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multiMiR specifications


Unique identifier OMICS_05795
Name multiMiR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus


No version available

Publication for multiMiR

multiMiR citations


Gene and miRNA expression profiles in PBMCs from patients with severe and mild emphysema and PiZZ alpha1 antitrypsin deficiency

PMCID: 5713702
PMID: 29238183
DOI: 10.2147/COPD.S145445

[…] for each functional group at a fisher’s exact p-value of 0.05. the same statistical approach was used for kegg analysis., integration of mirna degs and their target mrna degs was performed using the multimir r package with the web server at this is a comprehensive collection of predicted and validated mirna–target interactions and their associations with diseases […]


Discovering the 3′ UTR mediated regulation of alpha synuclein

PMCID: 5728410
PMID: 29149290
DOI: 10.1093/nar/gkx1048

[…] upon tiar depletion is very unlikely to occur in our cellular system. yet, we cannot exclude that mir-153 could play a role in tiar regulation in the nervous system., we then used the multimir algorithm () to systematically investigate other micrornas interacting with the long snca 3′utr (containing all other 3′utrs). we collected a total of 142 predicted and 9 experimentally […]


Exosomal microRNA signatures in multiple sclerosis reflect disease status

PMCID: 5662562
PMID: 29084979
DOI: 10.1038/s41598-017-14301-3

[…] functional analysis on targets of identified mirnas. for each signature, we retrieved validated targets of mirnas from three major mirna-target datasets, mirecords, mirtarbase, and tarbase using the multimir r analysis package. we then performed pathway overrepresentation analysis using kegg pathways retrieved from the molecular signatures database (msigdb)-v 6.0. among top 5% of significantly […]


Overexpression of Exportin 5 Overrides the Inhibitory Effect of miRNAs Regulation Control and Stabilize Proteins via Posttranslation Modifications in Prostate Cancer12

PMCID: 5587889
PMID: 28881308
DOI: 10.1016/j.neo.2017.07.008

[…] set an acceptable limit at less than or equal to 30%. we filtered out psms and associated protein with reporter ion ratio cvs greater than 30%., we identified regulatory micrornas targets using the multimir r package . the multimir package and database contain mirna-target information from 14 known databases. multimir subclassifies these databases as “predicted,” “validated,” and “disease-drug […]


Entrainment of Breast Cell Lines Results in Rhythmic Fluctuations of MicroRNAs

PMCID: 5535989
PMID: 28704935
DOI: 10.3390/ijms18071499

[…] opposite profiles (). see for the rhythmic features and statistical significance of the six mirnas determined by validation., after the six mirnas were validated, we sought their gene targets in multimir []. it lists the gene targets that were experimentally validated for each mirna. of the six mirnas, only mir-17-5p revealed targets (343 genes in total). we then performed an enrichment […]


Bioinformatics analysis of key genes and pathways for hepatocellular carcinoma transformed from cirrhosis

PMCID: 5484182
PMID: 28640074
DOI: 10.1097/MD.0000000000006938

[…] and cluepedia tool kits, and the key kegg pathway was analyzed using the r package pathview. the regulatory factor mirna of degs was extracted from 3 verified mirnas-target databases using the multimir r package. moreover, a protein-protein interaction (ppi) network was constructed using the cytoscape software., degs including cyclin-dependent kinase 1 (cdk1), pdz-binding kinase (pbk), […]

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multiMiR institution(s)
Department of Surgery, School of Medicine, University of Colorado Denver, Aurora, CO, USA; Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA; Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado Denver, Aurora, CO, USA; Department of Pharmacology, School of Medicine, University of Colorado Denver, Aurora, CO, USA; Department of Medicine, National Jewish Health, Denver, CO, USA; Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Biomedical Sciences, University of Minnesota Medical School Duluth Campus, Duluth, MN, USA; University of Colorado Comprehensive Cancer Center, Aurora, CO, USA

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