Correlation between gene mutation status and selected clinical features
Skin Cutaneous Melanoma (Metastatic)
22 February 2013
|
analyses__2013_02_22
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team
(Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as
Broad Institute TCGA Genome Data Analysis Center
(2013):
Correlation between gene mutation status and selected clinical features.
Broad Institute of MIT and Harvard.
doi:10.7908/C1X928HB
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 141 patients, 2 significant findings detected with Q value < 0.25.
-
PTEN mutation correlated to 'DISTANT.METASTASIS'.
-
MUC7 mutation correlated to 'AGE'.
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, 2 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 | 9 (6%) | 132 |
0.882 (1.00) |
0.815 (1.00) |
0.729 (1.00) |
2.63e-05 (0.0194) |
0.84 (1.00) |
0.0346 (1.00) |
|
| MUC7 | 11 (8%) | 130 |
0.465 (1.00) |
0.000201 (0.148) |
0.536 (1.00) |
0.962 (1.00) |
0.763 (1.00) |
0.722 (1.00) |
|
| TP53 | 25 (18%) | 116 |
0.496 (1.00) |
0.0922 (1.00) |
0.822 (1.00) |
0.665 (1.00) |
0.269 (1.00) |
0.305 (1.00) |
|
| BRAF | 70 (50%) | 71 |
0.136 (1.00) |
0.0582 (1.00) |
1 (1.00) |
0.379 (1.00) |
0.52 (1.00) |
0.849 (1.00) |
|
| C15ORF23 | 10 (7%) | 131 |
0.449 (1.00) |
0.698 (1.00) |
0.743 (1.00) |
0.975 (1.00) |
0.64 (1.00) |
0.414 (1.00) |
|
| CDKN2A | 21 (15%) | 120 |
0.67 (1.00) |
0.511 (1.00) |
1 (1.00) |
0.901 (1.00) |
0.551 (1.00) |
0.851 (1.00) |
|
| NRAS | 44 (31%) | 97 |
0.705 (1.00) |
0.156 (1.00) |
1 (1.00) |
0.564 (1.00) |
0.859 (1.00) |
0.269 (1.00) |
|
| OXA1L | 4 (3%) | 137 |
0.88 (1.00) |
0.807 (1.00) |
0.631 (1.00) |
0.995 (1.00) |
0.769 (1.00) |
0.541 (1.00) |
|
| STK19 | 9 (6%) | 132 |
0.334 (1.00) |
0.493 (1.00) |
0.296 (1.00) |
0.98 (1.00) |
0.799 (1.00) |
0.927 (1.00) |
|
| RAC1 | 11 (8%) | 130 |
0.0467 (1.00) |
0.523 (1.00) |
1 (1.00) |
0.975 (1.00) |
0.875 (1.00) |
0.34 (1.00) |
|
| ACSM2B | 28 (20%) | 113 |
0.163 (1.00) |
0.98 (1.00) |
0.0044 (1.00) |
0.813 (1.00) |
0.528 (1.00) |
0.68 (1.00) |
|
| CADM2 | 15 (11%) | 126 |
0.759 (1.00) |
0.91 (1.00) |
0.786 (1.00) |
0.93 (1.00) |
0.413 (1.00) |
0.416 (1.00) |
|
| OR51S1 | 16 (11%) | 125 |
0.443 (1.00) |
0.524 (1.00) |
1 (1.00) |
0.939 (1.00) |
0.47 (1.00) |
0.172 (1.00) |
|
| LCE1B | 10 (7%) | 131 |
