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 8 molecular subtypes across 295 patients, 26 significant findings detected with P value < 0.05 and Q value < 0.25.
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1p gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
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1q gain cnv correlated to 'CN_CNMF'.
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2p gain cnv correlated to 'CN_CNMF'.
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2q gain cnv correlated to 'CN_CNMF'.
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3q gain cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5p gain cnv correlated to 'CN_CNMF'.
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8q gain cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
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19q gain cnv correlated to 'CN_CNMF'.
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3p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.
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4p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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4q loss cnv correlated to 'CN_CNMF'.
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8p loss cnv correlated to 'CN_CNMF'.
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8q loss cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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9q loss cnv correlated to 'CN_CNMF'.
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11q loss cnv correlated to 'CN_CNMF'.
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18q loss cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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19p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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21q loss cnv correlated to 'CN_CNMF'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
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 | |
3q gain | 175 (59%) | 120 |
1e-05 (0.0064) |
0.00168 (0.983) |
0.0005 (0.305) |
0.00209 (1.00) |
0.357 (1.00) |
0.00028 (0.173) |
0.00345 (1.00) |
0.00023 (0.143) |
8q loss | 24 (8%) | 271 |
0.126 (1.00) |
0.0155 (1.00) |
5e-05 (0.0314) |
0.00034 (0.209) |
0.0169 (1.00) |
0.00027 (0.167) |
0.463 (1.00) |
0.0013 (0.764) |
18q loss | 73 (25%) | 222 |
0.616 (1.00) |
0.00083 (0.496) |
1e-05 (0.0064) |
0.0004 (0.246) |
0.0823 (1.00) |
0.00019 (0.118) |
0.078 (1.00) |
0.0195 (1.00) |
4p loss | 131 (44%) | 164 |
1e-05 (0.0064) |
0.068 (1.00) |
0.00119 (0.703) |
0.00047 (0.288) |
0.394 (1.00) |
0.00082 (0.492) |
