This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 79 arm-level events and 10 molecular subtypes across 56 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.
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4q loss cnv correlated to 'MIRSEQ_CNMF'.
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9p loss cnv correlated to 'RPPA_CHIERARCHICAL'.
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 | |
4q loss | 33 (59%) | 23 |
0.188 (0.744) |
0.0184 (0.479) |
0.292 (0.781) |
0.0902 (0.689) |
0.00495 (0.355) |
0.0388 (0.59) |
0.0001 (0.079) |
0.246 (0.769) |
0.0207 (0.479) |
0.135 (0.716) |
9p loss | 34 (61%) | 22 |
0.298 (0.781) |
0.00791 (0.375) |
0.0519 (0.595) |
0.00047 (0.186) |
0.673 (0.979) |
0.135 (0.716) |
0.864 (1.00) |
0.288 (0.781) |
1 (1.00) |
0.0608 (0.632) |
1p gain | 24 (43%) | 32 |
0.201 (0.744) |
0.754 (0.979) |
0.737 (0.979) |
0.693 (0.979) |
0.82 (1.00) |
0.902 (1.00) |
0.527 (0.944) |
0.284 (0.781) |
0.606 (0.952) |
0.567 (0.952) |
1q gain | 31 (55%) | 25 |
0.437 (0.907) |
0.767 (0.984) |
0.935 (1.00) |
0.594 (0.952) |
0.762 (0.979) |
0.618 (0.959) |
0.707 (0.979) |
0.456 (0.921) |
0.883 (1.00) |
0.815 (1) |
2p gain | 23 (41%) | 33 |
0.887 (1.00) |
0.00782 (0.375) |
0.109 (0.705) |
0.0348 (0.584) |
0.0193 (0.479) |
0.0561 (0.616) |
0.495 (0.938) |
0.0722 (0.663) |
0.101 (0.705) |
0.135 (0.716) |
2q gain | 21 (38%) | 35 |
0.373 (0.858) |
0.0185 (0.479) |
0.135 (0.716) |
0.313 (0.798) |
0.012 (0.432) |
0.112 (0.705) |
0.622 (0.959) |
0.0488 (0.595) |
0.195 (0.744) |
0.112 (0.705) |
3p gain | 12 (21%) | 44 |
0.212 (0.744) |
0.259 (0.781) |
0.104 (0.705) |
0.21 (0.744) |
0.431 (0.901) |
0.2 (0.744) |
0.861 (1.00) |
0.265 (0.781) |
0.451 (0.919) |
0.554 (0.952) |
3q gain | 23 (41%) | 33 |
0.101 (0.705) |
0.0486 (0.595) |
0.337 (0.824) |
0.566 (0.952) |
0.196 (0.744) |
0.12 (0.705) |
0.497 (0.938) |
0.19 (0.744) |
0.0738 (0.663) |
0.221 (0.747) |
4p gain | 9 (16%) | 47 |
0.73 (0.979) |
0.701 (0.979) |
0.0321 (0.552) |
0.0263 (0.524) |
0.823 (1.00) |
0.867 (1.00) |
0.775 (0.984) |
0.325 (0.809) |
0.261 (0.781) |
0.368 (0.853) |
4q gain | 3 (5%) | 53 |
1 (1.00) |
0.256 (0.781) |
0.514 (0.944) |
0.793 (0.995) |
0.675 (0.979) |
0.565 (0.952) |
0.598 (0.952) |
0.695 (0.979) |
||
5p gain | 23 (41%) | 33 |
0.0446 (0.595) |
0.375 (0.858) |
0.00605 (0.355) |
0.199 (0.744) |
0.451 (0.919) |
0.243 (0.768) |
0.743 (0.979) |
0.0288 (0.542) |
0.596 (0.952) |
0.152 (0.734) |
5q gain | 8 (14%) | 48 |
0.511 (0.944) |
0.565 (0.952) |
0.0224 (0.479) |
0.209 (0.744) |
0.311 (0.797) |
0.247 (0.769) |
0.0805 (0.664) |
0.154 (0.734) |
0.13 (0.716) |
