This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 57 arm-level results and 8 molecular subtypes across 66 patients, 49 significant findings detected with Q value < 0.25.
-
4p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
4q gain cnv correlated to 'MRNASEQ_CNMF'.
-
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'.
-
16q gain cnv correlated to 'MRNASEQ_CNMF'.
-
Xq gain cnv correlated to 'MRNASEQ_CNMF'.
-
1p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
1q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_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', and 'MRNASEQ_CHIERARCHICAL'.
-
6q loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
8p loss cnv correlated to 'CN_CNMF'.
-
8q loss cnv correlated to 'CN_CNMF'.
-
10p loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
10q loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
13q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
-
16q loss cnv correlated to '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'.
-
Xq loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Molecular subtypes |
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 | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | |
2p loss | 0 (0%) | 23 |
0.0828 (1.00) |
2.89e-06 (0.00127) |
8.31e-09 (3.77e-06) |
2.26e-07 (0.000102) |
0.0679 (1.00) |
0.000592 (0.242) |
0.0693 (1.00) |
0.000864 (0.348) |
2q loss | 0 (0%) | 23 |
0.0828 (1.00) |
2.89e-06 (0.00127) |
8.31e-09 (3.77e-06) |
2.26e-07 (0.000102) |
0.0679 (1.00) |
0.000592 (0.242) |
0.0693 (1.00) |
0.000864 (0.348) |
17p loss | 0 (0%) | 21 |
0.158 (1.00) |
8.78e-07 (0.000392) |
2.61e-09 (1.19e-06) |
3e-07 (0.000135) |
0.0256 (1.00) |
0.000255 (0.105) |
0.0183 (1.00) |
0.00074 (0.301) |
17q loss | 0 (0%) | 21 |
0.158 (1.00) |
8.78e-07 (0.000392) |
2.61e-09 (1.19e-06) |
3e-07 (0.000135) |
0.0256 (1.00) |
0.000255 (0.105) |
0.0183 (1.00) |
0.00074 (0.301) |
1p loss | 0 (0%) | 18 |
0.342 (1.00) |
8.27e-05 (0.0353) |
8.26e-06 (0.0036) |
1.79e-05 (0.0078) |
0.0572 (1.00) |
0.00103 (0.41) |
0.0195 (1.00) |
0.00549 (1.00) |
1q loss | 0 (0%) | 19 |
0.32 (1.00) |
0.000139 (0.0584) |
3.11e-05 (0.0134) |
6.59e-05 (0.0283) |
0.127 (1.00) |
0.00157 (0.615) |
0.0214 (1.00) |
0.00502 (1.00) |
6p loss | 0 (0%) | 19 |
0.32 (1.00) |
0.000139 (0.0584) |
1.26e-06 (0.000559) |
2.67e-05 (0.0116) |
0.127 (1.00) |
0.00157 (0.615) |
0.119 (1.00) |
0.00502 (1.00) |
6q loss | 0 (0%) | 19 |
0.32 (1.00) |
0.000139 (0.0584) |
1.26e-06 (0.000559) |
2.67e-05 (0.0116) |
0.127 (1.00) |
0.00157 (0.615) |
0.119 (1.00) |
0.00502 (1.00) |
Xq loss | 0 (0%) | 33 |
0.713 (1.00) |
9.23e-05 (0.039) |
