This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 80 arm-level events and 10 molecular subtypes across 264 patients, 26 significant findings detected with P value < 0.05 and Q value < 0.25.
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2p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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3q gain cnv correlated to 'CN_CNMF'.
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7p gain cnv correlated to 'CN_CNMF'.
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8p gain cnv correlated to 'CN_CNMF'.
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8q gain cnv correlated to 'CN_CNMF'.
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10p gain cnv correlated to 'CN_CNMF'.
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17q gain cnv correlated to 'CN_CNMF'.
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19q gain cnv correlated to 'CN_CNMF'.
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21q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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3p loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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6p loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
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6q loss cnv correlated to 'CN_CNMF'.
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8p loss cnv correlated to 'CN_CNMF'.
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9p loss cnv correlated to 'CN_CNMF'.
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9q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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11p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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11q loss cnv correlated to 'CN_CNMF'.
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14q loss cnv correlated to 'CN_CNMF'.
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15q loss cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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17p loss cnv correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 26 significant findings detected.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
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 | Fisher's exact test | Fisher's exact test | |
2p gain | 75 (28%) | 189 |
0.00018 (0.14) |
1e-05 (0.008) |
0.326 (1.00) |
0.735 (1.00) |
0.107 (1.00) |
0.063 (1.00) |
0.137 (1.00) |
0.0356 (1.00) |
0.199 (1.00) |
0.0367 (1.00) |
21q gain | 79 (30%) | 185 |
1e-05 (0.008) |
7e-05 (0.0549) |
0.653 (1.00) |
0.403 (1.00) |
0.0473 (1.00) |
0.00478 (1.00) |
0.00214 (1.00) |
0.00701 (1.00) |
0.00665 (1.00) |
0.00247 (1.00) |
3p loss | 31 (12%) | 233 |
0.832 (1.00) |
0.0413 (1.00) |
0.0223 (1.00) |
0.0248 (1.00) |
1e-05 (0.008) |
1e-05 (0.008) |
0.403 (1.00) |
0.13 (1.00) |
0.165 (1.00) |
0.103 (1.00) |
9q loss | 104 (39%) | 160 |
1e-05 (0.008) |
0.0119 (1.00) |
0.0279 (1.00) |
0.0099 (1.00) |
0.0284 (1.00) |
