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Authors: Sohei Ito 1 ; Shigeki Hagihara 2 and Naoki Yonezaki 2

Affiliations: 1 National Fisheries University, Japan ; 2 Tokyo Institute of Technology, Japan

Keyword(s): Gene Regulatory Network, Homeostasis, Temporal Logic, Strong Satisfiability, Network Motif, Systems Biology.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Systems Biology

Abstract: We proposed a novel framework to analyse homeostasis of gene networks using linear temporal logic. We formulate a kind of homeostasis as strong satisfiability of reactive system specifications. Both behaviours and properties of gene networks are specified in linear temporal logic and homeostasis of the network is checked by strong satisfiability checkers. Though this framework is simple and applicable for many networks, the computational complexity is heavy and large networks cannot be directly analysed. In this paper we present an approximate analysis method to mitigate this computational difficulty. We approximately specify a network specification using fewer propositions such that approximated specifications guarantee homeostasis of the network. However it is difficult to find such safely approximated specifications for any gene network. Thus we present approximate specifications for network motifs, which are common patterns appearing in many gene networks. We demonstrate our appr oximate method and see that our approximate method is quite efficient in analysing large networks. (More)

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Paper citation in several formats:
Ito, S.; Hagihara, S. and Yonezaki, N. (2015). Approximate Analysis of Homeostasis of Gene Networks by Linear Temporal Logic using Network Motifs. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2015) - BIOINFORMATICS; ISBN 978-989-758-070-3; ISSN 2184-4305, SciTePress, pages 93-101. DOI: 10.5220/0005177000930101

@conference{bioinformatics15,
author={Sohei Ito. and Shigeki Hagihara. and Naoki Yonezaki.},
title={Approximate Analysis of Homeostasis of Gene Networks by Linear Temporal Logic using Network Motifs},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2015) - BIOINFORMATICS},
year={2015},
pages={93-101},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005177000930101},
isbn={978-989-758-070-3},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2015) - BIOINFORMATICS
TI - Approximate Analysis of Homeostasis of Gene Networks by Linear Temporal Logic using Network Motifs
SN - 978-989-758-070-3
IS - 2184-4305
AU - Ito, S.
AU - Hagihara, S.
AU - Yonezaki, N.
PY - 2015
SP - 93
EP - 101
DO - 10.5220/0005177000930101
PB - SciTePress

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