parent for Protein stabilization

[gocentral]

Hi

please could you add the is_a parent term GO:0010628 positive regulation of gene expression to GO:0050821 protein stabilization synonym: positive regulation of protein stability

Thanks

Ruth

Reported by: RLovering

Original Ticket: geneontology/ontology-requests/11072

[gocentral]

• status: open --> closed-rejected
• assigned_to: Tanya Berardini

Original comment by: tberardini

[gocentral]

Hi Ruth,

After discussing with the rest of the GO editors, it seems to us that protein stabilization falls outside of the scope of the definition of 'positive regulation of gene expression'. For protein gene products, 'positive regulation of gene expression' includes translation and some protein processing (to active form) but not stabilization of an already translated protein.

Best,

Tanya

Original comment by: tberardini

[gocentral]

Hi Tanya

I kind of disagree with this decision, based on the existing placement of this term within the ontology. As from the existing placement protein stabilization is_a regulation of gene expression, so it seems that if it is_a regulation of gene expression then it would also be a positive regulation of gene expression.

However, if this is the final decision does that mean you are going to remove GO:0050821 protein stabilization from its current position in the ontology as a child of GO:0010468 regulation of gene expression

GO:0010608 posttranscriptional regulation of gene expression

GO:0031647 regulation of protein stability

GO:0050821 protein stabilization

and in which case what parent will it have? Perhaps: GO:0010468 regulation of gene expression

GO:0010608 posttranscriptional regulation of gene expression

NEW GO term posttranscriptional positive regulation of gene expression

GO:0050821 protein stabilization

Or will you be moving GO:0010608 posttranscriptional regulation of gene expression.

thanks

Ruth

Original comment by: RLovering

[gocentral]

You point out issues that need to be discussed further.

(1) Either:

broaden definition of 'reg of gene expr' to include 'reg of protein/RNA stability' based on existing children,

or

remove 'reg of x stability' from 'post-tsc reg of gene expr' and leave only parentage to 'reg of biol quality'

(2) Should clarify def of post-tsc reg of gene expr as this is very open-ended.

"Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript."

Original comment by: tberardini

[gocentral]

• status: closed-rejected --> open

Original comment by: tberardini

[gocentral]

Summary of GO editors' discussion:

Gene expression = making the functional protein or functional ncRNA, anything after this is not 'gene expression' anymore.

Protein stabilization can occur not just when the protein is initially translated, but also in a protein is hanging around in the cell.

Regulation of protein stability is POST-gene expression.

Proposed changes:

(1) Change in definition of 'gene expression' and in child terms that contain similar language:

"Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form."

TO

"Protein maturation is included when required to form an active form of a product from an inactive precursor form."

(2) Remove 'regulation of protein stability' from 'posttranscriptional regulation of gene expression'. Leave as an is_a child of 'regulation of biological quality'.

Original comment by: tberardini

[gocentral]

I agree with Tanya's proposed solution here. Gene expression = all steps up to formation of a functional gene product. Protein stabilisation can happen after this. I'm working on tidying up relationships that suggest a broader definition.

Original comment by: dosumis

[gocentral]

Thanks very much for your input, David. I will implement the edits described in comment dated 2014-08-25 next week.

Original comment by: tberardini

[gocentral]

• status: open --> closed

Original comment by: tberardini

[gocentral]

Edits implemented as described.

Original comment by: tberardini