7e-05 (0.0549) |
0.973 (1.00) |
0.137 (1.00) |
0.569 (1.00) |
0.285 (1.00) |
11p loss | 108 (41%) | 156 |
1e-05 (0.008) |
1e-05 (0.008) |
0.18 (1.00) |
0.748 (1.00) |
0.00202 (1.00) |
0.0005 (0.385) |
0.116 (1.00) |
0.0939 (1.00) |
0.00574 (1.00) |
0.0749 (1.00) |
15q loss | 88 (33%) | 176 |
0.00588 (1.00) |
0.00026 (0.201) |
0.107 (1.00) |
0.317 (1.00) |
0.452 (1.00) |
0.0706 (1.00) |
0.152 (1.00) |
4e-05 (0.0315) |
0.0927 (1.00) |
0.311 (1.00) |
3q gain | 118 (45%) | 146 |
5e-05 (0.0393) |
0.363 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.399 (1.00) |
0.197 (1.00) |
0.00918 (1.00) |
0.00057 (0.438) |
0.00128 (0.975) |
0.00044 (0.34) |
7p gain | 111 (42%) | 153 |
0.00024 (0.186) |
0.102 (1.00) |
0.0211 (1.00) |
0.445 (1.00) |
0.923 (1.00) |
0.795 (1.00) |
0.263 (1.00) |
0.333 (1.00) |
0.555 (1.00) |
0.279 (1.00) |
8p gain | 55 (21%) | 209 |
9e-05 (0.0704) |
0.0584 (1.00) |
0.0833 (1.00) |
0.0184 (1.00) |
0.523 (1.00) |
0.996 (1.00) |
0.26 (1.00) |
0.0178 (1.00) |
0.14 (1.00) |
0.161 (1.00) |
8q gain | 122 (46%) | 142 |
0.00017 (0.133) |
0.015 (1.00) |
0.0397 (1.00) |
0.186 (1.00) |
0.355 (1.00) |
0.84 (1.00) |
0.353 (1.00) |
0.0117 (1.00) |
0.109 (1.00) |
0.145 (1.00) |
10p gain | 75 (28%) | 189 |
6e-05 (0.0471) |
0.00414 (1.00) |
0.837 (1.00) |
0.431 (1.00) |
0.67 (1.00) |
0.083 (1.00) |
0.638 (1.00) |
0.786 (1.00) |
0.775 (1.00) |
0.982 (1.00) |
17q gain | 90 (34%) | 174 |
0.0002 (0.156) |
0.249 (1.00) |
0.497 (1.00) |
0.388 (1.00) |
0.149 (1.00) |
0.22 (1.00) |
0.111 (1.00) |
0.0028 (1.00) |
0.00346 (1.00) |
0.00458 (1.00) |
19q gain | 90 (34%) | 174 |
0.0001 (0.0781) |
0.0023 (1.00) |
0.32 (1.00) |
0.549 (1.00) |
0.267 (1.00) |
0.254 (1.00) |
0.806 (1.00) |
0.0272 (1.00) |
0.669 (1.00) |
0.0647 (1.00) |
6p loss | 64 (24%) | 200 |
0.00229 (1.00) |
0.0189 (1.00) |
0.755 (1.00) |
0.825 (1.00) |
0.0606 (1.00) |
0.0112 (1.00) |
0.655 (1.00) |
0.00024 (0.186) |
0.616 (1.00) |
0.0172 (1.00) |
6q loss | 97 (37%) | 167 |
1e-05 (0.008) |
0.00465 (1.00) |
0.833 (1.00) |
0.491 (1.00) |
0.229 (1.00) |
0.013 (1.00) |
0.8 (1.00) |
0.0125 (1.00) |
0.942 (1.00) |
0.218 (1.00) |
8p loss | 121 (46%) | 143 |
5e-05 (0.0393) |
0.00073 (0.56) |
0.216 (1.00) |
0.17 (1.00) |
0.0513 (1.00) |
0.61 (1.00) |
0.018 (1.00) |
0.0306 (1.00) |
0.0449 (1.00) |
0.0421 (1.00) |
9p loss | 114 (43%) | 150 |
1e-05 (0.008) |
0.175 (1.00) |
0.193 (1.00) |
0.0608 (1.00) |
0.419 (1.00) |
0.00276 (1.00) |
0.671 (1.00) |
0.348 (1.00) |
0.958 (1.00) |
1 (1.00) |
11q loss | 81 (31%) | 183 |
1e-05 (0.008) |
0.00132 (1.00) |
0.0573 (1.00) |
0.199 (1.00) |
0.0259 (1.00) |
0.0679 (1.00) |
0.516 (1.00) |
0.61 (1.00) |
0.0817 (1.00) |
0.317 (1.00) |
14q loss | 75 (28%) | 189 |
1e-05 (0.008) |
0.00039 (0.301) |
0.07 (1.00) |
0.0375 (1.00) |
0.0551 (1.00) |
0.00037 (0.286) |
0.0118 (1.00) |
0.0141 (1.00) |
0.0291 (1.00) |
0.396 (1.00) |
17p loss | 116 (44%) | 148 |
1e-05 (0.008) |
0.412 (1.00) |
0.957 (1.00) |
0.729 (1.00) |
0.408 (1.00) |
0.097 (1.00) |
0.264 (1.00) |
0.0963 (1.00) |
0.164 (1.00) |
0.453 (1.00) |
