This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 60 focal events and 12 molecular subtypes across 162 patients, 24 significant findings detected with P value < 0.05 and Q value < 0.25.
-
amp_1q21.3 cnv correlated to 'CN_CNMF'.
-
amp_6p21.1 cnv correlated to 'CN_CNMF'.
-
amp_8p11.23 cnv correlated to 'CN_CNMF'.
-
amp_8p11.21 cnv correlated to 'CN_CNMF'.
-
amp_8q24.21 cnv correlated to 'CN_CNMF'.
-
amp_12p12.1 cnv correlated to 'CN_CNMF'.
-
amp_13q12.13 cnv correlated to 'CN_CNMF'.
-
amp_13q12.2 cnv correlated to 'CN_CNMF'.
-
amp_13q22.1 cnv correlated to 'CN_CNMF'.
-
amp_16p11.2 cnv correlated to 'CN_CNMF'.
-
amp_17q12 cnv correlated to 'CN_CNMF'.
-
amp_17q24.1 cnv correlated to 'CN_CNMF'.
-
amp_20q11.21 cnv correlated to 'CN_CNMF'.
-
amp_20q11.23 cnv correlated to 'CN_CNMF'.
-
del_1p36.11 cnv correlated to 'CN_CNMF'.
-
del_1p33 cnv correlated to 'CN_CNMF'.
-
del_1p13.2 cnv correlated to 'CN_CNMF'.
-
del_4p13 cnv correlated to 'CN_CNMF'.
-
del_4q22.1 cnv correlated to 'CN_CNMF'.
-
del_4q35.1 cnv correlated to 'CN_CNMF'.
-
del_8p23.2 cnv correlated to 'CN_CNMF'.
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del_11q22.3 cnv correlated to 'CN_CNMF'.
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del_18q21.2 cnv correlated to 'CN_CNMF'.
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del_18q22.1 cnv correlated to 'CN_CNMF'.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
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 | Fisher's exact test | Fisher's exact test | |
amp 1q21 3 | 48 (30%) | 114 |
1 (1.00) |
0.852 (1.00) |
0.0001 (0.0697) |
0.96 (1.00) |
0.53 (1.00) |
0.227 (1.00) |
0.509 (1.00) |
0.36 (1.00) |
0.0577 (1.00) |
0.151 (1.00) |
0.0304 (1.00) |
0.659 (1.00) |
amp 6p21 1 | 53 (33%) | 109 |
0.0595 (1.00) |
0.106 (1.00) |
1e-05 (0.00715) |
0.0699 (1.00) |
0.809 (1.00) |
0.0446 (1.00) |
0.574 (1.00) |
0.337 (1.00) |
0.192 (1.00) |
0.387 (1.00) |
0.392 (1.00) |
0.794 (1.00) |
amp 8p11 23 | 52 (32%) | 110 |
0.00348 (1.00) |
0.206 (1.00) |
1e-05 (0.00715) |
0.31 (1.00) |
0.377 (1.00) |
0.129 (1.00) |
0.123 (1.00) |
0.0353 (1.00) |
0.047 (1.00) |
0.0275 (1.00) |
0.69 (1.00) |
0.468 (1.00) |
amp 8p11 21 | 69 (43%) | 93 |
0.0122 (1.00) |
0.213 (1.00) |
1e-05 (0.00715) |
0.256 (1.00) |
0.373 (1.00) |
0.519 (1.00) |
0.225 (1.00) |
0.134 (1.00) |
0.184 (1.00) |
0.274 (1.00) |
0.432 (1.00) |
