Yeast2Hybrid

Protein interactions

Hi. I really appreciate the effort to added protein interactions to the Gene Wiki pages. I have one small request. Currently these pages insert the citation after punctuation while you are doing the reverse. For consistency with the previous content, it would be desirable to follow the existing standard. (See also Manual of Style). Cheers. Boghog2 (talk)

Hi, Thank you for your message. I will change the way I display the citations ASAP.--Yeast2Hybrid (talk) 10:35, 17 July 2009 (UTC)

Great! Thanks for your quick response. Regards. Boghog2 (talk) 12:48, 17 July 2009 (UTC)

Citations

Your first run of adding protein interactions to Wiki Gene articles looks great, but there are a few glitches. I noticed that you started with the ARNTL article to group all the citations together at the end of the sentence instead of putting them directly after the appropriate protein. This is not as useful to the reader since it is difficult to track down which citation documents which interaction. In addition, with "well connected" proteins with many interactions (e.g., estrogen receptor alpha), the in-line reference list becomes quite long and runs off the side of the page. I would appreciate if you would modify your script so that the citations are linked directly to the appropriate protein as you had before but in addition have the citation after the punctuation. Cheers. Boghog2 (talk) 18:54, 19 July 2009 (UTC)

fixed (I hope)  :-) --Yeast2Hybrid (talk) 09:15, 20 July 2009 (UTC)

Another request. Linking journal names is creating a lot of red links. My own personal opinion is that is no need for this type of link since what is most important is the paper, not what journal it is published in. I am not sure how you are generating the citations, but if you are using WWW-Wikipedia-TemplateFiller, I there is an option to return the full journal name (see User_talk:Diberri/Template_filler#Full_Journal_Titles). If there is a journal article in Wikipedia, it is probably linked to the full journal name (e.g., Journal of Lipid Research and not J. Lipid Res.). While this could be solved by using redirects, introducing a lot of double redirects is also not desirable. Boghog2 (talk) 08:39, 20 July 2009 (UTC)

Fixed (I removed the link) --Yeast2Hybrid (talk) 09:15, 20 July 2009 (UTC)

OK great! Now everything looks good. Thanks for your quick response! Regards. Boghog2 (talk) 09:26, 20 July 2009 (UTC)

Article names or gene symbols

One more possible request for discussion. Right now, the links in the interactions sections display the WP page title. I wonder if those links should be changed to piped links, showing instead the gene symbol. Take for example RICS_(gene)#Interactions. Currently, it reads (without references):

RICS (gene) has been shown to interact with [[BCAR1]], [[FYN]], [[TrkA]], [[Src (gene)]]...

I wonder if it should really read:

RICS has been shown to interact with [[BCAR1]], [[FYN]], [[TrkA|NTRK1]], [[Src (gene)|SRC]]...

thoughts? AndrewGNF (talk) 20:59, 22 July 2009 (UTC)

I agree that the gene symbol should probably be used in preference to the page name because (1) the former is more compact (some of the page/gene names can be very long) and (2) for consistency with the other gene symbols in the sentence. Cheers. Boghog2 (talk) 21:32, 22 July 2009 (UTC)

PKMzeta changes

Yeast2Hybird, Almost all of the additions that you cited as proteins interacting with PKMzeta are incorrect because they bind to the regulatory domain of PKCzeta, not to PKMzeta, which is the independent zeta catalytic domain. The only 2 published interactions with PKMzeta that I am aware of are with KIBRA (as cited) and PDK1 (Kelly, M., Crary, J., Sacktor, T. C., Regulation of PKMζ synthesis by multiple kinases in long-term potentiation, J. Neurosci., 27:3439-3444 (2007)). Please remove all the others, unless you specifically know they interact with PKMzeta, which is expressed specifically in brain. Thanks, Tsacktor (talk) 00:59, 24 July 2009 (UTC)Tsacktor

Hi Tsacktor. I thought I'd chime in here because Yeast2Hybrid and I discussed the data beforehand. All the relationships are derived from BioGRID. Specifically, it looks like the data came from this page. The confusing part to me is actually the Protein kinase Mζ page itself here at WP. Clearly the title is "Protein kinase Mζ", but the protein infobox calls it "Protein kinase C, zeta" with symbol "PRKCZ". It seems like this is an area of your research. Can you clarify whether these should actually be two separate gene pages? Bottom line, the "interactions" section is tied to the data in the protein infobox, so once we get clarity on the "Protein kinase Mζ" versus "Protein kinase C, zeta" the rest should fall into place... Cheers, AndrewGNF (talk) 16:31, 24 July 2009 (UTC)

It appears that PKCζ and PKMζ are splice variants which are both derived from the same PRKCZ gene. Since this page deals with both the gene and expressed protein, one solution would be to rename the page as "protein kinase Cζ" and have separate sections discussing the PKCζ and PKMζ splice variants. In addition, as Andrew and I have suggested above, gene symbols rather than the full gene/protein name should be listed in interaction section. I am not familiar with BioGrid, but I assume that the PRKCZ entry should at least in theory include interactions involving all expressed spliced variants derived from this gene, in this case both PKCζ and PKMζ. Does renaming this article "protein kinase Cζ" sound reasonable? Boghog2 (talk) 17:37, 24 July 2009 (UTC)

Yes, this seems like a reasonable action to me. (As an aside, hopefully we'll get the interactions section cleaned up to gene symbols sometime. Due to constraints in real life, it was either get it done as is or have to wait indefinitely.) Cheers, AndrewGNF (talk) 18:30, 24 July 2009 (UTC)

OK, I went ahead and changed the page name to Protein kinase C, zeta and made some modifications to the lead and the protein interaction sections. Tsacktor, I hope this addresses your concerns. Cheers. Boghog2 (talk) 20:07, 24 July 2009 (UTC)

Proposed change to Reelin

I proposed a change to the citation style of the Reelin. I think it would make the article easier to navigate for editors (with virtually no change for readers). However, the effort to make the change is not trivial, so I would like to get feedback from editors before attempting a conversion. I've posting this message to editors who have a fair number of recent edits to that page. I've explained more details, along with a link to a test on the Talk PageSPhilbrickT 21:24, 8 October 2009 (UTC)

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