Talk:Group 8 Project - Microarray

From CellBiology

--Mark Hill 00:43, 27 May 2010 (UTC) The Project Page now locked, the discussion page is still available for additions and edits.


Our group has discussed the comments given by our peers. The following is the summary of their suggestions:

  1. more images
  2. more diagrams to illustrate some methods
  3. more glossary terms (proto-oncogene, cDNA, FISH, microtome, perturbations)
  4. more tables
  5. more bullet points to replace long paragraphs
  6. references to current research

We agreed most of the above suggestions and would edit our project accordingly. Additionally, we would add more information to the timeline and we would create a session for helpful links.

--Samantha Cabrera 07:44, 19 May 2010 (UTC)

--Rosita Pang 07:41, 19 May 2010 (UTC)

--Joseph Chuk 07:42, 19 May 2010 (UTC)


--Rosita Pang 07:47, 12 May 2010 (UTC) Dear group mates,

I think it maybe a good idea to include some helpful links, interesting facts (like current news on micorarrays) into our project. Additionally, we can do more research on the timeline and history. Adding a hyperlink for the glossary may also be a good idea.

For the Tissue MicroArray Slide image, it may be better to find another one from a proper journal with correct citations, instead from wiki.

There are still a lot of stuffs that we can do. Go go fighting!

Cheers, Rosita :)

--Mari Fushimi 05:23, 12 May 2010 (UTC) Hi group 8-here is my feedback

  • Great great work!!
  • Layout- I liked the impressive picture next to the contents as something eye-catching especially for someone who is not familiar with topic it was a good hook, the section of 'challenges' could have been broken up a bit more with pictures or diagrams; loved the break up of the rest though; language-was clear and not complicated; hand drawn diagram-good effort
  • References-pictures are very thoroughly referenced to a very high standard and has given our group something to aspire to

--Ozgur Tuna 05:10, 12 May 2010 (UTC) Good work guys. Your page is very well structured. The use of image showing the comparison between one colour and two colour expression analysis is great, makes it easy to understand.

My suggestions:

  • Definition and use Section can be added into the Introduction
  • History Section is a bit short. Is there no significant event/development since the 90’s? References for current research and development in Microarray would be great.
  • A few more definitions can be added into Glossary (like cDNA…etc)

--Jin Lee 04:51, 12 May 2010 (UTC) Hello Group 8, WOW! You guys have done great job! This page was very interesting and very visualised. Table forms and self drawn diagram were awesome! My only suggestion to improve this page will be just add few more words in glossary list.

--Shoahaib Karimi 04:45, 12 May 2010 (UTC)Great topic and great explanation of it all, your have a massive amount of references, you can include more in your glossay. Great use of table and student drawn image. can you get a better image for the first one the black and white one and also can you include pictures in your history and in some others.


--Mark Hill 04:28, 12 May 2010 (UTC) Lab 8 Assessment - 20 student reviews.

--z3252833 04:27, 12 May 2010 (UTC) Let me start by saying that your picture citations are really, really good. I mean, you even have summaries of the papers that the pictures for ci-ELISA and DNA microarray come from. It’s impressive. Your student diagram is nice to look at, relevant and informative, and well labelled, and all your in-text referencing is well done. You’ve used that table to present types of protein microarrays really well; the information is neat and concise. The text is quite dense, but it is written in a comprehensive way – I don’t know much about microarrays (or I didn’t before) but I still found it understandable, which means you’ve done a pretty great job with that. Just a few things to think about – perhaps move some of your pictures to the left of the page or move them around a bit to break up the text and make the format more interesting to look at; good use of a link to a video but would it be possible to add a screenshot to make it more noticeable; and would it be good to move your glossary up to before the references so people looking for terms could find it easier? It’s easy to miss the glossary if it’s hidden down the bottom of the page. Overall, well done! I really like this page.


--Jessie Tomkins 04:21, 12 May 2010 (UTC) Hey Group 8, some things to think about:

  • The first image next to the contents boxs looks a bit ill formatted.
  • The history could be expanded on to include scientists that were important.
  • The formatting of the table would work better if it was horizontal instead of vertical. The use of a table is great though. I like it alot.
  • Some paragraphs were a bit long and could be made more concise.
  • Move the glossary up before the references. Also expand the glossary.
  • As people have already said the conclusion was a bit odd.

