miRmap protocols

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miRmap specifications

Information


Unique identifier OMICS_06680
Name miRmap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_06680
Name miRmap
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for miRmap

miRmap in pipelines

 (3)
2017
PMCID: 5369021
PMID: 28347313
DOI: 10.1186/s12918-017-0419-z

[…] about the activity of regulators. to infer the associated transcriptional network, nested effects model (nem) [] structure learning is applied. an input mirna – gene network is constructed based on mirmap [] for 356 mirnas. the tf – target gene network with 344 tfs is compiled by computing tf binding affinities to promoter sequences according to the trap model [] using data from ensembl, […]

2017
PMCID: 5669919
PMID: 29137293
DOI: 10.18632/oncotarget.19752

[…] technology, usa). samples were applied to welgene biotechnology company (welgene, taipei, taiwan) for rna preparation and microarray analysis. the detailed protocol was described previously [, ]., mirmap is an open-source software library providing comprehensive microrna targets prediction (http://mirmap.ezlab.org/) []. the putative target genes can be identified based on calculating […]

2016
PMCID: 4936332
PMID: 27429792
DOI: 10.1556/1886.2016.00015

[…] version 3.0.2., to unravel the role of differentially expressed mirnas which have not yet been reported to play a role in bacterial infection, in silico prediction was used to identify mrna targets (mirmap, mirmap score <80) []. the list of potential target genes was applied to the david functional annotation tool [, ] to identify pathways in which these potential mrna targets accumulate., […]


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miRmap in publications

 (71)
PMCID: 5895658
PMID: 29674956
DOI: 10.3389/fncel.2018.00091

[…] genes by these following analysis: (1) target mrnas of mir-103 were first predicted by mirwalk 2.0 with six or above positive results by 12 methods (mirwalk, microt4, miranda, mirbridge, mirdb, mirmap, mirnamap, pictar2, pita, rna22, rnahybrid, targetscan, dweep et al., ); (2) genes correlated with ad pathology or risk were analyzed by disgenet, piñero et al., ); and (3) potential targeted […]

PMCID: 5919718
PMID: 29620192
DOI: 10.3892/ijo.2018.4342

[…] combines this information with a comparison of binding sites resulting from 12 existing mirna-target prediction programs (diana-microtv4.0, diana-microt-cds, miranda-rel2010, mirbridge, mirdb4.0, mirmap, mirnamap, dorina i.e., pictar2, pita, rna22v2, rnahybrid 2.1 and targetscan 6.2), we predicted 21 possible target genes in 7 databases (dianamt, miranda, mirdb, mirwalk pictar5, rna22 […]

PMCID: 5876433
PMID: 29616113
DOI: 10.3892/ol.2018.8088

[…] mirwalk and databases associated with mirwalk (targetscan, miranda, pictar2, rnahybrid, mirdb, rna22-has, targetminer, embl-ebi, diana-microt, mirbridge, mirmap, mirnamap and pita). the target genes of mir-452-5p were searched in the pubmed (https://www.ncbi.nlm.nih.gov/pubmed) and embase (https://www.embase.com) databases using the terms: ‘cancer’, […]

PMCID: 5841030
PMID: 29545842
DOI: 10.3892/etm.2018.5836

[…] were predicted using mirwalk 2.0 (http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/) (), which combined 12 existing mir-target prediction programs (mirwalk, microt4, miranda, mirbridge, mirdb, mirmap, mirnamap, pictar2, pita, rna22, rnahybrid and targetscan) to provide comprehensive potential targets for mir-449a. the genes predicted in more than five prediction software programs […]

PMCID: 5865962
PMID: 29393467
DOI: 10.3892/mmr.2018.8532

[…] significant., as for prediction tools, mirwalk 2.0 was applied to predict the potential target genes of mir-1-3p based on 12 online databases, namely mirwalk; microt4; miranda; mirbridge; mirdb; mirmap; mirnamap; pictar; pita; rna22; rnahybrid and targetscan. for the purpose of acquiring the possible target genes of mir-1-3p as complete as possible, genes were selected on condition […]


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miRmap institution(s)
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland

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