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Open Access Highly Accessed Research article

Information processing in the transcriptional regulatory network of yeast: Functional robustness

Frank Emmert-Streib1* and Matthias Dehmer2

Author Affiliations

1 Computational Biology and Machine Learning, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK

2 Center for Mathematics, Probability and Statistics, University of Coimbra, Apartado 3008, 3001-454 Coimbra, Portugal

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BMC Systems Biology 2009, 3:35  doi:10.1186/1752-0509-3-35

Published: 19 March 2009

Abstract

Background

Gene networks are considered to represent various aspects of molecular biological systems meaningfully because they naturally provide a systems perspective of molecular interactions. In this respect, the functional understanding of the transcriptional regulatory network is considered as key to elucidate the functional organization of an organism.

Results

In this paper we study the functional robustness of the transcriptional regulatory network of S. cerevisiae. We model the information processing in the network as a first order Markov chain and study the influence of single gene perturbations on the global, asymptotic communication among genes. Modification in the communication is measured by an information theoretic measure allowing to predict genes that are 'fragile' with respect to single gene knockouts. Our results demonstrate that the predicted set of fragile genes contains a statistically significant enrichment of so called essential genes that are experimentally found to be necessary to ensure vital yeast. Further, a structural analysis of the transcriptional regulatory network reveals that there are significant differences between fragile genes, hub genes and genes with a high betweenness centrality value.

Conclusion

Our study does not only demonstrate that a combination of graph theoretical, information theoretical and statistical methods leads to meaningful biological results but also that such methods allow to study information processing in gene networks instead of just their structural properties.