0.192 (0.744) |
6p gain | 30 (54%) | 26 |
0.195 (0.744) |
0.523 (0.944) |
0.552 (0.952) |
0.521 (0.944) |
0.601 (0.952) |
0.415 (0.896) |
1 (1.00) |
0.474 (0.926) |
0.737 (0.979) |
0.321 (0.809) |
6q gain | 27 (48%) | 29 |
0.208 (0.744) |
0.206 (0.744) |
0.608 (0.952) |
0.62 (0.959) |
0.224 (0.747) |
0.167 (0.744) |
1 (1.00) |
0.19 (0.744) |
0.65 (0.976) |
0.14 (0.716) |
7p gain | 21 (38%) | 35 |
0.201 (0.744) |
0.557 (0.952) |
0.908 (1.00) |
0.29 (0.781) |
0.151 (0.734) |
0.282 (0.781) |
0.593 (0.952) |
0.132 (0.716) |
0.329 (0.811) |
0.121 (0.705) |
7q gain | 17 (30%) | 39 |
0.585 (0.952) |
0.842 (1.00) |
0.692 (0.979) |
0.87 (1.00) |
0.339 (0.824) |
0.81 (0.997) |
0.742 (0.979) |
0.167 (0.744) |
1 (1.00) |
0.154 (0.734) |
8p gain | 19 (34%) | 37 |
0.188 (0.744) |
0.742 (0.979) |
0.503 (0.942) |
0.278 (0.781) |
0.445 (0.919) |
0.871 (1.00) |
0.97 (1.00) |
0.558 (0.952) |
0.665 (0.979) |
0.596 (0.952) |
8q gain | 30 (54%) | 26 |
0.0144 (0.474) |
0.197 (0.744) |
0.552 (0.952) |
0.594 (0.952) |
0.0505 (0.595) |
0.506 (0.942) |
0.215 (0.744) |
0.324 (0.809) |
0.0675 (0.65) |
0.122 (0.705) |
9p gain | 6 (11%) | 50 |
0.351 (0.839) |
0.703 (0.979) |
0.758 (0.979) |
0.124 (0.705) |
0.936 (1.00) |
0.665 (0.979) |
0.832 (1.00) |
0.804 (0.997) |
0.861 (1.00) |
1 (1.00) |
10p gain | 21 (38%) | 35 |
0.327 (0.809) |
0.0203 (0.479) |
0.173 (0.744) |
0.3 (0.781) |
0.04 (0.595) |
0.12 (0.705) |
0.326 (0.809) |
0.106 (0.705) |
0.678 (0.979) |
0.199 (0.744) |
10q gain | 17 (30%) | 39 |
0.874 (1.00) |
0.337 (0.824) |
0.239 (0.764) |
0.465 (0.926) |
0.551 (0.952) |
0.0481 (0.595) |
0.222 (0.747) |
0.182 (0.744) |
0.38 (0.858) |
0.0734 (0.663) |
11p gain | 5 (9%) | 51 |
0.72 (0.979) |
0.447 (0.919) |
0.209 (0.744) |
0.925 (1.00) |
0.264 (0.781) |
0.851 (1.00) |
0.493 (0.938) |
0.119 (0.705) |
0.519 (0.944) |
0.0933 (0.696) |
11q gain | 7 (12%) | 49 |
0.682 (0.979) |
0.388 (0.862) |
0.0192 (0.479) |
0.716 (0.979) |
0.227 (0.751) |
0.382 (0.859) |
0.755 (0.979) |
0.0363 (0.59) |
0.578 (0.952) |
0.0311 (0.552) |
12p gain | 22 (39%) | 34 |
0.262 (0.781) |
0.00431 (0.355) |
0.314 (0.799) |
0.594 (0.952) |
0.375 (0.858) |
0.0427 (0.595) |
0.81 (0.997) |
0.977 (1.00) |
0.529 (0.944) |
0.629 (0.961) |
12q gain | 11 (20%) | 45 |
0.537 (0.947) |
0.532 (0.945) |
0.652 (0.977) |
0.855 (1.00) |
0.805 (0.997) |
0.525 (0.944) |
1 (1.00) |
0.298 (0.781) |
0.91 (1.00) |
0.27 (0.781) |
13q gain | 15 (27%) | 41 |
0.648 (0.976) |
0.0703 (0.663) |
0.266 (0.781) |
0.544 (0.949) |
0.0215 (0.479) |
0.0243 (0.506) |
0.222 (0.747) |
0.046 (0.595) |
0.0101 (0.405) |
0.142 (0.718) |