1 (1.00) |
0.00029 (0.179) |
19p loss | 60 (20%) | 235 |
1e-05 (0.0064) |
0.0025 (1.00) |
0.00052 (0.317) |
0.00309 (1.00) |
0.0299 (1.00) |
0.00016 (0.0998) |
0.0503 (1.00) |
0.0145 (1.00) |
1p gain | 90 (31%) | 205 |
0.0094 (1.00) |
0.0148 (1.00) |
0.00125 (0.737) |
0.0429 (1.00) |
0.418 (1.00) |
6e-05 (0.0377) |
0.333 (1.00) |
0.0124 (1.00) |
1q gain | 140 (47%) | 155 |
0.00016 (0.0998) |
0.0164 (1.00) |
0.00762 (1.00) |
0.0797 (1.00) |
0.488 (1.00) |
0.00372 (1.00) |
0.155 (1.00) |
0.0101 (1.00) |
2p gain | 64 (22%) | 231 |
1e-05 (0.0064) |
0.153 (1.00) |
0.025 (1.00) |
0.0473 (1.00) |
0.169 (1.00) |
0.00085 (0.507) |
0.182 (1.00) |
0.389 (1.00) |
2q gain | 37 (13%) | 258 |
0.00016 (0.0998) |
0.397 (1.00) |
0.0181 (1.00) |
0.00592 (1.00) |
0.161 (1.00) |
0.00251 (1.00) |
0.157 (1.00) |
0.661 (1.00) |
5p gain | 113 (38%) | 182 |
1e-05 (0.0064) |
0.0975 (1.00) |
0.0271 (1.00) |
0.00489 (1.00) |
0.0345 (1.00) |
0.00788 (1.00) |
0.496 (1.00) |
0.0294 (1.00) |
8q gain | 91 (31%) | 204 |
0.271 (1.00) |
0.26 (1.00) |
0.0781 (1.00) |
0.00947 (1.00) |
0.166 (1.00) |
0.0067 (1.00) |
0.616 (1.00) |
0.00013 (0.0814) |
19q gain | 72 (24%) | 223 |
1e-05 (0.0064) |
0.102 (1.00) |
0.357 (1.00) |
0.0566 (1.00) |
0.68 (1.00) |
0.0952 (1.00) |
0.816 (1.00) |
0.802 (1.00) |
3p loss | 82 (28%) | 213 |
0.604 (1.00) |
0.00255 (1.00) |
0.00928 (1.00) |
3e-05 (0.0189) |
0.0269 (1.00) |
0.00385 (1.00) |
0.00213 (1.00) |
0.00082 (0.492) |
4q loss | 93 (32%) | 202 |
1e-05 (0.0064) |
0.399 (1.00) |
0.121 (1.00) |
0.00089 (0.53) |
0.961 (1.00) |
0.0506 (1.00) |
0.0545 (1.00) |
0.67 (1.00) |
8p loss | 82 (28%) | 213 |
7e-05 (0.0439) |
0.274 (1.00) |
0.014 (1.00) |
0.614 (1.00) |
0.0189 (1.00) |
0.0445 (1.00) |
0.0104 (1.00) |
0.0692 (1.00) |
9q loss | 51 (17%) | 244 |
0.00015 (0.0937) |
0.162 (1.00) |
0.0252 (1.00) |
0.0436 (1.00) |
0.471 (1.00) |
0.437 (1.00) |
0.00203 (1.00) |
0.175 (1.00) |
11q loss | 115 (39%) | 180 |
2e-05 (0.0126) |
0.321 (1.00) |
0.357 (1.00) |
0.305 (1.00) |
0.726 (1.00) |
0.00759 (1.00) |
0.805 (1.00) |
0.47 (1.00) |
21q loss | 49 (17%) | 246 |
2e-05 (0.0126) |
0.0387 (1.00) |
0.023 (1.00) |
0.00096 (0.571) |
0.303 (1.00) |
0.0275 (1.00) |
0.527 (1.00) |
0.774 (1.00) |
3p gain | 71 (24%) | 224 |
0.515 (1.00) |
0.111 (1.00) |
0.168 (1.00) |
0.328 (1.00) |
0.429 (1.00) |
0.579 (1.00) |
0.428 (1.00) |
0.557 (1.00) |
4p gain | 11 (4%) | 284 |
0.538 (1.00) |
0.893 (1.00) |
0.653 (1.00) |
0.454 (1.00) |
0.54 (1.00) |
0.598 (1.00) |
0.924 (1.00) |
0.875 (1.00) |
4q gain | 16 (5%) | 279 |
0.322 (1.00) |
0.0973 (1.00) |
0.94 (1.00) |
0.362 (1.00) |
0.897 (1.00) |
0.336 (1.00) |
0.898 (1.00) |
