This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 59 arm-level results and 8 molecular subtypes across 127 patients, 43 significant findings detected with Q value < 0.25.
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1q gain cnv correlated to 'METHLYATION_CNMF'.
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3p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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3q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
5p gain cnv correlated to 'CN_CNMF'.
-
5q gain cnv correlated to 'CN_CNMF'.
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7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
12p gain cnv correlated to 'CN_CNMF'.
-
12q gain cnv correlated to 'CN_CNMF'.
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16p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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16q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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17p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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17q gain cnv correlated to 'CN_CNMF'.
-
4p loss cnv correlated to 'CN_CNMF'.
-
5q loss cnv correlated to 'CN_CNMF'.
-
6p loss cnv correlated to 'CN_CNMF'.
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9p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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9q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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14q loss cnv correlated to 'CN_CNMF'.
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22q loss cnv correlated to 'CN_CNMF'.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Chi-square 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 | |
3q gain | 0 (0%) | 94 |
1.95e-12 (8.49e-10) |
0.00739 (1.00) |
3.65e-05 (0.015) |
6.94e-06 (0.00291) |
0.000679 (0.267) |
6.07e-08 (2.61e-05) |
0.197 (1.00) |
0.000241 (0.0969) |
17p gain | 0 (0%) | 61 |
9.52e-08 (4.09e-05) |
1.3e-06 (0.000555) |
3.49e-05 (0.0144) |
2.21e-06 (0.000937) |
0.0228 (1.00) |
7.75e-05 (0.0316) |
0.0197 (1.00) |
0.012 (1.00) |
3p gain | 0 (0%) | 98 |
7.99e-15 (3.49e-12) |
0.0132 (1.00) |
0.000268 (0.108) |
3.64e-07 (0.000156) |
0.00686 (1.00) |
4.64e-09 (2.01e-06) |
0.232 (1.00) |
0.00425 (1.00) |
7p gain | 0 (0%) | 60 |
2.69e-07 (0.000115) |
2.62e-06 (0.00111) |
5.65e-05 (0.0231) |
2.01e-05 (0.00834) |
0.0834 (1.00) |
0.00341 (1.00) |
0.156 (1.00) |
0.00708 (1.00) |
7q gain | 0 (0%) | 59 |
5.79e-08 (2.5e-05) |
9.37e-06 (0.00392) |
0.000181 (0.0735) |
3.74e-05 (0.0153) |
0.0474 (1.00) |
0.0042 (1.00) |
0.0832 (1.00) |
0.00741 (1.00) |
16p gain | 0 (0%) | 67 |
4.19e-06 (0.00177) |
0.221 (1.00) |
0.00874 (1.00) |
0.000182 (0.0738) |
0.0074 (1.00) |
1.89e-05 (0.00787) |
0.0997 (1.00) |
0.00401 (1.00) |
16q gain | 0 (0%) | 69 |
9.17e-06 (0.00384) |
0.0521 (1.00) |
0.00419 (1.00) |
1.46e-05 (0.00609) |
0.00489 (1.00) |
1.8e-06 (0.000764) |
0.134 (1.00) |
0.00254 (0.968) |
9p loss | 0 (0%) | 112 |