Other than that the content was easy to understand and obviously well researched. Well done.

--Erika Unsworth 03:35, 12 May 2010 (UTC) Group 8,

  • your content and language is great
  • great use of images- i especially like the first black & white image (looks great next to the contents box!)
  • the structure and flow of your page works well
  • I think the history section could be improved by putting the years in bold.
  • Overall, a great piece of work!

--Paula Ordonez 03:20, 12 May 2010 (UTC) Hi group 8, This is a very good page, with excellent choice of headings and paragraphs (though some paragraphs are too long and could make use of some bullet points.) I thoroughly enjoyed the table comparing analytical microarrays, functional protein microarrays, and reverse phase protein microarray (however could use clearer labels of what each row is comparing.) The reference list demonstrated your thorough research, however i think the glossary could do with some additions. Also, in the introduction perhaps a clearer definition of microarrays would be useful. Great job overall!

--Julianna Lam 02:47, 12 May 2010 (UTC) the defintion should go under the introduction.history is a bit short, would be good to go more in depth. the use of the table is really good, makes it easier to read. the content is informative. i liked the challenges section, though i think the word limitations sound better. i liked the use of the graphics and chart. overall good job !



--Joanne Raffel 01:54, 12 May 2010 (UTC) Your first image was rather large! You definition and use section should be included under the itnroduction heading. Your history section was rather short and your types of mecroarray was set out incorrectly and made it difficult to identify the subheadings and where the next section began. After your initial image, the rest of them I liked however they were quite small and made it difficult to reead the text included. Otherwise your page was very well set out.

--Darren Dizon 23:13, 11 May 2010 (UTC) Content was very well thought and and presented. I was able to gather all that you guys were gonna write just by reading the Intro (which is good). referencing was good in pictures and in-text. Gotta agree with others that i found it odd seeing a conclusion there. Overall. one of the better wiki pages

--z3254509 22:09, 11 May 2010 (UTC)

Excellent page, very detailed and informative. Crucial points:

  • Top references list, it is obvious a lot of research of has gone into this project.
  • The pictures are well referenced.
  • The formatting is spot on.

--Dougall Norris 06:58, 11 May 2010 (UTC)

Job well done guys, the page is set out differently to others, but i think it works well. Id like this page if i came by it looking for info on microarrays. Some points i wanted to make:

  • Awesome intro, perfect for wiki users.
  • Id probably put the definitions and use part after the history, because i feel like thatd lead well into the types (as the applications are also covered in types)
  • If you could, id consider putting in the scientists that played a role in the development of microarrays.
  • Not sure if u need a conclusion (its not an essay)
  • Glossary could be bigger
  • Solid list of references


Good stuff group 8. The project looks great, here are some points I thought might be useful: --Vishnnu Shanmugam 05:24, 11 May 2010 (UTC)

  • The images are very well referenced with both the source (link form) and copyright information. Excellent!
  • The project is well referenced however, in the protein microarray, tissue microarray and challenges section contains entire paragraphs with only a sigle reference at the end of each one. This is insufficient.
  • Glossary needs to be expanded.
  • Excellent images you created yourself. Even the table that compares Analytical microarrays, Functional protein microarrays, Reverse Phase Protein Microarray is impressive as it allows for easy comparisons of similarities and differences.
  • The timeline needs expanding to include more major historical landmarks
  • Not sure if a conclusion is necessary/appropriate as this section is typically found in projects answering that study and answer a particular question. Better title this section as “summary”.


--z3178608 04:19, 11 May 2010 (UTC) Hello Group 8 I enjoyed reading your project page, which is filled essential information for anyone interested in microarray.

  • The introduction gives a general overview of the technique and outline of the web-page that is useful to the reader.
  • Appropriate use of graphics along with the accompanying text.
  • Simplified history timeline that is easy to read.
  • Extensive coverage of information for the 3 microarray technique; comparison for the protein microarray presented in table that is easier to understand.
  • Under the challenges section, your group could probably put in point form or classified certain information under sub-headings (E.g. Problems with accuracy, and solutions etc.)

Overall, I think this project is excellent because of your great effort and intense literature research.

--Jae Choi 11:56, 10 May 2010 (UTC) Hi, You guys did a beautiful job. Well organised, clearly described, lots of interesting pictures including a link to video. It is really hard for me to point out the thing that I would like to comment on. But, in my opinion, it would be perfect if you add some more for the Glossary part. That is all I want to say. Cheers.


