Skin Cutaneous Melanoma: Correlation between gene mutation status and molecular subtypes
(All_Samples cohort)
(All_Samples 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 109 genes and 8 molecular subtypes across 264 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 109 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 | |
| BRAF | 140 (53%) | 124 |
0.036 (1.00) |
0.0552 (1.00) |
0.669 (1.00) |
0.898 (1.00) |
0.0432 (1.00) |
0.073 (1.00) |
0.705 (1.00) |
0.252 (1.00) |
| C15ORF23 | 14 (5%) | 250 |
0.912 (1.00) |
0.321 (1.00) |
1 (1.00) |
0.596 (1.00) |
0.718 (1.00) |
0.611 (1.00) |
0.574 (1.00) |
0.577 (1.00) |
| CDKN2A | 34 (13%) | 230 |
0.437 (1.00) |
0.311 (1.00) |
1 (1.00) |
0.544 (1.00) |
0.639 (1.00) |
0.714 (1.00) |
0.507 (1.00) |
1 (1.00) |
| NRAS | 73 (28%) | 191 |
0.0981 (1.00) |
0.201 (1.00) |
0.499 (1.00) |
0.0702 (1.00) |
0.553 (1.00) |
0.811 (1.00) |
0.812 (1.00) |
0.887 (1.00) |
| OXA1L | 8 (3%) | 256 |
0.618 (1.00) |
0.201 (1.00) |
1 (1.00) |
0.563 (1.00) |
0.296 (1.00) |
0.387 (1.00) |
0.384 (1.00) |
0.714 (1.00) |
| STK19 | 11 (4%) | 253 |
0.865 (1.00) |
0.13 (1.00) |
0.878 (1.00) |
1 (1.00) |
0.148 (1.00) |
0.283 (1.00) |
0.792 (1.00) |
0.54 (1.00) |
| TP53 | 39 (15%) | 225 |
0.328 (1.00) |
0.0542 (1.00) |
0.263 (1.00) |
0.364 (1.00) |
0.022 (1.00) |
0.204 (1.00) |
0.904 (1.00) |
0.107 (1.00) |
| TTN | 204 (77%) | 60 |
0.918 (1.00) |
0.00778 (1.00) |
0.179 (1.00) |
0.155 (1.00) |
0.365 (1.00) |
0.332 (1.00) |
0.0235 (1.00) |
0.223 (1.00) |
| UGT2B15 | 24 (9%) | 240 |
0.0936 (1.00) |
0.38 (1.00) |
0.342 (1.00) |
0.61 (1.00) |
0.384 (1.00) |
1 (1.00) |
0.313 (1.00) |
1 (1.00) |
| PTEN | 23 (9%) | 241 |
0.814 (1.00) |
0.288 (1.00) |
0.0107 (1.00) |
0.394 (1.00) |
0.417 (1.00) |
0.329 (1.00) |
0.924 (1.00) |
0.655 (1.00) |
| RAC1 | 17 (6%) | 247 |
0.294 (1.00) |
0.859 (1.00) |
0.704 (1.00) |
0.917 (1.00) |
0.238 (1.00) |
0.63 (1.00) |
0.333 (1.00) |
0.077 (1.00) |
| PPP6C | 23 (9%) | 241 |
0.279 (1.00) |
0.646 (1.00) |
0.768 (1.00) |
0.116 (1.00) |
0.475 (1.00) |
0.247 (1.00) |
0.0867 (1.00) |
0.0723 (1.00) |
| PRB2 | 39 (15%) | 225 |
0.349 (1.00) |
1 (1.00) |
1 (1.00) |
0.916 (1.00) |
0.033 (1.00) |
0.288 (1.00) |
0.652 (1.00) |
0.211 (1.00) |
| IDH1 | 15 (6%) | 249 |
0.0362 (1.00) |
0.345 (1.00) |
0.563 (1.00) |
0.83 (1.00) |
0.28 (1.00) |
0.302 (1.00) |
