Skin Cutaneous Melanoma: Correlation between gene mutation status and selected clinical features
(metastatic tumor cohort)
(metastatic tumor 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 selected clinical features.
Summary
Testing the association between mutation status of 125 genes and 7 clinical features across 146 patients, 3 significant findings detected with Q value < 0.25.
-
PTEN mutation correlated to 'DISTANT.METASTASIS'.
-
MUC7 mutation correlated to 'AGE'.
-
HAPLN1 mutation correlated to 'DISTANT.METASTASIS'.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between mutation status of 125 genes and 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 significant findings detected.
|
Clinical Features |
Time to Death |
AGE | GENDER |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
| nMutated (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Chi-square test | Chi-square test | t-test | Chi-square test | |
| PTEN | 11 (8%) | 135 |
0.999 (1.00) |
0.601 (1.00) |
0.34 (1.00) |
0.00018 (0.133) |
0.72 (1.00) |
0.0185 (1.00) |
|
| MUC7 | 11 (8%) | 135 |
0.466 (1.00) |
0.000185 (0.136) |
0.529 (1.00) |
0.965 (1.00) |
0.795 (1.00) |
0.668 (1.00) |
|
| HAPLN1 | 7 (5%) | 139 |
0.259 (1.00) |
0.178 (1.00) |
0.705 (1.00) |
0.000316 (0.233) |
0.93 (1.00) |
0.196 (1.00) |
|
| TP53 | 25 (17%) | 121 |
0.489 (1.00) |
0.0816 (1.00) |
1 (1.00) |
0.651 (1.00) |
0.295 (1.00) |
0.315 (1.00) |
|
| BRAF | 73 (50%) | 73 |
0.195 (1.00) |
0.0472 (1.00) |
1 (1.00) |
0.389 (1.00) |
0.684 (1.00) |
0.852 (1.00) |
|
| C15ORF23 | 10 (7%) | 136 |
0.452 (1.00) |
0.672 (1.00) |
0.741 (1.00) |
0.977 (1.00) |
0.69 (1.00) |
0.426 (1.00) |
|
| CDKN2A | 22 (15%) | 124 |
0.713 (1.00) |
0.654 (1.00) |
1 (1.00) |
0.898 (1.00) |
0.474 (1.00) |
0.729 (1.00) |
|
| NRAS | 45 (31%) | 101 |
0.73 (1.00) |
0.196 (1.00) |
0.857 (1.00) |
0.575 (1.00) |
0.928 (1.00) |
0.291 (1.00) |
|
| OXA1L | 4 (3%) | 142 |
0.885 (1.00) |
0.793 (1.00) |
0.644 (1.00) |
0.995 (1.00) |
0.738 (1.00) |
0.501 (1.00) |
|
| STK19 | 9 (6%) | 137 |
0.332 (1.00) |
0.516 (1.00) |
0.313 (1.00) |
0.981 (1.00) |
0.854 (1.00) |
0.913 (1.00) |
|
| RAC1 | 11 (8%) | 135 |
0.048 (1.00) |
0.497 (1.00) |
1 (1.00) |
0.977 (1.00) |
0.916 (1.00) |
0.384 (1.00) |
|
| ACSM2B | 28 (19%) | 118 |
0.164 (1.00) |
0.968 (1.00) |
0.00251 (1.00) |
0.827 (1.00) |
0.574 (1.00) |
0.665 (1.00) |
|
| CADM2 | 16 (11%) | 130 |
0.717 (1.00) |
0.736 (1.00) |
1 (1.00) |
0.927 (1.00) |
0.358 (1.00) |
0.337 (1.00) |
|
| OR51S1 | 16 (11%) | 130 |
