REVIEW Protein networking: insights into global functional organization of proteomes Enrico Pieroni 1 , Sergio de la Fuente van Bentem 2 , Gianmaria Mancosu 1 , Enrico Capobianco 1 , Heribert Hirt 2, 3 and Alberto de la Fuente 1 1 CRS4 Bioinformatica, c/o Parco Tecnologico POLARIS, Pula, Italy 2 Department of Plant Molecular Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria 3 Plant Genomics Research Unit, Unité de Recherche en Genomique Végétale (URGV), INRA/CNRS, Evry, France The formulation of network models from global protein studies is essential to understand the functioning of organisms. Network models of the proteome enable the application of Complex Network Analysis, a quantitative framework to investigate large complex networks using tech- niques from graph theory, statistical physics, dynamical systems and other fields. This approach has provided many insights into the functional organization of the proteome so far and will likely continue to do so. Currently, several network concepts have emerged in the field of proteomics. It is important to highlight the differences between these concepts, since different representations allow different insights into functional organization. One such concept is the protein interaction network, which contains proteins as nodes and undirected edges representing the occurrence of binding in large-scale protein-protein interaction studies. A second concept is the protein-sig- naling network, in which the nodes correspond to levels of post-translationally modified forms of proteins and directed edges to causal effects through post-translational modification, such as phosphorylation. Several other network concepts were introduced for proteomics. Although all formulated as networks, the concepts represent widely different physical systems. Therefore caution should be taken when applying relevant topological analysis. We review recent literature formulating and analyzing such networks. Received: August 7, 2007 Revised: November 1, 2007 Accepted: November 1, 2007 Keywords: Complex networks / Interactomics / Network biology / Protein networks / Systems biology Proteomics 2008, 8, 799–816 799 1 Introduction 1.1 General remarks Although large-scale high-throughput experimental tech- niques have greatly increased our knowledge, understanding the global organization of proteomes is still by far incom- plete. A global view on the proteome is hampered by the complexity: there are tens of thousands of proteins and potentially hundreds of thousands of relations between them. Abstract representations of the proteome and the relationships are needed to be able to analyze and interpret such huge collections of data. 1.2 Why networks? To understand living cells one must study them as systems rather than a collection of individual molecules. The study of systems consisting of thousands of interacting molecular species is very complicated and simplifying abstractions are necessary. The abstraction of intracellular processes into ‘networks’ is particularly fruitful [1, 2]. Networks provide a clear representation of complicated relationships between Correspondence: Dr. Alberto de la Fuente, CRS4 Bioinformatica, c/o Parco Tecnologico POLARIS, Edificio 1, Loc. Piscina Manna 09010 Pula, Italy E-mail: alf@crs4.it Fax: 139-070-9243-4114 Abbreviations: PIN, protein-interaction network; PSN, protein- signaling network; SCC, strongly connected component; TAP , tandem affinity purification; Y2H, yeast two-hybrid DOI 10.1002/pmic.200700767  2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com