1p gain | 57 (22%) | 207 |
0.0306 (1.00) |
0.0143 (1.00) |
0.691 (1.00) |
0.613 (1.00) |
0.795 (1.00) |
0.996 (1.00) |
0.696 (1.00) |
0.857 (1.00) |
0.96 (1.00) |
0.843 (1.00) |
1q gain | 83 (31%) | 181 |
0.00085 (0.649) |
0.251 (1.00) |
0.6 (1.00) |
0.885 (1.00) |
0.775 (1.00) |
0.951 (1.00) |
0.763 (1.00) |
0.977 (1.00) |
0.702 (1.00) |
0.818 (1.00) |
2q gain | 37 (14%) | 227 |
0.0965 (1.00) |
0.167 (1.00) |
0.308 (1.00) |
0.352 (1.00) |
0.428 (1.00) |
0.554 (1.00) |
0.502 (1.00) |
0.416 (1.00) |
0.728 (1.00) |
0.312 (1.00) |
3p gain | 92 (35%) | 172 |
0.00214 (1.00) |
0.229 (1.00) |
0.0981 (1.00) |
0.405 (1.00) |
0.00753 (1.00) |
0.0184 (1.00) |
0.0031 (1.00) |
0.00943 (1.00) |
0.00168 (1.00) |
0.00105 (0.801) |
4p gain | 33 (12%) | 231 |
0.00073 (0.56) |
0.0133 (1.00) |
0.608 (1.00) |
0.414 (1.00) |
0.034 (1.00) |
0.00577 (1.00) |
0.135 (1.00) |
0.00183 (1.00) |
0.0548 (1.00) |
0.00471 (1.00) |
4q gain | 19 (7%) | 245 |
0.00507 (1.00) |
0.0265 (1.00) |
0.544 (1.00) |
0.203 (1.00) |
0.0376 (1.00) |
0.09 (1.00) |
0.268 (1.00) |
0.132 (1.00) |
0.325 (1.00) |
0.409 (1.00) |
5p gain | 103 (39%) | 161 |
0.00283 (1.00) |
0.177 (1.00) |
0.0429 (1.00) |
0.24 (1.00) |
0.326 (1.00) |
0.123 (1.00) |
0.0702 (1.00) |
0.036 (1.00) |
0.346 (1.00) |
0.106 (1.00) |
5q gain | 37 (14%) | 227 |
0.368 (1.00) |
0.0401 (1.00) |
0.024 (1.00) |
0.283 (1.00) |
0.786 (1.00) |
0.738 (1.00) |
0.261 (1.00) |
0.144 (1.00) |
0.12 (1.00) |
0.503 (1.00) |
6p gain | 43 (16%) | 221 |
0.465 (1.00) |
0.743 (1.00) |
0.847 (1.00) |
0.133 (1.00) |
0.436 (1.00) |
0.305 (1.00) |
0.545 (1.00) |
0.75 (1.00) |
0.56 (1.00) |
0.833 (1.00) |
6q gain | 24 (9%) | 240 |
0.369 (1.00) |
0.816 (1.00) |
0.975 (1.00) |
0.0416 (1.00) |
0.306 (1.00) |
0.0545 (1.00) |
0.287 (1.00) |
0.409 (1.00) |
0.208 (1.00) |
0.741 (1.00) |
7q gain | 101 (38%) | 163 |
0.00237 (1.00) |
0.331 (1.00) |
0.194 (1.00) |
0.921 (1.00) |
0.825 (1.00) |
0.31 (1.00) |
0.331 (1.00) |
0.461 (1.00) |
0.396 (1.00) |
0.118 (1.00) |
9p gain | 40 (15%) | 224 |
0.00044 (0.34) |
0.66 (1.00) |
0.86 (1.00) |
0.381 (1.00) |
0.188 (1.00) |
0.1 (1.00) |
0.337 (1.00) |
0.129 (1.00) |
0.745 (1.00) |
0.297 (1.00) |
9q gain | 36 (14%) | 228 |
0.0165 (1.00) |
0.172 (1.00) |
0.881 (1.00) |
0.0293 (1.00) |
0.0065 (1.00) |
0.00076 (0.581) |
0.974 (1.00) |
0.371 (1.00) |
0.865 (1.00) |
0.0496 (1.00) |
10q gain | 23 (9%) | 241 |
0.044 (1.00) |
0.0924 (1.00) |
0.56 (1.00) |
0.549 (1.00) |
0.526 (1.00) |
0.0117 (1.00) |
0.787 (1.00) |
0.69 (1.00) |
0.773 (1.00) |
0.464 (1.00) |
11p gain | 25 (9%) | 239 |
0.428 (1.00) |
0.0829 (1.00) |
0.114 (1.00) |
0.122 (1.00) |
0.084 (1.00) |
0.0594 (1.00) |
0.489 (1.00) |
0.0138 (1.00) |
0.575 (1.00) |
0.0815 (1.00) |
11q gain | 37 (14%) | 227 |
0.577 (1.00) |
0.429 (1.00) |
0.2 (1.00) |
0.0472 (1.00) |
0.178 (1.00) |
0.0214 (1.00) |
0.633 (1.00) |
0.104 (1.00) |
0.753 (1.00) |
0.158 (1.00) |
12p gain | 75 (28%) | 189 |
0.0697 (1.00) |
0.198 (1.00) |
0.758 (1.00) |
0.531 (1.00) |
0.739 (1.00) |
0.953 (1.00) |
0.854 (1.00) |
0.138 (1.00) |