0.445 (1.00) |
0.495 (1.00) |
1 (1.00) |
0.944 (1.00) |
0.465 (1.00) |
0.16 (1.00) |
|
| LCE1B | 10 (7%) | 136 |
0.392 (1.00) |
0.684 (1.00) |
0.513 (1.00) |
0.977 (1.00) |
0.351 (1.00) |
0.637 (1.00) |
|
| IDH1 | 7 (5%) | 139 |
0.799 (1.00) |
0.0104 (1.00) |
0.432 (1.00) |
0.986 (1.00) |
0.923 (1.00) |
0.544 (1.00) |
|
| TAF1A | 8 (5%) | 138 |
0.291 (1.00) |
0.622 (1.00) |
0.712 (1.00) |
0.00355 (1.00) |
0.932 (1.00) |
0.864 (1.00) |
|
| NAP1L2 | 14 (10%) | 132 |
0.362 (1.00) |
0.077 (1.00) |
0.4 (1.00) |
0.951 (1.00) |
0.604 (1.00) |
0.447 (1.00) |
|
| PPP6C | 14 (10%) | 132 |
0.0327 (1.00) |
0.578 (1.00) |
1 (1.00) |
0.404 (1.00) |
0.135 (1.00) |
0.474 (1.00) |
|
| FRG2B | 10 (7%) | 136 |
0.525 (1.00) |
0.0205 (1.00) |
0.513 (1.00) |
0.971 (1.00) |
0.852 (1.00) |
0.599 (1.00) |
|
| USP29 | 25 (17%) | 121 |
0.0527 (1.00) |
0.0751 (1.00) |
0.264 (1.00) |
0.876 (1.00) |
0.677 (1.00) |
0.412 (1.00) |
|
| PRB4 | 16 (11%) | 130 |
0.125 (1.00) |
0.234 (1.00) |
0.284 (1.00) |
0.449 (1.00) |
0.759 (1.00) |
0.907 (1.00) |
|
| HIST1H2AA | 7 (5%) | 139 |
0.88 (1.00) |
0.961 (1.00) |
1 (1.00) |
0.986 (1.00) |
0.932 (1.00) |
0.718 (1.00) |
|
| RPTN | 23 (16%) | 123 |
0.639 (1.00) |
0.337 (1.00) |
0.816 (1.00) |
0.898 (1.00) |
0.482 (1.00) |
0.171 (1.00) |
|
| ZNF479 | 13 (9%) | 133 |
0.307 (1.00) |
0.175 (1.00) |
0.569 (1.00) |
0.355 (1.00) |
0.692 (1.00) |
0.782 (1.00) |
|
| C8A | 19 (13%) | 127 |
0.0477 (1.00) |
0.0291 (1.00) |
0.129 (1.00) |
0.0637 (1.00) |
0.747 (1.00) |
0.576 (1.00) |
|
| FUT9 | 16 (11%) | 130 |
0.986 (1.00) |
0.0241 (1.00) |
1 (1.00) |
0.936 (1.00) |
0.76 (1.00) |
0.589 (1.00) |
|
| ZNF679 | 15 (10%) | 131 |
0.696 (1.00) |
0.412 (1.00) |
0.783 (1.00) |
0.944 (1.00) |
0.713 (1.00) |
0.487 (1.00) |
|
| NRK | 18 (12%) | 128 |
0.364 (1.00) |
0.741 (1.00) |
0.797 (1.00) |
0.927 (1.00) |
0.709 (1.00) |
0.622 (1.00) |
|
| CDH9 | 26 (18%) | 120 |
0.431 (1.00) |
0.427 (1.00) |
1 (1.00) |
0.827 (1.00) |
0.434 (1.00) |
0.0723 (1.00) |
|
| PRAMEF11 | 13 (9%) | 133 |
0.108 (1.00) |
0.143 (1.00) |
0.569 (1.00) |
0.959 (1.00) |
0.238 (1.00) |
0.738 (1.00) |
|
| DDX3X | 15 (10%) | 131 |
0.584 (1.00) |
0.416 (1.00) |
0.162 (1.00) |
0.000441 (0.324) |
0.939 (1.00) |
0.744 (1.00) |
|
| GRXCR1 | 15 (10%) | 131 |
0.592 (1.00) |
0.0186 (1.00) |
0.783 (1.00) |
0.951 (1.00) |
0.795 (1.00) |
0.325 (1.00) |
|
| PRB2 | 21 (14%) | 125 |
0.576 (1.00) |
0.0107 (1.00) |
0.0532 (1.00) |
0.908 (1.00) |
0.659 (1.00) |
0.335 (1.00) |
|
| ELF5 | 4 (3%) | 142 |
0.422 (1.00) |
0.523 (1.00) |
