Talk:List of gene families

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1) I think that the concepts "gene family" and "gene complex" should have their own pages. They can be defined there. I'm not sure what a gene complex is, but if it is what I think it is, it should not be included in Gene Family. adam


A gene complex is really a gene family, it's an older terminology. The MHC is such a gene complex, since it consists of functionally related genes that appear that are also evolutionarily related. --Lexor|Talk 02:47, 7 Mar 2004 (UTC)

2) This page could get very big very fast. I threw in some more content just to get an idea of how we can organize the page. I think we should focus on protein superfamilies, and maybe we can note a few of the major subfamilies in parentheses. adam

You have to be careful about the distinction between the genes that encode the proteins and the proteins themselves. If you want to talk about protein families, e.g. along the lines of the SCOP database, which might include genes that are functionally related but not necessarily based on common descent, then it probably deserves a page protein family and/or List of protein families. --Lexor|Talk 02:47, 7 Mar 2004 (UTC)
As I understand the term, the essence of a gene families is common descent. Biochemical activity and organismal function are generally side effects of common descent, though I suppose that they could be considered as additional requirements for identifying a group of genes as a family. Also, if a gene family encodes proteins, I would think that "protein family" and "gene family" would be synonomous. If someone is using the term "protein family" in a way that is not analgous to "gene family", then we are heading for a clash of terminology (not like that's uncommon). I would suggest using a term like "protein class", but I guess that's not my decision. I did a PubMed search for "gene family" and it seems that many researchers use the term "gene family" as I described it. However, that doesn't mean that there isn't another usage. adam
Adam, yes your understanding is more or less my understanding. I perhaps worded my response a little carelessly. Yes, in general, gene families and protein families are both (or should be) based on common descent. However, I think that gene families are usually defined almost exclusively with regard to common descent, whereas when people are talking about protein families, sometimes biologists (especially molecular biologists), tend to lump functionally-related proteins with evolutionarily-related proteins by default without doing rigorous phylogenetic testing to establish that that is the case (e.g. convergent evolution can produce similar function and/or proteins that have similar binding sites and therefore functionally may be otherwise structurally, and therefore, evolutionarily, different). I just want to make sure that the list doesn't conflate the two, because they're already conflated enough in the literature. Am I making sense? --Lexor|Talk 04:25, 8 Mar 2004 (UTC)
In defense of us molecular biologists (feigned insult) we do at least do an allignment before declaring that a set of proteins are related...and we are learning that there is no such thing as "% homology"! Anyway, it seems the main issue is how we decide that some protein family in fact exists. Is it good enough if Albert's says so in Molecular Biology of the Cell? If any peer-reviewed work says so? Or are we going to dig thru ever reference and see which gene families really are justified? The last would be great, but it really seems excessive, especially considering that anyone can just come in and say "oh, my favorite gene family is not listed, I'll list it". I have to admit that I was not being careful when I added those gene families... they were just off of the top of my head and I have little or no idea of what justifies calling them a family. AdamRetchless 04:52, 8 Mar 2004 (UTC)
Sorry, I didn't know you were a molecular biologist. I know that most molecular biologists are aware of the distinction, it's more that occasionally in informal circumstances they are more likely to get a bit more sloppy than evolutionary biologists and systematists because it's not their bread and butter. Likewise systematists get sloppy when talking about molecules. No real slight intended... ;-) With regard to the issue on inclusion, it's probably not our role to get involved in angels on pinheads discussions about whether a given family is a true evolutionary family or not. So long as we note and carefully explain the possible conflation in the literature in the article, then we're doing our best to reflect the state of knowledge in the field (which includes the confusion over the exact definition of a protein and gene families!) that's fine with me. That's all we can really do as encyclopedists... --Lexor|Talk 05:08, 8 Mar 2004 (UTC)

Okay, I did pubmed and google searches on "gene complex". While I did not get a straight definition, I think I understand how the term is being used. As I read those articles, a gene complex is a region of a chromosome with several genes (loci?) of related function. This concept was in use long before we had any gene sequences so I can't see how it could involve any idea of gene homology. It has turned out that many gene complexes resulted from duplications of individual genes and therefore the genes in the complex also belong to the same family. However, a gene complex is not synonomous with a gene family. Now I just need to figure out if gene complex is synonomous with a "gene cluster", such as the globulin cluster. AdamRetchless 04:24, 8 Mar 2004 (UTC)


This could be a good resource for lists of gene families. As I understand copyright laws, lists cannot be copyrighted.
http://www.gene.ucl.ac.uk/nomenclature/genefamily.shtml
adam

Yes and no, if this database protection bill HR 3261 [1] that has been proposed in the US passes, we could be in for trouble for taking aggregation of mere facts. Not a problem now, but it is on the horizon and wikipedians should be alert to possibilities down the road. --Lexor|Talk 04:25, 8 Mar 2004 (UTC)


sigh Yeah. I forgot about that. Anyway, the link that I posted isn't really a list... it's a bunch of links to webpages. It would require a bit of work for us to extract what we really want from it, so I don't think that it would be a problem. AdamRetchless 04:52, 8 Mar 2004 (UTC)
It would be good to coordinate this page with the protein family page Gribskov 13:59, 20 September 2007 (UTC)