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Descriptive vs. Mechanistic Network Models in Plant Development in the Post-Genomic Era

  • J. Davila-Velderrain
  • J. C. Martinez-Garcia
  • E. R. Alvarez-BuyllaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1284)

Abstract

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.

Key words

Gene regulatory networks Root stem cell niche Cell differentiation Attractor Morphogenesis System dynamics Mathematical model Computational simulation Network inference Descriptive model Mechanistic model 

Notes

Acknowledgments

J.D.V acknowledges the support of CONACYT and the Centre for Genomic Regulation (CRG), Barcelona, Spain; while spending a research visit in the lab of Stephan Ossowski. This chapter constitutes a partial fulfillment of the graduate program Doctorado en Ciencias Biomédicas of the Universidad Nacional Autónoma de México, UNAM in which J.D.V. developed this project. This work was supported by grants CONACYT 180098, 180380, 167705, 152649 and UNAM-DGAPA-PAPIIT: IN203113, IN 203214, IN203814, UC Mexus ECO-IE415. The authors acknowledge logistical and administrative help of Diana Romo.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • J. Davila-Velderrain
    • 1
    • 2
  • J. C. Martinez-Garcia
    • 2
    • 3
  • E. R. Alvarez-Buylla
    • 1
    • 2
    Email author
  1. 1.Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de EcologíaUniversidad Nacional Autónoma de México, Ciudad UniversitariaMéxico D.F.Mexico
  2. 2.Centro de Ciencias de la Complejidad (C3)Universidad Nacional Autónoma de México, Ciudad UniversitariaMéxico D.F.Mexico
  3. 3.Departamento de Control AutomáticoCinvestav-IPNMéxico D.F.Mexico

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