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Dynamic network-based epistasis analysis: Boolean examples
estado: published
has publication venue: Frontiers in Plant Science
type: Article
type: Entity
freetext keyword: Boolean networks; Epistasis; Feed-forward loops; Feedback loops; Gene interactions; Gene regulatory networks; Modeling; Temporal dynamics
related by: authorship_17004
related by: authorship_17003
type: Document
type: Continuant
abstract: In this article we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the inference of gene regulatory networks. Here we emphasize the critical importance of dynamic analyses, and specifically illustrate the use of Boolean network models. Epistasis in a broad sense refers to gene interactions, however, as originally proposed by Bateson, epistasis is defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus (herein, classical epistasis). Classical epistasis analysis has proven powerful and useful, allowing researchers to infer and assign directionality to gene interactions. As larger data sets are becoming available, the analysis of classical epistasis is being complemented with computer science tools and system biology approaches.We show that when the hierarchical and single-path assumptions are not met in classical epistasis analysis, the access to relevant information and the correct inference of gene interaction topologies is hindered, and it becomes necessary to consider the temporal dynamics of gene interactions. The use of dynamical networks can overcome these limitations. We particularly focus on the use of Boolean networks that, like classical epis-tasis analysis, relies on logical formalisms, and hence can complement classical epistasis analysis and relax its assumptions. We develop a couple of theoretical examples and analyze them from a dynamic Boolean network model perspective. Boolean networks could help to guide additional experiments and discern among alternative regulatory schemes that would be impossible or difficult to infer without the elimination of these assumption from the classical epistasis analysis.We also use examples from the literature to show how a Boolean network-based approach has resolved ambiguities and guided epistasis analysis. Our article complements previous accounts, not only by focusing on the implications of the hierarchical and single-…
volume: 2
most specific type: Article
related by: authorship_17002
type: Information Content Entity
crisid: 2898
issue: DEC
origen: scopus
type: Generically Dependent Continuant
date time value: article date 2898
doi: 10.3389/fpls.2011.00092
type: Thing
e iscopus: 2-s2.0-84898834254
artnum: 92
accesstype: All Open Access, Gold, Green
related by: authorship_17006
related by: authorship_17005
most specific type: Document

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RDF description of Dynamic network-based epistasis analysis: Boolean examples - http://orbis.uaslp.mx/vivo/individual/scopus2897
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date: 2026-08-26T23:55:37
publisher: vivo
type: Document

Article
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Information Content Entity
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Frontiers in Plant Science
type: Document
type: Collection
type: Thing
type: Information Content Entity
publication venue for: Dynamic network-based epistasis analysis: Boolean examples
type: Generically Dependent Continuant
type: Periodical
type: Continuant
type: Journal
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