7.96e-05 (0.0341) |
0.000217 (0.0897) |
0.019 (1.00) |
0.00208 (0.806) |
0.00422 (1.00) |
0.00127 (0.5) |
4p gain | 0 (0%) | 48 |
0.383 (1.00) |
0.934 (1.00) |
4.56e-05 (0.0196) |
0.000161 (0.0672) |
0.239 (1.00) |
0.1 (1.00) |
0.777 (1.00) |
0.136 (1.00) |
11p gain | 0 (0%) | 53 |
0.517 (1.00) |
0.599 (1.00) |
0.000287 (0.118) |
0.000156 (0.0652) |
0.5 (1.00) |
0.186 (1.00) |
0.628 (1.00) |
0.1 (1.00) |
11q gain | 0 (0%) | 52 |
0.606 (1.00) |
0.613 (1.00) |
8.33e-05 (0.0355) |
2.78e-05 (0.012) |
0.698 (1.00) |
0.186 (1.00) |
0.801 (1.00) |
0.106 (1.00) |
10p loss | 0 (0%) | 22 |
0.261 (1.00) |
0.00329 (1.00) |
2.51e-06 (0.00111) |
3.03e-06 (0.00133) |
0.391 (1.00) |
0.0506 (1.00) |
0.11 (1.00) |
0.0517 (1.00) |
10q loss | 0 (0%) | 22 |
0.261 (1.00) |
0.00329 (1.00) |
2.51e-06 (0.00111) |
3.03e-06 (0.00133) |
0.391 (1.00) |
0.0506 (1.00) |
0.11 (1.00) |
0.0517 (1.00) |
4q gain | 0 (0%) | 49 |
0.362 (1.00) |
0.806 (1.00) |
0.000173 (0.0717) |
0.000784 (0.317) |
0.144 (1.00) |
0.0977 (1.00) |
0.522 (1.00) |
0.172 (1.00) |
16p gain | 0 (0%) | 51 |
0.556 (1.00) |
1 (1.00) |
9.21e-05 (0.039) |
0.000936 (0.375) |
0.137 (1.00) |
0.106 (1.00) |
0.491 (1.00) |
0.31 (1.00) |
16q gain | 0 (0%) | 51 |
0.556 (1.00) |
1 (1.00) |
9.21e-05 (0.039) |
0.000936 (0.375) |
0.137 (1.00) |
0.106 (1.00) |
0.491 (1.00) |
0.31 (1.00) |
Xq gain | 0 (0%) | 57 |
1 (1.00) |
1 (1.00) |
8.84e-05 (0.0375) |
0.00417 (1.00) |
0.294 (1.00) |
0.341 (1.00) |
0.533 (1.00) |
0.348 (1.00) |
8p loss | 0 (0%) | 57 |
8.11e-08 (3.67e-05) |
0.0857 (1.00) |
0.0531 (1.00) |
0.0036 (1.00) |
0.148 (1.00) |
0.341 (1.00) |
0.0122 (1.00) |
0.0254 (1.00) |
8q loss | 0 (0%) | 58 |
5.86e-07 (0.000262) |
0.0437 (1.00) |
0.134 (1.00) |
0.00434 (1.00) |
0.291 (1.00) |
0.586 (1.00) |
0.0267 (1.00) |
0.0851 (1.00) |
13q loss | 0 (0%) | 29 |
0.116 (1.00) |
0.00191 (0.743) |
0.00123 (0.488) |
0.000506 (0.207) |
0.743 (1.00) |
0.036 (1.00) |
0.514 (1.00) |
0.404 (1.00) |
16q loss | 0 (0%) | 62 |
0.685 (1.00) |
0.302 (1.00) |
0.00219 (0.844) |
8.58e-05 (0.0365) |
0.678 (1.00) |
0.452 (1.00) |
0.674 (1.00) |
0.577 (1.00) |
3p gain | 0 (0%) | 61 |
0.721 (1.00) |
1 (1.00) |
1 (1.00) |
0.942 (1.00) |
0.15 (1.00) |
0.134 (1.00) |
0.0544 (1.00) |
0.409 (1.00) |
3q gain | 0 (0%) | 61 |
0.721 (1.00) |
1 (1.00) |
1 (1.00) |
0.942 (1.00) |
0.15 (1.00) |
0.134 (1.00) |
0.0544 (1.00) |
0.409 (1.00) |
5p gain | 0 (0%) | 61 |
0.549 (1.00) |
1 (1.00) |
1 (1.00) |
0.839 (1.00) |
0.857 (1.00) |
0.134 (1.00) |
0.718 (1.00) |
0.343 (1.00) |
5q gain | 0 (0%) | 61 |
0.549 (1.00) |
1 (1.00) |
1 (1.00) |
0.839 (1.00) |
0.857 (1.00) |
0.134 (1.00) |
0.718 (1.00) |
0.343 (1.00) |
