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Bioinformatics Advance Access originally published online on June 18, 2008
Bioinformatics 2008 24(16):1779-1786; doi:10.1093/bioinformatics/btn309
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Predicting sub-Golgi localization of type II membrane proteins

A. D. J. van Dijk 1, D. Bosch 2, C. J. F. ter Braak 3, A. R. van der Krol 2 and R. C. H. J. van Ham 1,*

1Applied Bioinformatics, 2Metabolic Regulation, PRI, Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen and 3Biometris, PRI, Wageningen UR, Bornsesteeg 47, 6708 PD Wageningen, The Netherlands

*To whom correspondence should be addressed.


  Abstract

Motivation: Recent research underlines the importance of finegrained knowledge on protein localization. In particular, subcompartmental localization in the Golgi apparatus is important, for example, for the order of reactions performed in glycosylation pathways or the sorting functions of SNAREs, but is currently poorly understood.

Results: We assemble a dataset of type II transmembrane proteins with experimentally determined sub-Golgi localizations and use this information to develop a predictor based on the transmembrane domain of these proteins, making use of a dedicated proteinstructure based kernel in an SVM. Various applications demonstrate the power of our approach. In particular, comparison with a large set of glycan structures illustrates the applicability of our predictions on a ‘glycomic’ scale and demonstrates a significant correlation between sub-Golgi localization and the ordering of different steps in glycan biosynthesis.

Contact: roeland.vanham{at}wur.nl

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Burkhard Rhost

Received on March 28, 2008; revised on June 9, 2008; accepted on June 11, 2008

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