Talk:Gene expression

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Measurement[edit]

Need slow throughput techniques e.g. northern blot --Zven 12:12, 17 September 2006 (UTC)

I just updated this entire section, adding, for example, the northern blot, and a little more information on DNA microarrays. I also cleaned up the language to make it hopefully more accurate. I also updated the protein-level measurement part, since the original author was apparently unaware that Western blots are still the standard method of choice for reporting protein levels. Let me know what you think. -- Josh 03:36, 7 June 2007 (UTC)

Is human DNA homo- or hetero- encoding?[edit]

Consider the totality of all gene expressions within a chromosome. Are all genes on the same side of the DNA strand? In other words if you split the double helix are all the genes on one strand or are they staggered between the two strands?

If I remember correctly, which I think I do, each strand is just the mirror image of the other one. Codons on one strand match up with Anti-codons on the other.--Urthogie 21:37, 22 April 2007 (UTC)
Genes are dispersed among both strands in a single chromosome. With 100% confidence. -- Josh 03:39, 15 May 2007 (UTC)

Backing that up, open reading frames can occur on either strand in either direction Silasmellor (talk) 14:22, 10 May 2009 (UTC)

Patterns of Gene Expression[edit]

moved terms to Glossary of Scientific Terms related to Gene Expression. Removed empty section.

Housekeeping genes[edit]

Why does housekeeping genes redirect to this article? ώЇЌĩ Ѕαи Яоzε †αLҝ 21:50, 11 June 2007 (UTC)

  • I'm assuming because there is no 'housekeeping genes' article yet, that you need to underestand gene expression at least a bit to understand housekeeping genes, and that this article is the most informative one that the person making the redirect could find at the time. JetheroTalk 00:25, 9 July 2007 (UTC)

Intro Sentence[edit]

Was:

  • '''Gene expression''', or simply '''expression''', is the process by which a [[gene]]'s [[DNA sequence]] is converted into functional [[proteins]].

But:

  • DNA is not 'converted', but transcribed, leaving intact DNA behind
  • the term 'DNA sequence' does not capture epigenomic 'information', which may indeed be part of the inheritable trait, or genetic information, and have an effect on the amount or structure of the 'expressed' gene or trait.
  • not all 'gene expression', and perhaps not even most, results in protein production. Protein is not the only trait, or 'expression' of genetic information
  • Sentence from gene article was more comprehensive, but not quite what we need here. "The process of producing a biologically functional molecule of either RNA or protein is called gene expression, and the resulting molecule itself is called a gene product."
  • however, this still needs to be simple, so please continue to refine.

So is now:

  • '''Gene expression''', or simply '''expression''', is the process by which the inheritable information which comprises a [[gene]], such as the [[DNA sequence]], is made manifest as a physical and biologically functional [[gene product]], such as [[protein]] or [[RNA]].

JetheroTalk 00:49, 9 July 2007 (UTC)


Talking about proteins in the measurement of gene expression section[edit]

I removed the initial lines "The expression of many genes is regulated after transcription (i.e., by microRNAs or ubiquitin ligases), so an increase in mRNA concentration need not always increase expression. In fact, mRNA concentration has been shown to be a poor predictor of resultant protein abundance.[1][2]" because IMHO it serves as a pretty bad start for what essentially should just be a walk-through of the different methods that exists to quantify mRNA (ie. the de facto definition of gene expression in the litterature). Even if we do want to talk proteins, and I agree that this is relevant, it should come in another section. --LasseFolkersen (talk) 12:50, 31 March 2009 (UTC)

  • It might be useful here to talk about microarray technology in a bit more depth than just a mention. Thoughts? Contributions/160.94.10.132 (talk) 14:25, 15 June 2009 (UTC)
  • With regards to the sentence "The stability of the final gene product, whether it is RNA or protein, also contributes to the expression level of the gene - an unstable product results in a low expression level." Should an unstable protein not require a high gene expression level? Can anyone confirm this? Lady of the dead (talk) 21:00, 7 September 2009 (UTC)

What's on the to-do list?[edit]

