Skin Cutaneous Melanoma: Correlation between gene mutation status and molecular subtypes
(NF1_Any_Mutants cohort)
(NF1_Any_Mutants 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 75 genes and 8 molecular subtypes across 31 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 75 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 | Chi-square test | |
| NRAS | 9 (29%) | 22 |
0.704 (1.00) |
0.0207 (1.00) |
1 (1.00) |
1 (1.00) |
0.685 (1.00) |
0.866 (1.00) |
0.704 (1.00) |
0.594 (1.00) |
| TPTE | 15 (48%) | 16 |
0.289 (1.00) |
0.722 (1.00) |
1 (1.00) |
0.281 (1.00) |
0.901 (1.00) |
0.109 (1.00) |
0.289 (1.00) |
0.578 (1.00) |
| TP53 | 10 (32%) | 21 |
0.0538 (1.00) |
0.441 (1.00) |
0.366 (1.00) |
1 (1.00) |
0.0249 (1.00) |
0.0581 (1.00) |
1 (1.00) |
0.704 (1.00) |
| GRXCR1 | 10 (32%) | 21 |
0.704 (1.00) |
1 (1.00) |
0.621 (1.00) |
0.539 (1.00) |
0.312 (1.00) |
0.17 (1.00) |
0.458 (1.00) |
0.617 (1.00) |
| BRAF | 9 (29%) | 22 |
0.433 (1.00) |
0.693 (1.00) |
0.621 (1.00) |
0.539 (1.00) |
0.887 (1.00) |
0.829 (1.00) |
1 (1.00) |
0.356 (1.00) |
| TRAT1 | 7 (23%) | 24 |
0.685 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.225 (1.00) |
0.94 (1.00) |
0.0373 (1.00) |
0.286 (1.00) |
| ZNF585B | 9 (29%) | 22 |
1 (1.00) |
0.693 (1.00) |
0.052 (1.00) |
0.257 (1.00) |
0.372 (1.00) |
0.0602 (1.00) |
0.0538 (1.00) |
0.197 (1.00) |
| TPTE2 | 12 (39%) | 19 |
0.149 (1.00) |
1 (1.00) |
0.405 (1.00) |
0.604 (1.00) |
0.243 (1.00) |
0.0126 (1.00) |
0.473 (1.00) |
0.608 (1.00) |
| OR51S1 | 11 (35%) | 20 |
0.458 (1.00) |
0.153 (1.00) |
0.345 (1.00) |
0.257 (1.00) |
0.0425 (1.00) |
0.121 (1.00) |
1 (1.00) |
0.465 (1.00) |
| RAC1 | 5 (16%) | 26 |
0.333 (1.00) |
0.636 (1.00) |
1 (1.00) |
1 (1.00) |
0.0327 (1.00) |
0.0233 (1.00) |
1 (1.00) |
0.273 (1.00) |
| CDKN2A | 6 (19%) | 25 |
0.172 (1.00) |
0.37 (1.00) |
1 (1.00) |
1 (1.00) |
0.0277 (1.00) |
0.138 (1.00) |
1 (1.00) |
0.0201 (1.00) |
| C7 | 14 (45%) | 17 |
0.479 (1.00) |
0.149 (1.00) |
0.371 (1.00) |
0.59 (1.00) |
0.485 (1.00) |
0.157 (1.00) |
0.479 (1.00) |
0.366 (1.00) |
| C15ORF23 | 6 (19%) | 25 |
0.172 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0277 (1.00) |
0.0452 (1.00) |
0.394 (1.00) |
0.928 (1.00) |
| GLRB | 9 (29%) | 22 |
1 (1.00) |
0.693 (1.00) |
0.318 (1.00) |
0.27 (1.00) |
0.887 (1.00) |
1 (1.00) |
1 (1.00) |
0.171 (1.00) |
| FAM58A | 5 (16%) | 26 |
1 (1.00) |
0.148 (1.00) |
0.209 (1.00) |
0.453 (1.00) |
0.322 (1.00) |
0.911 (1.00) |
1 (1.00) |
0.046 (1.00) |
| EPHA6 | 15 (48%) | 16 |
0.156 (1.00) |
0.156 (1.00) |
1 (1.00) |
0.0932 (1.00) |
0.0155 (1.00) |
0.0135 (1.00) |
1 (1.00) |
0.0915 (1.00) |
| NAP1L2 | 9 (29%) | 22 |
0.252 (1.00) |
0.456 (1.00) |
1 (1.00) |
1 (1.00) |
0.685 (1.00) |
0.107 (1.00) |
0.704 (1.00) |
0.838 (1.00) |
| OR4K5 | 10 (32%) | 21 |
