Skin Cutaneous Melanoma: Correlation between gene mutation status and molecular subtypes
(Regional_LN cohort)
(Regional_LN cohort)
Maintained by TCGA GDAC Team
(Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction
This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Summary
Testing the association between mutation status of 74 genes and 8 molecular subtypes across 105 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
-
No gene mutations related to molecuar subtypes.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between mutation status of 74 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.
|
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
| nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
| BRAF | 59 (56%) | 46 |
0.0383 (1.00) |
0.242 (1.00) |
0.0794 (1.00) |
0.417 (1.00) |
0.274 (1.00) |
0.139 (1.00) |
0.117 (1.00) |
0.494 (1.00) |
| CDKN2A | 16 (15%) | 89 |
0.31 (1.00) |
0.979 (1.00) |
0.874 (1.00) |
0.04 (1.00) |
0.331 (1.00) |
0.46 (1.00) |
0.157 (1.00) |
0.31 (1.00) |
| NRAS | 29 (28%) | 76 |
0.0228 (1.00) |
0.0502 (1.00) |
0.072 (1.00) |
0.505 (1.00) |
0.574 (1.00) |
0.495 (1.00) |
0.444 (1.00) |
0.71 (1.00) |
| STK19 | 7 (7%) | 98 |
0.437 (1.00) |
0.534 (1.00) |
0.129 (1.00) |
0.358 (1.00) |
0.145 (1.00) |
0.0576 (1.00) |
0.0319 (1.00) |
0.713 (1.00) |
| TTN | 83 (79%) | 22 |
0.973 (1.00) |
0.803 (1.00) |
0.344 (1.00) |
0.236 (1.00) |
0.719 (1.00) |
0.738 (1.00) |
0.276 (1.00) |
0.571 (1.00) |
| TP53 | 18 (17%) | 87 |
0.128 (1.00) |
0.0813 (1.00) |
0.489 (1.00) |
0.699 (1.00) |
0.103 (1.00) |
0.0421 (1.00) |
0.00436 (1.00) |
0.077 (1.00) |
| PTEN | 11 (10%) | 94 |
0.459 (1.00) |
0.175 (1.00) |
0.387 (1.00) |
0.105 (1.00) |
0.559 (1.00) |
0.136 (1.00) |
0.25 (1.00) |
0.701 (1.00) |
| TPTE | 29 (28%) | 76 |
0.481 (1.00) |
0.587 (1.00) |
0.822 (1.00) |
0.206 (1.00) |
0.492 (1.00) |
0.952 (1.00) |
0.481 (1.00) |
1 (1.00) |
| PRB4 | 15 (14%) | 90 |
0.139 (1.00) |
0.922 (1.00) |
0.249 (1.00) |
0.154 (1.00) |
0.409 (1.00) |
0.689 (1.00) |
0.522 (1.00) |
0.47 (1.00) |
| CDH9 | 22 (21%) | 83 |
0.688 (1.00) |
0.24 (1.00) |
0.919 (1.00) |
0.667 (1.00) |
0.368 (1.00) |
0.525 (1.00) |
0.0811 (1.00) |
0.705 (1.00) |
| SERPINB4 | 17 (16%) | 88 |
0.724 (1.00) |
0.634 (1.00) |
0.0886 (1.00) |
0.0163 (1.00) |
0.795 (1.00) |
0.81 (1.00) |
0.491 (1.00) |
0.504 (1.00) |
| PRB2 | 19 (18%) | 86 |
