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 90 patients, 49 significant findings detected with P value < 0.05 and Q value < 0.25.
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2p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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4p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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4q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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5p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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5q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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7p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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7q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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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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9p gain cnv correlated to 'CN_CNMF'.
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10p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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10q gain cnv correlated to 'MRNASEQ_CNMF'.
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12p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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12q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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14q gain cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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16q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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19q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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20p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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20q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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xq gain cnv correlated to 'CN_CNMF'.
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9p loss cnv correlated to 'MRNASEQ_CNMF'.
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17p loss cnv correlated to 'METHLYATION_CNMF'.
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 | |
14q gain | 21 (23%) | 69 |
0.0142 (1.00) |
0.0561 (1.00) |
0.104 (1.00) |
0.427 (1.00) |
0.00031 (0.214) |
0.00105 (0.706) |
1e-05 (0.00736) |
0.00017 (0.118) |
3e-05 (0.0214) |
2e-05 (0.0144) |
4p gain | 37 (41%) | 53 |
1e-05 (0.00736) |
0.0444 (1.00) |
1 (1.00) |
0.464 (1.00) |
2e-05 (0.0144) |
4e-05 (0.0284) |
0.297 (1.00) |
0.00236 (1.00) |
0.343 (1.00) |
0.861 (1.00) |
4q gain | 33 (37%) | 57 |
2e-05 (0.0144) |
0.0367 (1.00) |
0.927 (1.00) |
0.729 (1.00) |
3e-05 (0.0214) |
2e-05 (0.0144) |
0.557 (1.00) |
0.0008 (0.542) |
0.361 (1.00) |
