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 10 molecular subtypes across 56 patients, 26 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_2q13 cnv correlated to 'MRNASEQ_CNMF'.
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amp_3p25.1 cnv correlated to 'CN_CNMF'.
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amp_3q26.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_4p16.3 cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
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amp_8q24.21 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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amp_13q31.3 cnv correlated to 'MIRSEQ_CNMF'.
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amp_16p11.2 cnv correlated to 'RPPA_CNMF'.
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amp_19q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_20q11.21 cnv correlated to 'CN_CNMF'.
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del_4q22.1 cnv correlated to 'MIRSEQ_MATURE_CNMF'.
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del_4q34.3 cnv correlated to 'MIRSEQ_MATURE_CNMF'.
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del_5q12.1 cnv correlated to 'METHLYATION_CNMF'.
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del_9p23 cnv correlated to 'RPPA_CNMF'.
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del_12q24.31 cnv correlated to 'RPPA_CHIERARCHICAL'.
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del_17p13.1 cnv correlated to 'MIRSEQ_MATURE_CNMF'.
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del_18q22.2 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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del_19p13.3 cnv correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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del_19q13.33 cnv correlated to 'MRNASEQ_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 | |
del 19p13 3 | 44 (79%) | 12 |
0.101 (0.427) |
0.102 (0.427) |
0.137 (0.458) |
0.103 (0.427) |
0.00737 (0.232) |
0.0886 (0.399) |
0.00285 (0.214) |
0.00923 (0.239) |
0.00141 (0.163) |
0.0215 (0.319) |
amp 3q26 2 | 37 (66%) | 19 |
0.00052 (0.104) |
0.00569 (0.232) |
0.45 (0.689) |
0.129 (0.451) |
0.262 (0.598) |
0.158 (0.478) |
1 (1.00) |
0.242 (0.573) |
0.0594 (0.39) |
0.184 (0.513) |
amp 4p16 3 | 25 (45%) | 31 |
0.0019 (0.163) |
0.456 (0.689) |
0.71 (0.862) |
0.01 (0.239) |
0.163 (0.48) |
0.187 (0.515) |
0.738 (0.872) |
0.289 (0.61) |
0.845 (0.927) |
0.532 (0.729) |
amp 8q24 21 | 40 (71%) | 16 |
0.00691 (0.232) |
0.446 (0.689) |
0.325 (0.615) |
0.645 (0.813) |
0.009 (0.239) |