0.725 (1.00) |
0.396 (1.00) |
12q gain | 56 (21%) | 208 |
0.00407 (1.00) |
0.00883 (1.00) |
0.0681 (1.00) |
0.0129 (1.00) |
0.114 (1.00) |
0.065 (1.00) |
0.517 (1.00) |
0.384 (1.00) |
0.366 (1.00) |
0.153 (1.00) |
13q gain | 70 (27%) | 194 |
0.24 (1.00) |
0.895 (1.00) |
0.976 (1.00) |
0.839 (1.00) |
0.24 (1.00) |
0.424 (1.00) |
0.755 (1.00) |
0.396 (1.00) |
0.808 (1.00) |
0.833 (1.00) |
14q gain | 44 (17%) | 220 |
0.153 (1.00) |
0.337 (1.00) |
0.378 (1.00) |
0.15 (1.00) |
0.0385 (1.00) |
0.234 (1.00) |
1 (1.00) |
0.0422 (1.00) |
0.531 (1.00) |
0.923 (1.00) |
15q gain | 24 (9%) | 240 |
0.00726 (1.00) |
0.0765 (1.00) |
0.715 (1.00) |
0.804 (1.00) |
0.655 (1.00) |
0.23 (1.00) |
0.308 (1.00) |
0.754 (1.00) |
1 (1.00) |
0.844 (1.00) |
16p gain | 42 (16%) | 222 |
0.166 (1.00) |
0.804 (1.00) |
0.374 (1.00) |
0.341 (1.00) |
0.635 (1.00) |
0.467 (1.00) |
0.222 (1.00) |
0.418 (1.00) |
0.474 (1.00) |
0.85 (1.00) |
16q gain | 52 (20%) | 212 |
0.271 (1.00) |
0.627 (1.00) |
0.135 (1.00) |
0.14 (1.00) |
0.381 (1.00) |
0.135 (1.00) |
0.102 (1.00) |
0.0875 (1.00) |
0.19 (1.00) |
0.544 (1.00) |
17p gain | 35 (13%) | 229 |
0.0869 (1.00) |
0.398 (1.00) |
0.55 (1.00) |
0.875 (1.00) |
0.735 (1.00) |
0.0414 (1.00) |
0.00269 (1.00) |
0.0138 (1.00) |
0.00134 (1.00) |
0.00341 (1.00) |
18p gain | 79 (30%) | 185 |
0.0261 (1.00) |
0.00303 (1.00) |
0.951 (1.00) |
0.912 (1.00) |
0.19 (1.00) |
0.039 (1.00) |
0.667 (1.00) |
0.102 (1.00) |
0.746 (1.00) |
0.983 (1.00) |
18q gain | 41 (16%) | 223 |
0.409 (1.00) |
0.0723 (1.00) |
0.321 (1.00) |
0.302 (1.00) |
0.677 (1.00) |
0.418 (1.00) |
0.525 (1.00) |
0.218 (1.00) |
0.534 (1.00) |
0.414 (1.00) |
19p gain | 55 (21%) | 209 |
0.00958 (1.00) |
0.0421 (1.00) |
0.267 (1.00) |
0.421 (1.00) |
0.0177 (1.00) |
0.0991 (1.00) |
0.746 (1.00) |
0.0337 (1.00) |
0.502 (1.00) |
0.061 (1.00) |
20p gain | 131 (50%) | 133 |
0.331 (1.00) |
0.437 (1.00) |
0.539 (1.00) |
0.0498 (1.00) |
0.694 (1.00) |
0.0269 (1.00) |
0.168 (1.00) |
0.0462 (1.00) |
0.0391 (1.00) |
0.177 (1.00) |
20q gain | 147 (56%) | 117 |
0.00892 (1.00) |
0.213 (1.00) |
0.4 (1.00) |
0.117 (1.00) |
0.962 (1.00) |
0.615 (1.00) |
0.144 (1.00) |
0.0129 (1.00) |
0.169 (1.00) |
0.134 (1.00) |
22q gain | 36 (14%) | 228 |
0.00298 (1.00) |
0.0066 (1.00) |
0.418 (1.00) |
0.337 (1.00) |
0.0183 (1.00) |
0.208 (1.00) |
0.195 (1.00) |
0.202 (1.00) |
0.405 (1.00) |
0.438 (1.00) |
xq gain | 33 (12%) | 231 |
0.0132 (1.00) |
0.366 (1.00) |
0.707 (1.00) |
0.574 (1.00) |
0.916 (1.00) |
0.922 (1.00) |
0.523 (1.00) |
0.669 (1.00) |
0.427 (1.00) |
0.338 (1.00) |
1p loss | 23 (9%) | 241 |
0.34 (1.00) |
0.305 (1.00) |
0.108 (1.00) |
0.081 (1.00) |
0.526 (1.00) |
0.111 (1.00) |
0.641 (1.00) |
0.196 (1.00) |
0.88 (1.00) |
0.959 (1.00) |
1q loss | 25 (9%) | 239 |
0.721 (1.00) |
0.598 (1.00) |
0.404 (1.00) |
0.956 (1.00) |
0.435 (1.00) |
0.132 (1.00) |
0.527 (1.00) |
0.00247 (1.00) |
1 (1.00) |
0.78 (1.00) |
2p loss | 27 (10%) | 237 |
0.424 (1.00) |
0.105 (1.00) |
0.961 (1.00) |
0.752 (1.00) |
0.732 (1.00) |
0.259 (1.00) |
0.179 (1.00) |