14q gain | 7 (12%) | 49 |
0.607 (0.952) |
0.577 (0.952) |
0.113 (0.705) |
0.0494 (0.595) |
0.255 (0.781) |
0.261 (0.781) |
0.206 (0.744) |
0.735 (0.979) |
0.226 (0.749) |
0.472 (0.926) |
15q gain | 4 (7%) | 52 |
0.189 (0.744) |
0.253 (0.781) |
0.759 (0.979) |
0.577 (0.952) |
0.576 (0.952) |
0.325 (0.809) |
0.756 (0.979) |
0.348 (0.832) |
0.425 (0.899) |
0.355 (0.842) |
16p gain | 10 (18%) | 46 |
0.11 (0.705) |
0.281 (0.781) |
0.18 (0.744) |
0.83 (1.00) |
0.197 (0.744) |
0.277 (0.781) |
1 (1.00) |
0.481 (0.933) |
0.904 (1.00) |
0.407 (0.887) |
16q gain | 6 (11%) | 50 |
0.172 (0.744) |
0.849 (1.00) |
0.746 (0.979) |
0.926 (1.00) |
0.546 (0.949) |
0.968 (1.00) |
0.771 (0.984) |
0.926 (1.00) |
0.475 (0.926) |
0.867 (1.00) |
17p gain | 9 (16%) | 47 |
0.39 (0.864) |
0.896 (1.00) |
0.953 (1.00) |
0.827 (1.00) |
0.569 (0.952) |
0.563 (0.952) |
0.284 (0.781) |
0.0607 (0.632) |
0.129 (0.716) |
0.173 (0.744) |
17q gain | 18 (32%) | 38 |
0.421 (0.896) |
0.272 (0.781) |
0.633 (0.963) |
0.8 (0.997) |
0.702 (0.979) |
0.514 (0.944) |
0.393 (0.869) |
0.306 (0.79) |
0.759 (0.979) |
0.432 (0.901) |
18p gain | 18 (32%) | 38 |
0.676 (0.979) |
0.0491 (0.595) |
0.689 (0.979) |
0.787 (0.993) |
0.0943 (0.697) |
0.345 (0.832) |
0.146 (0.728) |
0.199 (0.744) |
0.408 (0.887) |
0.431 (0.901) |
18q gain | 14 (25%) | 42 |
0.685 (0.979) |
0.0809 (0.664) |
0.597 (0.952) |
0.59 (0.952) |
0.154 (0.734) |
0.24 (0.764) |
0.204 (0.744) |
0.0848 (0.676) |
0.139 (0.716) |
0.169 (0.744) |
19p gain | 24 (43%) | 32 |
0.115 (0.705) |
0.177 (0.744) |
0.339 (0.824) |
0.724 (0.979) |
0.27 (0.781) |
0.364 (0.846) |
0.535 (0.945) |
0.229 (0.751) |
0.42 (0.896) |
0.51 (0.944) |
19q gain | 28 (50%) | 28 |
0.125 (0.705) |
0.0756 (0.664) |
0.733 (0.979) |
0.874 (1.00) |
0.379 (0.858) |
0.399 (0.878) |
0.93 (1.00) |
0.898 (1.00) |
0.886 (1.00) |
0.938 (1.00) |
20p gain | 37 (66%) | 19 |
0.287 (0.781) |
0.504 (0.942) |
0.109 (0.705) |
0.595 (0.952) |
0.923 (1.00) |
0.759 (0.979) |
0.875 (1.00) |
0.696 (0.979) |
0.223 (0.747) |
0.472 (0.926) |
20q gain | 44 (79%) | 12 |
0.0519 (0.595) |
0.919 (1.00) |
0.214 (0.744) |
0.952 (1.00) |
0.969 (1.00) |
0.996 (1.00) |
0.589 (0.952) |
0.576 (0.952) |
0.214 (0.744) |
0.68 (0.979) |
21q gain | 18 (32%) | 38 |
0.0732 (0.663) |
0.377 (0.858) |
0.489 (0.938) |
0.786 (0.993) |
0.901 (1.00) |
0.892 (1.00) |
0.915 (1.00) |
0.572 (0.952) |
1 (1.00) |
0.949 (1.00) |
22q gain | 8 (14%) | 48 |
0.711 (0.979) |
0.961 (1.00) |
0.454 (0.919) |
0.302 (0.786) |
0.805 (0.997) |
0.925 (1.00) |
0.886 (1.00) |
0.944 (1.00) |
1 (1.00) |
1 (1.00) |
xp gain | 18 (32%) | 38 |
0.938 (1.00) |
0.0101 (0.405) |