0.392 (1.00) |
0.647 (1.00) |
0.502 (1.00) |
0.975 (1.00) |
0.389 (1.00) |
0.664 (1.00) |
|
| IDH1 | 7 (5%) | 134 |
0.799 (1.00) |
0.0112 (1.00) |
0.425 (1.00) |
0.985 (1.00) |
0.934 (1.00) |
0.556 (1.00) |
|
| TAF1A | 8 (6%) | 133 |
0.296 (1.00) |
0.592 (1.00) |
0.474 (1.00) |
0.00466 (1.00) |
0.946 (1.00) |
0.875 (1.00) |
|
| NAP1L2 | 13 (9%) | 128 |
0.472 (1.00) |
0.0772 (1.00) |
0.555 (1.00) |
0.955 (1.00) |
0.619 (1.00) |
0.614 (1.00) |
|
| PPP6C | 13 (9%) | 128 |
0.0359 (1.00) |
0.788 (1.00) |
0.767 (1.00) |
0.379 (1.00) |
0.183 (1.00) |
0.558 (1.00) |
|
| FRG2B | 10 (7%) | 131 |
0.521 (1.00) |
0.022 (1.00) |
0.502 (1.00) |
0.969 (1.00) |
0.873 (1.00) |
0.666 (1.00) |
|
| USP29 | 25 (18%) | 116 |
0.052 (1.00) |
0.0857 (1.00) |
0.364 (1.00) |
0.866 (1.00) |
0.533 (1.00) |
0.497 (1.00) |
|
| PRB4 | 16 (11%) | 125 |
0.122 (1.00) |
0.252 (1.00) |
0.412 (1.00) |
0.472 (1.00) |
0.767 (1.00) |
0.923 (1.00) |
|
| HIST1H2AA | 7 (5%) | 134 |
0.882 (1.00) |
0.98 (1.00) |
1 (1.00) |
0.985 (1.00) |
0.936 (1.00) |
0.64 (1.00) |
|
| RPTN | 22 (16%) | 119 |
0.512 (1.00) |
0.355 (1.00) |
0.636 (1.00) |
0.901 (1.00) |
0.411 (1.00) |
0.181 (1.00) |
|
| ZNF479 | 12 (9%) | 129 |
0.338 (1.00) |
0.0858 (1.00) |
0.764 (1.00) |
0.326 (1.00) |
0.834 (1.00) |
0.592 (1.00) |
|
| C8A | 17 (12%) | 124 |
0.00444 (1.00) |
0.00404 (1.00) |
0.0299 (1.00) |
0.041 (1.00) |
0.779 (1.00) |
0.631 (1.00) |
|
| FUT9 | 16 (11%) | 125 |
0.992 (1.00) |
0.0264 (1.00) |
1 (1.00) |
0.93 (1.00) |
0.777 (1.00) |
0.646 (1.00) |
|
| ZNF679 | 15 (11%) | 126 |
0.698 (1.00) |
0.44 (1.00) |
0.786 (1.00) |
0.939 (1.00) |
0.746 (1.00) |
0.475 (1.00) |
|
| NRK | 18 (13%) | 123 |
0.365 (1.00) |
0.793 (1.00) |
0.798 (1.00) |
0.921 (1.00) |
0.532 (1.00) |
0.562 (1.00) |
|
| CDH9 | 26 (18%) | 115 |
0.422 (1.00) |
0.465 (1.00) |
1 (1.00) |
0.813 (1.00) |
0.359 (1.00) |
0.114 (1.00) |
|
| PRAMEF11 | 13 (9%) | 128 |
0.109 (1.00) |
0.159 (1.00) |
0.555 (1.00) |
0.955 (1.00) |
0.0802 (1.00) |
0.728 (1.00) |
|
| DDX3X | 15 (11%) | 126 |
0.583 (1.00) |
0.449 (1.00) |
0.167 (1.00) |
0.00064 (0.471) |
0.958 (1.00) |
0.75 (1.00) |
|
| GRXCR1 | 15 (11%) | 126 |
0.588 (1.00) |
0.0207 (1.00) |
0.786 (1.00) |
0.947 (1.00) |
0.804 (1.00) |
0.38 (1.00) |
|
| PRB2 | 21 (15%) | 120 |
0.58 (1.00) |
0.0121 (1.00) |
0.0857 (1.00) |
0.901 (1.00) |
0.512 (1.00) |