0.95 (1.00) |
7q gain | 48 (53%) | 42 |
1e-05 (0.00736) |
0.117 (1.00) |
0.139 (1.00) |
0.247 (1.00) |
1e-05 (0.00736) |
8e-05 (0.0563) |
0.915 (1.00) |
0.328 (1.00) |
0.277 (1.00) |
0.194 (1.00) |
12p gain | 64 (71%) | 26 |
1e-05 (0.00736) |
0.209 (1.00) |
0.204 (1.00) |
0.0668 (1.00) |
0.00011 (0.077) |
7e-05 (0.0494) |
0.243 (1.00) |
0.209 (1.00) |
0.13 (1.00) |
0.25 (1.00) |
16p gain | 49 (54%) | 41 |
1e-05 (0.00736) |
0.0107 (1.00) |
0.894 (1.00) |
0.0401 (1.00) |
1e-05 (0.00736) |
1e-05 (0.00736) |
0.0464 (1.00) |
0.0261 (1.00) |
0.0284 (1.00) |
0.276 (1.00) |
16q gain | 47 (52%) | 43 |
1e-05 (0.00736) |
0.00778 (1.00) |
0.954 (1.00) |
0.327 (1.00) |
8e-05 (0.0563) |
1e-05 (0.00736) |
0.0246 (1.00) |
0.0129 (1.00) |
0.0139 (1.00) |
0.462 (1.00) |
20p gain | 46 (51%) | 44 |
1e-05 (0.00736) |
0.234 (1.00) |
0.0228 (1.00) |
0.00851 (1.00) |
0.00016 (0.111) |
0.00011 (0.077) |
0.00475 (1.00) |
0.0893 (1.00) |
0.0095 (1.00) |
0.00428 (1.00) |
20q gain | 49 (54%) | 41 |
1e-05 (0.00736) |
0.0668 (1.00) |
0.00981 (1.00) |
0.078 (1.00) |
6e-05 (0.0425) |
0.00029 (0.2) |
0.0197 (1.00) |
0.277 (1.00) |
0.0114 (1.00) |
0.0146 (1.00) |
5p gain | 57 (63%) | 33 |
1e-05 (0.00736) |
0.0376 (1.00) |
0.0459 (1.00) |
0.0346 (1.00) |
0.00051 (0.349) |
2e-05 (0.0144) |
0.252 (1.00) |
0.228 (1.00) |
0.0724 (1.00) |
0.357 (1.00) |
5q gain | 53 (59%) | 37 |
1e-05 (0.00736) |
0.00851 (1.00) |
0.419 (1.00) |
0.148 (1.00) |
0.00063 (0.428) |
1e-05 (0.00736) |
0.336 (1.00) |
0.134 (1.00) |
0.209 (1.00) |
0.169 (1.00) |
7p gain | 48 (53%) | 42 |
5e-05 (0.0355) |
0.119 (1.00) |
0.139 (1.00) |
0.0929 (1.00) |
0.00011 (0.077) |
0.00165 (1.00) |
0.915 (1.00) |
0.551 (1.00) |
0.278 (1.00) |
0.288 (1.00) |
10p gain | 25 (28%) | 65 |
0.0019 (1.00) |
0.0597 (1.00) |
0.0193 (1.00) |
0.0137 (1.00) |
7e-05 (0.0494) |
0.00014 (0.0976) |
0.0343 (1.00) |
0.505 (1.00) |
0.0573 (1.00) |
0.454 (1.00) |
12q gain | 64 (71%) | 26 |
1e-05 (0.00736) |
0.308 (1.00) |
0.151 (1.00) |
0.028 (1.00) |
0.00049 (0.336) |
0.00021 (0.146) |
0.236 (1.00) |
0.455 (1.00) |
0.22 (1.00) |
0.591 (1.00) |
19q gain | 52 (58%) | 38 |
5e-05 (0.0355) |
0.0518 (1.00) |
0.295 (1.00) |
0.0558 (1.00) |
0.00031 (0.214) |
0.00097 (0.656) |
0.143 (1.00) |
0.111 (1.00) |
0.517 (1.00) |
0.119 (1.00) |
2p gain | 13 (14%) | 77 |
0.00738 (1.00) |
0.00142 (0.949) |
0.596 (1.00) |
0.34 (1.00) |
0.0121 (1.00) |
0.00025 (0.173) |
0.375 (1.00) |
0.0191 (1.00) |
0.125 (1.00) |
0.0741 (1.00) |
8p gain | 32 (36%) | 58 |
9e-05 (0.0632) |
0.14 (1.00) |
0.517 (1.00) |
0.441 (1.00) |
0.17 (1.00) |
0.147 (1.00) |
0.112 (1.00) |
0.172 (1.00) |
0.242 (1.00) |
0.517 (1.00) |
8q gain | 38 (42%) | 52 |
0.00022 (0.152) |
0.291 (1.00) |
0.723 (1.00) |
0.468 (1.00) |
0.418 (1.00) |
0.229 (1.00) |
0.499 (1.00) |
0.258 (1.00) |
0.52 (1.00) |
0.642 (1.00) |
9p gain | 20 (22%) | 70 |
6e-05 (0.0425) |
0.00218 (1.00) |
0.0878 (1.00) |
0.136 (1.00) |
0.00908 (1.00) |
0.0118 (1.00) |
0.382 (1.00) |
0.549 (1.00) |
