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![]() | The contents of the DNA microarray experiment page were merged into DNA microarray on 26 April 2016. For the contribution history and old versions of the redirected page, please see its history; for the discussion at that location, see its talk page. |
Here is a list of terms which are used in the article which should be defined:
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
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
Tiling arrays should be incorporated. Found a nice tutorial on http://www.biostat.ucsf.edu/cbmb/courses/Cawley-Lecture5.pdf
Array Design:
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)
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)
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)
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 they work, and why they are important. I am going to attempt to rewrite it to achieve this. -- Blacksun 07:44, 18 May 2006 (UTC)
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)
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 would argue that arrays *cannot* measure expression levels: they actually measure the steady state level of e.g. mRNA, which is equal to expression minus degradation. This is an important distinction (since both expression and degradation can vary greatly depending on environmental conditions) and it highlights a common misconception 128.249.106.194 ( talk) 20:38, 13 July 2010 (UTC)
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/
Would something on this be appropriate in this article? Aaadddaaammm 08:21, 4 November 2006 (UTC)
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)
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
== Online microarray data-analysis programs and tools == Several [[Open Directory Project]] categories list online microarray data analysis programs and tools: * {{dmoz|/Science/Biology/Bioinformatics/Online_Services/Gene_Expression_and_Regulation/|Bioinformatics : Online Services : Gene Expression and Regulation}} * [http://cybert.microarray.ics.uci.edu/ Cyber-T uses a Bayesian probabilistic framework for microarray data analysis] * {{dmoz|/Science/Biology/Biochemistry_and_Molecular_Biology/Gene_Expression/Databases/|Gene Expression : Databases}} * {{dmoz|/Science/Biology/Biochemistry_and_Molecular_Biology/Gene_Expression/Software/|Gene Expression : Software}} * {{dmoz|/Computers/Software/Databases/Data_Mining/Tool_Vendors/|Data Mining : Tool Vendors}} * [[Bioconductor]] - open source and open development software project for the analysis and comprehension of genomic data * [[Genevestigator]] : Web-based database and analysis tool to study gene expression across large sets of tissues, developmental stages, drugs, stimuli, and genetic modifications. * [http://genecat.mpg.de: GeneCAT (Gene Co-expression Analysis Toolbox): Web-based database of gene expression data and expression analysis tools for Arabidopsis thaliana and barley. ] * [http://gepas.org GEPAS]: Gene Expression Profile Analysis Suite developed in the [http://bioinfo.cipf.es Bioinformatics Department of the CIPF] in Spain. * [[DAVID bioinformatics]]: [http://david.abcc.ncifcrf.gov A free online bioinformatics resources provides functional interpretation of large lists of genes derived from genomic studies] * [http://www.ncbi.nlm.nih.gov/pubmed/17458699 caCORRECT] Chip Artifact Correction: [http://cacorrect.bme.gatech.edu A free online quality control tool for Affymetrix microarrays hosted at] [http://www.bme.gatech.edu Georgia Tech Biomedical Engineering Department] * [http://www.datascope.be/spm_page.htm "spm"] is an open source package developed in [[R_%28programming_language%29|R]] for the analysis of gene expression data by means of multivariate projection methods
-- Jethero Talk 04:16, 13 June 2008 (UTC)
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)
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)
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)
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)
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)
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 of Template: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)
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
DNA
oligonucleotides, 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.
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)
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)
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)
I'm surprised there isn't a section (or even a mention) of comparative analysis in this article. "comparative analysis" dna yields over 100,000 hits on Google Scholar. Is there another name I don't know? If not, it should definitely worked into this article. Cheers, Jack ( talk) 01:37, 18 June 2008 (UTC)
In the types and uses section of the article, it would be good to mention the use of exon arrays in addition to exon junction arrays for use in alternative splicing detection. An exon array has probes that specifically target exonic regions within a genome sequence, avoiding exon-exon junctions. They can be used to help discover novel splice isoforms without needing prior knowledge about which isoforms are expressed.
At present, only Affymetrix manufactures and sells exon arrays, such as the Human Exon 1.0 ST Array that targets all putatively transcribed exons within the human genome. Since I work for Affy, I have a conflict of interest in editing this article to add such a note, but I'd appreciate if someone could do this.