0.868 (1.00) |
5q gain | 44 (15%) | 251 |
0.00189 (1.00) |
0.88 (1.00) |
0.181 (1.00) |
0.771 (1.00) |
0.893 (1.00) |
0.956 (1.00) |
0.634 (1.00) |
0.874 (1.00) |
6p gain | 52 (18%) | 243 |
0.122 (1.00) |
0.00737 (1.00) |
0.00376 (1.00) |
0.035 (1.00) |
0.544 (1.00) |
0.0364 (1.00) |
0.308 (1.00) |
0.0995 (1.00) |
6q gain | 36 (12%) | 259 |
0.128 (1.00) |
0.114 (1.00) |
0.0854 (1.00) |
0.107 (1.00) |
0.337 (1.00) |
0.192 (1.00) |
0.337 (1.00) |
0.209 (1.00) |
7p gain | 38 (13%) | 257 |
0.211 (1.00) |
0.0377 (1.00) |
0.0161 (1.00) |
0.259 (1.00) |
0.00052 (0.317) |
0.0955 (1.00) |
0.0597 (1.00) |
0.137 (1.00) |
7q gain | 37 (13%) | 258 |
0.0491 (1.00) |
0.148 (1.00) |
0.13 (1.00) |
0.375 (1.00) |
0.00098 (0.582) |
0.19 (1.00) |
0.0104 (1.00) |
0.0615 (1.00) |
8p gain | 53 (18%) | 242 |
0.777 (1.00) |
0.787 (1.00) |
0.0955 (1.00) |
0.366 (1.00) |
0.722 (1.00) |
0.0266 (1.00) |
0.941 (1.00) |
0.0287 (1.00) |
9p gain | 49 (17%) | 246 |
0.645 (1.00) |
0.231 (1.00) |
0.528 (1.00) |
0.0352 (1.00) |
0.327 (1.00) |
0.0174 (1.00) |
0.787 (1.00) |
0.0268 (1.00) |
9q gain | 47 (16%) | 248 |
0.665 (1.00) |
0.00387 (1.00) |
0.0546 (1.00) |
0.00044 (0.27) |
0.0246 (1.00) |
0.00336 (1.00) |
0.291 (1.00) |
0.00053 (0.322) |
10p gain | 25 (8%) | 270 |
0.0749 (1.00) |
0.693 (1.00) |
0.155 (1.00) |
0.435 (1.00) |
0.105 (1.00) |
0.697 (1.00) |
0.862 (1.00) |
0.319 (1.00) |
10q gain | 17 (6%) | 278 |
0.623 (1.00) |
0.72 (1.00) |
0.624 (1.00) |
0.266 (1.00) |
0.356 (1.00) |
0.915 (1.00) |
0.624 (1.00) |
0.707 (1.00) |
11p gain | 9 (3%) | 286 |
0.761 (1.00) |
0.919 (1.00) |
0.523 (1.00) |
0.168 (1.00) |
0.632 (1.00) |
0.0201 (1.00) |
0.834 (1.00) |
0.805 (1.00) |
11q gain | 8 (3%) | 287 |
0.0182 (1.00) |
0.744 (1.00) |
0.0091 (1.00) |
0.00308 (1.00) |
0.202 (1.00) |
0.0224 (1.00) |
0.266 (1.00) |
0.579 (1.00) |
12p gain | 53 (18%) | 242 |
0.238 (1.00) |
0.266 (1.00) |
0.563 (1.00) |
0.413 (1.00) |
0.708 (1.00) |
0.347 (1.00) |
0.903 (1.00) |
0.902 (1.00) |
12q gain | 50 (17%) | 245 |
0.176 (1.00) |
0.158 (1.00) |
0.594 (1.00) |
0.397 (1.00) |
0.924 (1.00) |
0.27 (1.00) |
1 (1.00) |
0.88 (1.00) |
13q gain | 24 (8%) | 271 |
0.963 (1.00) |
0.233 (1.00) |
0.036 (1.00) |
0.107 (1.00) |
0.00596 (1.00) |
0.0681 (1.00) |
0.0995 (1.00) |
0.108 (1.00) |
14q gain | 47 (16%) | 248 |
0.047 (1.00) |
0.296 (1.00) |
0.26 (1.00) |
0.448 (1.00) |
0.284 (1.00) |
0.149 (1.00) |
0.496 (1.00) |
0.988 (1.00) |
15q gain | 52 (18%) | 243 |
0.109 (1.00) |
0.644 (1.00) |
0.931 (1.00) |
0.514 (1.00) |
0.733 (1.00) |
0.764 (1.00) |
0.604 (1.00) |
0.218 (1.00) |
16p gain | 44 (15%) | 251 |
0.00774 (1.00) |
0.312 (1.00) |
0.718 (1.00) |
0.136 (1.00) |
