期刊论文详细信息
BioData Mining
DAPPER: a data-mining resource for protein-protein interactions
Syed Haider1  Zoltan Lipinszki4  Marcin R. Przewloka4  Yaseen Ladak2  Pier Paolo D’Avino3  Yuu Kimata4  Pietro Lio’1  David M. Glover4 
[1] Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK
[2] Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
[3] Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
[4] Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
关键词: Drosophila melanogaster;    Data-integration;    Mass spectrometry;    Protein complexes;    Protein-protein interactions;    Proteomics data mining;   
Others  :  1226352
DOI  :  10.1186/s13040-015-0063-3
 received in 2015-04-25, accepted in 2015-09-16,  发布年份 2015
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【 摘 要 】

Background

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.

Results

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.

Conclusions

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.

【 授权许可】

   
2015 Haider et al.

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