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Network Approaches to the Functional Analysis of Microbial Proteins

Lookup NU author(s): Dr Jennifer Hallinan, Dr Katherine James, Professor Anil Wipat

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Abstract

Large amounts of detailed biological data have been generated over the past few decades. Much of these data is freely available in over 1000 online databases; an enticing, but frustrating resource for microbiologists interested in a systems-level view of the structure and function of microbial cells. The frustration engendered by the need to trawl manually through hundreds of databases in order to accumulate information about a gene, protein, pathway, or organism of interest can be alleviated by the use of computational data integration to generated network views of the system of interest. Biological networks can be constructed from a single type of data, such as protein protein binding information, or from data generated by multiple experimental approaches. In an integrated network, nodes usually represent genes or gene products, while edges represent some form of interaction between the nodes. Edges between nodes may be weighted to represent the probability that the edge exists in vivo. Networks may also be enriched with ontological annotations, facilitating both visual browsing and computational analysis via web service interfaces. In this review, we describe the construction, analysis of both single-data source and integrated networks, and their application to the inference of protein function in microbes.


Publication metadata

Author(s): Hallinan JS, James K, Wipat A

Publication type: Review

Publication status: Published

Journal: Advances in Microbial Physiology

Year: 2011

Volume: 59

Pages: 101-133

Print publication date: 21/11/2011

ISSN (print): 0065-2911

ISSN (electronic): 2162-5468

Publisher: ACADEMIC PRESS LTD-ELSEVIER SCIENCE LTD

URL: http://dx.doi.org/10.1016/B978-0-12-387661-4.00005-7

DOI: 10.1016/B978-0-12-387661-4.00005-7


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