0.461 (1.00) |
0.252 (1.00) |
10q gain | 26 (29%) | 64 |
0.00147 (0.979) |
0.0712 (1.00) |
0.0172 (1.00) |
0.0145 (1.00) |
1e-05 (0.00736) |
0.00056 (0.381) |
0.02 (1.00) |
0.343 (1.00) |
0.031 (1.00) |
0.844 (1.00) |
xq gain | 40 (44%) | 50 |
2e-05 (0.0144) |
0.165 (1.00) |
0.283 (1.00) |
0.0431 (1.00) |
0.00136 (0.91) |
0.0087 (1.00) |
0.796 (1.00) |
0.152 (1.00) |
0.343 (1.00) |
0.139 (1.00) |
9p loss | 20 (22%) | 70 |
0.00171 (1.00) |
0.048 (1.00) |
0.554 (1.00) |
0.117 (1.00) |
0.0001 (0.0701) |
0.001 (0.674) |
0.00901 (1.00) |
0.139 (1.00) |
0.00476 (1.00) |
0.938 (1.00) |
17p loss | 32 (36%) | 58 |
0.00305 (1.00) |
0.00016 (0.111) |
0.456 (1.00) |
0.197 (1.00) |
0.0116 (1.00) |
0.0134 (1.00) |
0.0811 (1.00) |
0.00285 (1.00) |
0.0142 (1.00) |
0.111 (1.00) |
1p gain | 4 (4%) | 86 |
0.183 (1.00) |
|||||||||
1q gain | 8 (9%) | 82 |
0.043 (1.00) |
0.658 (1.00) |
0.202 (1.00) |
0.559 (1.00) |
0.0459 (1.00) |
0.079 (1.00) |
0.0646 (1.00) |
0.241 (1.00) |
0.147 (1.00) |
0.85 (1.00) |
2q gain | 12 (13%) | 78 |
0.0522 (1.00) |
0.00249 (1.00) |
0.421 (1.00) |
0.176 (1.00) |
0.019 (1.00) |
0.0026 (1.00) |
0.0562 (1.00) |
0.00489 (1.00) |
0.0208 (1.00) |
0.0243 (1.00) |
3p gain | 13 (14%) | 77 |
0.286 (1.00) |
0.069 (1.00) |
0.45 (1.00) |
0.883 (1.00) |
0.332 (1.00) |
0.365 (1.00) |
0.409 (1.00) |
0.109 (1.00) |
0.634 (1.00) |
0.388 (1.00) |
3q gain | 15 (17%) | 75 |
0.398 (1.00) |
0.0508 (1.00) |
0.893 (1.00) |
0.822 (1.00) |
0.053 (1.00) |
0.792 (1.00) |
0.652 (1.00) |
0.246 (1.00) |
0.679 (1.00) |
0.711 (1.00) |
6p gain | 18 (20%) | 72 |
0.0171 (1.00) |
0.683 (1.00) |
1 (1.00) |
0.876 (1.00) |
0.0667 (1.00) |
0.472 (1.00) |
0.162 (1.00) |
0.055 (1.00) |
0.419 (1.00) |
0.236 (1.00) |
6q gain | 16 (18%) | 74 |
0.0732 (1.00) |
0.458 (1.00) |
0.607 (1.00) |
0.685 (1.00) |
0.2 (1.00) |
0.293 (1.00) |
0.298 (1.00) |
0.197 (1.00) |
0.15 (1.00) |
0.436 (1.00) |
9q gain | 29 (32%) | 61 |
0.00043 (0.295) |
0.0011 (0.737) |
0.0386 (1.00) |
0.0703 (1.00) |
0.0236 (1.00) |
0.00206 (1.00) |
0.0347 (1.00) |
0.353 (1.00) |
0.0894 (1.00) |
0.0831 (1.00) |
11p gain | 5 (6%) | 85 |
0.0917 (1.00) |
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11q gain | 6 (7%) | 84 |
0.126 (1.00) |
0.177 (1.00) |
0.201 (1.00) |
0.484 (1.00) |
0.0444 (1.00) |
0.0794 (1.00) |
0.186 (1.00) |
0.368 (1.00) |
0.00544 (1.00) |
0.39 (1.00) |
13q gain | 6 (7%) | 84 |
0.403 (1.00) |
0.463 (1.00) |
0.497 (1.00) |
0.724 (1.00) |
0.0391 (1.00) |
0.634 (1.00) |
0.141 (1.00) |
0.916 (1.00) |
0.185 (1.00) |
0.7 (1.00) |
15q gain | 11 (12%) | 79 |
0.0941 (1.00) |
0.0473 (1.00) |
0.445 (1.00) |
0.845 (1.00) |
0.0108 (1.00) |
0.00472 (1.00) |
0.36 (1.00) |
0.0007 (0.475) |
0.506 (1.00) |
0.257 (1.00) |
17p gain | 5 (6%) | 85 |
0.112 (1.00) |
0.336 (1.00) |
0.686 (1.00) |
0.144 (1.00) |
0.208 (1.00) |
0.795 (1.00) |
0.0595 (1.00) |
0.062 (1.00) |
||
17q gain | 7 (8%) | 83 |
0.0249 (1.00) |
0.338 (1.00) |
0.688 (1.00) |
0.142 (1.00) |
0.207 (1.00) |
0.794 (1.00) |