0.118 (0.446) |
0.0611 (0.39) |
0.0633 (0.39) |
0.0861 (0.397) |
0.0221 (0.319) |
amp 19q12 | 45 (80%) | 11 |
0.00027 (0.104) |
0.00037 (0.104) |
0.185 (0.513) |
0.248 (0.58) |
0.518 (0.725) |
0.02 (0.319) |
0.457 (0.689) |
0.502 (0.71) |
0.297 (0.612) |
0.433 (0.682) |
del 18q22 2 | 26 (46%) | 30 |
0.147 (0.467) |
0.527 (0.729) |
0.436 (0.682) |
0.537 (0.731) |
0.458 (0.689) |
0.357 (0.63) |
0.0065 (0.232) |
0.0771 (0.397) |
0.00934 (0.239) |
0.0253 (0.32) |
amp 2q13 | 29 (52%) | 27 |
0.432 (0.682) |
0.0972 (0.417) |
0.505 (0.711) |
0.488 (0.704) |
0.00773 (0.232) |
0.316 (0.614) |
1 (1.00) |
0.665 (0.828) |
0.721 (0.865) |
0.728 (0.867) |
amp 3p25 1 | 20 (36%) | 36 |
0.0103 (0.239) |
0.754 (0.877) |
0.762 (0.877) |
0.054 (0.39) |
0.32 (0.615) |
0.113 (0.446) |
0.0423 (0.379) |
0.0652 (0.39) |
0.229 (0.562) |
0.0671 (0.39) |
amp 13q31 3 | 25 (45%) | 31 |
0.486 (0.704) |
0.481 (0.703) |
0.228 (0.562) |
0.385 (0.652) |
0.23 (0.562) |
0.116 (0.446) |
0.00716 (0.232) |
0.0371 (0.379) |
0.0246 (0.32) |
0.0534 (0.39) |
amp 16p11 2 | 20 (36%) | 36 |
0.017 (0.309) |
0.0755 (0.397) |
0.00994 (0.239) |
0.0667 (0.39) |
0.766 (0.877) |
0.0727 (0.397) |
0.776 (0.878) |
0.411 (0.677) |
0.585 (0.771) |
0.209 (0.54) |
amp 20q11 21 | 48 (86%) | 8 |
0.00656 (0.232) |
0.0965 (0.417) |
0.113 (0.446) |
0.415 (0.677) |
0.464 (0.689) |
0.423 (0.677) |
0.0817 (0.397) |
0.14 (0.458) |
0.275 (0.6) |
0.275 (0.6) |
del 4q22 1 | 37 (66%) | 19 |
0.0326 (0.377) |
0.0675 (0.39) |
0.138 (0.458) |
0.238 (0.571) |
0.119 (0.446) |
0.154 (0.475) |
0.0203 (0.319) |
0.126 (0.45) |
0.00732 (0.232) |
0.057 (0.39) |
del 4q34 3 | 37 (66%) | 19 |
0.0379 (0.379) |
0.0228 (0.319) |
0.328 (0.615) |
0.135 (0.458) |
0.0413 (0.379) |
0.0409 (0.379) |
0.03 (0.367) |
0.201 (0.533) |
0.00688 (0.232) |
0.125 (0.45) |
del 5q12 1 | 26 (46%) | 30 |
0.207 (0.539) |
0.00516 (0.232) |
0.594 (0.778) |
0.159 (0.478) |
0.63 (0.804) |
0.452 (0.689) |
0.942 (0.98) |
0.297 (0.612) |
0.566 (0.756) |
0.445 (0.689) |
del 9p23 | 34 (61%) | 22 |
0.202 (0.533) |
0.67 (0.832) |
0.00502 (0.232) |
0.0156 (0.303) |
0.31 (0.613) |
0.325 (0.615) |
0.825 (0.915) |
0.426 (0.679) |
0.769 (0.877) |
0.121 (0.446) |
del 12q24 31 | 20 (36%) | 36 |
0.602 (0.781) |
0.756 (0.877) |
0.0234 (0.319) |
0.00166 (0.163) |
0.197 (0.533) |
0.256 (0.592) |
0.775 (0.878) |
0.888 (0.954) |
0.233 (0.562) |
0.931 (0.976) |
del 17p13 1 | 42 (75%) | 14 |
0.286 (0.608) |
0.0442 (0.385) |
0.13 (0.451) |
0.239 (0.571) |
0.0469 (0.387) |
0.423 (0.677) |
0.108 (0.446) |
0.182 (0.509) |
0.00487 (0.232) |
0.0837 (0.397) |
del 19q13 33 | 17 (30%) | 39 |
0.114 (0.446) |
0.0231 (0.319) |
