Skin Cutaneous Melanoma: Correlation between gene mutation status and selected clinical features
(BRAF_Hotspot_Mutants cohort)
(BRAF_Hotspot_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 selected clinical features.
Summary
Testing the association between mutation status of 98 genes and 8 clinical features across 65 patients, no significant finding detected with Q value < 0.25.
-
No gene mutations related to clinical features.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between mutation status of 98 genes and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.
|
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
GENDER |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
| nMutated (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Chi-square test | Chi-square test | t-test | Chi-square test | |
| CDKN2A | 8 (12%) | 57 |
0.434 (1.00) |
0.287 (1.00) |
0.739 (1.00) |
0.259 (1.00) |
0.947 (1.00) |
0.827 (1.00) |
0.484 (1.00) |
|
| PTEN | 8 (12%) | 57 |
0.539 (1.00) |
0.437 (1.00) |
0.386 (1.00) |
0.42 (1.00) |
0.135 (1.00) |
0.936 (1.00) |
0.0978 (1.00) |
|
| OR4K1 | 7 (11%) | 58 |
0.548 (1.00) |
0.731 (1.00) |
0.0733 (1.00) |
1 (1.00) |
0.961 (1.00) |
0.656 (1.00) |
0.352 (1.00) |
|
| RPTN | 11 (17%) | 54 |
0.475 (1.00) |
0.957 (1.00) |
0.0748 (1.00) |
1 (1.00) |
0.892 (1.00) |
0.582 (1.00) |
0.0912 (1.00) |
|
| TP53 | 7 (11%) | 58 |
0.136 (1.00) |
0.287 (1.00) |
0.119 (1.00) |
0.672 (1.00) |
0.308 (1.00) |
0.575 (1.00) |
0.328 (1.00) |
|
| ACSM2B | 13 (20%) | 52 |
0.676 (1.00) |
0.348 (1.00) |
0.231 (1.00) |
0.0463 (1.00) |
0.869 (1.00) |
0.531 (1.00) |
0.422 (1.00) |
|
| C7ORF58 | 8 (12%) | 57 |
0.667 (1.00) |
0.421 (1.00) |
1 (1.00) |
1 (1.00) |
0.0917 (1.00) |
0.816 (1.00) |
0.289 (1.00) |
|
| GFRAL | 7 (11%) | 58 |
0.295 (1.00) |
0.265 (1.00) |
0.413 (1.00) |
0.947 (1.00) |
0.683 (1.00) |
0.682 (1.00) |
||
| LILRA1 | 10 (15%) | 55 |
0.104 (1.00) |
0.422 (1.00) |
0.278 (1.00) |
1 (1.00) |
0.912 (1.00) |
0.37 (1.00) |
0.576 (1.00) |
|
| DSG3 | 12 (18%) | 53 |
0.471 (1.00) |
0.622 (1.00) |
0.493 (1.00) |
1 (1.00) |
0.134 (1.00) |
0.66 (1.00) |
0.289 (1.00) |
|
| PRAMEF11 | 4 (6%) | 61 |
0.0813 (1.00) |
1 (1.00) |
0.296 (1.00) |
0.983 (1.00) |
0.000614 (0.396) |
