This article is rated Start-class on Wikipedia's
content assessment scale. It is of interest to the following WikiProjects: | |||||||||||||||||
|
This article is currently the subject of an educational assignment. |
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)
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)
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 will give you some additional feedback once I have a chance to read through your sources. Richarnj ( talk) 13:27, 28 March 2014 (UTC)
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)
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)
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!
Let me know if you have any questions. Keilana| Parlez ici 15:55, 31 March 2014 (UTC)
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)
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)
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.
Keep up the good work! Klortho ( talk) 05:23, 14 April 2014 (UTC)
Great job so far! There is a lot of great information in your article. Here are a few suggestions:
PaleoBioJackie ( talk) 18:12, 14 April 2014 (UTC)
where you talk about related species, you had better mention that it's the same gene cluster. Hemoglobin is a
protein family, so it perhaps need slightly more explanation.
In the Coordinated gene expression, part the first sentence is unclear because we do not know what codominance is.
Better to explain what Coordinated gene expression, is first and then tell us the driving force and why it is so.
"A gene is duplicated during cell division" - this is completely normal, but it does not lead to "two end-to-end copies" normally, so please explain more clearly.
"It was theorized" better to say who theorized it. And this qualifer suggests that there is no evidence to support it. Whereas this idea may be widely supported.
"Gene converson" and "homogenized" both need to be explained in the sentence.
In the tandem arrays section there seems to be repetition about "essential"
Caenorhabditis elegans is a worm not a bacterium. Also Ciona intestinalis is not a procaryote.
It would be good to explain DAL and GAL a bit more as there are no Wikipedia articles on the topic yet.
more poor --> poorer
Terms to link in the lede: gene chromosome protein
More terms to link: Ciona intestinalis operon hybridizations bioinformatics (should be lower case b) dendogram chimaerism Digital transcriptome subtraction when talking about vector adaptor contamination 3p21.3 (mentioned so many times in Wikipedia but no article, closest is Chromosome 3 (human)); breast cancer lung cancer methylation, epigenetic Histone acetyltransferase
Grammar: organisms' (you are talking about one); " of genes on within" " despite it was initially thought" "programs exist which conducts"
Spelling to fix: ProtHox
Style: only the first word in a header should be capitalized.
Don't put terms in the see also section Wikipedia:See_also that are used and linked in the article. So for example link gene families in your article. Graeme Bartlett ( talk) 06:46, 26 April 2014 (UTC)
I do not share other editors' positive views about recent changes to the article. It appears to me that misunderstandings have been introduced.
In the lede:
In the "Coordinated Gene Expression" section, I find the first sentence hard to believe. It ignores the mechanism proposed by Ohno as the origin of gene clusters, and suggests two mechanisms which may explain the subsequent divergence of the genes within a cluster, but cannot explain its origin. The reference cited is behind a paywall, and I have been unable to read it; but its abstract, which is freely readable, is about identification of gene clusters, not about their origin. I also wonder if, when this section says "gene expression", it means "gene regulation". Maproom ( talk) 14:56, 28 April 2014 (UTC)
And most seriously, the word "clustering" appears 19 times in the article. In every instance, this is a result of an editor confusing genetic clustering (as described at Human genetic clustering) with gene clusters. These are entirely different phenomena. A gene cluster is a group of genes within a genome that are homologous in origin and have related functions. Genetic clustering is the use of cluster analysis to study the degree of relatedness of populations. Maproom ( talk) 15:16, 28 April 2014 (UTC)
Overall I really enjoyed learning about gene clusters. Your overall layout is very fluid and works nicely. I hope my suggestions are helpful in your future endeavors. Previte01 ( talk) 02:46, 30 April 2014 (UTC)
The following is copied from Wikipedia_talk:WikiProject_Genetics#Gene_cluster_article. Maproom ( talk) 11:06, 19 January 2015 (UTC)
Eight months ago, I wrote
No-one responded (and today, coincidentally, my request was archived). I am planning to work on the article myself soon. I shall copy this to its talk page.
While the students made many improvements to the article, they added a long section on formation, discussing various theories about the origin of gene clusters. But this is absurd; the origin of gene clusters (by duplication and divergence) was known in 1972, and is not in doubt. This is acknowledged in the second sentence of the article "A gene cluster is part of a gene family": The gene family article starts "A gene family is a set of several similar genes, formed by duplication of a single original gene."
