Talk:DNA microarray

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  • Requests: Illumina platform (polystyrene beads array) needed
  • Expand: Types of arrays list must be short (SNP arrays too long?) but complete, which it is not.


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[edit] Terms

Here is a list of terms which are used in the article which should be defined:

  • Disease gene" - ambiguous to a layman. Are you talking about genes that cause disease, or the genes of some virus or bacterium?
Could be either in this case, one is a foreign gene, the other is a mutation
  • reporters" - if this is the same as a "probe", you should say so
Yes, Reporters is a MIAME compliance term for what is historically a probe
  • eukaryotic" - ok, I know what this is, but there should be a link to the topic
  • oligonucleotides" - pretty technical for a non-journal article
See oligonucleotide
  • up-regulated" - no clue
Genes that are upregulated are more highly expressed in a (for example) diseased cell versus a normal cell.
  • down-regulated" - still no clue
Genes that are downregulated are expressed less (lower mRMA levels) in one cell type veruss another
  • fluorofores" - ditto
  • scanned" - with what? an electron microsope? Seems like a pretty important part of the process to skip.
Usually a lazer and photomultiplier tube to detect the emitted flourescence
  • piezoelectric deposition" - I know what piezoelectric is, but not the process. How about a link?
  • 60-mer: - no idea
the length of an oligonucleotide (60 bases in length) --Zven 23:40, 24 September 2006 (UTC)
  • define "spotted" or spotting. what does it mean

To spot means to deposit nucleic acid (or whatever material) via an aqueous solution onto a surface (typically glass). The nucleic acid contains the reporters or probes which will "attract" the corresponding labeled biological molecule.

After reading the article twice, I still don't understand how DNA microarrays work - how do you view the results, what steps do you take to cause the DNA to be transcribed, etc. From the link to "Gene expression", it seems like you might be processing the microarrays through a number of steps.

This article is only useful to people who *already* understand what a DNA microarray is, and not useful for people who want to learn what they are.

RESOLVED added glossary

[edit] Create a sub topic on potential pitfalls

The vastness and sheer magnitude of the data generated presents ample opportunities for misdiagnosing and misspoting of the genes. A detailed discussion i required to make readers of the challenges in analysing microarray data - Natarajan

I want to know about dna microarray in detail along with protocol and photographs

I think the article goes into quite a bit of detail. If you need photos, Google it! --Intimidated 11:06, 9 Mar 2005 (UTC)

Tiling arrays should be incorporated. Found a nice tutorial on http://www.biostat.ucsf.edu/cbmb/courses/Cawley-Lecture5.pdf

Its been quite a while since I monitored this page, but I would like to point out that many of the terms used here were discussed ad nauseum by the people who were directly involved with the development of the microarray platform and with the standards that experiments using microarrays must meet before they can be accepted by the community. Check the MGED.org pages for reports of the history of array development.
For instance, the sample that is spotted on the slide is NOT a probe. Because the role of the labeled nucleic acid in arrays is the opposite of the labeled nucleic acid in Southern or northern hybridization experiments, it was decided to NOT use the term PROBE to describe the attached nucleic acid nor for the labeled nucleic acid in solution(these are unknown species of molecules. If you read the Minimal Information About Microarray Experiments (or MIAME for short) which has been adopted as a standard for describing the data about array experiments before they can be published or deposited in public repositories (a prerequisite for most reputable journals), you will find that the attached nucleic acids are called REPORTERS, the site that the nucleic acid is attached is called a FEATURE, and the labeled nucleic acid in solution is called the BIOLOGICAL SAMPLES.
Furthermore, as one who uses microarrays, and developes the technology to use chip formats, I do not reserve the term chip for Affy arrays or Combi arrays, nor does anyone else I know.
That being said, I am going to correct the first couple of paragraphs of this article. I will try to get back to it soon to make it consistant throughout.srlasky 02:27, August 9, 2005 (UTC)
Hopefully, people who want to change reporter back to probe will look at this page first. I am including a quote from the MIAME document that defines reporters and features. This was a topic of heated discussion because everybody had a different definition that they wanted to use for the spots on the slide (probes were always labeled in other methods, in arrays, the spots on the slide that some people wanted to call probes, are not labeled), plus those spots had to have two different types of information; first, the sequence they contain and the gene they are complementary to, and second, the absolute position on the slide, the X-Y coordinates. It was decided to not use the term probe for the stuff on the slide, and to use the term reporter instead. Here is a section from the MIAMI document:

