TargetScan protocols

TargetScan specifications

Information


Unique identifier OMICS_00420
Name TargetScan
Alternative name TargetScanFly
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 7.2
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/TargetScan

Taxon


  • Primates
    • Homo sapiens

Maintainers


  • person_outline TargetScan Team <>
  • person_outline David Bartel <>

Information


Unique identifier OMICS_00420
Name TargetScan
Alternative name TargetScanFly
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, MATLAB, Perl, R, Shell (Bash)
License MIT License
Computer skills Advanced
Version 1.0.0
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

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Maintainers


  • person_outline TargetScan Team <>
  • person_outline David Bartel <>

Publications for TargetScan

TargetScan IN pipelines

 (14)
2018
PMCID: 5760646
PMID: 29317647
DOI: 10.1038/s41598-017-17518-4

[…] several databases including, mirbase (http://microrna.sanger.ac.uk), mirnasnp (http://www.bioguo.org/mirnasnp/index.php), microsniper http://vm24141.virt.gwdg.de/services/microsniper/index.php), targetscan (http:// targetscan.org/vert_71/) in order to predict mirnas that target hiwi2 3′ utr region. the predicted mirnas are including hsa-mir-4686, hsa-mir-3686, hsa-mir-4652-3p, […]

2017
PMCID: 5289111
PMID: 28168095
DOI: 10.7717/peerj.2831

[…] mirbase database (dennis et al., 2003; lewis, burge & bartel, 2005) and these mirna sequences were reorganized into fasta files. the target genes corresponding to the dems were predicted using targetscan software (lewis, burge & bartel, 2005), and the default parameters were adopted., the predicted target genes of the dems were mapped to david database (dennis et al., 2003), […]

2017
PMCID: 5513939
PMID: 28769761
DOI: 10.3389/fnmol.2017.00227

[…] korea (nrf), funded by the ministry of science, ict and future planning (nrf-2015r1c1a1a02036313)., 1 https://www.ncbi.nlm.nih.gov/geo/ , 2 http://hannonlab.cshl.edu/fastx_toolkit/ , 3 http://www.targetscan.org , 4 http://software.broadinstitute.org/gsea/msigdb , the supplementary material for this article can be found online at: […]

2017
PMCID: 5573442
PMID: 28878619
DOI: 10.3389/fnmol.2017.00259

[…] (anders et al., 2015). genes with low read count (<10) were filtered out to minimize false positives resulting from amplification. remaining genes were scanned for mirna target sites against the targetscan database (release 6.1). downstream analyses were performed in excel, and final gene lists underwent functional analysis using the gather (chang and nevins, 2006) the david fac tool (huang […]

2016
PMCID: 4756660
PMID: 26884323
DOI: 10.1038/srep21194

[…] sequences (mirbase release version 21) with the module of quantifier.pl in mirdeep2 (default parameters) to quantify known mirnas., the conservation of known mirnas was described based on the targetscan definitions for “highly conserved”, “conserved”, “poorly conserved”, and “bovine-specific”24. a highly conserved mirna is conserved across most vertebrates; a conserved mirna is conserved […]

TargetScan institution(s)
Whitehead Institute for Biomedical Research and Howard Hughes Medical Institute, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
TargetScan funding source(s)
Supported by a National Science Foundation Graduate Research Fellowship, a National Institutes of Health (NIH) Medical Scientist Training Program fellowship T32GM007753, a European Molecular Biology Organization (EMBO) long-term fellowship, NIH grants GM067031 and GM118135, and by the Howard Hughes Medical Institute.

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