0.0597 (1.00) |
0.0617 (1.00) |
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18p gain | 6 (7%) | 84 |
0.26 (1.00) |
|||||||||
18q gain | 5 (6%) | 85 |
0.493 (1.00) |
|||||||||
19p gain | 56 (62%) | 34 |
0.00387 (1.00) |
0.0546 (1.00) |
0.0617 (1.00) |
0.019 (1.00) |
0.00103 (0.693) |
0.00051 (0.349) |
0.466 (1.00) |
0.471 (1.00) |
0.639 (1.00) |
0.221 (1.00) |
21q gain | 31 (34%) | 59 |
0.0205 (1.00) |
0.00909 (1.00) |
0.06 (1.00) |
0.233 (1.00) |
0.0199 (1.00) |
0.00098 (0.661) |
0.0138 (1.00) |
0.02 (1.00) |
0.00288 (1.00) |
0.0829 (1.00) |
22q gain | 3 (3%) | 87 |
0.634 (1.00) |
|||||||||
1p loss | 29 (32%) | 61 |
0.117 (1.00) |
0.141 (1.00) |
0.949 (1.00) |
0.128 (1.00) |
0.438 (1.00) |
0.0645 (1.00) |
0.467 (1.00) |
0.41 (1.00) |
0.0278 (1.00) |
0.948 (1.00) |
1q loss | 20 (22%) | 70 |
0.204 (1.00) |
0.0904 (1.00) |
0.518 (1.00) |
0.0257 (1.00) |
0.961 (1.00) |
0.597 (1.00) |
0.37 (1.00) |
0.841 (1.00) |
0.0783 (1.00) |
0.49 (1.00) |
2p loss | 17 (19%) | 73 |
0.00676 (1.00) |
0.0276 (1.00) |
0.836 (1.00) |
0.659 (1.00) |
0.615 (1.00) |
0.268 (1.00) |
0.0385 (1.00) |
0.769 (1.00) |
0.228 (1.00) |
0.699 (1.00) |
2q loss | 15 (17%) | 75 |
0.00498 (1.00) |
0.00109 (0.731) |
0.734 (1.00) |
0.885 (1.00) |
0.114 (1.00) |
0.0525 (1.00) |
0.0315 (1.00) |
0.728 (1.00) |
0.0693 (1.00) |
0.537 (1.00) |
3p loss | 20 (22%) | 70 |
0.256 (1.00) |
0.142 (1.00) |
0.23 (1.00) |
0.29 (1.00) |
0.111 (1.00) |
0.137 (1.00) |
0.526 (1.00) |
0.388 (1.00) |
0.685 (1.00) |
0.316 (1.00) |
3q loss | 20 (22%) | 70 |
0.167 (1.00) |
0.165 (1.00) |
0.533 (1.00) |
0.603 (1.00) |
0.0221 (1.00) |
0.0299 (1.00) |
0.191 (1.00) |
0.341 (1.00) |
0.314 (1.00) |
0.117 (1.00) |
4p loss | 10 (11%) | 80 |
0.0955 (1.00) |
0.233 (1.00) |
1 (1.00) |
0.989 (1.00) |
0.0237 (1.00) |
0.0815 (1.00) |
0.307 (1.00) |
0.93 (1.00) |
0.0513 (1.00) |
1 (1.00) |
4q loss | 11 (12%) | 79 |
0.237 (1.00) |
0.0935 (1.00) |
0.879 (1.00) |
0.923 (1.00) |
0.0073 (1.00) |
0.0275 (1.00) |
0.248 (1.00) |
0.811 (1.00) |
0.013 (1.00) |
0.902 (1.00) |
5p loss | 8 (9%) | 82 |
0.287 (1.00) |
0.0524 (1.00) |
0.695 (1.00) |
0.192 (1.00) |
0.231 (1.00) |
0.0102 (1.00) |
0.774 (1.00) |
0.299 (1.00) |
0.695 (1.00) |
1 (1.00) |
5q loss | 7 (8%) | 83 |
0.899 (1.00) |
0.654 (1.00) |
0.276 (1.00) |
0.133 (1.00) |
0.658 (1.00) |
0.125 (1.00) |
0.66 (1.00) |
0.849 (1.00) |
||
6p loss | 19 (21%) | 71 |
0.145 (1.00) |
0.853 (1.00) |
0.573 (1.00) |
0.231 (1.00) |
0.62 (1.00) |
0.692 (1.00) |
0.627 (1.00) |
0.099 (1.00) |
0.726 (1.00) |
0.528 (1.00) |
6q loss | 22 (24%) | 68 |
0.0615 (1.00) |
0.86 (1.00) |
0.568 (1.00) |
0.274 (1.00) |
0.633 (1.00) |
0.692 (1.00) |
0.731 (1.00) |
0.173 (1.00) |
0.558 (1.00) |
0.323 (1.00) |
7p loss | 5 (6%) | 85 |
0.391 (1.00) |
0.585 (1.00) |
0.532 (1.00) |
0.204 (1.00) |
0.909 (1.00) |
0.892 (1.00) |
0.816 (1.00) |
0.414 (1.00) |
0.832 (1.00) |
0.114 (1.00) |
7q loss | 6 (7%) | 84 |
0.316 (1.00) |
0.303 (1.00) |
0.685 (1.00) |
0.779 (1.00) |
