Identification of microRNAs with regulatory potential using a matched microRNA-mRNA time-course data

Abstract

Over the past decade, a class of small RNA molecules called microRNAs (miRNAs) has been shown to regulate gene expression at the post-transcription stage. While early work focused on the identification of miRNAs using a combination of experimental and computational techniques, subsequent studies have focused on identification of miRNA-target mRNA pairs as each miRNA can have hundreds of mRNA targets. The experimental validation of some miRNAs as oncogenic has provided further motivation for research in this area. In this article we propose an odds-ratio (OR) statistic for identification of regulatory miRNAs. It is based on integrative analysis of matched miRNA and mRNA time-course microarray data. The OR-statistic was used for (i) identification of miRNAs with regulatory potential, (ii) identification of miRNA-target mRNA pairs and (iii) identification of time lags between changes in miRNA expression and those of its target mRNAs. We applied the OR-statistic to a cancer data set and identified a small set of miRNAs that were negatively correlated to mRNAs. A literature survey revealed that some of the miRNAs that were predicted to be regulatory, were indeed oncogenic or tumor suppressors. Finally, some of the predicted miRNA targets have been shown to be experimentally valid.

Figure 1.

Pair-wise concordance between miRNA rankings obtained for time-lag 0 using PicTar, TargetScanS, miRBase and miRGen. The plot is represented as a 4 × 4 grid with the upper-diagonal cells and the lower diagonal cells being mirror images. For example, while the graph in cell (1, 2) has PicTar rankings on the Y-axis and miRBase rankings on the X-axis, the graph in cell (2, 1) has PicTar rankings on the X-axis and miRBase rankings on the Y-axis.

Figure 2.

Log₂-fold change values for hsa-miR-16 and some of its targets mRNAs identified using OR-statistic. The horizontal blue lines correspond to 1.5-fold change (log₂ value of 0.58).

Figure 3.

Log₂-fold change values per miRNA probe/mRNA probeset. hsa-miR-16 had probes in duplicate and the target mRNAs map to multiple probesets, the number of probesets varying from one mRNA to another. Blue denotes over-expression with respect to time t = 0 and yellow denotes under-expression with respect to time t = 0. RAB11 corresponds to the gene RAB11FIP2.