0.94 (1.00) |
0.665 (1.00) |
0.296 (1.00) |
2q loss | 58 (22%) | 206 |
0.0954 (1.00) |
0.354 (1.00) |
0.748 (1.00) |
0.542 (1.00) |
0.292 (1.00) |
0.148 (1.00) |
0.699 (1.00) |
0.0497 (1.00) |
0.332 (1.00) |
0.0971 (1.00) |
3q loss | 13 (5%) | 251 |
0.935 (1.00) |
0.173 (1.00) |
0.0189 (1.00) |
0.0522 (1.00) |
0.1 (1.00) |
0.0106 (1.00) |
1 (1.00) |
0.621 (1.00) |
1 (1.00) |
0.746 (1.00) |
4p loss | 86 (33%) | 178 |
0.763 (1.00) |
0.809 (1.00) |
0.743 (1.00) |
0.78 (1.00) |
0.161 (1.00) |
0.027 (1.00) |
0.054 (1.00) |
0.481 (1.00) |
0.146 (1.00) |
0.0712 (1.00) |
4q loss | 91 (34%) | 173 |
0.545 (1.00) |
0.38 (1.00) |
0.304 (1.00) |
0.348 (1.00) |
0.238 (1.00) |
0.127 (1.00) |
0.17 (1.00) |
0.476 (1.00) |
0.158 (1.00) |
0.0763 (1.00) |
5p loss | 40 (15%) | 224 |
0.0174 (1.00) |
0.019 (1.00) |
0.316 (1.00) |
0.665 (1.00) |
0.634 (1.00) |
0.0479 (1.00) |
0.576 (1.00) |
0.905 (1.00) |
0.404 (1.00) |
1 (1.00) |
5q loss | 104 (39%) | 160 |
0.00229 (1.00) |
0.00555 (1.00) |
0.86 (1.00) |
0.346 (1.00) |
0.517 (1.00) |
0.0787 (1.00) |
0.75 (1.00) |
0.148 (1.00) |
0.738 (1.00) |
0.173 (1.00) |
7p loss | 11 (4%) | 253 |
0.257 (1.00) |
0.973 (1.00) |
0.322 (1.00) |
0.861 (1.00) |
0.74 (1.00) |
0.719 (1.00) |
0.25 (1.00) |
0.112 (1.00) |
0.0832 (1.00) |
0.192 (1.00) |
7q loss | 16 (6%) | 248 |
0.0862 (1.00) |
0.763 (1.00) |
0.231 (1.00) |
0.677 (1.00) |
0.61 (1.00) |
1 (1.00) |
0.252 (1.00) |
0.0825 (1.00) |
0.698 (1.00) |
0.942 (1.00) |
8q loss | 29 (11%) | 235 |
0.237 (1.00) |
0.0963 (1.00) |
0.498 (1.00) |
0.0107 (1.00) |
0.00307 (1.00) |
0.169 (1.00) |
0.0347 (1.00) |
0.0436 (1.00) |
0.00299 (1.00) |
0.137 (1.00) |
10p loss | 47 (18%) | 217 |
0.503 (1.00) |
0.013 (1.00) |
0.911 (1.00) |
0.264 (1.00) |
0.0242 (1.00) |
0.0627 (1.00) |
0.315 (1.00) |
0.293 (1.00) |
0.568 (1.00) |
0.305 (1.00) |
10q loss | 87 (33%) | 177 |
0.00066 (0.507) |
0.00914 (1.00) |
0.563 (1.00) |
0.73 (1.00) |
0.0425 (1.00) |
0.293 (1.00) |
0.299 (1.00) |
0.133 (1.00) |
0.262 (1.00) |
0.42 (1.00) |
12p loss | 28 (11%) | 236 |
0.227 (1.00) |
0.462 (1.00) |
0.943 (1.00) |
0.472 (1.00) |
0.399 (1.00) |
0.646 (1.00) |
0.374 (1.00) |
0.903 (1.00) |
0.699 (1.00) |
0.892 (1.00) |
12q loss | 34 (13%) | 230 |
0.587 (1.00) |
0.728 (1.00) |
0.369 (1.00) |
0.409 (1.00) |
0.973 (1.00) |
0.891 (1.00) |
0.486 (1.00) |
0.741 (1.00) |
0.914 (1.00) |
0.938 (1.00) |
13q loss | 53 (20%) | 211 |
0.00351 (1.00) |
0.872 (1.00) |
0.0106 (1.00) |
0.103 (1.00) |
0.0943 (1.00) |
0.609 (1.00) |
1 (1.00) |
0.0108 (1.00) |
0.861 (1.00) |
0.251 (1.00) |
16p loss | 68 (26%) | 196 |
0.0694 (1.00) |
0.0441 (1.00) |
0.657 (1.00) |
0.477 (1.00) |
0.634 (1.00) |
0.778 (1.00) |
0.774 (1.00) |
0.0507 (1.00) |
0.71 (1.00) |
0.499 (1.00) |
16q loss | 62 (23%) | 202 |
0.0277 (1.00) |
0.0365 (1.00) |
0.226 (1.00) |
0.792 (1.00) |
0.563 (1.00) |
0.799 (1.00) |
0.342 (1.00) |
0.0543 (1.00) |
0.575 (1.00) |
0.0795 (1.00) |
17q loss | 27 (10%) | 237 |
0.258 (1.00) |
0.27 (1.00) |
0.97 (1.00) |
0.942 (1.00) |
0.869 (1.00) |
0.864 (1.00) |
0.811 (1.00) |
0.571 (1.00) |