1 (1.00) |
1 (1.00) |
0.657 (1.00) |
0.589 (1.00) |
0.443 (1.00) |
0.952 (1.00) |
1 (1.00) |
0.209 (1.00) |
| SLC9A11 | 13 (42%) | 18 |
1 (1.00) |
0.0669 (1.00) |
0.371 (1.00) |
0.59 (1.00) |
0.729 (1.00) |
0.655 (1.00) |
0.285 (1.00) |
0.958 (1.00) |
| ADAMTS20 | 18 (58%) | 13 |
1 (1.00) |
0.481 (1.00) |
1 (1.00) |
1 (1.00) |
0.386 (1.00) |
0.887 (1.00) |
0.473 (1.00) |
0.605 (1.00) |
| SLC38A4 | 13 (42%) | 18 |
0.149 (1.00) |
0.00398 (1.00) |
0.405 (1.00) |
1 (1.00) |
0.0655 (1.00) |
0.458 (1.00) |
1 (1.00) |
0.172 (1.00) |
| OR2T2 | 8 (26%) | 23 |
0.685 (1.00) |
1 (1.00) |
1 (1.00) |
0.27 (1.00) |
0.606 (1.00) |
0.946 (1.00) |
0.685 (1.00) |
0.899 (1.00) |
| PRB2 | 11 (35%) | 20 |
0.458 (1.00) |
0.477 (1.00) |
1 (1.00) |
1 (1.00) |
0.161 (1.00) |
0.3 (1.00) |
1 (1.00) |
0.594 (1.00) |
| COL21A1 | 12 (39%) | 19 |
0.716 (1.00) |
0.288 (1.00) |
0.052 (1.00) |
0.257 (1.00) |
0.218 (1.00) |
0.643 (1.00) |
0.473 (1.00) |
0.335 (1.00) |
| OR4N2 | 10 (32%) | 21 |
0.704 (1.00) |
0.121 (1.00) |
1 (1.00) |
0.589 (1.00) |
0.443 (1.00) |
0.911 (1.00) |
1 (1.00) |
0.304 (1.00) |
| PROX1 | 7 (23%) | 24 |
1 (1.00) |
0.198 (1.00) |
0.621 (1.00) |
1 (1.00) |
0.485 (1.00) |
0.185 (1.00) |
0.22 (1.00) |
0.61 (1.00) |
| ANGPT1 | 10 (32%) | 21 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.312 (1.00) |
0.209 (1.00) |
0.252 (1.00) |
0.223 (1.00) |
| C8A | 11 (35%) | 20 |
0.135 (1.00) |
1 (1.00) |
0.345 (1.00) |
1 (1.00) |
0.182 (1.00) |
0.845 (1.00) |
0.716 (1.00) |
0.676 (1.00) |
| SERPINB11 | 7 (23%) | 24 |
0.22 (1.00) |
0.671 (1.00) |
1 (1.00) |
1 (1.00) |
0.418 (1.00) |
0.836 (1.00) |
1 (1.00) |
0.54 (1.00) |
| C18ORF34 | 11 (35%) | 20 |
0.458 (1.00) |
1 (1.00) |
0.657 (1.00) |
1 (1.00) |
0.182 (1.00) |
0.487 (1.00) |
0.716 (1.00) |
0.0518 (1.00) |
| FRG2B | 7 (23%) | 24 |
1 (1.00) |
0.412 (1.00) |
1 (1.00) |
1 (1.00) |
0.871 (1.00) |
0.94 (1.00) |
1 (1.00) |
0.756 (1.00) |
| LPPR1 | 5 (16%) | 26 |
1 (1.00) |
0.148 (1.00) |
0.621 (1.00) |
1 (1.00) |
0.596 (1.00) |
1 (1.00) |
1 (1.00) |
0.798 (1.00) |
| THEMIS | 10 (32%) | 21 |
1 (1.00) |
0.28 (1.00) |
1 (1.00) |
1 (1.00) |
0.555 (1.00) |
0.871 (1.00) |
1 (1.00) |
0.455 (1.00) |
| SNAP91 | 10 (32%) | 21 |
0.704 (1.00) |
0.441 (1.00) |
0.345 (1.00) |
1 (1.00) |
0.794 (1.00) |
0.837 (1.00) |
0.252 (1.00) |
0.48 (1.00) |
| SLC27A6 | 8 (26%) | 23 |
1 (1.00) |
0.24 (1.00) |
0.366 (1.00) |
1 (1.00) |
0.451 (1.00) |
0.207 (1.00) |
0.113 (1.00) |
0.487 (1.00) |
| CXORF22 | 11 (35%) | 20 |
0.0659 (1.00) |
0.707 (1.00) |
1 (1.00) |
1 (1.00) |
0.0336 (1.00) |
0.00731 (1.00) |
0.458 (1.00) |
0.118 (1.00) |
| NOBOX | 8 (26%) | 23 |
0.433 (1.00) |
0.698 (1.00) |
0.345 (1.00) |
1 (1.00) |
0.606 (1.00) |
0.773 (1.00) |
0.0155 (1.00) |
0.268 (1.00) |
| MUC7 | 8 (26%) | 23 |