0.483 (1.00) |
||
| RFX6 | 10 (15%) | 55 |
0.561 (1.00) |
0.224 (1.00) |
0.472 (1.00) |
0.715 (1.00) |
0.221 (1.00) |
0.942 (1.00) |
0.614 (1.00) |
|
| SLC4A10 | 10 (15%) | 55 |
0.918 (1.00) |
0.241 (1.00) |
0.472 (1.00) |
0.271 (1.00) |
0.66 (1.00) |
0.645 (1.00) |
0.702 (1.00) |
|
| SERPINB4 | 6 (9%) | 59 |
0.566 (1.00) |
0.761 (1.00) |
0.659 (1.00) |
0.166 (1.00) |
0.0532 (1.00) |
0.253 (1.00) |
0.605 (1.00) |
|
| NBPF1 | 10 (15%) | 55 |
0.615 (1.00) |
0.602 (1.00) |
0.68 (1.00) |
0.479 (1.00) |
0.931 (1.00) |
0.587 (1.00) |
0.612 (1.00) |
|
| NELL1 | 11 (17%) | 54 |
0.33 (1.00) |
0.00124 (0.792) |
0.796 (1.00) |
0.0878 (1.00) |
0.221 (1.00) |
0.281 (1.00) |
0.587 (1.00) |
|
| OR4C15 | 7 (11%) | 58 |
0.65 (1.00) |
0.172 (1.00) |
0.0106 (1.00) |
0.672 (1.00) |
0.947 (1.00) |
0.759 (1.00) |
0.808 (1.00) |
|
| CDR1 | 6 (9%) | 59 |
0.0957 (1.00) |
0.144 (1.00) |
0.242 (1.00) |
0.379 (1.00) |
0.0239 (1.00) |
0.98 (1.00) |
0.988 (1.00) |
|
| GK2 | 8 (12%) | 57 |
0.558 (1.00) |
0.201 (1.00) |
0.16 (1.00) |
0.706 (1.00) |
0.947 (1.00) |
0.819 (1.00) |
0.172 (1.00) |
|
| OR5D13 | 5 (8%) | 60 |
0.722 (1.00) |
0.26 (1.00) |
1 (1.00) |
1 (1.00) |
0.973 (1.00) |
0.000664 (0.427) |
0.299 (1.00) |
|
| ZNF215 | 7 (11%) | 58 |
0.393 (1.00) |
0.211 (1.00) |
0.839 (1.00) |
0.672 (1.00) |
0.523 (1.00) |
0.972 (1.00) |
0.947 (1.00) |
|
| MORF4 | 6 (9%) | 59 |
0.455 (1.00) |
0.0716 (1.00) |
0.0825 (1.00) |
0.379 (1.00) |
0.99 (1.00) |
0.9 (1.00) |
0.892 (1.00) |
|
| PRSS1 | 4 (6%) | 61 |
0.0922 (1.00) |
0.49 (1.00) |
0.296 (1.00) |
0.99 (1.00) |
0.962 (1.00) |
0.634 (1.00) |
||
| TRHR | 7 (11%) | 58 |
0.534 (1.00) |
0.11 (1.00) |
0.00667 (1.00) |
1 (1.00) |
0.0114 (1.00) |
0.77 (1.00) |
0.667 (1.00) |
|
| RGS21 | 5 (8%) | 60 |
0.575 (1.00) |
0.597 (1.00) |
1 (1.00) |
0.308 (1.00) |
0.809 (1.00) |
0.716 (1.00) |
||
| FUT9 | 5 (8%) | 60 |
0.253 (1.00) |
0.175 (1.00) |
1 (1.00) |
0.973 (1.00) |
0.938 (1.00) |
0.00508 (1.00) |
||
| CCDC102B | 9 (14%) | 56 |
0.365 (1.00) |
0.631 (1.00) |
0.0615 (1.00) |
0.455 (1.00) |
0.912 (1.00) |
0.396 (1.00) |
0.421 (1.00) |
|
| ST6GAL2 | 7 (11%) | 58 |
0.587 (1.00) |
0.425 (1.00) |
0.567 (1.00) |
0.413 (1.00) |
0.961 (1.00) |
0.294 (1.00) |
0.124 (1.00) |
|
| OR11L1 | 5 (8%) | 60 |
