The study of biological networks has led to the development of a variety of measures for characterizing network properties at different levels. Global analysis provides summary measures such as diameter, clustering coefficients, and degree distribution that describe the network as a whole, whereas local properties, such as the occurrences of motifs and graphlets allow us to focus on specific phenomena within the network. Local characteristics are suitable to study networks that are incompletely explored; in particular, they faithfully capture the neighborhoods of these parts of the networks that are better studied. In this talk I will describe several methods to analyze both protein-protein interaction (which are undirected graphs) as well as regulation networks (which are directed) along with the biological consequences that they have yielded.