1 (1.00) |
0.997 (1.00) |
0.255 (1.00) |
0.95 (1.00) |
|
| IL32 | 6 (4%) | 140 |
0.0674 (1.00) |
0.464 (1.00) |
0.679 (1.00) |
0.99 (1.00) |
0.868 (1.00) |
0.00533 (1.00) |
|
| LUZP2 | 13 (9%) | 133 |
0.887 (1.00) |
0.89 (1.00) |
0.569 (1.00) |
0.965 (1.00) |
0.736 (1.00) |
0.0149 (1.00) |
|
| PDE1A | 23 (16%) | 123 |
0.326 (1.00) |
0.139 (1.00) |
0.816 (1.00) |
0.887 (1.00) |
0.212 (1.00) |
0.523 (1.00) |
|
| RBM11 | 10 (7%) | 136 |
0.669 (1.00) |
0.262 (1.00) |
0.741 (1.00) |
0.248 (1.00) |
0.731 (1.00) |
0.567 (1.00) |
|
| GLRB | 16 (11%) | 130 |
0.339 (1.00) |
0.106 (1.00) |
1 (1.00) |
0.936 (1.00) |
0.755 (1.00) |
0.735 (1.00) |
|
| PRB1 | 12 (8%) | 134 |
0.367 (1.00) |
0.518 (1.00) |
0.127 (1.00) |
0.971 (1.00) |
0.517 (1.00) |
0.397 (1.00) |
|
| KIAA1257 | 7 (5%) | 139 |
0.0934 (1.00) |
0.0266 (1.00) |
0.247 (1.00) |
0.995 (1.00) |
0.676 (1.00) |
0.982 (1.00) |
|
| USP17L2 | 13 (9%) | 133 |
0.668 (1.00) |
0.991 (1.00) |
0.251 (1.00) |
0.959 (1.00) |
0.86 (1.00) |
0.239 (1.00) |
|
| SPAG16 | 13 (9%) | 133 |
0.151 (1.00) |
0.532 (1.00) |
0.251 (1.00) |
0.965 (1.00) |
0.814 (1.00) |
0.642 (1.00) |
|
| OR4M2 | 17 (12%) | 129 |
0.851 (1.00) |
0.0795 (1.00) |
1 (1.00) |
0.525 (1.00) |
0.965 (1.00) |
0.316 (1.00) |
|
| GFRAL | 20 (14%) | 126 |
0.506 (1.00) |
0.594 (1.00) |
0.807 (1.00) |
0.927 (1.00) |
0.481 (1.00) |
0.539 (1.00) |
|
| UNC119B | 3 (2%) | 143 |
0.873 (1.00) |
0.379 (1.00) |
1 (1.00) |
0.997 (1.00) |
0.984 (1.00) |
0.638 (1.00) |
|
| PHGDH | 5 (3%) | 141 |
0.7 (1.00) |
0.991 (1.00) |
0.157 (1.00) |
0.997 (1.00) |
0.984 (1.00) |
||
| STXBP5L | 31 (21%) | 115 |
0.102 (1.00) |
0.63 (1.00) |
0.684 (1.00) |
0.814 (1.00) |
0.963 (1.00) |
0.435 (1.00) |
|
| TRAT1 | 10 (7%) | 136 |
0.0153 (1.00) |
0.667 (1.00) |
0.513 (1.00) |
0.977 (1.00) |
0.741 (1.00) |
0.793 (1.00) |
|
| ZNF844 | 4 (3%) | 142 |
0.415 (1.00) |
0.0191 (1.00) |
0.644 (1.00) |
0.995 (1.00) |
0.465 (1.00) |
0.8 (1.00) |
|
| TTN | 114 (78%) | 32 |
0.566 (1.00) |
0.798 (1.00) |
0.0695 (1.00) |
0.225 (1.00) |
0.155 (1.00) |
0.145 (1.00) |
|
| DSG3 | 34 (23%) | 112 |
0.565 (1.00) |
0.11 (1.00) |
0.425 (1.00) |
0.244 (1.00) |
0.642 (1.00) |
0.376 (1.00) |
|
| GML | 8 (5%) | 138 |
0.967 (1.00) |
0.108 (1.00) |
0.15 (1.00) |
0.986 (1.00) |
0.543 (1.00) |
0.944 (1.00) |
|
| HHLA2 | 9 (6%) | 137 |
0.672 (1.00) |
0.312 (1.00) |
1 (1.00) |
0.981 (1.00) |
0.206 (1.00) |
0.818 (1.00) |
|
| LILRB4 | 22 (15%) | 124 |
0.419 (1.00) |
0.456 (1.00) |
0.818 (1.00) |
0.188 (1.00) |
0.686 (1.00) |
0.246 (1.00) |