Array Design:

  • General array design, including the platform type (whether the array is a spotted glass array, an in situ synthesized array, etc.); surface and coating specifications and spotting protocols used (for custom made arrays), or product identifiers (the name or make, catalogue reference numbers) for commercially available arrays.
  • Array feature and reporter annotation, normally represented as a table (for instance see Tables 1, 2 below), including
    • For each feature (spot) on the array, its location on the array (e.g., metacolumn, metarow, column, row) and the reporter present in the location (note that the same reporter may be present on several features).
    • For each reporter unambiguous characteristics of the reporter molecule, including
      • Reporter role – control or measurement
      • The sequence for oligonucleotide based reporters
      • The source, preparation and database accession number for long (e.g., cDNA or PCR product based) reporters
      • Primers for PCR product based reporters
If you want to look at the whole MIAME reference doc, it is available at the MGED.org site (MIAME_checklist). srlasky 17:54, August 18, 2005 (UTC)
I recognise what you are saying, but unfortunately the word probe has propagated into many scientific publications (e.g. The chipping forecast. Nature Genet.21(Suppl.) (1999). ) about microarray analysis, therefore I suggest that the MIAME use of Reporters for known material and the alternate word probe should be used. Something like; Reporters (also refered to as probes)... --Zven 22:48, 19 September 2006 (UTC)

[edit] About the edit that re-introduced British spelling

This is a fine edit, to reintroduce British spelling, but the page is in mixed dialect; consider the section header "Standardization". If an editor is going to insist on usage of one dialect, then that dialect should be used throughout the article and not randomly here and there. It is difficult to take the editor seriously when a word in the midst of text is pounced upon while a heading contrarily blazes a few lines away. Courtland 04:31, 30 October 2005 (UTC)

  • FYI, the usage of S vs. Z in British spelling varies. Some use it, some don't. So just because it has a Zed, don't assume that it is not British spelling. Fawcett5 13:57, 4 November 2005 (UTC)
    • True, but my understanding is that "standardization" vs. "standardisation" is an instance where the two typically differ. Further, "officially" the Z/S dichomtomy is not a part of the definitive distinction between the written dialects, but it is a significant part of the colloquial distinction (I don't recall where I read that and it would be good to dredge up a reference to support that statement .. i.e. to back up my accident-prone memory). Courtland 23:28, 4 November 2005 (UTC)

[edit] Oligos VS cDNA

I've always understood there being two main types of microarray - oligonucleotide arrays and cDNA arrays. The oligo arrays have 25bp oligos spotted onto the slide (I think these are Affy chips?) while the cDNA arrays have the cDNA from a single gene on each spot. Is this correct? It's not made clear by the article in its current form. If it is true, then I think this distinction should be emphasised as it can be quite confusing (I'm confused). Eirinn 11:44, 4 November 2005 (UTC)

There are two types of oligo arrays....one in which short oligos are synthesised in situ (affy style), and a second in which a spotted array approach is used. In the second case, the oligos are usually longer, typically a 70-mer. Fawcett5 13:55, 4 November 2005 (UTC)

[edit] List of companies

Someone added a bunch of companies that I am sure exist but don't believe they are important enough to mention here. I will remove all but the premiere ones like Agilent, Affymetrix etc. unless someone has any objections. --Blacksun 07:42, 18 May 2006 (UTC)

[edit] Lead is confusing

I don't like the way lead is written right now. The lead should be a clear and concise summary of what microarrays are, how do they work, and why are they important. I am going to attempt to rewrite it to achieve this. --Blacksun 07:44, 18 May 2006 (UTC)

[edit] Measuring expression level

Shouldn't we talk more about how expression levels are measured and name the common softwares used currently? It seems to be the missing piece in the article. I will try to write a bit on it. --Blacksun 07:53, 18 May 2006 (UTC)

[edit] Lead talks about expression arrays only

The lead talks only about expression arrays, but in later paragraphs it's made clear that there are many types of arrays (SNP, tiling, etc).