7p gain | 0 (0%) | 48 |
0.383 (1.00) |
0.934 (1.00) |
0.00906 (1.00) |
0.0191 (1.00) |
0.197 (1.00) |
1 (1.00) |
0.438 (1.00) |
0.35 (1.00) |
7q gain | 0 (0%) | 48 |
0.383 (1.00) |
0.934 (1.00) |
0.00906 (1.00) |
0.0191 (1.00) |
0.197 (1.00) |
1 (1.00) |
0.438 (1.00) |
0.35 (1.00) |
8p gain | 0 (0%) | 53 |
0.274 (1.00) |
0.599 (1.00) |
0.0276 (1.00) |
0.0848 (1.00) |
0.177 (1.00) |
1 (1.00) |
0.131 (1.00) |
0.665 (1.00) |
8q gain | 0 (0%) | 52 |
0.157 (1.00) |
0.613 (1.00) |
0.00994 (1.00) |
0.0317 (1.00) |
0.387 (1.00) |
1 (1.00) |
0.241 (1.00) |
0.761 (1.00) |
9p gain | 0 (0%) | 58 |
1 (1.00) |
0.779 (1.00) |
0.911 (1.00) |
0.841 (1.00) |
0.804 (1.00) |
0.298 (1.00) |
0.572 (1.00) |
0.603 (1.00) |
9q gain | 0 (0%) | 58 |
1 (1.00) |
0.779 (1.00) |
0.911 (1.00) |
0.841 (1.00) |
0.804 (1.00) |
0.298 (1.00) |
0.572 (1.00) |
0.603 (1.00) |
12p gain | 0 (0%) | 52 |
0.688 (1.00) |
1 (1.00) |
0.0129 (1.00) |
0.0542 (1.00) |
0.698 (1.00) |
1 (1.00) |
0.931 (1.00) |
0.726 (1.00) |
12q gain | 0 (0%) | 53 |
0.764 (1.00) |
0.772 (1.00) |
0.0135 (1.00) |
0.0191 (1.00) |
0.86 (1.00) |
0.675 (1.00) |
0.58 (1.00) |
0.592 (1.00) |
14q gain | 0 (0%) | 50 |
0.34 (1.00) |
0.928 (1.00) |
0.000706 (0.287) |
0.00332 (1.00) |
0.261 (1.00) |
0.436 (1.00) |
0.578 (1.00) |
0.587 (1.00) |
15q gain | 0 (0%) | 52 |
0.224 (1.00) |
0.664 (1.00) |
0.00113 (0.449) |
0.00646 (1.00) |
0.287 (1.00) |
0.671 (1.00) |
0.137 (1.00) |
0.363 (1.00) |
18p gain | 0 (0%) | 52 |
0.475 (1.00) |
0.562 (1.00) |
0.0062 (1.00) |
0.0191 (1.00) |
0.806 (1.00) |
0.386 (1.00) |
0.555 (1.00) |
0.26 (1.00) |
18q gain | 0 (0%) | 53 |
0.671 (1.00) |
0.772 (1.00) |
0.00409 (1.00) |
0.0183 (1.00) |
0.926 (1.00) |
1 (1.00) |
0.79 (1.00) |
0.311 (1.00) |
19p gain | 0 (0%) | 55 |
0.867 (1.00) |
0.904 (1.00) |
0.00206 (0.8) |
0.00219 (0.844) |
0.29 (1.00) |
0.337 (1.00) |
0.641 (1.00) |
0.27 (1.00) |
19q gain | 0 (0%) | 57 |
0.713 (1.00) |
0.712 (1.00) |
0.00269 (1.00) |
0.00372 (1.00) |
0.397 (1.00) |
0.341 (1.00) |
0.665 (1.00) |
0.406 (1.00) |
20p gain | 0 (0%) | 52 |
0.224 (1.00) |
0.562 (1.00) |
0.00468 (1.00) |
0.00377 (1.00) |
0.124 (1.00) |
0.671 (1.00) |
0.343 (1.00) |
0.639 (1.00) |
20q gain | 0 (0%) | 51 |
0.282 (1.00) |
0.283 (1.00) |
0.00713 (1.00) |
0.00743 (1.00) |
0.17 (1.00) |
1 (1.00) |
0.276 (1.00) |
0.757 (1.00) |
21q gain | 0 (0%) | 63 |
0.646 (1.00) |
0.158 (1.00) |
0.327 (1.00) |
0.333 (1.00) |
0.194 (1.00) |
0.361 (1.00) |
0.106 (1.00) |
0.528 (1.00) |
22q gain | 0 (0%) | 51 |
0.882 (1.00) |
0.53 (1.00) |
0.0748 (1.00) |
0.196 (1.00) |
0.466 (1.00) |
1 (1.00) |
0.491 (1.00) |
0.872 (1.00) |
3p loss | 0 (0%) | 59 |
0.0826 (1.00) |