|
| SLC38A4 | 16 (11%) | 130 |
0.748 (1.00) |
0.312 (1.00) |
0.104 (1.00) |
0.944 (1.00) |
0.874 (1.00) |
0.955 (1.00) |
|
| OR2L3 | 12 (8%) | 134 |
0.22 (1.00) |
0.725 (1.00) |
1 (1.00) |
0.00776 (1.00) |
0.834 (1.00) |
0.394 (1.00) |
|
| HBD | 8 (5%) | 138 |
0.0901 (1.00) |
0.604 (1.00) |
0.712 (1.00) |
0.981 (1.00) |
0.817 (1.00) |
0.273 (1.00) |
|
| TBC1D3B | 3 (2%) | 143 |
0.00283 (1.00) |
0.398 (1.00) |
1 (1.00) |
||||
| TCEB3C | 22 (15%) | 124 |
0.395 (1.00) |
0.218 (1.00) |
0.102 (1.00) |
0.876 (1.00) |
0.418 (1.00) |
0.411 (1.00) |
|
| CYLC2 | 16 (11%) | 130 |
0.6 (1.00) |
0.0886 (1.00) |
0.594 (1.00) |
0.951 (1.00) |
0.0427 (1.00) |
0.454 (1.00) |
|
| HBG2 | 6 (4%) | 140 |
0.619 (1.00) |
0.239 (1.00) |
1 (1.00) |
0.99 (1.00) |
0.953 (1.00) |
0.762 (1.00) |
|
| LOC649330 | 16 (11%) | 130 |
0.312 (1.00) |
0.0195 (1.00) |
0.594 (1.00) |
0.951 (1.00) |
0.788 (1.00) |
0.793 (1.00) |
|
| PARM1 | 11 (8%) | 135 |
0.00945 (1.00) |
0.197 (1.00) |
1 (1.00) |
0.977 (1.00) |
0.0223 (1.00) |
0.253 (1.00) |
|
| CCK | 5 (3%) | 141 |
0.124 (1.00) |
0.706 (1.00) |
0.649 (1.00) |
0.995 (1.00) |
0.00566 (1.00) |
0.545 (1.00) |
|
| ZFP106 | 5 (3%) | 141 |
0.808 (1.00) |
0.00424 (1.00) |
0.157 (1.00) |
0.993 (1.00) |
0.647 (1.00) |
0.207 (1.00) |
|
| UGT2B15 | 14 (10%) | 132 |
0.568 (1.00) |
0.644 (1.00) |
0.249 (1.00) |
0.355 (1.00) |
0.81 (1.00) |
0.156 (1.00) |
|
| DSG1 | 22 (15%) | 124 |
0.136 (1.00) |
0.5 (1.00) |
1 (1.00) |
0.887 (1.00) |
0.811 (1.00) |
0.273 (1.00) |
|
| ARL16 | 4 (3%) | 142 |
0.338 (1.00) |
0.0797 (1.00) |
1 (1.00) |
0.995 (1.00) |
0.738 (1.00) |
0.297 (1.00) |
|
| VEGFC | 14 (10%) | 132 |
0.938 (1.00) |
0.811 (1.00) |
0.4 (1.00) |
0.959 (1.00) |
0.0467 (1.00) |
0.0989 (1.00) |
|
| PSG4 | 15 (10%) | 131 |
0.941 (1.00) |
0.409 (1.00) |
1 (1.00) |
0.951 (1.00) |
0.921 (1.00) |
0.808 (1.00) |
|
| DEFB119 | 6 (4%) | 140 |
0.0591 (1.00) |
0.416 (1.00) |
1 (1.00) |
0.995 (1.00) |
0.908 (1.00) |
0.825 (1.00) |
|
| KLHL4 | 14 (10%) | 132 |
0.138 (1.00) |
0.727 (1.00) |
0.4 (1.00) |
0.965 (1.00) |
0.785 (1.00) |
0.657 (1.00) |
|
| EIF3D | 3 (2%) | 143 |
0.038 (1.00) |
0.474 (1.00) |
0.281 (1.00) |
0.997 (1.00) |
0.891 (1.00) |
0.578 (1.00) |
|
| OR2W1 | 12 (8%) | 134 |
0.7 (1.00) |
0.0687 (1.00) |
0.539 (1.00) |
0.965 (1.00) |
0.224 (1.00) |
0.86 (1.00) |
|
| OR4N2 | 17 (12%) | 129 |
0.856 (1.00) |
0.336 (1.00) |
0.0163 (1.00) |
0.0637 (1.00) |
0.937 (1.00) |
0.749 (1.00) |
|
| CCDC11 | 13 (9%) | 133 |
0.763 (1.00) |
0.909 (1.00) |
1 (1.00) |
0.959 (1.00) |
