title: Visualization and analysis of the complexome network of Saccharomyces cerevisiae.
abstract: Most processes in the cell are delivered by protein complexes, rather than individual proteins. While the association of proteins has been studied extensively in protein-protein interaction networks (the interactome), an intuitive and effective representation of complex-complex connections (the complexome) is not yet available. Here, we describe a new representation of the complexome of Saccharomyces cerevisiae. Using the core-module-attachment data of Gavin et al. (  Nature     2006  ,   440  ,   631 - 6  ), protein complexes in the network are represented as nodes; these are connected by edges that represent shared core and/or module protein subunits. To validate this network, we examined the network topology and its distribution of biological processes. The complexome network showed scale-free characteristics, with a power law-like node degree distribution and clustering coefficient independent of node degree. Connected complexes in the network showed similarities in biological process that were nonrandom. Furthermore, clusters of interacting complexes reflected a higher-level organization of many cellular functions. The strong functional relationships seen in these clusters, along with literature evidence, allowed 44 uncharacterized complexes to be assigned putative functions using guilt-by-association. We demonstrate our network model using the GEOMI visualization platform, on which we have developed capabilities to integrate and visualize complexome data.
authors.affiliation: Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia.
authors.forename: Simone S
authors.initials: SS
authors.lastname: Li
authors.forename: Kai
authors.initials: K
authors.lastname: Xu
authors.forename: Marc R
authors.initials: MR
authors.lastname: Wilkins
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D003593:Cytoplasm / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D005816:Genetic Complementation Test; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D020543:Proteome; D040901:Proteomics / Q000379:methods; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D012984:Software
chemical_list: D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins