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Bioinformatics. 2015 Sep 1;31(17):2822-8. doi: 10.1093/bioinformatics/btv220. Epub 2015 Apr 24.

Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from matched micro-RNA and gene expression data.

Author information

1
School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia.
2
CSIRO Mathematical & Information Sciences, Clayton South, VIC 3168, Australia and.
3
Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA.

Abstract

MOTIVATION:

In practice, identifying and interpreting the functional impacts of the regulatory relationships between micro-RNA and messenger-RNA is non-trivial. The sheer scale of possible micro-RNA and messenger-RNA interactions can make the interpretation of results difficult.

RESULTS:

We propose a supervised framework, pMim, built upon concepts of significance combination, for jointly ranking regulatory micro-RNA and their potential functional impacts with respect to a condition of interest. Here, pMim directly tests if a micro-RNA is differentially expressed and if its predicted targets, which lie in a common biological pathway, have changed in the opposite direction. We leverage the information within existing micro-RNA target and pathway databases to stabilize the estimation and annotation of micro-RNA regulation making our approach suitable for datasets with small sample sizes. In addition to outputting meaningful and interpretable results, we demonstrate in a variety of datasets that the micro-RNA identified by pMim, in comparison to simpler existing approaches, are also more concordant with what is described in the literature.

AVAILABILITY AND IMPLEMENTATION:

This framework is implemented as an R function, pMim, in the package sydSeq available from http://www.ellispatrick.com/r-packages.

CONTACT:

jean.yang@sydney.edu.au

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
25910695
PMCID:
PMC4635654
DOI:
10.1093/bioinformatics/btv220
[Indexed for MEDLINE]
Free PMC Article

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