Skin Cutaneous Melanoma: Correlation between gene mutation status and molecular subtypes
(Regional_Metastatic cohort)
(Regional_Metastatic 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 72 genes and 8 molecular subtypes across 137 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 72 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
| CDKN2A | 23 (17%) | 114 |
0.401 (1.00) |
0.297 (1.00) |
0.275 (1.00) |
0.252 (1.00) |
0.773 (1.00) |
0.797 (1.00) |
0.874 (1.00) |
0.942 (1.00) |
| TP53 | 23 (17%) | 114 |
0.223 (1.00) |
0.0372 (1.00) |
0.382 (1.00) |
0.535 (1.00) |
0.0742 (1.00) |
0.0594 (1.00) |
0.0154 (1.00) |
0.137 (1.00) |
| BRAF | 73 (53%) | 64 |
0.0593 (1.00) |
0.189 (1.00) |
0.578 (1.00) |
0.0411 (1.00) |
0.41 (1.00) |
0.186 (1.00) |
0.0126 (1.00) |
0.45 (1.00) |
| C15ORF23 | 10 (7%) | 127 |
0.4 (1.00) |
0.0666 (1.00) |
0.722 (1.00) |
1 (1.00) |
0.844 (1.00) |
1 (1.00) |
1 (1.00) |
0.884 (1.00) |
| ERVFRDE1 | 3 (2%) | 134 |
1 (1.00) |
0.49 (1.00) |
1 (1.00) |
1 (1.00) |
0.799 (1.00) |
1 (1.00) |
||
| NRAS | 39 (28%) | 98 |
0.00333 (1.00) |
0.0748 (1.00) |
0.533 (1.00) |
0.15 (1.00) |
0.679 (1.00) |
0.728 (1.00) |
0.393 (1.00) |
0.723 (1.00) |
| PTEN | 12 (9%) | 125 |
0.516 (1.00) |
0.236 (1.00) |
0.152 (1.00) |
0.375 (1.00) |
0.748 (1.00) |
0.276 (1.00) |
0.504 (1.00) |
0.82 (1.00) |
| PPP6C | 14 (10%) | 123 |
0.00801 (1.00) |
0.679 (1.00) |
0.753 (1.00) |
0.498 (1.00) |
0.726 (1.00) |
1 (1.00) |
0.131 (1.00) |
0.41 (1.00) |
| PRB4 | 16 (12%) | 121 |
0.867 (1.00) |
0.84 (1.00) |
0.0201 (1.00) |
0.0912 (1.00) |
0.259 (1.00) |
0.33 (1.00) |
0.582 (1.00) |
0.408 (1.00) |
| RAC1 | 9 (7%) | 128 |
0.777 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.673 (1.00) |
0.823 (1.00) |
0.0483 (1.00) |
| CDH9 | 23 (17%) | 114 |
0.922 (1.00) |
0.459 (1.00) |
0.742 (1.00) |
0.964 (1.00) |
0.807 (1.00) |
1 (1.00) |
0.0216 (1.00) |
0.892 (1.00) |
| STK19 | 9 (7%) | 128 |
0.777 (1.00) |
0.0969 (1.00) |
0.538 (1.00) |
0.659 (1.00) |
0.202 (1.00) |
0.33 (1.00) |
0.136 (1.00) |
0.686 (1.00) |
| ADH1C | 20 (15%) | 117 |
0.113 (1.00) |
0.439 (1.00) |
0.0941 (1.00) |
0.0668 (1.00) |
0.123 (1.00) |
0.397 (1.00) |
0.0594 (1.00) |
0.367 (1.00) |
| TCEB3C | 19 (14%) | 118 |
0.857 (1.00) |
