The increasing cost of drug development together with a significant drop in the number of new drug approvals raises the need for innovative approaches for drug-target identification and efficacy prediction. The emergence of most diseases cannot be explained by single-gene deficiency, but involve the breakdown of the coordinated function of distinct gene groups. Consequently, to be successful, drug interaction analysis must shift its focus from individual genes that carry disease-associated mutations towards a network-based perspective of disease mechanisms. In this tutorial, we show some theoretical approaches for network-based drug interaction analysis and review some of the most important insights into the relationships between drugs and genes achieved using network-based approaches.