(All_Metastatic cohort)
This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 111 genes and 8 clinical features across 161 patients, 11 significant findings detected with Q value < 0.25.
-
OXA1L mutation correlated to 'Time to Death' and 'LYMPH.NODE.METASTASIS'.
-
PTEN mutation correlated to 'DISTANT.METASTASIS'.
-
MUC7 mutation correlated to 'AGE'.
-
RAPGEF5 mutation correlated to 'LYMPH.NODE.METASTASIS'.
-
ANKRD20A4 mutation correlated to 'LYMPH.NODE.METASTASIS'.
-
C9ORF119 mutation correlated to 'LYMPH.NODE.METASTASIS'.
-
C2 mutation correlated to 'LYMPH.NODE.METASTASIS'.
-
SPINK13 mutation correlated to 'LYMPH.NODE.METASTASIS'.
-
GNAI2 mutation correlated to 'LYMPH.NODE.METASTASIS'.
-
SORT1 mutation correlated to 'Time to Death'.
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 | |
OXA1L | 5 (3%) | 156 |
1.05e-07 (7.88e-05) |
0.613 (1.00) |
0.656 (1.00) |
1 (1.00) |
0.992 (1.00) |
0.00012 (0.0891) |
0.48 (1.00) |
|
PTEN | 13 (8%) | 148 |
0.254 (1.00) |
0.234 (1.00) |
0.473 (1.00) |
0.551 (1.00) |
0.00028 (0.207) |
0.835 (1.00) |
0.0325 (1.00) |
|
MUC7 | 11 (7%) | 150 |
0.418 (1.00) |
0.000223 (0.166) |
0.819 (1.00) |
0.747 (1.00) |
0.964 (1.00) |
0.828 (1.00) |
0.576 (1.00) |
|
RAPGEF5 | 8 (5%) | 153 |
0.658 (1.00) |
0.36 (1.00) |
0.1 (1.00) |
0.26 (1.00) |
0.989 (1.00) |
0.000279 (0.207) |
0.331 (1.00) |
|
ANKRD20A4 | 4 (2%) | 157 |
0.247 (1.00) |
0.531 (1.00) |
0.778 (1.00) |
0.297 (1.00) |
0.995 (1.00) |
1.62e-05 (0.0121) |
0.564 (1.00) |
|
C9ORF119 | 5 (3%) | 156 |
0.832 (1.00) |
0.34 (1.00) |
1 (1.00) |
0.159 (1.00) |
0.992 (1.00) |
5.91e-05 (0.044) |
0.817 (1.00) |
|
C2 | 7 (4%) | 154 |
0.602 (1.00) |
0.883 (1.00) |
0.742 (1.00) |
1 (1.00) |
0.989 (1.00) |
0.000172 (0.128) |
0.349 (1.00) |
|
SPINK13 | 6 (4%) | 155 |
0.217 (1.00) |
0.168 (1.00) |
0.84 (1.00) |
0.416 (1.00) |
0.989 (1.00) |
3.89e-05 (0.029) |
0.817 (1.00) |
|
GNAI2 | 4 (2%) | 157 |
0.531 (1.00) |
0.44 (1.00) |
0.624 (1.00) |
0.997 (1.00) |
3.35e-09 (2.51e-06) |
0.572 (1.00) |
||
SORT1 | 5 (3%) | 156 |
9.47e-07 (0.000708) |
0.6 (1.00) |
0.0592 (1.00) |
0.653 (1.00) |
0.992 (1.00) |
0.696 (1.00) |
0.147 (1.00) |
|
TP53 | 26 (16%) | 135 |
0.611 (1.00) |
0.07 (1.00) |
0.221 (1.00) |
0.828 (1.00) |
0.59 (1.00) |
0.0964 (1.00) |
0.464 (1.00) |
|
BRAF | 82 (51%) | 79 |
0.265 (1.00) |