0.328 (1.00) |
0.552 (1.00) |
0.939 (1.00) |
0.407 (1.00) |
0.477 (1.00) |
0.815 (1.00) |
0.504 (1.00) |
| DDX3X | 14 (10%) | 123 |
0.204 (1.00) |
0.726 (1.00) |
0.317 (1.00) |
0.106 (1.00) |
0.307 (1.00) |
0.575 (1.00) |
0.542 (1.00) |
0.11 (1.00) |
| TRAT1 | 9 (7%) | 128 |
0.687 (1.00) |
0.829 (1.00) |
1 (1.00) |
1 (1.00) |
0.57 (1.00) |
0.747 (1.00) |
0.612 (1.00) |
0.686 (1.00) |
| TTN | 108 (79%) | 29 |
0.492 (1.00) |
0.35 (1.00) |
0.229 (1.00) |
0.114 (1.00) |
0.927 (1.00) |
0.727 (1.00) |
0.286 (1.00) |
0.644 (1.00) |
| GH2 | 10 (7%) | 127 |
0.0938 (1.00) |
0.919 (1.00) |
0.398 (1.00) |
0.653 (1.00) |
0.351 (1.00) |
0.637 (1.00) |
0.583 (1.00) |
0.788 (1.00) |
| TFEC | 13 (9%) | 124 |
0.875 (1.00) |
0.623 (1.00) |
0.247 (1.00) |
0.499 (1.00) |
1 (1.00) |
0.561 (1.00) |
0.524 (1.00) |
0.322 (1.00) |
| IDH1 | 7 (5%) | 130 |
0.666 (1.00) |
0.795 (1.00) |
0.568 (1.00) |
0.527 (1.00) |
0.332 (1.00) |
0.42 (1.00) |
0.0381 (1.00) |
0.15 (1.00) |
| WDR12 | 9 (7%) | 128 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.778 (1.00) |
0.682 (1.00) |
0.0837 (1.00) |
0.0182 (1.00) |
0.0373 (1.00) |
| RGS18 | 7 (5%) | 130 |
0.666 (1.00) |
1 (1.00) |
0.538 (1.00) |
0.426 (1.00) |
0.794 (1.00) |
0.78 (1.00) |
0.215 (1.00) |
0.731 (1.00) |
| POF1B | 17 (12%) | 120 |
0.0893 (1.00) |
0.145 (1.00) |
0.443 (1.00) |
0.627 (1.00) |
0.436 (1.00) |
0.892 (1.00) |
0.534 (1.00) |
0.467 (1.00) |
| OR5AC2 | 16 (12%) | 121 |
0.777 (1.00) |
0.71 (1.00) |
0.204 (1.00) |
0.943 (1.00) |
0.444 (1.00) |
0.291 (1.00) |
0.888 (1.00) |
1 (1.00) |
| VEGFC | 13 (9%) | 124 |
0.396 (1.00) |
0.466 (1.00) |
0.817 (1.00) |
0.00544 (1.00) |
0.0299 (1.00) |
0.012 (1.00) |
0.0637 (1.00) |
0.0495 (1.00) |
| RERG | 9 (7%) | 128 |
0.568 (1.00) |
0.683 (1.00) |
0.125 (1.00) |
0.067 (1.00) |
0.519 (1.00) |
0.24 (1.00) |
0.136 (1.00) |
0.386 (1.00) |
| CCNE2 | 10 (7%) | 127 |
0.506 (1.00) |
0.65 (1.00) |
0.258 (1.00) |
0.136 (1.00) |
0.844 (1.00) |
0.763 (1.00) |
0.0229 (1.00) |
0.561 (1.00) |
| GPR141 | 12 (9%) | 125 |
0.557 (1.00) |
0.0125 (1.00) |
0.00133 (0.761) |
0.00724 (1.00) |
0.552 (1.00) |
0.419 (1.00) |
0.221 (1.00) |
0.66 (1.00) |
| GK2 | 17 (12%) | 120 |
0.413 (1.00) |
0.76 (1.00) |
0.747 (1.00) |
1 (1.00) |
