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Open Access Research article

Model-based clustering reveals vitamin D dependent multi-centrality hubs in a network of vitamin-related proteins

Thanh-Phuong Nguyen1, Marco Scotti1*, Melissa J Morine1 and Corrado Priami12

Author Affiliations

1 The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura 1, 38068 Rovereto (Trento), Italy

2 Department of Information Engineering and Computer Science, University of Trento, Via Sommarive 14, 38123 Povo (Trento), Italy

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BMC Systems Biology 2011, 5:195  doi:10.1186/1752-0509-5-195

Published: 2 December 2011

Abstract

Background

Nutritional systems biology offers the potential for comprehensive predictions that account for all metabolic changes with the intricate biological organization and the multitudinous interactions between the cellular proteins. Protein-protein interaction (PPI) networks can be used for an integrative description of molecular processes. Although widely adopted in nutritional systems biology, these networks typically encompass a single category of functional interaction (i.e., metabolic, regulatory or signaling) or nutrient. Incorporating multiple nutrients and functional interaction categories under an integrated framework represents an informative approach for gaining system level insight on nutrient metabolism.

Results

We constructed a multi-level PPI network starting from the interactions of 200 vitamin-related proteins. Its final size was 1,657 proteins, with 2,700 interactions. To characterize the role of the proteins we computed 6 centrality indices and applied model-based clustering. We detected a subgroup of 22 proteins that were highly central and significantly related to vitamin D. Immune system and cancer-related processes were strongly represented among these proteins. Clustering of the centralities revealed a degree of redundancy among the indices; a repeated analysis using subsets of the centralities performed well in identifying the original set of 22 most central proteins.

Conclusions

Hierarchical and model-based clustering revealed multi-centrality hubs in a vitamin PPI network and redundancies among the centrality indices. Vitamin D-related proteins were strongly represented among network hubs, highlighting the pervasive effects of this nutrient. Our integrated approach to network construction identified promiscuous transcription factors, cytokines and enzymes - primarily related to immune system and cancer processes - representing potential gatekeepers linking vitamin intake to disease.