0.0963 (1.00) |
0.126 (1.00) |
0.746 (1.00) |
0.568 (1.00) |
0.835 (1.00) |
0.635 (1.00) |
|
C15ORF23 | 11 (7%) | 150 |
0.0921 (1.00) |
0.67 (1.00) |
0.819 (1.00) |
0.747 (1.00) |
0.97 (1.00) |
0.488 (1.00) |
0.679 (1.00) |
|
CDKN2A | 27 (17%) | 134 |
0.986 (1.00) |
0.995 (1.00) |
0.671 (1.00) |
1 (1.00) |
0.826 (1.00) |
0.746 (1.00) |
0.366 (1.00) |
|
NRAS | 49 (30%) | 112 |
0.459 (1.00) |
0.394 (1.00) |
0.454 (1.00) |
1 (1.00) |
0.618 (1.00) |
0.91 (1.00) |
0.591 (1.00) |
|
STK19 | 10 (6%) | 151 |
0.225 (1.00) |
0.335 (1.00) |
1 (1.00) |
0.5 (1.00) |
0.975 (1.00) |
0.965 (1.00) |
0.76 (1.00) |
|
RAC1 | 12 (7%) | 149 |
0.629 (1.00) |
0.415 (1.00) |
0.579 (1.00) |
1 (1.00) |
0.97 (1.00) |
0.895 (1.00) |
0.303 (1.00) |
|
IDH1 | 8 (5%) | 153 |
0.607 (1.00) |
0.00483 (1.00) |
1 (1.00) |
0.466 (1.00) |
0.981 (1.00) |
0.981 (1.00) |
0.703 (1.00) |
|
ACSM2B | 31 (19%) | 130 |
0.756 (1.00) |
0.861 (1.00) |
0.0877 (1.00) |
0.00183 (1.00) |
0.771 (1.00) |
0.351 (1.00) |
0.822 (1.00) |
|
PPP6C | 15 (9%) | 146 |
0.377 (1.00) |
0.647 (1.00) |
0.646 (1.00) |
1 (1.00) |
0.402 (1.00) |
0.0481 (1.00) |
0.755 (1.00) |
|
LCE1B | 9 (6%) | 152 |
0.564 (1.00) |
0.75 (1.00) |
0.0817 (1.00) |
0.726 (1.00) |
0.981 (1.00) |
0.933 (1.00) |
0.674 (1.00) |
|
OR51S1 | 17 (11%) | 144 |
0.471 (1.00) |
0.424 (1.00) |
0.197 (1.00) |
1 (1.00) |
0.934 (1.00) |
0.0496 (1.00) |
0.201 (1.00) |
|
NAP1L2 | 17 (11%) | 144 |
0.885 (1.00) |
0.0518 (1.00) |
0.0722 (1.00) |
0.426 (1.00) |
0.925 (1.00) |
0.0605 (1.00) |
0.635 (1.00) |
|
PRB2 | 24 (15%) | 137 |
0.274 (1.00) |
0.00385 (1.00) |
0.158 (1.00) |
0.0374 (1.00) |
0.862 (1.00) |
0.412 (1.00) |
0.287 (1.00) |
|
TAF1A | 10 (6%) | 151 |
0.133 (1.00) |
0.57 (1.00) |
0.893 (1.00) |
0.5 (1.00) |
0.179 (1.00) |
0.733 (1.00) |
0.823 (1.00) |
|
HIST1H2AA | 7 (4%) | 154 |
0.975 (1.00) |
0.0409 (1.00) |
0.708 (1.00) |
0.985 (1.00) |
0.955 (1.00) |
0.751 (1.00) |
||
FRG2B | 10 (6%) | 151 |
0.121 (1.00) |
0.0224 (1.00) |
0.808 (1.00) |
0.5 (1.00) |
0.97 (1.00) |
0.916 (1.00) |
0.566 (1.00) |
|
CDH9 | 27 (17%) | 134 |
0.546 (1.00) |
0.385 (1.00) |
0.0132 (1.00) |
1 (1.00) |
0.813 (1.00) |
0.204 (1.00) |
0.0904 (1.00) |
|
PRAMEF11 | 15 (9%) | 146 |
0.0301 (1.00) |
0.0848 (1.00) |
0.751 (1.00) |
0.784 (1.00) |
0.942 (1.00) |
0.0513 (1.00) |
0.854 (1.00) |
