Talk:DNA microarray

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Contents 1 Terms 2 Create a sub topic on potential pitfalls 3 About the edit that re-introduced British spelling 4 Oligos VS cDNA 5 List of companies 6 Lead is confusing 7 Measuring expression level 8 Lead talks about expression arrays only 9 Standardization: The FDA's MicroArray Quality Control (MAQC) Project 10 Dye Effect 11 Dyes used

[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

• down-regulated" - still no clue

Genes that are downregulated are expressed less

• 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

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.

[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)

[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)

[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