Predicting sub-Golgi localization of type II membrane proteins

A.D.J. van Dijk, H.J. Bosch, C.J.F. ter Braak, A.R. van der Krol, R.C.H.J. van Ham

Research output: Contribution to journalArticleAcademicpeer-review

36 Citations (Scopus)


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
Original languageEnglish
Pages (from-to)1779-1786
Issue number16
Publication statusPublished - 2008


  • subcellular-localization
  • transmembrane domains
  • lipid-bilayers
  • pathway
  • system
  • model
  • glycosyltransferases
  • glycosylation
  • retention
  • selection


Dive into the research topics of 'Predicting sub-Golgi localization of type II membrane proteins'. Together they form a unique fingerprint.

Cite this