Correlation between copy number variations of arm-level result and molecular subtypes
Cervical Squamous Cell Carcinoma (Primary solid tumor)
23 May 2013
|
analyses__2013_05_23
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team
(Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as
Broad Institute TCGA Genome Data Analysis Center
(2013):
Correlation between copy number variations of arm-level result and molecular subtypes.
Broad Institute of MIT and Harvard.
doi:10.7908/C1X63JZT
Overview
Introduction
This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Summary
Testing the association between copy number variation 73 arm-level results and 8 molecular subtypes across 126 patients, 3 significant findings detected with Q value < 0.25.
-
3q gain cnv correlated to 'CN_CNMF'.
-
4q loss cnv correlated to 'CN_CNMF'.
-
18q loss cnv correlated to 'MRNASEQ_CNMF'.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between significant copy number variation of 73 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 significant findings detected.
|
Molecular subtypes |
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 | 0 (0%) | 64 |
1.3e-05 (0.0076) |
0.463 (1.00) |
0.0191 (1.00) |
0.0478 (1.00) |
0.0537 (1.00) |
0.177 (1.00) |
0.49 (1.00) |
0.0133 (1.00) |
| 4q loss | 0 (0%) | 102 |
6.4e-06 (0.00373) |
1 (1.00) |
0.0976 (1.00) |
0.297 (1.00) |
0.627 (1.00) |
1 (1.00) |
0.959 (1.00) |
0.775 (1.00) |
| 18q loss | 0 (0%) | 102 |
0.112 (1.00) |
0.0114 (1.00) |
0.000428 (0.249) |
0.00334 (1.00) |
0.0132 (1.00) |
0.00661 (1.00) |
0.00367 (1.00) |
0.00289 (1.00) |
| 1p gain | 0 (0%) | 92 |
0.415 (1.00) |
0.584 (1.00) |
0.274 (1.00) |
0.904 (1.00) |
0.982 (1.00) |
0.828 (1.00) |
0.418 (1.00) |
0.766 (1.00) |
| 1q gain | 0 (0%) | 78 |
0.0208 (1.00) |
0.374 (1.00) |
0.345 (1.00) |
0.568 (1.00) |
0.252 (1.00) |
0.0764 (1.00) |
0.407 (1.00) |
0.257 (1.00) |
| 2p gain | 0 (0%) | 109 |
0.0833 (1.00) |
0.347 (1.00) |
0.1 (1.00) |
0.0951 (1.00) |
0.271 (1.00) |
0.0441 (1.00) |
0.181 (1.00) |
0.0369 (1.00) |
| 2q gain | 0 (0%) | 121 |
0.0843 (1.00) |
0.613 (1.00) |
0.0694 (1.00) |
0.153 (1.00) |
1 (1.00) |
0.637 (1.00) |
1 (1.00) |
0.732 (1.00) |
| 3p gain | 0 (0%) | 105 |
0.568 (1.00) |
0.407 (1.00) |
0.717 (1.00) |
0.0367 (1.00) |
0.483 (1.00) |
1 (1.00) |
1 (1.00) |
0.333 (1.00) |
| 4q gain | 0 (0%) | 123 |
0.115 (1.00) |
0.116 (1.00) |
0.453 (1.00) |
0.485 (1.00) |
0.487 (1.00) |
0.216 (1.00) |
0.267 (1.00) |
0.183 (1.00) |
| 5p gain | 0 (0%) | 85 |
0.0204 (1.00) |
0.914 (1.00) |
0.935 (1.00) |
0.728 (1.00) |
0.881 (1.00) |
0.304 (1.00) |
0.241 (1.00) |
0.289 (1.00) |
| 5q gain | 0 (0%) | 113 |
0.572 (1.00) |
0.422 (1.00) |
1 (1.00) |
1 (1.00) |
0.759 (1.00) |
0.53 (1.00) |
0.574 (1.00) |
0.87 (1.00) |