0.97 (1.00) |
0.835 (1.00) |
|
| LIN7A | 8 (5%) | 138 |
0.437 (1.00) |
0.703 (1.00) |
0.483 (1.00) |
0.99 (1.00) |
0.93 (1.00) |
0.567 (1.00) |
|
| RAPGEF5 | 6 (4%) | 140 |
0.957 (1.00) |
0.466 (1.00) |
0.404 (1.00) |
0.995 (1.00) |
0.738 (1.00) |
0.858 (1.00) |
|
| CD2 | 14 (10%) | 132 |
0.564 (1.00) |
0.323 (1.00) |
0.779 (1.00) |
0.011 (1.00) |
0.838 (1.00) |
0.397 (1.00) |
|
| C2ORF40 | 4 (3%) | 142 |
0.748 (1.00) |
0.392 (1.00) |
0.644 (1.00) |
0.997 (1.00) |
0.943 (1.00) |
||
| SGCZ | 16 (11%) | 130 |
0.11 (1.00) |
0.965 (1.00) |
1 (1.00) |
0.971 (1.00) |
0.265 (1.00) |
0.859 (1.00) |
|
| SPANXN2 | 13 (9%) | 133 |
0.0115 (1.00) |
0.794 (1.00) |
0.767 (1.00) |
0.971 (1.00) |
0.205 (1.00) |
0.394 (1.00) |
|
| TLL1 | 31 (21%) | 115 |
0.282 (1.00) |
0.205 (1.00) |
0.415 (1.00) |
0.729 (1.00) |
0.34 (1.00) |
0.205 (1.00) |
|
| C9ORF119 | 5 (3%) | 141 |
0.924 (1.00) |
0.968 (1.00) |
0.157 (1.00) |
0.993 (1.00) |
0.0348 (1.00) |
0.706 (1.00) |
|
| CCDC54 | 10 (7%) | 136 |
0.452 (1.00) |
0.653 (1.00) |
0.316 (1.00) |
0.981 (1.00) |
0.965 (1.00) |
0.82 (1.00) |
|
| DEFB118 | 6 (4%) | 140 |
0.135 (1.00) |
0.462 (1.00) |
1 (1.00) |
0.99 (1.00) |
0.965 (1.00) |
0.634 (1.00) |
|
| HTR3B | 10 (7%) | 136 |
0.0313 (1.00) |
0.745 (1.00) |
0.316 (1.00) |
0.977 (1.00) |
0.878 (1.00) |
0.693 (1.00) |
|
| MARCH11 | 7 (5%) | 139 |
0.321 (1.00) |
0.997 (1.00) |
0.705 (1.00) |
0.0875 (1.00) |
0.932 (1.00) |
0.469 (1.00) |
|
| MKX | 10 (7%) | 136 |
0.469 (1.00) |
0.798 (1.00) |
0.741 (1.00) |
0.986 (1.00) |
0.932 (1.00) |
0.0133 (1.00) |
|
| OR5H2 | 11 (8%) | 135 |
0.406 (1.00) |
0.0271 (1.00) |
0.751 (1.00) |
0.965 (1.00) |
0.318 (1.00) |
0.423 (1.00) |
|
| SIGLEC14 | 6 (4%) | 140 |
0.898 (1.00) |
0.154 (1.00) |
0.0817 (1.00) |
0.993 (1.00) |
0.945 (1.00) |
0.153 (1.00) |
|
| TUBB8 | 7 (5%) | 139 |
0.881 (1.00) |
0.22 (1.00) |
0.705 (1.00) |
0.993 (1.00) |
0.964 (1.00) |
0.696 (1.00) |
|
| ZIM3 | 12 (8%) | 134 |
0.0439 (1.00) |
0.916 (1.00) |
0.368 (1.00) |
0.971 (1.00) |
0.626 (1.00) |
0.521 (1.00) |
|
| PRC1 | 7 (5%) | 139 |
0.982 (1.00) |
0.907 (1.00) |
0.705 (1.00) |
0.99 (1.00) |
0.913 (1.00) |
0.842 (1.00) |
|
| MUM1L1 | 15 (10%) | 131 |
0.485 (1.00) |
0.775 (1.00) |
1 (1.00) |
0.936 (1.00) |
0.547 (1.00) |
0.681 (1.00) |
|
| TRIM58 | 12 (8%) | 134 |
0.391 (1.00) |
0.00222 (1.00) |
0.766 (1.00) |
0.965 (1.00) |
0.739 (1.00) |
0.826 (1.00) |
|
| ANKRD20A4 | 3 (2%) | 143 |
0.571 (1.00) |
0.865 (1.00) |
0.281 (1.00) |
0.997 (1.00) |
0.943 (1.00) |
0.623 (1.00) |
|