0.618 (1.00) |
0.656 (1.00) |
1 (1.00) |
0.236 (1.00) |
0.733 (1.00) |
0.15 (1.00) |
8p loss | 16 (18%) | 74 |
0.00546 (1.00) |
0.223 (1.00) |
0.104 (1.00) |
0.00064 (0.435) |
0.182 (1.00) |
0.141 (1.00) |
0.181 (1.00) |
0.0231 (1.00) |
0.254 (1.00) |
0.0297 (1.00) |
8q loss | 12 (13%) | 78 |
0.00444 (1.00) |
0.0866 (1.00) |
0.409 (1.00) |
0.0359 (1.00) |
0.034 (1.00) |
0.123 (1.00) |
0.0769 (1.00) |
0.0357 (1.00) |
0.18 (1.00) |
0.0378 (1.00) |
9q loss | 11 (12%) | 79 |
0.323 (1.00) |
0.936 (1.00) |
1 (1.00) |
0.037 (1.00) |
0.0812 (1.00) |
0.321 (1.00) |
0.557 (1.00) |
0.497 (1.00) |
0.214 (1.00) |
0.806 (1.00) |
10p loss | 12 (13%) | 78 |
0.223 (1.00) |
0.427 (1.00) |
1 (1.00) |
0.0555 (1.00) |
0.265 (1.00) |
1 (1.00) |
0.682 (1.00) |
0.707 (1.00) |
1 (1.00) |
0.326 (1.00) |
10q loss | 10 (11%) | 80 |
0.535 (1.00) |
0.625 (1.00) |
1 (1.00) |
0.238 (1.00) |
0.533 (1.00) |
1 (1.00) |
1 (1.00) |
0.707 (1.00) |
1 (1.00) |
0.288 (1.00) |
11p loss | 24 (27%) | 66 |
0.00644 (1.00) |
0.0179 (1.00) |
0.965 (1.00) |
0.799 (1.00) |
0.218 (1.00) |
0.19 (1.00) |
0.281 (1.00) |
0.892 (1.00) |
0.69 (1.00) |
1 (1.00) |
11q loss | 23 (26%) | 67 |
0.0119 (1.00) |
0.0029 (1.00) |
0.837 (1.00) |
0.396 (1.00) |
0.137 (1.00) |
0.128 (1.00) |
0.106 (1.00) |
0.826 (1.00) |
0.491 (1.00) |
0.781 (1.00) |
12p loss | 5 (6%) | 85 |
0.0907 (1.00) |
0.252 (1.00) |
0.254 (1.00) |
0.0826 (1.00) |
0.621 (1.00) |
0.0381 (1.00) |
0.103 (1.00) |
0.519 (1.00) |
0.431 (1.00) |
0.149 (1.00) |
12q loss | 4 (4%) | 86 |
0.183 (1.00) |
0.0478 (1.00) |
0.257 (1.00) |
0.0837 (1.00) |
0.443 (1.00) |
0.00936 (1.00) |
0.332 (1.00) |
0.239 (1.00) |
0.675 (1.00) |
0.114 (1.00) |
13q loss | 39 (43%) | 51 |
0.0144 (1.00) |
0.0826 (1.00) |
0.885 (1.00) |
0.943 (1.00) |
0.626 (1.00) |
0.886 (1.00) |
0.752 (1.00) |
0.306 (1.00) |
0.614 (1.00) |
0.491 (1.00) |
14q loss | 18 (20%) | 72 |
0.0275 (1.00) |
0.444 (1.00) |
0.249 (1.00) |
0.0531 (1.00) |
0.0182 (1.00) |
0.0474 (1.00) |
0.408 (1.00) |
0.53 (1.00) |
0.215 (1.00) |
0.147 (1.00) |
15q loss | 21 (23%) | 69 |
0.0818 (1.00) |
0.416 (1.00) |
0.554 (1.00) |
0.511 (1.00) |
0.11 (1.00) |
0.225 (1.00) |
0.606 (1.00) |
0.0411 (1.00) |
0.289 (1.00) |
0.876 (1.00) |
16p loss | 6 (7%) | 84 |
0.125 (1.00) |
0.0498 (1.00) |
0.138 (1.00) |
0.0474 (1.00) |
0.00215 (1.00) |
0.00426 (1.00) |
0.0132 (1.00) |
0.443 (1.00) |
0.0004 (0.275) |
0.467 (1.00) |
16q loss | 5 (6%) | 85 |
0.215 (1.00) |
0.0777 (1.00) |
0.196 (1.00) |
0.178 (1.00) |
0.058 (1.00) |
0.0848 (1.00) |
0.168 (1.00) |
0.305 (1.00) |
0.00145 (0.967) |
0.702 (1.00) |
17q loss | 24 (27%) | 66 |
0.0148 (1.00) |
0.00513 (1.00) |
0.639 (1.00) |
0.516 (1.00) |
0.118 (1.00) |
0.034 (1.00) |
0.0686 (1.00) |
0.0204 (1.00) |
0.228 (1.00) |
0.108 (1.00) |
18p loss | 37 (41%) | 53 |
0.0238 (1.00) |
0.26 (1.00) |
0.976 (1.00) |
0.687 (1.00) |
0.774 (1.00) |
0.645 (1.00) |
0.695 (1.00) |
0.693 (1.00) |
0.353 (1.00) |
0.34 (1.00) |
18q loss | 35 (39%) | 55 |
0.0364 (1.00) |
