Mathematical modeling of gene regulatory networks in Xenopus development

Yasushi Saka

doi:10.1007/978-1-61779-992-1_28

Mathematical modeling of gene regulatory networks in Xenopus development

Methods Mol Biol. 2012:917:497-513. doi: 10.1007/978-1-61779-992-1_28.

Author

Yasushi Saka¹

Affiliation

¹ Institute of Medical Sciences, University of Aberdeen, Scotland, UK. y.saka@abdn.ac.uk

PMID: 22956106
DOI: 10.1007/978-1-61779-992-1_28

Abstract

Mathematical modeling has become increasingly indispensable for scientists who study the dynamics of gene regulatory networks (GRN) that underlie cell differentiation and pattern formation in animal development including Xenopus embryogenesis. Here I outline a step-by-step procedure for constructing a mathematical model of GRN based on ordinary differential equations (ODE), using the network of Activin and its downstream target genes Xenopus Brachyury (Xbra) and Goosecoid (Gsc) as an example. I also briefly explain methods to analyse the dynamics described by an ODE model.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Animals
Embryo, Nonmammalian / embryology*
Embryonic Development / genetics*
Gene Regulatory Networks*
Kinetics
Models, Biological*
Software
Xenopus / embryology
Xenopus / genetics*