Talk:Housekeeping gene

Untitled
Please put new topics at the TOP.

New Data from 2013
I only found the Eisenberg/Levanon paper this week, but I've been corresponding with the authors so that I can update this page; this might take a little time; they generated a smaller, handier list which I think should take the place of this page. I also want to put up a disambiguation page that distinguishes between housekeeping genes, reference genes, and minimal gene set....all closely related but distinct terms that are often described loosely as "housekeeping genes." Then I'd like to store the big data file up here (if it's OK with the authors.) The one from their old paper in 2003 got moved so that the link that is in the 2003 paper is now broken: the new link is http://www.tau.ac.il/~elieis/Housekeeping_genes.html. doctorwolfie (talk) 15:09, 11 February 2015 (UTC)

I've updated the list through ribosomal proteins doctorwolfie (talk) 12:33, 23 February 2015 (UTC)

I'm up to apoptosis; page is getting pretty long, but there is method to this madness.... doctorwolfie (talk) 22:54, 23 February 2015 (UTC)

Down through proteosome bits... lost a lot of metabolism genes which was unexpected... I guess the liver just took over and shut em down for the other cells. doctorwolfie (talk) 22:53, 24 February 2015 (UTC)

Needs updating with new MIQE guidelines
Hello! The term "housekeeping gene" is now out of date. New publishing guidelines require them to be called "reference genes" now. Readingismyserenity (talk) 16:46, 4 February 2015 (UTC)

Awesome! Do you have a reference for reference genes? There was also a cool paper by Eli Eisenberg and Erez Levanon at http://www.sciencedirect.com/science/article/pii/S0168952513000899 which I'd like to incorporate. doctorwolfie (talk) 21:02, 5 February 2015 (UTC)

Sentence in introduction is a special, but not general topic
The sentence "In a recent study involving cardiac stem cells Actb and GADPH were found to be the most consistent, while β2M, HPRT-1 and RPLP-1 varied significantly between neonatal and adult cardiac cells.[4][5]" cites a study and is not suitable for an introduction. Please mention this particular finding later in the text. — Preceding unsigned comment added by 85.127.52.201 (talk) 20:33, 10 January 2012 (UTC)

The problem we were having was in defining precisely what we mean by "housekeeping gene" which is why the question is posed in the introduction...hoping that an expert could clear it up!doctorwolfie (talk) 18:15, 14 May 2012 (UTC)

Now I think 85.127.52.201 is probably right after all; I need a more succinct introduction; the most important point is that when scientists need to find a reference gene for their work that they get to the best, handiest and most up-to-date list. I arbitrarily chose to organize the list by proposed function for selfish study reasons, so as I work through the new list I plan to do the same. It should be a much shorter list, but as stated above, I hope to store the BIG data file (which is alphabetical) up here soon. doctorwolfie (talk) 15:09, 11 February 2015 (UTC)

2011 Draws to a close
Still not much traffic here; I sent some queries to Nature Genetics and Journal of Genetics but haven't got any help yet. doctorwolfie (talk) 14:43, 15 December 2011 (UTC)

New ideas for 2011
I've become so uncertain about the definition of a housekeeping gene, that I don't know what to do with this page. I finally found Dr. Koonin's group and am happily reading as many articles as I can find. Looks like the "minimal gene set" is quite literally "old hat". There are several orthologous clusters that seem to correspond to the idea of a "housekeeping niche" rather than a gene per se. There is also something a little disturbingly "de-localized" about some of the "housekeeping" functions; why bother to carry an important gene for metabolism if you live in close proximity to a symbiote that makes the product for you in abundance? Primates lost the ability to manufacture vitamin C, but that was OK because we lived in trees where there was plenty of vitamin C containing fruit!

