ABSTRACT
In this chapter we examine in some detail the experimental methods that are used to derive interaction networks. An interaction between two biological entities could be physical, for example an interaction between two proteins, between a protein and a length of DNA, or between a protein and a small molecule. An interaction could also be strictly informational, as in a genetic interaction. It is important to keep in mind that a physical interpretation of the latter is often difficult: a genetic interaction may or may not be due to a direct physical interaction, and often the basis of a genetic interaction remains abstract. Despite this difficulty, genetic interaction networks are considered vital to many important biological and medical goals. On the other hand, a physical interaction between two biological molecules can be simple to interpret but suffers from several uncertainties with respect to the relevance of the interaction for biological function. Thus, the two types of interactions-physical and genetic-often reveal complementary aspects of the biology of the organism.
