Recently, it occured to me that one reason microarrays often only show vague changes in gene expression is that gene regulation is often done by miRNA silencing of genes, rather than changes in level of expressed mRNA. I believe microarrays typically measure known mRNAs, and unless the array also contains relevant miRNAs, you're missing a lot of possibly crucial information.
Is this correct?
If so, do microarrays these days usually come with miRNA probes? How complete is our knowledge of miRNAs, anyway? And given today's densities, why not just include reverse-complement probes for the 3' UTR (where miRNAs usually bind)?