MiRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes

Andrew E Bruno,Li Li,James L Kalabus,Zihua Hu,Yuzhuo Pan,Aiming Yu

doi:10.1186/1471-2164-13-44

Abstract

BackgroundSingle nucleotide polymorphisms (SNPs) can lead to the susceptibility and onset of diseases through their effects on gene expression at the posttranscriptional level. Recent findings indicate that SNPs could create, destroy, or modify the efficiency of miRNA binding to the 3'UTR of a gene, resulting in gene dysregulation. With the rapidly growing number of published disease-associated SNPs (dSNPs), there is a strong need for resources specifically recording dSNPs on the 3'UTRs and their nucleotide distance from miRNA target sites. We present here miRdSNP, a database incorporating three important areas of dSNPs, miRNA target sites, and diseases.DescriptionmiRdSNP provides a unique database of dSNPs on the 3'UTRs of human genes manually curated from PubMed. The current release includes 786 dSNP-disease associations for 630 unique dSNPs and 204 disease types. miRdSNP annotates genes with experimentally confirmed targeting by miRNAs and indexes miRNA target sites predicted by TargetScan and PicTar as well as potential miRNA target sites newly generated by dSNPs. A robust web interface and search tools are provided for studying the proximity of miRNA binding sites to dSNPs in relation to human diseases. Searches can be dynamically filtered by gene name, miRBase ID, target prediction algorithm, disease, and any nucleotide distance between dSNPs and miRNA target sites. Results can be viewed at the sequence level showing the annotated locations for miRNA target sites and dSNPs on the entire 3'UTR sequences. The integration of dSNPs with the UCSC Genome browser is also supported.ConclusionmiRdSNP provides a comprehensive data source of dSNPs and robust tools for exploring their distance from miRNA target sites on the 3'UTRs of human genes. miRdSNP enables researchers to further explore the molecular mechanism of gene dysregulation for dSNPs at posttranscriptional level. miRdSNP is freely available on the web at http://mirdsnp.ccr.buffalo.edu.

Highlights

Single nucleotide polymorphisms (SNPs) can lead to the susceptibility and onset of diseases through their effects on gene expression at the posttranscriptional level
It is well known that non-coding disease-associated SNPs within regulatory regions of the genome can result in gene dysregulation at either transcriptional or posttranscriptional level
Aiming to provide a comprehensive data source of disease-associated SNPs (dSNPs) affecting posttranscriptional regulation of disease-related genes and tools for exploring the nucleotide distance between miRNA target sites and dSNPs, we present here miRdSNP, a database of manually curated dSNPs on the 3’UTRs of human genes from available publications in PubMed

Summary

Introduction

Single nucleotide polymorphisms (SNPs) can lead to the susceptibility and onset of diseases through their effects on gene expression at the posttranscriptional level. With the rapidly growing number of published disease-associated SNPs (dSNPs), there is a strong need for resources recording dSNPs on the 3’UTRs and their nucleotide distance from miRNA target sites. Single nucleotide polymorphisms (SNPs) underlie disease susceptibility through their effects on protein function and gene expression. It is well known that non-coding disease-associated SNPs (dSNPs) within regulatory regions of the genome can result in gene dysregulation at either transcriptional or posttranscriptional level. There is a strong need to have a database recording dSNPs and tools for capturing their proximity to miRNA target sites on the 3’UTRs so that researchers can explore further the molecular mechanism of gene dysregulation for dSNPs at posttranscriptional level

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