Announcement: Prediction of Mucin type O-glycosylation sites, NetOglyc version 2.0

Ian McFarlane I.McFarlane at icrf.icnet.uk
Fri May 16 12:25:50 EST 1997


Jan Have you any comment on the fact that there appears to be a family of
GalNAc Ts involved on O-glycosylation? Can your neural net give any info
on the possible specificites of the different transferase?

Ian Mc

In article <337C4DEE.41C6 at cbs.dtu.dk>, Jan Hansen <janhan at cbs.dtu.dk> wrote:

> Prediction of Mucin type O-glycosylation sites, NetOglyc version 2.0:
> 
> NetOglyc is a neural network algorithm recognizing Mucin type 
> O-glycosylation sites in mammalian proteins.
> 
> The method have been updated with increased performance.
> 
> The method is available at:
> http://www.cbs.dtu.dk/services/NetOGlyc/
> 
> both as a mail and www server.
> 
> The in vivo glycosylations sites used for making the method is
> listed in O-GLYCBASE available at:
> http://www.cbs.dtu.dk/databases/OGLYCBASE/
> 
> Abstract:
> 
> The specificities of the UDP-GalNAc:polypeptide
> N-acetylgalactosaminyltransferase family which links the carbohydrate
> GalNAc to the side chain of certain  serine and threonine residues in
> mucin type glycoproteins are presently unknown. The specificity seems
> to be modulated by sequence context,  secondary structure and surface
> accessibility.  The  sequence context  of glycosylated threonines was
> found to  differ from  that of serine, and  the sites  were  found to
> cluster.  Non-clustered  sites had a sequence context different  from 
> that  of  clustered  sites.  Charged  residues  were  disfavoured  at 
> position -1 and +3.  A jury of artificial neural networks was trained 
> to recognize  the sequence context  and surface  accessibility of 299 
> known and verified mucin type  O-glycosylation sites  extracted  from 
> O-GLYCBASE. The  cross-validated NetOglyc  network  system  correctly 
> found  83 % of  the  glycosylated  and  90 %  of the non-glycosylated 
> serine and threonine residues in independent test sets,  thus proving 
> more accurate than matrix statistics and vector projection methods.
> 
> -- 
> Jan Hansen
> 
> Center for Biological Sequence Analysis
> Department of Physical Chemistry
> The Technical University of Denmark
> Building 206
> DK-2800 Lyngby
> Denmark
> 
> Phone:  +45 4525 2485 
> Fax:    +45 4593 4808
> E-mail: janhan at cbs.dtu.dk
> WWW:    http://www.cbs.dtu.dk/janhan/homepage.html



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