0.424 (1.00) |
0.933 (1.00) |
0.533 (1.00) |
0.825 (1.00) |
0.935 (1.00) |
0.495 (1.00) |
0.915 (1.00) |
0.292 (1.00) |
0.354 (1.00) |
19p loss | 5 (6%) | 85 |
0.0923 (1.00) |
0.444 (1.00) |
0.158 (1.00) |
0.0133 (1.00) |
0.14 (1.00) |
0.718 (1.00) |
0.28 (1.00) |
0.111 (1.00) |
||
19q loss | 4 (4%) | 86 |
0.184 (1.00) |
0.706 (1.00) |
0.771 (1.00) |
0.118 (1.00) |
0.784 (1.00) |
0.206 (1.00) |
1 (1.00) |
0.432 (1.00) |
||
20p loss | 9 (10%) | 81 |
0.0418 (1.00) |
0.303 (1.00) |
0.544 (1.00) |
0.854 (1.00) |
0.214 (1.00) |
0.123 (1.00) |
0.0674 (1.00) |
0.447 (1.00) |
0.0203 (1.00) |
0.444 (1.00) |
20q loss | 3 (3%) | 87 |
0.18 (1.00) |
|||||||||
21q loss | 15 (17%) | 75 |
0.114 (1.00) |
0.339 (1.00) |
0.0498 (1.00) |
0.0521 (1.00) |
0.254 (1.00) |
0.251 (1.00) |
0.226 (1.00) |
0.509 (1.00) |
0.0836 (1.00) |
0.101 (1.00) |
22q loss | 48 (53%) | 42 |
0.0153 (1.00) |
0.0805 (1.00) |
0.974 (1.00) |
0.483 (1.00) |
0.621 (1.00) |
0.281 (1.00) |
0.876 (1.00) |
0.825 (1.00) |
0.682 (1.00) |
0.229 (1.00) |
xq loss | 17 (19%) | 73 |
0.00055 (0.375) |
0.244 (1.00) |
0.267 (1.00) |
0.264 (1.00) |
0.0329 (1.00) |
0.0456 (1.00) |
0.654 (1.00) |
0.168 (1.00) |
0.245 (1.00) |
0.798 (1.00) |
P value = 0.00025 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
2P GAIN MUTATED | 8 | 0 | 1 | 0 |
2P GAIN WILD-TYPE | 15 | 23 | 6 | 24 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
4P GAIN MUTATED | 4 | 13 | 12 | 8 |
4P GAIN WILD-TYPE | 32 | 13 | 4 | 4 |
P value = 2e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
4P GAIN MUTATED | 1 | 8 | 11 | 10 |
4P GAIN WILD-TYPE | 23 | 5 | 6 | 13 |
P value = 4e-05 (Fisher's exact test), Q value = 0.028
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
4P GAIN MUTATED | 2 | 15 | 0 | 13 |
4P GAIN WILD-TYPE | 21 | 8 | 7 | 11 |
P value = 2e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
4Q GAIN MUTATED | 3 | 12 | 11 | 7 |
4Q GAIN WILD-TYPE | 33 | 14 | 5 | 5 |
P value = 3e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
4Q GAIN MUTATED | 0 | 8 | 9 | 10 |
4Q GAIN WILD-TYPE | 24 | 5 | 8 | 13 |
P value = 2e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
4Q GAIN MUTATED | 1 | 15 | 0 | 11 |
4Q GAIN WILD-TYPE | 22 | 8 | 7 | 13 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
5P GAIN MUTATED | 10 | 24 | 14 | 9 |
5P GAIN WILD-TYPE | 26 | 2 | 2 | 3 |
P value = 2e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
5P GAIN MUTATED | 6 | 18 | 3 | 22 |
5P GAIN WILD-TYPE | 17 | 5 | 4 | 2 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
5Q GAIN MUTATED | 8 | 21 | 14 | 10 |
5Q GAIN WILD-TYPE | 28 | 5 | 2 | 2 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
5Q GAIN MUTATED | 5 | 19 | 3 | 20 |
5Q GAIN WILD-TYPE | 18 | 4 | 4 | 4 |
P value = 5e-05 (Fisher's exact test), Q value = 0.035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
7P GAIN MUTATED | 8 | 20 | 12 | 8 |
7P GAIN WILD-TYPE | 28 | 6 | 4 | 4 |
P value = 0.00011 (Fisher's exact test), Q value = 0.077