1 (1.00) |
0.252 (1.00) |
0.00554 (1.00) |
0.481 (1.00) |
0.581 (1.00) |
0.349 (1.00) |
0.198 (1.00) |
3q loss | 0 (0%) | 60 |
0.0326 (1.00) |
0.621 (1.00) |
0.135 (1.00) |
0.00126 (0.497) |
0.354 (1.00) |
0.585 (1.00) |
0.109 (1.00) |
0.107 (1.00) |
5p loss | 0 (0%) | 59 |
0.302 (1.00) |
0.141 (1.00) |
0.0329 (1.00) |
0.00478 (1.00) |
0.886 (1.00) |
0.581 (1.00) |
0.691 (1.00) |
0.225 (1.00) |
5q loss | 0 (0%) | 59 |
0.302 (1.00) |
0.141 (1.00) |
0.0329 (1.00) |
0.00478 (1.00) |
0.886 (1.00) |
0.581 (1.00) |
0.691 (1.00) |
0.225 (1.00) |
9p loss | 0 (0%) | 58 |
1 (1.00) |
0.888 (1.00) |
0.171 (1.00) |
0.579 (1.00) |
1 (1.00) |
0.298 (1.00) |
0.714 (1.00) |
0.843 (1.00) |
9q loss | 0 (0%) | 58 |
1 (1.00) |
0.888 (1.00) |
0.171 (1.00) |
0.579 (1.00) |
1 (1.00) |
0.298 (1.00) |
0.714 (1.00) |
0.843 (1.00) |
11p loss | 0 (0%) | 61 |
1 (1.00) |
0.696 (1.00) |
0.129 (1.00) |
0.408 (1.00) |
0.12 (1.00) |
1 (1.00) |
0.254 (1.00) |
0.161 (1.00) |
11q loss | 0 (0%) | 61 |
1 (1.00) |
0.696 (1.00) |
0.129 (1.00) |
0.408 (1.00) |
0.12 (1.00) |
1 (1.00) |
0.254 (1.00) |
0.161 (1.00) |
16p loss | 0 (0%) | 63 |
1 (1.00) |
0.418 (1.00) |
0.0126 (1.00) |
0.00148 (0.581) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.43 (1.00) |
18p loss | 0 (0%) | 61 |
0.257 (1.00) |
0.109 (1.00) |
0.0134 (1.00) |
0.0012 (0.476) |
0.12 (1.00) |
1 (1.00) |
0.254 (1.00) |
0.328 (1.00) |
18q loss | 0 (0%) | 59 |
0.222 (1.00) |
0.141 (1.00) |
0.0481 (1.00) |
0.0178 (1.00) |
0.203 (1.00) |
1 (1.00) |
0.349 (1.00) |
0.515 (1.00) |
21q loss | 0 (0%) | 38 |
1 (1.00) |
0.00704 (1.00) |
0.23 (1.00) |
0.0379 (1.00) |
0.575 (1.00) |
0.722 (1.00) |
0.152 (1.00) |
0.157 (1.00) |
22q loss | 0 (0%) | 61 |
0.721 (1.00) |
0.109 (1.00) |
0.745 (1.00) |
0.38 (1.00) |
1 (1.00) |
1 (1.00) |
0.849 (1.00) |
0.185 (1.00) |
P value = 4.56e-05 (Fisher's exact test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
4P GAIN CNV | 3 | 14 | 1 | 0 |
4P GAIN WILD-TYPE | 16 | 8 | 14 | 10 |
P value = 0.000161 (Chi-square test), Q value = 0.067
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
4P GAIN CNV | 1 | 1 | 12 | 0 | 4 |
4P GAIN WILD-TYPE | 9 | 9 | 5 | 6 | 19 |
P value = 0.000173 (Fisher's exact test), Q value = 0.072
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
4Q GAIN CNV | 3 | 13 | 1 | 0 |
4Q GAIN WILD-TYPE | 16 | 9 | 14 | 10 |
P value = 0.000287 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
11P GAIN CNV | 1 | 11 | 1 | 0 |
11P GAIN WILD-TYPE | 18 | 11 | 14 | 10 |
P value = 0.000156 (Chi-square test), Q value = 0.065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
11P GAIN CNV | 1 | 1 | 10 | 0 | 1 |
