DAPPER: A data-mining resource for protein-protein interactions
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Authors
Haider, Syed
Lipinszki, Zoltan
Ladak, Yaseen
D’Avino, Pier Paolo
Lio’, Pietro
Publication Date
2015-09-24Journal Title
BioData Mining
ISSN
1756-0381
Publisher
BioMed Central
Volume
8
Number
30
Language
English
Type
Article
Metadata
Show full item recordCitation
Haider, S., Lipinszki, Z., Przewloka, M., Ladak, Y., D’Avino, P. P., Kimata, Y., Lio’, P., & et al. (2015). DAPPER: A data-mining resource for protein-protein interactions. BioData Mining, 8 (30)https://doi.org/10.1186/s13040-015-0063-3
Abstract
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 pressing need for specialised tools, which can seamlessly collect, integrate and analyse these data. Here we describe a database and 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.
Keywords
proteomics data mining, protein-protein interactions, protein complexes, mass spectrometry, data-integration, Drosophila melanogaster
Sponsorship
This work was supported financially by grants from the Cancer Research UK (CRUK), the Biotechnology and Biological Sciences Research Council and the Medical Research Council to DMG (C3/A11431, BB/I013938/1, G1001696), by a Cancer Research UK Career Development Fellowship to YK (C40697/A12874), and by Cancer Research UK grants to PPD (C12296/A8039 and C12296/A12541). ZL is on leave from the Biological Research Centre of the Hungarian Academy of Sciences (Institute of Biochemistry, Szeged, Hungary) and was supported by a Long-Term Fellowship of the Federation of European Biochemical Societies (FEBS).
Funder references
BBSRC (BB/I013938/1)
MRC (G1001696)
Cancer Research UK (12874)
Cancer Research UK (A8039)
Cancer Research UK (11431)
Identifiers
External DOI: https://doi.org/10.1186/s13040-015-0063-3
This record's URL: https://www.repository.cam.ac.uk/handle/1810/251097
Rights
Attribution 2.0 UK: England & Wales
Licence URL: http://creativecommons.org/licenses/by/2.0/uk/
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