0.893 (1.00) |
0.826 (1.00) |
18p loss | 60 (23%) | 204 |
0.0184 (1.00) |
0.265 (1.00) |
0.464 (1.00) |
0.372 (1.00) |
0.652 (1.00) |
0.0409 (1.00) |
0.595 (1.00) |
0.24 (1.00) |
0.59 (1.00) |
0.708 (1.00) |
18q loss | 91 (34%) | 173 |
0.0477 (1.00) |
0.995 (1.00) |
0.683 (1.00) |
0.743 (1.00) |
0.891 (1.00) |
0.338 (1.00) |
0.0358 (1.00) |
0.0093 (1.00) |
0.116 (1.00) |
0.12 (1.00) |
19p loss | 67 (25%) | 197 |
0.0116 (1.00) |
0.196 (1.00) |
0.596 (1.00) |
0.398 (1.00) |
0.0142 (1.00) |
0.178 (1.00) |
0.828 (1.00) |
0.0341 (1.00) |
0.643 (1.00) |
0.29 (1.00) |
19q loss | 41 (16%) | 223 |
0.221 (1.00) |
0.618 (1.00) |
0.205 (1.00) |
0.0968 (1.00) |
0.335 (1.00) |
0.675 (1.00) |
0.422 (1.00) |
0.526 (1.00) |
0.357 (1.00) |
0.238 (1.00) |
20p loss | 23 (9%) | 241 |
0.101 (1.00) |
0.0325 (1.00) |
0.165 (1.00) |
0.0328 (1.00) |
0.757 (1.00) |
0.461 (1.00) |
0.394 (1.00) |
0.844 (1.00) |
0.167 (1.00) |
0.797 (1.00) |
20q loss | 9 (3%) | 255 |
0.0278 (1.00) |
0.444 (1.00) |
0.479 (1.00) |
0.346 (1.00) |
1 (1.00) |
0.873 (1.00) |
0.631 (1.00) |
0.817 (1.00) |
1 (1.00) |
0.527 (1.00) |
21q loss | 44 (17%) | 220 |
0.204 (1.00) |
0.0197 (1.00) |
0.106 (1.00) |
0.296 (1.00) |
0.0196 (1.00) |
0.0246 (1.00) |
0.77 (1.00) |
0.398 (1.00) |
0.194 (1.00) |
0.485 (1.00) |
22q loss | 102 (39%) | 162 |
0.0146 (1.00) |
0.0171 (1.00) |
0.581 (1.00) |
0.0116 (1.00) |
0.0294 (1.00) |
0.177 (1.00) |
0.222 (1.00) |
0.0303 (1.00) |
0.0976 (1.00) |
0.0881 (1.00) |
xq loss | 50 (19%) | 214 |
0.0314 (1.00) |
0.00403 (1.00) |
0.995 (1.00) |
0.714 (1.00) |
0.125 (1.00) |
0.763 (1.00) |
0.0285 (1.00) |
0.855 (1.00) |
0.0896 (1.00) |
0.398 (1.00) |
P value = 0.00018 (Fisher's exact test), Q value = 0.14
Table S1. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
2P GAIN MUTATED | 29 | 14 | 32 |
2P GAIN WILD-TYPE | 38 | 82 | 69 |
Figure S1. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D3V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.008
Table S2. Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 89 | 60 | 54 | 47 |
2P GAIN MUTATED | 20 | 33 | 12 | 7 |
2P GAIN WILD-TYPE | 69 | 27 | 42 | 40 |
Figure S2. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D3V2.png)
P value = 5e-05 (Fisher's exact test), Q value = 0.039
Table S3. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
3Q GAIN MUTATED | 44 | 29 | 45 |
3Q GAIN WILD-TYPE | 23 | 67 | 56 |
Figure S3. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D6V1.png)
P value = 0.00024 (Fisher's exact test), Q value = 0.19
Table S4. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
7P GAIN MUTATED | 36 | 25 | 50 |
7P GAIN WILD-TYPE | 31 | 71 | 51 |
Figure S4. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D13V1.png)
P value = 9e-05 (Fisher's exact test), Q value = 0.07
Table S5. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
8P GAIN MUTATED | 14 | 8 | 33 |
8P GAIN WILD-TYPE | 53 | 88 | 68 |
Figure S5. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D15V1.png)
P value = 0.00017 (Fisher's exact test), Q value = 0.13
