.774 (1.00) |
0.0105 (1.00) |
0.249 (1.00) |
0.195 (1.00) |
1 (1.00) |
0.128 (1.00) |
1 (1.00) |
0.0425 (1.00) |
22q loss | 8 (12%) | 58 |
0.829 (1.00) |
0.133 (1.00) |
0.246 (1.00) |
0.234 (1.00) |
0.898 (1.00) |
0.214 (1.00) |
0.687 (1.00) |
0.357 (1.00) |
xq loss | 39 (59%) | 27 |
0.599 (1.00) |
0.0735 (1.00) |
0.00689 (1.00) |
0.00361 (1.00) |
0.327 (1.00) |
0.00107 (0.456) |
0.77 (1.00) |
0.0372 (1.00) |
P value = 2e-05 (Fisher's exact test), Q value = 0.0093
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
4P GAIN MUTATED | 4 | 17 | 2 | 1 |
4P GAIN WILD-TYPE | 15 | 5 | 13 | 9 |
P value = 6e-05 (Fisher's exact test), Q value = 0.027
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
4P GAIN MUTATED | 4 | 14 | 3 | 1 | 1 | 1 | 0 |
4P GAIN WILD-TYPE | 15 | 2 | 4 | 5 | 9 | 3 | 4 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0093
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
4Q GAIN MUTATED | 4 | 17 | 2 | 1 |
4Q GAIN WILD-TYPE | 15 | 5 | 13 | 9 |
P value = 5e-05 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
4Q GAIN MUTATED | 4 | 14 | 3 | 1 | 1 | 1 | 0 |
4Q GAIN WILD-TYPE | 15 | 2 | 4 | 5 | 9 | 3 | 4 |
P value = 3e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
11P GAIN MUTATED | 1 | 13 | 1 | 0 |
11P GAIN WILD-TYPE | 18 | 9 | 14 | 10 |
P value = 0.00023 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
11P GAIN MUTATED | 1 | 11 | 1 | 1 | 1 | 0 | 0 |
11P GAIN WILD-TYPE | 18 | 5 | 6 | 5 | 9 | 4 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
11Q GAIN MUTATED | 1 | 14 | 0 | 0 |
11Q GAIN WILD-TYPE | 18 | 8 | 15 | 10 |
P value = 5e-05 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
11Q GAIN MUTATED | 1 | 12 | 1 | 1 | 0 | 0 | 0 |
11Q GAIN WILD-TYPE | 18 | 4 | 6 | 5 | 10 | 4 | 4 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0093
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
16P GAIN MUTATED | 4 | 16 | 1 | 0 |
16P GAIN WILD-TYPE | 15 | 6 | 14 | 10 |
P value = 8e-05 (Fisher's exact test), Q value = 0.036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
16P GAIN MUTATED | 4 | 13 | 2 | 1 | 0 | 1 | 0 |
16P GAIN WILD-TYPE | 15 | 3 | 5 | 5 | 10 | 3 | 4 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0093
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
16Q GAIN MUTATED | 4 | 16 | 1 | 0 |
16Q GAIN WILD-TYPE | 15 | 6 | 14 | 10 |
P value = 9e-05 (Fisher's exact test), Q value = 0.04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
16Q GAIN MUTATED | 4 | 13 | 2 | 1 | 0 | 1 | 0 |
16Q GAIN WILD-TYPE | 15 | 3 | 5 | 5 | 10 | 3 | 4 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0093
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
1P LOSS MUTATED | 17 | 32 | 4 |
1P LOSS WILD-TYPE | 1 | 3 | 9 |
P value = 0.00048 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
1P LOSS MUTATED | 19 | 16 | 14 | 4 |
1P LOSS WILD-TYPE | 0 | 6 | 1 | 6 |
P value = 0.00033 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
1P LOSS MUTATED | 19 | 11 | 6 | 4 | 9 | 4 | 0 |
1P LOSS WILD-TYPE | 0 | 5 | 1 | 2 | 1 | 0 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
1Q LOSS MUTATED | 17 | 32 | 3 |
1Q LOSS WILD-TYPE | 1 | 3 | 10 |
P value = 7e-05 (Fisher's exact test), Q value = 0.032