0.392 (1.00) |
0.789 (1.00) |
| NAP1L2 | 26 (10%) | 238 |
0.151 (1.00) |
0.966 (1.00) |
0.749 (1.00) |
0.705 (1.00) |
0.709 (1.00) |
0.702 (1.00) |
0.932 (1.00) |
1 (1.00) |
| FIGLA | 4 (2%) | 260 |
0.655 (1.00) |
0.367 (1.00) |
0.359 (1.00) |
0.377 (1.00) |
0.373 (1.00) |
0.301 (1.00) |
||
| RBM11 | 16 (6%) | 248 |
0.307 (1.00) |
0.0267 (1.00) |
0.792 (1.00) |
0.853 (1.00) |
0.399 (1.00) |
0.0237 (1.00) |
0.068 (1.00) |
0.426 (1.00) |
| HBG2 | 9 (3%) | 255 |
0.537 (1.00) |
0.195 (1.00) |
0.447 (1.00) |
0.444 (1.00) |
0.383 (1.00) |
0.431 (1.00) |
0.104 (1.00) |
0.309 (1.00) |
| LCE1B | 12 (5%) | 252 |
0.0811 (1.00) |
0.651 (1.00) |
0.92 (1.00) |
0.917 (1.00) |
0.45 (1.00) |
0.757 (1.00) |
0.93 (1.00) |
1 (1.00) |
| MUC7 | 19 (7%) | 245 |
0.806 (1.00) |
0.446 (1.00) |
0.376 (1.00) |
0.495 (1.00) |
0.399 (1.00) |
0.643 (1.00) |
0.402 (1.00) |
0.0483 (1.00) |
| DDX3X | 20 (8%) | 244 |
0.955 (1.00) |
0.44 (1.00) |
0.536 (1.00) |
0.278 (1.00) |
0.13 (1.00) |
0.407 (1.00) |
0.874 (1.00) |
1 (1.00) |
| CDH9 | 37 (14%) | 227 |
0.824 (1.00) |
0.0607 (1.00) |
0.642 (1.00) |
0.889 (1.00) |
0.763 (1.00) |
0.698 (1.00) |
0.0091 (1.00) |
0.198 (1.00) |
| HIST1H2AA | 10 (4%) | 254 |
0.804 (1.00) |
0.711 (1.00) |
0.659 (1.00) |
0.574 (1.00) |
0.105 (1.00) |
0.847 (1.00) |
0.298 (1.00) |
0.746 (1.00) |
| GFRAL | 33 (12%) | 231 |
0.763 (1.00) |
0.405 (1.00) |
0.609 (1.00) |
0.761 (1.00) |
0.124 (1.00) |
0.771 (1.00) |
0.664 (1.00) |
0.25 (1.00) |
| TBC1D3B | 6 (2%) | 258 |
0.0975 (1.00) |
0.661 (1.00) |
0.48 (1.00) |
0.0842 (1.00) |
0.0298 (1.00) |
0.858 (1.00) |
0.578 (1.00) |
1 (1.00) |
| HHLA2 | 18 (7%) | 246 |
0.229 (1.00) |
0.71 (1.00) |
0.284 (1.00) |
0.0117 (1.00) |
0.387 (1.00) |
0.267 (1.00) |
0.000705 (0.611) |
0.135 (1.00) |
| COPG2 | 10 (4%) | 254 |
0.972 (1.00) |
0.777 (1.00) |
0.202 (1.00) |
0.283 (1.00) |
0.893 (1.00) |
0.847 (1.00) |
0.298 (1.00) |
0.746 (1.00) |
| FGF16 | 8 (3%) | 256 |
0.677 (1.00) |
0.534 (1.00) |
0.0128 (1.00) |
0.0279 (1.00) |
0.11 (1.00) |
0.34 (1.00) |
0.273 (1.00) |
1 (1.00) |
| IL32 | 10 (4%) | 254 |
0.747 (1.00) |
0.0538 (1.00) |
1 (1.00) |
0.14 (1.00) |
0.893 (1.00) |
0.467 (1.00) |
0.655 (1.00) |
1 (1.00) |
| PRB4 | 19 (7%) | 245 |
0.868 (1.00) |
0.515 (1.00) |
0.0303 (1.00) |
0.0729 (1.00) |
0.101 (1.00) |
0.0409 (1.00) |
0.291 (1.00) |
0.0857 (1.00) |