| OR5J2 | 10 (7%) | 136 |
0.795 (1.00) |
0.886 (1.00) |
0.189 (1.00) |
0.981 (1.00) |
0.956 (1.00) |
0.795 (1.00) |
|
| CLEC14A | 14 (10%) | 132 |
0.245 (1.00) |
0.838 (1.00) |
0.249 (1.00) |
0.971 (1.00) |
0.51 (1.00) |
0.617 (1.00) |
|
| FAM19A1 | 7 (5%) | 139 |
0.354 (1.00) |
0.95 (1.00) |
1 (1.00) |
0.99 (1.00) |
0.6 (1.00) |
0.751 (1.00) |
|
| GK2 | 19 (13%) | 127 |
0.39 (1.00) |
0.984 (1.00) |
0.804 (1.00) |
0.918 (1.00) |
0.503 (1.00) |
0.0645 (1.00) |
|
| LONRF2 | 11 (8%) | 135 |
0.035 (1.00) |
0.909 (1.00) |
1 (1.00) |
0.986 (1.00) |
0.191 (1.00) |
0.673 (1.00) |
|
| NAP1L4 | 5 (3%) | 141 |
0.613 (1.00) |
0.369 (1.00) |
0.379 (1.00) |
0.993 (1.00) |
0.27 (1.00) |
0.693 (1.00) |
|
| CLCC1 | 7 (5%) | 139 |
0.122 (1.00) |
0.577 (1.00) |
0.705 (1.00) |
0.99 (1.00) |
0.457 (1.00) |
0.74 (1.00) |
|
| OR52J3 | 9 (6%) | 137 |
0.0699 (1.00) |
0.417 (1.00) |
0.737 (1.00) |
0.981 (1.00) |
0.923 (1.00) |
0.935 (1.00) |
|
| TMCO5A | 6 (4%) | 140 |
0.384 (1.00) |
0.29 (1.00) |
0.404 (1.00) |
0.993 (1.00) |
0.964 (1.00) |
0.273 (1.00) |
|
| C4ORF22 | 8 (5%) | 138 |
0.294 (1.00) |
0.654 (1.00) |
0.483 (1.00) |
0.99 (1.00) |
0.935 (1.00) |
0.868 (1.00) |
|
| MAP2K1 | 6 (4%) | 140 |
0.198 (1.00) |
0.636 (1.00) |
0.209 (1.00) |
0.99 (1.00) |
0.00585 (1.00) |
0.915 (1.00) |
|
| OR7D2 | 13 (9%) | 133 |
0.948 (1.00) |
0.479 (1.00) |
0.251 (1.00) |
0.959 (1.00) |
0.86 (1.00) |
0.274 (1.00) |
|
| CXCR2 | 9 (6%) | 137 |
0.181 (1.00) |
0.341 (1.00) |
0.737 (1.00) |
0.981 (1.00) |
0.841 (1.00) |
0.272 (1.00) |
|
| RBM22 | 4 (3%) | 142 |
0.579 (1.00) |
0.319 (1.00) |
0.156 (1.00) |
0.995 (1.00) |
0.964 (1.00) |
0.784 (1.00) |
|
| CX3CL1 | 3 (2%) | 143 |
0.495 (1.00) |
0.946 (1.00) |
1 (1.00) |
||||
| IGF2BP3 | 3 (2%) | 143 |
0.918 (1.00) |
0.678 (1.00) |
1 (1.00) |
||||
| KLRC3 | 4 (3%) | 142 |
0.532 (1.00) |
0.692 (1.00) |
0.644 (1.00) |
0.995 (1.00) |
0.169 (1.00) |
0.828 (1.00) |
|
| LRRIQ4 | 14 (10%) | 132 |
0.43 (1.00) |
0.135 (1.00) |
0.4 (1.00) |
0.944 (1.00) |
0.898 (1.00) |
0.628 (1.00) |
|
| NR1H4 | 8 (5%) | 138 |
0.362 (1.00) |
0.315 (1.00) |
0.483 (1.00) |
0.986 (1.00) |
0.195 (1.00) |
0.513 (1.00) |
|
| OR4A15 | 14 (10%) | 132 |
0.975 (1.00) |
0.0416 (1.00) |
0.0804 (1.00) |
0.965 (1.00) |
0.134 (1.00) |
0.37 (1.00) |
|
| MAGEA4 | 7 (5%) | 139 |
0.819 (1.00) |
0.57 (1.00) |
0.705 (1.00) |
0.0468 (1.00) |
0.853 (1.00) |
0.642 (1.00) |
|
| DGAT2L6 | 8 (5%) | 138 |
0.487 (1.00) |
0.437 (1.00) |
1 (1.00) |
0.981 (1.00) |
0.405 (1.00) |
0.56 (1.00) |
|
| RGS18 | 7 (5%) | 139 |