11P GAIN WILD-TYPE | 9 | 9 | 7 | 6 | 22 |
P value = 8.33e-05 (Fisher's exact test), Q value = 0.035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
11Q GAIN CNV | 1 | 12 | 1 | 0 |
11Q GAIN WILD-TYPE | 18 | 10 | 14 | 10 |
P value = 2.78e-05 (Chi-square test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
11Q GAIN CNV | 1 | 1 | 11 | 0 | 1 |
11Q GAIN WILD-TYPE | 9 | 9 | 6 | 6 | 22 |
P value = 9.21e-05 (Fisher's exact test), Q value = 0.039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
16P GAIN CNV | 3 | 12 | 0 | 0 |
16P GAIN WILD-TYPE | 16 | 10 | 15 | 10 |
P value = 9.21e-05 (Fisher's exact test), Q value = 0.039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
16Q GAIN CNV | 3 | 12 | 0 | 0 |
16Q GAIN WILD-TYPE | 16 | 10 | 15 | 10 |
P value = 8.84e-05 (Fisher's exact test), Q value = 0.037
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
XQ GAIN CNV | 0 | 9 | 0 | 0 |
XQ GAIN WILD-TYPE | 19 | 13 | 15 | 10 |
P value = 8.27e-05 (Fisher's exact test), Q value = 0.035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
1P LOSS CNV | 16 | 29 | 3 |
1P LOSS WILD-TYPE | 2 | 6 | 10 |
P value = 8.26e-06 (Fisher's exact test), Q value = 0.0036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
1P LOSS CNV | 19 | 12 | 14 | 3 |
1P LOSS WILD-TYPE | 0 | 10 | 1 | 7 |
P value = 1.79e-05 (Chi-square test), Q value = 0.0078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
1P LOSS CNV | 9 | 2 | 9 | 6 | 22 |
1P LOSS WILD-TYPE | 1 | 8 | 8 | 0 | 1 |
P value = 0.000139 (Fisher's exact test), Q value = 0.058
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
1Q LOSS CNV | 16 | 28 | 3 |
1Q LOSS WILD-TYPE | 2 | 7 | 10 |
P value = 3.11e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
1Q LOSS CNV | 19 | 12 | 13 | 3 |
1Q LOSS WILD-TYPE | 0 | 10 | 2 | 7 |
P value = 6.59e-05 (Chi-square test), Q value = 0.028
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
1Q LOSS CNV | 9 | 2 | 9 | 5 | 22 |
1Q LOSS WILD-TYPE | 1 | 8 | 8 | 1 | 1 |
P value = 2.89e-06 (Fisher's exact test), Q value = 0.0013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
2P LOSS CNV | 16 | 26 | 1 |
2P LOSS WILD-TYPE | 2 | 9 | 12 |
P value = 8.31e-09 (Fisher's exact test), Q value = 3.8e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
2P LOSS CNV | 19 | 11 | 13 | 0 |
2P LOSS WILD-TYPE | 0 | 11 | 2 | 10 |
P value = 2.26e-07 (Chi-square test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
2P LOSS CNV | 10 | 0 | 8 | 3 | 22 |
2P LOSS WILD-TYPE | 0 | 10 | 9 | 3 | 1 |
P value = 0.000592 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 9 | 57 |
2P LOSS CNV | 1 | 42 |
2P LOSS WILD-TYPE | 8 | 15 |
