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[go-helpdesk] membrane v plasma membrane

Susan Tweedie sart2 at gen.cam.ac.uk
Thu Jun 21 03:51:30 PDT 2012


Dear Christian

Thank you for contacting the GO Consortium with your question.

Your understanding is correct. Plasma membrane is a more specific type  
of membrane (an is_a child term of membrane) so all proteins annotated  
with plasma membrane are inferred from the hierarchy to be associated  
with membrane.

I am not sure what tool you used to do your analysis so it is  
difficult to trouble-shoot the problem without more information.  
However this situation could arise if the method you are using is only  
considering direct annotations with these terms rather than making use  
of the hierarchy to infer annotations to the parental terms. The  
underlying database of associations between terms and proteins  
contains only those that have been made directly to a specific term -  
the inferences from the hierarchy are not explicitly listed.

So if you search with one of your proteins associated with plasma  
membrane and view the associations you would expect to find at least  
one entry with plasma membrane but there may not be any direct  
annotations with membrane. However if you use tools such as our Term  
Enrichment or GO slimmer to analyze your proteins then the hierarchy  
will be taken into account.

If that doesn't answer your question please get back to us.

Best wishes,

Susan Tweedie


On 21 Jun 2012, at 21/Jun/2012 10:27:09, go-helpdesk-bounces at lists.stanford.edu 
  wrote:

>
> From: christian.moritz at biologie.uni-kl.de
> Date: 21 June 2012 10:07:06 BST
> To: go-helpdesk at mailman.stanford.edu
> Subject: GO Help query (from website)
>
>
>
> Email: christian.moritz at biologie.uni-kl.de
> Name: Annotation (from Christian Moritz)
> Text: Dear GO team,
> I have a (perhaps rather basic) question on the terms.
> In my analysis of a protein set, 125 out of about 600 ptoteins  
> belong to the term "plasma membrane". But only 59 out of the 600  
> belong to the term "membrane".
> Now I'm wondering how the hierarchy works: shouldn't all plasma  
> membrane proteine be included in membrane? Or do I have to add the 2  
> numbers to get the complete number of membrane proteins?
>
> To understand this would help me alot.
> Thanks and best regards,
> Christian
>
>
>

Susan Tweedie
FlyBase GO curator

s.tweedie at gen.cam.ac.uk



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