|
HBG2 | 7 (4%) | 154 |
0.969 (1.00) |
0.156 (1.00) |
0.854 (1.00) |
1 (1.00) |
0.985 (1.00) |
0.00722 (1.00) |
0.758 (1.00) |
|
DDX3X | 16 (10%) | 145 |
0.225 (1.00) |
0.538 (1.00) |
0.54 (1.00) |
0.172 (1.00) |
0.00456 (1.00) |
0.991 (1.00) |
0.704 (1.00) |
|
PRB4 | 18 (11%) | 143 |
0.0664 (1.00) |
0.123 (1.00) |
0.307 (1.00) |
0.205 (1.00) |
0.438 (1.00) |
0.12 (1.00) |
0.874 (1.00) |
|
GRXCR1 | 15 (9%) | 146 |
0.394 (1.00) |
0.0286 (1.00) |
0.517 (1.00) |
1 (1.00) |
0.942 (1.00) |
0.78 (1.00) |
0.318 (1.00) |
|
HHLA2 | 12 (7%) | 149 |
0.474 (1.00) |
0.301 (1.00) |
0.133 (1.00) |
1 (1.00) |
0.964 (1.00) |
0.0249 (1.00) |
0.908 (1.00) |
|
RBM11 | 11 (7%) | 150 |
0.62 (1.00) |
0.194 (1.00) |
0.673 (1.00) |
0.747 (1.00) |
0.227 (1.00) |
0.0329 (1.00) |
0.367 (1.00) |
|
FUT9 | 17 (11%) | 144 |
0.967 (1.00) |
0.0352 (1.00) |
0.389 (1.00) |
0.602 (1.00) |
0.916 (1.00) |
0.157 (1.00) |
0.256 (1.00) |
|
TTN | 127 (79%) | 34 |
0.883 (1.00) |
0.837 (1.00) |
1 (1.00) |
0.166 (1.00) |
0.496 (1.00) |
0.353 (1.00) |
0.376 (1.00) |
|
HBD | 9 (6%) | 152 |
0.233 (1.00) |
0.856 (1.00) |
0.376 (1.00) |
0.726 (1.00) |
0.975 (1.00) |
0.945 (1.00) |
0.349 (1.00) |
|
KIAA1257 | 7 (4%) | 154 |
0.333 (1.00) |
0.538 (1.00) |
0.424 (1.00) |
0.992 (1.00) |
0.885 (1.00) |
0.729 (1.00) |
||
USP17L2 | 16 (10%) | 145 |
0.371 (1.00) |
0.662 (1.00) |
0.0759 (1.00) |
0.172 (1.00) |
0.934 (1.00) |
0.145 (1.00) |
0.113 (1.00) |
|
CADM2 | 18 (11%) | 143 |
0.222 (1.00) |
0.944 (1.00) |
0.622 (1.00) |
1 (1.00) |
0.906 (1.00) |
0.136 (1.00) |
0.409 (1.00) |
|
GFRAL | 24 (15%) | 137 |
0.345 (1.00) |
0.82 (1.00) |
0.177 (1.00) |
0.82 (1.00) |
0.59 (1.00) |
0.122 (1.00) |
0.0761 (1.00) |
|
OR4N2 | 19 (12%) | 142 |
0.382 (1.00) |
0.363 (1.00) |
0.189 (1.00) |
0.0112 (1.00) |
0.0769 (1.00) |
0.277 (1.00) |
0.663 (1.00) |
|
UGT2B15 | 17 (11%) | 144 |
0.722 (1.00) |
0.36 (1.00) |
0.773 (1.00) |
0.112 (1.00) |
0.117 (1.00) |
0.126 (1.00) |
0.14 (1.00) |
|
UNC119B | 3 (2%) | 158 |
0.375 (1.00) |
1 (1.00) |
1 (1.00) |
0.997 (1.00) |
0.99 (1.00) |
0.555 (1.00) |
||
C8A | 21 (13%) | 140 |
0.128 (1.00) |
0.106 (1.00) |
1 (1.00) |
0.0906 (1.00) |
0.0914 (1.00) |
0.38 (1.00) |
0.426 (1.00) |
|
ELF5 | 4 (2%) | 157 |
0.775 (1.00) |
0.6 (1.00) |
1 (1.00) |
0.997 (1.00) |
0.28 (1.00) |
0.97 (1.00) |
||
