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Curator prediction of NOT kinase activity

Valerie Wood val at sanger.ac.uk
Wed Mar 8 03:36:16 PST 2006


I think I prefer ISS, because this is essentially a judgement which has
been made by assessing the sequence.....

Evelyn Camon wrote:
> 
> Hi,
> 
> I'm not keen on the GO_REF idea I'm afraid...could we propose that IC
> could be used without GO ID on these odd occasions...not sure what
> publication you would use though...
> 
> Ev
> 
> Sandra Orchard wrote:
> > Most kinase recognition patterns are HMMs which can only predict a
> > domain but will not tell you if it is active or not. The kinases in
> > these examples were hit by the HMMs. The only method which will give any
> > indication of activity are ProSite patterns which specifically say a
> > particular residue needs to be in a particulr position. The HMMs are
> > correct in that these are part of the kinase family, but are inactive
> > members of it, they are not false positives in that sense. This is true
> > for many different classes of enzyme.
> >
> > And I do not remove enzyme InterPro2GO annotation just because a family
> > contains a few inactive members - all the big enzyme families do and
> > they can only really be recognised by manual annotation.
> >
> > Sandra
> >
> > Valerie Wood wrote:
> >
> >> Hi Emily,
> >>
> >> A few comments which may be relevant:
> >>
> >> Out of interest, which protein kinase family is this (i.e. which
> >> Interpro domain). Is it a family where some (but not all) members are
> >> protein kinases, in
> >> which case the mapping should be removed?
> >>
> >> Alternatively, if this appears to be a spurious hit, instead of adding a
> >> NOT annotation, you can get spurious matches suppressed by Interpro as
> >> false positives (I often do this for S. pombe).
> >>
> >> Or, could it be a sequencing or gene predicition error?
> >>
> >>
> >>
> >> Val
> >>
> >>
> >> Midori Harris wrote:
> >>
> >>
> >>> Hi,
> >>>
> >>> I think there's no doubt whatsoever that this information should be
> >>> captured. The question is what to put for reference and evidence. The
> >>> best
> >>> evidence code is probably TAS, although one could possibly also make a
> >>> case for ISS (note that IC is restricted to inferences from other GO
> >>> annotations, so isn't suitable).
> >>>
> >>> For a reference, one possibility is to add an item to the GO_REF
> >>> collection; then there would be an ID to plug into the file.
> >>>
> >>> m
> >>>
> >>> On Wed, 8 Mar 2006, Emily Dimmer wrote:
> >>>
> >>>
> >>>
> >>>> Hi,
> >>>>
> >>>> One of our annotators, who is an expert on protein kinases, has looked
> >>>> at the sequence of a putative protein kinase and from noticing a couple
> >>>> of amino acids changes at its active site, has predicted that it does
> >>>> not possess any kinase activity - she did not use any software and
> >>>> there
> >>>> is no published work on this protein.
> >>>> Do you think this type of annotation should be represented in GO (we
> >>>> feel this annotation is of high quality and adds valuable
> >>>> information to
> >>>> a protein which has not yet been characterized), and if so how should
> >>>> this annotation be shown?
> >>>>
> >>>> Thanks,
> >>>> Emily
> >>>>
> >>>>
> >>>
> >>
> >>
> >>
> >
> 
> --
> Evelyn Camon
> GOA Coordinator
> Senior Scientific Curator
> European Bioinformatics Institute
> Tel:01223-494465
> Fax:01223-494468
> E-mail: camon at ebi.ac.uk
> URL: http://www.ebi.ac.uk/goa

-- 
----------------------------------------------------------------------------------
Valerie Wood		       Tel: 01223 494954
S. pombe Genome Project	       Fax: 01223 494919 		       
The Sanger Institute           email: val at sanger.ac.uk
Wellcome Trust Genome Campus   http://www.sanger.ac.uk/Projects/S_pombe 
Cambridge                      
CB10 1SA



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