0.685 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.201 (1.00) |
0.773 (1.00) |
1 (1.00) |
0.81 (1.00) |
| GIMAP7 | 6 (19%) | 25 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.28 (1.00) |
0.812 (1.00) |
1 (1.00) |
0.436 (1.00) |
| SYT17 | 6 (19%) | 25 |
0.394 (1.00) |
0.0209 (1.00) |
1 (1.00) |
1 (1.00) |
0.188 (1.00) |
0.602 (1.00) |
0.0068 (1.00) |
0.47 (1.00) |
| ASB15 | 9 (29%) | 22 |
0.704 (1.00) |
0.233 (1.00) |
0.366 (1.00) |
1 (1.00) |
1 (1.00) |
0.544 (1.00) |
1 (1.00) |
0.479 (1.00) |
| OR4A15 | 8 (26%) | 23 |
0.685 (1.00) |
1 (1.00) |
1 (1.00) |
0.27 (1.00) |
0.263 (1.00) |
0.332 (1.00) |
1 (1.00) |
0.547 (1.00) |
| PROL1 | 9 (29%) | 22 |
1 (1.00) |
0.233 (1.00) |
1 (1.00) |
1 (1.00) |
0.887 (1.00) |
0.906 (1.00) |
0.433 (1.00) |
0.0653 (1.00) |
| DSG3 | 16 (52%) | 15 |
1 (1.00) |
0.722 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.892 (1.00) |
1 (1.00) |
0.853 (1.00) |
| OPRK1 | 9 (29%) | 22 |
1 (1.00) |
1 (1.00) |
0.366 (1.00) |
0.273 (1.00) |
0.146 (1.00) |
0.0966 (1.00) |
0.704 (1.00) |
0.197 (1.00) |
| PCSK5 | 13 (42%) | 18 |
0.722 (1.00) |
0.717 (1.00) |
1 (1.00) |
1 (1.00) |
0.729 (1.00) |
0.887 (1.00) |
0.722 (1.00) |
0.905 (1.00) |
| OR52A1 | 8 (26%) | 23 |
0.685 (1.00) |
1 (1.00) |
0.273 (1.00) |
1 (1.00) |
0.451 (1.00) |
0.896 (1.00) |
0.685 (1.00) |
0.611 (1.00) |
| ACSM2B | 10 (32%) | 21 |
1 (1.00) |
0.441 (1.00) |
1 (1.00) |
0.589 (1.00) |
1 (1.00) |
0.837 (1.00) |
0.704 (1.00) |
0.304 (1.00) |
| NOL4 | 11 (35%) | 20 |
0.458 (1.00) |
0.477 (1.00) |
0.405 (1.00) |
0.604 (1.00) |
0.0659 (1.00) |
0.3 (1.00) |
0.0659 (1.00) |
0.356 (1.00) |
| OXA1L | 4 (13%) | 27 |
1 (1.00) |
0.304 (1.00) |
1 (1.00) |
1 (1.00) |
0.815 (1.00) |
0.813 (1.00) |
0.333 (1.00) |
0.367 (1.00) |
| PPFIA2 | 12 (39%) | 19 |
1 (1.00) |
0.724 (1.00) |
1 (1.00) |
1 (1.00) |
0.896 (1.00) |
0.956 (1.00) |
0.716 (1.00) |
0.933 (1.00) |
| IL1F8 | 6 (19%) | 25 |
1 (1.00) |
0.0671 (1.00) |
1 (1.00) |
0.453 (1.00) |
1 (1.00) |
0.0865 (1.00) |
0.0177 (1.00) |
0.169 (1.00) |
| UGT2A1 | 7 (23%) | 24 |
1 (1.00) |
0.412 (1.00) |
0.273 (1.00) |
1 (1.00) |
1 (1.00) |
0.606 (1.00) |
1 (1.00) |
0.756 (1.00) |
| SYT13 | 4 (13%) | 27 |
1 (1.00) |
1 (1.00) |
0.526 (1.00) |
1 (1.00) |
0.048 (1.00) |
0.18 (1.00) |
0.6 (1.00) |
0.0791 (1.00) |
| ASAH2 | 6 (19%) | 25 |
0.0829 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.445 (1.00) |
0.867 (1.00) |
0.0829 (1.00) |
0.544 (1.00) |
| ZNF679 | 7 (23%) | 24 |
0.22 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.645 (1.00) |
0.606 (1.00) |
0.22 (1.00) |
0.756 (1.00) |
| C10ORF54 | 6 (19%) | 25 |
0.172 (1.00) |
0.664 (1.00) |
1 (1.00) |
1 (1.00) |
0.151 (1.00) |
0.165 (1.00) |
1 (1.00) |
0.185 (1.00) |
| C10ORF120 | 7 (23%) | 24 |
0.394 (1.00) |
0.671 (1.00) |
0.621 (1.00) |
1 (1.00) |
0.102 (1.00) |