0.247 (0.58) |
0.0636 (0.39) |
0.00182 (0.163) |
0.0353 (0.379) |
0.281 (0.604) |
0.0382 (0.379) |
0.147 (0.467) |
0.0126 (0.28) |
amp 1q22 | 42 (75%) | 14 |
0.68 (0.841) |
0.431 (0.682) |
0.0772 (0.397) |
0.487 (0.704) |
0.459 (0.689) |
0.294 (0.612) |
0.13 (0.451) |
0.187 (0.515) |
0.0589 (0.39) |
0.267 (0.598) |
amp 2p14 | 28 (50%) | 28 |
0.384 (0.652) |
0.0871 (0.397) |
0.947 (0.983) |
0.489 (0.704) |
0.0137 (0.292) |
0.08 (0.397) |
0.314 (0.613) |
0.248 (0.58) |
0.252 (0.587) |
0.362 (0.635) |
amp 5p13 2 | 26 (46%) | 30 |
0.0919 (0.4) |
0.545 (0.737) |
0.233 (0.562) |
0.308 (0.613) |
0.127 (0.45) |
0.0556 (0.39) |
0.264 (0.598) |
0.0458 (0.387) |
0.327 (0.615) |
0.175 (0.496) |
amp 6p24 2 | 37 (66%) | 19 |
0.449 (0.689) |
0.98 (1.00) |
0.988 (1.00) |
0.326 (0.615) |
0.83 (0.918) |
0.356 (0.63) |
0.723 (0.865) |
0.497 (0.709) |
0.769 (0.877) |
0.768 (0.877) |
amp 8p11 21 | 33 (59%) | 23 |
0.351 (0.629) |
0.727 (0.867) |
0.15 (0.471) |
0.092 (0.4) |
0.435 (0.682) |
0.557 (0.749) |
0.687 (0.846) |
1 (1.00) |
0.641 (0.81) |
0.601 (0.781) |
amp 8q11 23 | 38 (68%) | 18 |
0.061 (0.39) |
0.0823 (0.397) |
0.312 (0.613) |
0.201 (0.533) |
0.0471 (0.387) |
0.166 (0.482) |
1 (1.00) |
0.922 (0.975) |
0.737 (0.872) |
0.857 (0.933) |
amp 8q24 21 | 42 (75%) | 14 |
0.0141 (0.292) |
0.753 (0.877) |
0.464 (0.689) |
0.952 (0.987) |
0.211 (0.54) |
0.337 (0.626) |
0.0504 (0.39) |
0.0326 (0.377) |
0.0598 (0.39) |
0.015 (0.301) |
amp 10q22 2 | 26 (46%) | 30 |
0.21 (0.54) |
0.732 (0.869) |
0.303 (0.613) |
0.344 (0.629) |
0.932 (0.976) |
0.925 (0.976) |
0.352 (0.629) |
0.739 (0.872) |
0.353 (0.629) |
0.428 (0.681) |
amp 11q13 1 | 19 (34%) | 37 |
0.323 (0.615) |
0.788 (0.886) |
0.422 (0.677) |
0.269 (0.598) |
0.109 (0.446) |
0.304 (0.613) |
0.582 (0.77) |
1 (1.00) |
0.514 (0.721) |
0.975 (1.00) |
amp 12q12 | 22 (39%) | 34 |
0.233 (0.562) |
0.232 (0.562) |
0.597 (0.78) |
0.0786 (0.397) |
0.314 (0.613) |
0.409 (0.677) |
0.501 (0.71) |
1 (1.00) |
0.529 (0.729) |
0.954 (0.987) |
amp 12q15 | 17 (30%) | 39 |
0.53 (0.729) |
0.661 (0.826) |
0.831 (0.918) |
0.708 (0.862) |
0.122 (0.446) |
0.698 (0.855) |
0.497 (0.709) |
0.164 (0.482) |
0.571 (0.758) |
0.231 (0.562) |
amp 17q12 | 27 (48%) | 29 |
1 (1.00) |
0.172 (0.493) |
0.934 (0.976) |
0.764 (0.877) |
0.322 (0.615) |
0.461 (0.689) |
0.135 (0.458) |
0.783 (0.883) |
0.498 (0.709) |
1 (1.00) |
amp 17q25 1 | 32 (57%) | 24 |
0.353 (0.629) |
0.123 (0.447) |
0.852 (0.931) |
0.724 (0.865) |
0.6 (0.781) |
0.307 (0.613) |
0.609 (0.787) |
0.719 (0.865) |
0.278 (0.602) |
0.66 (0.826) |
amp 19p13 2 | 19 (34%) | 37 |
0.0874 (0.397) |
0.35 (0.629) |
0.417 (0.677) |
0.663 (0.826) |