Table S6. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
8Q GAIN MUTATED | 37 | 28 | 57 |
8Q GAIN WILD-TYPE | 30 | 68 | 44 |
Figure S6. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D16V1.png)
P value = 6e-05 (Fisher's exact test), Q value = 0.047
Table S7. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
10P GAIN MUTATED | 33 | 17 | 25 |
10P GAIN WILD-TYPE | 34 | 79 | 76 |
Figure S7. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D19V1.png)
P value = 2e-04 (Fisher's exact test), Q value = 0.16
Table S8. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
17Q GAIN MUTATED | 30 | 18 | 42 |
17Q GAIN WILD-TYPE | 37 | 78 | 59 |
Figure S8. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D31V1.png)
P value = 1e-04 (Fisher's exact test), Q value = 0.078
Table S9. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
19Q GAIN MUTATED | 31 | 17 | 42 |
19Q GAIN WILD-TYPE | 36 | 79 | 59 |
Figure S9. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D35V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.008
Table S10. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
21Q GAIN MUTATED | 41 | 17 | 21 |
21Q GAIN WILD-TYPE | 26 | 79 | 80 |
Figure S10. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'
![](D38V1.png)
P value = 7e-05 (Fisher's exact test), Q value = 0.055
Table S11. Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 89 | 60 | 54 | 47 |
21Q GAIN MUTATED | 19 | 33 | 14 | 9 |
21Q GAIN WILD-TYPE | 70 | 27 | 40 | 38 |
Figure S11. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D38V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.008
Table S12. Gene #45: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 72 | 73 |
3P LOSS MUTATED | 7 | 3 | 21 |
3P LOSS WILD-TYPE | 111 | 69 | 52 |
Figure S12. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D45V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.008
Table S13. Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 44 | 64 | 59 |
3P LOSS MUTATED | 6 | 5 | 1 | 19 |
3P LOSS WILD-TYPE | 90 | 39 | 63 | 40 |
Figure S13. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D45V6.png)
P value = 0.00024 (Fisher's exact test), Q value = 0.19
Table S14. Gene #51: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 44 | 24 | 31 | 34 | 47 | 36 | 47 |
6P LOSS MUTATED | 16 | 4 | 12 | 12 | 13 | 5 | 2 |
6P LOSS WILD-TYPE | 28 | 20 | 19 | 22 | 34 | 31 | 45 |
Figure S14. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
![](D51V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.008
Table S15. Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
6Q LOSS MUTATED | 35 | 19 | 43 |
6Q LOSS WILD-TYPE | 32 | 77 | 58 |
Figure S15. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D52V1.png)
P value = 5e-05 (Fisher's exact test), Q value = 0.039
Table S16. Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
8P LOSS MUTATED | 45 | 45 | 31 |
8P LOSS WILD-TYPE | 22 | 51 | 70 |
Figure S16. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D55V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.008
