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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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positive regulation of GO:0042412 taurine biosynthetic process #16562

Closed RLovering closed 5 years ago

RLovering commented 6 years ago

Hi

for the annotation of GHR please could I have this term Ref PMID:18648510

I could just add the acts_upstream_of_positive_effect qualifier if that is more useful. Although I do wonder how analysis tools will 'group' data based on qualifiers

Thanks

Ruth

ukemi commented 6 years ago

Hi @RLovering,

Since you closed all of your similar requests, did you mean to close this one too?

-D

RLovering commented 5 years ago

Hi sorry I felt that overall there is better evidence that GHR regulates this process, it is regulating a lot of different process but for this there is regulation of the genes involved in the metabolism of taurine as well as a lack of taurine in the metabolites of these mice. But I could just add the acts_upstream_of_positive_effect qualifier Ruth

ukemi commented 5 years ago

If you know the mechanism, then the term is valid. I'll add it as long as you think that the GH pathway evolved to control the biosynthesis. I just wanted to double-check.

RLovering commented 5 years ago

Hi David

I have done a bit of digging and now I feel more confident that GHD should be associated with this term. I think the following paper PMID:24911144, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071367/ is based on similar data to the paper I listed above. However this paper has a nice figure (Fig 5J) included showing how the genes regulated by GHD and STAT are relevant to taurine synthesis, plus it is done by a different lab. Also there are other papers that describe the role of taurine in obesity, adipose tissue development, glucose and lipid metabolism, which all fit with the GHR role. Do you think MGI would like to annotate this paper, or shall I do this once the term is created?

Best

Ruth

ukemi commented 5 years ago

Thanks Ruth,

I will add this as a definition reference. I checked and the paper is already in our curation stream. I'd like to try to use it in a GO-CAM model.

-David

ukemi commented 5 years ago

Ruth,

Which of your groups dbxrefs do you want me to add to this?

RLovering commented 5 years ago

Oh yes, I forgot about that, thanks for the reminder. definition_xref:GOC:BHF please