Wikipedia talk:WikiProject Cell Signaling

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[edit] Cell Signaling Diagrams

check out Burke's Reconnections and the Visual Thesaurus.Wblakesx 22:52, 19 November 2006 (UTC)wblakesx


JWSchmidt and I were talking about adding in signaling diagrams on the relevant protein pages.

One thing I thing would be useful would be if the diagrams were actually hyper-linked, such that you could click from the protein name in the figure to the relevant article.

There are complications, obviously, to the idea of having such diagrams:

1) Some proteins, like Akt for example, link into multipe signaling pathways

2) Not everyone agrees on all the signaling points

3) Some signaling interactions are tissue specific.

4) Some signaling interactions are cell-stage specific (for example there are differences in signaling between the proliferation-competent cell and the cell once it is differentiated into a particular tissue-type and becomes post-mitotic).

But even with these problems, it seems that giving the signaling context to every protein that participates in signaling pathways would be extremely useful.

This would require coordinating with the large "Protein" project and their templates as well... and would require a section for every protein that is in a signaling pathway as to its role in that pathway.

Just some suggestions...


Gacggt 19:00, 18 June 2006 (UTC)

I was actually just reading your conversation with JWSchmidt. I've been thinking along the same lines. However, I imagine hyperlinked diagrams will be very restricted in what they can portray (looking at the examples on [1], I don't know how flexible the scripting language is). Here my thoughts on this: I was thinking of having a single pathway page with a diagram and links to individual proteins. This would get around point 1). The protein page could provide more detail on the protein's immediate interactions. I don't think it is appropriate to duplicate the signaling diagram for the entire pathway on protein pages. However, if a particular protein, say EGF-R, has a wide range of notable interactions, these could be illustrated, a sort of mini-pathway diagram. Regarding 2), I think controversial points should be discussed in the text, but avoided in diagrams. I am not sure if it's worth illustrating 3), it could get very messy.
This is a diagram I've done recently - Image:Sonic_hedgehog_pathway.png. Let me know what you think.
There is another problem - pathways differ considerably between species. What I was thinking of doing for Sonic hedgehog (which in my opinion should be moved to Hedgehog (cell signaling), with only protein SHH protein specific info remaining), is describing the insect and mammalian pathways in separate sections of the article. Peter Z.Talk 19:32, 18 June 2006 (UTC)
Clearly there needs to be conventions; for example, I'd suggest a bias to mammalian signaling. However, for pathways such as SHH where a lot of the work has been done in drosophila, there should be a distinct diagram to illustrate differences. Obviously, some pathways such as mating types in yeast are specific to the organism - and for those there would not be an issue about species.
I guess I agree with you about keeping things simple. So maybe the idea of hyper-linking from the actual diagram is too ambitious right now.
As for flash/animation - that would still be very useful to illustrate some points, like how phosphorylation alters protein-protein interactions... but if this ever becomes available, it can be put on the more general "phosphorylation" page.
So we're in agreement about having single pathway pages, with links to the proteins involved in the pathway.
But we still need to deal with significant differences/changes in terms of tissue specificity. For example in proliferation-competent cells, the Ras/Raf pathway synergizes with the PI3K/Akt pathway. But in differentiated muscle and nerve, Akt shuts down Raf. And Akt has distinct roles in muscle and nerve.
It is not a simple subject you've initiated!

Gacggt 12:03, 19 June 2006 (UTC)

Now that I think of it in Flash it would be really easy to hyperlink proteins. Another alternative is SVG, which also supports animations. However, I've had a lot of trouble with it lately and it'll take a while before it's readily usable. Peter Z.Talk 18:26, 19 June 2006 (UTC)

Okay, this is what I think the main ideas/questions are:

  • A single diagram for each major pathway; however, what constitutes a separate signaling pathway could be debatable in some cases;
  • Animated diagrams would be ideal - probably SWF format, hyperlinked to Wikipedia articles devoted to individual proteins;
  • Diagrams should be drawn to a single standard. My suggestions:
  1. a common colour scheme for receptors/kinases/transcription factors etc.
  2. an agreed way to portray protein domains and covalent modifications
  3. the same goes for membranes
  • Focus on human biology (there are sometimes differences between human and mouse, especially when you get to the details of transciptional regulation), keeping in mind the suggestions of Gacggt and myself above.
  • How to deal with cell type differences?
  • How to illustrate the steps of signal transduction with unknown mechanisms without introducing misunderstandings?

