© 2015 The Authors. Network analysis has been a recent focus in biological sciences due to its ability to synthesize global visualizations of cellular processes and predict functions based on inferences from network properties. A protein-protein interaction network, or interactome, captures the emergent cellular states from gene regulation and environmental conditions. Given that proteins are involved in extensive local and systemic molecular interactions such as signaling and metabolism, understanding protein functions and interactions are essential for a systems view of biology. However, in plant sciences these network-based approaches to data integration have been few and far between due to limited data, especially protein-protein interaction data. In this review, we cover network construction from experimental data, network analysis based on topological properties, and finally we discuss advances in networks in plants and other organisms in a comparative approach. We focus on applications of network biology to discover the dynamics of host-pathogen interactions as these have potential agricultural uses in improving disease resistance in commercial crops.