SPAG16 | 13 (8%) | 148 |
0.251 (1.00) |
0.753 (1.00) |
0.848 (1.00) |
0.377 (1.00) |
0.964 (1.00) |
0.0615 (1.00) |
0.582 (1.00) |
|
PHGDH | 8 (5%) | 153 |
0.83 (1.00) |
0.695 (1.00) |
0.588 (1.00) |
0.0273 (1.00) |
0.989 (1.00) |
0.00217 (1.00) |
0.143 (1.00) |
|
COPG2 | 3 (2%) | 158 |
0.997 (1.00) |
0.725 (1.00) |
1 (1.00) |
0.997 (1.00) |
0.99 (1.00) |
0.0442 (1.00) |
||
GML | 8 (5%) | 153 |
0.114 (1.00) |
1 (1.00) |
0.26 (1.00) |
0.985 (1.00) |
0.746 (1.00) |
0.965 (1.00) |
||
TBC1D3B | 3 (2%) | 158 |
0.404 (1.00) |
0.285 (1.00) |
1 (1.00) |
|||||
TFEC | 15 (9%) | 146 |
0.297 (1.00) |
0.111 (1.00) |
1 (1.00) |
1 (1.00) |
0.942 (1.00) |
0.00562 (1.00) |
0.571 (1.00) |
|
TRAT1 | 11 (7%) | 150 |
0.0516 (1.00) |
0.545 (1.00) |
0.0648 (1.00) |
0.533 (1.00) |
0.97 (1.00) |
0.0218 (1.00) |
0.86 (1.00) |
|
PRR23B | 11 (7%) | 150 |
0.0438 (1.00) |
0.813 (1.00) |
0.0825 (1.00) |
1 (1.00) |
0.97 (1.00) |
0.042 (1.00) |
0.907 (1.00) |
|
LIN7A | 9 (6%) | 152 |
0.00101 (0.746) |
0.581 (1.00) |
0.376 (1.00) |
0.488 (1.00) |
0.985 (1.00) |
0.00709 (1.00) |
0.576 (1.00) |
|
PARM1 | 14 (9%) | 147 |
0.0191 (1.00) |
0.234 (1.00) |
0.283 (1.00) |
0.577 (1.00) |
0.95 (1.00) |
0.00212 (1.00) |
0.167 (1.00) |
|
CCK | 5 (3%) | 156 |
0.0767 (1.00) |
0.725 (1.00) |
0.656 (1.00) |
0.653 (1.00) |
0.995 (1.00) |
0.024 (1.00) |
0.795 (1.00) |
|
TCEB3C | 23 (14%) | 138 |
0.16 (1.00) |
0.472 (1.00) |
0.864 (1.00) |
0.16 (1.00) |
0.862 (1.00) |
0.533 (1.00) |
0.458 (1.00) |
|
DEFB118 | 7 (4%) | 154 |
0.447 (1.00) |
0.64 (1.00) |
0.742 (1.00) |
1 (1.00) |
0.985 (1.00) |
0.0094 (1.00) |
0.762 (1.00) |
|
VEGFC | 16 (10%) | 145 |
0.479 (1.00) |
0.899 (1.00) |
0.394 (1.00) |
0.589 (1.00) |
0.942 (1.00) |
0.0142 (1.00) |
0.331 (1.00) |
|
MARCH11 | 8 (5%) | 153 |
0.789 (1.00) |
0.208 (1.00) |
0.711 (1.00) |
0.0895 (1.00) |
0.0156 (1.00) |
0.289 (1.00) |
||
ZFP106 | 6 (4%) | 155 |
0.000615 (0.454) |
0.491 (1.00) |
0.0864 (1.00) |
0.989 (1.00) |
0.81 (1.00) |
0.382 (1.00) |
||
PDE1A | 26 (16%) | 135 |
0.656 (1.00) |
0.13 (1.00) |
0.0187 (1.00) |
0.657 (1.00) |
0.838 (1.00) |
0.136 (1.00) |
0.708 (1.00) |
|
OR4F6 | 12 (7%) | 149 |
0.00169 (1.00) |
0.202 (1.00) |
0.916 (1.00) |
0.538 (1.00) |
0.227 (1.00) |
0.0866 (1.00) |
0.585 (1.00) |
|
CD2 | 15 (9%) | 146 |
0.753 (1.00) |
0.261 (1.00) |