0.659 (1.00) |
amp 8q24 21 | 107 (66%) | 55 |
0.017 (1.00) |
0.24 (1.00) |
1e-05 (0.00715) |
0.23 (1.00) |
0.63 (1.00) |
0.887 (1.00) |
0.0308 (1.00) |
0.00707 (1.00) |
0.542 (1.00) |
0.263 (1.00) |
0.938 (1.00) |
0.895 (1.00) |
amp 12p12 1 | 40 (25%) | 122 |
0.698 (1.00) |
0.468 (1.00) |
0.00029 (0.201) |
0.447 (1.00) |
0.0495 (1.00) |
0.00873 (1.00) |
0.705 (1.00) |
0.513 (1.00) |
0.694 (1.00) |
0.76 (1.00) |
0.0282 (1.00) |
0.834 (1.00) |
amp 13q12 13 | 123 (76%) | 39 |
0.415 (1.00) |
0.174 (1.00) |
6e-05 (0.0419) |
0.224 (1.00) |
0.324 (1.00) |
0.433 (1.00) |
0.00163 (1.00) |
0.00212 (1.00) |
0.00253 (1.00) |
0.00422 (1.00) |
0.839 (1.00) |
0.239 (1.00) |
amp 13q12 2 | 122 (75%) | 40 |
0.364 (1.00) |
0.236 (1.00) |
3e-05 (0.0211) |
0.151 (1.00) |
0.594 (1.00) |
0.587 (1.00) |
0.016 (1.00) |
0.012 (1.00) |
0.0215 (1.00) |
0.0218 (1.00) |
0.183 (1.00) |
0.248 (1.00) |
amp 13q22 1 | 117 (72%) | 45 |
0.265 (1.00) |
0.0653 (1.00) |
1e-05 (0.00715) |
0.0507 (1.00) |
0.908 (1.00) |
0.269 (1.00) |
0.00507 (1.00) |
0.00104 (0.714) |
0.00412 (1.00) |
0.0111 (1.00) |
0.156 (1.00) |
0.148 (1.00) |
amp 16p11 2 | 45 (28%) | 117 |
0.124 (1.00) |
0.581 (1.00) |
7e-05 (0.0489) |
0.231 (1.00) |
0.345 (1.00) |
0.668 (1.00) |
0.152 (1.00) |
0.118 (1.00) |
0.0972 (1.00) |
0.852 (1.00) |
0.197 (1.00) |
0.241 (1.00) |
amp 17q12 | 43 (27%) | 119 |
0.00651 (1.00) |
0.127 (1.00) |
2e-05 (0.0141) |
0.535 (1.00) |
0.177 (1.00) |
0.917 (1.00) |
0.433 (1.00) |
0.0251 (1.00) |
0.149 (1.00) |
0.597 (1.00) |
0.582 (1.00) |
0.882 (1.00) |
amp 17q24 1 | 37 (23%) | 125 |
0.291 (1.00) |
0.708 (1.00) |
0.00021 (0.146) |
0.124 (1.00) |
0.608 (1.00) |
0.748 (1.00) |
0.638 (1.00) |
0.172 (1.00) |
0.61 (1.00) |
0.209 (1.00) |
0.714 (1.00) |
0.746 (1.00) |
amp 20q11 21 | 143 (88%) | 19 |
0.00761 (1.00) |
0.162 (1.00) |
0.00018 (0.125) |
0.0239 (1.00) |
0.192 (1.00) |
0.368 (1.00) |
0.0578 (1.00) |
0.00319 (1.00) |
0.00761 (1.00) |
0.397 (1.00) |
0.191 (1.00) |
0.31 (1.00) |
amp 20q11 23 | 144 (89%) | 18 |
0.00784 (1.00) |
0.164 (1.00) |
0.00033 (0.228) |
0.056 (1.00) |
0.193 (1.00) |
0.368 (1.00) |
0.0397 (1.00) |
0.00247 (1.00) |
0.0144 (1.00) |
0.28 (1.00) |
0.478 (1.00) |
0.265 (1.00) |
del 1p36 11 | 72 (44%) | 90 |
0.115 (1.00) |
0.0637 (1.00) |
0.00031 (0.215) |
0.256 (1.00) |
0.703 (1.00) |
0.923 (1.00) |
0.726 (1.00) |
0.0212 (1.00) |
