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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