Talk:Gene cluster

Article Ideas

We are hoping to expand upon this article to include more information regarding current research on gene clusters, some relevant figures and images, and some more high quality references on this topic. We would also like to add some specific examples of gene clusters to the page to help demonstrate this concept. Mnemcek (talk) 22:21, 10 March 2014 (UTC)

I think it would also be beneficial to link this page to other, more robust Wikipedia articles relating to relevant genetics topics. Mnemcek (talk) 01:26, 11 March 2014 (UTC)

Specifically, we are planning to expand upon the definition of gene clusters using relevant figures and images. We also plan to incorporate the use of Bioinformatics to identify gene clusters as well as discuss gene cluster importance in research. Kneal0627 (talk) 02:22, 11 March 2014 (UTC)

Who do you both mean by "we"? Maproom (talk) 08:19, 11 March 2014 (UTC)

Users Kneal0627 and Mnemcek will be working together on this article for a molecular biology course assignment. We are always open to suggestions and collaboration, if you are interested in improving this article. Mnemcek (talk) 16:58, 11 March 2014 (UTC)

Thank you, that is reassuring. I had feared, from your use of "we", that you might represent a team of researchers, with a viewpoint to push.

What I know of gene clusters is from Ohno's book, and I found it fascinating. But it is over 40 years since I last read it, so I can't contribute anything myself. I look forward to learning more, plenty must have been learned since then. Here are some questions, which your additions to the article might answer:

• What is the oldest known gene cluster?
• What is the largest known gene cluster? Maybe different answers for functional genes and for all recognisable genes.
• I assume, or recall from Ohno, that the components of a cluster start by being adjacent, and then get spread across the genome by inversions and translocations. Is that right? Can you approximately date a cluster but how much it is spread across the chromosomes?

From my reading on the subject, this might be difficult to do because tandem arrayed gene clusters and dispersed gene clusters can interconvert between the two forms over time. If I come across any dating techniques using gene clusters, I will certainly add this to the article. Mnemcek (talk) 18:00, 8 April 2014 (UTC)

• The sentence "Hemoglobin molecules contain any two identical proteins from this gene cluster..." makes little sense to me. Perhaps you could clarify it?
• Do all sequenced species show gene clustering? Well – I know viruses don't, and I suspect bacteria don't. So what is the smallest genome that has been found to show clustering?

Bacteria have genes organized into operons which are a type of gene cluster. We are working on adding this to the article in the "Types of Gene Clusters" section. Mnemcek (talk) 18:00, 8 April 2014 (UTC)

Maproom (talk) 20:53, 11 March 2014 (UTC)

P.S. I wonder if you have looked at Human genetic clustering? It is a fork of this article, created on June 14th 2009. Maproom (talk) 20:58, 11 March 2014 (UTC)

Thank you for your comments and concerns about the article. We will take these into consideration as we continue our study on gene clusters and work to improve upon the article. Clusters occur as a result of duplication. As far as starting out as adjacent then spreading across the genome, I am unsure at this time. We will further investigate this theory. Bacteria actually do contain gene clusters in the form of coregulated genes aka operons. Kneal0627 (talk) 12:38, 1 April 2014 (UTC)

Comments from Richarnj

Overall your article is off to a great start. Each section is well written, and I think understandable for the average reader. The content also comes across with a neutral point of view with no original research, and has a much higher degree of verifiability with the addition of sources and inline citations.

The lead section is descriptive and concise, although would recommend rewording or explaining "products." Some readers may not know what genes encode so this description may be slightly too general. The content of your subsections are also descriptive and represent the subheaders well; however, I question if all of your current subheaders should be under "Creation of Gene Clusters." For example, "Types of Gene Clusters" could be its own header if expanded upon. This could even be placed immediately after the lead section with a separate subheader for each type of gene cluster. "Gene clusters vs. tandem repeats" may make more sense outside of the "Types of Gene Clusters" header.

To further expand your content consider addressing How were gene clusters discovered? What experiments or observations were made? Perhaps include a short history of the research of gene clusters. This could give the reader a better overview of the entire subject rather than just a description of the gene clusters themselves. Images may also help illustrate to the reader what a gene cluster looks like. I know it is likely difficult to find but it would be really helpful, especially in describing the difference of gene clusters and tandem repeats.

