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TargetSpy specifications

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Unique identifier OMICS_06685
Name TargetSpy
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for TargetSpy

TargetSpy citations

 (27)
library_books

Circulating microRNAs and Bioinformatics Tools to Discover Novel Diagnostic Biomarkers of Pediatric Diseases

2017
Genes
PMCID: 5615367
PMID: 28925938
DOI: 10.3390/genes8090234

[…] information, such as the presence of unexpected viral or bacterial rna molecules., mirnaconstarget: consensus target prediction on user-provided input data based on miranda [], pita [] and targetspy [] for animal micrornas and psrobot [] and tapir (target prediction for plant micrornas) [] for plant micrornas., srnajbrowser: visualization of srna expression data in a genome context […]

library_books

RNA Seq reveals MicroRNA expression signature and genetic polymorphism associated with growth and muscle quality traits in rainbow trout

2017
Sci Rep
PMCID: 5567286
PMID: 28831113
DOI: 10.1038/s41598-017-09515-4

[…] mrna were retrieved from the genome reference. due to difference in sensitivity and specificity of different target prediction algorithms, targets were predicted using 3 tools: miranda, pita and targetspy in small rna analysis server srnatoolbox. if the same target site is predicted by all 3 tools it was considered a potential microrna target. for pita, prediction parameters chosen were: […]

library_books

Genome wide profiling and differential expression of microRNA in rat pluripotent stem cells

2017
Sci Rep
PMCID: 5459850
PMID: 28584262
DOI: 10.1038/s41598-017-02632-0

[…] targets were kept if the corresponding mirna was upregulated (supplementary table )., mature sequences of novel mirnas were analysed for targets in the 3′ utrs of rat refseq transcripts using the targetspy v1.1, miranda v3.3a and targetscan v7.0 tools. to reduce the false positive rate, only targets that were predicted by all three programs were accepted (supplementary table )., lists […]

library_books

Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection

2017
BMC Genomics
PMCID: 5418855
PMID: 28472924
DOI: 10.1186/s12864-017-3741-3

[…] the sav groups (additional file ). however, this mirna may have been more accurately measured in the deseq2 analysis (4x times decrease, table )., the four mirna target prediction tools rnahybrid, targetspy, pita and miranda [, ] were applied to predict the target genes. two different approaches were used for selecting the genes used as input. first, we used a knowledge based approach […]

library_books

Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma

2017
Sci Rep
PMCID: 5382551
PMID: 28383034
DOI: 10.1038/srep46026

[…] five different prediction algorithms was applied: miranda: (http://www.microrna.org/microrna/getdownloads.do); pictar (www.pictar.org); pita: (genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html), targetspy (http://webclu.bio.wzw.tum.de/targetspy/index.php?down=true); target-scans: (genes.mit.edu/targetscan). only fully-consensus predicted targets were considered for initial target […]

library_books

The miR 125 family is an important regulator of the expression and maintenance of maternal effect genes during preimplantational embryo development

2016
Open Biol
PMCID: 5133438
PMID: 27906131
DOI: 10.1098/rsob.160181

[…] mirnas and proteins. numerous computational approaches for mirna target prediction have already been developed, such as targetscan, miranda, mirmap, diana-microt, targetboost, mitarget, mirtarget2, targetspy, targetminer, multimitar, nbmirtar and microt-ann []. because each algorithm has its own set of limitations, multiple computational algorithms are commonly used simultaneously to predict […]


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TargetSpy institution(s)
Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany

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