title: Interactive three-dimensional visualization and contextual analysis of protein interaction networks.
abstract: To understand the biology of the interactome, the covisualization of protein interactions and other protein-related data is required. In this study, we have adapted a 3-D network visualization platform, GEOMI, to allow the coanalysis of protein-protein interaction networks with proteomic parameters such as protein localization, abundance, physicochemical parameters, post-translational modifications, and gene ontology classification. Working with Saccharomyces cerevisiae data, we show that rich and interactive visualizations, constructed from multidimensional orthogonal data, provide insights on the complexity of the interactome and its role in biological processes and the architecture of the cell. We present the first organelle-specific interaction networks, that provide subinteractomes of high biological interest. We further present some of the first views of the interactome built from a new combination of yeast two-hybrid data and stable protein complexes, which are likely to approximate the true workings of stable and transient aspects of the interactome. The GEOMI tool and all interactome data are freely available by contacting the authors.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Edwin
authors.initials: E
authors.lastname: Ho
authors.forename: Richard
authors.initials: R
authors.lastname: Webber
authors.forename: Marc R
authors.initials: MR
authors.lastname: Wilkins
mesh_terms: D019295:Computational Biology; D003196:Computer Graphics; D030562:Databases, Protein; D015388:Organelles / Q000737:chemistry*; D011485:Protein Binding; D025941:Protein Interaction Mapping; D040901:Proteomics; D029701:Saccharomyces cerevisiae Proteins; D049490:Systems Biology / Q000379:methods*; D020798:Two-Hybrid System Techniques; D014584:User-Computer Interface
chemical_list: D029701:Saccharomyces cerevisiae Proteins