Peter Z.Talk 19:19, 19 June 2006 (UTC)

one last question...

  • How to edit pathways when new data comes along?

Gacggt 20:40, 19 June 2006 (UTC)

If we use a vector format (Flash and SVG both are) it shouldn't be a problem. Peter Z.Talk 20:53, 19 June 2006 (UTC)

Peter Z.Talk mentioned that he would incorporate the scheme used in my diagrams for the TGF beta signaling pathway, which he did in the JAK-STAT signaling pathway. I created a page in my sandbox proposing a scheme that we can use in images in the project. I agree that the images should be drawn to a single standard and I think we should work out one. Check it out here (proposed scheme) and tell me what you think and then we can move it over to the project page and iron out the details. --GAThrawn22 07:58, 3 July 2006 (UTC)

I moved the page the proposed page to Wikipedia:WikiProject Molecular and Cellular Biology/Diagram guide. Feel free to take a look and make any changes, additions, or discuss the scheme. --GAThrawn22 19:25, 8 July 2006 (UTC)

[edit] Article structure

I am not sure that a single sucture for signaling pathway articles is going to work. Pathways are pretty abstract concepts and exist only as a biologist's way of organising their research... PS Otherwise I think this project is a good idea. A lot of quite important (I would think) articles on this subject are in a really sad state. I'll try to encourage more people to participate. The Meaning of Liff 20:18, 6 June 2006 (UTC)

[edit] Template

Hey nice work on the templates, i'll start adding them to the appropriate articles and start expanding their content, one by one. Rockpocket 23:50, 6 June 2006 (UTC)

[edit] Cholesterol

Whoa!!! Adding choleseterol as a postranslation modification (what's the name of it - cholesteroylation or something? Do we have an article about this?) with roles in protein trafic and cell signaling?!? We thought we know everething about the ol' membrane fella - it's been researched for some half a century, at least. Why doesn't SHH-N stay anchored to the plasma membrane the way the mirystoylated proteins are (cholesterol in fully extended state is as long as myristate if not longer) but instead leaves the cell, does DISP have anything to do with it? Why is the presence of cholesterol moiety so important for the receptor/ligand recogntion? What would happen if the cholesterol moiety is cleaved off SHH-N outside the cell in a regulated manner? Would the reduction of cholesterol content inside the cells due to cholesterol lowering diets affect somehow these processes? Are there any drugs outthere that inhibit any of the cholesterol-dependent events - cholesterol attachment, excretion and PTCH binding? Sorry, i couldn't help it, i read this new stuff and my head started spinning around. -- Boris 03:25, 19 June 2006 (UTC)

Heh, it's a strange one, isn't it? Have a look here [2] in the hedgehog ligands section, they have a good set of references. The way SHH-N diffuses is very strange indeed, in vitro it diffuses freely in the culture medium, although secreting cells do retain plasma membrane SHH-immunoreactivity. SHH signals best when its multimerised, AFAIK under non-denaturing conditions it shows up as a massive (100s kDa) complex) on gels. The Patched receptor actually sequesters the hedgehog ligand, possibly through cholesterol binding to Patched sterol-sensing domain. The result is that the hedgehog signal weakens after passing thorugh a HH responsive field. In flies, removal of cholesterol results in increased range of signaling. DISP appears to be required only for signaling cholesterol modified SHH. See Entrez PubMed 15576405 for a good discussion of DISP and cholesterol. I don't know of any drugs that target the hedgehog pathway at the level of ligand, the absolute majority target Smoothened. I don't think anyone's looked if reduction of cellular cholesterol affects SHH modification. I think it's possible that it does. ADAM metalloproteases, for example, are modulated by cholesterol content of the cell. That's all I really know, I hope the links above help answer your questions. Peter Z.Talk 11:33, 19 June 2006 (UTC)
Btw the cholesterol is added is added by the C-terminal non-signaling domain of SHH, that catalyses the autocleavage. That makes it a cholesterol transferase! --Peter Z.Talk 11:36, 19 June 2006 (UTC)


