Second, microarray experiments reveal that overexpression of miRNA in cells cause the moderate down-regulation of a large number of transcripts, many of which contain the complementary sequences of the over-expressed miRNA in their 39-UTRs. Conversely, gene expression analysis from miRNA knockdown animals reveal that the miRNA recognition motifs are strongly enriched in the 39- UTRs of up-regulated genes, but depleted in the 39-UTRs of downregulated genes. Third, it has been shown that the 39-UTRs of certain class of ubiquitously expressed genes are specifically depleted of miRNA target sites and that the endogenous expression of several highly specific miRNAs is typically negatively correlated with the mRNA levels of their targets. Since the expression regulation at the mRNA level is common for miRNA functions, it is reasonable to expect that the activities of miRNAs can be reflected by the expression levels of their target mRNAs. As a matter of fact, the systematic negative correlations between expressions of miRNAs and those of their target transcripts have been observed in a number of studies as described above. With these observations, a natural question to us is: can we infer the modification of miRNA effective regulation from the expressions of their target genes? In this paper, we propose a method that BAY 43-9006 combines microarray expression data with miRNA target predictions to infer the relative activities of miRNAs underlying the gene expression changes. In a typical microarray expression experiment, the relative expression levels in two different biological samples or the absolute expression levels in a single biological sample are measured simultaneously for tens of thousands of genes. The expression levels of miRNA are generally not available from these gene expression data. Thus, the purpose of our method is to infer the relative miRNA activities, i.e. changes of miRNA effective regulations between two different conditions, based on the expression changes of their target genes, which are directly measured by cDNA arrays or calculated by comparing the absolute gene expression levels from different oligonucleotide arrays. Basically, our method examines the trend of expression changes of target genes of a miRNA. If these target genes tend to be down-regulated, it indicates that the effective activity of this miRNA is enhanced between the two conditions. Conversely, a prevalent up-regulation of these target genes would indicate a reduction of the miRNA activity. We apply this method to microarray data measuring gene expression changes in cell lines transfected with certain miRNAs or anti-miRNAs. It shows that the relative activities changes of the transfected miRNAs and the inhibited miRNAs can MG132 side effects indeed be inferred with high sensitivity and specificity.