TargetScan protocols

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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

 (93)
2018
PMCID: 5743562
PMID: 29290822
DOI: 10.7150/thno.22059

[…] and the sequence of mature hsa-mir-31-5p was downloaded from mirbase database (http://www.mirbase.org/). target prediction and context score analyses were performed using the targetscan_50.pl and targetscan_50_context_scores.pl perl scripts were downloaded from the targetscan website (http://www.targetscan.org/vert_50/). a sum context score of <0.2 was used to filter […]

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, […]

2018
PMCID: 5771341
PMID: 29344280
DOI: 10.7150/jca.18188

[…] hsa-mir-378 and hsa-mir-1827 targets were generated using publicly available programs: diana-microt-cds v5.0 (http://diana.imis.athena-innovation.gr/dianatools/index.php?r=microt_cds/index) and targetscan v7.1 (http://www.targetscan.org/vert_71/) . hypothetical mirna targets were subjected to gene-annotation enrichment analysis using database for annotation, visualization and integrated […]

2018
PMCID: 5776778
PMID: 29357938
DOI: 10.1186/s12958-017-0319-5

[…] expression profiles were analyzed by magia2 (http://gencomp.bio.unipd.it/magia2/) to identify mirna-tf-gene binary interactions and circuits []. the mirna-target interactions were predicted by the targetscan database [] with a z-score ≥ 0.7. tf-mirna interactions were identified from the mirgen2.0 [] and transmir [] databases, and tf-gene interactions were obtained from the ‘tfbs conserved’ […]

2018
PMCID: 5845524
PMID: 29682564
DOI: 10.1155/2018/8518563

[…] annotation system v4.0 (mas, http://bioinfo.capitalbio.com/mas3/). target mrnas of the mirnas were either identified from experimentally validated annotated in mirtarbase [] or predicted with targetscan []. based on the same predictive methods, the target mrnas of the isomirs were predicted after clustering multiple isomirs using seed sequences. we also further discussed the potential […]


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TargetScan in publications

 (6423)
PMCID: 5958082
PMID: 29773851
DOI: 10.1038/s41598-018-26163-4

[…] target genes out of all genes in individual clusters. transcription factor target gene sets from gsea (http://software.broadinstitute.org/gsea/msigdb/index.jsp) and mirna target gene sets from targetscan were used. we applied low stringency criteria to select enriched mirnas without correcting for multiple tests (fisher’s exact test p < 0.01), since we are interested in tf and mirna […]

PMCID: 5955976
PMID: 29769534
DOI: 10.1038/s41598-018-22493-5

[…] and specificity of the five-mirna signature model in predicting pancreatic adenocarcinoma patient survival risk (fig. ).figure 2, the target genes of prognostic mirnas were predicted using targetscan, mirdb, miranda, and mirtarbase analysis tools. to further enhance the reliability of the bioinformatic analysis, the overlapping target genes were identified using venn diagram (fig. ). […]

PMCID: 5952853
PMID: 29764374
DOI: 10.1186/s12864-018-4757-z

[…] two relatively closely related species: d. simulans and d. yakuba. mir310s cds targets are conserved between d.melanogaster and d.simulans. transcripts targeted by mir310s were identified using the targetscan algorithm [, , , ]. 3’utr annotation was extracted from bdgp6.83. the whole genome alignments were dm6, drosim1, and droyak3 available at the ucsc genome browser. mirna expression […]

PMCID: 5953401
PMID: 29764424
DOI: 10.1186/s12943-018-0838-5

[…] confirmed that micrornas are important target of lncrnas [, ]. to identify whether any micrornas represent potential targets that can be bind to atgl and neat1, we used three online software tools (targetscan: http://www.targetscan.org/; microrna.org: http://www.microrna.org/; starbase: http://starbase.sysu.edu.cn/.) to identify potential binding sites. we identified four micrornas […]

PMCID: 5951800
PMID: 29760470
DOI: 10.1038/s41598-018-25801-1

[…] for instance, we examined cnv embedded hsa-mir-4746-5p in 198 breast cancer cases; 52 cases exhibited copy gains and 146 were diploid. gene targets for the cnv-hsa-mir-4746-5p were predicted using targetscan and these predicted targets were identified in the mrna expression data sets (hiseq platform). a correlation analysis revealed 25 common target genes for both diploid and copy gain cases; […]


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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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