0.399 (1.00) |
|
| ELF5 | 4 (3%) | 137 |
0.426 (1.00) |
0.512 (1.00) |
1 (1.00) |
0.997 (1.00) |
0.159 (1.00) |
0.955 (1.00) |
|
| IL32 | 6 (4%) | 135 |
0.0666 (1.00) |
0.449 (1.00) |
0.672 (1.00) |
0.989 (1.00) |
0.868 (1.00) |
0.00823 (1.00) |
|
| LUZP2 | 13 (9%) | 128 |
0.881 (1.00) |
0.92 (1.00) |
0.555 (1.00) |
0.962 (1.00) |
0.696 (1.00) |
0.0144 (1.00) |
|
| PDE1A | 23 (16%) | 118 |
0.332 (1.00) |
0.154 (1.00) |
0.818 (1.00) |
0.878 (1.00) |
0.223 (1.00) |
0.456 (1.00) |
|
| RBM11 | 10 (7%) | 131 |
0.661 (1.00) |
0.279 (1.00) |
0.743 (1.00) |
0.27 (1.00) |
0.676 (1.00) |
0.575 (1.00) |
|
| GLRB | 16 (11%) | 125 |
0.34 (1.00) |
0.118 (1.00) |
1 (1.00) |
0.93 (1.00) |
0.793 (1.00) |
0.664 (1.00) |
|
| PRB1 | 12 (9%) | 129 |
0.363 (1.00) |
0.541 (1.00) |
0.211 (1.00) |
0.969 (1.00) |
0.572 (1.00) |
0.464 (1.00) |
|
| KIAA1257 | 7 (5%) | 134 |
0.0923 (1.00) |
0.0283 (1.00) |
0.255 (1.00) |
0.995 (1.00) |
0.71 (1.00) |
0.985 (1.00) |
|
| USP17L2 | 13 (9%) | 128 |
0.678 (1.00) |
0.949 (1.00) |
0.371 (1.00) |
0.955 (1.00) |
0.868 (1.00) |
0.276 (1.00) |
|
| SPAG16 | 13 (9%) | 128 |
0.153 (1.00) |
0.497 (1.00) |
0.371 (1.00) |
0.962 (1.00) |
0.837 (1.00) |
0.596 (1.00) |
|
| OR4M2 | 17 (12%) | 124 |
0.838 (1.00) |
0.0877 (1.00) |
0.793 (1.00) |
0.546 (1.00) |
0.972 (1.00) |
0.366 (1.00) |
|
| GFRAL | 20 (14%) | 121 |
0.507 (1.00) |
0.626 (1.00) |
1 (1.00) |
0.921 (1.00) |
0.342 (1.00) |
0.505 (1.00) |
|
| UNC119B | 3 (2%) | 138 |
0.873 (1.00) |
0.373 (1.00) |
1 (1.00) |
0.997 (1.00) |
0.984 (1.00) |
0.681 (1.00) |
|
| PHGDH | 5 (4%) | 136 |
0.701 (1.00) |
0.975 (1.00) |
0.157 (1.00) |
0.997 (1.00) |
0.984 (1.00) |
||
| STXBP5L | 30 (21%) | 111 |
0.088 (1.00) |
0.53 (1.00) |
0.674 (1.00) |
0.813 (1.00) |
0.939 (1.00) |
0.552 (1.00) |
|
| TRAT1 | 10 (7%) | 131 |
0.0155 (1.00) |
0.696 (1.00) |
0.502 (1.00) |
0.975 (1.00) |
0.681 (1.00) |
0.729 (1.00) |
|
| ZNF844 | 4 (3%) | 137 |
0.412 (1.00) |
0.0196 (1.00) |
0.631 (1.00) |
0.995 (1.00) |
0.509 (1.00) |
0.825 (1.00) |
|
| TTN | 113 (80%) | 28 |
0.561 (1.00) |
0.869 (1.00) |
0.19 (1.00) |
0.154 (1.00) |
0.152 (1.00) |
0.33 (1.00) |
|
| DSG3 | 34 (24%) | 107 |
0.563 (1.00) |
0.131 (1.00) |
0.545 (1.00) |
0.265 (1.00) |
0.693 (1.00) |
0.467 (1.00) |
|
| GML | 8 (6%) | 133 |
0.964 (1.00) |
0.114 (1.00) |
0.258 (1.00) |
0.985 (1.00) |