I'd like to generalize the lead a bit more to address the various types of arrays. A DNA microarray doesn't detect gene expression (as stated in the current lead), it detects the hybridization of complementary sequences to the array probes. This can measure various things depending on experimental protocol and array design, including (but not limited to) mRNA expression levels. gawp 20:26, 7 July 2006 (UTC)

  • I agree, why does Genome_tiling_arrays forward here when there is only once sentence about them with minimal content? --joshua orvis 15:00, 25 April 2007 (UTC)
  • agree. In an earlier edit, I made a first attempt (albeit rough) to generalize the lead to be about DNA Microarrays rather than expression arrays, and I put the existing expression array part in the intro paragraph. However, my edit it was pretty much undone by 193.1.68.18 (talk · contribs) in this revision. I agree that this article would be stronger and more inclusive if the lead were more general about DNA microarrays, and particular applications could be in a section. If there are others who agree or disagree, perhaps we could discuss here? JetheroTalk 05:01, 26 April 2007 (UTC)
Further information: Talk:DNA_microarray#New_Opening

[edit] Standardization: The FDA's MicroArray Quality Control (MAQC) Project

There is now an ongoing effort by the FDA to facillitate comparison of microarray (MA) data obtained from a variety of MA platforms. Detailed information about this project is available at http://www.fda.gov/nctr/science/centers/toxicoinformatics/maqc/

[edit] Dye Effect

Would something on this be appropriate in this article? Aaadddaaammm 08:21, 4 November 2006 (UTC)

I am a fan of the fact that when you go diving, red is the first colour to dissapear, a phenomenon that also accurs with these things, but to a less adrenaline pumping level... --Squidonius (talk) 21:24, 7 May 2008 (UTC)

[edit] Dyes used

I made a page for Cy3 and Cy5, but I am aweful at writing and I am new to wiki editing. could someone add a paragragh about dyes used in microarrays? - thanks

I modified the example for the dyes used for the 2-ways microarray. The correct emission for Cy3 is green and for Cy5 red. I removed the references to rhodamine and fluorescein because I think they are are not really used in that context, and are different from Cy3 and Cy5. aurel 14:21, 11 September 2007 (UTC)

http://en.wikipedia.org/wiki/Cyanine states: Cy3 possesses red fluorescence, and Cy5 - far-red. http://en.wikipedia.org/wiki/DNA_microarray states: Cy3, which has a fluorescence emission wavelength of 570 nm (corresponding to the green part of the light spectrum), and Cy5 with a fluorescence emission wavelength of 670 nm (corresponding to the red part of the light spectrum).

Personally, I disagree with both color assessments. I lean to the categorization at Biocompare (www.biocompare.com/documents/fluor_wavelengths.pdf) wherein Cy 3 emits Yellow, Cy5 emits Red.

Amazing how little agreement there is on the emission colors of these two dyes!! Dyeguy (talk) 13:20, 7 March 2008 (UTC)

[edit] links to online data repositories or microarray analysis programmes

I've re-instated the two links to Webarray and Arraypipe both of which are online programmes for microarray analysis free of charge that have undergone peer-review in the scientific literature(see: http://www.biomedcentral.com/1471-2105/6/306 and http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15215429 ). Please do not remove these links by merely replacing them with a hand wave to the Open Directory Project, which itself is a link jungle and not always reliable. Malljaja 10:17, 3 April 2007 (UTC)

