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Protocols

mirSVR specifications

Information


Unique identifier OMICS_23938
Name mirSVR

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus

Maintainer


This tool is not maintained anymore.

Additional information


http://34.236.212.39/microrna/faq.do

Publication for mirSVR

mirSVR citations

 (40)
library_books

MicroRNA 200a/200b Modulate High Glucose Induced Endothelial Inflammation by Targeting O linked N Acetylglucosamine Transferase Expression

2018
Front Physiol
PMCID: 5915961
PMID: 29720943
DOI: 10.3389/fphys.2018.00355

[…] g to the cellular protein O-GlcNAcylation levels (i.e., increase protein O-GlcNAcylation causing increase OGA expression and vice versa).In this study, web-based bioinformatics analysis using miRanda-mirSVR and miRDB database revealed that the members of the miR-200 functional group 1, but not of group 2, may bind to the 3′-UTR of human OGT mRNA. However, the miRanda-mirSVR database identified all […]

library_books

Fishing Into the MicroRNA Transcriptome

2018
Front Genet
PMCID: 5868305
PMID: 29616080
DOI: 10.3389/fgene.2018.00088

[…] et recognition are not completely understood and may vary for each miRNA-target interaction (Ritchie and Rasko, ). Moreover, several popular tools such as DIANNA-microT (Maragkakis et al., ), miRanda-miRSVR (Betel et al., ), and miRWalk (Dweep et al., ) were designed exclusively for predicting miRNAs in mammals. Other tools, such as TargetScan (Garcia et al., ), miRanda (Enright et al., ), PITA (K […]

library_books

Deciphering microRNA targets in pancreatic cancer using miRComb R package

2018
Oncotarget
PMCID: 5814228
PMID: 29464088
DOI: 10.18632/oncotarget.24034

[…] pancreatic cancer samples is 17401, that corresponds to a 22.6% of the 76878 potential miRNA targets predicted by at least one of the miRNA target prediction databases used in this study (TargetScan, miRSVR, miRDB). The expression of these 17401 miRNA-mRNA pairs is negatively correlated (FDR < 0.05) and predicted in at least one of the above mentioned databases. Although the experimental confirmat […]

library_books

miR 9a mediates the role of Lethal giant larvae as an epithelial growth inhibitor in Drosophila

2017
PMCID: 5829493
PMID: 29361610
DOI: 10.1242/bio.027391

[…] h were found to be upregulated in lgl tissues, matched 10 downregulated mRNAs. The remaining eight miRNAs, which were downregulated, matched 28 upregulated mRNAs. The strength of the miRNA targeting (mirSVR score, as computed by microRNA.org) as well as the logFC of miRNAs and mRNAs was visualized using Cytoscape (). Notably, our bioinformatics analyses combined with miRNA and mRNA profiling indic […]

library_books

In situ functional dissection of RNA cis regulatory elements by multiplex CRISPR Cas9 genome engineering

2017
Nat Commun
PMCID: 5727397
PMID: 29235467
DOI: 10.1038/s41467-017-00686-2

[…] he following putative RREs were considered based on their close proximity to miR-184 MREs (200 bp window centered on the MRE seed sequence): predicted target sites of most abundant S2 miRNAs (miRanda-mirSVR and TargetScanFly 6.2); AU-rich elements (AREScore; http://arescore.dkfz.de/arescore.pl); polyA signals (AATAAA/ATTAAA); HuR binding motifs (CISBP-RNA; http://cisbp-rna.ccbr.utoronto.ca/TFTools […]

library_books

Interplay of neuronal and non neuronal genes regulates intestinal DAF 16 mediated immune response during Fusarium infection of Caenorhabditis elegans

2017
PMCID: 5684781
PMID: 29152379
DOI: 10.1038/cddiscovery.2017.73

[…] miRNA-binding sites were obtained from Miranda with an mirSVR score (a measure of the likelihood that an miRNA targets a certain sequence) less than −0.3. Targets for piRNA were identified based on Bagjin et al. […]

Citations

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mirSVR institution(s)
Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Department of Computer Science, Columbia University, New York, NY, USA
mirSVR funding source(s)
Supported by NIH grants PO1GM073047 and 1U24CA143840.

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