I will replace the long "formation" section by a much shorter historical section, mentioning the various pre-1970 conjectures. Maproom ( talk) 11:01, 19 January 2015 (UTC)
The first paragraph of the article currently says that the members of a cluster "are located within a few thousand base pairs of each other"; and that "Genes found in a gene cluster may be ... on different ... chromosomes." I could accept either, but not both at once. I will appreciate some help in sorting out this mess. Maproom ( talk) 23:22, 14 February 2015 (UTC)
Hello fellow Wikipedians,
I have just modified one external link on Gene cluster. Please take a moment to review my edit. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit this simple FaQ for additional information. I made the following changes:
When you have finished reviewing my changes, you may follow the instructions on the template below to fix any issues with the URLs.
This message was posted before February 2018.
After February 2018, "External links modified" talk page sections are no longer generated or monitored by InternetArchiveBot. No special action is required regarding these talk page notices, other than
regular verification using the archive tool instructions below. Editors
have permission to delete these "External links modified" talk page sections if they want to de-clutter talk pages, but see the
RfC before doing mass systematic removals. This message is updated dynamically through the template {{
source check}}
(last update: 5 June 2024).
Cheers.— InternetArchiveBot ( Report bug) 01:27, 9 January 2017 (UTC)
I was shocked that the Gene cluster wikipedia page was devoted solely to a specific type of gene clusters (albeit very important to evo-devo studies), and ignores the more widespread use of the term, which includes secondary metabolism clusters and others from bacteria, fungi, plants and others. My quick review of the history of the article here seems to point to these getting pushed out some time ago because they did not fit the author's constrained definition of gene cluster. In fact, in comparative genomics, "gene cluster" has at least 4 connotations: 1. Clusters of orthologous genes (similarity groups), 2. Hox/tandem paralog clusters, and 3. Metabolic gene clusters (tightly linked non-homologous genes contributing to a common function), and 4. genes with coordinated expression in transcriptomes.
Probably the most parsimonious solution would be to have a disambiguation page, and rename the current gene cluster page into what it actually is, the Hox gene cluster page. Slotjc ( talk) 18:46, 15 March 2018 (UTC)
This article is rated Start-class on Wikipedia's
content assessment scale. It is of interest to the following WikiProjects: | |||||||||||||||||
|
This article is currently the subject of an educational assignment. |
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)
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)
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 will give you some additional feedback once I have a chance to read through your sources. Richarnj ( talk) 13:27, 28 March 2014 (UTC)
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)
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)
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!
Let me know if you have any questions. Keilana| Parlez ici 15:55, 31 March 2014 (UTC)
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)
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)
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.
Keep up the good work! Klortho ( talk) 05:23, 14 April 2014 (UTC)
Great job so far! There is a lot of great information in your article. Here are a few suggestions:
PaleoBioJackie ( talk) 18:12, 14 April 2014 (UTC)
where you talk about related species, you had better mention that it's the same gene cluster. Hemoglobin is a
protein family, so it perhaps need slightly more explanation.
In the Coordinated gene expression, part the first sentence is unclear because we do not know what codominance is.
Better to explain what Coordinated gene expression, is first and then tell us the driving force and why it is so.
"A gene is duplicated during cell division" - this is completely normal, but it does not lead to "two end-to-end copies" normally, so please explain more clearly.
"It was theorized" better to say who theorized it. And this qualifer suggests that there is no evidence to support it. Whereas this idea may be widely supported.
"Gene converson" and "homogenized" both need to be explained in the sentence.
In the tandem arrays section there seems to be repetition about "essential"
Caenorhabditis elegans is a worm not a bacterium. Also Ciona intestinalis is not a procaryote.
It would be good to explain DAL and GAL a bit more as there are no Wikipedia articles on the topic yet.
more poor --> poorer
Terms to link in the lede: gene chromosome protein
More terms to link: Ciona intestinalis operon hybridizations bioinformatics (should be lower case b) dendogram chimaerism Digital transcriptome subtraction when talking about vector adaptor contamination 3p21.3 (mentioned so many times in Wikipedia but no article, closest is Chromosome 3 (human)); breast cancer lung cancer methylation, epigenetic Histone acetyltransferase
Grammar: organisms' (you are talking about one); " of genes on within" " despite it was initially thought" "programs exist which conducts"
Spelling to fix: ProtHox
Style: only the first word in a header should be capitalized.