P value = 2.89e-06 (Fisher's exact test), Q value = 0.0013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
2Q LOSS CNV | 16 | 26 | 1 |
2Q LOSS WILD-TYPE | 2 | 9 | 12 |
P value = 8.31e-09 (Fisher's exact test), Q value = 3.8e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
2Q LOSS CNV | 19 | 11 | 13 | 0 |
2Q LOSS WILD-TYPE | 0 | 11 | 2 | 10 |
P value = 2.26e-07 (Chi-square test), Q value = 1e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
2Q LOSS CNV | 10 | 0 | 8 | 3 | 22 |
2Q LOSS WILD-TYPE | 0 | 10 | 9 | 3 | 1 |
P value = 0.000592 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 9 | 57 |
2Q LOSS CNV | 1 | 42 |
2Q LOSS WILD-TYPE | 8 | 15 |
P value = 0.000139 (Fisher's exact test), Q value = 0.058
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
6P LOSS CNV | 16 | 28 | 3 |
6P LOSS WILD-TYPE | 2 | 7 | 10 |
P value = 1.26e-06 (Fisher's exact test), Q value = 0.00056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
6P LOSS CNV | 19 | 12 | 14 | 2 |
6P LOSS WILD-TYPE | 0 | 10 | 1 | 8 |
P value = 2.67e-05 (Chi-square test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
6P LOSS CNV | 10 | 2 | 9 | 4 | 22 |
6P LOSS WILD-TYPE | 0 | 8 | 8 | 2 | 1 |
P value = 0.000139 (Fisher's exact test), Q value = 0.058
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
6Q LOSS CNV | 16 | 28 | 3 |
6Q LOSS WILD-TYPE | 2 | 7 | 10 |
P value = 1.26e-06 (Fisher's exact test), Q value = 0.00056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
6Q LOSS CNV | 19 | 12 | 14 | 2 |
6Q LOSS WILD-TYPE | 0 | 10 | 1 | 8 |
P value = 2.67e-05 (Chi-square test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
6Q LOSS CNV | 10 | 2 | 9 | 4 | 22 |
6Q LOSS WILD-TYPE | 0 | 8 | 8 | 2 | 1 |
P value = 8.11e-08 (Fisher's exact test), Q value = 3.7e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 5 | 47 | 14 |
8P LOSS CNV | 0 | 0 | 9 |
8P LOSS WILD-TYPE | 5 | 47 | 5 |
P value = 5.86e-07 (Fisher's exact test), Q value = 0.00026
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 5 | 47 | 14 |
8Q LOSS CNV | 0 | 0 | 8 |
8Q LOSS WILD-TYPE | 5 | 47 | 6 |
P value = 2.51e-06 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
10P LOSS CNV | 19 | 9 | 13 | 3 |
10P LOSS WILD-TYPE | 0 | 13 | 2 | 7 |
P value = 3.03e-06 (Chi-square test), Q value = 0.0013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
10P LOSS CNV | 10 | 2 | 6 | 4 | 22 |
10P LOSS WILD-TYPE | 0 | 8 | 11 | 2 | 1 |
P value = 2.51e-06 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
10Q LOSS CNV | 19 | 9 | 13 | 3 |
10Q LOSS WILD-TYPE | 0 | 13 | 2 | 7 |
P value = 3.03e-06 (Chi-square test), Q value = 0.0013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