0.495 (1.00) |
0.0632 (1.00) |
0.94 (1.00) |
0.293 (1.00) |
del 1p33 | 50 (31%) | 112 |
0.365 (1.00) |
0.00405 (1.00) |
3e-05 (0.0211) |
0.217 (1.00) |
0.801 (1.00) |
0.309 (1.00) |
0.697 (1.00) |
0.164 (1.00) |
0.44 (1.00) |
0.264 (1.00) |
0.871 (1.00) |
0.319 (1.00) |
del 1p13 2 | 52 (32%) | 110 |
0.475 (1.00) |
0.0237 (1.00) |
2e-05 (0.0141) |
0.628 (1.00) |
0.545 (1.00) |
0.569 (1.00) |
0.243 (1.00) |
0.0293 (1.00) |
0.508 (1.00) |
0.21 (1.00) |
0.804 (1.00) |
0.218 (1.00) |
del 4p13 | 59 (36%) | 103 |
0.779 (1.00) |
0.0395 (1.00) |
1e-05 (0.00715) |
0.0843 (1.00) |
0.837 (1.00) |
0.504 (1.00) |
0.712 (1.00) |
0.251 (1.00) |
0.979 (1.00) |
0.221 (1.00) |
0.415 (1.00) |
0.786 (1.00) |
del 4q22 1 | 72 (44%) | 90 |
0.62 (1.00) |
0.0239 (1.00) |
2e-05 (0.0141) |
0.257 (1.00) |
0.703 (1.00) |
0.475 (1.00) |
0.395 (1.00) |
0.312 (1.00) |
0.987 (1.00) |
0.256 (1.00) |
0.797 (1.00) |
0.504 (1.00) |
del 4q35 1 | 71 (44%) | 91 |
0.612 (1.00) |
0.0642 (1.00) |
4e-05 (0.028) |
0.119 (1.00) |
0.385 (1.00) |
0.654 (1.00) |
0.248 (1.00) |
0.0304 (1.00) |
0.486 (1.00) |
0.0513 (1.00) |
0.674 (1.00) |
0.796 (1.00) |
del 8p23 2 | 99 (61%) | 63 |
0.111 (1.00) |
0.0886 (1.00) |
1e-05 (0.00715) |
0.414 (1.00) |
1 (1.00) |
0.269 (1.00) |
0.0623 (1.00) |
0.0268 (1.00) |
0.782 (1.00) |
0.33 (1.00) |
0.289 (1.00) |
0.463 (1.00) |
del 11q22 3 | 38 (23%) | 124 |
0.0328 (1.00) |
0.0302 (1.00) |
1e-05 (0.00715) |
0.0391 (1.00) |
0.688 (1.00) |
0.135 (1.00) |
0.0722 (1.00) |
0.0724 (1.00) |
0.45 (1.00) |
0.966 (1.00) |
0.379 (1.00) |
0.169 (1.00) |
del 18q21 2 | 143 (88%) | 19 |
0.132 (1.00) |
0.334 (1.00) |
1e-05 (0.00715) |
0.112 (1.00) |
1 (1.00) |
0.771 (1.00) |
0.931 (1.00) |
0.719 (1.00) |
0.4 (1.00) |
0.123 (1.00) |
0.0435 (1.00) |
0.709 (1.00) |
del 18q22 1 | 138 (85%) | 24 |
0.0676 (1.00) |
0.0879 (1.00) |
1e-05 (0.00715) |
0.0311 (1.00) |
0.777 (1.00) |
0.653 (1.00) |
0.619 (1.00) |
0.676 (1.00) |
0.828 (1.00) |
0.299 (1.00) |
0.00126 (0.864) |
0.499 (1.00) |
amp 1q32 2 | 48 (30%) | 114 |
0.826 (1.00) |
0.938 (1.00) |
0.00273 (1.00) |
0.577 (1.00) |
0.186 (1.00) |
0.027 (1.00) |
0.508 (1.00) |
0.54 (1.00) |
0.0818 (1.00) |
0.65 (1.00) |
0.0303 (1.00) |
0.332 (1.00) |
amp 5q22 3 | 20 (12%) | 142 |
0.0227 (1.00) |
0.175 (1.00) |
0.36 (1.00) |
0.283 (1.00) |
0.105 (1.00) |
0.658 (1.00) |
0.719 (1.00) |
0.682 (1.00) |
0.454 (1.00) |