0.284 (1.00) |
0.941 (1.00) |
|
| HHLA2 | 9 (6%) | 132 |
0.666 (1.00) |
0.325 (1.00) |
1 (1.00) |
0.98 (1.00) |
0.246 (1.00) |
0.815 (1.00) |
|
| LILRB4 | 21 (15%) | 120 |
0.26 (1.00) |
0.367 (1.00) |
0.808 (1.00) |
0.185 (1.00) |
0.7 (1.00) |
0.248 (1.00) |
|
| SLC38A4 | 16 (11%) | 125 |
0.745 (1.00) |
0.338 (1.00) |
0.11 (1.00) |
0.939 (1.00) |
0.685 (1.00) |
0.945 (1.00) |
|
| OR2L3 | 11 (8%) | 130 |
0.295 (1.00) |
0.724 (1.00) |
1 (1.00) |
0.00466 (1.00) |
0.883 (1.00) |
0.213 (1.00) |
|
| HBD | 8 (6%) | 133 |
0.0887 (1.00) |
0.622 (1.00) |
0.474 (1.00) |
0.98 (1.00) |
0.845 (1.00) |
0.307 (1.00) |
|
| TBC1D3B | 3 (2%) | 138 |
0.00217 (1.00) |
0.404 (1.00) |
1 (1.00) |
||||
| TCEB3C | 21 (15%) | 120 |
0.36 (1.00) |
0.148 (1.00) |
0.0857 (1.00) |
0.878 (1.00) |
0.836 (1.00) |
0.599 (1.00) |
|
| CYLC2 | 16 (11%) | 125 |
0.596 (1.00) |
0.0981 (1.00) |
0.785 (1.00) |
0.947 (1.00) |
0.0327 (1.00) |
0.471 (1.00) |
|
| HBG2 | 6 (4%) | 135 |
0.619 (1.00) |
0.248 (1.00) |
1 (1.00) |
0.989 (1.00) |
0.961 (1.00) |
0.759 (1.00) |
|
| LOC649330 | 16 (11%) | 125 |
0.311 (1.00) |
0.0215 (1.00) |
0.785 (1.00) |
0.947 (1.00) |
0.633 (1.00) |
0.758 (1.00) |
|
| PARM1 | 11 (8%) | 130 |
0.00916 (1.00) |
0.208 (1.00) |
1 (1.00) |
0.975 (1.00) |
0.0106 (1.00) |
0.241 (1.00) |
|
| CCK | 5 (4%) | 136 |
0.123 (1.00) |
0.731 (1.00) |
0.65 (1.00) |
0.995 (1.00) |
0.00803 (1.00) |
0.447 (1.00) |
|
| ZFP106 | 5 (4%) | 136 |
0.81 (1.00) |
0.00439 (1.00) |
0.157 (1.00) |
0.992 (1.00) |
0.536 (1.00) |
0.184 (1.00) |
|
| UGT2B15 | 14 (10%) | 127 |
0.567 (1.00) |
0.609 (1.00) |
0.251 (1.00) |
0.379 (1.00) |
0.782 (1.00) |
0.204 (1.00) |
|
| DSG1 | 21 (15%) | 120 |
0.117 (1.00) |
0.379 (1.00) |
1 (1.00) |
0.89 (1.00) |
0.842 (1.00) |
0.434 (1.00) |
|
| ARL16 | 4 (3%) | 137 |
0.337 (1.00) |
0.0845 (1.00) |
1 (1.00) |
0.995 (1.00) |
0.769 (1.00) |
0.243 (1.00) |
|
| VEGFC | 12 (9%) | 129 |
0.68 (1.00) |
0.425 (1.00) |
0.764 (1.00) |
0.969 (1.00) |
0.331 (1.00) |
0.0664 (1.00) |
|
| PSG4 | 15 (11%) | 126 |
0.93 (1.00) |
0.443 (1.00) |
1 (1.00) |
0.947 (1.00) |
0.937 (1.00) |
0.838 (1.00) |
|
| DEFB119 | 6 (4%) | 135 |
0.056 (1.00) |
0.383 (1.00) |
1 (1.00) |
0.995 (1.00) |
0.919 (1.00) |
0.8 (1.00) |
|
| KLHL4 | 14 (10%) | 127 |
0.138 (1.00) |
0.687 (1.00) |
0.386 (1.00) |
0.962 (1.00) |
0.754 (1.00) |
