Talk:CYP4F2

Outdated ?

Hello Maxim Masiutin the page seems outdated - the protein name is usually given first followed by the named gene. The protein name as recommended by UniProt is Cytochrome P450 4F2. Also used on the other infobox entries. --Iztwoz (talk) 16:12, 24 November 2023 (UTC)

See other entries on Cytochrome P450 page and many entries there such as CYP4F8.--Iztwoz (talk) 16:21, 24 November 2023 (UTC)

You raised a valid point, I also noticed that there is no consitency on Wikipedia, I asked Boghog quite a while, a few years ago, but there were no consensus. Anyway, regardless of the gene/protein name, I guess that the Wikipedia article should be called as a name, not as an abbreviation, for example "Cytochrome P450 4F2", not CYP4F2, similar to 21-Hydroxylase (which is a GA) but not CYP21A2; or Histamine N-methyltransferase rather than HNMT.

Therefore, I have a few questions:

1. Since I didn't see any separate article when a protein-coding gene had one wikipedia article and the protein coded by this gene had another article; therefore, should we link articles Wikidata items for proteins, or for genes?
2. For enzyme proteins encoded by genes (or genes that encode protein, depending on what you select in p.), should we use names like "Histamine N-methyltransferase" or symbols like HNMT? (see nomenclature on PMID 32747822?

Boghog, do we have any written rule on that, or should we create such a rule? I searched, including wikiprojects for molecular biology and genetics but did not find anything.

Where do you think we should discuss that if we don't have any rule written so far? Whom should we attract to the discussion? Maxim Masiutin (talk) 16:34, 24 November 2023 (UTC)

Hi Maxim. In answer to your question, there is WP:MCBMOS (Molecular & Cellular Biology Manual of Style) which suggests the article name should be UniProt name. Furthermore, as discussed here and here, we have tried to make clear in the lead sentence that these articles are not only about the human gene/protein, but also paralogs that exist in other species. The wording that was reached through consensus is perhaps a little awkward, but it is both accurate and concise:

• <recommended UniProt name> is a protein that in humans is encoded by the <approved HUGO gene symbol> gene.

The "that" in the above sentence is non-limiting implying that the protein (and gene) exists in other species besides human. Boghog (talk) 16:54, 24 November 2023 (UTC)

Thank you for the information about WP:MCBMOS, I didn't know about it. Very useful. This implies that the article should link to Wikidata item about protein enzyme, not to human gene. I will try to change Wikidata item I D associated with the article. Maxim Masiutin (talk) 19:27, 24 November 2023 (UTC)

There are different Wikidata items:

1. Wikidata items on genes
2. Wikidata items on proteins

This article links to Wikidata item on genes. Therefore, the article presents the gene first.

You wrote about the protein name as recommended by UniProt, can you please give the link, as all the current links from the Infobox Enzyme point the the name of the enzyme (protein) used in the article.

According to Guidelines for Human Gene Nomenclature PMID 32747822, each gene has a name (longer one) and a symbol (shorter one). The name of a protein-coding genes should be based on a key normal function of the gene product (e.g. ABHD1 “abhydrolase domain containing 1”, HEATR1 “HEAT repeat containing 1”), whereas ABHD1 is a symbol of the gene and “abhydrolase domain containing 1” is a name of the gene. The symbols of the gene are italicyzed, and the abbreviation of a protein product is not italicized, e.g. ABHD1.

Can you please send a link to the Uniprot enzyme for CYP4F2? Maxim Masiutin (talk) 16:26, 24 November 2023 (UTC)

I also checked PubChem and it gives an old name for some reason:

https://pubchem.ncbi.nlm.nih.gov/protein/EC:1.14.14.94

I tried to search on "1.14.14.94" by protein number on UniProt but didn't find anything for human. I can only find "1.14.14.1" but when I search for this number in the other databases of enzymes, it gives a group of unspecifix monooxygenases. I am lost. Can you please help? Maxim Masiutin (talk) 16:45, 24 November 2023 (UTC)

The links are in the infobox on the page. There is more information on WP:MCBMOS --Iztwoz (talk) 17:02, 24 November 2023 (UTC)

Specifically UniProt link is P78329 and Entrez is 8529 --Iztwoz (talk) 17:05, 24 November 2023 (UTC)

Thank you, @Iztwoz!

Thank you, @Boghog!

I changed the article according to recommendations and observations and help that you provided! Maxim Masiutin (talk) 20:08, 24 November 2023 (UTC)

Thank you again, I hope I addressed the issues that you raised and added the following sections that were missed in the article but required per WP:MCBMOS:

• Gene
• Species
• Tissue and subcellular distribution
• Interactions
• Clinical significance
• History

Maxim Masiutin (talk) 04:36, 25 November 2023 (UTC)

Additional requirements of WP:MCBMOS

@Boghog: it seems that there are additional requirements of WP:MCBMOS:

1. list or mentin orthologs (as listed in HomoloGene) that exist in other species;
2. list or mention paralogs in humans (and by extension other species) or link to gene family article.

Is my understandging of these requirements correct? How can we implement those requirements? Maxim Masiutin (talk) 09:20, 25 November 2023 (UTC)

WP:MCBMOS at the momment is an WP:essay that has not yet been promoted to a WP:guideline, much less a WP:policy. Hence at most, WP:MCBMOS can be considered as a suggestion. (Disclaimer: I wrote a significant fraction of MCBMOS, so these are to some extent my personal opinions). That being said, I think they are reasonable suggestions. Futhermore, the article has already partially incorporated these suggestions. I will take another look to see if these suggestions can be expanded. Cheers. Boghog (talk) 14:47, 25 November 2023 (UTC)

Thank you very much! Those suggestions are more than reasonable! Still, there is one suggestion that is debatable:

while the following is not recommended:

• "the gene ALDOA is regulated" since it is redundant.

A reader may not know about the rule that italics means a gene and may be confused. Therefore, I would consider applying this rule up to the point where it cannot be deduced by context on whether it is about a protein or a gene. Maxim Masiutin (talk) 17:09, 25 November 2023 (UTC)