| 6p gain | 0 (0%) | 108 |
0.108 (1.00) |
0.00991 (1.00) |
0.0262 (1.00) |
0.0987 (1.00) |
0.188 (1.00) |
0.172 (1.00) |
0.0445 (1.00) |
0.0968 (1.00) |
| 6q gain | 0 (0%) | 117 |
0.501 (1.00) |
0.00483 (1.00) |
0.0536 (1.00) |
0.00601 (1.00) |
0.0953 (1.00) |
0.0216 (1.00) |
0.249 (1.00) |
0.0554 (1.00) |
| 7p gain | 0 (0%) | 119 |
0.48 (1.00) |
0.171 (1.00) |
0.198 (1.00) |
0.41 (1.00) |
0.316 (1.00) |
0.101 (1.00) |
0.00495 (1.00) |
0.0028 (1.00) |
| 7q gain | 0 (0%) | 115 |
0.109 (1.00) |
0.266 (1.00) |
0.285 (1.00) |
1 (1.00) |
0.482 (1.00) |
1 (1.00) |
0.107 (1.00) |
0.11 (1.00) |
| 8p gain | 0 (0%) | 116 |
0.644 (1.00) |
0.41 (1.00) |
0.12 (1.00) |
0.167 (1.00) |
0.38 (1.00) |
1 (1.00) |
0.266 (1.00) |
0.594 (1.00) |
| 8q gain | 0 (0%) | 104 |
0.0349 (1.00) |
0.0155 (1.00) |
0.104 (1.00) |
0.383 (1.00) |
0.104 (1.00) |
0.21 (1.00) |
0.0538 (1.00) |
0.0124 (1.00) |
| 9p gain | 0 (0%) | 114 |
0.32 (1.00) |
0.75 (1.00) |
0.47 (1.00) |
0.0148 (1.00) |
0.412 (1.00) |
0.509 (1.00) |
0.689 (1.00) |
0.407 (1.00) |
| 9q gain | 0 (0%) | 115 |
0.669 (1.00) |
0.223 (1.00) |
0.434 (1.00) |
0.0361 (1.00) |
0.128 (1.00) |
1 (1.00) |
0.621 (1.00) |
0.67 (1.00) |
| 10p gain | 0 (0%) | 118 |
0.653 (1.00) |
0.901 (1.00) |
0.883 (1.00) |
0.725 (1.00) |
0.156 (1.00) |
1 (1.00) |
0.809 (1.00) |
1 (1.00) |
| 10q gain | 0 (0%) | 122 |
0.457 (1.00) |
0.68 (1.00) |
0.81 (1.00) |
0.145 (1.00) |
0.33 (1.00) |
0.583 (1.00) |
0.564 (1.00) |
0.298 (1.00) |
| 12p gain | 0 (0%) | 112 |
0.0103 (1.00) |
0.486 (1.00) |
0.385 (1.00) |
0.00322 (1.00) |
0.378 (1.00) |
0.354 (1.00) |
0.936 (1.00) |
0.938 (1.00) |
| 12q gain | 0 (0%) | 116 |
0.0213 (1.00) |
0.842 (1.00) |
0.637 (1.00) |
0.0515 (1.00) |
0.244 (1.00) |
1 (1.00) |
0.592 (1.00) |
0.414 (1.00) |
| 13q gain | 0 (0%) | 120 |
0.0397 (1.00) |
0.496 (1.00) |
0.168 (1.00) |
0.488 (1.00) |
0.88 (1.00) |
0.365 (1.00) |
0.208 (1.00) |
0.436 (1.00) |
| 14q gain | 0 (0%) | 116 |
0.305 (1.00) |
0.593 (1.00) |
0.201 (1.00) |
0.124 (1.00) |
0.402 (1.00) |
0.487 (1.00) |
0.114 (1.00) |
0.0278 (1.00) |
| 15q gain | 0 (0%) | 113 |
0.00184 (1.00) |
1 (1.00) |
0.313 (1.00) |
0.794 (1.00) |
0.844 (1.00) |
1 (1.00) |
0.661 (1.00) |
1 (1.00) |
| 16p gain | 0 (0%) | 112 |
0.0456 (1.00) |
0.187 (1.00) |
0.506 (1.00) |
0.0615 (1.00) |
0.533 (1.00) |
0.121 (1.00) |
0.631 (1.00) |
0.318 (1.00) |
| 16q gain | 0 (0%) | 116 |
0.92 (1.00) |
0.643 (1.00) |
0.364 (1.00) |
0.0122 (1.00) |
0.402 (1.00) |
0.487 (1.00) |
0.451 (1.00) |
0.196 (1.00) |
| 17p gain | 0 (0%) | 121 |
0.616 (1.00) |
0.266 (1.00) |
0.269 (1.00) |
0.0126 (1.00) |
0.423 (1.00) |
0.0287 (1.00) |
0.272 (1.00) |
0.139 (1.00) |
| 17q gain | 0 (0%) | 113 |
0.0157 (1.00) |
0.0182 (1.00) |
0.0253 (1.00) |
0.0148 (1.00) |
0.394 (1.00) |
0.0208 (1.00) |
