User talk:Synapsin

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synapsin pages

Hello, just noticed your edits to the synapsin pages. Just wanted to note that there was previous consensus at WP:MCB that as a general rule, a single page would cover both the gene and its corresponding protein product. Feel free to discuss on the talk page if you think this should be an exception... Cheers, AndrewGNF (talk) 18:16, 14 September 2009 (UTC)

synapsin pages reply

If you notice, Syntaxin is also separated this way. A protein is not the same as the gene that encodes the protein and this is not apparent in the Wikipedia pages. Most of the pages incorrectly state that the name of the protein is the same as the gene. I will also speak on this on the page you referenced. Thank you for informing me.

Gene/protein pages

As discussed here, these Gene Wiki pages are really about both the protein and the gene that encodes it. The current lead sentence which implies that the page is only about the gene is misleading. We intend in the very near future to replace the lead sentence in all the ~9,000 Wiki Gene article with "X is a protein which in humans is encoded by the X gene". Sorry for the confusion. Boghog (talk) 18:37, 14 September 2009 (UTC)

Gene/protein pages response

This is a point of disambiguation. Regardless, the Wikipedia guidelines call for disambiguation of terms and separation of topics such as these. The protein is clearly not the gene and and the gene is clearly not the protein. Even with an improved lead sentence, the image of the protein is still displayed as though it is the same as the gene, which is obviously not to those familiar with the content. However, someone learning on the topic could easily be misled. To be more accurate, I would propose that in the place of the rendered protein image on the gene page, an image of the genetic sequence is provided. Everyone likes the pretty 3D rendered images, but really it should be on a separate page expounding on the protein.

Why can't we have a single page that is about both the protein and the gene that encodes it? There is no Wikipedia guideline or policy that precludes this. Please note that the {{GNF Protein box}} contains links to information about both the protein and the corresponding gene which is now transcluded into close to 10,000 articles. To split these articles up would be a tremendous amount of work with no added value. Quite to the contrary, it would be a mistake to split up information which is so closely intertwined. Boghog (talk) 19:20, 14 September 2009 (UTC)

These 10,000 articles are generated using templates. It would not take much to split those that are currently left untouched from when they were generated using template format. Also, it should not preclude the separation of the two topics manually as there is considerable information to be provided on both separately in many cases.

As for Wikipedia disambiguation, please refer to the information on Wikipedia disambiguation. You ask why? I say it's very confusing to have both the protein and gene integrally defined on the same page, when they are two distinctly different chemical compounds. Hence, the reason for disambiguation in Wikipedia.

Synapsin (talk) 19:38, 14 September 2009 (UTC)

The gene and the corresponding protein are so integrally interconnected, in most cases it makes no sense to place these on two separate pages. Normally there is much more published on the properties and function of the protein than the corresponding gene. The exception would be genes associated with common human diseases where there might be a large number of published linkage studies. In any case, information on the gene and the protein can be cleanly separated into different sections of the same article. Boghog (talk) 19:47, 14 September 2009 (UTC)

In response to:

• the image of the protein is still displayed as though it is the same as the gene

The title of the protein box is the official HUGO gene name which in most cases is identical to the protein name. This is certainly true of the protein boxes displayed on the SYN1 and SYN2 pages. So why is this misleading? Boghog (talk) 20:05, 14 September 2009 (UTC)

I agree that a gene and its protein products should be discussed on the same page. After all, I use (and hear many others use) "gene function" and "protein function" interchangeably. I think in the past, we'd only considered separating the gene and protein where there was such an overwhelming amount of material on each that to combine would have been unwieldy. In practice though, I don't know if this actually applies to any gene/protein pages currently. Among our most well-developed gene/protein articles, p53, reelin, and insulin all have managed to cover both topics in a single article.

Of course, this is a separate issue from cleaning up that opening intro sentence on the stubs, which I think we all agree is misleading and imprecise. Cheers, AndrewGNF (talk) 21:25, 14 September 2009 (UTC)

Exactly my point, the gene name and the protein name can be synonymous in some cases, but they are distinctly different entities. Research on the protein and subsequent information, may or may not be related to genomic research.

If you separate the two, it grants the opportunity to add a greater amount of information to a page, without making the page overwhelming. I plan to add more information to some of the pages and am in the process of editing them.

Synapsin (talk) 21:47, 14 September 2009 (UTC)

While you are expanding these articles, it is imperative that you add citations that are not co-authored by Greengard for balance. The difference between the reference lists in Synapsin I and SYN1 is quite striking. Please keep in mind WP:COI guidelines. Boghog (talk) 22:01, 14 September 2009 (UTC)

Obviously the references between the gene and the protein are going to be different, as these scientists are doing research on two completely different molecular compounds. I left the gene related references and those that speak to the SYN1 entry on the page for the gene intact. Those references that are related to the protein are listed on the page for the protein, and corrected the information on the interaction and heterodimerizations of the Synapsin proteins, not the genes as stated prior.