0.733 (0.869) |
0.323 (0.615) |
0.2 (0.533) |
0.276 (0.601) |
0.0611 (0.39) |
0.27 (0.598) |
amp 20q11 21 | 48 (86%) | 8 |
0.0861 (0.397) |
0.0704 (0.395) |
0.0468 (0.387) |
0.416 (0.677) |
0.162 (0.48) |
0.317 (0.614) |
0.159 (0.478) |
0.35 (0.629) |
0.273 (0.6) |
0.558 (0.749) |
amp xp11 21 | 28 (50%) | 28 |
0.142 (0.462) |
0.308 (0.613) |
0.18 (0.508) |
0.156 (0.478) |
0.242 (0.573) |
0.299 (0.612) |
0.0319 (0.377) |
0.101 (0.427) |
0.498 (0.709) |
0.0653 (0.39) |
del 1p36 21 | 19 (34%) | 37 |
0.188 (0.516) |
0.0638 (0.39) |
0.775 (0.878) |
0.896 (0.959) |
0.598 (0.78) |
0.0816 (0.397) |
0.0513 (0.39) |
0.0242 (0.32) |
0.288 (0.61) |
0.0586 (0.39) |
del 2q22 1 | 11 (20%) | 45 |
0.291 (0.61) |
0.333 (0.621) |
0.755 (0.877) |
0.473 (0.695) |
0.174 (0.495) |
0.168 (0.484) |
0.0184 (0.319) |
0.554 (0.747) |
0.459 (0.689) |
0.919 (0.975) |
del 3p14 2 | 37 (66%) | 19 |
0.419 (0.677) |
0.562 (0.753) |
0.702 (0.857) |
0.769 (0.877) |
0.503 (0.711) |
0.472 (0.695) |
1 (1.00) |
0.769 (0.877) |
0.36 (0.634) |
0.901 (0.959) |
del 3q13 31 | 22 (39%) | 34 |
0.192 (0.524) |
0.521 (0.726) |
0.217 (0.555) |
0.121 (0.446) |
0.64 (0.81) |
0.0666 (0.39) |
0.499 (0.709) |
0.456 (0.689) |
0.876 (0.947) |
0.825 (0.915) |
del 6q26 | 10 (18%) | 46 |
0.13 (0.451) |
0.963 (0.995) |
0.0497 (0.39) |
0.0807 (0.397) |
0.139 (0.458) |
0.697 (0.855) |
1 (1.00) |
0.298 (0.612) |
0.173 (0.495) |
0.314 (0.613) |
del 7q11 22 | 12 (21%) | 44 |
0.542 (0.736) |
0.8 (0.897) |
0.718 (0.865) |
0.721 (0.865) |
0.84 (0.923) |
0.836 (0.922) |
0.84 (0.923) |
0.531 (0.729) |
0.0647 (0.39) |
0.751 (0.877) |
del 7q36 2 | 20 (36%) | 36 |
0.29 (0.61) |
0.268 (0.598) |
0.723 (0.865) |
0.521 (0.726) |
0.422 (0.677) |
0.275 (0.6) |
0.0903 (0.4) |
0.0443 (0.385) |
0.466 (0.689) |
0.0816 (0.397) |
del 8p21 3 | 32 (57%) | 24 |
0.0362 (0.379) |
0.619 (0.796) |
0.489 (0.704) |
0.282 (0.604) |
0.346 (0.629) |
0.33 (0.618) |
0.885 (0.953) |
0.284 (0.607) |
0.402 (0.67) |
0.537 (0.731) |
del 9q21 13 | 39 (70%) | 17 |
0.0366 (0.379) |
0.572 (0.758) |
0.77 (0.877) |
0.452 (0.689) |
0.46 (0.689) |
0.257 (0.592) |
0.757 (0.877) |
0.322 (0.615) |
0.403 (0.67) |
0.399 (0.667) |
del 9q33 3 | 39 (70%) | 17 |
0.462 (0.689) |
0.801 (0.897) |
0.0816 (0.397) |
0.041 (0.379) |
0.227 (0.562) |
0.139 (0.458) |
0.646 (0.813) |
0.113 (0.446) |
0.378 (0.648) |
0.256 (0.592) |
del 10q23 31 | 20 (36%) | 36 |
0.159 (0.478) |
0.148 (0.467) |
0.927 (0.976) |
0.98 (1.00) |
0.375 (0.648) |
0.242 (0.573) |
0.879 (0.949) |
0.852 (0.931) |
0.572 (0.758) |
0.825 (0.915) |
del 11q14 1 | 26 (46%) | 30 |
0.0491 (0.39) |
0.638 (0.809) |
0.161 (0.48) |
0.228 (0.562) |
