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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Regulation of mRNA and protein levels #6299

Closed gocentral closed 9 years ago

gocentral commented 15 years ago

I would like to see "-/positive/negative regulation of transcript levels" added to the GO ontology under the parent terms "-/positive/negative regulation of cellular metabolic process" (GO:0031323, GO:0031325, GO:0031324) and “-/positive/ negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process” (GO:0019219, GO:0045935, GO:0045934). The definitions could be "Any process or processes that modulates/increases/decreases the levels of a specific mRNA or specific mRNAs in cells or tissue". An example can be found in PMID:19254430. Synonyms would be “upregulation of transcript levels”, “up-regulation of transcript levels”, “downregulation of transcript levels”, “down-regulation of transcript levels”.

I would like to see "-/positive/negative regulation of protein levels" added to the GO ontology under the parent terms "-/positive/negative regulation of cellular metabolic process" (GO:0031323, GO:0031325, GO:0031324) and “-/positive/ negative regulation of cellular protein metabolic process” (GO:0032268, GO:0032270, GO:0032269). The definitions could be "Any process or processes that modulates/increases/decreases the levels of a specific protein or specific proteins in cells or tissue". An example can be found in PMID:16595703. Synonyms would be “upregulation of protein levels”, “up-regulation of protein levels”, “downregulation of protein levels”, “down-regulation of protein levels”.

Reported by: gthayman

Original Ticket: geneontology/ontology-requests/6318

gocentral commented 15 years ago

Does ' GO:0010468 : regulation of gene expression ' cover this? Based on your description and the definition of this term, I would think it does? maybe some synonyms need to be added.

Cheers. Pascale

Original comment by: pgaudet

gocentral commented 15 years ago

I would suggest 'regulation of gene expression' as another parent term to the suggested terms. I am suggesting terms that are more granular, but take into account that message or protein turnover was not assessed, as is often the case, which would make 'regulation of transcription' (GO:0045449)/'regulation of translation' (GO:0006417) less appropriate. Thanks for the input. Tom

Original comment by: gthayman

gocentral commented 15 years ago

I'm turning this over to David and Tanya (our regulation team), and they will add synonyms or terms as they see fit.

m

Original comment by: mah11

gocentral commented 15 years ago

Original comment by: mah11

gocentral commented 15 years ago

This paper might be another example for "regulation of mRNA levels", in this case specifically for "regulation of histone mRNA levels".

Reis CC, Campbell JL (2007) Contribution of Trf4/5 and the nuclear exosome to genome stability through regulation of histone mRNA levels in Saccharomyces cerevisiae. Genetics 175(3):993-1010 PubMed ID: 17179095

-Karen

Original comment by: krchristie

gocentral commented 13 years ago

Hi Tanya and David,

Do you have any comment on this? We feel that it might be out of scope of GO (as well as out of date) because transcript levels are more about measuring assays than real processes. Therefore we're closing this item, but feel free to re-open it if people feel strongly about it. Tom, feel free to add a comment if you'd like this re-opened.

Thanks, J, B, P

Original comment by: paolaroncaglia

gocentral commented 13 years ago

Original comment by: paolaroncaglia