MeltDB: a software platform for the analysis and integration of metabolomics experiment data
MeltDB: a software platform for the analysis and integration of metabolomics experiment data
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DOI：
10.1093/bioinformatics/btn452
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发表时间：
2008-12-01
期刊：
影响因子：
5.8
通讯作者：
Goesmann, Alexander
中科院分区：
文献类型：
--
作者：
Neuweger, Heiko;Albaum, Stefan P.;Goesmann, Alexander
动机：新陈代谢组学的最新进展创造了测量数百种代谢物水平的可能性，这些代谢物是细胞调控过程的最终产物。在能够测量代谢物的高通量仪器中，样品采集和后续分析的自动化对实验数据集的必要的系统存储和计算处理提出了挑战。尽管存在用于单个仪器和前处理方法的大量专门软件系统，但显然需要一种自由且独立于平台的系统，以允许标准化和集成地存储和分析从代谢组学实验中获得的数据。目前还没有这样的系统，一方面支持原始数据集的预处理，另一方面允许在功能基因组学环境中可视化和集成更高级别的统计分析结果。结果：为了便于代谢组学实验的系统存储、分析和集成，我们实现了基于Web的代谢组学实验数据分析和注释软件平台MeltDB。MeltDB支持开放。LE格式(netCDF、mzXML、mzDATA)，并便于集成和评估现有的预处理方法。该系统为研究人员提供了一致地描述和存储他们的实验数据集的方法。代谢组学数据集的全面分析和可视化功能通过基于Web的用户界面提供给社区。该系统涵盖了在基于知识的背景下从原始数据到结果可视化的过程，并被整合到比勒费尔德大学现有的基因组学和转录学软件平台的背景下。我们通过一个样本实验展示了MeltDB的潜力，在这个实验中，我们剖析了三种不同碳源对革兰氏阴性菌野油菜黄单胞菌的影响。菜籽上测得的代谢物水平。实验数据在MeltDB中存储、分析和注释，并可通过公共MeltDB Web服务器访问。
Motivation: The recent advances in metabolomics have created the potential to measure the levels of hundreds of metabolites which are the end products of cellular regulatory processes. The automation of the sample acquisition and subsequent analysis in high-throughput instruments that are capable of measuring metabolites is posing a challenge on the necessary systematic storage and computational processing of the experimental datasets. Whereas a multitude of specialized software systems for individual instruments and preprocessing methods exists, there is clearly a need for a free and platform-independent system that allows the standardized and integrated storage and analysis of data obtained from metabolomics experiments. Currently there exists no such system that on the one hand supports preprocessing of raw datasets but also allows to visualize and integrate the results of higher level statistical analyses within a functional genomics context.Results: To facilitate the systematic storage, analysis and integration of metabolomics experiments, we have implemented MeltDB, a web-based software platform for the analysis and annotation of datasets from metabolomics experiments. MeltDB supports open. le formats (netCDF, mzXML, mzDATA) and facilitates the integration and evaluation of existing preprocessing methods. The system provides researchers with means to consistently describe and store their experimental datasets. Comprehensive analysis and visualization features of metabolomics datasets are offered to the community through a web-based user interface. The system covers the process from raw data to the visualization of results in a knowledge-based background and is integrated into the context of existing software platforms of genomics and transcriptomics at Bielefeld University. We demonstrate the potential of MeltDB by means of a sample experiment where we dissect the influence of three different carbon sources on the gram-negative bacterium Xanthomonas campestris pv. campestris on the level of measured metabolites. Experimental data are stored, analyzed and annotated within MeltDB and accessible via the public MeltDB web server.