0.404 (0.886) |
0.483 (0.933) |
0.0194 (0.479) |
0.246 (0.769) |
0.8 (0.997) |
0.561 (0.952) |
0.203 (0.744) |
0.433 (0.901) |
xq gain | 15 (27%) | 41 |
0.696 (0.979) |
0.364 (0.846) |
0.723 (0.979) |
0.761 (0.979) |
0.762 (0.979) |
0.714 (0.979) |
0.87 (1.00) |
0.293 (0.781) |
1 (1.00) |
0.0889 (0.689) |
1p loss | 9 (16%) | 47 |
0.596 (0.952) |
0.604 (0.952) |
0.486 (0.934) |
0.626 (0.959) |
0.922 (1.00) |
0.118 (0.705) |
0.111 (0.705) |
0.03 (0.551) |
0.0547 (0.608) |
0.0492 (0.595) |
1q loss | 9 (16%) | 47 |
0.483 (0.933) |
0.518 (0.944) |
0.736 (0.979) |
0.298 (0.781) |
0.513 (0.944) |
0.0778 (0.664) |
0.422 (0.896) |
0.156 (0.734) |
0.212 (0.744) |
0.146 (0.728) |
3p loss | 20 (36%) | 36 |
0.0102 (0.405) |
0.42 (0.896) |
0.407 (0.887) |
0.715 (0.979) |
0.0488 (0.595) |
0.23 (0.751) |
0.376 (0.858) |
0.928 (1.00) |
0.419 (0.896) |
0.43 (0.901) |
3q loss | 14 (25%) | 42 |
0.139 (0.716) |
0.458 (0.921) |
0.836 (1.00) |
0.796 (0.996) |
0.138 (0.716) |
0.602 (0.952) |
0.527 (0.944) |
0.879 (1.00) |
0.383 (0.859) |
1 (1.00) |
4p loss | 31 (55%) | 25 |
0.0659 (0.65) |
0.0628 (0.636) |
0.168 (0.744) |
0.0823 (0.664) |
0.257 (0.781) |
0.202 (0.744) |
0.0374 (0.59) |
0.713 (0.979) |
0.148 (0.73) |
0.446 (0.919) |
5p loss | 9 (16%) | 47 |
0.902 (1.00) |
0.476 (0.926) |
0.0159 (0.479) |
0.0624 (0.636) |
0.884 (1.00) |
0.135 (0.716) |
1 (1.00) |
0.299 (0.781) |
1 (1.00) |
0.417 (0.896) |
5q loss | 18 (32%) | 38 |
0.77 (0.984) |
0.308 (0.793) |
0.105 (0.705) |
0.078 (0.664) |
0.265 (0.781) |
0.232 (0.755) |
0.36 (0.842) |
0.947 (1.00) |
0.355 (0.842) |
0.948 (1.00) |
6p loss | 5 (9%) | 51 |
0.426 (0.899) |
0.956 (1.00) |
0.463 (0.926) |
0.751 (0.979) |
0.757 (0.979) |
0.955 (1.00) |
0.544 (0.949) |
0.91 (1.00) |
1 (1.00) |
1 (1.00) |
6q loss | 7 (12%) | 49 |
0.0641 (0.641) |
0.699 (0.979) |
0.387 (0.862) |
0.165 (0.744) |
0.64 (0.97) |
0.901 (1.00) |
0.706 (0.979) |
0.618 (0.959) |
0.672 (0.979) |
0.616 (0.959) |
7p loss | 13 (23%) | 43 |
1 (1.00) |
0.665 (0.979) |
0.545 (0.949) |
0.285 (0.781) |
0.737 (0.979) |
0.498 (0.938) |
0.312 (0.797) |
0.454 (0.919) |
0.774 (0.984) |
0.599 (0.952) |
7q loss | 13 (23%) | 43 |
0.119 (0.705) |
0.854 (1.00) |
0.325 (0.809) |
0.497 (0.938) |
0.92 (1.00) |
0.821 (1.00) |
0.717 (0.979) |
0.221 (0.747) |
1 (1.00) |
0.529 (0.944) |
8p loss | 23 (41%) | 33 |
0.289 (0.781) |
0.982 (1.00) |
0.539 (0.949) |
0.274 (0.781) |
0.83 (1.00) |
0.745 (0.979) |
0.687 (0.979) |
0.512 (0.944) |
0.605 (0.952) |
0.577 (0.952) |
8q loss | 9 (16%) | 47 |
1 (1.00) |
0.755 (0.979) |
0.811 (0.997) |
0.689 (0.979) |
0.298 (0.781) |
0.713 (0.979) |
