title: Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana.
abstract: Photosynthesis is one of the most important biological processes on the earth. So far, though the molecular mechanisms underlying photosynthesis is well understood, however, the regulatory networks of photosynthesis are poorly studied. Given the current interest in improving photosynthetic efficiency for greater crop yield, elucidating the detailed regulatory networks controlling the construction and maintenance of photosynthetic machinery is not only scientifically significant but also holding great potential in agricultural application. In this study, we first identified transcription factors (TFs) related to photosynthesis through the TRAP approach using position weight matrix information. Then, for TFs related to photosynthesis, interactions between them and their targets were also determined by the ARACNE approach. Finally, a gene regulatory network was established by combining TF-targets information generated by these two approaches. Topological analysis of the regulatory network suggested that (a) the regulatory network of photosynthesis has a property of "small world"; (b) there is substantial coordination mediated by transcription factors between different components in photosynthesis.
authors: Group of Plant System Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, China.
authors: Xianbin
authors: X
authors: Yu
authors: Group of Plant System Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, China.
authors: Guangyong
authors: G
authors: Zheng
authors: Group of Plant System Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, China.
authors: Lanlan
authors: L
authors: Shan
authors: Department of Computational Regulatory Genomics, CAS-MPG Partner Institutes for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, China.
authors: Guofeng
authors: G
authors: Meng
authors: Department of Computational Regulatory Genomics, CAS-MPG Partner Institutes for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, China.
authors: Martin
authors: M
authors: Vingron
authors: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China.
authors: Qi
authors: Q
authors: Liu
authors: Group of Plant System Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, China ; Group of Plant System Biology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences Shanghai, China.
authors: Xin-Guang
authors: XG
authors: Zhu
keywords: coordination; photosynthesis; regulatory network; small world; transcription factors