0.821 (0.915) |
0.923 (0.975) |
0.377 (0.648) |
0.265 (0.598) |
0.199 (0.533) |
0.0751 (0.397) |
del 11q23 2 | 26 (46%) | 30 |
0.437 (0.683) |
0.934 (0.976) |
0.613 (0.791) |
0.225 (0.562) |
0.151 (0.472) |
0.871 (0.943) |
0.514 (0.721) |
0.863 (0.938) |
0.0844 (0.397) |
0.357 (0.63) |
del 12q23 1 | 20 (36%) | 36 |
0.638 (0.809) |
0.943 (0.98) |
0.121 (0.446) |
0.0629 (0.39) |
0.629 (0.804) |
0.751 (0.877) |
1 (1.00) |
0.338 (0.626) |
0.622 (0.797) |
0.545 (0.737) |
del 13q12 11 | 30 (54%) | 26 |
0.165 (0.482) |
0.145 (0.467) |
0.435 (0.682) |
0.0692 (0.393) |
0.153 (0.475) |
0.206 (0.539) |
0.351 (0.629) |
0.0256 (0.32) |
0.127 (0.45) |
0.0619 (0.39) |
del 13q14 2 | 32 (57%) | 24 |
0.296 (0.612) |
0.0401 (0.379) |
0.227 (0.562) |
0.414 (0.677) |
0.0356 (0.379) |
0.0204 (0.319) |
0.303 (0.613) |
0.158 (0.478) |
0.0868 (0.397) |
0.193 (0.525) |
del 14q21 1 | 28 (50%) | 28 |
0.788 (0.886) |
0.115 (0.446) |
0.592 (0.777) |
0.132 (0.455) |
0.0676 (0.39) |
0.0545 (0.39) |
0.313 (0.613) |
0.381 (0.651) |
0.089 (0.399) |
0.369 (0.641) |
del 15q15 1 | 43 (77%) | 13 |
0.166 (0.482) |
0.0227 (0.319) |
0.447 (0.689) |
0.0395 (0.379) |
0.398 (0.667) |
0.771 (0.877) |
0.0712 (0.395) |
0.347 (0.629) |
0.115 (0.446) |
0.206 (0.539) |
del 16p13 3 | 33 (59%) | 23 |
0.421 (0.677) |
0.631 (0.804) |
0.708 (0.862) |
0.263 (0.598) |
0.366 (0.639) |
0.23 (0.562) |
0.0163 (0.306) |
0.388 (0.655) |
0.679 (0.841) |
0.716 (0.865) |
del 16q23 1 | 39 (70%) | 17 |
0.207 (0.539) |
0.14 (0.458) |
0.463 (0.689) |
0.279 (0.603) |
0.682 (0.841) |
0.393 (0.661) |
0.3 (0.613) |
0.814 (0.91) |
0.935 (0.976) |
0.621 (0.797) |
del 17q21 31 | 27 (48%) | 29 |
0.364 (0.636) |
0.0631 (0.39) |
0.525 (0.729) |
0.0914 (0.4) |
0.297 (0.612) |
0.347 (0.629) |
0.314 (0.613) |
0.085 (0.397) |
0.0564 (0.39) |
0.141 (0.458) |
del 19p13 3 | 47 (84%) | 9 |
0.138 (0.458) |
0.0417 (0.379) |
0.422 (0.677) |
0.121 (0.446) |
0.12 (0.446) |
0.378 (0.648) |
0.0817 (0.397) |
0.0846 (0.397) |
0.0401 (0.379) |
0.114 (0.446) |
del 20p12 1 | 9 (16%) | 47 |
0.534 (0.73) |
0.697 (0.855) |
0.0747 (0.397) |
0.0204 (0.319) |
0.42 (0.677) |
0.528 (0.729) |
0.269 (0.598) |
0.342 (0.629) |
0.766 (0.877) |
0.466 (0.689) |
del 22q13 31 | 40 (71%) | 16 |
0.485 (0.704) |
0.372 (0.644) |
0.115 (0.446) |
0.307 (0.613) |
0.481 (0.703) |
0.458 (0.689) |
1 (1.00) |
0.351 (0.629) |
0.974 (1.00) |
0.588 (0.773) |
del xp21 1 | 18 (32%) | 38 |
0.383 (0.652) |
0.659 (0.826) |
0.912 (0.969) |
0.895 (0.959) |
0.886 (0.953) |
0.868 (0.942) |
1 (1.00) |
1 (1.00) |
0.854 (0.931) |
0.901 (0.959) |
del xq25 | 23 (41%) | 33 |
0.783 (0.883) |
0.219 (0.557) |
0.265 (0.598) |
