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Table 3 Validation analysis of the seven potential SNPs identified by SurvEMVS using external database

From: Bayesian variable selection for parametric survival model with applications to cancer omics data

SNP (Cytoband)

Gene symbol (annotation)

TCGA

KEGG

PubMed

rs1506943_G (1q23.3)

LMX1A-RXRG (Intergenic)

RXRG: low expression in LUAD and LUSC tumor samples

RXRG participates in non-small cell lung cancer pathway and other cancer related pathways (hsa05200, 05222)

This gene is expressed at significantly lower levels in non-small cell lung cancer cells [46].

rs1921660_G (2q37.3)

GBX2-ASB18 (Intergenic)

GBX2: high expression is associated with bad prognosis (P = 0.0052)

a

Enhanced GBX2 expression stimulates growth of human prostate cancer cells [64, 65].

rs981852_C (3p14.2)

FHIT (Intron)

Low expression in LUSC tumor samples

FHIT participates in non-small cell lung cancer pathway and Small cell lung cancer pathway(hsa05222, 05223)

rs2044831_G (7p14.1)

EPDR1 (Coding)

Low expression in LUSC tumor samples

EPDR1 is highly expressed in colorectal tumor cells [66].

rs263264_G, (8q24.2)

ADCY8 (Intron)

ADCY8 participates multiple signal pathways and pathways in cancer

rs2074986_G (10q25.3)

GFRA1 (DHS)

Low expression in LUAD and LUSC tumor samples; High expression in LUAD is associated with good prognosis (P = 0.0025)

GFRA1 released by nerves enhances cancer cell perineural invasion [47];

Methylation changes of GFRA1 may be a potential biomarker for prediction of gastric carcinoma metastasis [67].

rs4885110_A (13q22.1)

LINC00393-KLF12 (Intergenic)

KLF12: low expression in LUAD tumor samples

KLF12 is an important regulator of gene expression during carcinogenesis [68,69,70].

  1. aNegative results of validation analysis