University of Colorado School of Public Health

The multiMiR R package and database:
Integration of microRNA-target interactions along with their disease and drug associations
(Nucleic Acids Res. 2014 Jul 24. pii: gku631)

Summary

microRNAs (miRNAs) regulate expression by promoting degradation or repressing translation of target transcripts. miRNA target sites have been catalogued in databases based on experimental validation and computational prediction using a variety of algorithms. Several online resources provide collections of multiple databases but need to be imported into other software, such as R, for processing, tabulation, graphing and computation. Currently available miRNA target site packages in R are limited in the number of databases, types of databases and flexibility.

The R package multiMiR, with web server at http://multimir.org, is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs.

Features

multiMiR includes several novel features not available in existing R packages:
  1. Compilation of nearly 50 million records from 14 different databases, more than any other collection
  2. Expansion of databases to those based on disease annotation and drug response, in addition to many experimental and computational databases
  3. User-defined cutoffs for predicted binding strength to provide the most confident selection
  4. Package enables retrieval of miRNA-target interactions from 14 external databases in R without the need to visit all these databases
  5. Advanced users can also submit SQL queries to the web server to retrieve results

Database v2.4 - updated 8/28/2024

CategoryExternal DatabaseVersionLast UpdateHuman RecordsMouse RecordsRat RecordsTotal Records
Validated miRNA-target InteractionsmiRecords4Apr 27, 20132,4254491713,045
miRTarBase9Sept, 2021544,58850,673652595,913
TarBase92023433,048209,8311,307644,186
Predicted miRNA-target InteractionsDIANA-microT-CDS5Sept, 20137,664,6023,747,171011,411,773
ElMMo5Jan, 20113,959,1121,449,133547,1915,955,436
MicroCosm5Sept, 2009762,987534,735353,3781,651,100
miRandaN/AAug, 20105,429,9552,379,881247,3688,057,204
miRDB6June, 20191,990,4251,091,263199,2503,280,938
PicTar2Dec 21, 2012404,066302,2360706,302
PITA6Aug 31, 20087,710,9365,163,153012,874,089
TargetScan8Sept 202113,964,42513,964,425013,964,425
miRNA-disease/drug AssociationsmiR2DiseaseN/AMar 14, 20112,875002,875
Pharmaco-miR (Verified Sets)N/AN/A30850313
PhenomiR2Feb 15, 201115,138491015,629

*Warning* There are issues with merging target IDs from older unmaintained databases. Databases that have been updated more recently (1-2 years) use current versions of annotated IDs. In each update these old target IDs are carried over due to a lack of a reliable method to disambiguate the original ID with current IDs. Please keep this in mind with results from older databases that have not been updated. We continue to look at methods to resolve these ambiguities and improve target agreement between databases. You can use the unique() R function to identify and then remove multiple target genes if needed.
Previous Database Versions

Software

Download Installation Documentation
Please see Bioconductor.
The version of the R package and Database have been seperated.
The R package has been set back to 1.0 for inclusion with Bioconductor while the
Database will continue from v2.1. The R package will now allow you to choose
pevious database versions if desired to reproduce previous results.
 Please install with bioconductor to simplify installation and maintenance.
http://bioconductor.org/packages/release/bioc/html/multiMiR.html 		Please see documentation on GitHub or Bioconductor.

More information about versions prior to inclusion in Bioconductor.

Feature Request/Bug Report:

If there is a feature you would like to suggest, or a bug you would like to report, please submit an issue through GitHub.

Contributors

multiMiR is developed by Yuanbin Ru at BioMarin Pharmaceutical Inc., Matt Mulvahill, Spencer Mahaffey, & Katerina Kechris at the University of Colorado Denver.

References

If you use multiMiR, please cite

Yuanbin Ru*, Katerina J. Kechris*, Boris Tabakoff, Paula Hoffman, Richard A. Radcliffe, Russell Bowler, Spencer Mahaffey, Simona Rossi, George A. Calin, Lynne Bemis, and Dan Theodorescu. (2014) The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations. Nucleic Acids Research, doi: 10.1093/nar/gku631. (* Equal contribution)