0.041 (1.00) |
0.0638 (1.00) |
| 18p gain | 0 (0%) | 114 |
0.408 (1.00) |
0.44 (1.00) |
0.606 (1.00) |
0.0271 (1.00) |
0.24 (1.00) |
0.345 (1.00) |
0.185 (1.00) |
0.295 (1.00) |
| 18q gain | 0 (0%) | 119 |
0.0757 (1.00) |
0.795 (1.00) |
0.486 (1.00) |
0.00832 (1.00) |
0.391 (1.00) |
1 (1.00) |
0.482 (1.00) |
0.89 (1.00) |
| 19p gain | 0 (0%) | 118 |
0.53 (1.00) |
0.808 (1.00) |
0.547 (1.00) |
0.331 (1.00) |
0.558 (1.00) |
1 (1.00) |
0.724 (1.00) |
0.899 (1.00) |
| 19q gain | 0 (0%) | 103 |
0.218 (1.00) |
0.804 (1.00) |
0.409 (1.00) |
0.0309 (1.00) |
0.126 (1.00) |
0.138 (1.00) |
0.00739 (1.00) |
0.0466 (1.00) |
| 20p gain | 0 (0%) | 94 |
0.000689 (0.397) |
0.401 (1.00) |
0.856 (1.00) |
0.083 (1.00) |
0.946 (1.00) |
0.18 (1.00) |
0.574 (1.00) |
0.39 (1.00) |
| 20q gain | 0 (0%) | 88 |
0.000534 (0.309) |
0.219 (1.00) |
0.512 (1.00) |
0.167 (1.00) |
0.632 (1.00) |
0.145 (1.00) |
0.645 (1.00) |
0.143 (1.00) |
| 21q gain | 0 (0%) | 112 |
0.556 (1.00) |
0.721 (1.00) |
0.266 (1.00) |
0.905 (1.00) |
0.332 (1.00) |
0.758 (1.00) |
0.229 (1.00) |
0.0868 (1.00) |
| 22q gain | 0 (0%) | 118 |
0.0403 (1.00) |
0.901 (1.00) |
0.326 (1.00) |
0.00377 (1.00) |
0.313 (1.00) |
1 (1.00) |
0.592 (1.00) |
0.467 (1.00) |
| Xq gain | 0 (0%) | 120 |
0.435 (1.00) |
0.201 (1.00) |
0.763 (1.00) |
0.332 (1.00) |
0.305 (1.00) |
0.365 (1.00) |
0.322 (1.00) |
0.164 (1.00) |
| 1q loss | 0 (0%) | 123 |
0.262 (1.00) |
0.617 (1.00) |
1 (1.00) |
0.485 (1.00) |
0.839 (1.00) |
1 (1.00) |
0.782 (1.00) |
0.474 (1.00) |
| 2p loss | 0 (0%) | 123 |
0.115 (1.00) |
0.184 (1.00) |
0.251 (1.00) |
0.673 (1.00) |
0.736 (1.00) |
0.553 (1.00) |
1 (1.00) |
0.784 (1.00) |
| 2q loss | 0 (0%) | 121 |
0.0843 (1.00) |
0.0303 (1.00) |
0.0859 (1.00) |
0.267 (1.00) |
0.723 (1.00) |
1 (1.00) |
0.381 (1.00) |
0.367 (1.00) |
| 3p loss | 0 (0%) | 99 |
0.32 (1.00) |
0.00125 (0.716) |
0.198 (1.00) |
0.000436 (0.254) |
0.0284 (1.00) |
0.0038 (1.00) |
0.000762 (0.439) |
0.000443 (0.257) |
| 4p loss | 0 (0%) | 85 |
0.00186 (1.00) |
0.111 (1.00) |
0.279 (1.00) |
0.956 (1.00) |
0.351 (1.00) |
0.215 (1.00) |
0.226 (1.00) |
0.102 (1.00) |
| 5p loss | 0 (0%) | 123 |
0.346 (1.00) |
0.617 (1.00) |
0.79 (1.00) |
1 (1.00) |
0.356 (1.00) |
1 (1.00) |
1 (1.00) |
0.349 (1.00) |
| 5q loss | 0 (0%) | 106 |
0.0316 (1.00) |
0.167 (1.00) |
0.527 (1.00) |
0.0345 (1.00) |
0.0788 (1.00) |
0.00686 (1.00) |
0.149 (1.00) |
0.202 (1.00) |
| 6p loss | 0 (0%) | 114 |
0.926 (1.00) |
0.0546 (1.00) |
0.384 (1.00) |
0.432 (1.00) |
0.725 (1.00) |
1 (1.00) |
0.551 (1.00) |
0.75 (1.00) |
| 6q loss | 0 (0%) | 103 |
0.208 (1.00) |
0.541 (1.00) |
0.287 (1.00) |
0.777 (1.00) |
0.395 (1.00) |
1 (1.00) |
0.564 (1.00) |
1 (1.00) |
| 7p loss | 0 (0%) | 120 |
0.0625 (1.00) |
0.496 (1.00) |
0.558 (1.00) |
0.332 (1.00) |