Additions wiki-linking may so help a less knowledgeable reader. Consider gene, evolution, eukaryote, protein, chromosome, and tandem repeat.

I agree with you here. This article has a lot of complex topics that some readers may not understand, but it is not really the place to go into detail about them. So, we will definitely add wiki-links to help guide understanding of the topics. Mnemcek (talk) 02:22, 8 April 2014 (UTC)

I will give you some additional feedback once I have a chance to read through your sources. Richarnj (talk) 13:27, 28 March 2014 (UTC)

I think you have some great references to start from. You have provided information from your sources without getting too close to the orginal wording and have also made this information less technical which will help the typical wiki audience. I focused mostly on your first reference since you use it most often and for good reason. I would recommend using it even more, if not directly then to gather ideas of new areas to research. While I was reading it I was thinking you could add a discussion of the difference between gene clusters in prokaryotes vs. eukaryotes. You could also discuss how gene clusters are found in a genome and the affects gene clusters have compared with the traditional randomly located genes. You may also want to expand on your discussion of the evolutionary aspects of gene clusters. Richarnj (talk) 13:04, 31 March 2014 (UTC)

Thank you so much for your comments and feedback. We will certainly take these in consideration over the course of our next article contribution as well as throughout the remainder of the project. Kneal0627 (talk) 12:12, 1 April 2014 (UTC)

Thank you for your feedback. We have taken several of your recommendations into consideration. The subheaders under the section Creation of Gene clusters were consolidated. Figures were also added in this section and the content was greatly expanded. We are planning on adding a research section pertaining to gene clusters. While the history of experiments that lead to the discovery of gene clusters is difficult to find, we intend to focus on how gene clusters can/are being used in current research (i.e. treatment of diseases). We have also added several wiki links throughout the article that will hopefully give readers a better understanding of the material without going into so much detail in the article itself. Kneal0627 (talk) 23:44, 8 April 2014 (UTC)

The changes you have made look great, and it is really helpful to have the addition of the figures and wikilinks. A suggestion for working with wikilinks, if you want to link to a page but not use its exact wording you can use the pipe symbol | within the double square brackets. Whatever is before the | is the article to which you are linking and after the | is the text you want displayed to the reader. For example, if phenotype | phenotypic were in square brackets like a wikilink, phenotypic would appear to the reader and the link would redirect to the phenotype page. This could be helpful when you have instances of (biology) in the title of a wikipage. You may also consider shortening the third header to "Types of gene clusters" and using subheadings for prokaryotes and eukaryotes. Can't wait to see how you continue to improve the article in the coming weeks. Richarnj (talk) 12:07, 10 April 2014 (UTC)

Thank you so much for the suggestion with wikilinks. We will definitely use this throughout the article! I think we could shorten the heading and use subheaders. Thanks! Kneal0627 (talk) 21:25, 14 April 2014 (UTC)

The article is now hard to understand

This article used to be short but easy to understand. Recent additions make it impossible to understand. Some examples:

From the first sentence: "closer to one another than anticipated". Anticipated by whom? How close did this person anticipate that such genes would be?

From the second sentence: "varieties of gene clusters". What is a "variety" of a gene cluster?

From the third sentence: "to identify ethnic groups within Homo sapiens". Are there groups within Homo sapiens that differ in their gene clusters? This seems most unlikely, and if true should be supported by a reference.

The fourth sentence "The presence of gene clusters suggests that a cluster provides an evolutionary advantage for the organism". No, it suggests that the genes with the cluster derive from a common ancestor, by duplication and divergence, as described by Ohno. Maproom (talk) 21:48, 29 March 2014 (UTC)

I have deleted the second and third sentences. I realised that their writer had confused the concepts of "gene cluster" and "genetic clustering". Maproom (talk) 08:41, 30 March 2014 (UTC)