0.638 (1.00) |
|
| EIF3D | 3 (2%) | 138 |
0.0386 (1.00) |
0.482 (1.00) |
0.291 (1.00) |
0.997 (1.00) |
0.904 (1.00) |
0.548 (1.00) |
|
| OR2W1 | 12 (9%) | 129 |
0.698 (1.00) |
0.0759 (1.00) |
0.367 (1.00) |
0.962 (1.00) |
0.269 (1.00) |
0.862 (1.00) |
|
| OR4N2 | 17 (12%) | 124 |
0.862 (1.00) |
0.36 (1.00) |
0.0299 (1.00) |
0.0728 (1.00) |
0.949 (1.00) |
0.736 (1.00) |
|
| CCDC11 | 13 (9%) | 128 |
0.753 (1.00) |
0.944 (1.00) |
1 (1.00) |
0.955 (1.00) |
0.981 (1.00) |
0.845 (1.00) |
|
| LIN7A | 8 (6%) | 133 |
0.437 (1.00) |
0.724 (1.00) |
0.71 (1.00) |
0.989 (1.00) |
0.936 (1.00) |
0.624 (1.00) |
|
| RAPGEF5 | 6 (4%) | 135 |
0.951 (1.00) |
0.479 (1.00) |
0.41 (1.00) |
0.995 (1.00) |
0.769 (1.00) |
0.877 (1.00) |
|
| CD2 | 14 (10%) | 127 |
0.56 (1.00) |
0.345 (1.00) |
0.773 (1.00) |
0.014 (1.00) |
0.871 (1.00) |
0.358 (1.00) |
|
| C2ORF40 | 4 (3%) | 137 |
0.749 (1.00) |
0.406 (1.00) |
0.631 (1.00) |
0.997 (1.00) |
0.951 (1.00) |
||
| SGCZ | 15 (11%) | 126 |
0.0876 (1.00) |
0.848 (1.00) |
0.786 (1.00) |
0.975 (1.00) |
0.474 (1.00) |
0.685 (1.00) |
|
| SPANXN2 | 13 (9%) | 128 |
0.0114 (1.00) |
0.76 (1.00) |
0.767 (1.00) |
0.969 (1.00) |
0.248 (1.00) |
0.373 (1.00) |
|
| TLL1 | 31 (22%) | 110 |
0.277 (1.00) |
0.231 (1.00) |
0.535 (1.00) |
0.732 (1.00) |
0.369 (1.00) |
0.279 (1.00) |
|
| C9ORF119 | 5 (4%) | 136 |
0.925 (1.00) |
0.954 (1.00) |
0.157 (1.00) |
0.992 (1.00) |
0.045 (1.00) |
0.744 (1.00) |
|
| CCDC54 | 10 (7%) | 131 |
0.452 (1.00) |
0.683 (1.00) |
0.32 (1.00) |
0.98 (1.00) |
0.97 (1.00) |
0.858 (1.00) |
|
| DEFB118 | 6 (4%) | 135 |
0.135 (1.00) |
0.444 (1.00) |
1 (1.00) |
0.989 (1.00) |
0.972 (1.00) |
0.684 (1.00) |
|
| HTR3B | 9 (6%) | 132 |
0.0534 (1.00) |
0.903 (1.00) |
0.153 (1.00) |
0.98 (1.00) |
0.9 (1.00) |
0.822 (1.00) |
|
| MARCH11 | 7 (5%) | 134 |
0.319 (1.00) |
0.971 (1.00) |
0.711 (1.00) |
0.101 (1.00) |
0.936 (1.00) |
0.388 (1.00) |
|
| MKX | 10 (7%) | 131 |
0.467 (1.00) |
0.823 (1.00) |
0.743 (1.00) |
0.985 (1.00) |
0.936 (1.00) |
0.0165 (1.00) |
|
| OR5H2 | 11 (8%) | 130 |
0.403 (1.00) |
0.0302 (1.00) |
0.747 (1.00) |
0.962 (1.00) |
0.366 (1.00) |
0.46 (1.00) |
|
| SIGLEC14 | 6 (4%) | 135 |
0.899 (1.00) |
0.161 (1.00) |
0.0834 (1.00) |
0.992 (1.00) |
0.955 (1.00) |
0.188 (1.00) |
|
| TUBB8 | 7 (5%) | 134 |
0.879 (1.00) |
0.208 (1.00) |
0.711 (1.00) |