0.662 (1.00) |
0.0615 (1.00) |
0.664 (1.00) |
amp 10q22 2 | 11 (7%) | 151 |
0.499 (1.00) |
0.931 (1.00) |
0.817 (1.00) |
1 (1.00) |
1 (1.00) |
0.972 (1.00) |
0.222 (1.00) |
0.191 (1.00) |
0.38 (1.00) |
0.187 (1.00) |
0.229 (1.00) |
1 (1.00) |
amp 11p15 5 | 44 (27%) | 118 |
0.382 (1.00) |
0.0961 (1.00) |
0.0278 (1.00) |
0.695 (1.00) |
0.726 (1.00) |
0.588 (1.00) |
0.137 (1.00) |
0.034 (1.00) |
0.0966 (1.00) |
0.538 (1.00) |
0.344 (1.00) |
0.104 (1.00) |
amp 11q13 3 | 27 (17%) | 135 |
0.329 (1.00) |
0.332 (1.00) |
0.00527 (1.00) |
0.00753 (1.00) |
0.911 (1.00) |
0.731 (1.00) |
0.141 (1.00) |
0.00204 (1.00) |
0.0132 (1.00) |
0.341 (1.00) |
0.43 (1.00) |
0.534 (1.00) |
amp 12p13 33 | 41 (25%) | 121 |
0.689 (1.00) |
0.483 (1.00) |
0.00184 (1.00) |
0.654 (1.00) |
0.116 (1.00) |
0.214 (1.00) |
0.809 (1.00) |
0.836 (1.00) |
0.579 (1.00) |
0.815 (1.00) |
0.207 (1.00) |
0.511 (1.00) |
amp 15q26 1 | 13 (8%) | 149 |
0.111 (1.00) |
0.212 (1.00) |
0.151 (1.00) |
0.507 (1.00) |
0.156 (1.00) |
0.348 (1.00) |
0.0921 (1.00) |
0.122 (1.00) |
0.908 (1.00) |
1 (1.00) |
0.79 (1.00) |
0.104 (1.00) |
amp 19p13 2 | 34 (21%) | 128 |
0.0206 (1.00) |
0.25 (1.00) |
0.00158 (1.00) |
0.854 (1.00) |
0.545 (1.00) |
0.0852 (1.00) |
0.0577 (1.00) |
0.704 (1.00) |
0.588 (1.00) |
0.696 (1.00) |
0.977 (1.00) |
0.322 (1.00) |
amp 20q13 33 | 143 (88%) | 19 |
0.0365 (1.00) |
0.234 (1.00) |
0.0196 (1.00) |
0.242 (1.00) |
0.259 (1.00) |
0.562 (1.00) |
0.173 (1.00) |
0.0452 (1.00) |
0.0777 (1.00) |
0.396 (1.00) |
0.338 (1.00) |
0.711 (1.00) |
amp xp22 2 | 31 (19%) | 131 |
0.0503 (1.00) |
0.219 (1.00) |
0.646 (1.00) |
0.317 (1.00) |
0.96 (1.00) |
0.235 (1.00) |
0.708 (1.00) |
0.175 (1.00) |
0.813 (1.00) |
0.87 (1.00) |
0.414 (1.00) |
0.184 (1.00) |
amp xq27 3 | 36 (22%) | 126 |
0.362 (1.00) |
0.325 (1.00) |
0.0148 (1.00) |
0.0202 (1.00) |
0.648 (1.00) |
0.21 (1.00) |
0.0197 (1.00) |
0.123 (1.00) |
0.383 (1.00) |
0.278 (1.00) |
0.291 (1.00) |
0.305 (1.00) |
del 2p12 | 18 (11%) | 144 |
0.354 (1.00) |
0.821 (1.00) |
0.00143 (0.978) |
0.406 (1.00) |
0.449 (1.00) |
0.142 (1.00) |
0.646 (1.00) |
0.432 (1.00) |
0.359 (1.00) |
0.545 (1.00) |
0.267 (1.00) |
0.884 (1.00) |
del 3p14 2 | 29 (18%) | 133 |
0.801 (1.00) |
0.701 (1.00) |
0.783 (1.00) |
1 (1.00) |
0.218 (1.00) |
0.716 (1.00) |
0.342 (1.00) |
0.764 (1.00) |
0.81 (1.00) |
0.96 (1.00) |
0.72 (1.00) |
0.768 (1.00) |
