Título del libro: Plant Functional Genomics: Methods And Protocols: Second Edition
Título del capítulo: Descriptive vs. mechanistic network models in plant development in the post-genomic era
MARIA ELENA ALVAREZ BUYLLA ROCES;
Autores externos:
Idioma:
Inglés
Año de publicación:
2015
Palabras clave:
Attractor; Cell differentiation; Computational simulation; Descriptive model; Gene regulatory networks; Mathematical model; Mechanistic model; Morphogenesis; Network inference; Root stem cell niche; System dynamics
Resumen:
Network modeling is now a widespread practice in systems biology, as well as in integrative genomics, and it constitutes a rich and diverse scientific research field. A conceptually clear understanding of the reasoning behind the main existing modeling approaches, and their associated technical terminologies, is required to avoid confusions and accelerate the transition towards an undeniable necessary more quantitative, multidisciplinary approach to biology. Herein, we focus on two main network-based modeling approaches that are commonly used depending on the information available and the intended goals: inference-based methods and system dynamics approaches. As far as data-based network inference methods are concerned, they enable the discovery of potential functional influences among molecular components. On the other hand, experimentally grounded network dynamical models have been shown to be perfectly suited for the mechanistic study of developmental processes. How do these two perspectives relate to each other? In this chapter, we describe and compare both approaches and then apply them to a given specific developmental module. Along with the step-by-step practical implementation of each approach, we also focus on discussing their respective goals, utility, assumptions, and associated limitations. We use the gene regulatory network (GRN) involved in Arabidopsis thaliana Root Stem Cell Niche patterning as our illustrative example. We show that descriptive models based on functional genomics data can provide important background information consistent with experimentally supported functional relationships integrated in mechanistic GRN models. The rationale of analysis and modeling can be applied to any other well-characterized functional developmental module in multicellular organisms, like plants and animals. © Springer Science+Business Media New York 2015. All rights are reserved.
Entidades citadas de la UNAM:
ISBN:
9781493924448
Editorial:
Springer New York Nombre de la publicación:
Descriptive vs. mechanistic network models in plant development in the post-genomic era
Página inicial:
455
Página final:
479
Tipo de producto:
Capítulo de un Libro
