title: A functional genomics approach using metabolomics and in silico pathway analysis.
abstract: In the field of functional genomics increasing effort is being undertaken to analyze the function of orphan genes using metabolome data. Improved analytical equipment allows screening simultaneously for a high number of metabolites. Such metabolite profiles are analyzed using multivariate data analysis techniques and changes in the genotype will in many cases lead to different metabolite profiles. Here, a theoretical framework that may be applied to identify the function of orphan genes is presented. The approach is based on a combination of metabolome analysis combined with in silico pathway analysis. Pathway analysis may be carried out using convex analysis and a change in the active pathway structure of deletion mutants expressed in a different metabolite profile may disclose the function or the functional class of an orphan gene. The concept is illustrated using a simplified model for growth of Saccharomyces cerevisiae.
authors.affiliation: Center for Process Biotechnology, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark.
authors.forename: Jochen
authors.initials: J
authors.lastname: Förster
authors.forename: Andreas Karoly
authors.initials: AK
authors.lastname: Gombert
authors.forename: Jens
authors.initials: J
authors.lastname: Nielsen
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004734:Energy Metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D023281:Genomics; D008954:Models, Biological; D008956:Models, Chemical; D008957:Models, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D013329:Structure-Activity Relationship