Integrating network motifs into a genetic network: A case of study based on the Phop/PhoQ two-component system

Oscar Harari, Coral Del Val, Igor Zwir

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Genetic and genomic approaches have been successfully employed to assign genes to distinct regulatory networks. The strength of the connections in these networks must be specified to define the kinetics of a group of genes, but the uncertainty concerning the connections between genes, the ambiguity inherent to the biological processes, and the impossibility of experimentally determining the underlying biological properties only allow a rough prediction of gene interaction. Here we describe a framework that examines promoter sequences and identifies those cis-acting features that define transcriptional network motifs. Then, we employ an iterative process, based on Ordinary Differential Equations, to learn a network architecture that appropriately integrates these motifs into a full structure. The application of this method to the two component systems PhoP/PhoQ and the PmrA/PmrB in Salmonella enterica uncovered novel mechanisms that enable the inter-connection of these networks. The predictions were experimentally verified.

Original languageEnglish
Title of host publicationProceedings of the 2011 11th International Conference on Intelligent Systems Design and Applications, ISDA'11
Pages1371-1376
Number of pages6
DOIs
StatePublished - Dec 1 2011
Event2011 11th International Conference on Intelligent Systems Design and Applications, ISDA'11 - Cordoba, Spain
Duration: Nov 22 2011Nov 24 2011

Publication series

NameInternational Conference on Intelligent Systems Design and Applications, ISDA
ISSN (Print)2164-7143
ISSN (Electronic)2164-7151

Conference

Conference2011 11th International Conference on Intelligent Systems Design and Applications, ISDA'11
CountrySpain
CityCordoba
Period11/22/1111/24/11

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    Harari, O., Del Val, C., & Zwir, I. (2011). Integrating network motifs into a genetic network: A case of study based on the Phop/PhoQ two-component system. In Proceedings of the 2011 11th International Conference on Intelligent Systems Design and Applications, ISDA'11 (pp. 1371-1376). [6121851] (International Conference on Intelligent Systems Design and Applications, ISDA). https://doi.org/10.1109/ISDA.2011.6121851