Qualitative Analysis of Gene Regulatory Networks using Network Motifs

Sohei Ito, Takuma Ichinose, Masaya Shimakawa, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki

2013

Abstract

We developed a method for analysing gene regulatory networks in a purely qualitative fashion. Behaviours of networks are captured as transition systems using propositions for gene states (ON or OFF), and those related to threshold values for gene activation/inhibition. Possible behaviours of networks are specified by logical formulae in Linear Temporal Logic (LTL). With this specification, it is possible to check whether some/all behaviours satisfy a biological property, which is difficult for quantitative analyses like an ordinary differential equation approach. Our method uses satisfiability checking of LTL. Due to the complexity of LTL satisfiability checking, analyses of large networks are generally intractable in this method. To tackle this issue, in this paper, we propose approximate analysis method in which we specify behaviours in simpler formulae which compress/expand the possible behaviours of networks. We present approximate specifications for some network patterns called network motifs.

Paper Citation

in Harvard Style

Ito S., Ichinose T., Shimakawa M., Izumi N., Hagihara S. and Yonezaki N. (2013). Qualitative Analysis of Gene Regulatory Networks using Network Motifs . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013) ISBN 978-989-8565-35-8, pages 15-24. DOI: 10.5220/0004188400150024

in Bibtex Style

@conference{bioinformatics13,
author={Sohei Ito and Takuma Ichinose and Masaya Shimakawa and Naoko Izumi and Shigeki Hagihara and Naoki Yonezaki},
title={Qualitative Analysis of Gene Regulatory Networks using Network Motifs},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)},
year={2013},
pages={15-24},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004188400150024},
isbn={978-989-8565-35-8},
}

in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)
TI - Qualitative Analysis of Gene Regulatory Networks using Network Motifs
SN - 978-989-8565-35-8
AU - Ito S.
AU - Ichinose T.
AU - Shimakawa M.
AU - Izumi N.
AU - Hagihara S.
AU - Yonezaki N.
PY - 2013
SP - 15
EP - 24
DO - 10.5220/0004188400150024