0.0406 (1.00) |
0.784 (1.00) |
0.0891 (1.00) |
0.182 (1.00) |
0.439 (1.00) |
|
EIF3D | 3 (2%) | 158 |
0.481 (1.00) |
0.725 (1.00) |
0.299 (1.00) |
0.997 (1.00) |
0.979 (1.00) |
0.628 (1.00) |
||
MKX | 11 (7%) | 150 |
0.175 (1.00) |
0.684 (1.00) |
0.0593 (1.00) |
0.747 (1.00) |
0.981 (1.00) |
0.0156 (1.00) |
0.0422 (1.00) |
|
ARL16 | 5 (3%) | 156 |
0.0271 (1.00) |
0.0592 (1.00) |
0.653 (1.00) |
0.992 (1.00) |
0.885 (1.00) |
0.157 (1.00) |
||
OR2L3 | 13 (8%) | 148 |
0.282 (1.00) |
0.928 (1.00) |
0.222 (1.00) |
1 (1.00) |
0.0189 (1.00) |
0.057 (1.00) |
0.0699 (1.00) |
|
DEFB119 | 6 (4%) | 155 |
0.867 (1.00) |
0.188 (1.00) |
0.155 (1.00) |
1 (1.00) |
0.992 (1.00) |
0.943 (1.00) |
0.513 (1.00) |
|
KLHL4 | 16 (10%) | 145 |
0.731 (1.00) |
0.902 (1.00) |
0.252 (1.00) |
0.589 (1.00) |
0.95 (1.00) |
0.124 (1.00) |
0.59 (1.00) |
|
NR1H4 | 10 (6%) | 151 |
0.084 (1.00) |
0.448 (1.00) |
1 (1.00) |
0.328 (1.00) |
0.975 (1.00) |
0.0042 (1.00) |
0.363 (1.00) |
|
IL32 | 7 (4%) | 154 |
0.702 (1.00) |
0.538 (1.00) |
0.708 (1.00) |
0.985 (1.00) |
0.833 (1.00) |
0.00832 (1.00) |
||
DGAT2L6 | 9 (6%) | 152 |
0.6 (1.00) |
0.349 (1.00) |
0.0312 (1.00) |
1 (1.00) |
0.975 (1.00) |
0.0113 (1.00) |
0.762 (1.00) |
|
OR8D4 | 9 (6%) | 152 |
0.327 (1.00) |
0.625 (1.00) |
0.482 (1.00) |
1 (1.00) |
0.981 (1.00) |
0.014 (1.00) |
0.967 (1.00) |
|
GRXCR2 | 12 (7%) | 149 |
0.268 (1.00) |
0.951 (1.00) |
0.055 (1.00) |
1 (1.00) |
0.97 (1.00) |
0.0342 (1.00) |
0.683 (1.00) |
|
OR5H2 | 12 (7%) | 149 |
0.315 (1.00) |
0.0158 (1.00) |
1 (1.00) |
0.76 (1.00) |
0.957 (1.00) |
0.023 (1.00) |
0.515 (1.00) |
|
SIGLEC14 | 8 (5%) | 153 |
0.702 (1.00) |
0.042 (1.00) |
0.118 (1.00) |
0.0273 (1.00) |
0.985 (1.00) |
0.0094 (1.00) |
0.42 (1.00) |
|
ZNF479 | 15 (9%) | 146 |
0.528 (1.00) |
0.267 (1.00) |
0.806 (1.00) |
0.784 (1.00) |
0.362 (1.00) |
0.125 (1.00) |
0.785 (1.00) |
|
GH2 | 10 (6%) | 151 |
0.85 (1.00) |
0.483 (1.00) |
0.466 (1.00) |
0.747 (1.00) |
0.981 (1.00) |
0.00432 (1.00) |
0.0533 (1.00) |
|
GK2 | 21 (13%) | 140 |
0.706 (1.00) |
0.727 (1.00) |
0.105 (1.00) |
1 (1.00) |
0.896 (1.00) |
0.0829 (1.00) |
0.0679 (1.00) |
|
C2ORF40 | 4 (2%) | 157 |
0.404 (1.00) |
0.0637 (1.00) |
0.624 (1.00) |
0.997 (1.00) |
0.979 (1.00) |
|||
CXCR2 | 11 (7%) | 150 |
0.89 (1.00) |
0.675 (1.00) |
0.606 (1.00) |
1 (1.00) |
0.964 (1.00) |