--Angama Yaquobi 07:16, 10 May 2010 (UTC)Hi group 8 I must say a well-researched project. Overall structure is very logical and the references seem very comprehensive. Adding more words in glossary makes it easy for a reader to attain the meaning and also placing the glossary before references makes the page look better. I would like to see few more pictures in your webpage. Overall well done group 8!


--David Williamson 06:26, 10 May 2010 (UTC)

  • Good project guys, and I’m sure it’ll be even better by the time you guys are done with it.
  • The choice of subheadings and layout seems logical and well thought out.
  • Good choice of pictures- they’re useful in aiding understanding.
  • I liked the way the project was written- the language is clear and direct
  • Going through the project as a whole and making it flow a bit better between sections could further improve this project (I know our group has this problem too as we haven’t really integrated everyone’s work that well yet).
  • It could be worth including some extra words in the glossary, eg: I didn’t know what ‘perturbations’ meant.
  • In the introduction- I think it could be good to give a single sentence at the start saying what microarrays are, or it might be worth merging the intro and ‘definition and use’? The intro gives readers a great sense of applications and types of microarrays but not what they physically are, and often someone visiting a page will only want to know what the technique is in a very basic sense.
  • The table in ‘protein microaray’ section is a great idea, but I found it a little confusing to read. Would it be possible to have clearly laid out rows that directly compare the types eg: a row for what it measures, a row for significance, a row for uses etc.

--Katiana Shaw 03:25, 10 May 2010 (UTC) Hey Group 8 - Here are my thoughts on your project:

  • The information is very comprehensive and shows that you have done a lot of research. Well Done!
  • I really like the setup where you have broken the project into the different types of microarray. It flows well and is easy to read. One suggestion is to put the glossary above the references (I actually missed them the first time I looked at your page).
  • I really like the use of video but would also like to see a few more pictures throughout, just to break up the text a little.

A great project overall - well done!


--z3252005 12:06, 9 May 2010 (UTC) Hey Group 8. This project is very well constructed. The headings and sub-headings were appropriate. The sections were well put together. The introduction is good as it includes an outline of the page which is nice and the history section is clear and concise. Some improvements I could suggest are:

  • I think you should keep consistency in the history section by writing the names of the researchers for all the developments which are mentioned and not for just a few.
  • More images would be nice especially for the challenges section. Maybe you guys could include a picture of "Spot". This isn't a major issue but you guys should put the author for the student drawn diagram and also put up a copyright. To see what to include just have a look at the editing basics section of the webpage.
  • The glossary section would be better if it was placed before the references as it maybe missed at times. Also you guys could include some more terms in the glossary as well.

Overall this project was well put together and explains effectively the microarray technique. Good work guys.


--z3256682 07:07, 9 May 2010 (UTC) Hi,

I was very impressed by this project - you have made it understandable and I haven't been overwhelmed by endless text. The intro that provided an outline of your project was appreciated. A few suggestions to improve include the following for your consideration:

- good idea to put protein microarray types into table, however you may like to add an extra 1st column containing something like 'What is it, What happens, What uses, How common is it' so the reader can find the question and quickly see the answer in your table. (not a problem - just my thoughts)

- in tissue microarray, you could, but not absolutely needed, add a picture of this MTA-1 tissue arrayer. A picture of SPOT and other equipment/kits is also possible.

- add more definitions to your glossary, eg. microtome.

Kind regards,


Definately the best project I've seen so far, good work Group 8! The ordering and layout of the sections is really effective- not too many things that can be faulted! The addition of a table that allows the direct comparison between the 3 types of microarrays you've covered would be a useful addition, as would a few more terms in the Glossary (things like proto-oncogene, cDNA, FISH etc). Overall, the referencing is pretty good but a list of references to current research that uses microarray would be a valuable resource too. Nice work! --Louisa Frew 14:32, 8 May 2010 (UTC)


--Begum Sonmez 23:50, 7 May 2010 (UTC)

Hello group 8. Your project page on Microarray looks appealing overall. Some specific things that I really liked were the intro, the brief history, the use of a table for Protein Microarray. Although, here are some changes that you all might like to consider:

