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miRdSNP: A Database of Disease-Associated SNPs and microRNA Target Sites on 3'UTRs of Human Genes

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miRdSNP: A Database of Disease-Associated SNPs and microRNA Target Sites on 3'UTRs of Human Genes

Andrew E Bruno et al. BMC Genomics.

Abstract

Background: Single 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.

Description: miRdSNP 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.

Conclusion: miRdSNP 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.

Figures

Figure 1
Figure 1
Histogram of the number of dSNPs associated with individual diseases.
Figure 2
Figure 2
Overview of miRdSNP web interface. (A) The search results in tabular format, (B) detail view for miRNA target and dSNP, and (C) sequence view for the selected gene.
Figure 3
Figure 3
(A) Distribution of dSNPs, miRNA target sites, and SNPs on individual chromosomes. The green area curve represents miRNA target site (TargetScan) density, red area curve is SNP density, and red circles represent dSNP density where the larger the radius the more dSNPs in the chromosomal location. (B) Linking dSNPs to the UCSC Genome browser.

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