ToDo list: Definition 1 (see below under "Update"): see if we can find the original usage of the term Definition 2: speak to a good bench-researcher to see if a table of standards is common use and build a list for those purposes Definition 3: although this suits my personal goals (looking at evolutionary biology, etc, compounding lists of "proposed housekeeping genes" may not be useful to anyone, especially if the goal is to construct a list of "minimal gene set" which has been accomplished by datasets like the KOG dataset (ftp://ftp.ncbi.nih.gov/pub/COG/KOG) and which has been solved in practical terms by the design of mycobacterium laboratorium (newly synthesized organism born in May 2010)....does anyone have a list of those genes? — Preceding unsigned comment added by Doctorwolfie (talk • contribs) 00:41, 2 January 2011 (UTC) doctorwolfie (talk) 00:45, 2 January 2011 (UTC)

Update
Although this is an ongoing project, I'm considering rolling back to a simpler version of this page, but would love some feedback if anyone ever reads this page as to what would be useful....how about something like a list of common uses such as: 1. used originally by James Watson to refer to tRNA, mRNA, etc 2. used to refer to certain genes that are beleived to be present at constant levels for purposes of laboratory standardization. 3. used conceptually to define the "minimum gene set" that a single cell needs to operate. (A model like #3 would be really useful to biology teachers as a great "starting point" or syllabus for a course on cellular and molecular biology. Furthermore, mimicking the evolutionary mechanisms of gene duplication/modification it subsequently becomes easier to trace how genes evolved and explains why genes have structural similarity and functional overlap.) doctorwolfie (talk) 20:54, 19 October 2010 (UTC)

I've read through the Housekeeping gene article and would like to suggest an additional article in wikipedia entitled, List of housekeeping genes, or words to that effect, which could be linked to this page. From reading other sections of this talk page, my suggestion may already be a work in progress. Cheers! Marshallsumter (talk) 20:17, 21 October 2010 (UTC)

Lonely thoughts
Not much traffic coming through here...I hope what I'm doing has relevance; I'm certainly learning a lot. I'm trying to to build a set of truly constitutive genes that will guide students in their study. However, I have a sneaking suspicion that technical limitations of the current tag-technology (non-specificity) will place a lot of genes on the list that don't really belong. I'm hoping that grouping them by (apparent) function that somebody may be able to spot the redundancy and simplify the list (when 2 tags seem to identify 2 different genes because they tag a homologous sequence that is shared between them; a longer more specific tag might correctly identify the real gene)

In other gloomy news I included a reference by some workers who found that genes that we thought were constitutive may NOT be present at constant levels (which calls into question the validity of using them as standards). This is hardly surprising, because as in the case of cyclins, surely they wouldn't be hangin around through the entire cell cycle? Or the fact that at least the mRNA might, it's just that they aren't translated raises the question as to whether tagging mRNAs is truly identifying whether a protein is REALLY "expressed"(translated) After all, that looks like how cyclins work; mRNA hangs out, but the protein products are either silenced by an inhibitor or ubiquinated and disposed. Does anybody know how long mRNA hangs out and/or how it goes away? Ubiquination? Enzymatic degradation? HELLLLPPP!!!!!!doctorwolfie (talk) 13:16, 25 April 2010 (UTC)

Oh, I get it; Ribonuclease is extremely ancient...wellll, duh!doctorwolfie (talk) 01:40, 27 April 2010 (UTC)

What if we're tagging dead exons?
Despite the statement contained on this page about the quantitative definition of a housekeeping gene (ie:greater than 25 copies per cell) I'm finding more of them that seem a little more restricted to the 5-10 copy baseline that almost every gene exhibits (looking at the BiooGPS site). I asked hem abouut this (ie: whether it's real, or just represents background noise) and was referred back to the primary literature which didn't answer the question.

I'm still only vaguely familiar with the techniques used and keep hoping for someone who knows more to help. Is it possible that some of the tags used just happen to correspond to non-translated exonic material? Afterall, LINE elements look like retrotransposed polII genes. Are we 100% sure that we're really tagging mRNA that is expressed?

Expanding this page
I've uploaded a working draft at http://en.wikipedia.org/wiki/User:Doctorwolfie/new_article_name_here I'd be very greatful for some constructive criticismdoctorwolfie (talk) 20:55, 18 February 2010 (UTC)

I'm working on adding some references, but I needed some help with formatting. I would like to expand this list (a lot), but I was wondering if there was a more efficient way of notating. I'm working with two reference lists; some entries are mentioned in one, and some in both of the references. Is there a short cut (rather than cutting and pasting the entire reference each time?  It's going to be several hundred references to either one of two sources.)doctorwolfie (talk) 16:42, 15 February 2010 (UTC)

Sandbox Discussion
First, I know the formatting is a mess. I need some help cleaning it up (there are two main references, lists that I'm pulling the names from) I have not found an ORGANIZED list, so I thought Wikipedia would be the best place for it. HHHEEEELLLLPPPPP!

