SUBA: The Arabidopsis subcellular database
SUBA: The Arabidopsis subcellular database
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DOI：
10.1093/nar/gkl863
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发表时间：
2007-01-01
影响因子：
14.9
通讯作者：
Millar, A. Harvey
中科院分区：
文献类型：
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作者：
Heazlewood, Joshua L.;Verboom, Robert E.;Millar, A. Harvey
蛋白质定位的知识有助于我们理解蛋白质功能和生物学相互关系。目前正在使用各种实验方法来产生需要以综合方式提供的定位数据。嵌合荧光融合蛋白已被用于定义亚细胞定位，至少有1100个相关的实验在拟南芥中完成。最近，许多研究采用质谱进行蛋白质组学调查的亚细胞成分在拟南芥产生定位信息类似于2600蛋白质。进一步的蛋白质定位信息可以从其他参考文献中获得，以分析位置（AmiGO：类似于900种蛋白质）、来自Swiss-Prot注释的位置信息（类似于2000种蛋白质）;以及从基因描述推断的位置（类似于2700种蛋白质）。此外，越来越多的可用软件提供基于氨基酸序列的蛋白质的位置预测信息。我们已着手将这些不同的数据源整合在一起来构建SUBA，这是一个拟南芥蛋白质的亚细胞定位数据库。SUBA中的定位数据包括10个不同的亚细胞位置，> 6743个非冗余蛋白质，并且代表了在负责51%的拟南芥表达序列标签的转录物中编码的蛋白质。SUBA数据库提供了一个强有力的手段，通过它来评估蛋白质亚细胞定位在拟南芥（http：www.suba.bcs.uwa.edu.au）。
Knowledge of protein localisation contributes towards our understanding of protein function and of biological inter-relationships. A variety of experimental methods are currently being used to produce localisation data that need to be made accessible in an integrated manner. Chimeric fluorescent fusion proteins have been used to define subcellular localisations with at least 1100 related experiments completed in Arabidopsis. More recently, many studies have employed mass spectrometry to undertake proteomic surveys of subcellular components in Arabidopsis yielding localisation information for similar to 2600 proteins. Further protein localisation information may be obtained from other literature references to analysis of locations (AmiGO: similar to 900 proteins), location information from Swiss-Prot annotations (similar to 2000 proteins); and location inferred from gene descriptions (similar to 2700 proteins). Additionally, an increasing volume of available software provides location prediction information for proteins based on amino acid sequence. We have undertaken to bring these various data sources together to build SUBA, a SUBcellular location database for Arabidopsis proteins. The localisation data in SUBA encompasses 10 distinct subcellular locations, > 6743 non-redundant proteins and represents the proteins encoded in the transcripts responsible for 51% of Arabidopsis expressed sequence tags. The SUBA database provides a powerful means by which to assess protein subcellular localisation in Arabidopsis (http://www.suba.bcs.uwa.edu.au).