We presented a computational pipeline to investigate connections between small molecules and miRNAs in AD through comparative analysis of transcriptional responses of small molecules perturbations and miRNAs regulations in AD. We introduced miRNA expression profiles to identify biological insights into small molecules and miRNAs.
For each ADM, if the up-regulated target genes of the ADM tended to appear in the bottom of the ranked small molecule signatures, while the down-regulated target genes inclined to fall in the top of the ranked small molecule signatures, we inferred that the ADM mediated expression alterations was opposite to that of the small molecule perturbation. In this situation, a negative Similarity (S) score was calculated to measure the opposite connection between the small molecule and the ADM, which may helpful to develop anti-miRNA drugs. Analogously, a positive Similarity score of one pair of small molecule and ADM represented the similar transcriptional responses of small molecule treatment and miRNA perturbation, which may helpful to develop miRNA mimic drugs.