title: Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data.
abstract: Although large-scale gene expression data have been studied from many perspectives, they have not been systematically integrated to infer the regulatory potentials of individual genes in specific pathways. Here we report the analysis of expression patterns of genes in the Calvin cycle from 95 Arabidopsis microarray experiments, which revealed a consistent gene regulation pattern in most experiments. This identified pattern, likely due to gene regulation by light rather than feedback regulations of the metabolite fluxes in the Calvin cycle, is remarkably consistent with the rate-limiting roles of the enzymes encoded by these genes reported from both experimental and modeling approaches. Therefore, the regulatory potential of the genes in a pathway may be inferred from their expression patterns. Furthermore, gene expression analysis in the context of a known pathway helps to categorize various biological perturbations that would not be recognized with the prevailing methods.
authors.affiliation: Department of Epidemiology and Public Health, Yale University School of Medicine, 60 College Street, New Haven, CT 06520, USA. ning.sun@yale.edu
authors.forename: Ning
authors.initials: N
authors.lastname: Sun
authors.forename: Ligeng
authors.initials: L
authors.lastname: Ma
authors.forename: Deyun
authors.initials: D
authors.lastname: Pan
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism / Q000528:radiation effects*; D002241:Carbohydrates / Q000096:biosynthesis*; D002245:Carbon Dioxide / Q000378:metabolism*; D030561:Databases, Nucleic Acid; D004798:Enzymes / Q000235:genetics; D020869:Gene Expression Profiling; D015971:Gene Expression Regulation, Enzymologic / Q000528:radiation effects; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects; D008027:Light; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D010641:Phenotype; D020218:Response Elements / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics / Q000528:radiation effects
chemical_list: D002241:Carbohydrates; D004798:Enzymes; D002245:Carbon Dioxide