The task of developing a list of housekeeping genes, may be a purely academic one; let's give students a place to start learning genes by giving them a true representation of a true representative set of genes that are present in all (most?) cells. I used to think that these might align with something like a LUCA complement of minimally required genes...but it's entirely posible that some functions may have been deleted from the "list" just because a particular organ has taken over a function to obviate its expression in all cells. Conversely, it may be that a key regulatory step is expressed differently in different cell types.

It may be very dangerous to assume that "housekeeping genes" are expressed at constant levels. They may need to be dramatically up or down regulated depending on the cell type.

I've been working with two lists, which has been frustrating because the terminology (gene names) changes so frequently. I try to link to wikipedia pages that contain some plausible human genes when possible, but there are so many isoenzymes, that it's hard to be sure if a particular gene is truly constitutive (or whether the one that we've identified just happens to be a homolog of the true constitutive gene.) Some of the studies seem to be flawed because they use relatively short tags to locate the respective genes...but are they REALLY able to distinguish between isoenzymes? It also looks like two tags are sometimes used for different parts of the same gene. This is also problematic because genes evolve by being duplicated and then changing function. So weirdly, just because one has a match for a piece of a gene which appears ubiquitous, the actual function that is being carried out may not be intuitively indicated by the gene's name. For example: the crystallins evolved from piles of old metabolic enzymes. Similarly, glycogen synthase kinase has a lot more functions than simply synthesizing glycogen.

Ideally the list should read like a joyous reunion of undergraduate molecular biology, with many familiar friends and faces (and a couple of surprises). Notably missing from the lists are the tRNA's which are probably present; I'm assuming that tRNA is so folded in on itself that it's not possible to construct an EST mRNA-like thread that could read them. It makes me wonder what other little bits of RNA are floating around in there!

Carbohydrate metabolism Most of the glycolysis enzymes seem to be represented in at least one of the lists. Although the original page I was building from listed hexokinase, I couldn't find hexokinase (which is the rate limiting step, right?) Maybe it has another name?

Ribosomal proteins Are all ribosomal proteins present in all cells? Are ribosomes specialized in different cells? In my two lists there were some notable missing members...I just listed what was found in either one or the other of the two lists.

Cytoskeletal Different genes are referenced in the sources for actin: alpha, beta, and gamma

Heat shock The nomenclature for heat shock proteins seems a little primitive. Are they really that well conserved?

I studied some of Boghog2's user pages, and the Gene Ontology website to try to get a somewhat logical organization to the page. I am actively editing this page, but today I finally got brave and just redid it since I found the work by Samatha Greer contradicts the original statement on the stub: (that all housekeeping genes are expressed at equal levels and can thus safely be used as standardization tools.)

There! I've done it. This is the first time I've attempted a whole article (expanding a stub, etc)....although I realize that it's more of a list. Please be gentle with me! doctorwolfie (talk) 21:11, 10 March 2010 (UTC) doctorwolfie (talk) 21:11, 10 March 2010 (UTC)

Not turned on by TATA boxes?
Imagine my surprise when I found out that my genes weren't turned on by TATAs! I stumbled across this rather casual comment in the textbook of Molecular Cell Biology (Lodish et.al. from MIT)that Housekeeping genes tended to be initiated by CpG islands rather than by the more usual TATA boxes of more characteristically eukaryotic genes. Could this mean that CpG islands may represent an older form of transcription initiation, while the TATA box represents a more eukaryotic innovation? As far as this article goes, it might revise the way that we select entries for inclusion as "housekeeping genes." The more I study this, the more definitions that I seem to find for what constitutes a "housekeeping gene." doctorwolfie (talk) 16:25, 13 August 2010 (UTC)