Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network.

Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network. Research Abstract Details 

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Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network. Abstract Text:

David J Irons,Nicholas A M Monk,David J Irons,Nicholas A M Monk,

BACKGROUND: It is widely accepted that genetic regulatory systems are 'modular', in that the whole system is made up of smaller 'subsystems' corresponding to specific biological functions. Most attempts to identify modules in genetic regulatory systems have relied on the topology of the underlying network. However, it is the temporal activity (dynamics) of genes and proteins that corresponds to biological functions, and hence it is dynamics that we focus on here for identifying subsystems. RESULTS: Using Boolean network models as an exemplar, we present a new technique to identify subsystems, based on their dynamical properties. The main part of the method depends only on the stable dynamics (attractors) of the system, thus requiring no prior knowledge of the underlying network. However, knowledge of the logical relationships between the network components can be used to describe how each subsystem is regulated. To demonstrate its applicability to genetic regulatory systems, we apply the method to a model of the Drosophila segment polarity network, providing a detailed breakdown of the system. CONCLUSION: We have designed a technique for decomposing any set of discrete-state, discrete-time attractors into subsystems. Having a suitable mathematical model also allows us to describe how each subsystem is regulated and how robust each subsystem is against perturbations. However, since the subsystems are found directly from the attractors, a mathematical model or underlying network topology is not necessarily required to identify them, potentially allowing the method to be applied directly to experimental expression data.

Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network. Publishing Authors By Initials

DJ Irons,NA Monk,DJ Irons,NA Monk,

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Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: BMC bioinformatics

VOLUME: 8

Page Numbers: 413

Journal Abbreviation: BMC Bioinformatics

ISSN: 1471-2105

DAY: 25

MONTH: 10

YEAR: 2007

Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network. Information

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LANGUAGE: eng

NlmUniqueID: 100965194

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AFFILIATION: Department of Computer Science, University of Sheffield, UK. d.irons@sheffield.ac.uk

Country: England

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MEDLINETA: BMC Bioinformatics

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