0.847 (1.00) |
0.411 (1.00) |
0.502 (1.00) |
0.804 (1.00) |
| NAP1L2 | 12 (9%) | 125 |
0.645 (1.00) |
0.35 (1.00) |
0.722 (1.00) |
0.157 (1.00) |
0.593 (1.00) |
0.791 (1.00) |
0.544 (1.00) |
1 (1.00) |
| SNAP91 | 18 (13%) | 119 |
0.703 (1.00) |
0.566 (1.00) |
0.869 (1.00) |
0.622 (1.00) |
0.625 (1.00) |
0.488 (1.00) |
0.898 (1.00) |
0.331 (1.00) |
| PRB2 | 20 (15%) | 117 |
0.386 (1.00) |
0.953 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.0492 (1.00) |
0.188 (1.00) |
0.00145 (0.827) |
0.0268 (1.00) |
| TLL1 | 27 (20%) | 110 |
0.766 (1.00) |
0.316 (1.00) |
0.765 (1.00) |
0.179 (1.00) |
0.0938 (1.00) |
0.0459 (1.00) |
0.4 (1.00) |
0.407 (1.00) |
| HBD | 8 (6%) | 129 |
0.499 (1.00) |
0.733 (1.00) |
1 (1.00) |
0.158 (1.00) |
0.213 (1.00) |
0.0612 (1.00) |
0.0721 (1.00) |
0.143 (1.00) |
| GRXCR2 | 11 (8%) | 126 |
0.846 (1.00) |
1 (1.00) |
0.371 (1.00) |
0.719 (1.00) |
0.624 (1.00) |
0.467 (1.00) |
0.611 (1.00) |
0.801 (1.00) |
| NOTCH2NL | 9 (7%) | 128 |
0.21 (1.00) |
0.569 (1.00) |
0.194 (1.00) |
0.107 (1.00) |
0.0409 (1.00) |
0.299 (1.00) |
0.553 (1.00) |
0.0373 (1.00) |
| OXA1L | 4 (3%) | 133 |
0.685 (1.00) |
0.183 (1.00) |
0.827 (1.00) |
0.545 (1.00) |
0.835 (1.00) |
0.44 (1.00) |
||
| AREG | 6 (4%) | 131 |
0.717 (1.00) |
0.38 (1.00) |
0.832 (1.00) |
0.689 (1.00) |
0.879 (1.00) |
0.49 (1.00) |
1 (1.00) |
0.694 (1.00) |
| HBG2 | 6 (4%) | 131 |
0.294 (1.00) |
0.38 (1.00) |
1 (1.00) |
1 (1.00) |
0.504 (1.00) |
0.562 (1.00) |
||
| SERPINB4 | 20 (15%) | 117 |
0.487 (1.00) |
0.75 (1.00) |
0.0154 (1.00) |
0.0183 (1.00) |
0.483 (1.00) |
0.397 (1.00) |
0.951 (1.00) |
0.486 (1.00) |
| SPTLC3 | 14 (10%) | 123 |
1 (1.00) |
0.638 (1.00) |
0.418 (1.00) |
0.859 (1.00) |
0.0414 (1.00) |
0.439 (1.00) |
0.234 (1.00) |
0.638 (1.00) |
| TAF1A | 9 (7%) | 128 |
0.964 (1.00) |
0.911 (1.00) |
0.722 (1.00) |
0.212 (1.00) |
0.345 (1.00) |
0.602 (1.00) |
0.908 (1.00) |
0.454 (1.00) |
| CLVS2 | 13 (9%) | 124 |
0.194 (1.00) |
0.542 (1.00) |
0.609 (1.00) |
0.964 (1.00) |
0.0299 (1.00) |
0.19 (1.00) |
0.808 (1.00) |
0.831 (1.00) |
| CCDC102B | 15 (11%) | 122 |
0.219 (1.00) |
0.889 (1.00) |
0.15 (1.00) |
0.921 (1.00) |
0.695 (1.00) |
0.558 (1.00) |
0.881 (1.00) |
0.92 (1.00) |
| OR4N2 | 15 (11%) | 122 |
