Table 2 Significantly mutated genes in tumor samples of 510 patients with LUAD. The genes were classified as oncogene (OG) and tumor suppressor gene (TSG) based on their scores and the cancer gene census information by SomInaClust R package
From: Analysis of genomic and transcriptomic variations as prognostic signature for lung adenocarcinoma
Gene | # Mutations | qDG | OG Score | TSG Score | Classification | CGCa |
|---|---|---|---|---|---|---|
KRAS | 143 | 1.97e-250 | 97.8 | 0 | OG | Dom |
TP53 | 253 | 2.52e-135 | 79.7 | 38 | TSG | Rec |
EGFR | 73 | 8.97e-84 | 73.8 | 10 | OG | Dom |
STK11 | 83 | 4.6e-61 | 27.8 | 72 | TSG | Rec |
BRAF | 44 | 8.07e-51 | 67.5 | 7.4 | OG | Dom |
RBM10 | 39 | 9.06e-31 | 0 | 78.9 | TSG | NA |
NF1 | 63 | 5.37e-25 | 0 | 54.2 | TSG | Rec |
MGA | 52 | 6.46e-23 | 0 | 58.3 | TSG | NA |
SETD2 | 44 | 1.34e-20 | 16.7 | 58.1 | TSG | Rec |
RB1 | 32 | 4.99e-20 | 0 | 68.8 | TSG | Rec |
PIK3CA | 27 | 1.36e-19 | 61.5 | 0 | OG | Dom |
ATM | 48 | 5.18e-18 | 25 | 45.7 | TSG | Rec |
CTNNB1 | 21 | 3.32e-15 | 61.1 | 12.5 | OG | Dom |
ARID1A | 30 | 1.76e-14 | 12.5 | 60 | TSG | Rec |
ARID2 | 29 | 2.83e-12 | 0 | 57.1 | TSG | Rec |
SMARCA4 | 48 | 2.23e-11 | 16.7 | 42.9 | TSG | Rec |
CSMD3 | 324 | 6.25e-10 | 0 | 17.5 | NA | NA |
ATF7IP | 17 | 1.84e-08 | 0 | 71.4 | TSG | NA |
KEAP1 | 90 | 1.91e-08 | 9.8 | 24.1 | TSG | NA |
NFE2L2 | 14 | 2.83e-07 | 58.3 | 0 | OG | Dom |
KDM5C | 16 | 1.76e-06 | 0 | 60 | TSG | Rec |
ERBB2 | 13 | 6.94e-06 | 55.6 | 14.3 | OG | Dom |
LRP1B | 267 | 6.04e-05 | 0 | 15.6 | NA | Rec |
HMCN1 | 97 | 8.93e-05 | 0 | 24.1 | TSG | NA |
MAP2K1 | 9 | 0.000263 | 66.7 | 0 | OG | Dom |
APC | 24 | 0.000272 | 0 | 37.5 | TSG | Rec |
PNISR | 6 | 0.000626 | 0 | 83.3 | TSG | NA |
RPL5 | 7 | 0.000626 | 0 | 83.3 | TSG | Dom |
GNAS | 19 | 0.000962 | 28.6 | 0 | OG | Dom |
COL11A1 | 129 | 0.00139 | 0 | 18.1 | NA | NA |
EPHA5 | 66 | 0.00221 | 0 | 23.4 | TSG | NA |
TTK | 18 | 0.00221 | 0 | 41.2 | TSG | NA |
FBXW7 | 12 | 0.0028 | 40 | 50 | TSG | Rec |
DMD | 99 | 0.00349 | 0 | 18.8 | NA | NA |
SMAD4 | 20 | 0.00379 | 30 | 35 | TSG | Rec |