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
7P GAIN MUTATED | 6 | 12 | 13 | 11 |
7P GAIN WILD-TYPE | 18 | 1 | 4 | 12 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
7Q GAIN MUTATED | 7 | 20 | 13 | 8 |
7Q GAIN WILD-TYPE | 29 | 6 | 3 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
7Q GAIN MUTATED | 5 | 13 | 13 | 11 |
7Q GAIN WILD-TYPE | 19 | 0 | 4 | 12 |
P value = 8e-05 (Fisher's exact test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
7Q GAIN MUTATED | 6 | 20 | 2 | 14 |
7Q GAIN WILD-TYPE | 17 | 3 | 5 | 10 |
P value = 9e-05 (Fisher's exact test), Q value = 0.063
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
8P GAIN MUTATED | 5 | 18 | 4 | 5 |
8P GAIN WILD-TYPE | 31 | 8 | 12 | 7 |
P value = 0.00022 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
8Q GAIN MUTATED | 9 | 20 | 4 | 5 |
8Q GAIN WILD-TYPE | 27 | 6 | 12 | 7 |
P value = 6e-05 (Fisher's exact test), Q value = 0.042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
9P GAIN MUTATED | 2 | 4 | 10 | 4 |
9P GAIN WILD-TYPE | 34 | 22 | 6 | 8 |
P value = 7e-05 (Fisher's exact test), Q value = 0.049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
10P GAIN MUTATED | 6 | 11 | 4 | 2 |
10P GAIN WILD-TYPE | 18 | 2 | 13 | 21 |
P value = 0.00014 (Fisher's exact test), Q value = 0.098
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
10P GAIN MUTATED | 7 | 14 | 1 | 1 |
10P GAIN WILD-TYPE | 16 | 9 | 6 | 23 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
10Q GAIN MUTATED | 7 | 11 | 3 | 2 |
10Q GAIN WILD-TYPE | 17 | 2 | 14 | 21 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
12P GAIN MUTATED | 14 | 26 | 15 | 9 |
12P GAIN WILD-TYPE | 22 | 0 | 1 | 3 |
P value = 0.00011 (Fisher's exact test), Q value = 0.077
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
12P GAIN MUTATED | 9 | 13 | 14 | 18 |
12P GAIN WILD-TYPE | 15 | 0 | 3 | 5 |
P value = 7e-05 (Fisher's exact test), Q value = 0.049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
12P GAIN MUTATED | 10 | 20 | 2 | 22 |
12P GAIN WILD-TYPE | 13 | 3 | 5 | 2 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
12Q GAIN MUTATED | 13 | 26 | 16 | 9 |
12Q GAIN WILD-TYPE | 23 | 0 | 0 | 3 |
P value = 0.00021 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
12Q GAIN MUTATED | 11 | 20 | 2 | 22 |
12Q GAIN WILD-TYPE | 12 | 3 | 5 | 2 |
P value = 0.00031 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
14Q GAIN MUTATED | 2 | 6 | 8 | 1 |
14Q GAIN WILD-TYPE | 22 | 7 | 9 | 22 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 36 | 16 | 26 |
14Q GAIN MUTATED | 17 | 0 | 1 |
14Q GAIN WILD-TYPE | 19 | 16 | 25 |
P value = 0.00017 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 16 | 27 | 11 | 20 | 4 |
14Q GAIN MUTATED | 7 | 0 | 3 | 5 | 3 |
14Q GAIN WILD-TYPE | 9 | 27 | 8 | 15 | 1 |
P value = 3e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 22 | 27 |
14Q GAIN MUTATED | 14 | 2 | 1 |
14Q GAIN WILD-TYPE | 14 | 20 | 26 |
