A Qualitative Framework for Analysing Homeostasis in Gene Networks

Sohei Ito, Shigeki Hagihara, Naoki Yonezaki

2014

Abstract

Toward the system level understanding of the mechanisms contributing homeostasis in organisms, a computational framework to model a system and analyse its properties is indispensable. The purpose of this work is to provide a framework which enables testing and validating homeostatic properties on gene regulatory networks in silico. Based on a qualitative analysis framework for gene networks using temporal logic, we proposed a novel formulation of homeostasis by the notion of realisability. This formulation of homeostasis yields a qualitative method to analyse homeostasis of gene networks. In this formulation, homeostasis is captured by a response not for just an instantaneous stimulation such as dose-response relationships but for any input scenario e.g. oscillating or continuous inputs, which is difficult to be captured by quantitative models. Moreover, we can consider any number of inputs from an environment without difficulty. Such flexibility is a notable advantage of our framework. We demonstrate the usefulness of our framework in analysing a number of small but tricky networks.

Paper Citation

in Harvard Style

Ito S., Hagihara S. and Yonezaki N. (2014). A Qualitative Framework for Analysing Homeostasis in Gene Networks . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014) ISBN 978-989-758-012-3, pages 5-16. DOI: 10.5220/0004731400050016

in Bibtex Style

@conference{bioinformatics14,
author={Sohei Ito and Shigeki Hagihara and Naoki Yonezaki},
title={A Qualitative Framework for Analysing Homeostasis in Gene Networks},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014)},
year={2014},
pages={5-16},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004731400050016},
isbn={978-989-758-012-3},
}

in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014)
TI - A Qualitative Framework for Analysing Homeostasis in Gene Networks
SN - 978-989-758-012-3
AU - Ito S.
AU - Hagihara S.
AU - Yonezaki N.
PY - 2014
SP - 5
EP - 16
DO - 10.5220/0004731400050016