title: Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast.
abstract: Composed of linear difference equations, a discrete dynamical system (DDS) model was designed to reconstruct transcriptional regulations in gene regulatory networks (GRNs) for ethanologenic yeast Saccharomyces cerevisiae in response to 5-hydroxymethylfurfural (HMF), a bioethanol conversion inhibitor. The modelling aims at identification of a system of linear difference equations to represent temporal interactions among significantly expressed genes. Power stability is imposed on a system model under the normal condition in the absence of the inhibitor. Non-uniform sampling, typical in a time-course experimental design, is addressed by a log-time domain interpolation. A statistically significant DDS model of the yeast GRN derived from time-course gene expression measurements by exposure to HMF, revealed several verified transcriptional regulation events. These events implicate Yap1 and Pdr3, transcription factors consistently known for their regulatory roles by other studies or postulated by independent sequence motif analysis, suggesting their involvement in yeast tolerance and detoxification of the inhibitor.
authors.affiliation: Department of Computer Science, New Mexico State University, Las Cruces, NM 88003, USA. joemsong@cs.nmsu.edu
authors.forename: M
authors.initials: M
authors.lastname: Song
authors.forename: Z
authors.initials: Z
authors.lastname: Ouyang
authors.forename: Z L
authors.initials: ZL
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D016000:Cluster Analysis; D003198:Computer Simulation; D004361:Drug Tolerance; D005662:Furaldehyde / Q000031:analogs & derivatives* / Q000494:pharmacology; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal / Q000187:drug effects; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis; D012441:Saccharomyces cerevisiae / Q000187:drug effects* / Q000235:genetics; D013997:Time Factors
chemical_list: C008046:5-hydroxymethylfurfural; D005662:Furaldehyde