0.031 (1.00) |
0.792 (1.00) |
0.27 (1.00) |
0.625 (1.00) |
0.0353 (1.00) |
0.142 (1.00) |
0.158 (1.00) |
0.359 (1.00) |
| OR8D4 | 9 (7%) | 128 |
0.568 (1.00) |
0.829 (1.00) |
0.0528 (1.00) |
0.756 (1.00) |
0.519 (1.00) |
0.747 (1.00) |
0.612 (1.00) |
0.386 (1.00) |
| RBM11 | 10 (7%) | 127 |
0.45 (1.00) |
0.919 (1.00) |
0.32 (1.00) |
0.917 (1.00) |
0.65 (1.00) |
0.697 (1.00) |
0.523 (1.00) |
0.495 (1.00) |
| DEFB118 | 7 (5%) | 130 |
0.455 (1.00) |
0.374 (1.00) |
0.538 (1.00) |
0.225 (1.00) |
0.706 (1.00) |
0.319 (1.00) |
0.474 (1.00) |
0.613 (1.00) |
| GRXCR1 | 13 (9%) | 124 |
0.561 (1.00) |
0.329 (1.00) |
1 (1.00) |
0.574 (1.00) |
0.247 (1.00) |
0.866 (1.00) |
0.361 (1.00) |
0.559 (1.00) |
| RGPD3 | 22 (16%) | 115 |
0.347 (1.00) |
0.838 (1.00) |
0.672 (1.00) |
0.768 (1.00) |
0.188 (1.00) |
0.446 (1.00) |
0.546 (1.00) |
0.652 (1.00) |
| CA1 | 8 (6%) | 129 |
0.201 (1.00) |
0.241 (1.00) |
0.0149 (1.00) |
0.415 (1.00) |
0.151 (1.00) |
0.637 (1.00) |
0.0596 (1.00) |
0.0689 (1.00) |
| HNF4G | 15 (11%) | 122 |
0.533 (1.00) |
0.287 (1.00) |
1 (1.00) |
0.894 (1.00) |
0.94 (1.00) |
0.881 (1.00) |
0.495 (1.00) |
0.163 (1.00) |
| ACTL7B | 8 (6%) | 129 |
0.574 (1.00) |
0.594 (1.00) |
0.371 (1.00) |
0.0892 (1.00) |
0.473 (1.00) |
0.369 (1.00) |
0.46 (1.00) |
0.493 (1.00) |
| SPAG16 | 12 (9%) | 125 |
0.59 (1.00) |
0.551 (1.00) |
0.785 (1.00) |
0.86 (1.00) |
0.642 (1.00) |
0.497 (1.00) |
0.125 (1.00) |
0.327 (1.00) |
| PCDHB8 | 23 (17%) | 114 |
0.0658 (1.00) |
0.0646 (1.00) |
0.26 (1.00) |
0.781 (1.00) |
0.354 (1.00) |
0.228 (1.00) |
0.109 (1.00) |
0.892 (1.00) |
| HIST1H2AA | 5 (4%) | 132 |
0.404 (1.00) |
0.523 (1.00) |
0.832 (1.00) |
0.572 (1.00) |
0.375 (1.00) |
0.434 (1.00) |
0.631 (1.00) |
0.806 (1.00) |
| OR10K2 | 14 (10%) | 123 |
1 (1.00) |
0.94 (1.00) |
0.71 (1.00) |
0.611 (1.00) |
0.68 (1.00) |
0.666 (1.00) |
0.293 (1.00) |
0.313 (1.00) |
| PHGDH | 8 (6%) | 129 |
0.707 (1.00) |
0.812 (1.00) |
0.601 (1.00) |
0.317 (1.00) |
0.594 (1.00) |
1 (1.00) |
0.514 (1.00) |
0.348 (1.00) |
| OR9K2 | 11 (8%) | 126 |
0.375 (1.00) |
1 (1.00) |
0.0592 (1.00) |
0.0905 (1.00) |
0.211 (1.00) |
0.55 (1.00) |
0.233 (1.00) |
1 (1.00) |
| LIN7A | 8 (6%) | 129 |
0.297 (1.00) |
0.0512 (1.00) |
0.538 (1.00) |