0.0973 (1.00) |
0.099 (1.00) |
0.881 (1.00) |
0.58 (1.00) |
16q gain | 40 (14%) | 255 |
0.456 (1.00) |
0.0775 (1.00) |
0.373 (1.00) |
0.0468 (1.00) |
0.0919 (1.00) |
0.0871 (1.00) |
0.477 (1.00) |
0.467 (1.00) |
17p gain | 22 (7%) | 273 |
0.00075 (0.451) |
0.00049 (0.3) |
0.593 (1.00) |
0.398 (1.00) |
0.247 (1.00) |
0.65 (1.00) |
0.078 (1.00) |
0.504 (1.00) |
17q gain | 42 (14%) | 253 |
0.0155 (1.00) |
0.0961 (1.00) |
0.426 (1.00) |
0.193 (1.00) |
0.158 (1.00) |
0.809 (1.00) |
0.266 (1.00) |
0.787 (1.00) |
18p gain | 49 (17%) | 246 |
0.0342 (1.00) |
0.165 (1.00) |
0.45 (1.00) |
0.238 (1.00) |
0.92 (1.00) |
0.286 (1.00) |
0.786 (1.00) |
0.689 (1.00) |
18q gain | 32 (11%) | 263 |
0.133 (1.00) |
0.277 (1.00) |
0.683 (1.00) |
0.288 (1.00) |
0.339 (1.00) |
0.339 (1.00) |
0.425 (1.00) |
0.393 (1.00) |
19p gain | 44 (15%) | 251 |
0.0166 (1.00) |
0.169 (1.00) |
0.541 (1.00) |
0.839 (1.00) |
0.936 (1.00) |
0.193 (1.00) |
0.635 (1.00) |
0.593 (1.00) |
20p gain | 100 (34%) | 195 |
0.00065 (0.393) |
0.0312 (1.00) |
0.273 (1.00) |
0.0444 (1.00) |
0.0501 (1.00) |
0.102 (1.00) |
0.661 (1.00) |
0.593 (1.00) |
20q gain | 115 (39%) | 180 |
0.00466 (1.00) |
0.0996 (1.00) |
0.265 (1.00) |
0.0294 (1.00) |
0.462 (1.00) |
0.0331 (1.00) |
0.807 (1.00) |
0.345 (1.00) |
21q gain | 37 (13%) | 258 |
0.355 (1.00) |
0.704 (1.00) |
0.164 (1.00) |
0.518 (1.00) |
0.754 (1.00) |
0.756 (1.00) |
0.922 (1.00) |
0.602 (1.00) |
22q gain | 29 (10%) | 266 |
0.148 (1.00) |
0.489 (1.00) |
0.751 (1.00) |
0.209 (1.00) |
0.778 (1.00) |
0.332 (1.00) |
0.147 (1.00) |
0.961 (1.00) |
xq gain | 40 (14%) | 255 |
0.0145 (1.00) |
0.0439 (1.00) |
0.136 (1.00) |
0.189 (1.00) |
0.228 (1.00) |
0.17 (1.00) |
0.313 (1.00) |
0.149 (1.00) |
1p loss | 13 (4%) | 282 |
0.0539 (1.00) |
0.139 (1.00) |
0.0111 (1.00) |
0.0545 (1.00) |
0.134 (1.00) |
0.201 (1.00) |
0.445 (1.00) |
0.675 (1.00) |
1q loss | 9 (3%) | 286 |
0.0205 (1.00) |
0.33 (1.00) |
0.0233 (1.00) |
0.169 (1.00) |
0.0916 (1.00) |
0.441 (1.00) |
0.475 (1.00) |
0.742 (1.00) |
2p loss | 19 (6%) | 276 |
0.653 (1.00) |
0.829 (1.00) |
0.193 (1.00) |
0.257 (1.00) |
0.524 (1.00) |
0.214 (1.00) |
0.511 (1.00) |
0.347 (1.00) |
2q loss | 35 (12%) | 260 |
0.801 (1.00) |
0.36 (1.00) |
0.052 (1.00) |
0.0628 (1.00) |
0.146 (1.00) |
0.0216 (1.00) |
0.862 (1.00) |
0.205 (1.00) |
3q loss | 14 (5%) | 281 |
0.3 (1.00) |
0.247 (1.00) |
0.227 (1.00) |
0.562 (1.00) |
0.0731 (1.00) |
0.371 (1.00) |
0.257 (1.00) |
0.151 (1.00) |
5p loss | 19 (6%) | 276 |
0.719 (1.00) |
0.539 (1.00) |
0.901 (1.00) |
0.573 (1.00) |
0.599 (1.00) |
0.592 (1.00) |
0.685 (1.00) |
0.108 (1.00) |
5q loss | 51 (17%) | 244 |
0.00182 (1.00) |
