title: Modelling the yeast interactome.
abstract: The topology behind biological interaction networks has been studied for over a decade. Yet, there is no definite agreement on the theoretical models which best describe protein-protein interaction (PPI) networks. Such models are critical to quantifying the significance of any empirical observation regarding those networks. Here, we perform a comprehensive analysis of yeast PPI networks in order to gain insights into their topology and its dependency on interaction-screening technology. We find that: (1) interaction-detection technology has little effect on the topology of PPI networks; (2) topology of these interaction networks differs in organisms with different cellular complexity (human and yeast); (3) clear topological difference is present between PPI networks, their functional sub-modules, and their inter-functional "linkers"; (4) high confidence PPI networks have more "geometrical" topology compared to predicted, incomplete, or noisy PPI networks; and (5) inter-functional "linker" proteins serve as mediators in signal transduction, transport, regulation and organisational cellular processes.
authors.affiliation: Department of Computing, Imperial College London, London, United Kingdom.
authors.forename: Vuk
authors.initials: V
authors.lastname: Janjić
authors.affiliation: Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel.
authors.forename: Roded
authors.initials: R
authors.lastname: Sharan
authors.affiliation: Department of Computing, Imperial College London, London, United Kingdom.
authors.forename: Nataša
authors.initials: N
authors.lastname: Pržulj
mesh_terms: D005656:Fungal Proteins / Q000378:metabolism*; D008954:Models, Biological; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D015003:Yeasts / Q000378:metabolism*
chemical_list: D005656:Fungal Proteins