Protein networking: Insights into global functional organization of proteomes

Enrico Pieroni, Sergio De La Fuente Van Bentem, Gianmaria Mancosu, Enrico Capobianco, Heribert Hirt, Alberto De La Fuente*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

71 Scopus citations

Abstract

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 techniques 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-signaling 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.

Original languageEnglish (US)
Pages (from-to)799-816
Number of pages18
JournalProteomics
Volume8
Issue number4
DOIs
StatePublished - Feb 2008

Keywords

  • Complex networks
  • Interactomics
  • Network biology
  • Protein networks
  • Systems biology

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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