title: Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana.
abstract: BACKGROUND
  Photosynthetic light acclimation is an important process that allows plants to optimize the efficiency of photosynthesis, which is the core technology for green energy. However, currently little is known about the molecular mechanisms behind the regulation of the photosynthetic light acclimation response. In this study, a systematic method is proposed to investigate this mechanism by constructing gene regulatory networks from microarray data of Arabidopsis thaliana.
  
  
  METHODS
  The potential TF-gene regulatory pairs of photosynthetic light acclimation have been obtained by data mining of literature and databases. Following the identification of these potential TF-gene pairs, they have been refined using Pearson's correlation, allowing the construction of a rough gene regulatory network. This rough gene regulatory network is then pruned using time series microarray data of Arabidopsis thaliana via the maximum likelihood system identification method and Akaike's system order detection method to approach the real gene regulatory network of photosynthetic light acclimation.
  
  
  RESULTS
  By comparing the gene regulatory networks under the PSI-to-PSII light shift and the PSII-to-PSI light shift, it is possible to identify important transcription factors for the different light shift conditions. Furthermore, the robustness of the gene network, in particular the hubs and weak linkage points, are also discussed under the different light conditions to gain further insight into the mechanisms of photosynthesis.
  
  
  CONCLUSIONS
  This study investigates the molecular mechanisms of photosynthetic light acclimation for Arabidopsis thaliana from the physiological level. This has been achieved through the construction of gene regulatory networks from the limited data sources and literature via an efficient computation method. If more experimental data for whole-genome ChIP-chip data and microarray data with multiple sampling points becomes available in the future, the proposed method will be improved on by constructing the whole-genome gene regulatory network. These advances will greatly improve our understanding of the mechanisms of the photosynthetic system.
authors.affiliation: Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsin-Chu, 300, Taiwan.
authors.forename: Cheng-Wei
authors.initials: CW
authors.lastname: Yao
authors.forename: Ban-Dar
authors.initials: BD
authors.lastname: Hsu
authors.forename: Bor-Sen
authors.initials: BS
authors.lastname: Chen
mesh_terms: D000064:Acclimatization; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D018744:DNA, Plant / Q000378:metabolism; D053263:Gene Regulatory Networks; D008027:Light; D020411:Oligonucleotide Array Sequence Analysis; D010788:Photosynthesis; D045331:Photosystem I Protein Complex / Q000378:metabolism; D045332:Photosystem II Protein Complex / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; D045331:Photosystem I Protein Complex; D045332:Photosystem II Protein Complex