0.279 (1.00) |
0.207 (1.00) |
0.0975 (1.00) |
0.655 (1.00) |
0.973 (1.00) |
0.381 (1.00) |
0.279 (1.00) |
|
| GIMAP4 | 3 (5%) | 62 |
0.993 (1.00) |
0.15 (1.00) |
0.545 (1.00) |
0.99 (1.00) |
0.946 (1.00) |
0.913 (1.00) |
||
| ICA1L | 3 (5%) | 62 |
0.395 (1.00) |
1 (1.00) |
0.545 (1.00) |
|||||
| CADM2 | 7 (11%) | 58 |
0.446 (1.00) |
0.521 (1.00) |
0.474 (1.00) |
0.413 (1.00) |
0.947 (1.00) |
0.816 (1.00) |
0.353 (1.00) |
|
| GUCA1C | 3 (5%) | 62 |
0.415 (1.00) |
0.368 (1.00) |
1 (1.00) |
|||||
| C15ORF23 | 4 (6%) | 61 |
0.287 (1.00) |
0.731 (1.00) |
1 (1.00) |
0.983 (1.00) |
0.954 (1.00) |
0.895 (1.00) |
||
| HTR3B | 5 (8%) | 60 |
0.0774 (1.00) |
0.764 (1.00) |
0.763 (1.00) |
1 (1.00) |
0.973 (1.00) |
0.909 (1.00) |
0.385 (1.00) |
|
| RGPD4 | 13 (20%) | 52 |
0.16 (1.00) |
0.993 (1.00) |
0.281 (1.00) |
0.194 (1.00) |
0.845 (1.00) |
0.925 (1.00) |
0.767 (1.00) |
|
| PENK | 5 (8%) | 60 |
0.123 (1.00) |
0.415 (1.00) |
0.0755 (1.00) |
1 (1.00) |
0.973 (1.00) |
0.947 (1.00) |
0.801 (1.00) |
|
| RBM11 | 4 (6%) | 61 |
0.882 (1.00) |
0.355 (1.00) |
0.589 (1.00) |
0.181 (1.00) |
0.725 (1.00) |
0.289 (1.00) |
||
| WBSCR17 | 11 (17%) | 54 |
0.787 (1.00) |
0.299 (1.00) |
1 (1.00) |
0.0119 (1.00) |
0.0316 (1.00) |
0.57 (1.00) |
0.619 (1.00) |
|
| MORC1 | 12 (18%) | 53 |
0.452 (1.00) |
0.197 (1.00) |
0.292 (1.00) |
0.0845 (1.00) |
0.892 (1.00) |
0.977 (1.00) |
0.275 (1.00) |
|
| FAM83A | 3 (5%) | 62 |
0.302 (1.00) |
1 (1.00) |
0.545 (1.00) |
0.000753 (0.484) |
0.868 (1.00) |
|||
| SPANXN2 | 5 (8%) | 60 |
0.616 (1.00) |
0.37 (1.00) |
1 (1.00) |
1 (1.00) |
0.973 (1.00) |
0.0861 (1.00) |
0.00749 (1.00) |
|
| OR2M3 | 9 (14%) | 56 |
0.0271 (1.00) |
0.00399 (1.00) |
0.0615 (1.00) |
1 (1.00) |
0.6 (1.00) |
0.775 (1.00) |
0.551 (1.00) |
|
| TLL1 | 14 (22%) | 51 |
0.0894 (1.00) |
0.995 (1.00) |
0.0677 (1.00) |
1 (1.00) |
0.791 (1.00) |
0.406 (1.00) |
0.0803 (1.00) |
|
| ZNF331 | 5 (8%) | 60 |
0.853 (1.00) |
0.689 (1.00) |
0.0975 (1.00) |
1 (1.00) |
0.0239 (1.00) |
0.953 (1.00) |
0.853 (1.00) |
|
| OR2L3 | 6 (9%) | 59 |
0.714 (1.00) |
0.0692 (1.00) |
1 (1.00) |
0.0239 (1.00) |
0.955 (1.00) |
0.34 (1.00) |
||
| NCR1 | 5 (8%) | 60 |
0.42 (1.00) |
0.0357 (1.00) |
0.0975 (1.00) |
0.655 (1.00) |
0.983 (1.00) |
0.905 (1.00) |