0.000169 (0.069) |
0.000318 (0.127) |
0.00782 (1.00) |
0.0678 (1.00) |
0.114 (1.00) |
0.314 (1.00) |
1 (1.00) |
0.0241 (1.00) |
9q loss | 0 (0%) | 110 |
0.000445 (0.177) |
3.17e-05 (0.0131) |
0.0256 (1.00) |
0.131 (1.00) |
0.0751 (1.00) |
0.0814 (1.00) |
1 (1.00) |
0.00493 (1.00) |
1q gain | 0 (0%) | 118 |
0.00553 (1.00) |
0.000353 (0.141) |
0.00232 (0.89) |
0.00827 (1.00) |
0.446 (1.00) |
0.112 (1.00) |
0.812 (1.00) |
0.128 (1.00) |
5p gain | 0 (0%) | 113 |
1.96e-08 (8.45e-06) |
0.0521 (1.00) |
0.156 (1.00) |
0.8 (1.00) |
0.835 (1.00) |
0.411 (1.00) |
0.437 (1.00) |
0.536 (1.00) |
5q gain | 0 (0%) | 113 |
2.18e-10 (9.48e-08) |
0.0521 (1.00) |
0.579 (1.00) |
0.8 (1.00) |
0.851 (1.00) |
0.411 (1.00) |
0.437 (1.00) |
0.536 (1.00) |
12p gain | 0 (0%) | 87 |
0.00055 (0.218) |
0.833 (1.00) |
0.161 (1.00) |
0.0648 (1.00) |
0.0938 (1.00) |
0.103 (1.00) |
0.465 (1.00) |
0.11 (1.00) |
12q gain | 0 (0%) | 87 |
0.00055 (0.218) |
0.833 (1.00) |
0.161 (1.00) |
0.0648 (1.00) |
0.0938 (1.00) |
0.103 (1.00) |
0.465 (1.00) |
0.11 (1.00) |
17q gain | 0 (0%) | 50 |
5.4e-06 (0.00227) |
0.00104 (0.404) |
0.0144 (1.00) |
0.000926 (0.362) |
0.0536 (1.00) |
0.0135 (1.00) |
0.0442 (1.00) |
0.05 (1.00) |
4p loss | 0 (0%) | 116 |
0.000247 (0.0993) |
0.00449 (1.00) |
0.0129 (1.00) |
0.18 (1.00) |
0.181 (1.00) |
0.657 (1.00) |
0.346 (1.00) |
0.0408 (1.00) |
5q loss | 0 (0%) | 121 |
1.96e-05 (0.00815) |
0.23 (1.00) |
0.41 (1.00) |
0.211 (1.00) |
0.547 (1.00) |
0.665 (1.00) |
0.239 (1.00) |
0.615 (1.00) |
6p loss | 0 (0%) | 118 |
0.00043 (0.171) |
0.443 (1.00) |
0.468 (1.00) |
1 (1.00) |
0.214 (1.00) |
0.546 (1.00) |
0.812 (1.00) |
1 (1.00) |
14q loss | 0 (0%) | 104 |
1.54e-11 (6.7e-09) |
0.267 (1.00) |
0.135 (1.00) |
0.0977 (1.00) |
0.757 (1.00) |
0.934 (1.00) |
1 (1.00) |
0.458 (1.00) |
22q loss | 0 (0%) | 103 |
0.000233 (0.0942) |
0.00271 (1.00) |
0.673 (1.00) |
0.0477 (1.00) |
0.0178 (1.00) |
0.0721 (1.00) |
0.0885 (1.00) |
0.0331 (1.00) |
2p gain | 0 (0%) | 114 |
0.0607 (1.00) |
0.132 (1.00) |
0.585 (1.00) |
0.338 (1.00) |
0.788 (1.00) |
0.227 (1.00) |
0.0415 (1.00) |
0.155 (1.00) |
2q gain | 0 (0%) | 112 |
0.0309 (1.00) |
0.354 (1.00) |
0.329 (1.00) |
0.205 (1.00) |
0.877 (1.00) |
0.441 (1.00) |
0.27 (1.00) |
0.291 (1.00) |
4p gain | 0 (0%) | 123 |
0.382 (1.00) |
0.457 (1.00) |
1 (1.00) |
0.754 (1.00) |
0.874 (1.00) |
|||
4q gain | 0 (0%) | 124 |
0.572 (1.00) |
0.645 (1.00) |
0.602 (1.00) |
0.759 (1.00) |
0.604 (1.00) |
|||
6p gain | 0 (0%) | 123 |
0.503 (1.00) |
0.44 (1.00) |
0.114 (1.00) |
0.677 (1.00) |
0.282 (1.00) |
0.514 (1.00) |
0.279 (1.00) |
1 (1.00) |
6q gain | 0 (0%) | 124 |
0.213 (1.00) |
0.41 (1.00) |
1 (1.00) |
0.429 (1.00) |
0.518 (1.00) |
|||
8p gain | 0 (0%) | 118 |
0.318 (1.00) |
0.087 (1.00) |
0.732 (1.00) |
0.232 (1.00) |
0.502 (1.00) |
0.389 (1.00) |
0.424 (1.00) |
0.128 (1.00) |
8q gain | 0 (0%) | 116 |
0.00446 (1.00) |
0.0131 (1.00) |
0.243 (1.00) |
0.0683 (1.00) |
0.0899 (1.00) |
0.396 (1.00) |
0.246 (1.00) |
0.0765 (1.00) |
10p gain | 0 (0%) | 123 |
0.184 (1.00) |
0.645 (1.00) |
0.602 (1.00) |
0.138 (1.00) |