0.0472 (1.00) |
0.269 (1.00) |
|
RPTN | 27 (17%) | 134 |
0.452 (1.00) |
0.165 (1.00) |
0.062 (1.00) |
0.513 (1.00) |
0.838 (1.00) |
0.0846 (1.00) |
0.0456 (1.00) |
|
PRIM2 | 9 (6%) | 152 |
0.955 (1.00) |
0.5 (1.00) |
0.299 (1.00) |
0.156 (1.00) |
0.132 (1.00) |
0.0067 (1.00) |
0.0239 (1.00) |
|
MUM1L1 | 17 (11%) | 144 |
0.655 (1.00) |
0.675 (1.00) |
0.498 (1.00) |
1 (1.00) |
0.916 (1.00) |
0.0802 (1.00) |
0.349 (1.00) |
|
TLL1 | 33 (20%) | 128 |
0.816 (1.00) |
0.169 (1.00) |
0.293 (1.00) |
0.426 (1.00) |
0.674 (1.00) |
0.146 (1.00) |
0.405 (1.00) |
|
PRC1 | 9 (6%) | 152 |
0.82 (1.00) |
0.445 (1.00) |
0.551 (1.00) |
0.488 (1.00) |
0.981 (1.00) |
0.717 (1.00) |
0.931 (1.00) |
|
GLRB | 19 (12%) | 142 |
0.0995 (1.00) |
0.189 (1.00) |
0.0396 (1.00) |
0.801 (1.00) |
0.896 (1.00) |
0.241 (1.00) |
0.818 (1.00) |
|
AREG | 6 (4%) | 155 |
0.0117 (1.00) |
0.294 (1.00) |
0.84 (1.00) |
0.67 (1.00) |
0.992 (1.00) |
0.000342 (0.253) |
0.454 (1.00) |
|
ACD | 7 (4%) | 154 |
0.459 (1.00) |
0.563 (1.00) |
0.0286 (1.00) |
0.424 (1.00) |
0.985 (1.00) |
0.00442 (1.00) |
0.384 (1.00) |
|
C2ORF39 | 8 (5%) | 153 |
0.069 (1.00) |
0.22 (1.00) |
1 (1.00) |
0.711 (1.00) |
0.053 (1.00) |
0.00709 (1.00) |
0.576 (1.00) |
|
RERG | 9 (6%) | 152 |
0.726 (1.00) |
0.0961 (1.00) |
0.482 (1.00) |
0.488 (1.00) |
0.985 (1.00) |
0.0016 (1.00) |
0.438 (1.00) |
|
TUBB8 | 8 (5%) | 153 |
0.0913 (1.00) |
0.352 (1.00) |
1 (1.00) |
0.711 (1.00) |
0.989 (1.00) |
0.00217 (1.00) |
0.693 (1.00) |
|
AGXT2 | 16 (10%) | 145 |
0.511 (1.00) |
0.386 (1.00) |
0.216 (1.00) |
1 (1.00) |
0.942 (1.00) |
0.113 (1.00) |
0.611 (1.00) |
|
C9 | 12 (7%) | 149 |
0.00975 (1.00) |
0.679 (1.00) |
0.834 (1.00) |
0.76 (1.00) |
0.97 (1.00) |
0.0321 (1.00) |
0.901 (1.00) |
|
CX3CL1 | 3 (2%) | 158 |
0.938 (1.00) |
0.469 (1.00) |
1 (1.00) |
|||||
DEFB112 | 6 (4%) | 155 |
0.137 (1.00) |
0.462 (1.00) |
0.0332 (1.00) |
1 (1.00) |
0.989 (1.00) |
0.00157 (1.00) |
0.727 (1.00) |
|
FAM19A1 | 7 (4%) | 154 |
0.466 (1.00) |
0.964 (1.00) |
1 (1.00) |
0.708 (1.00) |
0.989 (1.00) |
0.76 (1.00) |
0.813 (1.00) |
|
LONRF2 | 13 (8%) | 148 |
0.162 (1.00) |
0.885 (1.00) |
0.558 (1.00) |
0.77 (1.00) |
0.975 (1.00) |
0.297 (1.00) |
0.458 (1.00) |
|
NAP1L4 | 6 (4%) | 155 |
0.855 (1.00) |
0.34 (1.00) |
0.84 (1.00) |
0.67 (1.00) |
0.989 (1.00) |