[edit] Pathway names

What do you think of these names? (source)

  • Two-component system
  • MAPK signaling pathway
  • Wnt signaling pathway
  • Notch signaling pathway
  • Hedgehog signaling pathway
  • TGF-beta signaling pathway
  • VEGF signaling pathway
  • Jak-STAT signaling pathway
  • Calcium signaling pathway
  • Phosphatidylinositol signaling system
  • mTOR signaling pathway

--JWSchmidt 03:30, 25 June 2006 (UTC)

John, I hope you don't mind me moving your suggestions here. This list looks good. When it comes to naming articles I think we could drop the "pathway" from the title. It's quite meaningless and I wouldn't really describe calcium signaling as a single pathway, for instance. Obviously, this list isn't complete, but we can accept as guide/convention for naming articles in the future.
I think we could mentioned a proposed rename on the talk pages of the articles involved and leave a link to this page. If there are no objections after a few days we could go ahead and move them. --Peter Z.Talk 18:28, 25 June 2006 (UTC)

[edit] Notable labs

I propose to add links to most notable labs working on a particular pathway in external links sections of articles. It is too much to hope that the articles will always be maintained up to date. It could help students and researchers new to the subject get up to speed on the latest developments. As this could become a vehicle of shameless self promotion, we need strict criteria for inclusion. Generally, the lab must be accepted among the majority of researchers in the subject area as influential, but this is near impossible to verify. I suggest these rules:

  • Limit the list to 4-5 groups and use these criteria for notability:
  • The pathway must the central research interest of the lab;
  • The lab must have published a large number of papers describing one of the following:
  1. a novel component of the pathway;
  2. the precise role of a component in the pathway;
  3. a new role of the pathway in human development/homeostasis/disease.

--Peter Z.Talk 20:21, 26 June 2006 (UTC)

Hi... actually I think this is too much of a judgement call. It seems fine to list references, and to point to seminal papers - but annointing a sub-set of signaling labs as the most important seems fraught with problems. Just my opinion. Also, one would point to different labs for different contexts, even in the same pathway. Sorry but I strongly disagree with this idea. Gacggt 20:28, 26 June 2006 (UTC)

Yep, I do have the same concerns. The idea is that by following links to lab homepages a reader could find out about papers that had not been published when the article was last updated. Although, I guess a more experienced reader could simply check what the authors of the key referenced papers have been up to lately. Peter Z.Talk 20:34, 26 June 2006 (UTC)

[edit] Categories

I have just realised that we have both Category:Signal transduction and Category:Cell signaling. Now, we do need separate articles for these terms, but I don't think separate categories are justified. I suggest to move all articles to Cell signaling and get rid of signal transduction. I am not sure how category mechanics/bureaucracy works, need to look it up.

It is also about time we agreed on a category system. I suggest we create these subcategories in Category:Cell signaling: Signaling pathways, Ligands (alternatively Cell signaling ligands), Receptors (alternatively Cell signaling receptors), Kinases, Transcription factors. Articles relevant to a particular pathway could be linked together using navboxes, modelled after TGF_beta_signaling_pathway#Summary_table. If there are no objections, I'll proceed to sort things out. It's the best I can do until I get full text access to journals and can get back to writing. Peter Z.Talk 13:28, 8 July 2006 (UTC)

I agree. --GAThrawn22 19:17, 8 July 2006 (UTC)

OK, I have to cross the continent tomorrow. I'll sort things out next week. --Peter Z.Talk 20:37, 14 July 2006 (UTC)

[edit] Willing to Help

Hi, I noticed an invitation to help on this project from some edit I had done on another page and so I wandered here and I'm willing to help, if you can use me (also, didn't mean to put up a big "new discussion" headline for this comment, but I didn't know where else to put it). Unfortunately I'm relatively new to the Wikipedia community, so I'm not really sure how to help.