Thank you for expressing your concerns and specifying examples of confusion. We will take these into consideration as we continue to improve upon the article. Addressing your concern for the sentence "The presence of gene clusters suggests that a cluster provides an evolutionary advantage for the organism." Yes, genes within a cluster are indicative that they arise from a common ancestor; however, genes within a cluster encode for the same function or variations of that function. Also, gene clusters aid in the horizontal transfer of the complete gene cluster from one species to another. This has become evident through various research and will be further clarified. Kneal0627 (talk) 12:31, 1 April 2014 (UTC)

Because this article is part of a semester project and we are graded on our contributions, we ask that you please refrain from making deletions. Please express your concerns on the article talk page and allow us ample time to respond. If you feel the need to make a deletion, please ensure that the reference is retained if used throughout the remainder of the article. Thanks! Kneal0627 (talk) 12:40, 1 April 2014 (UTC)

I am here to try to improve Wikipedia, not to help you achieve a good grade for your project. However, I can probably hold off making further edits until your project has been graded – when will that be?

Meanwhile, I have a suggestion for how you might improve the article. Start by defining "gene cluster"; then provide information on what is observed about gene clusters; and finally report on knowledge and speculation on how gene clusters are generated and maintained. At present, this material is all there in the article, but in a rather jumbled order. Maproom (talk) 14:31, 1 April 2014 (UTC)

Thank you. We simply ask that you please consider that we are continually working on improving this article as well. The citation that you deleted was correct and did mention coinheritance. I have replaced it. Please take a careful look at the fourth paragraph under the Introduction section of the reference. It states, 'Alternatively, coinheritance may provide the motive force for driving the clustering of genes.' Our project will be fully graded by May 6. Thank you for your suggestions. We will take these into consideration as we work to make our corrections/edits for this week. Kneal0627 (talk) 20:36, 1 April 2014 (UTC)

I apologise. I now realise that what I read was merely the abstract of the cited paper, which does not include the word "coinheritance". However, I believe that if you are to use the word "coinheritance" in the article, you should provide an explanation of its meaning. The paper cited is behind a paywall, and Google yields nothing clearly relevant, so it is not a term you can expect readers here to understand. Maproom (talk) 21:04, 1 April 2014 (UTC)

Comments from mmehta10

Great Start! This topic seems extremely interesting and will probably have great viewership on Wikipedia. I would like to provide some feedback so the learning community can benefit more from this article. I like that you have followed most of the criterion of a good article on Wikipedia platform such as it has been written with a neutral point of view and broadly covers the main aspects of the topic.

I did notice a few points which you may want to improve, one of which is perhaps adding some references for the information under "creation of gene clusters". Also, adding some images along-side the text will surely be appreciated by our visual learners as the readers can grasp the concepts better. Additional detail regarding how these gene clusters are being identified and used currently can also help in making the article more complete. I really like that you have added Wiki-links in order to give readers access to expand their knowledge of this topic easily. The references have been accurately cited and are all from reliable sources.Mmehta10 (talk) 03:17, 31 March 2014 (UTC)

Thank your for your feedback and suggestions for the article. We will take these into considerations as we work to improve upon the content. Initially, there was a reference for the information under "Creation of gene clusters"; however, a deletion in another area by a different user resulted in the loss of the citation. This will be corrected very soon. Kneal0627 (talk) 12:43, 1 April 2014 (UTC)

Thank you for your recommendations! Figures were added under the section "Creation of Gene Clusters." References were also corrected in this area, and the content was greatly expanded. We intend to add a "Research" section that will be aimed in the use of gene clusters in current and future research for the treatment of diseases; however, we are still gathering more information for this section. It will be added relatively soon.

Sorry, I forgot my signature. Kneal0627 (talk) 23:48, 8 April 2014 (UTC)

Hi all, the article seems to be shaping up quite well! Keep up the good work! One quick comment, some detail seems to be "missing" in reference 11: http://david.abcc.ncifcrf.gov/home.jsp. Missing or empty |title= (help). Perhaps this can be recited? Mmehta10 (talk) 01:02, 16 April 2014 (UTC)

I will try to improve the citation, thanks for the heads up. 71.237.32.30 (talk) 02:14, 23 April 2014 (UTC)

Comments from Keilana

Hi guys, great work so far! I have some suggestions for you that I hope you'll find helpful. Please feel free to ask me via email or on my talk page if you have any questions about what I've suggested. Thank you!

