title: Biochemical systems analysis of genome-wide expression data.
abstract: BACKGROUND
  Modern methods of genomics have produced an unprecedented amount of raw data. The interpretation and explanation of these data constitute a major, well-recognized challenge.
  
  
  RESULTS
  Biochemical Systems Theory (BST) is the mathematical basis of a well-established methodological framework for analyzing networks of biochemical reactions. An existing BST model of yeast glycolysis is used here to explain and interpret the glycolytic gene expression pattern of heat shocked yeast. Our analysis demonstrates that the observed gene expression profile satisfies the primary goals of increased ATP, trehalose, and NADPH production, while maintaining intermediate metabolites at reasonable levels. Based on a systematic exploration of alternative, hypothetical expression profiles, we show that the observed profile outperforms other profiles.
  
  
  CONCLUSIONS
  BST is a useful framework for combining DNA microarray data with enzymatic process information to yield new insights into metabolic pathway regulation.
  
  
  BACKGROUND
  All analyses were executed with the software PLAS(Copyright), which is freely available at http://correio.cc.fc.ul.pt/~aenf/plas.html for academic use.
  
  
  BACKGROUND
  VoitEO@MUSC.edu
authors.affiliation: Department of Biometry and Epidemiology, 135 Rutledge Avenue, Medical University of South Carolina, Charleston, SC 29425, USA. VoitEO@MUSC.edu
authors.forename: E O
authors.initials: EO
authors.lastname: Voit
authors.forename: T
authors.initials: T
authors.lastname: Radivoyevitch
mesh_terms: D019295:Computational Biology; D003627:Data Interpretation, Statistical; D016208:Databases, Factual; D020869:Gene Expression Profiling / Q000706:statistics & numerical data*; D016681:Genome, Fungal; D006019:Glycolysis / Q000235:genetics; D018869:Heat-Shock Response; D008954:Models, Biological; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D013597:Systems Analysis