0.513 (1.00) |
0.485 (1.00) |
0.77 (1.00) |
0.0286 (1.00) |
0.267 (1.00) |
0.426 (1.00) |
0.0456 (1.00) |
6p loss | 47 (16%) | 248 |
0.15 (1.00) |
0.0904 (1.00) |
0.0456 (1.00) |
0.117 (1.00) |
0.445 (1.00) |
0.123 (1.00) |
0.897 (1.00) |
0.123 (1.00) |
6q loss | 74 (25%) | 221 |
0.00479 (1.00) |
0.0472 (1.00) |
0.105 (1.00) |
0.201 (1.00) |
0.207 (1.00) |
0.0342 (1.00) |
0.244 (1.00) |
0.163 (1.00) |
7p loss | 26 (9%) | 269 |
0.0465 (1.00) |
0.34 (1.00) |
0.027 (1.00) |
0.0191 (1.00) |
0.214 (1.00) |
0.826 (1.00) |
0.556 (1.00) |
0.0542 (1.00) |
7q loss | 37 (13%) | 258 |
0.0972 (1.00) |
0.177 (1.00) |
0.0402 (1.00) |
0.196 (1.00) |
0.145 (1.00) |
0.254 (1.00) |
0.57 (1.00) |
0.572 (1.00) |
9p loss | 54 (18%) | 241 |
0.00132 (0.775) |
0.967 (1.00) |
0.411 (1.00) |
0.672 (1.00) |
0.928 (1.00) |
0.953 (1.00) |
0.0512 (1.00) |
0.796 (1.00) |
10p loss | 66 (22%) | 229 |
0.00053 (0.322) |
0.579 (1.00) |
0.732 (1.00) |
0.232 (1.00) |
0.711 (1.00) |
0.602 (1.00) |
0.113 (1.00) |
0.739 (1.00) |
10q loss | 74 (25%) | 221 |
0.00068 (0.411) |
0.8 (1.00) |
0.781 (1.00) |
0.162 (1.00) |
0.76 (1.00) |
0.137 (1.00) |
0.243 (1.00) |
0.554 (1.00) |
11p loss | 100 (34%) | 195 |
0.00127 (0.748) |
0.152 (1.00) |
0.332 (1.00) |
0.188 (1.00) |
0.635 (1.00) |
0.0613 (1.00) |
0.947 (1.00) |
0.221 (1.00) |
12p loss | 40 (14%) | 255 |
0.0222 (1.00) |
0.32 (1.00) |
0.463 (1.00) |
0.67 (1.00) |
0.27 (1.00) |
0.803 (1.00) |
0.308 (1.00) |
0.207 (1.00) |
12q loss | 15 (5%) | 280 |
0.361 (1.00) |
0.498 (1.00) |
1 (1.00) |
0.455 (1.00) |
0.196 (1.00) |
0.536 (1.00) |
0.238 (1.00) |
0.91 (1.00) |
13q loss | 80 (27%) | 215 |
0.00074 (0.446) |
0.202 (1.00) |
0.0154 (1.00) |
0.00978 (1.00) |
0.102 (1.00) |
0.00318 (1.00) |
0.636 (1.00) |
0.107 (1.00) |
14q loss | 35 (12%) | 260 |
0.00103 (0.611) |
0.358 (1.00) |
0.0335 (1.00) |
0.0861 (1.00) |
0.851 (1.00) |
0.0991 (1.00) |
0.0154 (1.00) |
0.625 (1.00) |
15q loss | 47 (16%) | 248 |
0.0584 (1.00) |
0.414 (1.00) |
0.48 (1.00) |
0.336 (1.00) |
0.294 (1.00) |
0.511 (1.00) |
0.263 (1.00) |
0.693 (1.00) |
16p loss | 34 (12%) | 261 |
0.103 (1.00) |
0.0818 (1.00) |
0.162 (1.00) |
0.224 (1.00) |
0.412 (1.00) |
0.0104 (1.00) |
0.0539 (1.00) |
0.202 (1.00) |
16q loss | 44 (15%) | 251 |
0.142 (1.00) |
0.0151 (1.00) |
0.00607 (1.00) |
0.0473 (1.00) |
0.00949 (1.00) |
0.00117 (0.693) |
0.0899 (1.00) |
0.0137 (1.00) |
17p loss | 95 (32%) | 200 |
0.00133 (0.779) |
0.191 (1.00) |
0.104 (1.00) |
0.0426 (1.00) |
0.137 (1.00) |
0.056 (1.00) |
0.541 (1.00) |
0.292 (1.00) |
17q loss | 37 (13%) | 258 |
0.173 (1.00) |
0.456 (1.00) |
0.152 (1.00) |
0.0786 (1.00) |
0.0484 (1.00) |
0.332 (1.00) |
0.568 (1.00) |
