University of Colorado Cancer Center, A National Cancer Institute-designated Comprehensive Cancer Center

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.ucdenver.edu, 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
CategoryExternal DatabaseVersionLast UpdateHuman RecordsMouse RecordsTotal Records
Validated miRNA-target InteractionsmiRecords4Apr 27, 201324254492874
miRTarBase4.5Nov 1, 201347003944856451
TarBase6201223447902432471
Predicted miRNA-target InteractionsDIANA-microT-CDS5Sept, 20137664602374717111411773
ElMMo5Jan, 2011395911214491335408245
MicroCosm5Sept, 20097629875347351297722
miRandaN/AAug, 2010542995523798817809836
miRDB4Jan, 20127222693487781071047
PicTar2Dec 21, 2012404066302236706302
PITA6Aug 31, 20087710936516315312874089
TargetScan6.2Jun, 2012629812225908148888936
miRNA-disease/drug AssociationsmiR2DiseaseN/AMar 14, 2011287502875
Pharmaco-miR (Verified Sets)N/AN/A3085313
PhenomiR2Feb 15, 20111513849115629

Software

Download Installation Documentation
The current version of multiMiR is 1.0.1 and can be downloaded from
http://multimir.ucdenver.edu/multiMiR_1.0.1.tar.gz.
multiMiR requires the XML and RCurl packages from R. The packages can be installed from R by typing:
install.packages("XML")
install.packages("RCurl")
install.packages("/pathname/multiMiR_1.0.1.tar.gz", repos=NULL, type="source")

NOTE: Change “pathname” to your own directory path.
multiMiR is distributed with a User’s Guide illustrating examples of package functions and queries.

The User's Guide can be downloaded here or viewed from R by typing:
vignette("multiMiR")

More information about version 1.0.1.

Feature Request/Bug Report:

If there is a feature you would like to suggest, or a bug you would like to report, please email multimir.ucdenver at gmail.com

Contributors

multiMiR is developed by Yuanbin Ru at Windber Research Institute & 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)