This article is the MCB Wikiprojects Collaboration of the Month. What does it need? It appears to me that each of the sections should have a "main article: bla" link in it, for starters. Then we need to decide how much detail goes into those sections, as each step (i.e. Transcription, Translation, etc.) has its own article already. Should we be trying to improve the overall understanding of the whole process of expression here? It's not entirely clear to me what the goal of the article is. Agathman (talk) 00:11, 28 May 2009 (UTC)

The two core questions in any article are "what is it" and "why is it important". The article could do with a better lead that would give a broad and simple overview, less emphasis on techniques (which are of limited interest to most of our audience) and a much expanded section on the various levels of regulation. Tim Vickers (talk) 02:57, 28 May 2009 (UTC)

Eukaryote bias[edit]

This article currently has a significant eukaryoitic bias; please try to avoid this! I will make some edits to clarify the differences between prokaryotic and eukaryotic gene expression, particularly with respect to co-translation in prok's, RNA processing, nuclear export, folding location and secretion via exocytic pathways. - Zephyris Talk 10:33, 29 July 2009 (UTC)

Remove Article on Protein Expression?[edit]

The protein expression article seems abandoned. Should it be deleted and redirected to gene expression? Pdcook (talk) 19:38, 11 September 2009 (UTC)

Oppose. Protein expression is related to gene expression but nevertheless is a distinct subject. A quick search of PubMed and Google Books reveals an enormous amount of material that has been published on this subject (a few citations to review articles and monographs has now been added to the article). Therefore I believe protein expression deserves its own article. Boghog (talk) 10:34, 12 September 2009 (UTC)
I do see your point, but most of the information contained within protein expression is already present within the gene expression article. We could perhaps have a section within the gene expression article entitled protein expression. I have also noticed that many times when we say protein expression we actually do mean gene expression. Pdcook (talk) 15:07, 14 September 2009 (UTC)
More often mRNA expression is meant. Redirecting from a non-synonym will only cause confusion and/or force awkward layout here; this article is prominently linked from protein expression anyway. Plus this article already has problems with clearly separating protein and RNA. Narayanese (talk) 15:44, 14 September 2009 (UTC)
I wonder if the definitions of these terms vary depending on field of study. A geneticist versus a protein biochemist might define them differently, and certainly the distinction is nebulous at best. I guess from my perspective, protein expression can only be a subset of gene expression, unless you're including artificial peptide synthesis. I'm curious how others differentiate these two terms.Pdcook (talk) 22:43, 14 September 2009 (UTC)
I have a feeling it's the same across the fields, i e that its a subset. Narayanese (talk) 22:00, 16 September 2009 (UTC)
In one of my second year introductory lectures, we were asked at what stage we considered that a gene was expressed. The biochemists and geneticists said it was as soon as mRNA is transcribed, the microbiologists said it was once protein was produced, and the biologists were mostly split between those two with a few that saw it as being at the point of the gene's phenotypic manifestation. I'm generalising of course, but that was the general trend. So in that crowd at least, there was a divide (sorry about the mini-essay to make the point).
I don't think there should be a page dedicated solely to the protein expression side of gene expression; we'd just be repeating ourselves. It seems to me that the citations in the protein expression article focus on the biotechnology side of protein production? Yes, this is a very important line of research, but there's a distinction to be made. Is there not a more suitably titled page for the biotech. aspect? Or could we move some of it to more suitable pages? For instance one of those cited articles (>>) at least seemed to me like it would be more at home in the expression vector article. Ribrob (talk) 16:01, 18 September 2009 (UTC)
As you might imagine, I agree with Ribrob. It doesn't seem like we're saying anything new in the protein expression article. Even the biotechnological aspect is covered to a greater extent in the gene expression article. Pdcook (talk) 17:20, 18 September 2009 (UTC)

It would be nice if we could make a decision on this soon. Pdcook (talk) 03:22, 27 September 2009 (UTC)

