Visualisation and analysis of the complexome network of Saccharomyces cerevisiae.

Article


Li, S., Xu, K. and Wilkins, M. 2011. Visualisation and analysis of the complexome network of Saccharomyces cerevisiae. Journal of Proteome Research. 10 (10), pp. 4744-4756. https://doi.org/10.1021/pr200548c
TypeArticle
TitleVisualisation and analysis of the complexome network of Saccharomyces cerevisiae.
AuthorsLi, S., Xu, K. and Wilkins, M.
Abstract

Most processes in the cell are delivered by protein complexes, rather than individual proteins. While the association of proteins has been studied extensively in protein–protein interaction networks (the interactome), an intuitive and effective representation of complex–complex connections (the complexome) is not yet available. Here, we describe a new representation of the complexome of Saccharomyces cerevisiae. Using the core-module-attachment data of Gavin et al. ( Nature 2006, 440, 631−6), protein complexes in the network are represented as nodes; these are connected by edges that represent shared core and/or module protein subunits. To validate this network, we examined the network topology and its distribution of biological processes. The complexome network showed scale-free characteristics, with a power law-like node degree distribution and clustering coefficient independent of node degree. Connected complexes in the network showed similarities in biological process that were nonrandom. Furthermore, clusters of interacting complexes reflected a higher-level organization of many cellular functions. The strong functional relationships seen in these clusters, along with literature evidence, allowed 44 uncharacterized complexes to be assigned putative functions using guilt-by-association. We demonstrate our network model using the GEOMI visualization platform, on which we have developed capabilities to integrate and visualize complexome data.

PublisherAmerican Chemical Society
JournalJournal of Proteome Research
ISSN1535-3893
Publication process dates
Deposited17 Feb 2012
Output statusPublished
Digital Object Identifier (DOI)https://doi.org/10.1021/pr200548c
LanguageEnglish
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