Protein networking: insights into global functional organization of proteomes
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,...
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Published in | Proteomics (Weinheim) Vol. 8; no. 4; pp. 799 - 816 |
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Main Authors | , , , , , |
Format | Journal Article |
Language | English |
Published |
Weinheim
Wiley-VCH Verlag
01.02.2008
WILEY-VCH Verlag WILEY‐VCH Verlag Wiley-VCH |
Subjects | |
Online Access | Get full text |
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Summary: | 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. |
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Bibliography: | http://dx.doi.org/10.1002/pmic.200700767 Regione Autonoma della Sardegna ArticleID:PMIC200700767 European Union Sardegna Ricerche Vienna Science and Technology Fund istex:64A7BE1C87EE1747F60BC2574ADBF6F182AB7819 ark:/67375/WNG-1PZZRRFP-G Austrian Science Foundation ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-3 content type line 23 ObjectType-Review-1 |
ISSN: | 1615-9853 1615-9861 |
DOI: | 10.1002/pmic.200700767 |