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Open Access Highly Accessed Database

dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation

Jinlian Wang1, Manabu Torii2, Hongfang Liu3, Gerald W Hart4 and Zhang-Zhi Hu1*

Author Affiliations

1 Department of Oncology, Georgetown University Medical Center, 3300 Whitehaven Street, Suite 1200, NW, Washington, DC 20007, USA

2 ISIS Center, Georgetown University Medical Center, 2115 Wisconsin Avenue, Suite 603, Washington, DC 20007, USA

3 Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University Medical Center, 4000 Reservoir Road, Building D, Suite 180, NW, Washington, DC 20057, USA

4 Biological Chemistry, School of Medicine, Johns Hopkins University, 725 N. Wolfe Street, 515 WBSB, Baltimore, MD 21205, USA

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BMC Bioinformatics 2011, 12:91  doi:10.1186/1471-2105-12-91

Published: 6 April 2011

Abstract

Background

Protein O-GlcNAcylation (or O-GlcNAc-ylation) is an O-linked glycosylation involving the transfer of β-N-acetylglucosamine to the hydroxyl group of serine or threonine residues of proteins. Growing evidences suggest that protein O-GlcNAcylation is common and is analogous to phosphorylation in modulating broad ranges of biological processes. However, compared to phosphorylation, the amount of protein O-GlcNAcylation data is relatively limited and its annotation in databases is scarce. Furthermore, a bioinformatics resource for O-GlcNAcylation is lacking, and an O-GlcNAcylation site prediction tool is much needed.

Description

We developed a database of O-GlcNAcylated proteins and sites, dbOGAP, primarily based on literature published since O-GlcNAcylation was first described in 1984. The database currently contains ~800 proteins with experimental O-GlcNAcylation information, of which ~61% are of humans, and 172 proteins have a total of ~400 O-GlcNAcylation sites identified. The O-GlcNAcylated proteins are primarily nucleocytoplasmic, including membrane- and non-membrane bounded organelle-associated proteins. The known O-GlcNAcylated proteins exert a broad range of functions including transcriptional regulation, macromolecular complex assembly, intracellular transport, translation, and regulation of cell growth or death. The database also contains ~365 potential O-GlcNAcylated proteins inferred from known O-GlcNAcylated orthologs. Additional annotations, including other protein posttranslational modifications, biological pathways and disease information are integrated into the database. We developed an O-GlcNAcylation site prediction system, OGlcNAcScan, based on Support Vector Machine and trained using protein sequences with known O-GlcNAcylation sites from dbOGAP. The site prediction system achieved an area under ROC curve of 74.3% in five-fold cross-validation. The dbOGAP website was developed to allow for performing search and query on O-GlcNAcylated proteins and associated literature, as well as for browsing by gene names, organisms or pathways, and downloading of the database. Also available from the website, the OGlcNAcScan tool presents a list of predicted O-GlcNAcylation sites for given protein sequences.

Conclusions

dbOGAP is the first public bioinformatics resource to allow systematic access to the O-GlcNAcylated proteins, and related functional information and bibliography, as well as to an O-GlcNAcylation site prediction tool. The resource will facilitate research on O-GlcNAcylation and its proteomic identification.