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Protocols

TargetScanS specifications

Information


Unique identifier OMICS_06691
Name TargetScanS
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Ben Lewis

Publication for TargetScanS

TargetScanS citations

 (28)
library_books

Tools for Sequence Based miRNA Target Prediction: What to Choose?

2016
Int J Mol Sci
PMCID: 5187787
PMID: 27941681
DOI: 10.3390/ijms17121987

[…] lgorithm used to predict miRNA targets in vertebrates []. Since then, this tool has been improved through new versions and additional algorithms that have helped to improve match prediction accuracy: TargetScanS [], TargetScan PCT [], TargetScan context+ score [,,]. All of these are described below. These web-based tools have two search options: the gene symbol and/or the species-specific miRNA na […]

library_books

MicroRNA: Biological and Computational Perspective

2016
PMCID: 5172550
PMID: 16393143
DOI: 10.1016/S1672-0229(05)03011-1

[…] r target predictions in Arabidopsis. In the past few years progress has also been made in the prediction of targets in other species , , , , , , , , , , , .Commonly used programs are TargetScan and TargetScanS , miRanda , , DIANA-microT , RNAhybrid , PicTar , and others.Although the programs differ in technical details, many of the programs use basically the same principles in their target findi […]

call_split

Identifying microRNA targets in different gene regions

2014
BMC Bioinformatics
PMCID: 4110731
PMID: 25077573
DOI: 10.1186/1471-2105-15-S7-S4
call_split See protocol

[…] e pSILAC method [] and evaluated how our target predictions correlate with the results in the pSILAC dataset. To achieve a comparable predicted number of targets with other well-known methods such as TargetScanS and PicTar, we set the cut-off values ΔGduplexcutoff=-15.0 kcal/mol and ΔΔGcutoff=-10.0kcal/mol, respectively.Figure shows the ratio of the fraction of predicted miRNA targets for which p […]

library_books

A Positive Feedback Mechanism That Regulates Expression of miR 9 during Neurogenesis

2014
PLoS One
PMCID: 3979806
PMID: 24714615
DOI: 10.1371/journal.pone.0094348

[…] th Mef2C.Since we predict that Mef2C and miR-9 are coordinately involved in neurogenesis and HDAC4 opposes this mechanism, we searched for potential feedback networks between Mef2C and miR-9. We used TargetScanS , to determine if any of these mRNAs were potential targets of miR-9. The 3′UTR of HDAC4 contained four predicted miR-9 response elements (RE) including one closest to the coding sequence […]

call_split

Functional divergence of the rapidly evolving miR 513 subfamily in primates

2013
BMC Evol Biol
PMCID: 3840687
PMID: 24252134
DOI: 10.1186/1471-2148-13-255
call_split See protocol

[…] otung (http://www.cs.cmu.edu/~durand/Notung/). The species tree was based on the NCBI taxonomy tree (http://www.ncbi.nlm.nih.gov/taxonomy). To identify potential targets of miR-513 sequences, we used TargetScanS [], and eight genes with top rank values were selected for functional testing. […]

library_books

Target Gene and Function Prediction of Differentially Expressed MicroRNAs in Lactating Mammary Glands of Dairy Goats

2013
Int J Genomics
PMCID: 3806118
PMID: 24195063
DOI: 10.1155/2013/917342

[…] e database, miRGen v3 [] is an integrated database that includes the prediction results of six algorithms, DIANA-microT, miRanda (microran.org), miRanda (miRBase), PicTar (4-way), PicTar (5-way), and TargetScanS. In miRGen, all PicTar targets were downloaded as UCSC Tracks from the UCSC Genome Browser Database. “4-way” refers to a 4-species conservation constraint (human/mouse/rat/dog), and “5-way […]

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