0.948 (1.00) |
0.758 (0.979) |
0.26 (0.781) |
0.669 (0.979) |
9q loss | 39 (70%) | 17 |
0.19 (0.744) |
0.00161 (0.318) |
0.141 (0.716) |
0.0218 (0.479) |
0.496 (0.938) |
0.0387 (0.59) |
0.664 (0.979) |
0.119 (0.705) |
1 (1.00) |
0.162 (0.744) |
10p loss | 23 (41%) | 33 |
0.626 (0.959) |
0.0133 (0.457) |
0.666 (0.979) |
0.721 (0.979) |
0.0288 (0.542) |
0.187 (0.744) |
0.246 (0.769) |
0.79 (0.994) |
0.88 (1.00) |
0.896 (1.00) |
10q loss | 21 (38%) | 35 |
0.886 (1.00) |
0.298 (0.781) |
0.275 (0.781) |
0.783 (0.991) |
0.176 (0.744) |
0.17 (0.744) |
0.124 (0.705) |
0.471 (0.926) |
0.398 (0.878) |
0.738 (0.979) |
11p loss | 26 (46%) | 30 |
1 (1.00) |
0.00374 (0.355) |
0.88 (1.00) |
0.858 (1.00) |
0.378 (0.858) |
0.517 (0.944) |
0.269 (0.781) |
0.58 (0.952) |
0.505 (0.942) |
0.36 (0.842) |
11q loss | 24 (43%) | 32 |
0.626 (0.959) |
0.00807 (0.375) |
0.718 (0.979) |
0.806 (0.997) |
0.805 (0.997) |
0.892 (1.00) |
0.294 (0.781) |
0.59 (0.952) |
0.22 (0.747) |
0.183 (0.744) |
12p loss | 13 (23%) | 43 |
0.305 (0.789) |
0.276 (0.781) |
0.528 (0.944) |
0.74 (0.979) |
0.58 (0.952) |
0.734 (0.979) |
0.547 (0.949) |
0.578 (0.952) |
1 (1.00) |
0.217 (0.747) |
12q loss | 14 (25%) | 42 |
0.427 (0.9) |
0.88 (1.00) |
0.873 (1.00) |
0.125 (0.705) |
0.82 (1.00) |
0.915 (1.00) |
0.965 (1.00) |
0.907 (1.00) |
0.92 (1.00) |
0.604 (0.952) |
13q loss | 26 (46%) | 30 |
0.417 (0.896) |
0.00113 (0.298) |
0.847 (1.00) |
0.148 (0.73) |
0.0586 (0.627) |
0.0265 (0.524) |
0.357 (0.842) |
0.119 (0.705) |
0.0386 (0.59) |
0.197 (0.744) |
14q loss | 27 (48%) | 29 |
0.943 (1.00) |
0.0933 (0.696) |
0.527 (0.944) |
0.118 (0.705) |
0.121 (0.705) |
0.123 (0.705) |
0.616 (0.959) |
0.898 (1.00) |
0.939 (1.00) |
0.938 (1.00) |
15q loss | 32 (57%) | 24 |
0.0063 (0.355) |
0.713 (0.979) |
0.772 (0.984) |
0.052 (0.595) |
0.93 (1.00) |
0.981 (1.00) |
0.931 (1.00) |
0.978 (1.00) |
1 (1.00) |
0.895 (1.00) |
16p loss | 32 (57%) | 24 |
0.242 (0.767) |
0.492 (0.938) |
0.977 (1.00) |
0.089 (0.689) |
0.346 (0.832) |
0.102 (0.705) |
0.811 (0.997) |
0.913 (1.00) |
0.47 (0.926) |
0.895 (1.00) |
16q loss | 37 (66%) | 19 |
0.777 (0.985) |
0.794 (0.996) |
0.739 (0.979) |
0.13 (0.716) |
0.45 (0.919) |
0.0907 (0.689) |
0.683 (0.979) |
0.924 (1.00) |
0.14 (0.716) |
0.859 (1.00) |
17p loss | 34 (61%) | 22 |
0.546 (0.949) |
0.282 (0.781) |
0.0439 (0.595) |
0.274 (0.781) |
0.981 (1.00) |
0.759 (0.979) |
0.806 (0.997) |
0.891 (1.00) |
0.235 (0.76) |
0.89 (1.00) |
17q loss | 17 (30%) | 39 |
0.164 (0.744) |
0.358 (0.842) |
0.527 (0.944) |
0.633 (0.963) |
0.716 (0.979) |
0.385 (0.862) |
0.967 (1.00) |
0.214 (0.744) |