0.0694 (0.393) |
0.147 (0.467) |
0.898 (0.959) |
0.482 (0.703) |
0.567 (0.756) |
0.12 (0.446) |
0.386 (0.652) |
P value = 0.00773 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 19 | 12 | 10 |
AMP PEAK 3(2Q13) MUTATED | 8 | 7 | 11 | 3 |
AMP PEAK 3(2Q13) WILD-TYPE | 7 | 12 | 1 | 7 |
P value = 0.0103 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 22 | 13 |
AMP PEAK 4(3P25.1) MUTATED | 7 | 4 | 9 |
AMP PEAK 4(3P25.1) WILD-TYPE | 14 | 18 | 4 |
P value = 0.00052 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 22 | 13 |
AMP PEAK 5(3Q26.2) MUTATED | 20 | 10 | 7 |
AMP PEAK 5(3Q26.2) WILD-TYPE | 1 | 12 | 6 |
P value = 0.00569 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 13 | 13 | 11 |
AMP PEAK 5(3Q26.2) MUTATED | 16 | 4 | 11 | 6 |
AMP PEAK 5(3Q26.2) WILD-TYPE | 3 | 9 | 2 | 5 |
P value = 0.0019 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 22 | 13 |
AMP PEAK 6(4P16.3) MUTATED | 15 | 4 | 6 |
AMP PEAK 6(4P16.3) WILD-TYPE | 6 | 18 | 7 |
P value = 0.01 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 8 | 8 | 7 | 7 | 7 | 5 | 5 |
AMP PEAK 6(4P16.3) MUTATED | 7 | 3 | 0 | 1 | 3 | 3 | 3 |
AMP PEAK 6(4P16.3) WILD-TYPE | 1 | 5 | 7 | 6 | 4 | 2 | 2 |
P value = 0.00691 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 22 | 13 |
AMP PEAK 12(8Q24.21) MUTATED | 11 | 16 | 13 |
AMP PEAK 12(8Q24.21) WILD-TYPE | 10 | 6 | 0 |
P value = 0.009 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 19 | 12 | 10 |
AMP PEAK 12(8Q24.21) MUTATED | 11 | 17 | 4 | 8 |
AMP PEAK 12(8Q24.21) WILD-TYPE | 4 | 2 | 8 | 2 |
P value = 0.00716 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 24 | 17 |
AMP PEAK 17(13Q31.3) MUTATED | 6 | 16 | 3 |
AMP PEAK 17(13Q31.3) WILD-TYPE | 8 | 8 | 14 |
P value = 0.00994 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 9 | 12 | 6 | 9 |
AMP PEAK 18(16P11.2) MUTATED | 7 | 3 | 1 | 4 | 1 |
AMP PEAK 18(16P11.2) WILD-TYPE | 4 | 6 | 11 | 2 | 8 |
P value = 0.00027 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 22 | 13 |
AMP PEAK 22(19Q12) MUTATED | 21 | 12 | 12 |
AMP PEAK 22(19Q12) WILD-TYPE | 0 | 10 | 1 |
P value = 0.00037 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 13 | 13 | 11 |
AMP PEAK 22(19Q12) MUTATED | 17 | 5 | 12 | 11 |
AMP PEAK 22(19Q12) WILD-TYPE | 2 | 8 | 1 | 0 |
P value = 0.00656 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 22 | 13 |
AMP PEAK 23(20Q11.21) MUTATED | 21 | 15 | 12 |
AMP PEAK 23(20Q11.21) WILD-TYPE | 0 | 7 | 1 |
P value = 0.00732 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 9 | 14 | 14 | 18 |
DEL PEAK 5(4Q22.1) MUTATED | 9 | 10 | 11 | 7 |
DEL PEAK 5(4Q22.1) WILD-TYPE | 0 | 4 | 3 | 11 |
