Disentangling the multigenic and pleiotropic nature of molecular function

Stoney, R. A., Ames, R. M., Nenadic, G., Robertson, D. L. and Schwartz, J.-M. (2015) Disentangling the multigenic and pleiotropic nature of molecular function. BMC Systems Biology, 9(Suppl6), S3. (doi:10.1186/1752-0509-9-S6-S3) (PMID:26678917) (PMCID:PMC4674882)

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Abstract

Background: Biological processes at the molecular level are usually represented by molecular interaction networks. Function is organised and modularity identified based on network topology, however, this approach often fails to account for the dynamic and multifunctional nature of molecular components. For example, a molecule engaging in spatially or temporally independent functions may be inappropriately clustered into a single functional module. To capture biologically meaningful sets of interacting molecules, we use experimentally defined pathways as spatial/temporal units of molecular activity. Results: We defined functional profiles of Saccharomyces cerevisiae based on a minimal set of Gene Ontology terms sufficient to represent each pathway's genes. The Gene Ontology terms were used to annotate 271 pathways, accounting for pathway multi-functionality and gene pleiotropy. Pathways were then arranged into a network, linked by shared functionality. Of the genes in our data set, 44% appeared in multiple pathways performing a diverse set of functions. Linking pathways by overlapping functionality revealed a modular network with energy metabolism forming a sparse centre, surrounded by several denser clusters comprised of regulatory and metabolic pathways. Signalling pathways formed a relatively discrete cluster connected to the centre of the network. Genetic interactions were enriched within the clusters of pathways by a factor of 5.5, confirming the organisation of our pathway network is biologically significant. Conclusions: Our representation of molecular function according to pathway relationships enables analysis of gene/protein activity in the context of specific functional roles, as an alternative to typical molecule-centric graph-based methods. The pathway network demonstrates the cooperation of multiple pathways to perform biological processes and organises pathways into functionally related clusters with interdependent outcomes.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Robertson, Professor David
Authors: Stoney, R. A., Ames, R. M., Nenadic, G., Robertson, D. L., and Schwartz, J.-M.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:BMC Systems Biology
Publisher:BioMed Central
ISSN:1752-0509
ISSN (Online):1752-0509
Copyright Holders:Copyright © 2015 Stoney et al.
First Published:First published in BMC Systems Biology 9(Suppl 6): S3
Publisher Policy:Reproduced under a Creative Commons License

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