I also want to point out that "GeneChip" is a registered trademark of Affymetrix, as noted here: http://www.affymetrix.com/site/terms.affx. So it would be good if someone could note this as well. Thanks. SteveChervitzTrutane ( talk) 08:28, 10 September 2008 (UTC)
Overall the article is rate B. I think it deserves more. Where is it lacking? -- Squidonius ( talk) 09:44, 21 October 2009 (UTC)
I don't find the section on statistics very helpful. To my eye, it says, yah there are all these problems with multiple hypotheses and normalization. True, but the article should either go into these issues or redirect the reader. There is a raft interesting literature on this topic. We should read it, summarize it and cite it, or avoid highlighting the issue. Tombadog ( talk) 01:59, 22 October 2009 (UTC)
My edit on statistics was changed to resemble how it was before, despite being misinformative: Microarray analysis is a pain because the data is Relative (condition A vs. B, not gene xx in A is xx pmol) and you start with an image, Analysis of SAGE data has only a fraction of the problems microarrays have, yet have lots and lots of data, so size is not #1 issue. If someone else feels so, please amend. -- Squidonius ( talk) 12:48, 16 November 2009 (UTC)
Better to use the term probe than feature, because it is microarray (northern blot)-specific. — Preceding unsigned comment added by Pain-proof ( talk • contribs) 01:07, 7 January 2015 (UTC)
Under the Data analysis section is "...in the case of commercial platforms, the analysis may be proprietary.[citation needed] " Here is one citation, where the company clearly states their algorithm is proprietary: [1] — Preceding unsigned comment added by 184.100.44.130 ( talk) 00:29, 9 June 2017 (UTC)
I like to think of myself as fairly scientifically literate, but after skimming through this page, and a couple of other web descriptions, I still don't understand what DNA chips are.
The most fundamental issue to explain seems missing: is this an actual biological sample taken from a living being (human or whatever) that's somehow affixed to a solid surface, or is this a purely synthetic pattern affixed to a microscope slide or other support? If the latter, why not just encode it into a computer program, why bother with a physical form at all?
I think that the people who've written about this (here on Wikipedia and elsewhere) know too much about the subject, and don't know how to introduce it to an audience who know nothing about it. I think the page should start with a much more basic explanation of what's being discussed. — Preceding unsigned comment added by 74.104.100.218 ( talk) 20:53, 30 August 2019 (UTC)
I agree with this. It's a comprehensive article, but very difficult to get into for the beginner.
Would it be OK to rewrite the introduction using some assumptions/simplifications? Like, for example, I think it would help if the introduction just mentioned that DNA microarray can measure SNPs and gene expression, define what that is, and then briefly mention that other types exists. Because right now it's written in such a comprehensive way, keeping open to all the many different types of microarray (tilling, microRNA, etc). But that makes it hard to read. And really gene expression and SNP genotyping, is by far the largest applications by count of samples (and I'd even argue SNP genotyping alone would be the most important, given gwas+DTC industry) Yinwang888 ( talk) 05:32, 11 February 2020 (UTC)
This is the
talk page for discussing improvements to the
DNA microarray article. This is not a forum for general discussion of the article's subject. |
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Find sources: Google ( books · news · scholar · free images · WP refs) · FENS · JSTOR · TWL |
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![]() | The contents of the DNA microarray experiment page were merged into DNA microarray on 26 April 2016. For the contribution history and old versions of the redirected page, please see its history; for the discussion at that location, see its talk page. |
Here is a list of terms which are used in the article which should be defined:
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
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
Tiling arrays should be incorporated. Found a nice tutorial on http://www.biostat.ucsf.edu/cbmb/courses/Cawley-Lecture5.pdf
Array Design:
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)
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)
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)
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 they work, and why they are important. I am going to attempt to rewrite it to achieve this. -- Blacksun 07:44, 18 May 2006 (UTC)
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)
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 would argue that arrays *cannot* measure expression levels: they actually measure the steady state level of e.g. mRNA, which is equal to expression minus degradation. This is an important distinction (since both expression and degradation can vary greatly depending on environmental conditions) and it highlights a common misconception 128.249.106.194 ( talk) 20:38, 13 July 2010 (UTC)
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/
Would something on this be appropriate in this article? Aaadddaaammm 08:21, 4 November 2006 (UTC)
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)
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
== Online microarray data-analysis programs and tools == Several [[Open Directory Project]] categories list online microarray data analysis programs and tools: * {{dmoz|/Science/Biology/Bioinformatics/Online_Services/Gene_Expression_and_Regulation/|Bioinformatics : Online Services : Gene Expression and Regulation}} * [http://cybert.microarray.ics.uci.edu/ Cyber-T uses a Bayesian probabilistic framework for microarray data analysis] * {{dmoz|/Science/Biology/Biochemistry_and_Molecular_Biology/Gene_Expression/Databases/|Gene Expression : Databases}} * {{dmoz|/Science/Biology/Biochemistry_and_Molecular_Biology/Gene_Expression/Software/|Gene Expression : Software}} * {{dmoz|/Computers/Software/Databases/Data_Mining/Tool_Vendors/|Data Mining : Tool Vendors}} * [[Bioconductor]] - open source and open development software project for the analysis and comprehension of genomic data * [[Genevestigator]] : Web-based database and analysis tool to study gene expression across large sets of tissues, developmental stages, drugs, stimuli, and genetic modifications. * [http://genecat.mpg.de: GeneCAT (Gene Co-expression Analysis Toolbox): Web-based database of gene expression data and expression analysis tools for Arabidopsis thaliana and barley. ] * [http://gepas.org GEPAS]: Gene Expression Profile Analysis Suite developed in the [http://bioinfo.cipf.es Bioinformatics Department of the CIPF] in Spain. * [[DAVID bioinformatics]]: [http://david.abcc.ncifcrf.gov A free online bioinformatics resources provides functional interpretation of large lists of genes derived from genomic studies] * [http://www.ncbi.nlm.nih.gov/pubmed/17458699 caCORRECT] Chip Artifact Correction: [http://cacorrect.bme.gatech.edu A free online quality control tool for Affymetrix microarrays hosted at] [http://www.bme.gatech.edu Georgia Tech Biomedical Engineering Department] * [http://www.datascope.be/spm_page.htm "spm"] is an open source package developed in [[R_%28programming_language%29|R]] for the analysis of gene expression data by means of multivariate projection methods
-- Jethero Talk 04:16, 13 June 2008 (UTC)
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)
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)
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)
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)
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)
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 of Template: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)
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
DNA
oligonucleotides, 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.