P value = 2e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 39 | 24 | 14 |
14Q GAIN MUTATED | 17 | 0 | 0 |
14Q GAIN WILD-TYPE | 22 | 24 | 14 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
16P GAIN MUTATED | 6 | 26 | 11 | 6 |
16P GAIN WILD-TYPE | 30 | 0 | 5 | 6 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
16P GAIN MUTATED | 3 | 10 | 13 | 16 |
16P GAIN WILD-TYPE | 21 | 3 | 4 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
16P GAIN MUTATED | 4 | 20 | 0 | 18 |
16P GAIN WILD-TYPE | 19 | 3 | 7 | 6 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
16Q GAIN MUTATED | 5 | 25 | 11 | 6 |
16Q GAIN WILD-TYPE | 31 | 1 | 5 | 6 |
P value = 8e-05 (Fisher's exact test), Q value = 0.056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
16Q GAIN MUTATED | 4 | 9 | 13 | 16 |
16Q GAIN WILD-TYPE | 20 | 4 | 4 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
16Q GAIN MUTATED | 4 | 19 | 1 | 18 |
16Q GAIN WILD-TYPE | 19 | 4 | 6 | 6 |
P value = 5e-05 (Fisher's exact test), Q value = 0.035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
19Q GAIN MUTATED | 13 | 16 | 16 | 7 |
19Q GAIN WILD-TYPE | 23 | 10 | 0 | 5 |
P value = 0.00031 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
19Q GAIN MUTATED | 10 | 13 | 12 | 9 |
19Q GAIN WILD-TYPE | 14 | 0 | 5 | 14 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
20P GAIN MUTATED | 6 | 22 | 11 | 7 |
20P GAIN WILD-TYPE | 30 | 4 | 5 | 5 |
P value = 0.00016 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
20P GAIN MUTATED | 4 | 9 | 8 | 18 |
20P GAIN WILD-TYPE | 20 | 4 | 9 | 5 |
P value = 0.00011 (Fisher's exact test), Q value = 0.077
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
20P GAIN MUTATED | 6 | 12 | 1 | 20 |
20P GAIN WILD-TYPE | 17 | 11 | 6 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0074
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
20Q GAIN MUTATED | 8 | 22 | 12 | 7 |
20Q GAIN WILD-TYPE | 28 | 4 | 4 | 5 |
P value = 6e-05 (Fisher's exact test), Q value = 0.042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
20Q GAIN MUTATED | 5 | 11 | 8 | 18 |
20Q GAIN WILD-TYPE | 19 | 2 | 9 | 5 |
P value = 0.00029 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 23 | 7 | 24 |
20Q GAIN MUTATED | 6 | 14 | 2 | 20 |
20Q GAIN WILD-TYPE | 17 | 9 | 5 | 4 |
P value = 2e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 26 | 16 | 12 |
XQ GAIN MUTATED | 6 | 21 | 8 | 5 |
XQ GAIN WILD-TYPE | 30 | 5 | 8 | 7 |
P value = 1e-04 (Fisher's exact test), Q value = 0.07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 13 | 17 | 23 |
9P LOSS MUTATED | 14 | 1 | 3 | 1 |
9P LOSS WILD-TYPE | 10 | 12 | 14 | 22 |
P value = 0.00016 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 11 | 20 | 18 | 11 |
17P LOSS MUTATED | 11 | 0 | 12 | 4 | 1 |
17P LOSS WILD-TYPE | 7 | 11 | 8 | 14 | 10 |
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtypes file = ACC-TP.transferedmergedcluster.txt
-
Number of patients = 90
-
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.