MetAssimulo: simulation of realistic NMR metabolic profiles.
MetAssimulo: simulation of realistic NMR metabolic profiles.
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DOI：
10.1186/1471-2105-11-496
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发表时间：
2010-10-06
影响因子：
3
通讯作者：
Ebbels TM
中科院分区：
文献类型：
--
作者：
Muncey HJ;Jones R;De Iorio M;Ebbels TM
探索遗传和环境相互作用的复杂融合、代谢谱（或代谢组学/代谢组学）以及代谢反应中涉及的小分子的研究，是一个快速扩展的“组学”领域。捕获代谢物数据的主要技术是 1H-NMR 光谱，它会产生高度复杂的谱图，需要复杂的统计分析方法。然而，实验数据难以控制且获取成本昂贵。因此，数据模拟是帮助算法开发的有效途径。 MetAssimulo 是一个基于 MATLAB 的软件包，开发用于模拟复杂混合物的 1H-NMR 谱，例如代谢曲线。 MetAssimulo 从代谢物标准光谱数据库中提取数据，结合用户输入的浓度信息或从人类代谢组数据库自动构建的浓度信息，能够创建包含大量具有一系列用户定义属性的代谢物的真实代谢图谱。当前的功能包括通过每种代谢物浓度的平均值和标准差指定的两组（“病例”和“对照”）的模拟。该软件能够在用户可控的水平上添加具有真实自相关结构的频谱噪声。该算法的一个关键特征是它能够模拟代谢物内和代谢物间的相关性，其分析是该领域许多技术的基础。此外，MetAssimulo 能够模拟 NMR 峰位置的变化，这些变化是由基质效应（例如 pH 差异）引起的，这种变化经常在代谢 NMR 光谱中观察到，并对统计算法提出了严峻的挑战。目前没有其他软件能够如此复杂和灵活地模拟 NMR 代谢谱。本文描述了 MetAssimulo 背后的算法，并演示了如何使用它来模拟真实的 NMR 代谢谱，从而开发和测试新的数据分析技术。 MetAssimulo 可免费用于学术用途，网址为：http://cisbic.bioinformatics.ic.ac.uk/metassimulo/。
Probing the complex fusion of genetic and environmental interactions, metabolic profiling (or metabolomics/metabonomics), the study of small molecules involved in metabolic reactions, is a rapidly expanding 'omics' field. A major technique for capturing metabolite data is 1H-NMR spectroscopy and this yields highly complex profiles that require sophisticated statistical analysis methods. However, experimental data is difficult to control and expensive to obtain. Thus data simulation is a productive route to aid algorithm development. MetAssimulo is a MATLAB-based package that has been developed to simulate 1H-NMR spectra of complex mixtures such as metabolic profiles. Drawing data from a metabolite standard spectral database in conjunction with concentration information input by the user or constructed automatically from the Human Metabolome Database, MetAssimulo is able to create realistic metabolic profiles containing large numbers of metabolites with a range of user-defined properties. Current features include the simulation of two groups ('case' and 'control') specified by means and standard deviations of concentrations for each metabolite. The software enables addition of spectral noise with a realistic autocorrelation structure at user controllable levels. A crucial feature of the algorithm is its ability to simulate both intra- and inter-metabolite correlations, the analysis of which is fundamental to many techniques in the field. Further, MetAssimulo is able to simulate shifts in NMR peak positions that result from matrix effects such as pH differences which are often observed in metabolic NMR spectra and pose serious challenges for statistical algorithms. No other software is currently able to simulate NMR metabolic profiles with such complexity and flexibility. This paper describes the algorithm behind MetAssimulo and demonstrates how it can be used to simulate realistic NMR metabolic profiles with which to develop and test new data analysis techniques. MetAssimulo is freely available for academic use at http://cisbic.bioinformatics.ic.ac.uk/metassimulo/.
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HMDB：人类代谢组数据库。
影响因子：
14.9
作者：
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3
作者：
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影响因子：
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作者：
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