MitoMiner, an integrated database for the storage and analysis of mitochondrial proteomics data.
MitoMiner, an integrated database for the storage and analysis of mitochondrial proteomics data.
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DOI：
10.1074/mcp.m800373-mcp200
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发表时间：
2009-06
期刊：
影响因子：
--
通讯作者：
Robinson AJ
中科院分区：
文献类型：
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作者：
Smith AC;Robinson AJ
线粒体是真核细胞的重要组成部分，其功能超出能量产生，包括代谢，信号传导，细胞生长和凋亡。它们的功能障碍与大量的代谢、退行性和年龄相关的人类疾病有关。因此，重要的是要表征和理解的微扰子。许多实验试图定义线粒体蛋白质组，导致难以分析的大型复杂数据集。为了解决这个问题，我们开发了一个新的公共资源来存储和研究这种线粒体蛋白质组学数据，称为MitoMiner，它使用一个模型来描述蛋白质组学数据和相关的生物信息。导入来自质谱和绿色荧光蛋白标记实验的33篇出版物的蛋白质组学数据，并将其与来自UniProt和基因组计划的蛋白质注释、来自京都基因和基因组百科全书的代谢途径数据、来自HomoloGene的同源关系、我们通过调查这些数据集证明了MitoMiner的优势，并表明，已报道的不同线粒体蛋白的数量约为3700种，尽管动物和酵母共有的蛋白的数量约为1400种，并且膜蛋白似乎代表不足。此外，分析表明，在线粒体蛋白质组学实验中经常检测到一些细胞溶质代谢途径的酶，这表明它们与线粒体外膜的外部相关。MitoMiner的数据和先进功能为进一步的线粒体分析和线粒体生理学的未来系统级建模提供了框架。
Mitochondria are a vital component of eukaryotic cells with functions that extend beyond energy production to include metabolism, signaling, cell growth, and apoptosis. Their dysfunction is implicated in a large number of metabolic, degenerative, and age-related human diseases. Therefore, it is important to characterize and understand the mitochondrion. Many experiments have attempted to define the mitochondrial proteome, resulting in large and complex data sets that are difficult to analyze. To address this, we developed a new public resource for the storage and investigation of this mitochondrial proteomics data, called MitoMiner, that uses a model to describe the proteomics data and associated biological information. The proteomics data of 33 publications from both mass spectrometry and green fluorescent protein tagging experiments were imported and integrated with protein annotation from UniProt and genome projects, metabolic pathway data from Kyoto Encyclopedia of Genes and Genomes, homology relationships from HomoloGene, and disease information from Online Mendelian Inheritance in Man. We demonstrate the strengths of MitoMiner by investigating these data sets and show that the number of different mitochondrial proteins that have been reported is about 3700, although the number of proteins common to both animals and yeast is about 1400, and membrane proteins appear to be underrepresented. Furthermore analysis indicated that enzymes of some cytosolic metabolic pathways are regularly detected in mitochondrial proteomics experiments, suggesting that they are associated with the outside of the outer mitochondrial membrane. The data and advanced capabilities of MitoMiner provide a framework for further mitochondrial analysis and future systems level modeling of mitochondrial physiology.