title: Minimum network constraint on reverse engineering to develop biological regulatory networks.
abstract: Reconstructing the topological structure of biological regulatory networks from microarray expression data or data of protein expression profiles is one of major tasks in systems biology. In recent years, various mathematical methods have been developed to meet this task. Here, based on our previously reported reverse engineering method, we propose a new constraint, i.e., the minimum network constraint, to facilitate the reconstruction of biological networks. Three well studied regulatory networks (the budding yeast cell cycle network, the fission yeast cell cycle network, and the SOS network of Escherichia coli) were used as the test sets to verify the performance of this method. Numerical results show that the biological networks prefer to use the minimal networks to fulfill their functional tasks, making it possible to apply minimal network criteria in the network reconstruction process. Two scenarios were considered in the reconstruction process: generating data using different initial conditions; and generating data from knock out and over-expression experiments. In both cases, network structures are revealed faithfully in a few steps using our approach.
authors.affiliation: Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences at Peking University, Beijing 100871, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Shao
authors.affiliation: School of Physics and the State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Peking University, Beijing 100871, China.
authors.forename: Jiayi
authors.initials: J
authors.lastname: Wu
authors.affiliation: Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences at Peking University, Beijing 100871, China.
authors.forename: Binghui
authors.initials: B
authors.lastname: Tian
authors.affiliation: Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences at Peking University, Beijing 100871, China; School of Physics and the State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Peking University, Beijing 100871, China. Electronic address: qi@pku.edu.cn.
authors.forename: Qi
authors.initials: Q
authors.lastname: Ouyang
mesh_terms: D002453:Cell Cycle; D004926:Escherichia coli / Q000166:cytology; D008954:Models, Biological; D012568:Schizosaccharomyces / Q000166:cytology; D049490:Systems Biology
keywords: Biological network; Boolean mathematics; Minimum network; Reverse engineering