PicTar protocols

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PicTar specifications

Information


Unique identifier OMICS_00411
Name PicTar
Interface Web user interface
Restrictions to use None
Input data A fixed search set of microRNAs and multiple alignments of orthologous nucleotide sequences.
Computer skills Basic
Maintained Yes

Taxon


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

Maintainer


  • person_outline Nikolaus Rajewsky <>

Publication for PicTar

PicTar in pipelines

 (2)
2017
PMCID: 5647044
PMID: 28849135
DOI: 10.3892/mmr.2017.7304

[…] in order to predict which genes to target with screening mirnas, three databases were used: targetscan (targetscan.org); microcosm targets (ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5); and pictar (pictar.mdc-berlin.de/cgi-bin/pictar_vertebrate.cgi). genes which were identified using all of the three databases were used, in order to limit the number of false positive results. […]

2014
PMCID: 4100108
PMID: 24879525
DOI: 10.3390/ijms15069531

[…] expressed mirnas are listed in ., to understand the function of the differentially expressed mirnas in goat hair follicles, we predicted the target genes of the mirnas using the target scan website, pictar and diana-microt v3.0, and counted mirnas that were predicted by two of these software tools. as a result, 981 genes were found to be targeted by five differentially expressed mirnas, except […]


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PicTar in publications

 (1904)
PMCID: 5945737
PMID: 29748604
DOI: 10.1038/s41419-018-0605-y

[…] the manufacturers’ protocol., at least two databases of the following five usual prediction databases: targetscan (http://www.targetscan.org) and miranda (http://www.microrna.org/microrna/home.do), pictar (http://pictar.mdc-berlin.de/), mirtarget2 from mirdb (http://mirdb.org/mirdb/ download.html) and pita (http://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html) were used to predict mirna […]

PMCID: 5938708
PMID: 29724992
DOI: 10.1038/s41419-018-0545-6

[…] in msc could show effect on mirna biogenesis and take part in cell senescence, we detected a number of specific mirnas which possibly target senescence-associated molecules, such as p21. mirbase, pictar and targetscans were performed to screen targets. mir-20a expression was significantly decreased in dicer1-kd mscs in comparison with both control mscs and the negative group (fig. ). […]

PMCID: 5923206
PMID: 29703907
DOI: 10.1038/s41598-018-24932-9

[…]  h post-ang ii stimulation, the cells were harvested for mrna, microrna, and western blot analyses., the target genes for mir-199a-5p were predicted using bioinformatic tools targetscan, mirbase, and pictar, and the specific primers for these genes were designed by primer 5.0., protein samples were prepared from h9c2 cells with radioimmunoprecipitation assay (ripa) lysis buffer, and the protein co […]

PMCID: 5916892
PMID: 29695718
DOI: 10.1038/s41467-018-04083-1

[…] (fig. ). in contrast, we did find that mir-222 inhibition increased expression of ccng2 (cyclin g2), a relevant cell cycle regulator, but could not find ccng2 as a predicted mir-222 target (through pictar and targetscan). we went on to specifically check ccng2 expression in mir-222 overexpressing neonatal rat ventricular cardiomyocytes (nrvms), and found an increase in ccng2 expression, […]

PMCID: 5941226
PMID: 29739921
DOI: 10.1038/s41419-018-0490-4

[…] the molecular mechanisms responsible for the proangiogenic function of mir-181a, we searched for the downstream target genes of mir-181a by using mirna target prediction software (targetscan, pictar, and rnahybrid)–, srcin1 was chosen for further experimental confirmation because it was not only predicted to be targeted by mir-181a but also exhibited a potential role in inhibiting […]


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PicTar institution(s)
Center for Comparative Functional Genomics, Department of Biology, New York University, New York, NY, USA; Department of Physics, New York University, New York, NY USA; Laboratory of Metabolic Diseases, The Rockefeller University, New York, NY, USA
PicTar funding source(s)
Supported in part by a grant from the US National Institutes of Health, a scholarship by the German Academic Exchange Service, grants from the US National Institutes of Health and the US National Science Foundation, and by the Howard Hughes Medical Institute grant through the Undergraduate Biological Sciences Education Program to New York University.

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