0.788 (1.00) |
0.763 (1.00) |
0.36 (1.00) |
0.943 (1.00) |
0.855 (1.00) |
0.21 (1.00) |
0.0312 (1.00) |
0.0609 (1.00) |
| TCEB3C | 14 (13%) | 91 |
0.184 (1.00) |
0.0621 (1.00) |
0.898 (1.00) |
0.472 (1.00) |
0.255 (1.00) |
0.596 (1.00) |
0.574 (1.00) |
0.14 (1.00) |
| ADH1C | 17 (16%) | 88 |
0.861 (1.00) |
0.761 (1.00) |
0.103 (1.00) |
0.607 (1.00) |
0.0191 (1.00) |
0.0241 (1.00) |
0.788 (1.00) |
0.187 (1.00) |
| C15ORF23 | 7 (7%) | 98 |
0.261 (1.00) |
0.587 (1.00) |
0.869 (1.00) |
0.763 (1.00) |
0.478 (1.00) |
0.3 (1.00) |
0.786 (1.00) |
0.575 (1.00) |
| CCNE2 | 10 (10%) | 95 |
1 (1.00) |
0.314 (1.00) |
0.171 (1.00) |
0.0854 (1.00) |
0.84 (1.00) |
0.648 (1.00) |
0.399 (1.00) |
0.773 (1.00) |
| SDR16C5 | 16 (15%) | 89 |
0.895 (1.00) |
0.0422 (1.00) |
0.0534 (1.00) |
0.406 (1.00) |
0.0515 (1.00) |
0.00901 (1.00) |
0.504 (1.00) |
0.919 (1.00) |
| PDE1A | 19 (18%) | 86 |
0.901 (1.00) |
0.54 (1.00) |
0.641 (1.00) |
0.852 (1.00) |
0.855 (1.00) |
0.413 (1.00) |
0.444 (1.00) |
0.41 (1.00) |
| TLL1 | 24 (23%) | 81 |
0.584 (1.00) |
0.733 (1.00) |
0.462 (1.00) |
0.0468 (1.00) |
0.298 (1.00) |
0.336 (1.00) |
0.576 (1.00) |
0.1 (1.00) |
| RAC1 | 7 (7%) | 98 |
0.95 (1.00) |
0.857 (1.00) |
0.857 (1.00) |
0.858 (1.00) |
1 (1.00) |
0.869 (1.00) |
1 (1.00) |
0.452 (1.00) |
| RERG | 8 (8%) | 97 |
1 (1.00) |
1 (1.00) |
0.025 (1.00) |
0.721 (1.00) |
0.335 (1.00) |
0.467 (1.00) |
0.356 (1.00) |
0.161 (1.00) |
| OR52L1 | 12 (11%) | 93 |
0.528 (1.00) |
0.343 (1.00) |
0.078 (1.00) |
0.165 (1.00) |
0.316 (1.00) |
0.121 (1.00) |
0.857 (1.00) |
0.349 (1.00) |
| HBD | 8 (8%) | 97 |
0.0565 (1.00) |
1 (1.00) |
0.26 (1.00) |
0.315 (1.00) |
0.238 (1.00) |
0.142 (1.00) |
0.23 (1.00) |
0.161 (1.00) |
| VEGFC | 12 (11%) | 93 |
0.394 (1.00) |
0.527 (1.00) |
0.0865 (1.00) |
0.141 (1.00) |
0.16 (1.00) |
0.0144 (1.00) |
0.0816 (1.00) |
0.0334 (1.00) |
| BAGE2 | 7 (7%) | 98 |
0.354 (1.00) |
0.264 (1.00) |
0.661 (1.00) |
0.927 (1.00) |
0.253 (1.00) |
0.229 (1.00) |
0.524 (1.00) |
0.575 (1.00) |
| OR1N2 | 13 (12%) | 92 |
0.548 (1.00) |
0.337 (1.00) |
0.254 (1.00) |
0.353 (1.00) |
0.651 (1.00) |
0.741 (1.00) |
1 (1.00) |
0.207 (1.00) |
| PPP6C | 10 (10%) | 95 |
0.521 (1.00) |
0.85 (1.00) |
0.323 (1.00) |
0.507 (1.00) |
0.54 (1.00) |
0.966 (1.00) |
0.121 (1.00) |
0.237 (1.00) |
| HNF4G | 12 (11%) | 93 |
0.859 (1.00) |
1 (1.00) |
0.744 (1.00) |
