title: Modular analysis of gene networks by linear temporal logic.
abstract: Despite a lot of advances in biology and genomics, it is still difficult to utilise such valuable knowledge and information to understand and analyse large biological systems due to high computational complexity. In this paper we propose a modular method with which from several small network analyses we analyse a large network by integrating them. This method is based on the qualitative framework proposed by authors in which an analysis of gene networks is reduced to checking satisfiability of linear temporal logic formulae. The problem of linear temporal logic satisfiability checking needs exponential time in the size of a formula. Thus it is difficult to analyse large networks directly in this method since the size of a formula grows linearly to the size of a network. The modular method alleviates this computational difficulty. We show some experimental results and see how we benefit from the modular analysis method.
authors.affiliation: The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
authors.forename: Sohei
authors.initials: S
authors.lastname: Ito
authors.forename: Takuma
authors.initials: T
authors.lastname: Ichinose
authors.forename: Masaya
authors.initials: M
authors.lastname: Shimakawa
authors.forename: Naoko
authors.initials: N
authors.lastname: Izumi
authors.forename: Shigeki
authors.initials: S
authors.lastname: Hagihara
authors.forename: Naoki
authors.initials: N
authors.lastname: Yonezaki
mesh_terms: D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D005798:Genes, Bacterial / Q000235:genetics; D008128:Logic; D008957:Models, Genetic; D011550:Pseudomonas aeruginosa / Q000235:genetics; D013997:Time Factors