• The next thing you should be thinking about is expanding the lead.
• Also, once you've expanded the lead, Wikipedia house style has it that we don't cite facts in the lead as long as they are discussed and cited elsewhere in the article - just something to keep in mind as you expand it.
• As you've noted with the citation needed tags, the section on creation needs citations.
• The writing in general could be simplified a little bit, and I also suggest you gloss complex concepts. One thing that can help with that is wikilinks to other articles that discuss the concepts in greater detail.
• You don't need to repeat citations in each sentence, for example, in the second paragraph of the co-expression sections, you only need the Yi citation at the end.
• Please paraphrase more carefully. The second paragraph of co-expression is far too closely paraphrased from the source, and that's just what I found from my spot check. Close paraphrasing qualifies as plagiarism.

Let me know if you have any questions. Keilana|^{Parlez ici} 15:55, 31 March 2014 (UTC)

Thank your for your feedback and suggestions for the article. We will take these into considerations as we work to improve upon the content. Initially, there was a reference for the information under "Creation of gene clusters"; however, a deletion in another area by a different user resulted in the loss of the citation. This will be corrected very soon. Thank you for your note regarding paraphrasing. I ran this through turnitin.com and it did not come up flagged; however, I will work to correct this. — Preceding unsigned comment added by Kneal0627 (talk • contribs) 12:49, 1 April 2014 (UTC)

Thank you for your recommendations! The lead has been expanded. Citations have been added under the section "Creation of Gene Clusters." Sections were rewritten in order to avoid close paraphrasing. The material under this section has also been further expanded in order to provide a better understanding for readers. Also, wiki links were added throughout the article to provide a means for the audience to understand concepts without going into further detail within the article itself. Once a wikilink has been used for one term, should we continue to use it each time the term is used throughout the article or just the initial one time? Kneal0627 (talk) 23:53, 8 April 2014 (UTC)

Comments from Maproom

I am doubtful of the sentence "Coordinated gene expression, or co-expression as a result of codominance, is considered to be the most common mechanism driving the formation of gene clusters; however, coinheritance has also been considered as a driving force for the formation of gene clusters."

I don't understand how codominance could provide a mechanism for the creation of gene clusters; though it could explain their evolutionary success, once created. I have been unable to find any explanation of the term "coinheritance", in Wikipedia or elsewhere. The source cited is a paper unavailable to me online; its abstract is about the identification of gene clusters, not their origin. Maproom (talk) 06:58, 4 April 2014 (UTC)

Also, there is something wrong with "Gene clusters may be similar to that of an operon.". What does "that" refer to? Maproom (talk) 07:03, 4 April 2014 (UTC)

The term "coinheritance" simply means joint inheritance. That is, the genes are inherited together. Google provides a definition as well as several other free journal articles. We will take all your concerns under consideration as we continue to elaborate on concepts and edit the article. Thanks! 96.36.136.218 (talk) 02:28, 5 April 2014 (UTC)

Comments from Tatabox8

Great job on your article it looks great! The article is well written and I can tell you have spent a great deal of time on it. The writing is informative and unbiased. The researchers that come upon this article will definitely have their questions answered and be informed on the subject matter. The wikilinks are great and will help readers expand on topics they are unfamiliar with. I agree with Richarnj on shortening the heading "Types of gene clusters: Prokaryotic gene clusters vs. Eukaryotic gene clusters" the title is simply too long and will look simple and straightforward if shorten and using subheaders within the section. I was informed by Keilana we don't have to cite the same source back to back sentences. I noticed in the creation of gene clusters source 7 was cited back to back. Also, looking at your reference list it looks like reference 4 and 5 are the exact same reference somehow listed twice. Reference number 11 is missing some information to be a complete source. Perhaps you're waiting on the website to get more information on how to cite the material. I like the addition of the images and the simple description under each one. I find that sometimes looking at the images gives me a good concept of the topic and then reading the material reinforces it. Keep up the good work!Tatabox8 (talk) 04:55, 11 April 2014 (UTC)

Thank you so much for all your suggestions. We will take this under consideration as we work to improve upon the article. Thank you for pointing out the references. I hadn't notice that but will correct it. Kneal0627 (talk) 21:29, 14 April 2014 (UTC)

Comments from Klortho

The comments below are just my suggestions for a couple of ways it might be improved. Keep in mind that they are just suggestions, and if you disagree, or these conflict with other reviewers' suggestions, then do what you think is best.

