An overview of constructing influential miRNA-GeneSignature interactions. A. miRNA gene signature is identified by transfecting cells with pre-miRNA and then identify gene down-regulated upon the transfection. B. Using the context-specific effects of miRNAs (genes affected by miRNAs directly and indirectly) to build functional associations between miRNAs and GeneSignatures via elastic-net regression model. This step sheds light on the functional associations between miRNA and pathways, miRNAs and diseases. It is also used as a miRNA enrichment method to identify miRNAs whose targets are enriched in gene lists. Using miRNA-gene networks and disease or pathway gene networks, the model predicts functional interactions between diseases and miRNAs or pathways and miRNAs.