0.582 (1.00) |
|
| PPP6C | 5 (8%) | 60 |
0.654 (1.00) |
0.343 (1.00) |
1 (1.00) |
0.308 (1.00) |
0.777 (1.00) |
0.573 (1.00) |
||
| UGT2B15 | 7 (11%) | 58 |
0.456 (1.00) |
0.229 (1.00) |
0.223 (1.00) |
0.413 (1.00) |
0.425 (1.00) |
0.923 (1.00) |
0.176 (1.00) |
|
| DISP1 | 8 (12%) | 57 |
0.21 (1.00) |
0.0391 (1.00) |
0.739 (1.00) |
0.706 (1.00) |
0.983 (1.00) |
0.905 (1.00) |
0.717 (1.00) |
|
| ADAM18 | 13 (20%) | 52 |
0.425 (1.00) |
0.84 (1.00) |
0.347 (1.00) |
0.522 (1.00) |
0.845 (1.00) |
0.906 (1.00) |
0.678 (1.00) |
|
| ZNF160 | 6 (9%) | 59 |
0.679 (1.00) |
0.707 (1.00) |
0.415 (1.00) |
0.655 (1.00) |
0.961 (1.00) |
0.0102 (1.00) |
0.00325 (1.00) |
|
| MAEL | 4 (6%) | 61 |
0.242 (1.00) |
0.0175 (1.00) |
1 (1.00) |
0.983 (1.00) |
0.725 (1.00) |
0.441 (1.00) |
||
| NRK | 7 (11%) | 58 |
0.783 (1.00) |
0.726 (1.00) |
0.265 (1.00) |
0.672 (1.00) |
0.961 (1.00) |
0.874 (1.00) |
0.698 (1.00) |
|
| ADAM32 | 8 (12%) | 57 |
0.374 (1.00) |
0.617 (1.00) |
0.259 (1.00) |
0.947 (1.00) |
0.683 (1.00) |
0.54 (1.00) |
||
| SNTG1 | 6 (9%) | 59 |
0.758 (1.00) |
0.24 (1.00) |
0.0447 (1.00) |
1 (1.00) |
0.961 (1.00) |
0.656 (1.00) |
0.0137 (1.00) |
|
| NDST4 | 9 (14%) | 56 |
0.727 (1.00) |
0.414 (1.00) |
0.255 (1.00) |
0.0259 (1.00) |
0.931 (1.00) |
0.558 (1.00) |
0.428 (1.00) |
|
| B2M | 3 (5%) | 62 |
0.937 (1.00) |
1 (1.00) |
0.545 (1.00) |
|||||
| RGPD3 | 8 (12%) | 57 |
0.732 (1.00) |
0.0659 (1.00) |
0.21 (1.00) |
0.259 (1.00) |
0.931 (1.00) |
0.519 (1.00) |
0.236 (1.00) |
|
| WDR12 | 6 (9%) | 59 |
0.882 (1.00) |
0.679 (1.00) |
0.659 (1.00) |
0.655 (1.00) |
0.983 (1.00) |
0.417 (1.00) |
0.966 (1.00) |
|
| PCDP1 | 6 (9%) | 59 |
0.623 (1.00) |
0.819 (1.00) |
0.415 (1.00) |
1 (1.00) |
0.961 (1.00) |
0.923 (1.00) |
0.192 (1.00) |
|
| ZNF679 | 4 (6%) | 61 |
0.203 (1.00) |
0.288 (1.00) |
0.0722 (1.00) |
0.589 (1.00) |
0.983 (1.00) |
0.176 (1.00) |
0.0714 (1.00) |
|
| NAP1L2 | 5 (8%) | 60 |
0.724 (1.00) |
0.99 (1.00) |
0.0755 (1.00) |
0.655 (1.00) |
0.973 (1.00) |
0.575 (1.00) |
0.583 (1.00) |
|
| OR4A16 | 5 (8%) | 60 |
0.487 (1.00) |
0.65 (1.00) |
0.12 (1.00) |
1 (1.00) |
0.00299 (1.00) |
0.587 (1.00) |
0.0267 (1.00) |
|
| PDE1A | 9 (14%) | 56 |
0.532 (1.00) |
0.0928 (1.00) |
0.0891 (1.00) |
0.455 (1.00) |
