The multiMiR R package and database: Integration of microRNA-target interactions along with their disease and drug associations

Yuanbin Ru, Katerina J. Kechris, Boris Tabakoff, Paula Hoffman, Richard A. Radcliffe, Russell Bowler, Spencer Mahaffey, Simona Rossi, George A. Calin, Lynne Bemis, Dan Theodorescu

Research output: Contribution to journalArticlepeer-review

99 Scopus citations

Abstract

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 various 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. We present multiMiR, a new miRNA-target interaction R package and database, which includes several novel features not available in existing R packages: (i) compilation of nearly 50 million records in human and mouse from 14 different databases, more than any other collection; (ii) expansion of databases to those based on disease annotation and drug microRNAresponse, in addition to many experimental and computational databases; and (iii) user-defined cutoffs for predicted binding strength to provide the most confident selection. Case studies are reported on various biomedical applications including mouse models of alcohol consumption, studies of chronic obstructive pulmonary disease in human subjects, and human cell line models of bladder cancer metastasis. We also demonstrate how multiMiR was used to generate testable hypotheses that were pursued experimentally.

Original languageEnglish (US)
Article numbere133
JournalNucleic acids research
Volume42
Issue number17
DOIs
StatePublished - Jun 27 2014

Bibliographical note

Funding Information:
National Institutes of Health [R01CA075115 to D.T., K01AA16922, R01AA021131 to K.J.K., R01AA016957 to R.A.R., R24AA013162 to B.T.]; a Butcher Seed Grant [to K.J.K., R.B.]; the Banbury Fund [to B.T.]. Funding for open access charge: National Institutes of Health. Conflict of interest statement. None declared.

Publisher Copyright:
© © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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