0.932 (1.00) |
0.277 (0.781) |
18p loss | 18 (32%) | 38 |
0.0321 (0.552) |
0.0168 (0.479) |
0.41 (0.889) |
0.285 (0.781) |
0.0538 (0.608) |
0.0892 (0.689) |
0.0674 (0.65) |
0.0794 (0.664) |
0.0587 (0.627) |
0.0463 (0.595) |
18q loss | 20 (36%) | 36 |
0.117 (0.705) |
0.0726 (0.663) |
0.317 (0.802) |
0.295 (0.781) |
0.184 (0.744) |
0.119 (0.705) |
0.0117 (0.432) |
0.00577 (0.355) |
0.00615 (0.355) |
0.00224 (0.339) |
19p loss | 15 (27%) | 41 |
0.561 (0.952) |
0.46 (0.923) |
0.163 (0.744) |
0.472 (0.926) |
0.203 (0.744) |
0.358 (0.842) |
0.346 (0.832) |
0.718 (0.979) |
0.211 (0.744) |
0.702 (0.979) |
19q loss | 13 (23%) | 43 |
0.735 (0.979) |
0.153 (0.734) |
0.195 (0.744) |
0.818 (1.00) |
0.944 (1.00) |
0.619 (0.959) |
0.229 (0.751) |
0.874 (1.00) |
0.237 (0.762) |
1 (1.00) |
20p loss | 7 (12%) | 49 |
0.535 (0.945) |
0.208 (0.744) |
0.00285 (0.339) |
0.003 (0.339) |
0.0816 (0.664) |
0.0758 (0.664) |
0.617 (0.959) |
0.692 (0.979) |
0.578 (0.952) |
0.693 (0.979) |
20q loss | 4 (7%) | 52 |
0.372 (0.858) |
0.603 (0.952) |
0.0804 (0.664) |
0.192 (0.744) |
0.118 (0.705) |
0.473 (0.926) |
1 (1.00) |
0.885 (1.00) |
0.669 (0.979) |
0.789 (0.994) |
21q loss | 17 (30%) | 39 |
0.667 (0.979) |
0.179 (0.744) |
0.734 (0.979) |
0.33 (0.811) |
0.634 (0.963) |
0.744 (0.979) |
0.681 (0.979) |
0.972 (1.00) |
0.931 (1.00) |
0.943 (1.00) |
22q loss | 33 (59%) | 23 |
0.176 (0.744) |
0.969 (1.00) |
0.253 (0.781) |
0.0209 (0.479) |
0.962 (1.00) |
0.902 (1.00) |
0.706 (0.979) |
0.291 (0.781) |
0.466 (0.926) |
0.759 (0.979) |
xp loss | 15 (27%) | 41 |
0.648 (0.976) |
0.839 (1.00) |
0.264 (0.781) |
0.345 (0.832) |
0.927 (1.00) |
0.928 (1.00) |
0.448 (0.919) |
0.65 (0.976) |
0.504 (0.942) |
0.761 (0.979) |
xq loss | 18 (32%) | 38 |
0.77 (0.984) |
0.155 (0.734) |
0.485 (0.934) |
0.219 (0.747) |
0.236 (0.76) |
0.626 (0.959) |
0.457 (0.921) |
0.648 (0.976) |
0.532 (0.945) |
0.708 (0.979) |
P value = 1e-04 (Fisher's exact test), Q value = 0.079
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 10 | 22 | 4 | 19 |
4Q LOSS MUTATED | 10 | 16 | 0 | 7 |
4Q LOSS WILD-TYPE | 0 | 6 | 4 | 12 |
P value = 0.00047 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 8 | 8 | 7 | 7 | 7 | 5 | 5 |
9P LOSS MUTATED | 8 | 6 | 7 | 1 | 4 | 2 | 1 |
9P LOSS WILD-TYPE | 0 | 2 | 0 | 6 | 3 | 3 | 4 |
-
Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCS-TP/19782451/transformed.cor.cli.txt
-
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/20140950/UCS-TP.transferedmergedcluster.txt
-
Number of patients = 56
-
Number of significantly arm-level cnvs = 79
-
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.