Don't put terms in the see also section Wikipedia:See_also that are used and linked in the article. So for example link gene families in your article. Graeme Bartlett ( talk) 06:46, 26 April 2014 (UTC)
I do not share other editors' positive views about recent changes to the article. It appears to me that misunderstandings have been introduced.
In the lede:
In the "Coordinated Gene Expression" section, I find the first sentence hard to believe. It ignores the mechanism proposed by Ohno as the origin of gene clusters, and suggests two mechanisms which may explain the subsequent divergence of the genes within a cluster, but cannot explain its origin. The reference cited is behind a paywall, and I have been unable to read it; but its abstract, which is freely readable, is about identification of gene clusters, not about their origin. I also wonder if, when this section says "gene expression", it means "gene regulation". Maproom ( talk) 14:56, 28 April 2014 (UTC)
And most seriously, the word "clustering" appears 19 times in the article. In every instance, this is a result of an editor confusing genetic clustering (as described at Human genetic clustering) with gene clusters. These are entirely different phenomena. A gene cluster is a group of genes within a genome that are homologous in origin and have related functions. Genetic clustering is the use of cluster analysis to study the degree of relatedness of populations. Maproom ( talk) 15:16, 28 April 2014 (UTC)
Overall I really enjoyed learning about gene clusters. Your overall layout is very fluid and works nicely. I hope my suggestions are helpful in your future endeavors. Previte01 ( talk) 02:46, 30 April 2014 (UTC)
The following is copied from Wikipedia_talk:WikiProject_Genetics#Gene_cluster_article. Maproom ( talk) 11:06, 19 January 2015 (UTC)
Eight months ago, I wrote
No-one responded (and today, coincidentally, my request was archived). I am planning to work on the article myself soon. I shall copy this to its talk page.
While the students made many improvements to the article, they added a long section on formation, discussing various theories about the origin of gene clusters. But this is absurd; the origin of gene clusters (by duplication and divergence) was known in 1972, and is not in doubt. This is acknowledged in the second sentence of the article "A gene cluster is part of a gene family": The gene family article starts "A gene family is a set of several similar genes, formed by duplication of a single original gene."
I will replace the long "formation" section by a much shorter historical section, mentioning the various pre-1970 conjectures. Maproom ( talk) 11:01, 19 January 2015 (UTC)
The first paragraph of the article currently says that the members of a cluster "are located within a few thousand base pairs of each other"; and that "Genes found in a gene cluster may be ... on different ... chromosomes." I could accept either, but not both at once. I will appreciate some help in sorting out this mess. Maproom ( talk) 23:22, 14 February 2015 (UTC)
Hello fellow Wikipedians,
I have just modified one external link on Gene cluster. Please take a moment to review my edit. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit this simple FaQ for additional information. I made the following changes:
When you have finished reviewing my changes, you may follow the instructions on the template below to fix any issues with the URLs.
This message was posted before February 2018.
After February 2018, "External links modified" talk page sections are no longer generated or monitored by InternetArchiveBot. No special action is required regarding these talk page notices, other than
regular verification using the archive tool instructions below. Editors
have permission to delete these "External links modified" talk page sections if they want to de-clutter talk pages, but see the
RfC before doing mass systematic removals. This message is updated dynamically through the template {{
source check}}
(last update: 5 June 2024).
Cheers.— InternetArchiveBot ( Report bug) 01:27, 9 January 2017 (UTC)
I was shocked that the Gene cluster wikipedia page was devoted solely to a specific type of gene clusters (albeit very important to evo-devo studies), and ignores the more widespread use of the term, which includes secondary metabolism clusters and others from bacteria, fungi, plants and others. My quick review of the history of the article here seems to point to these getting pushed out some time ago because they did not fit the author's constrained definition of gene cluster. In fact, in comparative genomics, "gene cluster" has at least 4 connotations: 1. Clusters of orthologous genes (similarity groups), 2. Hox/tandem paralog clusters, and 3. Metabolic gene clusters (tightly linked non-homologous genes contributing to a common function), and 4. genes with coordinated expression in transcriptomes.
Probably the most parsimonious solution would be to have a disambiguation page, and rename the current gene cluster page into what it actually is, the Hox gene cluster page. Slotjc ( talk) 18:46, 15 March 2018 (UTC)