Correlation between gene mutation status and selected clinical features
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.
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)