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
1Q LOSS MUTATED | 19 | 16 | 14 | 3 |
1Q LOSS WILD-TYPE | 0 | 6 | 1 | 7 |
P value = 5e-05 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
1Q LOSS MUTATED | 19 | 11 | 5 | 3 | 10 | 4 | 0 |
1Q LOSS WILD-TYPE | 0 | 5 | 2 | 3 | 0 | 0 | 4 |
P value = 0.00051 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
1Q LOSS MUTATED | 18 | 8 | 11 | 3 | 4 | 5 | 3 |
1Q LOSS WILD-TYPE | 0 | 3 | 1 | 3 | 1 | 0 | 6 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
2P LOSS MUTATED | 17 | 28 | 1 |
2P LOSS WILD-TYPE | 1 | 7 | 12 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
2P LOSS MUTATED | 19 | 14 | 13 | 0 |
2P LOSS WILD-TYPE | 0 | 8 | 2 | 10 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
2P LOSS MUTATED | 19 | 10 | 4 | 0 | 10 | 3 | 0 |
2P LOSS WILD-TYPE | 0 | 6 | 3 | 6 | 0 | 1 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
2P LOSS MUTATED | 18 | 7 | 10 | 2 | 3 | 5 | 1 |
2P LOSS WILD-TYPE | 0 | 4 | 2 | 4 | 2 | 0 | 8 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
2Q LOSS MUTATED | 17 | 28 | 1 |
2Q LOSS WILD-TYPE | 1 | 7 | 12 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
2Q LOSS MUTATED | 19 | 14 | 13 | 0 |
2Q LOSS WILD-TYPE | 0 | 8 | 2 | 10 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
2Q LOSS MUTATED | 19 | 10 | 4 | 0 | 10 | 3 | 0 |
2Q LOSS WILD-TYPE | 0 | 6 | 3 | 6 | 0 | 1 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
2Q LOSS MUTATED | 18 | 7 | 10 | 2 | 3 | 5 | 1 |
2Q LOSS WILD-TYPE | 0 | 4 | 2 | 4 | 2 | 0 | 8 |
P value = 0.00014 (Fisher's exact test), Q value = 0.063
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
6P LOSS MUTATED | 17 | 30 | 4 |
6P LOSS WILD-TYPE | 1 | 5 | 9 |
P value = 3e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
6P LOSS MUTATED | 19 | 15 | 14 | 3 |
6P LOSS WILD-TYPE | 0 | 7 | 1 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
6P LOSS MUTATED | 19 | 11 | 6 | 1 | 10 | 4 | 0 |
6P LOSS WILD-TYPE | 0 | 5 | 1 | 5 | 0 | 0 | 4 |
P value = 4e-04 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 10 | 6 | 5 | 8 | 4 | 6 | 5 | 4 |
6P LOSS MUTATED | 8 | 3 | 5 | 8 | 4 | 6 | 2 | 0 |
6P LOSS WILD-TYPE | 2 | 3 | 0 | 0 | 0 | 0 | 3 | 4 |
P value = 0.00016 (Fisher's exact test), Q value = 0.071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
6Q LOSS MUTATED | 17 | 30 | 4 |
6Q LOSS WILD-TYPE | 1 | 5 | 9 |
P value = 3e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
6Q LOSS MUTATED | 19 | 15 | 14 | 3 |
6Q LOSS WILD-TYPE | 0 | 7 | 1 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
6Q LOSS MUTATED | 19 | 11 | 6 | 1 | 10 | 4 | 0 |
6Q LOSS WILD-TYPE | 0 | 5 | 1 | 5 | 0 | 0 | 4 |
P value = 0.00032 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 10 | 6 | 5 | 8 | 4 | 6 | 5 | 4 |
6Q LOSS MUTATED | 8 | 3 | 5 | 8 | 4 | 6 | 2 | 0 |
6Q LOSS WILD-TYPE | 2 | 3 | 0 | 0 | 0 | 0 | 3 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 5 | 47 | 14 |
8P LOSS MUTATED | 0 | 0 | 9 |
8P LOSS WILD-TYPE | 5 | 47 | 5 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0093
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 5 | 47 | 14 |
8Q LOSS MUTATED | 0 | 0 | 8 |
8Q LOSS WILD-TYPE | 5 | 47 | 6 |
P value = 0.00029 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