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)
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)
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)
I'm surprised there isn't a section (or even a mention) of comparative analysis in this article. "comparative analysis" dna yields over 100,000 hits on Google Scholar. Is there another name I don't know? If not, it should definitely worked into this article. Cheers, Jack ( talk) 01:37, 18 June 2008 (UTC)
In the types and uses section of the article, it would be good to mention the use of exon arrays in addition to exon junction arrays for use in alternative splicing detection. An exon array has probes that specifically target exonic regions within a genome sequence, avoiding exon-exon junctions. They can be used to help discover novel splice isoforms without needing prior knowledge about which isoforms are expressed.
At present, only Affymetrix manufactures and sells exon arrays, such as the Human Exon 1.0 ST Array that targets all putatively transcribed exons within the human genome. Since I work for Affy, I have a conflict of interest in editing this article to add such a note, but I'd appreciate if someone could do this.
I also want to point out that "GeneChip" is a registered trademark of Affymetrix, as noted here: http://www.affymetrix.com/site/terms.affx. So it would be good if someone could note this as well. Thanks. SteveChervitzTrutane ( talk) 08:28, 10 September 2008 (UTC)
Overall the article is rate B. I think it deserves more. Where is it lacking? -- Squidonius ( talk) 09:44, 21 October 2009 (UTC)
I don't find the section on statistics very helpful. To my eye, it says, yah there are all these problems with multiple hypotheses and normalization. True, but the article should either go into these issues or redirect the reader. There is a raft interesting literature on this topic. We should read it, summarize it and cite it, or avoid highlighting the issue. Tombadog ( talk) 01:59, 22 October 2009 (UTC)
My edit on statistics was changed to resemble how it was before, despite being misinformative: Microarray analysis is a pain because the data is Relative (condition A vs. B, not gene xx in A is xx pmol) and you start with an image, Analysis of SAGE data has only a fraction of the problems microarrays have, yet have lots and lots of data, so size is not #1 issue. If someone else feels so, please amend. -- Squidonius ( talk) 12:48, 16 November 2009 (UTC)
Better to use the term probe than feature, because it is microarray (northern blot)-specific. — Preceding unsigned comment added by Pain-proof ( talk • contribs) 01:07, 7 January 2015 (UTC)
Under the Data analysis section is "...in the case of commercial platforms, the analysis may be proprietary.[citation needed] " Here is one citation, where the company clearly states their algorithm is proprietary: [1] — Preceding unsigned comment added by 184.100.44.130 ( talk) 00:29, 9 June 2017 (UTC)
I like to think of myself as fairly scientifically literate, but after skimming through this page, and a couple of other web descriptions, I still don't understand what DNA chips are.
The most fundamental issue to explain seems missing: is this an actual biological sample taken from a living being (human or whatever) that's somehow affixed to a solid surface, or is this a purely synthetic pattern affixed to a microscope slide or other support? If the latter, why not just encode it into a computer program, why bother with a physical form at all?
I think that the people who've written about this (here on Wikipedia and elsewhere) know too much about the subject, and don't know how to introduce it to an audience who know nothing about it. I think the page should start with a much more basic explanation of what's being discussed. — Preceding unsigned comment added by 74.104.100.218 ( talk) 20:53, 30 August 2019 (UTC)
I agree with this. It's a comprehensive article, but very difficult to get into for the beginner.
Would it be OK to rewrite the introduction using some assumptions/simplifications? Like, for example, I think it would help if the introduction just mentioned that DNA microarray can measure SNPs and gene expression, define what that is, and then briefly mention that other types exists. Because right now it's written in such a comprehensive way, keeping open to all the many different types of microarray (tilling, microRNA, etc). But that makes it hard to read. And really gene expression and SNP genotyping, is by far the largest applications by count of samples (and I'd even argue SNP genotyping alone would be the most important, given gwas+DTC industry) Yinwang888 ( talk) 05:32, 11 February 2020 (UTC)