Expression dynamics of a cellular metabolic network.
Toward the goal of understanding system properties of biological networks, we investigate the global and local regulation of gene expression in the Saccharomyces cerevisiae metabolic network. Our results demonstrate predominance of local gene regulation in metabolism. Metabolic genes display significant coexpression on distances smaller than the average network distance, a behavior supported by the distribution of transcription factor binding sites in the metabolic network and genome context associations. Positive gene coexpression decreases monotonically with distance in the network, while negative coexpression is strongest at intermediate network distances. We show that basic topological motifs of the metabolic network exhibit statistically significant differences in coexpression behavior.
Kharchenko
Peter
P
Department of Genetics, Harvard Medical School, Boston, MA, USA.
Church
George M
GM
Vitkup
Dennis
D
D001665:Binding Sites; D004271:DNA, Fungal / Q000235:genetics / Q000378:metabolism; D004790:Enzyme Induction; D004798:Enzymes / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D008954:Models, Biological; D008957:Models, Genetic; D011401:Promoter Regions, Genetic / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D049490:Systems Biology; D014157:Transcription Factors / Q000378:metabolism
D004271:DNA, Fungal; D004798:Enzymes; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors