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Nucleic Acids Res. 2015 Jan;43(Database issue):D335-8. doi: 10.1093/nar/gku1131. Epub 2014 Nov 11.

RaftProt: mammalian lipid raft proteome database.

Author information

1
The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.
2
School of Information and Communication Technology, Griffith University, Brisbane, QLD, Australia.
3
Centre for High-Throughput Biology, University of British Columbia, British Columbia, Canada.
4
Systems Biology Laboratory, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC, Australia.
5
The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia m.hill2@uq.edu.au.

Abstract

RaftProt (http://lipid-raft-database.di.uq.edu.au/) is a database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids thought to act as dynamic signalling and sorting platforms. Given their fundamental roles in cellular regulation, there is a plethora of information on the size, composition and regulation of these membrane microdomains, including a large number of proteomics studies. To facilitate the mining and analysis of published lipid raft proteomics studies, we have developed a searchable database RaftProt. In addition to browsing the studies, performing basic queries by protein and gene names, searching experiments by cell, tissue and organisms; we have implemented several advanced features to facilitate data mining. To address the issue of potential bias due to biochemical preparation procedures used, we have captured the lipid raft preparation methods and implemented advanced search option for methodology and sample treatment conditions, such as cholesterol depletion. Furthermore, we have identified a list of high confidence proteins, and enabled searching only from this list of likely bona fide lipid raft proteins. Given the apparent biological importance of lipid raft and their associated proteins, this database would constitute a key resource for the scientific community.

PMID:
25392410
PMCID:
PMC4383944
DOI:
10.1093/nar/gku1131
[Indexed for MEDLINE]
Free PMC Article

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