| NBPF7 | 16 (6%) | 248 |
0.0502 (1.00) |
0.208 (1.00) |
0.861 (1.00) |
1 (1.00) |
0.449 (1.00) |
0.943 (1.00) |
0.158 (1.00) |
1 (1.00) |
| POM121 | 18 (7%) | 246 |
1 (1.00) |
0.255 (1.00) |
0.73 (1.00) |
0.785 (1.00) |
0.829 (1.00) |
0.581 (1.00) |
0.245 (1.00) |
0.454 (1.00) |
| ARID2 | 38 (14%) | 226 |
0.29 (1.00) |
0.426 (1.00) |
0.679 (1.00) |
0.0266 (1.00) |
0.0734 (1.00) |
1 (1.00) |
0.363 (1.00) |
0.373 (1.00) |
| MAP2K1 | 13 (5%) | 251 |
0.859 (1.00) |
0.587 (1.00) |
0.00234 (1.00) |
0.0237 (1.00) |
0.205 (1.00) |
0.171 (1.00) |
0.877 (1.00) |
1 (1.00) |
| DEFB118 | 10 (4%) | 254 |
0.804 (1.00) |
0.0978 (1.00) |
1 (1.00) |
1 (1.00) |
0.893 (1.00) |
0.467 (1.00) |
1 (1.00) |
0.746 (1.00) |
| HBD | 10 (4%) | 254 |
0.918 (1.00) |
0.847 (1.00) |
0.886 (1.00) |
0.14 (1.00) |
0.282 (1.00) |
0.0378 (1.00) |
0.922 (1.00) |
0.746 (1.00) |
| ANKRD20A4 | 5 (2%) | 259 |
0.189 (1.00) |
0.452 (1.00) |
0.201 (1.00) |
0.278 (1.00) |
0.0471 (1.00) |
0.18 (1.00) |
0.528 (1.00) |
1 (1.00) |
| GLRB | 26 (10%) | 238 |
0.765 (1.00) |
0.455 (1.00) |
0.108 (1.00) |
0.0242 (1.00) |
0.363 (1.00) |
0.567 (1.00) |
0.352 (1.00) |
0.135 (1.00) |
| NR1H4 | 14 (5%) | 250 |
0.982 (1.00) |
0.152 (1.00) |
0.228 (1.00) |
0.471 (1.00) |
0.743 (1.00) |
0.877 (1.00) |
0.819 (1.00) |
0.253 (1.00) |
| OR51S1 | 30 (11%) | 234 |
0.105 (1.00) |
0.94 (1.00) |
0.742 (1.00) |
0.039 (1.00) |
0.233 (1.00) |
0.163 (1.00) |
0.939 (1.00) |
1 (1.00) |
| TFEC | 16 (6%) | 248 |
0.35 (1.00) |
0.439 (1.00) |
0.0836 (1.00) |
0.247 (1.00) |
0.596 (1.00) |
0.943 (1.00) |
0.807 (1.00) |
1 (1.00) |
| UNC119B | 6 (2%) | 258 |
0.14 (1.00) |
0.447 (1.00) |
0.424 (1.00) |
0.668 (1.00) |
0.805 (1.00) |
0.153 (1.00) |
1 (1.00) |
0.677 (1.00) |
| ZNF479 | 27 (10%) | 237 |
0.532 (1.00) |
0.842 (1.00) |
0.279 (1.00) |
0.348 (1.00) |
0.891 (1.00) |
0.485 (1.00) |
0.157 (1.00) |
0.674 (1.00) |
| FAM19A1 | 10 (4%) | 254 |
0.056 (1.00) |
0.605 (1.00) |
0.173 (1.00) |
0.0133 (1.00) |
0.0744 (1.00) |
1 (1.00) |
0.847 (1.00) |
0.513 (1.00) |
| GIMAP7 | 24 (9%) | 240 |
0.00153 (1.00) |
0.483 (1.00) |
0.181 (1.00) |
0.239 (1.00) |
0.238 (1.00) |
0.79 (1.00) |
0.521 (1.00) |
0.27 (1.00) |
| KLHL4 | 23 (9%) | 241 |
0.693 (1.00) |
0.383 (1.00) |
0.94 (1.00) |
0.733 (1.00) |
0.633 (1.00) |
0.064 (1.00) |
0.537 (1.00) |
0.496 (1.00) |
| NOTCH2NL | 13 (5%) | 251 |