FER | 16 | 0.0043 | 0 | 46.2 | TSG | NA |
MARK1 | 21 | 0.0043 | 0 | 46.2 | TSG | NA |
TEP1 | 29 | 0.0043 | 0 | 46.2 | TSG | NA |
ATRX | 35 | 0.00463 | 0 | 26.5 | TSG | Rec |
CDKN2A | 21 | 0.00585 | 37.5 | 35 | TSG | Rec |
MYO9A | 19 | 0.00615 | 0 | 42.9 | TSG | NA |
ZNF800 | 17 | 0.00615 | 0 | 42.9 | TSG | NA |
CMTR2 | 26 | 0.00674 | 0 | 55.6 | TSG | NA |
RASA1 | 9 | 0.00674 | 0 | 55.6 | TSG | NA |
CDKN1B | 5 | 0.00674 | 0 | 80 | TSG | Rec |
DHX15 | 7 | 0.00674 | 0 | 80 | TSG | NA |
IQGAP2 | 28 | 0.00816 | 0 | 40 | TSG | NA |
LTN1 | 19 | 0.00816 | 0 | 40 | TSG | NA |
SMARCA1 | 19 | 0.00816 | 0 | 40 | TSG | NA |
SPTA1 | 164 | 0.00971 | 0 | 17.6 | NA | NA |
FHOD3 | 31 | 0.0122 | 0 | 30.4 | TSG | NA |
CPVL | 8 | 0.0161 | 0 | 66.7 | TSG | NA |
MAP3K12 | 8 | 0.0161 | 0 | 66.7 | TSG | NA |
TOP2B | 9 | 0.0161 | 0 | 66.7 | TSG | NA |
ROCK1 | 21 | 0.0163 | 0 | 35.3 | TSG | NA |
PBRM1 | 12 | 0.0172 | 0 | 45.5 | TSG | Rec |
AKAP6 | 40 | 0.0195 | 0 | 28 | TSG | NA |
SENP1 | 3 | 0.0241 | 0 | 100 | TSG | NA |
SP1 | 4 | 0.0241 | 0 | 100 | TSG | NA |
WISP3 | 4 | 0.0241 | 0 | 100 | TSG | NA |
RAD50 | 13 | 0.0243 | 20 | 41.7 | TSG | NA |
COL28A1 | 19 | 0.0243 | 0 | 41.7 | TSG | NA |
SCAF8 | 18 | 0.0243 | 0 | 41.7 | TSG | NA |
STK31 | 19 | 0.0243 | 0 | 41.7 | TSG | NA |
IDH1 | 6 | 0.0248 | 40 | 25 | TSG | Dom |
USH2A | 240 | 0.0263 | 0 | 13.2 | NA | NA |
YLPM1 | 23 | 0.0269 | 0 | 31.6 | TSG | NA |
IQUB | 12 | 0.0272 | 0 | 57.1 | TSG | NA |
MARK2 | 10 | 0.0272 | 0 | 57.1 | TSG | NA |
NAA15 | 8 | 0.0272 | 0 | 57.1 | TSG | NA |
CDH10 | 99 | 0.028 | 0 | 16.4 | NA | NA |
AKT1 | 3 | 0.0296 | 66.7 | 0 | OG | Dom |
RAF1 | 7 | 0.031 | 66.7 | 0 | OG | Dom |
VPS13C | 39 | 0.0332 | 0 | 25 | TSG | NA |
ZBBX | 28 | 0.0333 | 0 | 30 | TSG | NA |
DST | 67 | 0.0333 | 0 | 19.1 | NA | NA |
KMT2C | 52 | 0.0388 | 0 | 18.8 | NA | Rec |
DGKB | 38 | 0.0431 | 0 | 28.6 | TSG | NA |
MAP2K4 | 8 | 0.045 | 33.3 | 50 | TSG | Rec |
FBN2 | 93 | 0.045 | 0 | 20.5 | TSG | NA |
B2M | 8 | 0.045 | 0 | 50 | TSG | Rec |
BAP1 | 8 | 0.045 | 0 | 50 | TSG | Rec |