Cakmak Ali, Qi Xinjian, Cicek A Ercument, Bederman Ilya, Henderson Leigh, Drumm Mitchell, Ozsoyoglu Gultekin
Department of Electrical Engineering and Computer Science, Case Western Reserve University, 10900 Euclid Ave. Cleveland, OH 44106, USA.
J Bioinform Comput Biol. 2012 Feb;10(1):1240003. doi: 10.1142/S0219720012400033.
With the recent advances in experimental technologies, such as gas chromatography and mass spectrometry, the number of metabolites that can be measured in biofluids of individuals has markedly increased. Given a set of such measurements, a very common task encountered by biologists is to identify the metabolic mechanisms that lead to changes in the concentrations of given metabolites and interpret the metabolic consequences of the observed changes in terms of physiological problems, nutritional deficiencies, or diseases. In this paper, we present the steady-state metabolic network dynamics analysis (SMDA) approach in detail, together with its application in a cystic fibrosis study. We also present a computational performance evaluation of the SMDA tool against a mammalian metabolic network database. The query output space of the SMDA tool is exponentially large in the number of reactions of the network. However, (i) larger numbers of observations exponentially reduce the output size, and (ii) exploratory search and browsing of the query output space is provided to allow users to search for what they are looking for.
随着实验技术的最新进展，如气相色谱法和质谱分析法，个体生物流体中可测量的代谢物数量显著增加。给定一组这样的测量数据，生物学家经常遇到的一项任务是确定导致给定代谢物浓度变化的代谢机制，并根据生理问题、营养缺乏或疾病来解释观察到的变化的代谢后果。在本文中，我们详细介绍了稳态代谢网络动力学分析（SMDA）方法及其在囊性纤维化研究中的应用。我们还针对哺乳动物代谢网络数据库对SMDA工具进行了计算性能评估。SMDA工具的查询输出空间在网络反应数量上呈指数级增长。然而，（i）更多的观测值会以指数方式减小输出大小，并且（ii）提供了对查询输出空间的探索性搜索和浏览功能，以允许用户搜索他们想要查找的内容。