del 3q26 31 | 16 (10%) | 146 |
1 (1.00) |
0.497 (1.00) |
0.331 (1.00) |
1 (1.00) |
0.725 (1.00) |
0.836 (1.00) |
0.799 (1.00) |
0.295 (1.00) |
0.0834 (1.00) |
0.372 (1.00) |
0.0671 (1.00) |
0.865 (1.00) |
del 5q11 2 | 51 (31%) | 111 |
0.066 (1.00) |
0.00202 (1.00) |
0.0119 (1.00) |
0.00184 (1.00) |
0.857 (1.00) |
0.341 (1.00) |
0.557 (1.00) |
0.0342 (1.00) |
0.552 (1.00) |
0.289 (1.00) |
0.675 (1.00) |
0.252 (1.00) |
del 5q22 2 | 57 (35%) | 105 |
0.183 (1.00) |
0.00082 (0.564) |
0.0556 (1.00) |
0.323 (1.00) |
0.546 (1.00) |
0.728 (1.00) |
1 (1.00) |
0.0982 (1.00) |
0.739 (1.00) |
0.238 (1.00) |
0.213 (1.00) |
0.444 (1.00) |
del 6p25 3 | 24 (15%) | 138 |
1 (1.00) |
0.939 (1.00) |
0.264 (1.00) |
0.0217 (1.00) |
0.653 (1.00) |
0.985 (1.00) |
0.95 (1.00) |
0.867 (1.00) |
0.753 (1.00) |
0.783 (1.00) |
0.469 (1.00) |
0.173 (1.00) |
del 6q26 | 30 (19%) | 132 |
0.158 (1.00) |
0.744 (1.00) |
0.213 (1.00) |
0.682 (1.00) |
0.101 (1.00) |
0.199 (1.00) |
0.265 (1.00) |
0.119 (1.00) |
0.0558 (1.00) |
0.334 (1.00) |
0.0967 (1.00) |
0.114 (1.00) |
del 7q31 1 | 4 (2%) | 158 |
0.0623 (1.00) |
1 (1.00) |
0.952 (1.00) |
0.759 (1.00) |
0.767 (1.00) |
1 (1.00) |
1 (1.00) |
|||||
del 8p11 21 | 24 (15%) | 138 |
0.317 (1.00) |
0.823 (1.00) |
0.00427 (1.00) |
0.203 (1.00) |
0.112 (1.00) |
0.702 (1.00) |
0.166 (1.00) |
0.0989 (1.00) |
0.0463 (1.00) |
0.0685 (1.00) |
0.378 (1.00) |
0.163 (1.00) |
del 10q21 1 | 37 (23%) | 125 |
0.37 (1.00) |
0.417 (1.00) |
0.0293 (1.00) |
0.302 (1.00) |
0.0605 (1.00) |
0.186 (1.00) |
0.431 (1.00) |
0.793 (1.00) |
0.833 (1.00) |
0.28 (1.00) |
0.822 (1.00) |
0.315 (1.00) |
del 10q25 2 | 47 (29%) | 115 |
0.761 (1.00) |
0.772 (1.00) |
0.0715 (1.00) |
0.671 (1.00) |
0.456 (1.00) |
0.241 (1.00) |
0.687 (1.00) |
0.223 (1.00) |
0.624 (1.00) |
0.275 (1.00) |
0.713 (1.00) |
0.349 (1.00) |
del 12p13 1 | 33 (20%) | 129 |
1 (1.00) |
0.261 (1.00) |
0.26 (1.00) |
0.287 (1.00) |
0.536 (1.00) |
0.276 (1.00) |
0.532 (1.00) |
0.149 (1.00) |
0.295 (1.00) |
0.528 (1.00) |
0.771 (1.00) |
0.537 (1.00) |
del 12q22 | 24 (15%) | 138 |
0.607 (1.00) |
0.408 (1.00) |
0.0227 (1.00) |
0.774 (1.00) |
0.9 (1.00) |
0.315 (1.00) |
0.851 (1.00) |
0.403 (1.00) |
0.365 (1.00) |
0.617 (1.00) |
0.304 (1.00) |
0.362 (1.00) |
del 14q11 2 | 68 (42%) | 94 |
0.483 (1.00) |
0.128 (1.00) |
0.029 (1.00) |
0.931 (1.00) |
0.702 (1.00) |
0.694 (1.00) |
0.0662 (1.00) |