0.992 (1.00) |
0.968 (1.00) |
0.689 (1.00) |
|
| ZIM3 | 12 (9%) | 129 |
0.043 (1.00) |
0.95 (1.00) |
0.535 (1.00) |
0.969 (1.00) |
0.561 (1.00) |
0.566 (1.00) |
|
| PRC1 | 7 (5%) | 134 |
0.977 (1.00) |
0.878 (1.00) |
0.711 (1.00) |
0.989 (1.00) |
0.92 (1.00) |
0.803 (1.00) |
|
| MUM1L1 | 14 (10%) | 127 |
0.515 (1.00) |
0.56 (1.00) |
1 (1.00) |
0.939 (1.00) |
0.665 (1.00) |
0.505 (1.00) |
|
| TRIM58 | 12 (9%) | 129 |
0.389 (1.00) |
0.00251 (1.00) |
1 (1.00) |
0.962 (1.00) |
0.479 (1.00) |
0.86 (1.00) |
|
| ANKRD20A4 | 3 (2%) | 138 |
0.57 (1.00) |
0.802 (1.00) |
0.291 (1.00) |
0.997 (1.00) |
0.951 (1.00) |
0.652 (1.00) |
|
| OR5J2 | 10 (7%) | 131 |
0.798 (1.00) |
0.923 (1.00) |
0.177 (1.00) |
0.98 (1.00) |
0.962 (1.00) |
0.813 (1.00) |
|
| CLEC14A | 14 (10%) | 127 |
0.243 (1.00) |
0.882 (1.00) |
0.251 (1.00) |
0.969 (1.00) |
0.491 (1.00) |
0.56 (1.00) |
|
| FAM19A1 | 7 (5%) | 134 |
0.356 (1.00) |
0.969 (1.00) |
1 (1.00) |
0.989 (1.00) |
0.642 (1.00) |
0.789 (1.00) |
|
| GK2 | 18 (13%) | 123 |
0.292 (1.00) |
0.963 (1.00) |
1 (1.00) |
0.921 (1.00) |
0.577 (1.00) |
0.07 (1.00) |
|
| LONRF2 | 11 (8%) | 130 |
0.0348 (1.00) |
0.868 (1.00) |
1 (1.00) |
0.985 (1.00) |
0.222 (1.00) |
0.647 (1.00) |
|
| HAPLN1 | 7 (5%) | 134 |
0.258 (1.00) |
0.168 (1.00) |
0.711 (1.00) |
0.00046 (0.339) |
0.936 (1.00) |
0.236 (1.00) |
|
| NAP1L4 | 5 (4%) | 136 |
0.615 (1.00) |
0.39 (1.00) |
0.364 (1.00) |
0.992 (1.00) |
0.0856 (1.00) |
0.74 (1.00) |
|
| CLCC1 | 7 (5%) | 134 |
0.128 (1.00) |
0.552 (1.00) |
0.711 (1.00) |
0.989 (1.00) |
0.197 (1.00) |
0.779 (1.00) |
|
| OR52J3 | 9 (6%) | 132 |
0.0717 (1.00) |
0.445 (1.00) |
0.729 (1.00) |
0.98 (1.00) |
0.933 (1.00) |
0.941 (1.00) |
|
| TMCO5A | 6 (4%) | 135 |
0.381 (1.00) |
0.28 (1.00) |
0.41 (1.00) |
0.992 (1.00) |
0.968 (1.00) |
0.321 (1.00) |
|
| C4ORF22 | 8 (6%) | 133 |
0.29 (1.00) |
0.628 (1.00) |
0.71 (1.00) |
0.989 (1.00) |
0.95 (1.00) |
0.867 (1.00) |
|
| MAP2K1 | 5 (4%) | 136 |
0.221 (1.00) |
0.927 (1.00) |
0.364 (1.00) |
0.992 (1.00) |
0.0212 (1.00) |
0.847 (1.00) |
|
| OR7D2 | 13 (9%) | 128 |
0.952 (1.00) |
0.507 (1.00) |
0.371 (1.00) |
0.955 (1.00) |
0.868 (1.00) |
0.329 (1.00) |
|
| CXCR2 | 9 (6%) | 132 |
0.179 (1.00) |
0.366 (1.00) |
0.729 (1.00) |
0.98 (1.00) |
0.776 (1.00) |
0.271 (1.00) |
|
| RBM22 | 4 (3%) | 137 |
0.578 (1.00) |
0.328 (1.00) |