0.628 (1.00) |
0.606 (1.00) |
|
OR5J2 | 11 (7%) | 150 |
0.187 (1.00) |
0.757 (1.00) |
0.673 (1.00) |
0.213 (1.00) |
0.975 (1.00) |
0.996 (1.00) |
0.833 (1.00) |
|
POM121 | 11 (7%) | 150 |
0.0787 (1.00) |
0.984 (1.00) |
0.338 (1.00) |
0.747 (1.00) |
0.97 (1.00) |
0.0371 (1.00) |
0.0149 (1.00) |
|
RBM22 | 4 (2%) | 157 |
0.327 (1.00) |
0.6 (1.00) |
0.297 (1.00) |
0.995 (1.00) |
0.985 (1.00) |
0.721 (1.00) |
||
SLC10A2 | 15 (9%) | 146 |
0.173 (1.00) |
0.238 (1.00) |
0.154 (1.00) |
0.784 (1.00) |
0.942 (1.00) |
0.032 (1.00) |
0.0825 (1.00) |
|
C4ORF22 | 8 (5%) | 153 |
0.56 (1.00) |
0.545 (1.00) |
0.281 (1.00) |
0.711 (1.00) |
0.985 (1.00) |
0.993 (1.00) |
0.771 (1.00) |
|
CLEC14A | 15 (9%) | 146 |
0.618 (1.00) |
0.926 (1.00) |
1 (1.00) |
0.26 (1.00) |
0.957 (1.00) |
0.0304 (1.00) |
0.422 (1.00) |
|
IGF2BP3 | 3 (2%) | 158 |
0.687 (1.00) |
0.469 (1.00) |
1 (1.00) |
|||||
RBM46 | 11 (7%) | 150 |
0.313 (1.00) |
0.134 (1.00) |
0.0703 (1.00) |
0.533 (1.00) |
0.964 (1.00) |
0.0653 (1.00) |
0.829 (1.00) |
|
SERPINB4 | 21 (13%) | 140 |
0.714 (1.00) |
0.209 (1.00) |
0.378 (1.00) |
0.0278 (1.00) |
0.121 (1.00) |
0.348 (1.00) |
0.902 (1.00) |
P value = 1.05e-07 (logrank test), Q value = 7.9e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 49 | 0.2 - 98.8 (12.2) |
OXA1L MUTATED | 3 | 2 | 1.0 - 4.9 (1.1) |
OXA1L WILD-TYPE | 82 | 47 | 0.2 - 98.8 (12.6) |
P value = 0.00012 (Chi-square test), Q value = 0.089
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 88 | 2 | 7 | 15 | 1 | 4 | 10 | 5 | 15 | 1 |
OXA1L MUTATED | 2 | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
OXA1L WILD-TYPE | 86 | 2 | 6 | 14 | 0 | 4 | 10 | 5 | 15 | 1 |
P value = 0.00028 (Chi-square test), Q value = 0.21
nPatients | M0 | M1 | M1A | M1B | M1C |
---|---|---|---|---|---|
ALL | 140 | 2 | 1 | 2 | 2 |
PTEN MUTATED | 11 | 2 | 0 | 0 | 0 |
PTEN WILD-TYPE | 129 | 0 | 1 | 2 | 2 |
P value = 0.000223 (t-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 160 | 56.3 (15.8) |
MUC7 MUTATED | 11 | 72.7 (10.9) |
MUC7 WILD-TYPE | 149 | 55.1 (15.5) |
P value = 0.000279 (Chi-square test), Q value = 0.21
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 88 | 2 | 7 | 15 | 1 | 4 | 10 | 5 | 15 | 1 |
RAPGEF5 MUTATED | 2 | 0 | 1 | 2 | 1 | 0 | 0 | 0 | 0 | 0 |
RAPGEF5 WILD-TYPE | 86 | 2 | 6 | 13 | 0 | 4 | 10 | 5 | 15 | 1 |
