Content deleted Content added
m Removing tag |
Harryboyles (talk | contribs) m →top: removing unsupported parameters in WikiProject banners |
||
| (39 intermediate revisions by 29 users not shown) | |||
Line 1:
{{
{{WikiProject banner shell|class=B|vital=yes|1=
}}
{{merged-from|DNA microarray experiment|26 April 2016}}
▲{{Todo}}
==Terms==
Line 91 ⟶ 89:
==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
==Measuring expression level==
Line 107 ⟶ 105:
'''{{further|[[Talk:DNA_microarray#New_Opening]]}}'''
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 [[Special:Contributions/128.249.106.194|128.249.106.194]] ([[User talk:128.249.106.194|talk]]) 20:38, 13 July 2010 (UTC)
==Standardization: The FDA's MicroArray Quality Control (MAQC) Project==
Line 137:
: 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. [[User:Jethero|Jethero]]<sup>[[User_Talk:Jethero|Talk]]</sup> 04:48, 12 April 2007 (UTC)
: I've respectfully removed the 'link-farm' again, since [[WP:NOT#DIR]] These resources are not mentioned in the text, and there is no mention of why these are notable with resepct to 'DNA Microarray'. Since it's obviously an 'invitation' to advertise, I've removed the entire 'software' section this time. If specific software can be tied to advances or watersheds in DNA Microarray fabrication or analysis, then perhaps they can be included in the text directly? Or if there is an interesting tid-bit about how the development of these tools were driven by the technology or visa versa?
<nowiki>
== 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
</nowiki>
--[[User:Jethero|Jethero]]<sup>[[User_Talk:Jethero|Talk]]</sup> 04:16, 13 June 2008 (UTC)
==Merger of Gene chip technology into DNA microarray==
Line 169 ⟶ 188:
== 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)--[[User:Squidonius|Squidonius]] ([[User talk:Squidonius|talk]]) 12:17, 5 April 2008 (UTC)
==New template for talk pages, expecially the larger ones==
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 {{tl|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{{twlh|Unanswered}} and not here.
Line 206 ⟶ 224:
: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). --[[User:Squidonius|Squidonius]] ([[User talk:Squidonius|talk]]) 10:53, 10 May 2008 (UTC)
== Comparative analysis ==
I'm surprised there isn't a section (or even a mention) of [[comparative analysis]] in this article. [http://scholar.google.co.uk/scholar?hl=en&lr=&safe=off&client=firefox-a&q=%22comparative+analysis%22+dna&btnG=Search "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, [[User:Jackhynes|Jack]] ([[User talk:Jackhynes|talk]]) 01:37, 18 June 2008 (UTC)
==Affymetrix Exon arrays and "GeneChip®"==
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 [http://www.affymetrix.com/products/arrays/specific/exon.affx 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. [[User:SteveChervitzTrutane|SteveChervitzTrutane]] ([[User talk:SteveChervitzTrutane|talk]]) 08:28, 10 September 2008 (UTC)
== Article Rating ==
Overall the article is rate '''B'''. I think it deserves more. Where is it lacking? --[[User:Squidonius|Squidonius]] ([[User talk: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. [[User:Tombadog|Tombadog]] ([[User talk:Tombadog|talk]]) 01:59, 22 October 2009 (UTC)
: The next mark up is [[Wikipedia:Good article criteria|Good article]]. I gave Statistics a bit of a clean (from mystical to list) and I added a section better explaining hybridization in hopefully understandable terms. Possible improvements:
:* Is History too short?
:* Maybe splitting the analysis part, say creating [[DNA microarray statistical analysis]] and expanding that?
:* Is the jargon simple and constant? I think it is. (I am advocating the correct jargon to be used, such as probe, feature/spot, channel, platform and not fixed DNA, dot, colour and machine)
:* Nothing is said about proteomics and ancillary techniques
:* some images don't seem too relevant. Image gallery? --[[User:Squidonius|Squidonius]] ([[User talk:Squidonius|talk]]) 16:38, 5 November 2009 (UTC)
== Statistics ==
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. --[[User:Squidonius|Squidonius]] ([[User talk:Squidonius|talk]]) 12:48, 16 November 2009 (UTC)
:Since I was the one changing the section in question, here is my response. The previous version was quite poorly worded, inviting exactly those sorts of misconceptions that it was trying to resolve. One issue that you raise is the "relativity" of the data in microarrays, which is misleading as most data are expressed as relative values (eg. concentrations, gene expression relative to a normalization genes). Overall, what you may be referring to, but what was not properly addressed, are the challenges posed by the signal-to-noise ratio, whose magnitude in microarray analysis is affected by things like hybridization (chemical noise), scanning (electronic noise), and probably most important, biological variation. So, to overcome these distinct set of challenges, algorithms have been developed, such as background subtraction, data normalization, and biological replication coupled with statistical methods that deal with issues such as multiple testing, normalization of variances, etc. that attempt to address these issues. I'm open to meaningful delineation of these issues in a new section that looks at these from a measured perspective, but I'm opposed to lumping them all together by merely saying that there are "sheer volumes of data" and "several normalization methods in the published literature" (without referencing these)—this is not helpful, as it only restates the well-known fact that microarray analysis is difficult. My modifications were aimed at recasting somewhat meandering sentences, thus trying to focus the discussion to invite further additions. [[User:Malljaja|Malljaja]] ([[User talk:Malljaja|talk]]) 15:47, 16 November 2009 (UTC)
== principle figure ==
Better to use the term probe than feature, because it is microarray (northern blot)-specific. <small><span class="autosigned">— Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[User:Pain-proof|Pain-proof]] ([[User talk:Pain-proof|talk]] • [[Special:Contributions/Pain-proof|contribs]]) 01:07, 7 January 2015 (UTC)</span></small><!-- Template:Unsigned --> <!--Autosigned by SineBot-->
== "citation needed" ==
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: [http://prosigna.com/x-us/overview/prosigna-algorithm/] <!-- Template:Unsigned IP --><small class="autosigned">— Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/184.100.44.130|184.100.44.130]] ([[User talk:184.100.44.130#top|talk]]) 00:29, 9 June 2017 (UTC)</small> <!--Autosigned by SineBot-->
== Huh? ==
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. <!-- Template:Unsigned IP --><small class="autosigned">— Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/74.104.100.218|74.104.100.218]] ([[User talk:74.104.100.218#top|talk]]) 20:53, 30 August 2019 (UTC)</small> <!--Autosigned by SineBot-->
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) [[User:Yinwang888|Yinwang888]] ([[User talk:Yinwang888|talk]]) 05:32, 11 February 2020 (UTC)
: I replaced the header figure. It was very specific on a sub-aspect on where probes of gene expression microarrays bind. Instead there now is an overview video. I hope that helps. I didn't delete the previous figure though, merely moved it down a bit [[User:Lassefolkersen|LasseFolkersen]] ([[User talk:Lassefolkersen|talk]]) 10:42, 14 May 2020 (UTC)
:: Very nice video! Very illustrative. Cool that you have made a Chinese version, but your pronounciation sucks. Good thing you put in subtitles. May I ask if you are Lasse Folkersen of impute.me? I am a big fan of that site. Why is there no wikipedia article for that? [[User:Yinwang888|Yinwang888]] ([[User talk:Yinwang888|talk]]) 08:56, 27 May 2020 (UTC)
| |||