Characterization of Nested Complexes in Protein Interaction Networks

This paper provides a novel characterization of nested complexes in protein interaction networks, stressing definition and representation issues, quantification, biological validation, network metrics, motifs, modularity and gene ontology (GO) terms. This characterization can be used in the design of a nested protein complex prediction algorithm. We introduce the "nested group" concept as a way to represent nested complexes. We also show that enrichment in essential proteins, GO terms related to regulation, imperfect 5-clique motifs, as well as higher GO homogeneity, can be used to identify proteins in nested complexes. Supplementary materials, data and programs are available at http://faculty.uaeu.ac.ae/nzaki/Research.htm.