P value = 1.62e-05 (Chi-square test), Q value = 0.012
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 88 | 2 | 7 | 15 | 1 | 4 | 10 | 5 | 15 | 1 |
ANKRD20A4 MUTATED | 2 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
ANKRD20A4 WILD-TYPE | 86 | 2 | 7 | 14 | 0 | 4 | 10 | 5 | 15 | 1 |
P value = 5.91e-05 (Chi-square test), Q value = 0.044
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 88 | 2 | 7 | 15 | 1 | 4 | 10 | 5 | 15 | 1 |
C9ORF119 MUTATED | 2 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 0 | 0 |
C9ORF119 WILD-TYPE | 86 | 2 | 7 | 13 | 0 | 4 | 10 | 5 | 15 | 1 |
P value = 0.000172 (Chi-square test), Q value = 0.13
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 88 | 2 | 7 | 15 | 1 | 4 | 10 | 5 | 15 | 1 |
C2 MUTATED | 3 | 0 | 0 | 0 | 1 | 0 | 2 | 0 | 0 | 0 |
C2 WILD-TYPE | 85 | 2 | 7 | 15 | 0 | 4 | 8 | 5 | 15 | 1 |
P value = 3.89e-05 (Chi-square test), Q value = 0.029
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 88 | 2 | 7 | 15 | 1 | 4 | 10 | 5 | 15 | 1 |
SPINK13 MUTATED | 2 | 0 | 0 | 3 | 1 | 0 | 0 | 0 | 0 | 0 |
SPINK13 WILD-TYPE | 86 | 2 | 7 | 12 | 0 | 4 | 10 | 5 | 15 | 1 |
P value = 3.35e-09 (Chi-square test), Q value = 2.5e-06
nPatients | N0 | N1 | N1A | N1B | N2 | N2A | N2B | N2C | N3 | NX |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 88 | 2 | 7 | 15 | 1 | 4 | 10 | 5 | 15 | 1 |
GNAI2 MUTATED | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 |
GNAI2 WILD-TYPE | 87 | 2 | 7 | 15 | 0 | 4 | 10 | 4 | 15 | 1 |
P value = 9.47e-07 (logrank test), Q value = 0.00071
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 85 | 49 | 0.2 - 98.8 (12.2) |
SORT1 MUTATED | 3 | 2 | 1.4 - 4.0 (2.4) |
SORT1 WILD-TYPE | 82 | 47 | 0.2 - 98.8 (12.6) |
-
Mutation data file = SKCM-All_Metastatic.mutsig.cluster.txt
-
Clinical data file = SKCM-All_Metastatic.clin.merged.picked.txt
-
Number of patients = 161
-
Number of significantly mutated genes = 111
-
Number of selected clinical features = 8
-
Exclude genes that fewer than K tumors have mutations, K = 3
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
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
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
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
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.