title: Time series dependent analysis of unparametrized Thomas networks.
abstract: This paper is concerned with the analysis of labeled Thomas networks using discrete time series. It focuses on refining the given edge labels and on assessing the data quality. The results are aimed at being exploitable for experimental design and include the prediction of new activatory or inhibitory effects of given interactions and yet unobserved oscillations of specific components in between specific sampling intervals. On the formal side, we generalize the concept of edge labels and introduce a discrete time series interpretation. This interpretation features two original concepts: 1) Incomplete measurements are admissible, and 2) it allows qualitative assumptions about the changes in gene expression by means of monotonicity. On the computational side, we provide a Python script, erda.py, that automates the suggested workflow by model checking and constraint satisfaction. We illustrate the workflow by investigating the yeast network IRMA.
authors.affiliation: DFG Research Center Matheon, Freie Universität Berlin, Berlin, Germany. Hannes.Klarner@FU-Berlin.de
authors.forename: Hannes
authors.initials: H
authors.lastname: Klarner
authors.forename: Heike
authors.initials: H
authors.lastname: Siebert
authors.forename: Alexander
authors.initials: A
authors.lastname: Bockmayr
mesh_terms: D019295:Computational Biology / Q000379:methods*; D053263:Gene Regulatory Networks; D008962:Models, Theoretical; D012107:Research Design; D012441:Saccharomyces cerevisiae / Q000235:genetics