ArrayPipe--A Microarray Analysis Pipeline
Webarray
I've respectfully removed them again as Wikipedia is not a directory WP:NOT#DIR, even for peer reviewed open source software. You can suggest to create a section in Open Directory Project for "Peer Reviewed Free Open Source Software for DNA Microarray", or you can use the original paper references for these tools somewhere in the text, indicating of course their notability and relevance to this topic, or you can reference a third party comprehensive review of FLOSS microarray tools. Simply listing them does not indicate notability, and invites spam. Furtehr, your decision to highlight these particular tools and not others is WP:POV and so needs to be explained in text and supported by references. JetheroTalk 04:48, 12 April 2007 (UTC)


[edit] Merger of Gene chip technology into DNA microarray

The way the Gene chip technology article stands right now, it just seems like a summary of the microarray article or, at least, one commercial term for microarray, so I figured out would find out the opinion of whether other people think these are the same thing or different?? Ciar 23:16, 5 May 2007 (UTC)

I agree. It's a weird article and basically a confusing stub of this one, with a name that seems to refer to the Affymetrix chip but is spelled wrong. I think you should just make it redirect here. Madeleine 00:36, 9 May 2007 (UTC)
I agree too. It's just a summary of the main article. Merge it. --LasseFolkersen 20:43, 10 May 2007 (UTC)
I went ahead and redirected the gene chip article to here. (NoQuarter 15:40, 29 May 2007 (UTC))

[edit] no mention of nanopore devices?

Are these considered "DNA microarrays"? - UNSIGNED

I am not that familiar with it, but nanopore is a hypothetical/early experimental sequencing method. An array of pores is not a DNA microarray, but a microchip biosensor-kinda thing. --Squidonius (talk) 12:24, 5 April 2008 (UTC)

[edit] Proposed section merges

The following discussion is archived. Please do not modify it. Subsequent comments should be made in a new section.
The result was no merge into DESTINATION PAGE. -- Squidonius (talk) 15:26, 13 April 2008 (UTC)

I found two nearly identical sections on microarray fabrication via oligonucleotide synthesis at phosphoramidite and oligonucleotide synthesis and proposed merging them into this article as they seem more relevant here. - tameeria (talk) 14:57, 6 December 2007 (UTC)

I agree, they should be shortened and linked to here --LasseFolkersen (talk) 12:05, 7 February 2008 (UTC)

Do not merge oligonucleotide synthesis with microarray fabrication. Oligonculeotide synthesis is applicable to many other areas such as siRNA, antisense, aptamers, PCR, etc. —Preceding unsigned comment added by 71.120.222.65 (talk) 20:15, 21 February 2008 (UTC)

Disagree Those articles need that section. I have put a ((main|DNA microarray#Fabrication)) tag on them. —Preceding unsigned comment added by Squidonius (talk • contribs) 11:51, 26 February 2008 (UTC)

The above discussion is preserved as an archive. Please do not modify it. Subsequent comments should be made in a new section.


[edit] Sugar coat

On the Spotted vs. oligonucleotide arrays, the fact that home made spotted arrays give pourer results is putting it lightly and is actually humourus. The reason people use spotted arrays is that there is no alternative as they want a custom one. cDNA spotted arrays cost 100-200$ vs 400$ slides + reagents. self printed, 20$ the polylysine coated but you need the library, a cDNA one is about 10k$. with commercial slides you get a nice protocol and proprietary reagents, whereas spotted arrays you have to make the yourself (and there is not a standard one, they all are terrible). the failure rate is so much higher too. I am complaning here and not fixing it myself because this is not something referenceble to a textbook/article and it probably would be edited out. I am asking that that section be changed --Squidonius (talk) 12:12, 26 February 2008 (UTC)

[edit] Channel and Colour

this article uses the word colour to describe the two differently "coloured" dyes. In reality when talking about dyes one uses the word "channel", which is much more precise (there is not only the dye but also the laser and filters) and used in the official lingo (not only reguarding flourescence: it is even in photoshop, say, to do a colour overlay) but not socially. furthermore Cy3 and Cy5 when you look at them in solution they are deep blue and purple! Is colour used for ease of comprehension or is it a minor error? 3-channel microarrays also exist (red, blue and UV)--Squidonius (talk) 12:17, 5 April 2008 (UTC)

[edit] New template for talk pages, expecially the larger ones

Unanswered query This question or request has not been resolved
Remove this tag when this is resolved.