0.931 (1.00) |
0.265 (1.00) |
0.266 (1.00) |
|
| GABRE | 7 (11%) | 58 |
0.454 (1.00) |
0.242 (1.00) |
0.0507 (1.00) |
0.2 (1.00) |
0.947 (1.00) |
0.618 (1.00) |
0.256 (1.00) |
|
| PRC1 | 5 (8%) | 60 |
0.268 (1.00) |
0.188 (1.00) |
1 (1.00) |
0.166 (1.00) |
0.983 (1.00) |
0.905 (1.00) |
0.814 (1.00) |
|
| KLHL4 | 4 (6%) | 61 |
0.122 (1.00) |
0.379 (1.00) |
1 (1.00) |
0.589 (1.00) |
0.99 (1.00) |
0.97 (1.00) |
0.269 (1.00) |
|
| BAZ2B | 8 (12%) | 57 |
0.28 (1.00) |
0.522 (1.00) |
0.0941 (1.00) |
0.42 (1.00) |
0.523 (1.00) |
0.149 (1.00) |
0.188 (1.00) |
|
| CYP4Z1 | 5 (8%) | 60 |
0.987 (1.00) |
0.343 (1.00) |
0.655 (1.00) |
0.0239 (1.00) |
0.119 (1.00) |
0.269 (1.00) |
||
| C1ORF168 | 10 (15%) | 55 |
0.154 (1.00) |
0.661 (1.00) |
0.189 (1.00) |
0.715 (1.00) |
0.912 (1.00) |
0.919 (1.00) |
0.0848 (1.00) |
|
| FAM65C | 7 (11%) | 58 |
0.321 (1.00) |
0.179 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.961 (1.00) |
0.984 (1.00) |
0.303 (1.00) |
|
| NOTCH2NL | 5 (8%) | 60 |
0.203 (1.00) |
1 (1.00) |
0.166 (1.00) |
0.983 (1.00) |
0.417 (1.00) |
0.542 (1.00) |
||
| TRHDE | 11 (17%) | 54 |
0.0463 (1.00) |
0.0871 (1.00) |
0.259 (1.00) |
1 (1.00) |
0.705 (1.00) |
0.48 (1.00) |
0.639 (1.00) |
|
| USP17L2 | 6 (9%) | 59 |
0.486 (1.00) |
0.862 (1.00) |
0.015 (1.00) |
1 (1.00) |
0.961 (1.00) |
0.955 (1.00) |
0.722 (1.00) |
|
| RXFP2 | 7 (11%) | 58 |
0.111 (1.00) |
0.541 (1.00) |
0.697 (1.00) |
1 (1.00) |
0.973 (1.00) |
0.507 (1.00) |
0.273 (1.00) |
|
| TAF1A | 3 (5%) | 62 |
0.769 (1.00) |
1 (1.00) |
1 (1.00) |
0.000753 (0.484) |
0.494 (1.00) |
|||
| ANO4 | 10 (15%) | 55 |
0.105 (1.00) |
0.44 (1.00) |
0.168 (1.00) |
0.479 (1.00) |
0.912 (1.00) |
0.594 (1.00) |
0.814 (1.00) |
|
| MNDA | 7 (11%) | 58 |
0.372 (1.00) |
0.0125 (1.00) |
0.0507 (1.00) |
0.413 (1.00) |
0.961 (1.00) |
0.955 (1.00) |
0.356 (1.00) |
|
| ADAM7 | 10 (15%) | 55 |
0.105 (1.00) |
0.101 (1.00) |
0.0775 (1.00) |
1 (1.00) |
0.705 (1.00) |
0.568 (1.00) |
0.715 (1.00) |
|
| FOLH1B | 4 (6%) | 61 |
0.893 (1.00) |
0.377 (1.00) |
0.731 (1.00) |
1 (1.00) |
0.983 (1.00) |
0.417 (1.00) |
0.479 (1.00) |
|
| C10ORF71 | 8 (12%) | 57 |
0.674 (1.00) |
0.468 (1.00) |
0.509 (1.00) |
0.0463 (1.00) |
0.961 (1.00) |
0.615 (1.00) |
0.436 (1.00) |
|
| CXCR2 | 3 (5%) | 62 |
