Encyclopedia of Systems Biology

2013 Edition
| Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota

Protein–Protein Interaction Networks, Distributed Analysis

  • Pietro Hiram Guzzi
Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_970

Definition

The whole set of protein interactions in a cell is often modeled by using graphs. Usually these graphs are referred to as Protein Interaction Networks. Currently, there is a large number of laboratories that are producing data about protein interaction networks as well as a large number of laboratories that mine these data to extract biologically relevant knowledge. In this scenario, the distributed analysis of protein interaction networks is a set of complex activities that can be structured on: (1) the Sharing and dissemination of PPI data among different databases; (2) the collection of data stored in heterogeneous databases; and (3) the Distributed analysis based on distributed and high-performance infrastructures.

Characteristics

Information representable as a network is mostly modeled using graph theory Lesne (2006). Informally, a graph is a structure composed of a set of nodes and edges linking them. A graph G is defined as G = {V, E}, where V is a set of nodes, Eis...

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References

  1. Aittokallio T, Schwikowski B (2006) Graph-based methods for analysing networks in cell biology. Brief Bioinform 7(3):243–255. doi:10.1093/bib/bbl022PubMedGoogle Scholar
  2. Cannataro M, Guzzi PH, Veltri P (2010) Protein-to-protein interactions: technologies, databases, and algorithms. ACM Comput Surv 43:1:1–1:36, ISSN 0360–0300, doi: http://doi.acm.org/10.1145/1824795.1824796
  3. Cerami E, Bader G, Gross BE, Sander C (2006) cpath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics 7(497):1–9. doi:10.1186/1471-2105-7-497Google Scholar
  4. Lesne A (2006) Complex networks: from graph theory to biology. Lett Math Phys 78(3):235–262. doi:10.1007/s11005-006-0123-1, ISSN 0377–9017, http://dx.doi.org/10.1007/s11005-006-0123-1

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Department of Experimental Medicine and ClinicUniversity Magna Gratia of CatanzaroCatanzaroItaly