0.779 (1.00) |
0.365 (1.00) |
0.661 (1.00) |
0.5 (1.00) |
| 7q loss | 0 (0%) | 113 |
0.0129 (1.00) |
0.422 (1.00) |
0.0352 (1.00) |
0.188 (1.00) |
0.106 (1.00) |
0.753 (1.00) |
0.221 (1.00) |
0.075 (1.00) |
| 8p loss | 0 (0%) | 99 |
0.435 (1.00) |
0.23 (1.00) |
0.445 (1.00) |
0.795 (1.00) |
0.803 (1.00) |
1 (1.00) |
0.734 (1.00) |
0.961 (1.00) |
| 8q loss | 0 (0%) | 120 |
1 (1.00) |
0.496 (1.00) |
0.326 (1.00) |
0.332 (1.00) |
0.359 (1.00) |
0.0669 (1.00) |
0.148 (1.00) |
0.436 (1.00) |
| 9p loss | 0 (0%) | 114 |
0.32 (1.00) |
0.926 (1.00) |
0.74 (1.00) |
0.776 (1.00) |
0.97 (1.00) |
1 (1.00) |
0.864 (1.00) |
0.75 (1.00) |
| 9q loss | 0 (0%) | 115 |
0.669 (1.00) |
0.117 (1.00) |
0.0145 (1.00) |
0.275 (1.00) |
0.366 (1.00) |
0.0864 (1.00) |
0.291 (1.00) |
0.0921 (1.00) |
| 10p loss | 0 (0%) | 104 |
0.0152 (1.00) |
0.835 (1.00) |
0.139 (1.00) |
0.102 (1.00) |
0.765 (1.00) |
0.61 (1.00) |
0.798 (1.00) |
1 (1.00) |
| 10q loss | 0 (0%) | 102 |
0.0129 (1.00) |
0.958 (1.00) |
0.79 (1.00) |
0.181 (1.00) |
0.477 (1.00) |
0.459 (1.00) |
0.466 (1.00) |
0.576 (1.00) |
| 11p loss | 0 (0%) | 99 |
0.0822 (1.00) |
0.454 (1.00) |
0.874 (1.00) |
0.941 (1.00) |
0.782 (1.00) |
0.644 (1.00) |
0.734 (1.00) |
0.421 (1.00) |
| 11q loss | 0 (0%) | 96 |
0.00965 (1.00) |
0.463 (1.00) |
0.771 (1.00) |
0.177 (1.00) |
0.952 (1.00) |
0.373 (1.00) |
0.836 (1.00) |
0.964 (1.00) |
| 12p loss | 0 (0%) | 107 |
0.00218 (1.00) |
0.169 (1.00) |
0.739 (1.00) |
0.72 (1.00) |
0.589 (1.00) |
0.18 (1.00) |
0.518 (1.00) |
0.246 (1.00) |
| 12q loss | 0 (0%) | 122 |
0.0356 (1.00) |
0.459 (1.00) |
0.286 (1.00) |
0.298 (1.00) |
1 (1.00) |
1 (1.00) |
0.38 (1.00) |
0.677 (1.00) |
| 13q loss | 0 (0%) | 103 |
0.43 (1.00) |
0.0226 (1.00) |
0.489 (1.00) |
0.0659 (1.00) |
0.0301 (1.00) |
0.208 (1.00) |
0.101 (1.00) |
0.0488 (1.00) |
| 14q loss | 0 (0%) | 119 |
0.424 (1.00) |
0.146 (1.00) |
0.0234 (1.00) |
0.00355 (1.00) |
0.2 (1.00) |
0.0258 (1.00) |
0.0563 (1.00) |
0.0103 (1.00) |
| 15q loss | 0 (0%) | 118 |
0.00157 (0.901) |
1 (1.00) |
0.316 (1.00) |
0.116 (1.00) |
0.772 (1.00) |
0.697 (1.00) |
1 (1.00) |
1 (1.00) |
| 16p loss | 0 (0%) | 118 |
0.415 (1.00) |
0.148 (1.00) |
0.129 (1.00) |
0.00638 (1.00) |
0.117 (1.00) |
0.241 (1.00) |
0.211 (1.00) |
0.33 (1.00) |
| 16q loss | 0 (0%) | 112 |
0.821 (1.00) |
0.0314 (1.00) |
0.00107 (0.614) |
0.000523 (0.303) |
0.0574 (1.00) |
0.00554 (1.00) |
0.0298 (1.00) |
0.0244 (1.00) |
| 17p loss | 0 (0%) | 99 |
0.0148 (1.00) |
0.00292 (1.00) |
0.0411 (1.00) |
0.0596 (1.00) |
0.0202 (1.00) |
0.0173 (1.00) |
0.0241 (1.00) |
0.0913 (1.00) |
| 17q loss | 0 (0%) | 121 |
0.616 (1.00) |
0.0303 (1.00) |
0.0859 (1.00) |
0.267 (1.00) |
0.296 (1.00) |
0.321 (1.00) |
0.326 (1.00) |
0.367 (1.00) |
| 18p loss | 0 (0%) | 110 |
0.55 (1.00) |