Some pages, such as this one have lots of post, and it requires some work to see what has been answered or acknowledged. therefore I have helped make the {{Unanswered}} template that can be put above a section allowing one to quickly glimpse what has been answered. If you were waiting for an answer but never got one as the post in somewhere in the middle tag it! please voice any queries or comments in the talk page ofTemplate:Unanswered (links, talk) and not here.

This article in particular is strange as I think it has reached a critical mass and all overly-long sections are continuously trimmed. I would give it a {{tl|toolong} tag which requests that it be split up a bit and summarised and the new articles explanded. Although it may need a bit of reordering first. Gibson's primer of genome science is a bit messy too, but I think this can be improved a great deal, I have not tagged it so, as it is relatively short. Cheers --Squidonius (talk) 15:22, 13 April 2008 (UTC)

[edit] New Opening

I am going through this discussion page in order to revamp the article. the problem is I got stuck at fixing the intro:

PROPOSED

A DNA microarray is an arrayed series of microscopic spots of DNAoligonucleotides, called features, where each feauture contains picomoles of a specific unique sequence, such a stretch of a gene sequence.
These molecules are the used as probes) to which only the correct target sequence will hybridise under high-stringency conditions; where the target is the labelled mix of either RNA or DNA to be analysed, in the majority of case with a fluorophore-based detection system.
The probes are bound to a solid surface by covalent attachment to a chemical matrix. The solid surface can either be glass or a silicon chip, in which case they are commonly known as gene,genome chip or colloquially Affy Chip when an Affymetrix chip is used. DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system. DNA arrays are commonly used for expression profiling, i.e., monitoring expression levels of thousands of genes simultaneously, or for comparative genomic hybridization.

ORIGINAL

A DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array) is a collection of microscopic DNA spots, commonly representing single genes, arrayed on a solid surface by covalent attachment to a chemical matrix. DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system. Qualitative or quantitative measurements with DNA microarrays utilize the selective nature of DNA-DNA or DNA-RNA hybridization under high-stringency conditions and fluorophore-based detection. DNA arrays are commonly used for expression profiling, i.e., monitoring expression levels of thousands of genes simultaneously, or for comparative genomic hybridization.

is it too dense? Thanks, any feedback welcome (even insults)--Squidonius (talk) 18:10, 15 April 2008 (UTC)
I changed the lead over as I noticed that a unusual vandalalism was removed, it was not really vandalism but a comment about the bad lead, reguardless of feedback.

I apologise for the large amount of comments I have added, but I think this article is back to shape, now. thanks to all that helped with the making the text more readable --Squidonius (talk) 13:45, 18 April 2008 (UTC)

[edit] Radioactive microarrays

the exception to the rule that microarrays are fluorescent is with μ-imager from Biomesure (A novel sensitive microarray approach for differential screening using probes labelled with two different radioelements . al, Salin H et. 4, s.l. : Nucleic acid research, 2002, Vol. 30.), but it is not in the text because the machine reads only the area of a coverslip, which in my humble personal opinion I believe is utterly ridicoulus. you can put agilent or 22k cDNA microarrays in a phosphoimager screen with P33 (if you have a reason to do that). --Squidonius (talk) 21:20, 7 May 2008 (UTC)

[edit] Lead

I've re-instated and slightly re-worded the lead according to wiki guidelines found here. As any good lead, it should provide a good summary that will draw the interested reader into the article. As such, it needs to be a little more extensive than a couple of sentences and is already in fairly good shape (and has been for some time, imho)--other sections that still require some real work are those dealing with the stats analyses (problems with multiple testings etc), and making the different technical platforms a little more transparent and confluent. Thanks. Malljaja (talk) 01:31, 10 May 2008 (UTC)

Oh, m'kay. I was not aware of that. I concur, it is fine now. This article will be FA one day, so I was starting at the top and eventually get to the bottom (or procrastinating from it). Next... types has a bit too much white (maybe a table like in ncRNA might work). --Squidonius (talk) 10:53, 10 May 2008 (UTC)