Skip Navigation



Bioinformatics Advance Access published online on June 18, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn309
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrow All Versions of this Article:
24/16/1779    most recent
btn309v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Dijk, A.D.J. v.
Right arrow Articles by Ham, R. C. H. J. v.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Dijk, A.D.J. v.
Right arrow Articles by Ham, R. C. H. J. v.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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,*

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

*To whom correspondence should be addressed. Dr. R. C. H. J. van Ham, E-mail: roeland.vanham{at}wur.nl


  Abstract

Motivation: Recent research underlines the importance of fine-grained knowledge on protein localization. In particular, sub-compartmental 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 protein-structure 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

Associate Editor: Prof. Burkhard Rost

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.