0.874 (1.00) |
|||
10q gain | 0 (0%) | 124 |
0.393 (1.00) |
0.317 (1.00) |
0.442 (1.00) |
|||||
13q gain | 0 (0%) | 113 |
0.00662 (1.00) |
0.179 (1.00) |
0.324 (1.00) |
0.0445 (1.00) |
0.638 (1.00) |
0.307 (1.00) |
0.928 (1.00) |
0.414 (1.00) |
18p gain | 0 (0%) | 121 |
0.16 (1.00) |
0.329 (1.00) |
0.863 (1.00) |
1 (1.00) |
0.885 (1.00) |
0.804 (1.00) |
0.188 (1.00) |
0.761 (1.00) |
18q gain | 0 (0%) | 123 |
0.0227 (1.00) |
0.329 (1.00) |
0.77 (1.00) |
0.432 (1.00) |
0.827 (1.00) |
0.32 (1.00) |
0.188 (1.00) |
0.761 (1.00) |
20p gain | 0 (0%) | 88 |
0.0185 (1.00) |
0.0743 (1.00) |
0.000722 (0.284) |
0.0152 (1.00) |
0.256 (1.00) |
0.267 (1.00) |
0.0791 (1.00) |
0.189 (1.00) |
20q gain | 0 (0%) | 87 |
0.0107 (1.00) |
0.142 (1.00) |
0.000813 (0.319) |
0.0381 (1.00) |
0.166 (1.00) |
0.524 (1.00) |
0.0213 (1.00) |
0.259 (1.00) |
21q gain | 0 (0%) | 122 |
0.637 (1.00) |
0.468 (1.00) |
0.0267 (1.00) |
0.193 (1.00) |
0.00525 (1.00) |
1 (1.00) |
||
Xq gain | 0 (0%) | 122 |
0.121 (1.00) |
0.137 (1.00) |
0.457 (1.00) |
1 (1.00) |
0.278 (1.00) |
0.752 (1.00) |
0.827 (1.00) |
0.204 (1.00) |
1p loss | 0 (0%) | 113 |
0.0256 (1.00) |
0.328 (1.00) |
0.611 (1.00) |
0.589 (1.00) |
0.417 (1.00) |
0.283 (1.00) |
0.162 (1.00) |
0.472 (1.00) |
1q loss | 0 (0%) | 120 |
0.0171 (1.00) |
0.193 (1.00) |
0.103 (1.00) |
0.432 (1.00) |
0.111 (1.00) |
0.00803 (1.00) |
0.377 (1.00) |
0.123 (1.00) |
3p loss | 0 (0%) | 119 |
0.00138 (0.536) |
0.00142 (0.549) |
0.058 (1.00) |
0.0149 (1.00) |
0.0923 (1.00) |
0.073 (1.00) |
0.426 (1.00) |
0.00239 (0.914) |
3q loss | 0 (0%) | 124 |
0.248 (1.00) |
0.0335 (1.00) |
0.0288 (1.00) |
0.0762 (1.00) |
0.106 (1.00) |
0.518 (1.00) |
0.778 (1.00) |
0.0539 (1.00) |
4q loss | 0 (0%) | 115 |
0.00104 (0.404) |
0.00153 (0.59) |
0.0999 (1.00) |
0.0683 (1.00) |
0.394 (1.00) |
0.802 (1.00) |
0.671 (1.00) |
0.163 (1.00) |
5p loss | 0 (0%) | 122 |
0.00932 (1.00) |
0.246 (1.00) |
0.114 (1.00) |
0.0626 (1.00) |
0.805 (1.00) |
0.831 (1.00) |
0.438 (1.00) |
0.848 (1.00) |
6q loss | 0 (0%) | 115 |
0.00107 (0.415) |
0.066 (1.00) |
0.374 (1.00) |
0.558 (1.00) |
0.151 (1.00) |
0.802 (1.00) |
0.618 (1.00) |
0.163 (1.00) |
8p loss | 0 (0%) | 124 |
0.846 (1.00) |
1 (1.00) |
0.604 (1.00) |
|||||
10p loss | 0 (0%) | 120 |
0.0171 (1.00) |
0.056 (1.00) |
0.269 (1.00) |
0.18 (1.00) |
0.273 (1.00) |
0.51 (1.00) |
0.438 (1.00) |
0.222 (1.00) |
10q loss | 0 (0%) | 119 |
0.00696 (1.00) |
0.0362 (1.00) |
0.269 (1.00) |
0.0871 (1.00) |
0.0171 (1.00) |
0.134 (1.00) |
0.171 (1.00) |
0.0667 (1.00) |
11p loss | 0 (0%) | 118 |
0.167 (1.00) |
0.113 (1.00) |
0.269 (1.00) |
0.145 (1.00) |
0.446 (1.00) |
0.585 (1.00) |
0.899 (1.00) |
0.366 (1.00) |
11q loss | 0 (0%) | 116 |
0.00512 (1.00) |
0.00354 (1.00) |
0.296 (1.00) |
0.0563 (1.00) |
0.355 (1.00) |
0.936 (1.00) |
0.671 (1.00) |
0.911 (1.00) |
13q loss | 0 (0%) | 115 |
0.019 (1.00) |
0.00153 (0.59) |
0.091 (1.00) |
0.403 (1.00) |
0.016 (1.00) |
0.0706 (1.00) |
0.186 (1.00) |
0.00342 (1.00) |
15q loss | 0 (0%) | 116 |
0.00407 (1.00) |
0.119 (1.00) |
0.579 (1.00) |
0.487 (1.00) |
0.727 (1.00) |