0.266 (1.00) |
0.0389 (1.00) |
0.0988 (1.00) |
0.1 (1.00) |
0.0818 (1.00) |
0.00617 (1.00) |
0.0609 (1.00) |
| 19p loss | 0 (0%) | 114 |
0.44 (1.00) |
0.693 (1.00) |
0.258 (1.00) |
0.397 (1.00) |
0.19 (1.00) |
0.509 (1.00) |
0.638 (1.00) |
0.349 (1.00) |
| 19q loss | 0 (0%) | 120 |
0.495 (1.00) |
0.57 (1.00) |
0.486 (1.00) |
0.173 (1.00) |
0.779 (1.00) |
0.365 (1.00) |
1 (1.00) |
1 (1.00) |
| 20p loss | 0 (0%) | 118 |
0.53 (1.00) |
0.42 (1.00) |
0.596 (1.00) |
0.376 (1.00) |
0.955 (1.00) |
0.697 (1.00) |
0.724 (1.00) |
0.413 (1.00) |
| 21q loss | 0 (0%) | 113 |
0.000976 (0.561) |
0.458 (1.00) |
0.858 (1.00) |
0.81 (1.00) |
0.328 (1.00) |
0.753 (1.00) |
0.708 (1.00) |
1 (1.00) |
| 22q loss | 0 (0%) | 113 |
0.87 (1.00) |
1 (1.00) |
0.867 (1.00) |
0.512 (1.00) |
0.759 (1.00) |
1 (1.00) |
0.756 (1.00) |
0.87 (1.00) |
'3q gain' versus 'CN_CNMF'
P value = 1.3e-05 (Fisher's exact test), Q value = 0.0076
Table S1. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 32 | 52 |
| 3Q GAIN CNV | 33 | 12 | 17 |
| 3Q GAIN WILD-TYPE | 9 | 20 | 35 |
Figure S1. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'
'4q loss' versus 'CN_CNMF'
P value = 6.4e-06 (Fisher's exact test), Q value = 0.0037
Table S2. Gene #43: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 32 | 52 |
| 4Q LOSS CNV | 7 | 15 | 2 |
| 4Q LOSS WILD-TYPE | 35 | 17 | 50 |
Figure S2. Get High-res Image Gene #43: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'
'18q loss' versus 'MRNASEQ_CNMF'
P value = 0.000428 (Fisher's exact test), Q value = 0.25
Table S3. Gene #68: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 30 | 31 |
| 18Q LOSS CNV | 3 | 6 | 13 |
| 18Q LOSS WILD-TYPE | 47 | 24 | 18 |
Figure S3. Get High-res Image Gene #68: '18q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
Methods & Data
Input
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Molecular subtypes file = CESC-TP.transferedmergedcluster.txt
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Number of patients = 126
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Number of significantly arm-level cnvs = 73
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Number of molecular subtypes = 8
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Exclude genes that fewer than K tumors have mutations, K = 3
Fisher's exact test
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
Q value calculation
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.
Download Results
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.
References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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Broad Institute TCGA GDAC as part of the TCGA Research Network.
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