Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

allergene annotation

Alexander Diehl adiehl at informatics.jax.org
Tue Mar 14 07:56:14 PST 2006


Jane,

What we call hypersensitivity is, in many cases, an extreme or 
disregulated immune-mediated inflammatory response.  But the mechanisms 
involved occur routinely in our bodies on a small scale with a real 
defensive function (PMID: 12860528 has a nice discussion of this).  
Because no other nomenclature exists for these processes in the 
literature, I choose to stick with the word "hypersensitivity" for lack 
of another terse description, despite its pathological connotations.

-- Alex


Jane Lomax wrote:
> LOL!
>
> Okay, okay - I take your point - the hay-fever example wasn't entirely 
> serious. Although I do remain to be convinced that there are _no_ cases 
> where inducing a hypersensitive response in another organism doesn't 
> confer some selective advantage, but I don't know enough about this 
> field and will bow to your superior knowledge ;)
>
> Out of interest (and I remember having this discussion with you before 
> Alex, I just can't remember the conclusion) what's the rationale behind 
> having GO:0016068 (type I hypersensitivity) in the ontology if all 
> hypersensitivities are disregulations?
>
> thanks,
>
> jane
>
>
>
> On Tue, 14 Mar 2006, Alexander Diehl wrote:
>
>   
>> No,
>>
>> Allergen and antigens are simply the substrates of the immune system.  
>> What makes something an allergen or an antigen is  dependent on the 
>> responding immune system, and varies by both individual and species.  A 
>> response to a particular allergen or antigen is a phenotypic quality of 
>> the responding organism.  Furthermore, allergies are far more prevalent 
>> in "western" human populations than in societies with less 
>> well-developed systems of sanitation and medicine, and thus reflect 
>> largely an inappropriate refocusing of the immune system in the absence 
>> of the threats humans faced in evolution, primarily parasites.  The 
>> suggestion that an allergen confers an advantage to plant reproduction 
>> also seems amazingly far fetched, given that the vast majority of plant 
>> pollen ends up somewhere else than up a person's nose.  Even in sneezing 
>> (if I am to pursue what may be intended facetiously here), the pollen 
>> would be primarily expelled covered in mucus and probably inactivated.
>>
>> Allergies are pathogenic disregulations of the normal "hypersensitivity" 
>> responses.  We should not be stretching the GO to become a disease 
>> ontology unless that is what we want to do with it.  If we want to make 
>> the GO into a disease ontology then let's do it officially and not on 
>> the sly.
>>
>> -- Alex
>>
>>
>> Jane Lomax wrote:
>>     
>>> I concede that the argument doesn't hold up as well for allergens as it 
>>> does for pathogenic organisms.
>>>
>>> But aren't you making a value judgement about what constitutes a 'normal' 
>>> interaction? How do we know that the fact that the plant protein induces a 
>>> hypersensitive response in another organism doesn't confer some advantage 
>>> to the plant? Perhaps hay-fever promotes the spreading of pollen?!
>>>
>>> jane
>>>
>>>
>>> On Tue, 14 Mar 2006, Alexander Diehl wrote:
>>>
>>>   
>>>       
>>>> Sorry to be a few minutes late on this.
>>>>
>>>> The function of a protein, any protein, is not to be an allergen, or 
>>>> antigen, for another organism's immune system.  This is not appropriate 
>>>> annotation at all.  Indeed, nearly any protein can be made antigenic 
>>>> when given in the right context.  The plant proteins in question may be 
>>>> known allergens, but that is not their natural role in the plant or for 
>>>> the plant.  Annotation of allergenic potential would be appropriate with 
>>>> an ontology focused on disease and pathology, but not for the GO.
>>>>
>>>> We can discuss at the meeting, but I am quite firm in my conviction here,
>>>>
>>>> Alex
>>>>
>>>>
>>>> Jane Lomax wrote:
>>>>     
>>>>         
>>>>> But I think when you're talking about interactions between organisms, 
>>>>> there really isn't a 'normal' or 'abnormal' - the interaction just 
>>>>> occurs. And remember that you'll record two taxon ids; one for the species 
>>>>> producing the allergen, and one for the 'allergic' species. So it isn't 
>>>>> the usual case of 'is it normal for the species I'm annotating' because 
>>>>> you're annotating both.
>>>>>
>>>>> jane
>>>>>
>>>>> On Tue, 14 Mar 2006, Harold Drabkin wrote:
>>>>>
>>>>>   
>>>>>       
>>>>>           
>>>>>> Yes, a new term would work much better.  However, it may or may not be 
>>>>>> the "normal " function or process.