0.277 (1.00) |
0.109 (1.00) |
0.343 (1.00) |
0.576 (1.00) |
0.343 (1.00) |
del 14q31 1 | 70 (43%) | 92 |
0.483 (1.00) |
0.237 (1.00) |
0.0297 (1.00) |
1 (1.00) |
0.708 (1.00) |
0.2 (1.00) |
0.08 (1.00) |
0.141 (1.00) |
0.2 (1.00) |
0.239 (1.00) |
0.87 (1.00) |
0.632 (1.00) |
del 15q22 33 | 76 (47%) | 86 |
0.623 (1.00) |
0.154 (1.00) |
0.00078 (0.537) |
0.697 (1.00) |
0.148 (1.00) |
0.0578 (1.00) |
0.784 (1.00) |
0.187 (1.00) |
0.421 (1.00) |
0.744 (1.00) |
0.932 (1.00) |
0.724 (1.00) |
del 16p13 3 | 13 (8%) | 149 |
0.887 (1.00) |
0.677 (1.00) |
0.0158 (1.00) |
0.0204 (1.00) |
0.724 (1.00) |
0.6 (1.00) |
0.912 (1.00) |
0.832 (1.00) |
0.355 (1.00) |
0.633 (1.00) |
0.675 (1.00) |
0.573 (1.00) |
del 16q23 1 | 23 (14%) | 139 |
0.152 (1.00) |
0.351 (1.00) |
0.0411 (1.00) |
0.136 (1.00) |
0.588 (1.00) |
0.952 (1.00) |
0.586 (1.00) |
0.658 (1.00) |
0.76 (1.00) |
0.843 (1.00) |
0.511 (1.00) |
0.307 (1.00) |
del 17p11 2 | 110 (68%) | 52 |
0.0848 (1.00) |
0.757 (1.00) |
0.00582 (1.00) |
0.281 (1.00) |
0.829 (1.00) |
0.358 (1.00) |
0.864 (1.00) |
0.972 (1.00) |
0.935 (1.00) |
0.352 (1.00) |
0.634 (1.00) |
0.807 (1.00) |
del 19p13 3 | 36 (22%) | 126 |
0.273 (1.00) |
0.952 (1.00) |
0.0183 (1.00) |
0.0303 (1.00) |
1 (1.00) |
0.705 (1.00) |
0.809 (1.00) |
0.518 (1.00) |
0.46 (1.00) |
0.00606 (1.00) |
0.759 (1.00) |
0.579 (1.00) |
del 20p12 1 | 60 (37%) | 102 |
0.622 (1.00) |
0.0322 (1.00) |
0.00051 (0.352) |
0.788 (1.00) |
0.541 (1.00) |
0.179 (1.00) |
0.707 (1.00) |
0.0382 (1.00) |
0.0411 (1.00) |
0.0727 (1.00) |
0.984 (1.00) |
0.612 (1.00) |
del 20p12 1 | 60 (37%) | 102 |
0.619 (1.00) |
0.0323 (1.00) |
0.00058 (0.4) |
0.788 (1.00) |
0.54 (1.00) |
0.182 (1.00) |
0.706 (1.00) |
0.0394 (1.00) |
0.0424 (1.00) |
0.0751 (1.00) |
0.984 (1.00) |
0.614 (1.00) |
del 21q11 2 | 71 (44%) | 91 |
0.315 (1.00) |
0.0609 (1.00) |
0.0194 (1.00) |
0.836 (1.00) |
0.922 (1.00) |
0.214 (1.00) |
0.249 (1.00) |
0.482 (1.00) |
0.0639 (1.00) |
0.726 (1.00) |
0.273 (1.00) |
0.316 (1.00) |
del 22q13 31 | 67 (41%) | 95 |
0.906 (1.00) |
0.293 (1.00) |
0.00611 (1.00) |
0.834 (1.00) |
0.409 (1.00) |
0.352 (1.00) |
0.0623 (1.00) |
0.123 (1.00) |
0.00608 (1.00) |
0.113 (1.00) |
0.23 (1.00) |
0.123 (1.00) |
del xp22 33 | 33 (20%) | 129 |
0.774 (1.00) |
0.916 (1.00) |
0.00131 (0.897) |
0.00318 (1.00) |
0.726 (1.00) |
0.897 (1.00) |
0.674 (1.00) |
0.5 (1.00) |