I currently work in a signaling laboratory that focuses on nutrient signalling to the mTOR-S6 Kinase pathway. We do mostly in-vitro studies and have recently been interested in transcriptional regulation by the pathway.

I think this project is a great idea. I also think that the best way to organize it would be through diagrams, i.e. clickable diagrams akin to how Cell Signaling does it, although I understand that this would be extremely complicated. Best, Mhsia 18:17, 3 August 2006 (UTC)

Bravo guys. Wish I could help. How to depict information seems a point of interest. Hmmm, maybe I'll have something to say after boning up on it a bit. There is often a trade off between clarity and density, but a good 'architecture' can allow both. One problem seems to occur when one item has several different 'meanings' or functions. Perhaps some help from other communities, like logic, graphics, programmers, who?. How about Flash that splits/merges to show alternatives? Wblakesx 23:46, 18 October 2006 (UTC)wblakesx

[edit] Project directory

Hello. The WikiProject Council has recently updated the Wikipedia:WikiProject Council/Directory. This new directory includes a variety of categories and subcategories which will, with luck, potentially draw new members to the projects who are interested in those specific subjects. Please review the directory and make any changes to the entries for your project that you see fit. There is also a directory of portals, at User:B2T2/Portal, listing all the existing portals. Feel free to add any of them to the portals or comments section of your entries in the directory. The three columns regarding assessment, peer review, and collaboration are included in the directory for both the use of the projects themselves and for that of others. Having such departments will allow a project to more quickly and easily identify its most important articles and its articles in greatest need of improvement. If you have not already done so, please consider whether your project would benefit from having departments which deal in these matters. It is my hope that all the changes to the directory can be finished by the first of next month. Please feel free to make any changes you see fit to the entries for your project before then. If you should have any questions regarding this matter, please do not hesitate to contact me. Thank you. B2T2 23:35, 25 October 2006 (UTC)

[edit] Regarding Kisspeptin

Would anyone like to help me make a page for the GnRH regulating protein kisspeptin. There isn't one on Wikipedia yet.--JE.at.UWOU|T 18:35, 14 November 2006 (UTC)

[edit] PAC-1

Cross-posted at Wikipedia talk:WikiProject Molecular and Cellular Biology.

An editor has raised awareness to PAC-1 on WP:DRUGS. I thought some project contributors may have heard of it/be interested in contributing to the article. Thanks, Fvasconcellos 16:46, 26 December 2006 (UTC)

[edit] Wikipedia Day Awards

Hello, all. It was initially my hope to try to have this done as part of Esperanza's proposal for an appreciation week to end on Wikipedia Day, January 15. However, several people have once again proposed the entirety of Esperanza for deletion, so that might not work. It was the intention of the Appreciation Week proposal to set aside a given time when the various individuals who have made significant, valuable contributions to the encyclopedia would be recognized and honored. I believe that, with some effort, this could still be done. My proposal is to, with luck, try to organize the various WikiProjects and other entities of wikipedia to take part in a larger celebrartion of its contributors to take place in January, probably beginning January 15, 2007. I have created yet another new subpage for myself (a weakness of mine, I'm afraid) at User talk:Badbilltucker/Appreciation Week where I would greatly appreciate any indications from the members of this project as to whether and how they might be willing and/or able to assist in recognizing the contributions of our editors. Thank you for your attention. Badbilltucker 17:03, 30 December 2006 (UTC)

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