0.924 (1.00) |
0.241 (1.00) |
0.456 (1.00) |
0.201 (1.00) |
0.869 (1.00) |
| USP17L2 | 13 (9%) | 124 |
0.55 (1.00) |
0.542 (1.00) |
0.361 (1.00) |
0.197 (1.00) |
0.581 (1.00) |
0.414 (1.00) |
0.698 (1.00) |
0.616 (1.00) |
| ANKRD20A4 | 4 (3%) | 133 |
0.555 (1.00) |
0.307 (1.00) |
0.117 (1.00) |
0.0461 (1.00) |
0.185 (1.00) |
0.34 (1.00) |
0.433 (1.00) |
0.758 (1.00) |
| CYLC2 | 14 (10%) | 123 |
0.433 (1.00) |
0.823 (1.00) |
0.258 (1.00) |
0.631 (1.00) |
0.1 (1.00) |
0.043 (1.00) |
0.316 (1.00) |
0.283 (1.00) |
| VGLL1 | 5 (4%) | 132 |
0.749 (1.00) |
0.149 (1.00) |
0.832 (1.00) |
0.831 (1.00) |
0.735 (1.00) |
1 (1.00) |
0.276 (1.00) |
0.643 (1.00) |
| DEFB110 | 5 (4%) | 132 |
0.696 (1.00) |
0.149 (1.00) |
0.237 (1.00) |
0.121 (1.00) |
0.522 (1.00) |
0.847 (1.00) |
0.535 (1.00) |
1 (1.00) |
| LCE1B | 7 (5%) | 130 |
0.151 (1.00) |
1 (1.00) |
0.873 (1.00) |
1 (1.00) |
0.794 (1.00) |
0.78 (1.00) |
0.884 (1.00) |
0.858 (1.00) |
| PARM1 | 10 (7%) | 127 |
0.45 (1.00) |
0.546 (1.00) |
0.722 (1.00) |
0.698 (1.00) |
1 (1.00) |
0.479 (1.00) |
0.837 (1.00) |
0.884 (1.00) |
| ACSM2B | 24 (18%) | 113 |
0.369 (1.00) |
0.514 (1.00) |
0.828 (1.00) |
0.744 (1.00) |
0.219 (1.00) |
0.0832 (1.00) |
0.0209 (1.00) |
0.32 (1.00) |
| BAGE2 | 7 (5%) | 130 |
0.492 (1.00) |
0.332 (1.00) |
1 (1.00) |
0.805 (1.00) |
0.0814 (1.00) |
0.78 (1.00) |
0.375 (1.00) |
0.858 (1.00) |
| CECR6 | 6 (4%) | 131 |
0.792 (1.00) |
0.173 (1.00) |
0.632 (1.00) |
0.0102 (1.00) |
0.281 (1.00) |
0.662 (1.00) |
0.262 (1.00) |
0.842 (1.00) |
| OR4M2 | 15 (11%) | 122 |
0.517 (1.00) |
0.271 (1.00) |
0.574 (1.00) |
0.488 (1.00) |
1 (1.00) |
0.632 (1.00) |
0.147 (1.00) |
0.559 (1.00) |
| CERKL | 10 (7%) | 127 |
0.44 (1.00) |
0.35 (1.00) |
1 (1.00) |
0.588 (1.00) |
1 (1.00) |
0.431 (1.00) |
0.837 (1.00) |
0.884 (1.00) |
Methods & Data
Input
-
Mutation data file = SKCM-Regional_Metastatic.mutsig.cluster.txt
-
Molecular subtypes file = SKCM-Regional_Metastatic.transferedmergedcluster.txt
-
Number of patients = 137
-
Number of significantly mutated genes = 72
-
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
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)
Copyright © 2013
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.