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Protocols

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 citations

 (259)
library_books

Bioinformatics based identification of potential microRNA biomarkers in frequent and non frequent exacerbators of COPD

2018
PMCID: 5909781
PMID: 29713155
DOI: 10.2147/COPD.S163459

[…] tivity by handling the various types of data and performing multiple testing corrections on P-values.The accuracy for the predicted targets of candidate miRNAs was improved by the following software: PicTar, miRDB and TargetScan. Validated targets were acquired from TarBase. Briefly, we took the intersection of the three series of predicted targets and validated the targets using TarBase. […]

library_books

Salivary microRNAs as new molecular markers in cleft lip and palate: a new frontier in molecular medicine

2018
Oncotarget
PMCID: 5922367
PMID: 29721173
DOI: 10.18632/oncotarget.24838

[…] e different miRNA set expression in the two study populations see also the heat map shown in Figure . Moreover, we analyzed the results using the TargetScan program http://www.targetscan.org/, http://pictar.mdc-berlin.de/, http://www.microrna.org/microrna/home.do) that contain the miR-binding site(s) in the UTR. TargetScan analysis predicted the binding of miR-324-3p e miR-223 to the 3′-UTR of met […]

library_books

Tumor suppressor role of miR 139 5p in endometrial cancer

2018
PMCID: 5879796
PMID: 29618950
DOI: 10.1186/s12935-018-0545-8

[…] mediated by p21 []. However, the regulatory mechanisms that underlie the expression of HOXA10 in EC have yet to be studied. We predicted that miR-139-5p, is a regulator of HOXA10 expression, based on PicTar, TargetScan, and miRBase database. However, the role of miR-139-5p in EC development, especially regarding its link with HOXA10, has not been explored yet. In the present study, we investigated […]

call_split

Inhibition of breast cancer metastasis by co transfection of miR 31/193b mimics

2018
PMCID: 5960762
PMID: 29796229
DOI: 10.22038/IJBMS.2018.26614.6522
call_split See protocol

[…] 6.2gw/ EmGFP vector. To identify potential target genes of miR-193b and miR-31, the TargetScan (http://www.targetscan.org), miRanda (http://www.microrna.org), miRDB (http://www.mirdb.org/miRDB/) and PicTar (http://pictar.mdc-berlin.de) databases were used. […]

call_split

MicroRNA 671 3p inhibits the development of breast cancer: A study based on in vitro experiments, in house quantitative polymerase chain reaction and bioinformatics analysis

2018
PMCID: 5919715
PMID: 29620195
DOI: 10.3892/ijo.2018.4339
call_split See protocol

[…] ted target genes of miR-671-3p were determined using the miRWalk 2.0 database (zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2), which contains 12 online tools, namely Targetscan, RNAhybrid, RNA22, PITA, Pictar2, miRWalk, Microt4, miRNAMap, miRDB, mirbridge, miRanda and miRMap. Targets predicted by >3 algorithms were selected for GO functional annotation and KEGG pathway analyses using the DAVID onlin […]

call_split

Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression

2018
Nat Commun
PMCID: 5862881
PMID: 29563510
DOI: 10.1038/s41467-018-03573-6
call_split See protocol

[…] eter values: Input parameters Promoter 2 kb, 3′ UTR, minimum seed length 7 and/or p-value 0.05. We considered mRNA to be a target for miRNA if targeting was predicted by 2/3 of the databases miRanda, PICTAR2, and Targetscan–. Differentially expressed miRNAs were defined as having an absolute median ratio between two conditions >1.5, and the Benjamini-Hochberg adjusted p-value of a non-parametric W […]

Citations

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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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