Three examples of modular decomposition of protein-protein interaction networks. In each case from top to bottom: schema of complexes, the corresponding protein-protein interaction network as determined from PCP experiments, and its modular decomposition (MOD). (a) Protein phosphatase 2A. Parallel modules group proteins that do not interact but are functionally equivalent. Here these are the catalytic Pph21 and Pph22 (module 2) and the regulatory Cdc55 and Rts1 (module 3). (b) RNA polymerases (RNAP) I, II and III. A good layout of the corresponding network gives an intuitive idea of what the constitutive units of the complexes are. Modular decomposition extracts them and makes their logical combinations explicit. (c) Transcriptional regulator complexes (see text for details). Modular decomposition condenses the network to its backbone prime structure (root of the tree) and identifies its constitutive units.