0.714 (1.00) |
0.772 (1.00) |
0.667 (1.00) |
16q loss | 0 (0%) | 124 |
0.632 (1.00) |
0.139 (1.00) |
0.871 (1.00) |
0.22 (1.00) |
0.498 (1.00) |
0.283 (1.00) |
||
17p loss | 0 (0%) | 122 |
0.756 (1.00) |
0.0436 (1.00) |
0.0288 (1.00) |
0.0762 (1.00) |
0.301 (1.00) |
0.267 (1.00) |
0.309 (1.00) |
0.116 (1.00) |
18p loss | 0 (0%) | 108 |
0.0863 (1.00) |
0.0306 (1.00) |
0.0772 (1.00) |
0.0114 (1.00) |
0.543 (1.00) |
0.426 (1.00) |
0.373 (1.00) |
0.94 (1.00) |
18q loss | 0 (0%) | 107 |
0.209 (1.00) |
0.0155 (1.00) |
0.0392 (1.00) |
0.00363 (1.00) |
0.755 (1.00) |
0.349 (1.00) |
0.63 (1.00) |
0.836 (1.00) |
19p loss | 0 (0%) | 123 |
0.0513 (1.00) |
1 (1.00) |
1 (1.00) |
0.32 (1.00) |
0.555 (1.00) |
0.38 (1.00) |
||
19q loss | 0 (0%) | 123 |
0.0513 (1.00) |
1 (1.00) |
1 (1.00) |
0.697 (1.00) |
0.555 (1.00) |
1 (1.00) |
||
21q loss | 0 (0%) | 112 |
0.504 (1.00) |
0.231 (1.00) |
0.246 (1.00) |
0.728 (1.00) |
0.472 (1.00) |
0.376 (1.00) |
0.863 (1.00) |
0.173 (1.00) |
Xq loss | 0 (0%) | 124 |
0.632 (1.00) |
0.665 (1.00) |
0.442 (1.00) |
P value = 0.000353 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 53 | 31 |
1Q GAIN CNV | 1 | 0 | 7 |
1Q GAIN WILD-TYPE | 26 | 53 | 24 |
P value = 7.99e-15 (Chi-square test), Q value = 3.5e-12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
3P GAIN CNV | 1 | 3 | 1 | 5 | 19 |
3P GAIN WILD-TYPE | 23 | 41 | 12 | 21 | 1 |
P value = 0.000268 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 25 |
3P GAIN CNV | 12 | 0 | 7 |
3P GAIN WILD-TYPE | 15 | 24 | 18 |
P value = 3.64e-07 (Fisher's exact test), Q value = 0.00016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 37 | 21 |
3P GAIN CNV | 0 | 19 | 0 |
3P GAIN WILD-TYPE | 18 | 18 | 21 |
P value = 4.64e-09 (Fisher's exact test), Q value = 2e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 48 | 33 | 11 | 35 |
3P GAIN CNV | 4 | 2 | 10 | 13 |
3P GAIN WILD-TYPE | 44 | 31 | 1 | 22 |
P value = 1.95e-12 (Chi-square test), Q value = 8.5e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
3Q GAIN CNV | 2 | 4 | 2 | 6 | 19 |
3Q GAIN WILD-TYPE | 22 | 40 | 11 | 20 | 1 |
P value = 3.65e-05 (Fisher's exact test), Q value = 0.015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 25 |
3Q GAIN CNV | 14 | 0 | 8 |
3Q GAIN WILD-TYPE | 13 | 24 | 17 |
P value = 6.94e-06 (Fisher's exact test), Q value = 0.0029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 37 | 21 |
3Q GAIN CNV | 1 | 20 | 1 |
3Q GAIN WILD-TYPE | 17 | 17 | 20 |
P value = 6.07e-08 (Fisher's exact test), Q value = 2.6e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 48 | 33 | 11 | 35 |
3Q GAIN CNV | 4 | 5 | 10 | 14 |
3Q GAIN WILD-TYPE | 44 | 28 | 1 | 21 |
P value = 0.000241 (Fisher's exact test), Q value = 0.097
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 47 | 16 | 48 |
3Q GAIN CNV | 20 | 0 | 7 |
3Q GAIN WILD-TYPE | 27 | 16 | 41 |
P value = 1.96e-08 (Chi-square test), Q value = 8.4e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
5P GAIN CNV | 1 | 0 | 0 | 12 | 1 |
5P GAIN WILD-TYPE | 23 | 44 | 13 | 14 | 19 |