0.504 (1.00) |
1 (1.00) |
0.926 (1.00) |
1 (1.00) |
0.454 (1.00) |
| TRAT1 | 6 (6%) | 99 |
0.429 (1.00) |
0.492 (1.00) |
0.7 (1.00) |
0.727 (1.00) |
0.103 (1.00) |
0.222 (1.00) |
0.373 (1.00) |
0.326 (1.00) |
| AREG | 5 (5%) | 100 |
0.864 (1.00) |
0.644 (1.00) |
0.496 (1.00) |
1 (1.00) |
0.365 (1.00) |
0.529 (1.00) |
0.84 (1.00) |
1 (1.00) |
| ST18 | 24 (23%) | 81 |
1 (1.00) |
0.815 (1.00) |
0.559 (1.00) |
0.327 (1.00) |
0.408 (1.00) |
0.863 (1.00) |
0.437 (1.00) |
0.554 (1.00) |
| TAF1A | 8 (8%) | 97 |
0.284 (1.00) |
0.375 (1.00) |
0.319 (1.00) |
0.487 (1.00) |
0.41 (1.00) |
0.579 (1.00) |
0.64 (1.00) |
0.868 (1.00) |
| GRXCR2 | 9 (9%) | 96 |
0.0843 (1.00) |
0.168 (1.00) |
0.447 (1.00) |
1 (1.00) |
0.103 (1.00) |
0.261 (1.00) |
0.136 (1.00) |
0.338 (1.00) |
| OR9K2 | 11 (10%) | 94 |
0.663 (1.00) |
0.305 (1.00) |
0.414 (1.00) |
0.0221 (1.00) |
0.723 (1.00) |
0.606 (1.00) |
0.208 (1.00) |
1 (1.00) |
| OXA1L | 4 (4%) | 101 |
0.328 (1.00) |
0.306 (1.00) |
0.833 (1.00) |
0.913 (1.00) |
0.834 (1.00) |
0.261 (1.00) |
||
| A2BP1 | 14 (13%) | 91 |
0.729 (1.00) |
0.845 (1.00) |
0.0228 (1.00) |
0.723 (1.00) |
0.273 (1.00) |
0.28 (1.00) |
0.0675 (1.00) |
0.496 (1.00) |
| HIST1H2AA | 5 (5%) | 100 |
0.612 (1.00) |
0.644 (1.00) |
0.638 (1.00) |
0.453 (1.00) |
0.437 (1.00) |
0.935 (1.00) |
0.731 (1.00) |
0.616 (1.00) |
| LILRA1 | 21 (20%) | 84 |
0.264 (1.00) |
0.49 (1.00) |
0.759 (1.00) |
0.31 (1.00) |
0.413 (1.00) |
0.769 (1.00) |
0.739 (1.00) |
0.808 (1.00) |
| LIN7A | 8 (8%) | 97 |
0.424 (1.00) |
0.0151 (1.00) |
0.476 (1.00) |
0.664 (1.00) |
0.238 (1.00) |
0.336 (1.00) |
0.64 (1.00) |
0.738 (1.00) |
| VGLL1 | 3 (3%) | 102 |
1 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
0.794 (1.00) |
1 (1.00) |
||
| GALNTL5 | 10 (10%) | 95 |
0.125 (1.00) |
0.195 (1.00) |
0.289 (1.00) |
0.104 (1.00) |
0.131 (1.00) |
0.372 (1.00) |
0.215 (1.00) |
0.773 (1.00) |
| HSD11B1 | 6 (6%) | 99 |
0.712 (1.00) |
0.602 (1.00) |
0.234 (1.00) |
0.28 (1.00) |
0.764 (1.00) |
1 (1.00) |
0.12 (1.00) |
0.662 (1.00) |
| ANKRD20A4 | 4 (4%) | 101 |
0.361 (1.00) |
0.901 (1.00) |
0.0982 (1.00) |
0.296 (1.00) |
0.833 (1.00) |
0.415 (1.00) |
0.677 (1.00) |
0.725 (1.00) |
| GPR141 | 8 (8%) | 97 |
0.384 (1.00) |
0.473 (1.00) |
0.00297 (1.00) |
0.0173 (1.00) |
0.301 (1.00) |
0.348 (1.00) |
0.512 (1.00) |
1 (1.00) |
| NAP1L2 | 10 (10%) | 95 |
0.386 (1.00) |
1 (1.00) |
