Formal Analysis of Gene Networks Using Network Motifs View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2014

AUTHORS

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

ABSTRACT

We developed a theoretical framework to analyse gene regulatory networks. Our framework is based on the formal methods which are well-known techniques to analyse software/hardware systems. Behaviours of gene networks are abstracted into transition systems which has discrete time structure. We characterise possible behaviours of given networks by linear temporal logic (LTL) formulae. By checking the satisfiability of LTL formulae, we analyse whether all/some behaviours of given networks satisfy given biological properties. Due to the complexity of LTL satisfiability checking, analyses of large networks are generally intractable in this method. To mitigate this computational difficulty, we proposed approximate analysis method using network motifs to circumvent the computational difficulty of LTL satisfiability checking. Experiments show that our approximate method is surprisingly efficient. More... »

PAGES

131-146

References to SciGraph publications

  • 1993-09. Logical identification of all steady states: The concept of feedback loop characteristic states in BULLETIN OF MATHEMATICAL BIOLOGY
  • 2002. ω-Automata in AUTOMATA LOGICS, AND INFINITE GAMES
  • 2005-11-29. Realizable and unrealizable specifications of reactive systems in AUTOMATA, LANGUAGES AND PROGRAMMING
  • 2007-06. Network motifs: theory and experimental approaches in NATURE REVIEWS GENETICS
  • Book

    TITLE

    Biomedical Engineering Systems and Technologies

    ISBN

    978-3-662-44484-9
    978-3-662-44485-6

    From Grant

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/978-3-662-44485-6_10

    DOI

    http://dx.doi.org/10.1007/978-3-662-44485-6_10

    DIMENSIONS

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