MSEA: metabolite set enrichment analysis in the MeltDB metabolomics software platform: metabolic profiling of Corynebacterium glutamicum as an example
MSEA: metabolite set enrichment analysis in the MeltDB metabolomics software platform: metabolic profiling of Corynebacterium glutamicum as an example
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DOI：
10.1007/s11306-011-0311-6
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发表时间：
2012-04-01
期刊：
影响因子：
3.6
通讯作者：
Neuweger, Heiko
中科院分区：
文献类型：
--
作者：
Persicke, Marcus;Rueckert, Christian;Neuweger, Heiko
基因集富集分析（GSEA）已成功地应用于转录组学和蛋白质组学研究超过5年。我们将一种改进的GSEA方法应用于代谢组学，称为代谢物集富集分析（MSEA），并将该方法集成到MeltDB平台中。与新的集成功能，我们评估代谢组学研究的方法的适用性，通过分析工业氨基酸生产菌株谷氨酸棒杆菌的代谢谱。代谢物集是从KEGG和新创建的CglCyc数据库中定义的代谢途径获得的。在使用MSEA的第一个实验中，代谢谱分析比较了葡萄糖和乙酸盐生长的菌株，并且在第二个实验中，比较了碳流从赖氨酸途径逐步转移到分支苏氨酸、异亮氨酸和甲硫氨酸途径的生产菌株系列。通过识别代谢谱的变化，MSEA能够识别在利用不同碳源或经遗传修饰的碳源时激活的代谢途径。所呈现的实验结果可在http://meltdb.cebitec.unibielefeld.de公开获得。
Gene set enrichment analysis (GSEA) has been successfully employed in transcriptomics and proteomics research for over 5 years. We have applied a modified GSEA approach to metabolomics, called metabolite set enrichment analysis (MSEA), and have integrated this method into the MeltDB platform. With the novel integrated functionality, we evaluate the applicability of the approach for metabolomics research by analyzing the metabolic profiles of industrial amino acid producer strains of Corynebacterium glutamicum. Metabolite sets are obtained from metabolic pathways defined in the KEGG and the newly created CglCyc databases. In the first experiment using MSEA, the metabolic profiling analyses compared glucose- and acetate-grown strains, and, in the second, a production strain series in which the carbon flow is shifted step-wise from the lysine pathway to the branching threonine, isoleucine, and methionine pathways. By identifying changes of the metabolic profile MSEA was able to identify the metabolic pathways activated while utilizing different carbon sources or those that have been genetically modified. The presented experimental results are publicly available at http://meltdb.cebitec.unibielefeld.de.