0.402 (1.00) |
0.139 (1.00) |
0.84 (1.00) |
0.783 (1.00) |
0.638 (1.00) |
1 (1.00) |
| C18ORF26 | 13 (12%) | 92 |
0.181 (1.00) |
0.642 (1.00) |
0.622 (1.00) |
0.0587 (1.00) |
1 (1.00) |
0.419 (1.00) |
0.278 (1.00) |
0.428 (1.00) |
| DEFB110 | 5 (5%) | 100 |
0.702 (1.00) |
0.744 (1.00) |
0.103 (1.00) |
0.131 (1.00) |
0.365 (1.00) |
0.288 (1.00) |
0.632 (1.00) |
1 (1.00) |
| IDH1 | 6 (6%) | 99 |
0.313 (1.00) |
0.602 (1.00) |
0.121 (1.00) |
0.405 (1.00) |
0.764 (1.00) |
0.551 (1.00) |
0.502 (1.00) |
0.0972 (1.00) |
| SNAP91 | 15 (14%) | 90 |
0.59 (1.00) |
0.00172 (1.00) |
0.933 (1.00) |
1 (1.00) |
0.162 (1.00) |
0.268 (1.00) |
1 (1.00) |
0.47 (1.00) |
| CA1 | 6 (6%) | 99 |
0.00987 (1.00) |
0.142 (1.00) |
0.751 (1.00) |
0.733 (1.00) |
0.386 (1.00) |
0.271 (1.00) |
0.046 (1.00) |
0.176 (1.00) |
| SERPINB11 | 12 (11%) | 93 |
0.129 (1.00) |
0.478 (1.00) |
0.872 (1.00) |
0.947 (1.00) |
0.292 (1.00) |
0.0606 (1.00) |
0.79 (1.00) |
0.51 (1.00) |
| UGT2B15 | 13 (12%) | 92 |
0.89 (1.00) |
0.284 (1.00) |
0.924 (1.00) |
0.407 (1.00) |
1 (1.00) |
0.852 (1.00) |
0.596 (1.00) |
0.0892 (1.00) |
| ACSM2B | 21 (20%) | 84 |
0.769 (1.00) |
0.0497 (1.00) |
0.236 (1.00) |
0.166 (1.00) |
0.556 (1.00) |
0.207 (1.00) |
0.00697 (1.00) |
0.155 (1.00) |
| C16ORF78 | 8 (8%) | 97 |
0.0199 (1.00) |
0.49 (1.00) |
0.87 (1.00) |
0.27 (1.00) |
0.814 (1.00) |
0.79 (1.00) |
0.23 (1.00) |
0.614 (1.00) |
| TFEC | 10 (10%) | 95 |
0.828 (1.00) |
0.559 (1.00) |
0.154 (1.00) |
0.206 (1.00) |
0.918 (1.00) |
0.275 (1.00) |
0.576 (1.00) |
0.19 (1.00) |
| TRHDE | 24 (23%) | 81 |
0.788 (1.00) |
0.00627 (1.00) |
0.798 (1.00) |
0.058 (1.00) |
0.536 (1.00) |
0.6 (1.00) |
0.797 (1.00) |
0.144 (1.00) |
| OR5AC2 | 13 (12%) | 92 |
0.742 (1.00) |
0.869 (1.00) |
0.647 (1.00) |
0.624 (1.00) |
0.205 (1.00) |
0.0246 (1.00) |
1 (1.00) |
0.896 (1.00) |
| CCDC102B | 11 (10%) | 94 |
0.056 (1.00) |
0.629 (1.00) |
0.722 (1.00) |
0.18 (1.00) |
0.262 (1.00) |
0.606 (1.00) |
0.228 (1.00) |
0.316 (1.00) |
| GRXCR1 | 12 (11%) | 93 |
0.311 (1.00) |
0.202 (1.00) |
0.949 (1.00) |
0.485 (1.00) |
1 (1.00) |
0.926 (1.00) |
0.538 (1.00) |
0.791 (1.00) |
| OR4M2 | 13 (12%) | 92 |
0.726 (1.00) |
0.125 (1.00) |
0.779 (1.00) |
0.666 (1.00) |
0.526 (1.00) |
0.601 (1.00) |
0.185 (1.00) |
0.896 (1.00) |
| PLAC8L1 | 3 (3%) | 102 |
0.187 (1.00) |
0.863 (1.00) |
0.171 (1.00) |
1 (1.00) |
0.259 (1.00) |