0.944 (1.00) |
0.328 (1.00) |
0.0428 (1.00) |
0.99 (1.00) |
0.853 (1.00) |
0.763 (1.00) |
|
| TSGA13 | 6 (4%) | 140 |
0.3 (1.00) |
0.873 (1.00) |
0.404 (1.00) |
0.993 (1.00) |
0.921 (1.00) |
0.308 (1.00) |
|
| OPN5 | 5 (3%) | 141 |
0.329 (1.00) |
0.656 (1.00) |
0.649 (1.00) |
0.995 (1.00) |
0.847 (1.00) |
0.754 (1.00) |
|
| SPINK13 | 4 (3%) | 142 |
0.191 (1.00) |
0.326 (1.00) |
1 (1.00) |
0.995 (1.00) |
0.359 (1.00) |
0.956 (1.00) |
'PTEN MUTATION STATUS' versus 'DISTANT.METASTASIS'
P value = 0.00018 (Chi-square test), Q value = 0.13
Table S1. Gene #8: 'PTEN MUTATION STATUS' versus Clinical Feature #4: 'DISTANT.METASTASIS'
| nPatients | M0 | M1 | M1A | M1B | M1C |
|---|---|---|---|---|---|
| ALL | 124 | 2 | 1 | 1 | 2 |
| PTEN MUTATED | 9 | 2 | 0 | 0 | 0 |
| PTEN WILD-TYPE | 115 | 0 | 1 | 1 | 2 |
Figure S1. Get High-res Image Gene #8: 'PTEN MUTATION STATUS' versus Clinical Feature #4: 'DISTANT.METASTASIS'
'MUC7 MUTATION STATUS' versus 'AGE'
P value = 0.000185 (t-test), Q value = 0.14
Table S2. Gene #17: 'MUC7 MUTATION STATUS' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 144 | 56.1 (16.0) |
| MUC7 MUTATED | 11 | 72.7 (10.9) |
| MUC7 WILD-TYPE | 133 | 54.8 (15.6) |
Figure S2. Get High-res Image Gene #17: 'MUC7 MUTATION STATUS' versus Clinical Feature #2: 'AGE'
'HAPLN1 MUTATION STATUS' versus 'DISTANT.METASTASIS'
P value = 0.000316 (Chi-square test), Q value = 0.23
Table S3. Gene #104: 'HAPLN1 MUTATION STATUS' versus Clinical Feature #4: 'DISTANT.METASTASIS'
| nPatients | M0 | M1 | M1A | M1B | M1C |
|---|---|---|---|---|---|
| ALL | 124 | 2 | 1 | 1 | 2 |
| HAPLN1 MUTATED | 5 | 0 | 0 | 1 | 0 |
| HAPLN1 WILD-TYPE | 119 | 2 | 1 | 0 | 2 |
Figure S3. Get High-res Image Gene #104: 'HAPLN1 MUTATION STATUS' versus Clinical Feature #4: 'DISTANT.METASTASIS'
Methods & Data
Input
-
Mutation data file = SKCM-TM.mutsig.cluster.txt
-
Clinical data file = SKCM-TM.clin.merged.picked.txt
-
Number of patients = 146
-
Number of significantly mutated genes = 125
-
Number of selected clinical features = 7
-
Exclude genes that fewer than K tumors have mutations, K = 3
Survival analysis
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
Student's t-test analysis
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
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] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] 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)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] 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.