a comprehensive database of putative human microRNA target site (MTS) SNVs and their functional predictions
dbMTS collects all potential SNVs microRNA target seed regions in human 3’UTRs and provides their functional predictions and annotations to facilitate the steps of filtering and prioritizing SNVs from a huge list of all SNVs discovered in a whole exome sequencing (WES) study. The core functional annotations in the database are the targeting efficacy scores for the reference and mutant loci based on three microRNA target prediction algorithms, TargetScan v7.0, RNAhybrid, and miRanda. Based on their predictions, we further classify the effect of each SNV into three categories, substitution, target loss and target gain. The maximum difference between the reference score and variant-induced score was calculated to estimate how the microRNA targeting efficacy was changed after introducing the variant. Additional functional annotations of the SNVs were also collected in dbMTS including variant consequences by SnpEff, VEP and ANNOVAR, dbSNP variant IDs, GWAS Catalog entries, allele frequencies from various populations, clinical consequences from ClinVar, expression quantitative trait loci (eQTLs) from GTEx, mappability scores etc.
dbMTS v1.0 is available, you could compose your query at the next section below. A description of the columns can be found here.
dbMTS can be queried as an attached database for dbNSFP. More information can be found on the dbNSFP website.
Selected output resources:
Chang Li, Michael D. Swartz, Bing Yu, Yongsheng Bai, Xiaoming Liu. dbMTS: a comprehensive database of putative human microRNA target site SNVs and their functional predictions. bioRxiv 554485; doi: https://doi.org/10.1101/554485
Xiaoming Liu, Ph.D.
Lab Page: http://liulab.scienceUniversity of South Florida,