0.0187 (1.00) |
0.22 (1.00) |
0.61 (1.00) |
| CHSY1 | 5 (16%) | 26 |
0.172 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.178 (1.00) |
0.592 (1.00) |
0.172 (1.00) |
0.401 (1.00) |
| CSF2RA | 6 (19%) | 25 |
0.394 (1.00) |
0.664 (1.00) |
0.142 (1.00) |
0.194 (1.00) |
0.862 (1.00) |
0.637 (1.00) |
1 (1.00) |
0.786 (1.00) |
| KCND2 | 10 (32%) | 21 |
1 (1.00) |
1 (1.00) |
0.366 (1.00) |
1 (1.00) |
0.312 (1.00) |
0.618 (1.00) |
0.704 (1.00) |
0.646 (1.00) |
| SPEF2 | 12 (39%) | 19 |
0.273 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0816 (1.00) |
0.737 (1.00) |
0.716 (1.00) |
0.0422 (1.00) |
| RPGRIP1 | 8 (26%) | 23 |
1 (1.00) |
0.412 (1.00) |
0.621 (1.00) |
1 (1.00) |
0.606 (1.00) |
0.737 (1.00) |
0.433 (1.00) |
0.711 (1.00) |
| OR2L3 | 4 (13%) | 27 |
0.6 (1.00) |
0.304 (1.00) |
0.526 (1.00) |
1 (1.00) |
0.53 (1.00) |
0.744 (1.00) |
1 (1.00) |
0.727 (1.00) |
| CCDC54 | 6 (19%) | 25 |
0.172 (1.00) |
0.664 (1.00) |
0.621 (1.00) |
0.539 (1.00) |
0.231 (1.00) |
0.411 (1.00) |
1 (1.00) |
0.29 (1.00) |
| KLHL14 | 7 (23%) | 24 |
0.394 (1.00) |
1 (1.00) |
1 (1.00) |
0.27 (1.00) |
0.485 (1.00) |
0.606 (1.00) |
1 (1.00) |
0.682 (1.00) |
| ZFX | 7 (23%) | 24 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.755 (1.00) |
0.94 (1.00) |
0.685 (1.00) |
0.86 (1.00) |
| KLHL13 | 10 (32%) | 21 |
1 (1.00) |
0.068 (1.00) |
1 (1.00) |
1 (1.00) |
0.794 (1.00) |
1 (1.00) |
0.704 (1.00) |
0.131 (1.00) |
| NSUN7 | 5 (16%) | 26 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.453 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.478 (1.00) |
| VEGFC | 6 (19%) | 25 |
1 (1.00) |
0.185 (1.00) |
1 (1.00) |
0.539 (1.00) |
0.52 (1.00) |
0.411 (1.00) |
0.0829 (1.00) |
0.203 (1.00) |
| TMEM202 | 5 (16%) | 26 |
0.172 (1.00) |
0.636 (1.00) |
0.621 (1.00) |
0.194 (1.00) |
0.829 (1.00) |
0.681 (1.00) |
0.654 (1.00) |
0.657 (1.00) |
| ERC2 | 15 (48%) | 16 |
0.156 (1.00) |
0.156 (1.00) |
0.0186 (1.00) |
0.281 (1.00) |
0.0845 (1.00) |
0.214 (1.00) |
0.289 (1.00) |
0.263 (1.00) |
| GRM3 | 12 (39%) | 19 |
0.716 (1.00) |
0.288 (1.00) |
0.176 (1.00) |
0.127 (1.00) |
0.0816 (1.00) |
0.111 (1.00) |
0.149 (1.00) |
0.114 (1.00) |
| CDH12 | 9 (29%) | 22 |
0.252 (1.00) |
0.132 (1.00) |
1 (1.00) |
0.273 (1.00) |
0.887 (1.00) |
0.201 (1.00) |
0.252 (1.00) |
0.402 (1.00) |
| SIRPB1 | 7 (23%) | 24 |
1 (1.00) |
0.671 (1.00) |
0.124 (1.00) |
0.539 (1.00) |
0.485 (1.00) |
0.325 (1.00) |
0.685 (1.00) |
0.574 (1.00) |
Methods & Data
Input
-
Mutation data file = SKCM-NF1_Any_Mutants.mutsig.cluster.txt
-
Molecular subtypes file = SKCM-NF1_Any_Mutants.transferedmergedcluster.txt
-
Number of patients = 31
-
Number of significantly mutated genes = 75
-
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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