Table S17. Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
9P LOSS MUTATED | 23 | 20 | 71 |
9P LOSS WILD-TYPE | 44 | 76 | 30 |
Figure S17. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D57V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.008
Table S18. Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
9Q LOSS MUTATED | 22 | 20 | 62 |
9Q LOSS WILD-TYPE | 45 | 76 | 39 |
Figure S18. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D58V1.png)
P value = 7e-05 (Fisher's exact test), Q value = 0.055
Table S19. Gene #58: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 96 | 44 | 64 | 59 |
9Q LOSS MUTATED | 43 | 10 | 37 | 14 |
9Q LOSS WILD-TYPE | 53 | 34 | 27 | 45 |
Figure S19. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D58V6.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.008
Table S20. Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
11P LOSS MUTATED | 38 | 11 | 59 |
11P LOSS WILD-TYPE | 29 | 85 | 42 |
Figure S20. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D61V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.008
Table S21. Gene #61: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 89 | 60 | 54 | 47 |
11P LOSS MUTATED | 18 | 34 | 28 | 24 |
11P LOSS WILD-TYPE | 71 | 26 | 26 | 23 |
Figure S21. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D61V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.008
Table S22. Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
11Q LOSS MUTATED | 32 | 8 | 41 |
11Q LOSS WILD-TYPE | 35 | 88 | 60 |
Figure S22. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D62V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.008
Table S23. Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
14Q LOSS MUTATED | 34 | 11 | 30 |
14Q LOSS WILD-TYPE | 33 | 85 | 71 |
Figure S23. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D66V1.png)
P value = 0.00026 (Fisher's exact test), Q value = 0.2
Table S24. Gene #67: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 89 | 60 | 54 | 47 |
15Q LOSS MUTATED | 38 | 27 | 15 | 5 |
15Q LOSS WILD-TYPE | 51 | 33 | 39 | 42 |
Figure S24. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D67V2.png)
P value = 4e-05 (Fisher's exact test), Q value = 0.032
Table S25. Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 44 | 24 | 31 | 34 | 47 | 36 | 47 |
15Q LOSS MUTATED | 18 | 13 | 16 | 15 | 11 | 11 | 4 |
15Q LOSS WILD-TYPE | 26 | 11 | 15 | 19 | 36 | 25 | 43 |
Figure S25. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
![](D67V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.008
Table S26. Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 96 | 101 |
17P LOSS MUTATED | 34 | 22 | 60 |
17P LOSS WILD-TYPE | 33 | 74 | 41 |
Figure S26. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'
![](D70V1.png)
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtypes file = BLCA-TP.transferedmergedcluster.txt
-
Number of patients = 264
-
Number of significantly arm-level cnvs = 80
-
Number of molecular subtypes = 10
-
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.