The yeast protein-protein interaction map is a highly modular network with a staircase community structure

Summary: The construction of genome wide protein–protein interaction maps makes it feasible to study the global organization of proteins in a biological cell. Here the module organization of the protein–protein interaction network (PPIN) of budding yeast are investigated by Netwalk, an algorithm based on biased random (Brownian) walks. The yeast PPIN is a highly modular network, it has a modularity value of Q ≃ 0.62. Measured by a dissimilarity index, the giant component of yeast PPIN contains 449 elementary modules that organize into a staircase community structure. The elementary modules at the lowest level of this staircase are mainly responsible for protein production; and an expanding central community is formed by the addition of other elementary modules at increasingly higher dissimilarity levels, which are responsible for protein synthesis regulation, protein transport, cell cycle control, and so on. Many proteins that function as bridges between different elementary modules are also identified. Availability and supporting information: The Netwalk algorithm is available upon request ([email protected]). Information on the identified elementary modules is also deposited at http://www.mpikg-golm.mpg.de/theory/people/zhou/EModule.html.