Methods are described for detecting
protein-
protein interactions, among two populations of proteins, each having a complexity of at least 1,000. For example, proteins are fused either to the
DNA-
binding domain of a
transcriptional activator or to the activation domain of a
transcriptional activator. Two
yeast strains, of the opposite
mating type and carrying one type each of the fusion proteins are mated together. Productive interactions between the two halves due to
protein-protein interactions lead to the reconstitution of the
transcriptional activator, which in turn leads to the activation of a
reporter gene containing a
binding site for the
DNA-
binding domain. This analysis can be carried out for two or more populations of proteins. The differences in the genes encoding the proteins involved in the protein-protein interactions are characterized, thus leading to the identification of
specific protein-protein interactions, and the genes encoding the interacting proteins, relevant to a particular tissue, stage or
disease. Furthermore, inhibitors that interfere with these protein-protein interactions are identified by their ability to inactivate a
reporter gene. The screening for such inhibitors can be in a multiplexed format where a set of inhibitors will be screened against a
library of interactors. Further, information-
processing methods and systems are described. These methods and systems provide for identification of the genes coding for detected interacting proteins, for assembling a unified
database of protein-protein interaction data, and for
processing this unified
database to obtain protein interaction domain and protein pathway information.