• The section beginning "Gene clusters may also be formed ..." is giving me a similarity match in Turnitin, but I don't have access to the original source book "Evolution by Gene Duplication". From what Turnitin is saying, though, the paraphrasing is too close. Could you have another look and make sure that it is written in your own words?

• You need to do some copy-editing for grammar. For example, in the lead paragraph, there are two number-disagreements: "protein" should be "proteins", and "Portions of the DNA ... is ...". One trick is to copy-paste the article into MS Word or a similar word processor, and turn on its grammar checker.

• In the link in your lead to "homology", code it this way, so that the reader doesn't see the "(biology)": "[[Homology (biology)|homology]]".

• In the lead, it is not immediately clear that you are talking about different genes across species. I started out thinking it was a cluster of genes on the same chromosome, and it wasn't until the last part that I realized these are homologous genes in different species. It would be nice if that were clear right away.

• But wait: as I read on, it seems that you switched to talking about them as I originally thought the term meant: a cluster of similar genes located close together within a chromosome. So now I am confused. What do gene clusters have to do with phylogeny? Please try to make the lead more clear.

• In general, your headings should be shorter, and you can remove "gene cluster" from them. So, for example, "Creation of gene clusters" -> "Creation". (But, I like "Formation" better, I think.)

• You don't need the sentence, "The process was described by Susumu Ohno in his book Evolution by Gene Duplication (1970)." Just the reference is fine. In later sentences, you don't need "Ohno contended", "Ohno argued", etc., unless these statements are controversial. If they are controversial, make that clear. If not, then just state them as facts.

• You're paragraphs should be shorter.

• I would change the title of the section "Bioinformatics" to "Identification", or "Methods of identification".

• I think it would be nice to expand that section a bit. What are the challenges of identifying gene clusters?

• I think the outline of your article could use a little work. Right now, you have a lot of content in "Creation", and not very much in each of the other sections. I'm not sure what to suggest, but you might take a look at some similar articles, to see how they are organized, and then think about moving your content around a bit.

• I think you have found some very nice figures, and you make good use of them.

Keep up the good work! Klortho (talk) 05:23, 14 April 2014 (UTC)

Thank you so much for all your suggestions! We will take all of these into consideration as we work to improve upon the article. Kneal0627 (talk) 21:32, 14 April 2014 (UTC)

Comments from PaleoBioJackie

Great job so far! There is a lot of great information in your article. Here are a few suggestions:

• You're diagrams are great and there is a lot of information there, but they are too small to read! Especially the second photo, where one would have to click in to it to see it, but then click the back button to read the description. They cannot view the diagram and the description at the same time. It is easy to resize images, you need to add |300px| (or whichever size you choose) into the editing area of the photos. If this is unclear, try finding a Wikipedia article that has a larger image and click edit to learn how they made it bigger.

• I would love to see an image closer to the beginning of the article to help draw people in.

• The body of the article is good, but the introduction could use some work. It is a little difficult to understand and there are some grammatical errors, specifically plural vs singular form seems to switch within the same sentence a couple of times.

• For the WikiLinks, if the context word you want to use is plural (i.e. proteins) but the article is singular, you could code : "[[Protein|proteins]]". In context, this would look like: "Some proteins have been found to ....." for example.

• It might be helpful to clarify in the intro: Are gene clusters found in each organism, or are they a means of comparing similar genes across several organisms/species?

• The topic is written pretty well for a layman to understand, but I think there is still more that can be done in this area. Overall, good job making a tough subject easily accessible to non-scientists!

PaleoBioJackie (talk) 18:12, 14 April 2014 (UTC)

I have tried playing around with the size of the images. This is the best I could come up with. Anything passed this causes the images to overshadow the text, making the article look funny. I'll keep trying though! Thank you so much for all your suggestions! We will take all of these into consideration as we work to improve upon the article. — Preceding unsigned comment added by Kneal0627 (talk • contribs) 21:35, 14 April 2014 (UTC)