0.183 (1.00) |
0.794 (1.00) |
1 (1.00) |
| POM121 | 10 (10%) | 95 |
0.758 (1.00) |
0.366 (1.00) |
0.517 (1.00) |
0.272 (1.00) |
0.766 (1.00) |
0.738 (1.00) |
0.399 (1.00) |
0.388 (1.00) |
| RBM11 | 9 (9%) | 96 |
0.895 (1.00) |
0.378 (1.00) |
0.715 (1.00) |
0.629 (1.00) |
1 (1.00) |
0.835 (1.00) |
0.673 (1.00) |
0.562 (1.00) |
| RUNX1T1 | 16 (15%) | 89 |
0.168 (1.00) |
0.533 (1.00) |
0.0103 (1.00) |
0.0403 (1.00) |
1 (1.00) |
0.46 (1.00) |
0.575 (1.00) |
0.842 (1.00) |
| RGS7 | 17 (16%) | 88 |
0.65 (1.00) |
0.544 (1.00) |
0.795 (1.00) |
0.701 (1.00) |
0.376 (1.00) |
0.314 (1.00) |
0.385 (1.00) |
0.923 (1.00) |
| CLVS2 | 11 (10%) | 94 |
0.386 (1.00) |
0.685 (1.00) |
0.319 (1.00) |
0.629 (1.00) |
0.216 (1.00) |
0.263 (1.00) |
1 (1.00) |
0.701 (1.00) |
| DEFB118 | 6 (6%) | 99 |
0.0237 (1.00) |
0.492 (1.00) |
0.44 (1.00) |
0.604 (1.00) |
0.386 (1.00) |
0.791 (1.00) |
0.645 (1.00) |
1 (1.00) |
| OR52A5 | 12 (11%) | 93 |
0.647 (1.00) |
0.00302 (1.00) |
0.0805 (1.00) |
0.575 (1.00) |
0.0886 (1.00) |
0.0104 (1.00) |
0.927 (1.00) |
0.454 (1.00) |
| SPTLC3 | 13 (12%) | 92 |
0.539 (1.00) |
0.573 (1.00) |
0.787 (1.00) |
0.935 (1.00) |
0.0359 (1.00) |
0.601 (1.00) |
0.414 (1.00) |
0.896 (1.00) |
| ACTL7B | 7 (7%) | 98 |
0.203 (1.00) |
1 (1.00) |
0.712 (1.00) |
0.682 (1.00) |
0.693 (1.00) |
0.454 (1.00) |
0.885 (1.00) |
0.853 (1.00) |
| PHGDH | 7 (7%) | 98 |
0.698 (1.00) |
0.613 (1.00) |
0.708 (1.00) |
0.682 (1.00) |
0.376 (1.00) |
1 (1.00) |
0.471 (1.00) |
0.452 (1.00) |
| RGPD3 | 18 (17%) | 87 |
0.156 (1.00) |
0.321 (1.00) |
0.565 (1.00) |
0.564 (1.00) |
0.458 (1.00) |
0.166 (1.00) |
0.428 (1.00) |
0.561 (1.00) |
| WDR12 | 7 (7%) | 98 |
0.698 (1.00) |
0.951 (1.00) |
0.712 (1.00) |
0.415 (1.00) |
0.693 (1.00) |
0.108 (1.00) |
0.055 (1.00) |
0.0567 (1.00) |
| MPP7 | 13 (12%) | 92 |
0.487 (1.00) |
0.36 (1.00) |
0.622 (1.00) |
0.506 (1.00) |
0.334 (1.00) |
0.149 (1.00) |
0.929 (1.00) |
1 (1.00) |
Methods & Data
Input
-
Mutation data file = SKCM-Regional_LN.mutsig.cluster.txt
-
Molecular subtypes file = SKCM-Regional_LN.transferedmergedcluster.txt
-
Number of patients = 105
-
Number of significantly mutated genes = 74
-
Number of Molecular subtypes = 8
-
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
Chi-square test
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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