Authors:
Sohei Ito
1
;
Takuma Ichinose
2
;
Masaya Shimakawa
2
;
Naoko Izumi
3
;
Shigeki Hagihara
2
and
Naoki Yonezaki
2
Affiliations:
1
The University of Tokyo, Japan
;
2
Tokyo Institute of Technology, Japan
;
3
Jumonji University, Japan
Keyword(s):
Gene Regulatory Network, Temporal Logic, Formal Methods, Network Motif.
Related
Ontology
Subjects/Areas/Topics:
Algorithms and Software Tools
;
Bioinformatics
;
Biomedical Engineering
;
Systems Biology
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.
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