Understanding hormonal crosstalk in \textit{Arabidopsis} root development via emulation and history matching

DOI10.1515/SAGMB-2018-0053zbMATH Open1461.92011arXiv1801.01538OpenAlexW2980794949WikidataQ97561915 ScholiaQ97561915MaRDI QIDQ830633FDOQ830633

Authors: Samuel E. Jackson, Ian Vernon, Keith Lindsey, Junli Liu 

Publication date: 7 May 2021

Published in: Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Abstract: A major challenge in plant developmental biology is to understand how plant growth is coordinated by interacting hormones and genes. To meet this challenge, it is important to not only use experimental data, but also formulate a mathematical model. For the mathematical model to best describe the true biological system, it is necessary to understand the parameter space of the model, along with the links between the model, the parameter space and experimental observations. We develop sequential history matching methodology, using Bayesian emulation, to gain substantial insight into biological model parameter spaces. This is achieved by finding sets of acceptable parameters in accordance with successive sets of physical observations. These methods are then applied to a complex hormonal crosstalk model for Arabidopsis root growth. In this application, we demonstrate how an initial set of 22 observed trends reduce the volume of the set of acceptable inputs to a proportion of 6.1 x 10^(-7) of the original space. Additional sets of biologically relevant experimental data, each of size 5, reduce the size of this space by a further three and two orders of magnitude respectively. Hence, we provide insight into the constraints placed upon the model structure by, and the biological consequences of, measuring subsets of observations.

Full work available at URL: https://arxiv.org/abs/1801.01538

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zbMATH Keywords

emulationhistory matching\textit{Arabidopsis}Bayesian uncertainty analysisparameter search

Mathematics Subject Classification ID

Qualitative investigation and simulation of ordinary differential equation models (34C60) Developmental biology, pattern formation (92C15) Plant biology (92C80)

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Cited In (1)

• Modeling of gene regulative networks in developmental systems.

Uses Software

• GPfit
• GPy
• GitHub

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