As for balance, Greengard (as the PI) and various associates of his, have done much of the work regarding Syanpsin I, and contributed to the reasons for the Nobel Prize he was awarded. There are several other authors listed in the references cited and if you refer to the papers, the citations are all relevant to the information provided. Additionally, I am hoping to add some more recent books to the further reading list in the near future, in order to provide books which might be more easily accessed. Synapsin (talk) 15:03, 15 September 2009 (UTC)

OK, I see Greengard has obviously has coauthored many papers in this area. In addition, Greengard was buried in the "et al." of some of the citations in the SYN1 article. However I wanted to point out that many of the citations listed in the further reading section of SYN1 are primarily about the protein and are not co-authored by Greengard. There a abundant papers published by other research groups on Synapsin 1 hence it is important to include at least some of these in the article for balance. Boghog (talk) 19:05, 15 September 2009 (UTC)

Actually, on reviewing the list of protein articles in the Further Reading section of SYN1, Greengard is one of the co-authors a good number of "et al."s. Many of the remaining citations related to the work on the protein, list an author who was at one time associated with Greengard in his laboratory or collaborations. If you prefer, I can change the format of the citations not to list all the authors and switch to the use of et al. and it will make it look more balanced, but personally I think it's artificial. Neither being co-authored by Greengard or being an associate should be a disqualification for being cited. I am happy to move the Further Reading on proteins to the Synapsin I page as any significant findings related to the protein in articles that aren't general reviews should be added on review. Synapsin (talk) 21:30, 16 September 2009 (UTC)

Edits

In response to this edit:

• The interaction is between the Synapsin I & II, as well as Synapsin II proteins, not the genes, SYN1, SYN2, and SYN3. Read the paper.

Please read the lead sentence in the SYN2 article.

In addition, please do not take down the merger templates until a consensus has been reached. Right now there is no consensus and the purpose of adding the template is to build a consensus. Thank you. Boghog (talk) 05:34, 15 September 2009 (UTC)

Please do not keep changing the correction edits to the lead sentences to SYN2 and SYN1. The lead sentence of the SYN2 entry as it currently reads is misleading as it incorrectly states that the protein, Synapsin II, is also known as SYN2. The gene is only known as SYN2, not the protein. Also by convention, gene names are typically italicized, to provide further clarity.

Synapsin II, also known as SYN2, is a protein which in humans is encoded by the SYN2 gene.[1][2]

I propose it should read something like:

SYN2, also known as the Synapsin II gene, is the human gene which encodes the nervous system protein Synapsin II.

Synapsin (talk) 15:23, 15 September 2009 (UTC)

Please read this: gene and protein symbol conventions. Boghog (talk) 15:35, 15 September 2009 (UTC)

I actually agree with Synapsin that "SYN2" (and similar) is most often used to refer to the gene and not the protein. In my experience anyway. But regardless, I think the formulation of the lead sentence will be clear once we decide the bigger issue of whether the gene and protein articles should be merged. Synapsin, are you mostly done editing SYN2 and Synapsin 2? If so, then we can try to reach a consensus as to whether there is sufficient material there to justify keeping these two articles separate. Cheers, AndrewGNF (talk) 16:08, 15 September 2009 (UTC)

Thank you for your agreement. The following may clarify the issues we are contending with proper nomenclature. Often, proteins are alternatively named by a symbol or acronym name, which is by convention italicized and used the name of the gene corresponding to the protein. In those cases, stating, "<protein>" also known as <SYMBOL> is the protein the human gene <SYMBOL> encodes. " may be accurate.

However, in the case of Synapsin I, the symbolic name is only used in reference to the gene name. Both SYN1 and Syn1 (more properly SYN1 per gene nomenclature guidelines) are registered as the gene name for the Synapsin I gene in many databases, but the protein is still referenced as Synapsin 1 and not SYN1. (UniProtKB/Swiss-Prot, RCSB PDB, HPRD, Entrez Gene) It may be because another protein, Syntaxin 1, has sometimes been seen to be abbreviated SYN-1, instead of STX1 as it common is referred to now.

At the very least I would request that you consider this case as an exception for deriving a same symbolic name for the protein and the gene, differentiated by italics for the gene name.Synapsin (talk) 18:11, 15 September 2009 (UTC)

I will post when I'm done editing the Synapsin 2 page. Synapsin (talk) 18:13, 15 September 2009 (UTC)

OK, I stand corrected. Again, correct me if I am wrong, but I believe part of the confusion is that apparently there is no central authority (although UniProt may come close) for establishing official protein names and symbols analogous to HUGO which establishes official gene names and symbols. So I agree that we need to be flexible and adapt to special cases such as Synapsin. Cheers. Boghog (talk) 18:42, 15 September 2009 (UTC)