0.695 (1.00) |
0.342 (1.00) |
0.374 (1.00) |
0.0669 (1.00) |
0.017 (1.00) |
0.00564 (1.00) |
0.32 (1.00) |
0.0859 (1.00) |
| PRC1 | 15 (6%) | 249 |
0.295 (1.00) |
0.367 (1.00) |
0.257 (1.00) |
0.378 (1.00) |
0.368 (1.00) |
0.625 (1.00) |
0.214 (1.00) |
0.421 (1.00) |
| ZMAT4 | 10 (4%) | 254 |
0.325 (1.00) |
0.0783 (1.00) |
0.703 (1.00) |
0.249 (1.00) |
0.944 (1.00) |
0.847 (1.00) |
0.385 (1.00) |
0.513 (1.00) |
| PDE1A | 34 (13%) | 230 |
0.831 (1.00) |
0.945 (1.00) |
0.663 (1.00) |
0.4 (1.00) |
0.057 (1.00) |
0.208 (1.00) |
0.453 (1.00) |
0.344 (1.00) |
| GML | 10 (4%) | 254 |
0.844 (1.00) |
0.429 (1.00) |
0.202 (1.00) |
0.326 (1.00) |
0.604 (1.00) |
0.467 (1.00) |
0.124 (1.00) |
1 (1.00) |
| OR4N2 | 25 (9%) | 239 |
0.318 (1.00) |
0.302 (1.00) |
0.364 (1.00) |
0.445 (1.00) |
0.00231 (1.00) |
0.0986 (1.00) |
0.574 (1.00) |
0.0536 (1.00) |
| ACSM2B | 40 (15%) | 224 |
0.378 (1.00) |
0.58 (1.00) |
0.69 (1.00) |
0.719 (1.00) |
0.314 (1.00) |
0.336 (1.00) |
0.229 (1.00) |
0.482 (1.00) |
| USP17L2 | 19 (7%) | 245 |
0.265 (1.00) |
0.0489 (1.00) |
0.242 (1.00) |
0.45 (1.00) |
0.00514 (1.00) |
0.239 (1.00) |
0.334 (1.00) |
0.464 (1.00) |
| TAF1A | 13 (5%) | 251 |
0.479 (1.00) |
0.876 (1.00) |
0.67 (1.00) |
0.785 (1.00) |
0.783 (1.00) |
0.445 (1.00) |
0.819 (1.00) |
0.772 (1.00) |
| OR5H2 | 19 (7%) | 245 |
0.342 (1.00) |
0.755 (1.00) |
0.792 (1.00) |
0.666 (1.00) |
0.829 (1.00) |
0.745 (1.00) |
0.754 (1.00) |
1 (1.00) |
| PHGDH | 9 (3%) | 255 |
0.936 (1.00) |
0.911 (1.00) |
0.79 (1.00) |
0.483 (1.00) |
0.394 (1.00) |
0.358 (1.00) |
0.91 (1.00) |
0.309 (1.00) |
| BAGE2 | 14 (5%) | 250 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.904 (1.00) |
0.578 (1.00) |
0.82 (1.00) |
0.41 (1.00) |
0.78 (1.00) |
| FUT9 | 25 (9%) | 239 |
0.639 (1.00) |
0.00568 (1.00) |
0.47 (1.00) |
0.328 (1.00) |
0.273 (1.00) |
0.562 (1.00) |
0.326 (1.00) |
0.832 (1.00) |
| MPP7 | 29 (11%) | 235 |
0.388 (1.00) |
0.746 (1.00) |
0.918 (1.00) |
0.742 (1.00) |
0.12 (1.00) |
0.497 (1.00) |
0.741 (1.00) |
1 (1.00) |
| TSPAN9 | 4 (2%) | 260 |
0.473 (1.00) |
1 (1.00) |
0.164 (1.00) |
0.606 (1.00) |
0.834 (1.00) |
0.572 (1.00) |
0.686 (1.00) |
1 (1.00) |
| TRAT1 | 13 (5%) | 251 |
0.532 (1.00) |
0.256 (1.00) |
0.497 (1.00) |
0.765 (1.00) |
0.183 (1.00) |
0.457 (1.00) |
0.63 (1.00) |
0.772 (1.00) |