10P LOSS MUTATED | 17 | 27 | 4 |
10P LOSS WILD-TYPE | 1 | 8 | 9 |
P value = 7e-05 (Fisher's exact test), Q value = 0.032
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
10P LOSS MUTATED | 19 | 13 | 13 | 3 |
10P LOSS WILD-TYPE | 0 | 9 | 2 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
10P LOSS MUTATED | 19 | 8 | 6 | 2 | 10 | 3 | 0 |
10P LOSS WILD-TYPE | 0 | 8 | 1 | 4 | 0 | 1 | 4 |
P value = 0.00014 (Fisher's exact test), Q value = 0.063
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
10P LOSS MUTATED | 18 | 6 | 11 | 2 | 4 | 4 | 3 |
10P LOSS WILD-TYPE | 0 | 5 | 1 | 4 | 1 | 1 | 6 |
P value = 0.00031 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
10Q LOSS MUTATED | 17 | 28 | 4 |
10Q LOSS WILD-TYPE | 1 | 7 | 9 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0093
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
10Q LOSS MUTATED | 19 | 13 | 14 | 3 |
10Q LOSS WILD-TYPE | 0 | 9 | 1 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
10Q LOSS MUTATED | 19 | 8 | 6 | 2 | 10 | 4 | 0 |
10Q LOSS WILD-TYPE | 0 | 8 | 1 | 4 | 0 | 0 | 4 |
P value = 2e-04 (Fisher's exact test), Q value = 0.089
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
10Q LOSS MUTATED | 18 | 7 | 11 | 2 | 4 | 4 | 3 |
10Q LOSS WILD-TYPE | 0 | 4 | 1 | 4 | 1 | 1 | 6 |
P value = 0.00049 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
13Q LOSS MUTATED | 11 | 29 | 3 |
13Q LOSS WILD-TYPE | 7 | 6 | 10 |
P value = 0.00015 (Fisher's exact test), Q value = 0.067
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
13Q LOSS MUTATED | 15 | 10 | 5 | 0 | 10 | 3 | 0 |
13Q LOSS WILD-TYPE | 4 | 6 | 2 | 6 | 0 | 1 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
17P LOSS MUTATED | 17 | 31 | 2 |
17P LOSS WILD-TYPE | 1 | 4 | 11 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
17P LOSS MUTATED | 19 | 16 | 14 | 1 |
17P LOSS WILD-TYPE | 0 | 6 | 1 | 9 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
17P LOSS MUTATED | 19 | 11 | 6 | 0 | 10 | 4 | 0 |
17P LOSS WILD-TYPE | 0 | 5 | 1 | 6 | 0 | 0 | 4 |
P value = 9e-05 (Fisher's exact test), Q value = 0.04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
17P LOSS MUTATED | 18 | 8 | 11 | 3 | 3 | 5 | 2 |
17P LOSS WILD-TYPE | 0 | 3 | 1 | 3 | 2 | 0 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
17Q LOSS MUTATED | 17 | 31 | 2 |
17Q LOSS WILD-TYPE | 1 | 4 | 11 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
17Q LOSS MUTATED | 19 | 16 | 14 | 1 |
17Q LOSS WILD-TYPE | 0 | 6 | 1 | 9 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 19 | 16 | 7 | 6 | 10 | 4 | 4 |
17Q LOSS MUTATED | 19 | 11 | 6 | 0 | 10 | 4 | 0 |
17Q LOSS WILD-TYPE | 0 | 5 | 1 | 6 | 0 | 0 | 4 |
P value = 1e-04 (Fisher's exact test), Q value = 0.045
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 18 | 11 | 12 | 6 | 5 | 5 | 9 |
17Q LOSS MUTATED | 18 | 8 | 11 | 3 | 3 | 5 | 2 |
17Q LOSS WILD-TYPE | 0 | 3 | 1 | 3 | 2 | 0 | 7 |
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtypes file = KICH-TP.transferedmergedcluster.txt
-
Number of patients = 66
-
Number of significantly arm-level cnvs = 61
-
Number of molecular subtypes = 8
-
Exclude genes that fewer than K tumors have mutations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.