A functional genomics approach using metabolomics and in silico pathway analysis

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 analy...

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Bibliographic Details
Published in:Biotechnology and bioengineering 2002-09, Vol.79 (7), p.703-712
Main Authors: Förster, Jochen, Gombert, Andreas Karoly, Nielsen, Jens
Format: Article
Language:English
Subjects:
Algorithms
Biological and medical sciences
Biotechnology
Computer Simulation
convex analysis
elementary flux modes
Energy Metabolism
functional genomics
Fundamental and applied biological sciences. Psychology
Gene Expression Profiling - methods
Gene Expression Regulation, Fungal
Genetic engineering
Genetic technics
Genome, Fungal
Genomics
metabolome analysis
metabolomics
Methods. Procedures. Technologies
Models, Biological
Models, Chemical
Models, Genetic
pathway structure
Saccharomyces cerevisiae
Saccharomyces cerevisiae - genetics
Saccharomyces cerevisiae - growth & development
Saccharomyces cerevisiae - metabolism
Structure-Activity Relationship
Vectors (cloning, transfer, expression). Insertion sequences and transposons
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Summary: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. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 79: 703–712, 2002.
ISSN:0006-3592
1097-0290
DOI:10.1002/bit.10378