| C9ORF119 | 8 (3%) | 256 |
0.677 (1.00) |
0.668 (1.00) |
0.617 (1.00) |
0.606 (1.00) |
0.385 (1.00) |
1 (1.00) |
0.273 (1.00) |
0.266 (1.00) |
| TUBB8 | 15 (6%) | 249 |
0.292 (1.00) |
0.747 (1.00) |
0.411 (1.00) |
0.651 (1.00) |
0.839 (1.00) |
0.941 (1.00) |
0.527 (1.00) |
0.421 (1.00) |
| ACD | 10 (4%) | 254 |
0.918 (1.00) |
0.429 (1.00) |
0.657 (1.00) |
0.239 (1.00) |
0.66 (1.00) |
0.388 (1.00) |
0.171 (1.00) |
0.188 (1.00) |
| NUDT4 | 5 (2%) | 259 |
0.134 (1.00) |
0.373 (1.00) |
0.218 (1.00) |
0.0409 (1.00) |
1 (1.00) |
0.617 (1.00) |
0.224 (1.00) |
0.373 (1.00) |
| C8A | 30 (11%) | 234 |
0.215 (1.00) |
0.202 (1.00) |
0.268 (1.00) |
0.0673 (1.00) |
0.0293 (1.00) |
0.289 (1.00) |
0.605 (1.00) |
0.324 (1.00) |
| KIAA1257 | 15 (6%) | 249 |
0.92 (1.00) |
0.747 (1.00) |
0.67 (1.00) |
0.282 (1.00) |
0.802 (1.00) |
0.472 (1.00) |
0.707 (1.00) |
0.421 (1.00) |
| SNAP91 | 28 (11%) | 236 |
0.313 (1.00) |
0.876 (1.00) |
0.176 (1.00) |
0.469 (1.00) |
0.861 (1.00) |
1 (1.00) |
0.275 (1.00) |
0.298 (1.00) |
| CCK | 7 (3%) | 257 |
1 (1.00) |
0.703 (1.00) |
0.0415 (1.00) |
0.16 (1.00) |
0.609 (1.00) |
0.802 (1.00) |
0.379 (1.00) |
0.712 (1.00) |
| SPINK13 | 9 (3%) | 255 |
0.153 (1.00) |
0.575 (1.00) |
0.621 (1.00) |
0.612 (1.00) |
0.0683 (1.00) |
0.117 (1.00) |
0.203 (1.00) |
0.735 (1.00) |
| ANXA10 | 14 (5%) | 250 |
0.198 (1.00) |
0.0145 (1.00) |
0.258 (1.00) |
0.45 (1.00) |
0.0977 (1.00) |
0.0276 (1.00) |
0.343 (1.00) |
0.161 (1.00) |
| LIN7A | 11 (4%) | 253 |
0.416 (1.00) |
0.179 (1.00) |
0.202 (1.00) |
0.283 (1.00) |
0.0278 (1.00) |
0.117 (1.00) |
0.39 (1.00) |
0.54 (1.00) |
| C2 | 14 (5%) | 250 |
0.151 (1.00) |
0.414 (1.00) |
0.911 (1.00) |
0.83 (1.00) |
0.00374 (1.00) |
0.117 (1.00) |
0.299 (1.00) |
0.772 (1.00) |
| DGAT2L6 | 12 (5%) | 252 |
0.345 (1.00) |
0.604 (1.00) |
0.619 (1.00) |
0.343 (1.00) |
0.747 (1.00) |
0.93 (1.00) |
0.813 (1.00) |
1 (1.00) |
| RAPGEF5 | 13 (5%) | 251 |
0.339 (1.00) |
0.628 (1.00) |
0.703 (1.00) |
0.541 (1.00) |
0.0702 (1.00) |
0.767 (1.00) |
0.177 (1.00) |
0.253 (1.00) |
| OR2L3 | 17 (6%) | 247 |
0.884 (1.00) |
0.0637 (1.00) |
0.41 (1.00) |
0.527 (1.00) |
0.76 (1.00) |
0.596 (1.00) |
0.902 (1.00) |
0.449 (1.00) |
| ZNF679 | 20 (8%) | 244 |
0.512 (1.00) |
0.511 (1.00) |
0.736 (1.00) |
0.653 (1.00) |
0.146 (1.00) |
0.802 (1.00) |
0.159 (1.00) |
0.483 (1.00) |
