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 journalArticle

71 Citations (Scopus)

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

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MicroRNAs
Databases
Pharmaceutical Preparations
Urinary Bladder Neoplasms
Alcohol Drinking
Chronic Obstructive Pulmonary Disease
Software
Neoplasm Metastasis
Cell Line

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Ru, Y., Kechris, K. J., Tabakoff, B., Hoffman, P., Radcliffe, R. A., Bowler, R., ... Theodorescu, D. (2014). The multiMiR R package and database: Integration of microRNA-target interactions along with their disease and drug associations. Nucleic acids research, 42(17), [e133]. https://doi.org/10.1093/nar/gku631

The multiMiR R package and database : Integration of microRNA-target interactions along with their disease and drug associations. / Ru, Yuanbin; Kechris, Katerina J.; Tabakoff, Boris; Hoffman, Paula; Radcliffe, Richard A.; Bowler, Russell; Mahaffey, Spencer; Rossi, Simona; Calin, George A.; Bemis, Lynne; Theodorescu, Dan.

In: Nucleic acids research, Vol. 42, No. 17, e133, 27.06.2014.

Research output: Contribution to journalArticle

Ru, Y, Kechris, KJ, Tabakoff, B, Hoffman, P, Radcliffe, RA, Bowler, R, Mahaffey, S, Rossi, S, Calin, GA, Bemis, L & Theodorescu, D 2014, 'The multiMiR R package and database: Integration of microRNA-target interactions along with their disease and drug associations', Nucleic acids research, vol. 42, no. 17, e133. https://doi.org/10.1093/nar/gku631
Ru, Yuanbin ; Kechris, Katerina J. ; Tabakoff, Boris ; Hoffman, Paula ; Radcliffe, Richard A. ; Bowler, Russell ; Mahaffey, Spencer ; Rossi, Simona ; Calin, George A. ; Bemis, Lynne ; Theodorescu, Dan. / The multiMiR R package and database : Integration of microRNA-target interactions along with their disease and drug associations. In: Nucleic acids research. 2014 ; Vol. 42, No. 17.
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