P value = 2.18e-10 (Chi-square test), Q value = 9.5e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
5Q GAIN CNV | 0 | 0 | 0 | 13 | 1 |
5Q GAIN WILD-TYPE | 24 | 44 | 13 | 13 | 19 |
P value = 2.69e-07 (Chi-square test), Q value = 0.00012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
7P GAIN CNV | 5 | 22 | 13 | 9 | 18 |
7P GAIN WILD-TYPE | 19 | 22 | 0 | 17 | 2 |
P value = 2.62e-06 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 53 | 31 |
7P GAIN CNV | 10 | 40 | 7 |
7P GAIN WILD-TYPE | 17 | 13 | 24 |
P value = 5.65e-05 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 25 |
7P GAIN CNV | 22 | 5 | 12 |
7P GAIN WILD-TYPE | 5 | 19 | 13 |
P value = 2.01e-05 (Fisher's exact test), Q value = 0.0083
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 37 | 21 |
7P GAIN CNV | 5 | 29 | 5 |
7P GAIN WILD-TYPE | 13 | 8 | 16 |
P value = 5.79e-08 (Chi-square test), Q value = 2.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
7Q GAIN CNV | 5 | 22 | 13 | 9 | 19 |
7Q GAIN WILD-TYPE | 19 | 22 | 0 | 17 | 1 |
P value = 9.37e-06 (Fisher's exact test), Q value = 0.0039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 53 | 31 |
7Q GAIN CNV | 10 | 40 | 8 |
7Q GAIN WILD-TYPE | 17 | 13 | 23 |
P value = 0.000181 (Fisher's exact test), Q value = 0.073
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 25 |
7Q GAIN CNV | 22 | 6 | 12 |
7Q GAIN WILD-TYPE | 5 | 18 | 13 |
P value = 3.74e-05 (Fisher's exact test), Q value = 0.015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 37 | 21 |
7Q GAIN CNV | 6 | 29 | 5 |
7Q GAIN WILD-TYPE | 12 | 8 | 16 |
P value = 0.00055 (Chi-square test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
12P GAIN CNV | 7 | 6 | 10 | 9 | 8 |
12P GAIN WILD-TYPE | 17 | 38 | 3 | 17 | 12 |
P value = 0.00055 (Chi-square test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
12Q GAIN CNV | 7 | 6 | 10 | 9 | 8 |
12Q GAIN WILD-TYPE | 17 | 38 | 3 | 17 | 12 |
P value = 4.19e-06 (Chi-square test), Q value = 0.0018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
16P GAIN CNV | 6 | 16 | 3 | 16 | 19 |
16P GAIN WILD-TYPE | 18 | 28 | 10 | 10 | 1 |
P value = 0.000182 (Fisher's exact test), Q value = 0.074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 37 | 21 |
16P GAIN CNV | 2 | 24 | 6 |
16P GAIN WILD-TYPE | 16 | 13 | 15 |
P value = 1.89e-05 (Fisher's exact test), Q value = 0.0079
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 48 | 33 | 11 | 35 |
16P GAIN CNV | 13 | 13 | 10 | 24 |
16P GAIN WILD-TYPE | 35 | 20 | 1 | 11 |
P value = 9.17e-06 (Chi-square test), Q value = 0.0038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
16Q GAIN CNV | 6 | 16 | 3 | 14 | 19 |
16Q GAIN WILD-TYPE | 18 | 28 | 10 | 12 | 1 |
P value = 1.46e-05 (Fisher's exact test), Q value = 0.0061
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 37 | 21 |
16Q GAIN CNV | 2 | 24 | 3 |
16Q GAIN WILD-TYPE | 16 | 13 | 18 |
P value = 1.8e-06 (Fisher's exact test), Q value = 0.00076
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 48 | 33 | 11 | 35 |
16Q GAIN CNV | 13 | 10 | 10 | 25 |
16Q GAIN WILD-TYPE | 35 | 23 | 1 | 10 |
