Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

    We have a manual that explains all the features 

Record number 368220
Title Predicting sub-Golgi localization of type II membrane proteins
Author(s) Dijk, A.D.J. van; Bosch, H.J.; Braak, C.J.F. ter; Krol, A.R. van der; Ham, R.C.H.J. van
Source Bioinformatics 24 (2008)16. - ISSN 1367-4803 - p. 1779 - 1786.
DOI https://doi.org/10.1093/bioinformatics/btn309
Department(s) PRI BIOS Applied Bioinformatics
PRI Bioscience
Biometris (WU MAT)
PRI Biometris
Laboratory of Plant Physiology
Bioinformatics
EPS-1
Publication type Refereed Article in a scientific journal
Publication year 2008
Keyword(s) subcellular-localization - transmembrane domains - lipid-bilayers - pathway - system - model - glycosyltransferases - glycosylation - retention - selection
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
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