0.698 (1.00) |
1 (1.00) |
0.731 (1.00) |
0.934 (1.00) |
P value = 1e-04 (Fisher's exact test), Q value = 0.07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 1(1Q21.3) MUTATED | 7 | 7 | 6 | 16 | 9 | 3 |
AMP PEAK 1(1Q21.3) WILD-TYPE | 3 | 27 | 36 | 14 | 15 | 19 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 4(6P21.1) MUTATED | 6 | 16 | 4 | 10 | 15 | 2 |
AMP PEAK 4(6P21.1) WILD-TYPE | 4 | 18 | 38 | 20 | 9 | 20 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 5(8P11.23) MUTATED | 3 | 15 | 4 | 5 | 8 | 17 |
AMP PEAK 5(8P11.23) WILD-TYPE | 7 | 19 | 38 | 25 | 16 | 5 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 6(8P11.21) MUTATED | 5 | 17 | 6 | 10 | 9 | 22 |
AMP PEAK 6(8P11.21) WILD-TYPE | 5 | 17 | 36 | 20 | 15 | 0 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 7(8Q24.21) MUTATED | 6 | 29 | 14 | 24 | 12 | 22 |
AMP PEAK 7(8Q24.21) WILD-TYPE | 4 | 5 | 28 | 6 | 12 | 0 |
P value = 0.00029 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 12(12P12.1) MUTATED | 1 | 5 | 7 | 18 | 6 | 3 |
AMP PEAK 12(12P12.1) WILD-TYPE | 9 | 29 | 35 | 12 | 18 | 19 |
P value = 6e-05 (Fisher's exact test), Q value = 0.042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 13(13Q12.13) MUTATED | 8 | 29 | 23 | 19 | 24 | 20 |
AMP PEAK 13(13Q12.13) WILD-TYPE | 2 | 5 | 19 | 11 | 0 | 2 |
P value = 3e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 14(13Q12.2) MUTATED | 8 | 29 | 21 | 20 | 24 | 20 |
AMP PEAK 14(13Q12.2) WILD-TYPE | 2 | 5 | 21 | 10 | 0 | 2 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 15(13Q22.1) MUTATED | 8 | 29 | 19 | 18 | 24 | 19 |
AMP PEAK 15(13Q22.1) WILD-TYPE | 2 | 5 | 23 | 12 | 0 | 3 |
P value = 7e-05 (Fisher's exact test), Q value = 0.049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 17(16P11.2) MUTATED | 3 | 17 | 2 | 6 | 11 | 6 |
AMP PEAK 17(16P11.2) WILD-TYPE | 7 | 17 | 40 | 24 | 13 | 16 |
P value = 2e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 18(17Q12) MUTATED | 2 | 19 | 7 | 10 | 0 | 5 |
AMP PEAK 18(17Q12) WILD-TYPE | 8 | 15 | 35 | 20 | 24 | 17 |
P value = 0.00021 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 19(17Q24.1) MUTATED | 1 | 17 | 7 | 8 | 0 | 4 |
AMP PEAK 19(17Q24.1) WILD-TYPE | 9 | 17 | 35 | 22 | 24 | 18 |
P value = 0.00018 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 21(20Q11.21) MUTATED | 10 | 34 | 31 | 23 | 24 | 21 |