| NAP1L4 | 10 (4%) | 254 |
0.0587 (1.00) |
0.0295 (1.00) |
0.878 (1.00) |
0.431 (1.00) |
0.13 (1.00) |
0.124 (1.00) |
0.922 (1.00) |
0.513 (1.00) |
| PARM1 | 18 (7%) | 246 |
0.0276 (1.00) |
1 (1.00) |
0.814 (1.00) |
0.22 (1.00) |
0.924 (1.00) |
0.862 (1.00) |
0.178 (1.00) |
0.0458 (1.00) |
| DEFB119 | 6 (2%) | 258 |
0.531 (1.00) |
0.768 (1.00) |
0.812 (1.00) |
0.819 (1.00) |
0.946 (1.00) |
1 (1.00) |
0.336 (1.00) |
1 (1.00) |
| RGS18 | 10 (4%) | 254 |
0.369 (1.00) |
0.223 (1.00) |
0.218 (1.00) |
0.16 (1.00) |
0.394 (1.00) |
1 (1.00) |
0.323 (1.00) |
1 (1.00) |
| VEGFC | 17 (6%) | 247 |
0.0588 (1.00) |
0.408 (1.00) |
1 (1.00) |
0.273 (1.00) |
0.295 (1.00) |
0.0489 (1.00) |
0.189 (1.00) |
0.119 (1.00) |
| ARL16 | 7 (3%) | 257 |
0.687 (1.00) |
0.796 (1.00) |
0.159 (1.00) |
0.684 (1.00) |
0.519 (1.00) |
0.181 (1.00) |
1 (1.00) |
1 (1.00) |
| CACNA1H | 24 (9%) | 240 |
0.436 (1.00) |
0.0911 (1.00) |
0.897 (1.00) |
0.645 (1.00) |
0.414 (1.00) |
0.767 (1.00) |
0.542 (1.00) |
0.826 (1.00) |
| CCNE2 | 13 (5%) | 251 |
0.303 (1.00) |
0.77 (1.00) |
0.116 (1.00) |
0.102 (1.00) |
0.436 (1.00) |
0.721 (1.00) |
0.0417 (1.00) |
0.381 (1.00) |
| FRG2B | 17 (6%) | 247 |
0.771 (1.00) |
0.508 (1.00) |
0.929 (1.00) |
0.8 (1.00) |
0.372 (1.00) |
0.736 (1.00) |
0.154 (1.00) |
0.207 (1.00) |
| SPAG16 | 17 (6%) | 247 |
0.222 (1.00) |
0.732 (1.00) |
0.619 (1.00) |
0.379 (1.00) |
0.149 (1.00) |
0.147 (1.00) |
0.2 (1.00) |
0.449 (1.00) |
| USP29 | 40 (15%) | 224 |
0.858 (1.00) |
1 (1.00) |
0.758 (1.00) |
0.62 (1.00) |
0.701 (1.00) |
0.778 (1.00) |
0.319 (1.00) |
0.217 (1.00) |
| GH2 | 10 (4%) | 254 |
0.176 (1.00) |
0.556 (1.00) |
0.589 (1.00) |
0.585 (1.00) |
0.0664 (1.00) |
0.425 (1.00) |
0.607 (1.00) |
0.513 (1.00) |
| ST18 | 47 (18%) | 217 |
0.3 (1.00) |
0.62 (1.00) |
0.369 (1.00) |
0.192 (1.00) |
0.55 (1.00) |
0.159 (1.00) |
0.877 (1.00) |
0.408 (1.00) |
| CCDC102B | 22 (8%) | 242 |
0.914 (1.00) |
0.885 (1.00) |
0.324 (1.00) |
0.303 (1.00) |
0.671 (1.00) |
0.919 (1.00) |
1 (1.00) |
0.496 (1.00) |
| B2M | 6 (2%) | 258 |
0.946 (1.00) |
1 (1.00) |
0.766 (1.00) |
0.87 (1.00) |
0.495 (1.00) |
0.226 (1.00) |
0.0227 (1.00) |
0.677 (1.00) |
| CD2 | 17 (6%) | 247 |
0.92 (1.00) |
0.596 (1.00) |
0.41 (1.00) |
0.411 (1.00) |
0.416 (1.00) |
0.903 (1.00) |
0.697 (1.00) |
0.607 (1.00) |
| SLC38A4 | 30 (11%) | 234 |
0.545 (1.00) |
