miRonTop protocols

View miRonTop computational protocol

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miRonTop specifications

Information


Unique identifier OMICS_14645
Name miRonTop
Interface Web user interface
Restrictions to use None
Input data Results of a global mRNA expression data
Input format TXT
Programming languages Java
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Publication for miRonTop

miRonTop in pipeline

2017
PMCID: 5698490
PMID: 29162888
DOI: 10.1038/s41598-017-16226-3

[…] e genes were further analyzed to determine functional pathways and ontology enrichment using enrichr, and david web tools. mir-500a in silico predictions were obtained with the online database mirdb. mirontop was used for predictions of mirna enrichment on the gene expression dataset (in silico validation) using the following parameters of significance: aveexp > 4, abs(logfc) > 0.15, and b & […]


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miRonTop in publications

 (10)
PMCID: 5698490
PMID: 29162888
DOI: 10.1038/s41598-017-16226-3

[…] a similar overlap was found with other algorithms for mirna target prediction (fig. )., finally, we performed an in silico validation of our gene expression approach. to this end, we used the mirontop mining tool to infer the most enriched mirnas in our expression dataset after mir500a-5p modulation (see methods). for this particular analysis, we used the complementarity of the seed […]

PMCID: 4705652
PMID: 26578605
DOI: 10.1093/nar/gkv1221

[…] target prediction with expression data. some tools that use mirna expression data are described above (table ). the list of studies that have used these tools is reported as supporting material s2., mirontop () is an online java application that identifies the potential involvement of mirnas in a given biological system using dna microarrays or hits data. it provides fast characterization […]

PMCID: 3927079
PMID: 24600468
DOI: 10.3389/fgene.2014.00023

[…] tools, such as mirmap (vejnar et al., ), that combine multiple mirna target identification tools to overcome the limitations of individual tools. in addition, some integrated tools, such as mirontop (le brigand et al., ) and comir (coronnello and benos, ), incorporate expression data in the ranking of mirna target predictions., this review highlights the common features of mirna target […]

PMCID: 3615727
PMID: 23492775
DOI: 10.1038/cddis.2013.71

[…] 66 up- and 84 downregulated genes in the pmir-210 cell line (). several mir-210 predicted targets were found in the set of downregulated transcripts (). we next analyzed this set using our web tool ‘mirontop' to better characterize this effect. the results indicated an overrepresentation of mir-210-predicted targets in the set of downregulated transcripts (enrichment factor=6.55; p<0.0001), […]

PMCID: 3573122
PMID: 23459460
DOI: 10.1371/journal.pgen.1003291

[…] differences between two biological states , . hierarchical clusterings were done with the multiexperiment viewer (mev) program version 4.3, using a manhattan distance metric and average linkage., mirontop is an online java web tool (available at http://www.microarray.fr:8080/mirontop/index) that integrates dna microarrays data to identify the potential implication of mirnas on a specific […]


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miRonTop institution(s)
Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, UMR6097, Sophia-Antipolis, France; University of Nice Sophia Antipolis, Nice, France
miRonTop funding source(s)
Supported by MICROENVIMET, FP7-HEALTH-F2-2008-201279, ARC, INCa and Vaincre la Mucoviscidose.

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