  • In the intro I liked the link: ‘Links: - Using DNA microarrays to monitor the expression of thousands of genes simultaneously’, but I think it belongs under ‘Definition and Use’.
  • Some of the dates under history didn’t have their corresponding researchers mentioned, but others did. It would be more informative to have the names of the main researchers, or the name of the foundation/group.
  • The beginning of the Video (under DNA Microarray) was helpful.
  • The table under Types of Protein Microarrays was helpful, but I think it deserves an extra column added to the far left side to Identify what each row is mentioning/comparing. This is helpful for the reader.
  • Challenges:
    • ‘Background signals can also be introduced due to non-specific binding of the labeled nucleic acids to the array substrate (COMMA) and its fluorescence and these backgrounds signals may vary in location.’ (Under ‘Accuracy’, which is under ‘Challenges’). Nothing major with this, though just add a comma as indicated.
    • Under ‘Accuracy’, try and make use of bullets. A bullet for ‘deviations in the positions of subarray grids’, "dilution effect", and one for the ‘solution’ to this problem for example.
    • The heading ‘Reproducibility’ under Challenges seems misleading to me. I thought it was the Reproducibility of the technique, not the results of the technique. That’s something to think about changing If you like, but If not, it’s really nothing major. It’s just something I found along the way.
    • ‘Microarray-based studies may report findings that are not only difficult to reproduce, but not reproducible [Did you mean ‘not reliable’?]
  • Put the Glossary before referencing mainly because the glossary is also referenced itself. It makes more sense to put it there.

Overall, I have no major comments. This page seems to me very well researched. The overall structure is logical. Thanks for teaching me about microarray (I never new what it was before!).


Hey Guys, your page is hard to fault. The references seem very comprehensive and well done. There are some good diagrams but i think a few more would be a good option. Also a glossary might be a good idea for your topic as there are a lot of acronyms and terms which would be less confusing in a glossary. That's really the only thing i can suggest as the page is flawless otherwise.--z3253199 04:22, 7 May 2010 (UTC)

--z3252340 11:11, 5 May 2010 (UTC) I found your page to be really well put together and well organised. it is obvious that you have done a lot of work on the page. There is alot of information on the page so one thing you could do to improve the page would be to reduce some of the information by including a couple of more tables or summarising some of the parts. Also include some more images if possible or use diagrams to illustrate some of the methods.



Referencing

Hey guys,

Actually, we should do the referencing properly by using something like:

<ref> Hornshøj H, Conley LN, Hedegaard J, Sørensen P, Panitz F, et al. (2007) Microarray Expression Profiles of 20.000 Genes across 23 Healthy Porcine Tissues. PLoS ONE 2(11): e1203. doi:10.1371/journal.pone.0001203 [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001203;jsessionid=DBF480686BE7D530C3063820824A92CD] </ref>

And it would automatically be added in the reference below.

Cheers, Rosita :)

http://www.ramaciotti.unsw.edu.au/index.html

Protein Microarray

http://www.ncbi.nlm.nih.gov/pubmed/20204849

Our Plan

how it works

flow diagrams

references

current applications

include a diagram the group has drawn

Microarray Database

Sam's references

Brown PO & Botstein D (1999). “Exploring the new world of the genome with DNA microarrays”. Nature Genetics Supplement 21: 33-37. doi:

Quackenbush J (2002). “Microarray data normalization and transformation”. Nature Genetics Supplement 32: 496-501. doi:10.1038/ng1032.

Lockhart DJ & Winzeler EA (2000). “Genomics, gene expression and DNA arrays”. Nature 405 (6788): 827-836. doi:10.1038/35015701.

Shalon D, Smith SJ & Brown PO (1996). “A DNA Microarray System for Analyzing Complex DNA Samples Using Two-color Fluorescent Probe Hybridization”. Genome Research 6 (7): 639-645. doi:10.1101/gr.6.7.639. PMID 8796352.

Simon R, Radmacher MD, Dobbin K & McShane LM (2003). "Pitfalls in the Use of DNA Microarray Data for Diagnostic and Prognostic Classification". Journal of the National Cancer Institute 95 (1): 14-18. doi:10.1093/jnci/95.1.14.


King, H.C. & Sinha, A.A. (2001). "Gene Expression Profile Analysis by DNA Microarrays". The Journal of the American Medical Association, 286(18):2280-2288. http://jama.ama-assn.org/cgi/content/abstract/286/18/2280