10Q LOSS CNV | 10 | 2 | 6 | 4 | 22 |
10Q LOSS WILD-TYPE | 0 | 8 | 11 | 2 | 1 |
P value = 0.000506 (Chi-square test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
13Q LOSS CNV | 10 | 1 | 8 | 2 | 16 |
13Q LOSS WILD-TYPE | 0 | 9 | 9 | 4 | 7 |
P value = 8.58e-05 (Chi-square test), Q value = 0.036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
16Q LOSS CNV | 4 | 0 | 0 | 0 | 0 |
16Q LOSS WILD-TYPE | 6 | 10 | 17 | 6 | 23 |
P value = 8.78e-07 (Fisher's exact test), Q value = 0.00039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
17P LOSS CNV | 16 | 28 | 1 |
17P LOSS WILD-TYPE | 2 | 7 | 12 |
P value = 2.61e-09 (Fisher's exact test), Q value = 1.2e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
17P LOSS CNV | 19 | 12 | 14 | 0 |
17P LOSS WILD-TYPE | 0 | 10 | 1 | 10 |
P value = 3e-07 (Chi-square test), Q value = 0.00013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
17P LOSS CNV | 10 | 0 | 9 | 4 | 22 |
17P LOSS WILD-TYPE | 0 | 10 | 8 | 2 | 1 |
P value = 0.000255 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 9 | 57 |
17P LOSS CNV | 1 | 44 |
17P LOSS WILD-TYPE | 8 | 13 |
P value = 8.78e-07 (Fisher's exact test), Q value = 0.00039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
17Q LOSS CNV | 16 | 28 | 1 |
17Q LOSS WILD-TYPE | 2 | 7 | 12 |
P value = 2.61e-09 (Fisher's exact test), Q value = 1.2e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
17Q LOSS CNV | 19 | 12 | 14 | 0 |
17Q LOSS WILD-TYPE | 0 | 10 | 1 | 10 |
P value = 3e-07 (Chi-square test), Q value = 0.00013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
17Q LOSS CNV | 10 | 0 | 9 | 4 | 22 |
17Q LOSS WILD-TYPE | 0 | 10 | 8 | 2 | 1 |
P value = 0.000255 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 9 | 57 |
17Q LOSS CNV | 1 | 44 |
17Q LOSS WILD-TYPE | 8 | 13 |
P value = 9.23e-05 (Fisher's exact test), Q value = 0.039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 35 | 13 |
XQ LOSS CNV | 12 | 21 | 0 |
XQ LOSS WILD-TYPE | 6 | 14 | 13 |
P value = 7.96e-05 (Fisher's exact test), Q value = 0.034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
XQ LOSS CNV | 15 | 8 | 10 | 0 |
XQ LOSS WILD-TYPE | 4 | 14 | 5 | 10 |
P value = 0.000217 (Chi-square test), Q value = 0.09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
XQ LOSS CNV | 7 | 0 | 5 | 3 | 18 |
XQ LOSS WILD-TYPE | 3 | 10 | 12 | 3 | 5 |
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Molecular subtypes file = KICH-TP.transferedmergedcluster.txt
-
Number of patients = 66
-
Number of significantly arm-level cnvs = 57
-
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 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.