0.19 (1.00) |
18p loss | 55 (19%) | 240 |
0.392 (1.00) |
0.0376 (1.00) |
0.00063 (0.382) |
0.0109 (1.00) |
0.42 (1.00) |
0.0346 (1.00) |
0.303 (1.00) |
0.151 (1.00) |
19q loss | 29 (10%) | 266 |
0.22 (1.00) |
0.0533 (1.00) |
0.559 (1.00) |
0.42 (1.00) |
0.271 (1.00) |
0.107 (1.00) |
0.2 (1.00) |
0.0253 (1.00) |
20p loss | 23 (8%) | 272 |
0.791 (1.00) |
0.0549 (1.00) |
0.0555 (1.00) |
0.224 (1.00) |
0.116 (1.00) |
0.148 (1.00) |
0.135 (1.00) |
0.366 (1.00) |
20q loss | 10 (3%) | 285 |
0.509 (1.00) |
0.0183 (1.00) |
0.235 (1.00) |
0.0461 (1.00) |
1 (1.00) |
0.65 (1.00) |
1 (1.00) |
0.516 (1.00) |
22q loss | 71 (24%) | 224 |
0.00242 (1.00) |
0.196 (1.00) |
0.023 (1.00) |
0.00078 (0.469) |
0.912 (1.00) |
0.211 (1.00) |
0.627 (1.00) |
0.794 (1.00) |
xq loss | 58 (20%) | 237 |
0.0303 (1.00) |
0.0638 (1.00) |
0.15 (1.00) |
0.179 (1.00) |
0.204 (1.00) |
0.941 (1.00) |
0.0461 (1.00) |
0.471 (1.00) |
P value = 6e-05 (Fisher's exact test), Q value = 0.038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 95 | 72 | 25 | 43 |
1P GAIN MUTATED | 9 | 31 | 35 | 9 | 6 |
1P GAIN WILD-TYPE | 51 | 64 | 37 | 16 | 37 |
P value = 0.00016 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
1Q GAIN MUTATED | 46 | 34 | 60 |
1Q GAIN WILD-TYPE | 83 | 39 | 33 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
2P GAIN MUTATED | 14 | 32 | 18 |
2P GAIN WILD-TYPE | 115 | 41 | 75 |
P value = 0.00016 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
2Q GAIN MUTATED | 8 | 20 | 9 |
2Q GAIN WILD-TYPE | 121 | 53 | 84 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
3Q GAIN MUTATED | 61 | 40 | 74 |
3Q GAIN WILD-TYPE | 68 | 33 | 19 |
P value = 0.00028 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 95 | 72 | 25 | 43 |
3Q GAIN MUTATED | 23 | 59 | 55 | 16 | 22 |
3Q GAIN WILD-TYPE | 37 | 36 | 17 | 9 | 21 |
P value = 0.00023 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 64 | 50 | 26 | 142 |
3Q GAIN MUTATED | 26 | 36 | 22 | 83 |
3Q GAIN WILD-TYPE | 38 | 14 | 4 | 59 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
5P GAIN MUTATED | 31 | 48 | 34 |
5P GAIN WILD-TYPE | 98 | 25 | 59 |
P value = 0.00013 (Fisher's exact test), Q value = 0.081
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 64 | 50 | 26 | 142 |
8Q GAIN MUTATED | 7 | 15 | 7 | 57 |
8Q GAIN WILD-TYPE | 57 | 35 | 19 | 85 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
19Q GAIN MUTATED | 16 | 38 | 18 |
19Q GAIN WILD-TYPE | 113 | 35 | 75 |
P value = 3e-05 (Fisher's exact test), Q value = 0.019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 154 | 33 |
3P LOSS MUTATED | 5 | 59 | 6 |
3P LOSS WILD-TYPE | 51 | 95 | 27 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
