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Curator prediction of NOT kinase activity

jyoti khadake jyoti at ebi.ac.uk
Wed Mar 8 04:08:55 PST 2006


Hi,

In this particular instance would the reference which identifies 
residues important for the kinase activity in members of the family be 
the appropriate reference?

JK

Midori Harris wrote:

>The reference has to identify the source of the information. In this case,
>it comes from what the curator knows, and from the work she did examining
>the protein sequence. So I don't think the protein ID would suffice,
>because it would capture nothing of the curator's involvement. The
>advantage of a GO_REF is that we could include everything the curator did,
>and make it unambiguous ... but it's not for me to decide whether that
>advantage outweighs the problems (btw, what are the arguments against a
>GO_REF?)
>
>m
>
>On Wed, 8 Mar 2006, Emily Dimmer wrote:
>
>  
>
>>So if using the ISS code with these kinds of annotations, what reference 
>>information should be provided? Should the reference field refer back to 
>>the protein's identifier? Or to a specific GO_REF (which isn't ideal)
>>e.g.
>>UniProt     P12345      GO:0004672      UniProt:P12345     ISS   F   
>>protein    taxon:9606 20060308       UniProt
>>
>>Midori Harris wrote:
>>
>>    
>>
>>>The documentation for ISS says that it can be used for predicted or 
>>>observed sequence features, and that in such cases the 'with' field can be 
>>>left blank. If we choose to regard altered 'active' site residues as 
>>>features -- which seems reasonable -- ISS will work.
>>>
>>>Also, using IC would not solve the reference problem, so you would still 
>>>have to either (a) make a GO_REF entry or (b) think of something else to 
>>>use as the reference.
>>>
>>>m
>>>
>>>On Wed, 8 Mar 2006, Evelyn Camon wrote:
>>>
>>> 
>>>
>>>      
>>>
>>>>ok..so sequence similar to what?? the sequence/domain for the active 
>>>>kinase??? or could we have Inferred by Curator from Sequence (ICS??)..hmmm
>>>>
>>>>Ev
>>>>
>>>>Valerie Wood wrote:
>>>>   
>>>>
>>>>        
>>>>
>>>>>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
>>>>>>       
>>>>>>
>>>>>>            
>>>>>>
>>>>>     
>>>>>
>>>>>          
>>>>>
>>>>-- 
>>>>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
>>>>
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>> 
>>>
>>>      
>>>
>>    
>>
>
>  
>

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