SUB-cellular location database for Arabidopsis proteins

The SUB-cellular location database for Arabidopsis proteins (SUBA) provides a powerful tool to investigate subcellular localisation in Arabidopsis through the unification of disparate datasets and through the provision of a web accessible interface for the construction of powerful user based queries resulting in a one-stop-shop for protein localisation in this model plant. Subcellular localisation information can contribute towards our understanding of protein function, protein redundancy and of biological inter-relationships. While a variety of technologies are currently employed to determine the sub-cellular location of proteins much of this information is not available in an integrated manner. In an attempt to get a clearer picture of their experimental data and to more generally understand subcellular partitioning we have brought together various data sources to build SUBA. The database has a web accessible interface that allows advanced combinatorial queries to be undertaken on the contained data.
SUBA houses large scale proteomic data sets and GFP localisation from cellular compartments of Arabidopsis. It also contains precompiled bioinformatic predictions for protein subcellular localisations. With the upgrade to SUBA3, protein-protein-interaction data was added and more recently a classification algorithm SUBAcon was integrated for forming a localisation consensus call. SUBA was last updated in June 2014 and is based on the TAIR10 genome annotation release. The experimental data sets are generally updated annually mid year.
SUBA3 in January 2015 contains 4725 entries based on chimeric fusion studies (GFP), comprising 2987 distinct proteins from 1414 publications as well as 27601 entries based on subcellular proteomic studies, comprising 8787 distinct proteins from 143 publications. There are 27385 protein-protein-interaction pairs stored in SUBA3.

拟南芥蛋白质亚细胞定位数据库（SUB-cellular location database for Arabidopsis proteins，简称SUBA）通过整合异质数据集，并提供网页可访问的交互界面以支持用户开展高级查询，为研究拟南芥的蛋白质亚细胞定位提供了强有力的工具，成为该模式植物蛋白质定位研究的一站式服务平台。
亚细胞定位信息有助于我们理解蛋白质功能、蛋白质冗余性以及生物间相互关系。尽管当前已采用多种技术测定蛋白质的亚细胞定位，但多数此类信息尚未以整合形式公开。为了更清晰地梳理实验数据并更全面地理解亚细胞分区机制，研究团队整合了多类数据源构建了SUBA数据库。该数据库配备网页访问界面，支持对库内数据进行高级组合查询。
SUBA收录了大规模蛋白质组数据集以及拟南芥细胞组分的绿色荧光蛋白（Green Fluorescent Protein，GFP）定位数据，同时还包含预先编译完成的蛋白质亚细胞定位生物信息学预测结果。在升级至SUBA3版本时，数据库新增了蛋白质-蛋白质相互作用数据；近期还集成了分类算法SUBAcon，以生成定位一致性判定结果。SUBA最近一次更新于2014年6月，其数据基于TAIR10基因组注释版本发布；实验数据集通常于每年年中进行更新。
截至2015年1月，SUBA3共包含4725条基于嵌合融合研究（绿色荧光蛋白，Green Fluorescent Protein，GFP）的条目，涵盖来自1414篇文献的2987个独特蛋白质；同时包含27601条基于亚细胞蛋白质组学研究的条目，涵盖来自143篇文献的8787个独特蛋白质。SUBA3中共存储了27385对蛋白质-蛋白质相互作用数据对。