P value = 0.00688 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 9 | 14 | 14 | 18 |
DEL PEAK 6(4Q34.3) MUTATED | 9 | 11 | 10 | 7 |
DEL PEAK 6(4Q34.3) WILD-TYPE | 0 | 3 | 4 | 11 |
P value = 0.00516 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 13 | 13 | 11 |
DEL PEAK 7(5Q12.1) MUTATED | 11 | 1 | 6 | 8 |
DEL PEAK 7(5Q12.1) WILD-TYPE | 8 | 12 | 7 | 3 |
P value = 0.00502 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 9 | 12 | 6 | 9 |
DEL PEAK 12(9P23) MUTATED | 11 | 5 | 7 | 4 | 2 |
DEL PEAK 12(9P23) WILD-TYPE | 0 | 4 | 5 | 2 | 7 |
P value = 0.00166 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 8 | 8 | 7 | 7 | 7 | 5 | 5 |
DEL PEAK 19(12Q24.31) MUTATED | 2 | 7 | 5 | 3 | 1 | 0 | 0 |
DEL PEAK 19(12Q24.31) WILD-TYPE | 6 | 1 | 2 | 4 | 6 | 5 | 5 |
P value = 0.00487 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 9 | 14 | 14 | 18 |
DEL PEAK 26(17P13.1) MUTATED | 8 | 14 | 11 | 9 |
DEL PEAK 26(17P13.1) WILD-TYPE | 1 | 0 | 3 | 9 |
P value = 0.0065 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 24 | 17 |
DEL PEAK 28(18Q22.2) MUTATED | 5 | 17 | 4 |
DEL PEAK 28(18Q22.2) WILD-TYPE | 9 | 7 | 13 |
P value = 0.00934 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 9 | 14 | 14 | 18 |
DEL PEAK 28(18Q22.2) MUTATED | 6 | 4 | 11 | 5 |
DEL PEAK 28(18Q22.2) WILD-TYPE | 3 | 10 | 3 | 13 |
P value = 0.00737 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 19 | 12 | 10 |
DEL PEAK 30(19P13.3) MUTATED | 13 | 10 | 12 | 9 |
DEL PEAK 30(19P13.3) WILD-TYPE | 2 | 9 | 0 | 1 |
P value = 0.00285 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 14 | 24 | 17 |
DEL PEAK 30(19P13.3) MUTATED | 12 | 23 | 9 |
DEL PEAK 30(19P13.3) WILD-TYPE | 2 | 1 | 8 |
P value = 0.00923 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 8 | 18 | 6 |
DEL PEAK 30(19P13.3) MUTATED | 16 | 7 | 18 | 3 |
DEL PEAK 30(19P13.3) WILD-TYPE | 7 | 1 | 0 | 3 |
P value = 0.00141 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 9 | 14 | 14 | 18 |
DEL PEAK 30(19P13.3) MUTATED | 8 | 13 | 14 | 9 |
DEL PEAK 30(19P13.3) WILD-TYPE | 1 | 1 | 0 | 9 |
P value = 0.00182 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 19 | 12 | 10 |
DEL PEAK 31(19Q13.33) MUTATED | 9 | 2 | 1 | 5 |
DEL PEAK 31(19Q13.33) WILD-TYPE | 6 | 17 | 11 | 5 |
-
Copy number data file = all_lesions.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCS-TP/22533741/transformed.cor.cli.txt
-
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/22541488/UCS-TP.transferedmergedcluster.txt
-
Number of patients = 56
-
Number of significantly focal cnvs = 60
-
Number of molecular subtypes = 10
-
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.