P value = 9.52e-08 (Chi-square test), Q value = 4.1e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
17P GAIN CNV | 6 | 19 | 13 | 9 | 19 |
17P GAIN WILD-TYPE | 18 | 25 | 0 | 17 | 1 |
P value = 1.3e-06 (Fisher's exact test), Q value = 0.00056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 53 | 31 |
17P GAIN CNV | 9 | 40 | 7 |
17P GAIN WILD-TYPE | 18 | 13 | 24 |
P value = 3.49e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 25 |
17P GAIN CNV | 20 | 3 | 10 |
17P GAIN WILD-TYPE | 7 | 21 | 15 |
P value = 2.21e-06 (Fisher's exact test), Q value = 0.00094
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 37 | 21 |
17P GAIN CNV | 3 | 27 | 3 |
17P GAIN WILD-TYPE | 15 | 10 | 18 |
P value = 7.75e-05 (Fisher's exact test), Q value = 0.032
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 48 | 33 | 11 | 35 |
17P GAIN CNV | 22 | 9 | 10 | 25 |
17P GAIN WILD-TYPE | 26 | 24 | 1 | 10 |
P value = 5.4e-06 (Chi-square test), Q value = 0.0023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
17Q GAIN CNV | 7 | 25 | 13 | 13 | 19 |
17Q GAIN WILD-TYPE | 17 | 19 | 0 | 13 | 1 |
P value = 0.000247 (Chi-square test), Q value = 0.099
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
4P LOSS CNV | 7 | 0 | 0 | 4 | 0 |
4P LOSS WILD-TYPE | 17 | 44 | 13 | 22 | 20 |
P value = 1.96e-05 (Chi-square test), Q value = 0.0081
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
5Q LOSS CNV | 6 | 0 | 0 | 0 | 0 |
5Q LOSS WILD-TYPE | 18 | 44 | 13 | 26 | 20 |
P value = 0.00043 (Chi-square test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
6P LOSS CNV | 1 | 0 | 0 | 7 | 1 |
6P LOSS WILD-TYPE | 23 | 44 | 13 | 19 | 19 |
P value = 0.000169 (Chi-square test), Q value = 0.069
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
9P LOSS CNV | 8 | 0 | 0 | 6 | 1 |
9P LOSS WILD-TYPE | 16 | 44 | 13 | 20 | 19 |
P value = 0.000318 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 53 | 31 |
9P LOSS CNV | 5 | 0 | 7 |
9P LOSS WILD-TYPE | 22 | 53 | 24 |
P value = 0.000445 (Chi-square test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
9Q LOSS CNV | 8 | 1 | 0 | 7 | 1 |
9Q LOSS WILD-TYPE | 16 | 43 | 13 | 19 | 19 |
P value = 3.17e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 53 | 31 |
9Q LOSS CNV | 6 | 0 | 9 |
9Q LOSS WILD-TYPE | 21 | 53 | 22 |
P value = 1.54e-11 (Chi-square test), Q value = 6.7e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
14Q LOSS CNV | 16 | 0 | 0 | 7 | 0 |
14Q LOSS WILD-TYPE | 8 | 44 | 13 | 19 | 20 |
P value = 0.000233 (Chi-square test), Q value = 0.094
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 44 | 13 | 26 | 20 |
22Q LOSS CNV | 6 | 6 | 0 | 12 | 0 |
22Q LOSS WILD-TYPE | 18 | 38 | 13 | 14 | 20 |
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Molecular subtypes file = KIRP-TP.transferedmergedcluster.txt
-
Number of patients = 127
-
Number of significantly arm-level cnvs = 59
-
Number of molecular subtypes = 8
-
Exclude genes that fewer than K tumors have mutations, K = 3
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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.