0.783 (1.00) |
0.226 (1.00) |
1 (1.00) |
0.99 (1.00) |
0.451 (1.00) |
0.248 (1.00) |
||
| OR4E2 | 5 (8%) | 60 |
0.933 (1.00) |
0.354 (1.00) |
0.175 (1.00) |
1 (1.00) |
0.308 (1.00) |
0.947 (1.00) |
0.458 (1.00) |
|
| POTEG | 6 (9%) | 59 |
0.887 (1.00) |
0.0765 (1.00) |
0.0447 (1.00) |
0.655 (1.00) |
0.0239 (1.00) |
0.712 (1.00) |
0.901 (1.00) |
|
| TCEB3C | 7 (11%) | 58 |
0.931 (1.00) |
0.34 (1.00) |
0.697 (1.00) |
0.413 (1.00) |
0.947 (1.00) |
0.0322 (1.00) |
0.324 (1.00) |
|
| TCP10L2 | 3 (5%) | 62 |
0.382 (1.00) |
0.652 (1.00) |
1 (1.00) |
|||||
| BAGE2 | 4 (6%) | 61 |
0.861 (1.00) |
0.0946 (1.00) |
0.589 (1.00) |
0.181 (1.00) |
0.168 (1.00) |
0.265 (1.00) |
||
| CLEC14A | 5 (8%) | 60 |
0.852 (1.00) |
0.958 (1.00) |
0.225 (1.00) |
0.655 (1.00) |
0.983 (1.00) |
0.129 (1.00) |
0.388 (1.00) |
|
| SLC6A13 | 7 (11%) | 58 |
0.0727 (1.00) |
0.621 (1.00) |
0.0141 (1.00) |
0.2 (1.00) |
0.425 (1.00) |
0.656 (1.00) |
0.127 (1.00) |
|
| BCLAF1 | 10 (15%) | 55 |
0.0915 (1.00) |
0.132 (1.00) |
0.168 (1.00) |
0.479 (1.00) |
0.135 (1.00) |
0.709 (1.00) |
0.808 (1.00) |
|
| UPF2 | 8 (12%) | 57 |
0.25 (1.00) |
0.394 (1.00) |
0.866 (1.00) |
0.42 (1.00) |
0.961 (1.00) |
0.656 (1.00) |
0.657 (1.00) |
|
| GPR141 | 6 (9%) | 59 |
0.759 (1.00) |
0.203 (1.00) |
1 (1.00) |
0.655 (1.00) |
0.961 (1.00) |
0.904 (1.00) |
0.675 (1.00) |
|
| ZNF334 | 4 (6%) | 61 |
0.44 (1.00) |
0.245 (1.00) |
1 (1.00) |
|||||
| HAPLN1 | 4 (6%) | 61 |
0.159 (1.00) |
1 (1.00) |
1 (1.00) |
0.00677 (1.00) |
0.961 (1.00) |
0.301 (1.00) |
||
| MUM1L1 | 7 (11%) | 58 |
0.412 (1.00) |
0.671 (1.00) |
1 (1.00) |
1 (1.00) |
0.947 (1.00) |
0.972 (1.00) |
0.604 (1.00) |
|
| ST18 | 7 (11%) | 58 |
0.706 (1.00) |
0.787 (1.00) |
1 (1.00) |
0.672 (1.00) |
0.973 (1.00) |
0.507 (1.00) |
0.725 (1.00) |
|
| OR5H15 | 5 (8%) | 60 |
0.104 (1.00) |
0.471 (1.00) |
1 (1.00) |
0.166 (1.00) |
0.973 (1.00) |
0.381 (1.00) |
0.215 (1.00) |
Methods & Data
Input
-
Mutation data file = SKCM-BRAF_Hotspot_Mutants.mutsig.cluster.txt
-
Clinical data file = SKCM-BRAF_Hotspot_Mutants.clin.merged.picked.txt
-
Number of patients = 65
-
Number of significantly mutated genes = 98
-
Number of selected clinical features = 8
-
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.