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]. |