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allergene annotation
Michelle Gwinn Giglio
mlgwinn at tigr.org
Wed Mar 15 08:46:24 PST 2006
Hi Jane, Alex, and all,
It's funny this is coming up now since at the recent PAMGO workshop held
here at TIGR, we needed to annotate a gene from a pathogen to the
process of inducing hypersensitive response in a plant.
In fact we were planning on requesting just such a term as "induction of
hypersensitive response in other organisms".
However, we also then started into a discussion of whether this was the
best annotation approach to deal with this kind of situation - as it
appears that pathogens (or at least plant ones) have the ability to
manipulate and effect MANY plant systems and we fear a duplication of
much of the process tree under "interaction between organism" - so we
were wondering if the dual-taxon thing could work for this too.
Anyway - my point here was really to say that, yes indeed, there are
cases where organims have proteins which induce the hypersensitive
response in orther organisms.
I forget why they do this (at least the ones we were looking at) - its
not my field - but I think it has to do with feeding - but I'm not sure.
Michelle
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
>
>
>
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