DAPPER: a data-mining resource for protein-protein interactions.
DAPPER: a data-mining resource for protein-protein interactions.
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DOI：
10.1186/s13040-015-0063-3
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发表时间：
2015
期刊：
影响因子：
4.5
通讯作者：
Glover DM
中科院分区：
文献类型：
--
作者：
Haider S;Lipinszki Z;Przewloka MR;Ladak Y;D'Avino PP;Kimata Y;Lio' P;Glover DM
蛋白质和复合物之间的相互作用网络的识别，提供了新的见解，调节许多生物过程的分子机制的承诺。随着此类数据集的数量不断增加，特别是在模式生物（如果蝇）中，迫切需要能够无缝收集、整合和分析这些数据的专业工具。在这里，我们描述了一个数据库，再加上挖掘工具的蛋白质-蛋白质相互作用（DAPPER），开发作为一个丰富的资源，研究多蛋白质复合物在果蝇。这个蛋白质组学数据库是通过对从果蝇组织和培养细胞中亲和纯化的许多蛋白质复合物进行质谱分析而编制的。通过BioMart软件的加速版本提供对DAPPER的网络访问，通过定制的查询和输出格式实现数据挖掘。蛋白质-蛋白质相互作用数据集使用FlyBase标识符进行注释，并使用BioMart的数据联合模型进一步链接到Ensembl数据库，从而实现复杂的多数据集查询。DAPPER是开源的，其所有内容和源代码都可以免费获得。DAPPER提供了一个易于导航和可扩展的平台，用于实时集成包含新的和现有的果蝇蛋白质-蛋白质相互作用数据集的各种资源。本文的在线版本（doi：10.1186/s13040-015-0063-3）包含补充材料，可供授权用户使用。
The identification of interaction networks between proteins and complexes holds the promise of offering novel insights into the molecular mechanisms that regulate many biological processes. With increasing volumes of such datasets, especially in model organisms such as Drosophila melanogaster, there exists a pressing need for specialised tools, which can seamlessly collect, integrate and analyse these data. Here we describe a database coupled with a mining tool for protein-protein interactions (DAPPER), developed as a rich resource for studying multi-protein complexes in Drosophila melanogaster. This proteomics database is compiled through mass spectrometric analyses of many protein complexes affinity purified from Drosophila tissues and cultured cells. The web access to DAPPER is provided via an accelerated version of BioMart software enabling data-mining through customised querying and output formats. The protein-protein interaction dataset is annotated with FlyBase identifiers, and further linked to the Ensembl database using BioMart’s data-federation model, thereby enabling complex multi-dataset queries. DAPPER is open source, with all its contents and source code are freely available. DAPPER offers an easy-to-navigate and extensible platform for real-time integration of diverse resources containing new and existing protein-protein interaction datasets of Drosophila melanogaster. The online version of this article (doi:10.1186/s13040-015-0063-3) contains supplementary material, which is available to authorized users.