title: A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae.
abstract: Existing machine-readable resources for large-scale gene regulatory networks usually do not provide context information characterizing the activating conditions for a regulation and how targeted genes are affected. Although this information is essentially required for data interpretation, available networks are often restricted to not condition-dependent, non-quantitative, plain binary interactions as derived from high-throughput screens. In this article, we present a comprehensive Petri net based regulatory network that controls the diauxic shift in Saccharomyces cerevisiae. For 100 specific enzymatic genes, we collected regulations from public databases as well as identified and manually curated >400 relevant scientific articles. The resulting network consists of >300 multi-input regulatory interactions providing (i) activating conditions for the regulators; (ii) semi-quantitative effects on their targets; and (iii) classification of the experimental evidence. The diauxic shift network compiles widespread distributed regulatory information and is available in an easy-to-use machine-readable form. Additionally, we developed a browsable system organizing the network into pathway maps, which allows to inspect and trace the evidence for each annotated regulation in the model.
authors.affiliation: Practical Informatics and Bioinformatics, Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 17, 80333 Munich, Germany.
authors.forename: Ludwig
authors.initials: L
authors.lastname: Geistlinger
authors.forename: Gergely
authors.initials: G
authors.lastname: Csaba
authors.forename: Simon
authors.initials: S
authors.lastname: Dirmeier
authors.forename: Robert
authors.initials: R
authors.lastname: Küffner
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
mesh_terms: D002952:Citric Acid Cycle / Q000235:genetics; D005227:Fatty Acids / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D005943:Gluconeogenesis / Q000235:genetics; D008957:Models, Genetic; D019764:Phosphoenolpyruvate Carboxykinase (ATP) / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics
chemical_list: D005227:Fatty Acids; D029701:Saccharomyces cerevisiae Proteins; D019764:Phosphoenolpyruvate Carboxykinase (ATP)