AMP PEAK 21(20Q11.21) WILD-TYPE | 0 | 0 | 11 | 7 | 0 | 1 |
P value = 0.00033 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
AMP PEAK 22(20Q11.23) MUTATED | 10 | 34 | 32 | 23 | 24 | 21 |
AMP PEAK 22(20Q11.23) WILD-TYPE | 0 | 0 | 10 | 7 | 0 | 1 |
P value = 0.00031 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
DEL PEAK 1(1P36.11) MUTATED | 4 | 19 | 10 | 21 | 13 | 5 |
DEL PEAK 1(1P36.11) WILD-TYPE | 6 | 15 | 32 | 9 | 11 | 17 |
P value = 3e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
DEL PEAK 2(1P33) MUTATED | 7 | 17 | 3 | 11 | 10 | 2 |
DEL PEAK 2(1P33) WILD-TYPE | 3 | 17 | 39 | 19 | 14 | 20 |
P value = 2e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
DEL PEAK 3(1P13.2) MUTATED | 7 | 15 | 2 | 12 | 10 | 6 |
DEL PEAK 3(1P13.2) WILD-TYPE | 3 | 19 | 40 | 18 | 14 | 16 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
DEL PEAK 7(4P13) MUTATED | 4 | 13 | 5 | 16 | 17 | 4 |
DEL PEAK 7(4P13) WILD-TYPE | 6 | 21 | 37 | 14 | 7 | 18 |
P value = 2e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
DEL PEAK 8(4Q22.1) MUTATED | 5 | 19 | 8 | 18 | 18 | 4 |
DEL PEAK 8(4Q22.1) WILD-TYPE | 5 | 15 | 34 | 12 | 6 | 18 |
P value = 4e-05 (Fisher's exact test), Q value = 0.028
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
DEL PEAK 9(4Q35.1) MUTATED | 4 | 17 | 8 | 19 | 18 | 5 |
DEL PEAK 9(4Q35.1) WILD-TYPE | 6 | 17 | 34 | 11 | 6 | 17 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
DEL PEAK 15(8P23.2) MUTATED | 7 | 24 | 11 | 23 | 15 | 19 |
DEL PEAK 15(8P23.2) WILD-TYPE | 3 | 10 | 31 | 7 | 9 | 3 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
DEL PEAK 19(11Q22.3) MUTATED | 2 | 0 | 7 | 16 | 8 | 5 |
DEL PEAK 19(11Q22.3) WILD-TYPE | 8 | 34 | 35 | 14 | 16 | 17 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
DEL PEAK 28(18Q21.2) MUTATED | 10 | 34 | 27 | 27 | 23 | 22 |
DEL PEAK 28(18Q21.2) WILD-TYPE | 0 | 0 | 15 | 3 | 1 | 0 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
DEL PEAK 29(18Q22.1) MUTATED | 10 | 34 | 25 | 25 | 23 | 21 |
DEL PEAK 29(18Q22.1) WILD-TYPE | 0 | 0 | 17 | 5 | 1 | 1 |
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtype file = READ-TP.transferedmergedcluster.txt
-
Number of patients = 162
-
Number of significantly focal cnvs = 60
-
Number of molecular subtypes = 12
-
Exclude genes that fewer than K tumors have alterations, 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.