4P LOSS MUTATED | 32 | 48 | 51 |
4P LOSS WILD-TYPE | 97 | 25 | 42 |
P value = 0.00029 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 64 | 50 | 26 | 142 |
4P LOSS MUTATED | 15 | 26 | 17 | 66 |
4P LOSS WILD-TYPE | 49 | 24 | 9 | 76 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
4Q LOSS MUTATED | 16 | 45 | 32 |
4Q LOSS WILD-TYPE | 113 | 28 | 61 |
P value = 7e-05 (Fisher's exact test), Q value = 0.044
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
8P LOSS MUTATED | 23 | 34 | 25 |
8P LOSS WILD-TYPE | 106 | 39 | 68 |
P value = 5e-05 (Fisher's exact test), Q value = 0.031
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 77 | 101 | 65 |
8Q LOSS MUTATED | 12 | 0 | 8 |
8Q LOSS WILD-TYPE | 65 | 101 | 57 |
P value = 0.00034 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 154 | 33 |
8Q LOSS MUTATED | 11 | 5 | 4 |
8Q LOSS WILD-TYPE | 45 | 149 | 29 |
P value = 0.00027 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 95 | 72 | 25 | 43 |
8Q LOSS MUTATED | 12 | 3 | 1 | 2 | 6 |
8Q LOSS WILD-TYPE | 48 | 92 | 71 | 23 | 37 |
P value = 0.00015 (Fisher's exact test), Q value = 0.094
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
9Q LOSS MUTATED | 11 | 23 | 17 |
9Q LOSS WILD-TYPE | 118 | 50 | 76 |
P value = 2e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
11Q LOSS MUTATED | 33 | 28 | 54 |
11Q LOSS WILD-TYPE | 96 | 45 | 39 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 77 | 101 | 65 |
18Q LOSS MUTATED | 26 | 9 | 25 |
18Q LOSS WILD-TYPE | 51 | 92 | 40 |
P value = 4e-04 (Fisher's exact test), Q value = 0.25
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 154 | 33 |
18Q LOSS MUTATED | 23 | 25 | 12 |
18Q LOSS WILD-TYPE | 33 | 129 | 21 |
P value = 0.00019 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 95 | 72 | 25 | 43 |
18Q LOSS MUTATED | 25 | 15 | 11 | 5 | 17 |
18Q LOSS WILD-TYPE | 35 | 80 | 61 | 20 | 26 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
19P LOSS MUTATED | 14 | 31 | 15 |
19P LOSS WILD-TYPE | 115 | 42 | 78 |
P value = 0.00016 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 60 | 95 | 72 | 25 | 43 |
19P LOSS MUTATED | 13 | 15 | 6 | 12 | 14 |
19P LOSS WILD-TYPE | 47 | 80 | 66 | 13 | 29 |
P value = 2e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 73 | 93 |
21Q LOSS MUTATED | 9 | 24 | 16 |
21Q LOSS WILD-TYPE | 120 | 49 | 77 |
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtypes file = CESC-TP.transferedmergedcluster.txt
-
Number of patients = 295
-
Number of significantly arm-level cnvs = 80
-
Number of molecular subtypes = 8
-
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.