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pheromone-dependent #20417
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Maybe not, since there is a single subclass:
Similarly for the non-regulatory terms:
Should we merge ? |
Hmm, it sounds phenotype-y (assay readout) I can't speak for Candida albicans or cerevisiae, but I think that in pombe we only need pheromone response MAPK cascade |
I donwloaded SGD (33EXP) and CGD (15 EXP) annotations https://docs.google.com/spreadsheets/d/1mregahtFd6w50ZlOj_-skWQuvZHP1o2ZVz9R_rlmLls/edit#gid=0 @srengel @marekskrzypek Can you please have a look and let us know if merging/replacing the terms by 'pheromone response MAPK cascade' would work for you ? I spot checked a few and there seems to a a single, MAPK pathway. Thanks, Pascale |
I think the confusion comes from that there are so many upstream signaling events preceding cells deciding to sexually reproduce (and initiate pheromone signaling to find a mating partner) I guess it is quite a big thing genetically since the organism must "decide" conditions are so bad that the best thing to do is to shuffle up its genome and make spores to hopefully survive the bad times. A few more terms need to move...here is a nice summary |
could you make a negative regulation of pheromone responsive mapk cascade @pgaudet and I'll move sxa2 & gap1 to that term |
BUT the pheromone response is all through the GO:0071507 pheromone response MAPK cascade The stress is only transcribing thee pheromone. That is a "response to stress" not a "response to pheromone"? |
@Antonialock that is what you said above... |
Remember that this is not universal -- some microorganisms, including budding yeast, mate pretty much any time haploids of "opposite" mating types encounter each other, often under favorable growth conditions; the resulting diploids also grow vegetatively as long as times are good. Pheromone production is not a stress response in these species. I don't think this point affects the original question, though, since it's about what happens after one cell meets a pheromone from another cell. |
Thanks, Yes, I was refering to the plethora of pombe annotations that I (guess I) made! TOR, glucose sensing pathway and the stress MAPK pathway all feed into it |
ah! I forgot how specific this term is ("A MAPK cascade that is part of a pheromone response ending in conjugation with cellular fusion") so for this pathway should we annotate the GCPRs to the "pheromone response MAPK cascade" term, or something broader? there is only 1 term for the glucose/gpcr pathway: so (sounds terrible! I am happy with just one term...do the mapk components need their own "module" @ValWood ?) |
Good question. Personally I'm not sure they do, but this was an outcome of the signalling meeting, and it kind of works OK. So now I co-annotate to a) the module, and b) the "signalling " role. So The G protein signalling pathway will have GO:0007186 G protein-coupled receptor signaling pathway or even It's a bit similar to phosphorelay system where I have done https://www.pombase.org/gene/SPAC27E2.09 It's a little clunky but I think it works OK. Remember that everything upstream of the MAPK module becomes "positive regulation of blah" We don't need more precomposed terms.... |
Hang. on, isn't GO:0007186 G protein-coupled receptor signaling pathway I wouldn't even couple this signalling together with intervening transcription. This really is somewhere where we need causally upstream because we would be linking together upstream-downstream processes. The model for "positive regulation of conjugation with cellular fusion" will be something like: GO:0007186 G protein-coupled receptor signaling pathway - > transcription (pheromone) -> MAPK cascase -> downstream conjugation processes. (the G-protein signalling and the MAPK part aren't even in the same cell, they will be in opposite mating types so they can't be modelled as a single signalling pathway). |
Oh actually there are 2 pathways from adenylate cycles, you are referring to the one directly upstream of the pheromone MAPK so it is the first solution. |
pheromone activates gpcr, activates g protein, activates mapk cascade, activates TF -> transcription I don't think of the GPCR as regulating the MAPK module, it's all part of the same pathway It seems inconsistent with how the glucose sensing pathway is annotated. |
I know but that was the outcome of the signalling meeting... @ukemi is there a link to the documentation that describes this? I am looking here: |
I found this ticket MAPK signalling cascade is part_of "overall signalling pathway" Possible the difference is that the pathway I was annotating (p38 MAPK) is linear in that the module upstream (phosphorelay), is only known to regulaete MAPK cascade, so in that case it seemed OK. But really the stress activated MAPK pathway, to a biologist, begins with mcs4. The mating pheromone MAPK pathway begins with the receptor and includes the MAPK module. I am inclined to agree that the "MAPK module" is probably surplus....but i don't know how this would work for higher eukaryotes which have lots of pathway duplication. This is a great example of why the ontology and process starts and ends need to be clearer before models can be build, otherwise all of the models will be inconsistent. |
Yeah ok. There is much more crosstalk in higher eukaryotes
…On Thu, 3 Dec 2020 at 19:34, Val Wood ***@***.***> wrote:
I found this ticket
geneontology/go-annotation#1592
<geneontology/go-annotation#1592>
which leads to this model
http://noctua.berkeleybop.org/editor/graph/gomodel:5437882f00000024
so I think we need to say that
MAPK signalling cascade is part_of "overall signalling pathway"
Possible the difference is that the pathway I was annotating (p38 MAPK) is
linear in that the module upstream (phosphorelay), is only known to
regulaete MAPK cascade, so in that case it seemed OK. But really the stress
activated MAPK pathway, to a biologist, begins with mcs4.
The mating pheromone MAPK pathway begins with the receptor and includes
the MAPK module.
I am inclined to agree that the "MAPK module" is probably surplus....but i
don't know how this would work for higher eukaryotes which have lots of
pathway duplication.
This is a great example of why the ontology and process starts and ends
need to be clearer before models can be build, otherwise all of the models
will be inconsistent.
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I think that is the rationale. We can put the modules together to create the pathway. The pathway is just a label really. For example here ras1 and Gpa1 are 2 independent pathways feeding in to byr1. Both can be "positive regulation of |
regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion (GO:0010969)
I'm wondering why we have pheromone depednet terms.
Do we need them @Antonialock ?
Presumably we know they are pheromom=ne dependent if they start from a pheromone?
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