0.297 (1.00) |
0.995 (1.00) |
0.969 (1.00) |
0.82 (1.00) |
|
| CX3CL1 | 3 (2%) | 138 |
0.495 (1.00) |
0.935 (1.00) |
1 (1.00) |
||||
| IGF2BP3 | 3 (2%) | 138 |
0.92 (1.00) |
0.69 (1.00) |
1 (1.00) |
||||
| KLRC3 | 4 (3%) | 137 |
0.53 (1.00) |
0.678 (1.00) |
0.631 (1.00) |
0.995 (1.00) |
0.0356 (1.00) |
0.844 (1.00) |
|
| LRRIQ4 | 14 (10%) | 127 |
0.424 (1.00) |
0.146 (1.00) |
0.386 (1.00) |
0.939 (1.00) |
0.909 (1.00) |
0.556 (1.00) |
|
| NR1H4 | 8 (6%) | 133 |
0.357 (1.00) |
0.296 (1.00) |
0.71 (1.00) |
0.985 (1.00) |
0.179 (1.00) |
0.482 (1.00) |
|
| OR4A15 | 14 (10%) | 127 |
0.973 (1.00) |
0.046 (1.00) |
0.0805 (1.00) |
0.962 (1.00) |
0.164 (1.00) |
0.44 (1.00) |
|
| MAGEA4 | 7 (5%) | 134 |
0.821 (1.00) |
0.551 (1.00) |
0.711 (1.00) |
0.0554 (1.00) |
0.865 (1.00) |
0.688 (1.00) |
|
| DGAT2L6 | 8 (6%) | 133 |
0.484 (1.00) |
0.451 (1.00) |
1 (1.00) |
0.98 (1.00) |
0.225 (1.00) |
0.587 (1.00) |
|
| RGS18 | 7 (5%) | 134 |
0.945 (1.00) |
0.343 (1.00) |
0.0451 (1.00) |
0.989 (1.00) |
0.873 (1.00) |
0.743 (1.00) |
|
| TSGA13 | 6 (4%) | 135 |
0.298 (1.00) |
0.896 (1.00) |
0.41 (1.00) |
0.992 (1.00) |
0.921 (1.00) |
0.358 (1.00) |
|
| OPN5 | 5 (4%) | 136 |
0.328 (1.00) |
0.641 (1.00) |
0.65 (1.00) |
0.995 (1.00) |
0.869 (1.00) |
0.749 (1.00) |
|
| SPINK13 | 4 (3%) | 137 |
0.192 (1.00) |
0.336 (1.00) |
1 (1.00) |
0.995 (1.00) |
0.397 (1.00) |
0.966 (1.00) |
'PTEN MUTATION STATUS' versus 'DISTANT.METASTASIS'
P value = 2.63e-05 (Chi-square test), Q value = 0.019
Table S1. Gene #8: 'PTEN MUTATION STATUS' versus Clinical Feature #4: 'DISTANT.METASTASIS'
| nPatients | M0 | M1 | M1A | M1B | M1C |
|---|---|---|---|---|---|
| ALL | 119 | 2 | 1 | 1 | 2 |
| PTEN MUTATED | 7 | 2 | 0 | 0 | 0 |
| PTEN WILD-TYPE | 112 | 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 = 0.000201 (t-test), Q value = 0.15
Table S2. Gene #17: 'MUC7 MUTATION STATUS' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 139 | 56.3 (16.1) |
| MUC7 MUTATED | 11 | 72.7 (10.9) |
| MUC7 WILD-TYPE | 128 | 54.9 (15.7) |
Figure S2. Get High-res Image Gene #17: 'MUC7 MUTATION STATUS' versus Clinical Feature #2: 'AGE'
Methods & Data
Input
-
Mutation data file = SKCM-TM.mutsig.cluster.txt
-
Clinical data file = SKCM-TM.clin.merged.picked.txt
-
Number of patients = 141
-
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.