Module Finding Approaches for Protein Interaction Networks

This chapter provides an overview of the computational approaches developed for exploring the modular organization of protein interaction networks. A special emphasis is placed on the module finding tools implemented in three freely available software packages, VisANT, Cytoscape and MATISSE, as well as on their biomedical applications. The selected methods are presented in the broader context of module discovery options, ranging from approaches that rely merely on topological properties of the underlying network to those that take into account also other complementary data sources, such as the mRNA levels of the proteins. The author will also highlight some current limitations in the measured network data that should be understood when developing and applying module finding methodology, and discuss some key future trends and promising research directions with potential implications for clinical research.