>>>>>> A virus or symbiont host interaction is a bit different, because those 
>>>>>> interactions are most likely critical for the life cycle (eg, if you 
>>>>>> don't have a host, the virus can't replicate, etc.).  Many people are 
>>>>>> allergic to gluten, but is that a normal function/process of  gluten? 
>>>>>>
>>>>>>
>>>>>> Jane Lomax wrote:
>>>>>>     
>>>>>>         
>>>>>>             
>>>>>>> Unfortunately that term only works where one organism is living in 
>>>>>>> symbiosis with another organism (e.g. host/pathogen) which is why I 
>>>>>>> suggested that new term...
>>>>>>>
>>>>>>>
>>>>>>> On Tue, 14 Mar 2006, Harold Drabkin wrote:
>>>>>>>
>>>>>>>   
>>>>>>>       
>>>>>>>           
>>>>>>>               
>>>>>>>> But, I did find this term, and related?
>>>>>>>>
>>>>>>>> GO term: 	*induction of host defense response*
>>>>>>>> GO id: 	*GO:0044416*
>>>>>>>> Definition: 	*The elicitation by an organism of the defense response of 
>>>>>>>> the host. The host is defined as the larger of the organisms involved in 
>>>>>>>> a symbiotic interaction. *
>>>>>>>>
>>>>>>>>
>>>>>>>> which I think might be more in line with a direct annotation to 
>>>>>>>> something like this???
>>>>>>>>
>>>>>>>>
>>>>>>>> Harold Drabkin wrote:
>>>>>>>>     
>>>>>>>>         
>>>>>>>>             
>>>>>>>>                 
>>>>>>>>> I would not; they are the a cause, but they are not involved in the 
>>>>>>>>> process (which is not occurring in the plant).
>>>>>>>>> The GO is used to indicate the normal function and process of a gene 
>>>>>>>>> product. You need to look at it from the point of view of the organism 
>>>>>>>>> that produces the gene product. If these perform some function for the 
>>>>>>>>> plant, that is what you would annotate them to. Perhaps there are 
>>>>>>>>> terms associated with defense in a plant (ie, along the lines of 
>>>>>>>>> something that is released to deter the plant from being eaten???__?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> adepto at cribi.unipd.it wrote:
>>>>>>>>>       
>>>>>>>>>           
>>>>>>>>>               
>>>>>>>>>                   
>>>>>>>>>> Hi All
>>>>>>>>>> I have to annotate plant genes described as "allergenic peptides" in 
>>>>>>>>>> pFam these
>>>>>>>>>> genes are described as:
>>>>>>>>>> "Allergies are hypersensitivity reactions of the immune system to 
>>>>>>>>>> specific
>>>>>>>>>> substances called allergens (such as pollen, stings, drugs, or food) 
>>>>>>>>>> that, in
>>>>>>>>>> most people, result in no symptoms. A nomenclature system has been 
>>>>>>>>>> established
>>>>>>>>>> for antigens (allergens) that cause IgE-mediated atopic allergies in 
>>>>>>>>>> humans..."
>>>>>>>>>>
>>>>>>>>>> So, where may I annotate these allergenes? It is GO:0016068 (type I
>>>>>>>>>> hypersensitivity) the right term? Thanks in advance.
>>>>>>>>>> Alessandro
>>>>>>>>>>   
>>>>>>>>>>         
>>>>>>>>>>             
>>>>>>>>>>                 
>>>>>>>>>>                     
>>>>>>>>     
>>>>>>>>         
>>>>>>>>             
>>>>>>>>                 
>>>>>>> Dr Jane Lomax
>>>>>>> GO Editorial Office
>>>>>>> EMBL-EBI
>>>>>>> Wellcome Trust Genome Campus
>>>>>>> Hinxton
>>>>>>> Cambridgeshire, UK
>>>>>>> CB10 1SD
>>>>>>>
>>>>>>> p: +44 1223 492516
>>>>>>> f: +44 1223 494468
>>>>>>>
>>>>>>>   
>>>>>>>       
>>>>>>>           
>>>>>>>               
>>>>>>     
>>>>>>         
>>>>>>             
>>>>> Dr Jane Lomax
>>>>> GO Editorial Office
>>>>> EMBL-EBI
>>>>> Wellcome Trust Genome Campus
>>>>> Hinxton
>>>>> Cambridgeshire, UK
>>>>> CB10 1SD
>>>>>
>>>>> p: +44 1223 492516
>>>>> f: +44 1223 494468
>>>>>
>>>>>   
>>>>>       
>>>>>           
>>>> -- 
>>>> Alexander Diehl, Ph.D.
>>>> Scientific Curator
>>>> Mouse Genome Informatics
>>>> The Jackson Laboratory
>>>> 600 Main Street
>>>> Bar Harbor, ME  04609
>>>>
>>>> email:  adiehl at informatics.jax.org
>>>> work:  +1 (207) 288-6427
>>>> fax:  +1 (207) 288-6131 
>>>>
>>>>
>>>>     
>>>>         
>>> Dr Jane Lomax
>>> GO Editorial Office
>>> EMBL-EBI
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridgeshire, UK
>>> CB10 1SD
>>>
>>> p: +44 1223 492516
>>> f: +44 1223 494468
>>>
>>>   
>>>       
>> -- 
>> Alexander Diehl, Ph.D.
>> Scientific Curator
>> Mouse Genome Informatics
>> The Jackson Laboratory
>> 600 Main Street
>> Bar Harbor, ME  04609
>>
>> email:  adiehl at informatics.jax.org
>> work:  +1 (207) 288-6427
>> fax:  +1 (207) 288-6131 
>>
>>
>>     
>
> Dr Jane Lomax
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
>
> p: +44 1223 492516
> f: +44 1223 494468
>
>   

-- 
Alexander Diehl, Ph.D.
Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131 




More information about the go-discuss mailing list