Collection And Analysis Of Functional Variants In Human And Mouse LncRNAs

Long non-coding RNAs(lncRNAs)are emerging as important regulators in different biological processes through various ways.Recently,there is a rapid growth of identified lncRNAs and variants including SNPs(Single Nucleotide Polymorphism)and mutations.For the facility of lncRNA related research,we collected and annotated lncRNA and variants on them,and developed the lncRNASNP2 database.Took the advantage of the resources in public databases including dbSNP,TCGA(The Cancer Genome Atlas)and COSMIC(Catalogue of Somatic Mutations in Cancer),we identified 7,260,238 SNPs on 141,353 human lncRNA transcripts and 3,921,448 SNPs on 117,405 mouse lncRNA transcripts;859,534 noncoding variants from COSMIC cancer data in lncRNAs and 158,806 TCGA cancer mutations in lncRNAs.Besides,lncRNA expression in tumor-adjacent and tumor samples of 20 cancer types and lncRNA related diseases were collected,experiment validated and predicted miRNA-lncRNA interactions were included.For each variant we mentioned above,the impact of the variant on the function and structure of lncRNA as well as the variant causing miRNA target gain or loss on lncRNA were predicted.Besides,SNPs located in linkage disequilibrium(LD)regions were identified using the information in GWAS(Genome-wide association study)Catalog.All these data for human and mouse lncRNAs were imported into lncRNASNP2 database(http://bioinfo.life.hust.edu.cn/lncRNASNP/),which includes two sub-databases lncRNASNP-human and lncRNASNP-mouse.The lncRNASNP2 database has a userfriendly interface for searching and browsing through the SNP,mutation,lncRNA and miRNA sections.Besides,we developed online tools for users to analyze new variants in lncRNA.