Table 1.

Specific genomic alterations of cancer driver genes to predict tumor microenvironment immune type (TMIT)

GeneGenomic alterationOdds ratioP valueFDR
VHLMutation3.372.21 × 10−204.15 × 10−18
CASP8Mutation3.132.56 × 10−88.81 × 10−7
PBRM1Mutation2.406.59 × 10−128.23 × 10−10
NCOR1Mutation2.372.58 × 10−88.81 × 10−7
MXRA5Mutation2.135.93 × 10−104.44 × 10−8
FAT1Mutation1.991.44 × 10−86.00 × 10−7
ANK3Mutation1.951.20 × 10−85.64 × 10−7
MUC17Mutation1.941.90 × 10−111.78 × 10−9
BRAFMutation1.705.50 × 10−93.44 × 10−7
FLGMutation1.697.05 × 10−93.78 × 10−7
CD274Amplification3.462.05 × 10−147.43 × 10−12
APCAmplification3.336.10 × 10−93.68 × 10−7
DIAPH1Amplification3.091.16 × 10−91.40 × 10−7
CDX1Amplification2.731.69 × 10−88.75 × 10−7
NPM1Amplification2.542.27 × 10−91.65 × 10−7
PIGZAmplification1.674.94 × 10−108.94 × 10−8
MUC4Amplification1.642.03 × 10−91.65 × 10−7
ACVR2BDeletion4.501.54 × 10−115.57 × 10−9
MYD88Deletion4.323.56 × 10−115.58 × 10−9
TGFBR2Deletion3.424.64 × 10−115.58 × 10−9
RPSADeletion4.261.52 × 10−101.31 × 10−8
SLC22A14Deletion3.921.81 × 10−101.31 × 10−8
EAF1Deletion4.106.79 × 10−103.50 × 10−8
MRPS25Deletion4.196.45 × 10−103.50 × 10−8
CTNNB1Deletion3.507.86 × 10−103.55 × 10−8
ZNF620Deletion3.781.55 × 10−96.21 × 10−8
  • Please see Supplementary Table S3 for raw data of all significance genomic alterations of genes.

  • Odds ratio was calculated that the proportion of TMIT I in each genomic alteration-positive divided by those in the genomic alteration-negative, by logistic regression.

  • Filtering condition of this table is odds ratio > 1.5 and FDR < 1.00 × 10−7.

  • FDR, false discovery rate.