Bioinformatic Prediction of SNPs within miRNA Binding Sites of Inflammatory Genes Associated with Gastric Cancer


Polymorphisms in miRNA binding sites have been shown to affect miRNA binding to target genes, resultingin differential mRNA and protein expression and susceptibility to common diseases. Our purpose was to predictSNPs (single nucleotide polymorphisms) within miRNA binding sites of inflammatory genes in relation to gastriccancer. A complete list of SNPs in the 3’UTR regions of all inflammatory genes associated with gastric cancer wasobtained from Pubmed. miRNA target prediction databases (MirSNP, Targetscan Human 6.2, PolymiRTS 3.0,miRNASNP 2.0, and Patrocles) were used to predict miRNA target sites. There were 99 SNPs with MAF>0.05within the miRNA binding sites of 41 genes among 72 inflammation-related genes associated with gastric cancer.NF-κB and JAK-STAT are the two most important signaling pathways. 47 SNPs of 25 genes with 95 miRNAswere predicted. CCL2 and IL1F5 were found to be the shared target genes of hsa-miRNA-624-3p. Bioinformaticmethods could identify a set of SNPs within miRNA binding sites of inflammatory genes, and provide data anddirection for subsequent functional verification research.