Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Jan 25:13:44.
doi: 10.1186/1471-2164-13-44.

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

Andrew E Bruno  1 , Li Li, James L Kalabus, Yuzhuo Pan, Aiming Yu, Zihua Hu
Affiliations

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.

PubMed Disclaimer

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.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Dickson DW, Baker M, Rademakers R. Common variant in GRN is a genetic risk factor for hippocampal sclerosis in the elderly. Neurodegener Dis. 2010;7(1-3):170–174. doi: 10.1159/000289231. - DOI - PMC - PubMed
    1. Wang G, van der Walt JM, Mayhew G, Li YJ, Züchner S, Scott WK, Martin ER, Vance JM. Variation in the miRNA-433 binding site of FGF20 confers risk for Parkinson disease by overexpression of alpha-synuclein. Am J Hum Genet. 2008;82(2):283–289. doi: 10.1016/j.ajhg.2007.09.021. - DOI - PMC - PubMed
    1. Abelson JF, Kwan KY, O'Roak BJ, Baek DY, Stillman AA, Morgan TM, Mathews CA, Pauls DL, Rasin MR, Gunel M, Davis NR, Ercan-Sencicek AG, Guez DH, Spertus JA, Leckman JF, Dure LS, Kurlan R, Singer HS, Gilbert DL, Farhi A, Louvi A, Lifton RP, Sestan N, State MW. Sequence variants in SLITRK1 are associated with Tourette's syndrome. Science. 2005;310(5746):317–320. doi: 10.1126/science.1116502. - DOI - PubMed
    1. Tan Z, Randall G, Fan J, Camoretti-Mercado B, Brockman-Schneider R, Pan L, Solway J, Gern JE, Lemanske RF, Nicolae D, Ober C. Allele-specific targeting of microRNAs to HLA-G and risk of asthma. Am J Hum Genet. 2007;81(4):829–834. doi: 10.1086/521200. - DOI - PMC - PubMed
    1. Martin MM, Buckenberger JA, Jiang J, Malana GE, Nuovo GJ, Chotani M, Feldman DS, Schmittgen TD, Elton TS. The human angiotensin II type 1 receptor +1166 A/C polymorphism attenuates microrna-155 binding. J Biol Chem. 2007;282(33):24262–24269. doi: 10.1074/jbc.M701050200. - DOI - PMC - PubMed

Publication types

LinkOut - more resources