title: Bioinformatic prediction of SNPs within miRNA binding sites of inflammatory genes associated with gastric cancer.
abstract: Polymorphisms in miRNA binding sites have been shown to affect miRNA binding to target genes, resulting in differential mRNA and protein expression and susceptibility to common diseases. Our purpose was to predict SNPs (single nucleotide polymorphisms) within miRNA binding sites of inflammatory genes in relation to gastric cancer. A complete list of SNPs in the 3'UTR regions of all inflammatory genes associated with gastric cancer was obtained 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>0.05 within 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 miRNAs were predicted. CCL2 and IL1F5 were found to be the shared target genes of hsa-miRNA-624-3p. Bioinformatic methods could identify a set of SNPs within miRNA binding sites of inflammatory genes, and provide data and direction for subsequent functional verification research.
authors.affiliation: Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China E-mail : kjwang@163.com.
authors.forename: Chuan-Qing
authors.initials: CQ
authors.lastname: Song
authors.forename: Jun-Hui
authors.initials: JH
authors.lastname: Zhang
authors.forename: Jia-Chen
authors.initials: JC
authors.lastname: Shi
authors.forename: Xiao-Qin
authors.initials: XQ
authors.lastname: Cao
authors.forename: Chun-Hua
authors.initials: CH
authors.lastname: Song
authors.forename: Adil
authors.initials: A
authors.lastname: Hassan
authors.forename: Peng
authors.initials: P
authors.lastname: Wang
authors.forename: Li-Ping
authors.initials: LP
authors.lastname: Dai
authors.forename: Jian-Ying
authors.initials: JY
authors.lastname: Zhang
authors.forename: Kai-Juan
authors.initials: KJ
authors.lastname: Wang
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics*; D001665:Binding Sites; D018932:Chemokine CCL2 / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D053263:Gene Regulatory Networks; D006801:Humans; D018836:Inflammation Mediators / Q000378:metabolism*; D007378:Interleukins / Q000235:genetics / Q000378:metabolism; D053613:Janus Kinase 1 / Q000235:genetics / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics*; D016328:NF-kappa B / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D050791:STAT Transcription Factors / Q000235:genetics / Q000378:metabolism; D013274:Stomach Neoplasms / Q000235:genetics* / Q000378:metabolism*
chemical_list: D020413:3' Untranslated Regions; C111835:CCL2 protein, human; D018932:Chemokine CCL2; C122187:IL36RN protein, human; D018836:Inflammation Mediators; D007378:Interleukins; D035683:MicroRNAs; D016328:NF-kappa B; D050791:STAT Transcription Factors; C507904:JAK1 protein, human; D053613:Janus Kinase 1