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