0.584 (1.00) |
0.693 (1.00) |
0.948 (1.00) |
0.0602 (1.00) |
0.557 (1.00) |
0.774 (1.00) |
1 (1.00) |
| OR8D4 | 11 (4%) | 253 |
0.114 (1.00) |
0.537 (1.00) |
0.159 (1.00) |
0.213 (1.00) |
0.171 (1.00) |
0.283 (1.00) |
0.859 (1.00) |
1 (1.00) |
| MKX | 16 (6%) | 248 |
0.313 (1.00) |
0.347 (1.00) |
0.841 (1.00) |
0.841 (1.00) |
0.317 (1.00) |
0.0741 (1.00) |
0.218 (1.00) |
1 (1.00) |
| SPATA8 | 11 (4%) | 253 |
0.416 (1.00) |
0.461 (1.00) |
0.342 (1.00) |
0.556 (1.00) |
0.306 (1.00) |
0.214 (1.00) |
||
| GPR137 | 10 (4%) | 254 |
0.275 (1.00) |
0.392 (1.00) |
1 (1.00) |
0.87 (1.00) |
0.944 (1.00) |
0.716 (1.00) |
1 (1.00) |
0.513 (1.00) |
| GRXCR2 | 15 (6%) | 249 |
0.683 (1.00) |
0.944 (1.00) |
0.0937 (1.00) |
0.83 (1.00) |
0.0161 (1.00) |
0.304 (1.00) |
0.666 (1.00) |
0.586 (1.00) |
| C2ORF40 | 7 (3%) | 257 |
0.441 (1.00) |
0.896 (1.00) |
0.287 (1.00) |
0.431 (1.00) |
0.362 (1.00) |
1 (1.00) |
1 (1.00) |
0.712 (1.00) |
| CADM2 | 23 (9%) | 241 |
0.97 (1.00) |
0.0738 (1.00) |
0.346 (1.00) |
0.348 (1.00) |
0.794 (1.00) |
0.728 (1.00) |
0.469 (1.00) |
0.00265 (1.00) |
| OR5J2 | 16 (6%) | 248 |
0.816 (1.00) |
0.761 (1.00) |
1 (1.00) |
0.176 (1.00) |
0.196 (1.00) |
0.518 (1.00) |
0.0463 (1.00) |
0.302 (1.00) |
| SIGLEC14 | 12 (5%) | 252 |
0.12 (1.00) |
0.604 (1.00) |
1 (1.00) |
0.444 (1.00) |
0.344 (1.00) |
0.704 (1.00) |
1 (1.00) |
1 (1.00) |
| CX3CL1 | 4 (2%) | 260 |
0.513 (1.00) |
0.131 (1.00) |
1 (1.00) |
0.377 (1.00) |
0.0951 (1.00) |
0.301 (1.00) |
||
| GNAI2 | 4 (2%) | 260 |
0.334 (1.00) |
0.367 (1.00) |
0.792 (1.00) |
1 (1.00) |
0.173 (1.00) |
0.572 (1.00) |
0.17 (1.00) |
0.157 (1.00) |
| OR52J3 | 17 (6%) | 247 |
0.642 (1.00) |
0.282 (1.00) |
0.342 (1.00) |
0.61 (1.00) |
0.838 (1.00) |
0.946 (1.00) |
0.393 (1.00) |
0.801 (1.00) |
| AREG | 6 (2%) | 258 |
1 (1.00) |
0.579 (1.00) |
0.585 (1.00) |
0.684 (1.00) |
0.67 (1.00) |
0.335 (1.00) |
0.441 (1.00) |
0.206 (1.00) |
| RUNDC3B | 15 (6%) | 249 |
0.494 (1.00) |
0.0111 (1.00) |
0.897 (1.00) |
0.904 (1.00) |
0.912 (1.00) |
1 (1.00) |
0.527 (1.00) |
0.789 (1.00) |
Methods & Data
Input
-
Mutation data file = SKCM-All_Samples.mutsig.cluster.txt
-
Molecular subtypes file = SKCM-All_Samples.transferedmergedcluster.txt
-
Number of patients = 264
-
Number of significantly mutated genes = 109
-
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.