We tested and measured the strength of heterospecific interactions between microRNAs and their targets by carrying out transgenic experiments across Drosophila species, by over-expressing the miR310s cluster of D. melanogaster (Dm310s) and D. pseudoobscura (Dp310s) in D. melanogaster. A knockout line, referred to as Dm310s (−), was also included for comparison. The whole-genome expression (WGE) of the Dp310s and Dm310s transgenic lines were compared on two platforms of both Affymetrix tiling array and DGRC cDNA array. The WGE of knockout line was assayed on only Affymetrix tiling array. In the Dm310s lines, overexpression was more common than underexpression among misregulated genes while the pattern appeared to be reversed in the Dm310s(−) line. The number of genes significantly misexpressed under the influence of Dp310s is 3-10 times greater than under Dm310s. Importantly, the numbers of predicted targets are similar between them. Expression analysis of the predicted target genes suggests that miRNAs may sometimes function to buffer fluctuations in the transcriptome output. After the buffering function has evolved, heterospecific combinations may cause adverse effects. This SuperSeries is composed of the SubSeries listed below. Overall design: The three data sets are all parts of the same overall study, in which we over-expressed the Dm310s and Dp310s in D. melanogaster, and analyzed the transcriptional consequences by using microarrays. A knockout line was also used to provide supplementary information. For more details, refer to individual Series.