Integrated MicroRNA-mRNA Analysis for Multi-Component Activity Monitoring of Herbal Medicine in Mouse Primary Hepatocytes

MicroRNAs (miRNAs) are involved in diverse cellular effects of herbal medicine by regulating post-transcriptional gene expression. However, the miRNA-mRNA regulatory network is far from being fully understood. In present study, we measured the molecular effects of herbal medicines on primary hepatocytes to gain some insights into the underlined mechanisms. Using bioinformatic approach with whole gene expression microarray and whole miRNA microarray, we selected the genes regulated by miRNA in whole gene level and then analyzed the functional involvement. Correlation matrix between expression of miRNA and putative target genes was constructed and then genes with correlation coefficient of under -0.8 (FDR< 0.01) were selected as being regulated by miRNA. The function of these genes was associated with diverse signaling and drug-metabolism using ontological and pathway analysis. From the network of interaction, we identified key regulatory elements acting as cores in multiple pathways that were regulated by herbal medicine via miRNA. Taken together, we have identified miRNA targets and its functional association by herbal medicine in hepatocytes in whole gene level using bioinformatics approach. We anticipate that the unique miRNA targets predicted by the proposed method will advance the understanding of the molecular mechanism of herbal medicines and will suggest novel therapeutic targets after further experimental validations.