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mrSNP specifications

Information


Unique identifier OMICS_03509
Name mrSNP
Interface Web user interface
Restrictions to use None
Programming languages Javascript, PHP, Python
Computer skills Basic
Stability No
Maintained No

Publication for mrSNP

mrSNP citations

 (6)
call_split

Association of the PLCB1 gene with drug dependence

2017
Sci Rep
PMCID: 5579249
PMID: 28860459
DOI: 10.1038/s41598-017-10207-2
call_split See protocol

[…] luciferase reporter system to test the possible impact of these SNPs on the regulation of gene expression mediated by miRNAs, as previously described. The prediction tools FuncPred, mirWalk, mirSNP, mrSNP, mirdSNP, miRNASNP and RNAhybrid were used to select miRNAs which binding sites in PLCB1 is potentially affected by these SNPs. We chose the best predictions for each SNP: for rs1047383, hsa-miR […]

library_books

Cis acting single nucleotide polymorphisms alter MicroRNA mediated regulation of human brain expressed transcripts

2016
Hum Mol Genet
PMCID: 5418741
PMID: 28171541
DOI: 10.1093/hmg/ddw317

[…] E interactions will be captured. The PolymiRTS () database identifies and annotates SNPs in MREs which have been biologically tested, but again focuses on miRNA binding regions in the 3’UTR. Finally, mrSNP () provides a web service for researchers working with RNA-seq data to predict the impact of an SNP in the 3’UTR on miRNA binding. While all these approaches are useful to some degree, we develo […]

library_books

Rare intronic variants of TCF7L2 arising by selective sweeps in an indigenous population from Mexico

2016
BMC Genet
PMCID: 4880969
PMID: 27230431
DOI: 10.1186/s12863-016-0372-7

[…] iency of miRNA binding to the 3’UTR of a gene, resulting in gene dysregulation. Consequently, we explored each mutation identified in the Indigenous population in the following databases: miRdSNP [], mrSNP [] and RNAsnp []. We plotted our results using the UCSC browser (http://genome.ucsc.edu/cgi-bin/hgGateway). […]

call_split

Variations in ORAI1 Gene Associated with Kawasaki Disease

2016
PLoS One
PMCID: 4720480
PMID: 26789410
DOI: 10.1371/journal.pone.0145486
call_split See protocol

[…] pact of amino acid changes of ORAI1 on its protein function. miRNA target sequences within the 3’-UTR of ORAI1 mRNA and the impact of the nucleotide changes within the targets was predicted using the mrSNP web service []. […]

library_books

Altered Gene Expression Associated with microRNA Binding Site Polymorphisms

2015
PLoS One
PMCID: 4619707
PMID: 26496489
DOI: 10.1371/journal.pone.0141351

[…] y SNPs with the potential to disrupt existing MREs or create new MREs (referred to as MRE-SNPs), we used three databases utilizing different miRNA target prediction algorithms (PolymiRTS, miRSNP, and mrSNP). We identified 27,126 SNP-probe combinations involving a cis-acting eQTL SNP or its proxy in the predicted MRE of a cis-regulated gene, accounting for approximately 4% of all cis-eQTLs identifi […]

library_books

Genetic variation in the 3′ UTR of CYP1A2, CYP2B6, CYP2D6, CYP3A4, NR1I2, and UGT2B7: potential effects on regulation by microRNA and pharmacogenomics relevance

2014
Front Genet
PMCID: 4044583
PMID: 24926315
DOI: 10.3389/fgene.2014.00167

[…] le, aiding in prioritizing miRSNPs with potential effect instead of showing miRSNPs that significantly alter microRNA binding (Bhattacharya et al., ).To assess the potential effect of novel SNPs, the mrSNP software was used by selecting assembly hg19 of the human genome, using default cut-offs and inserting the chromosome position and two alleles. The prediction method applied is adapted from Dian […]

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mrSNP institution(s)
Biomedical Informatics, Computer Science and Engineering, The Ohio State University, Columbus, OH, USA

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