In think Ribrob's comments are very helpful. In the field of molecular biology, protein expression is certainly a subset of gene expression while in the fields of biotechnology and proteomics it is distinct. Furthermore in the field of expression profiling, (gene expression) ≠ (protein expression) since the mRNA levels do not necessarily correlate to the amount of expressed protein. So I propose that the protein expression article be renamed to something like "protein expression (biotechnology)" and the material in the gene expression article relating to biotechnology be moved to the "protein expression (biotechnology)" article. Boghog (talk) 06:33, 27 September 2009 (UTC)
I think that is a great idea, Boghog. Pdcook (talk) 19:29, 30 September 2009 (UTC)
Keep per WP:NOEFFORT, WP:PNJCS etc. --Kkmurray (talk) 17:15, 19 October 2009 (UTC)
Concur with BogHog . Additional bird killed with that stone: The gene expression article is nice and short, while clearly directs to the various subtopics. only longer section there is gene expression systems which would fit perfectly in protein expression (biotechnology). I think that is decided! --Squidonius (talk) 10:26, 20 October 2009 (UTC)
Yes check.svg Done Thanks for everyones support. Per the discussion above, I have moved most of the material in the Gene_expression#Expression_system section to the newly renamed protein expression (biotechnology) article. Cheers. Boghog (talk) 06:33, 28 October 2009 (UTC)
Thanks. I think it's a big improvement. Pdcook (talk) 23:08, 9 November 2009 (UTC)

Transcription[edit]

The previous version of this text explained correctly, that the produced RNA strand is complimentary to the used template DNA strand. DNA "TAC" to RNA "AUG" (encoding for methionine and also serving as start codon for translation) was given as an example. However, the template DNA strand is itself read in "reverse" 3' → 5' direction to create the new strand in 5' → 3' "sense" direction. The newly generated 5' → 3' RNA is therefore identical to the 5' → 3' coding strand of the DNA (complimentary strand of a complimentary strand), with the difference that T is replaced by U in RNA, of course. This new version is in concordance with the more detailed Transcription (genetics) article and, I believe, less confusing to the first time reader. --Firefly's luciferase (talk) 03:01, 26 February 2010 (UTC)

inducible genes[edit]

The words inducible gene redirect here and yet there's absolutely no trace of the word "inducible" in this article. Someone fix this please or remove the redirect and create a separate article for what an inducible gene is. 98.176.12.43 (talk) 19:34, 9 October 2010 (UTC)

The term inducible gene was defined in a previous version of this article but lost in subsequent edits. I have reintroduced these definitions. In addition, I have changed the redirect of inducible gene to the more specific Gene_expression#Regulation_of_gene_expression. Boghog (talk) 20:52, 9 October 2010 (UTC)
I also just noticed that a definition of an inducible gene was included in the Glossary_of_gene_expression_terms#I. Boghog (talk) 07:25, 10 October 2010 (UTC)

Tools[edit]

Regulation of gene expression#Methods has a more extensive section on tools, albeit it has a focus on whether the abundance measured is relative or absolute (e.i. protein foo @ condition B is n times higher than @ condition A or foo is n pM ), as the article is about change in expression levels. Maybe a copy-paste possibility? --Squidonius (talk) 03:21, 10 October 2010 (UTC)

Overexpression?[edit]

Overexpression redirects to this article. What does it mean? --Abdull (talk) 12:29, 2 June 2012 (UTC)

Overexpression = gene expression above the normal amount. This can be done in the laboratory for example by gene knockin (inserting extra copies of the gene into a cell). Overexpression is also a possible mechanism by which pathogens or cancer cells can become resistant to drugs. Boghog (talk) 12:46, 2 June 2012 (UTC)

The articles Gene expression and Protein biosynthesis are similar[edit]

Both the articles refer to the same thing. I see no dissimilarities. The ultimate goal of gene expression is protein synthesis. These two articles are like seeing a snake from its mouth and from the tail. So I propose to merge the two articles. This message will also be posted on Gene expression article. --G.Kiruthikan (talk) 13:58, 1 March 2014 (UTC)

Overexpress and Overexpression undefined[edit]

Overexpress and Overexpression redirect to this article but are not defined. Should the article cover the term or should redirects be removed? pgr94 (talk) 10:41, 12 May 2014 (UTC)