基元模式分析在生物网络和途径分析中的应用

Applications of elementary mode analysis in biological network and pathway analysis

摘要:

基元模式分析是应用最广泛的代谢途径分析方法。基元模式分析的研究对象从代谢网络发展到信号传导网络；研究尺度从细胞到生物反应器，甚至生态系统；数学描述从稳态分解到动态解析；研究领域从微生物代谢到人类疾病。以下综述了基元模式分析的算法和软件开发现状，以及其在代谢途径与鲁棒性、代谢通量分解、稳态代谢通量分析、动态模型与生物过程模拟、网络结构与调控、菌株设计和信号传导网络等方面的应用。开发新的算法解决组合爆炸问题，探索基元模式与代谢调控的关系以及提高菌株设计算法效率是今后基元模式的重要发展方向。

Abstract:

Elementary mode analysis is the widely applied tool in metabolic pathway analysis. Studies based on elementary mode analysis (EMA) were performed for both metabolic network and signal transduction network. Its analytical objective is from cell to bioreactor, and even ecological system. EMA is available to describe biological behaviors by steady state and dynamic models. Not only microorganism metabolism but also human health could be evaluated by EMA. The algorithms and software for calculating elementary mode (EM) were analyzed. The applications of EMA are reviewed such as special metabolic pathway and robustness of metabolic network, metabolic flux decomposition, metabolic flux analysis at steady state, dynamic model and bioprocess simulation, network structure and regulation, strain design and signal transduction network. Solving combinatorial explosion, exploring the relations between EM and metabolic regulation, and improving the algorithm efficiency of strain design are important issues of EMA in future.