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Bioinformatics Vol. 18 no. 8 2002
Pages 1109-1115
© 2002 Oxford University Press

Prediction of Golgi Type II membrane proteins based on their transmembrane domains

Zheng Yuan 1,2 and Rohan D. Teasdale 1,*

1 Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, and
2 Department of Mathematics, University of Queensland, St Lucia, 4072, Australia

Received on December 14, 2001 ; revised on January 30, 2002 ; accepted on February 19, 2002

Motivation: A major issue in cell biology today is how distinct intracellular regions of the cell, like the Golgi Apparatus, maintain their unique composition of proteins and lipids. The cell differentially separates Golgi resident proteins from proteins that move through the organelle to other subcellular destinations. We set out to determine if we could distinguish these two types of transmembrane proteins using computational approaches.

Results: A new method has been developed to predict Golgi membrane proteins based on their transmembrane domains. To establish the prediction procedure, we took the hydrophobicity values and frequencies of different residues within the transmembrane domains into consideration. A simple linear discriminant function was developed with a small number of parameters derived from a dataset of Type II transmembrane proteins of known localization. This can discriminate between proteins destined for Golgi apparatus or other locations (post-Golgi) with a success rate of 89.3% or 85.2%, respectively on our redundancy-reduced data sets.

Availability: See http://microarray.imb.uq.edu.au/golgi/

Contact: r.teasdale{at}imb.uq.edu.au

* To whom correspondence should be addressed.


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