Week 7

Under Construction

The content in this page has not been finalized and is still subject to change. Use the current information at your own risk.

This journal entry is due on Friday, October 11, at midnight PDT. (Thursday night/Friday morning)

Individual Journal Assignment

• Store this journal entry as "username Week 7" (i.e., this is the text to place between the square brackets when you link to this page).
• Link from your user page to this Assignment page.
• Link to your journal entry from your user page.
• Link back from your journal entry to your user page.
• Don't forget to add the "Journal Entry" category to the end of your wiki page.
  • Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.

Background Readings

<biblio>

1. Paper1 pmid=9915498

//Brown & Botstein (1999) link to full text

1. Paper2 Chapter 4 of Campbell & Heyer, Discovering Genomics, Proteomics, and Bioinformatics. Available on MyLMUConnect under the "Information" section.

</biblio>

Overview of Microarray Data Analysis

This is a list of steps required to analyze DNA microarray data.

1. Quantitate the fluorescence signal in each spot in the microarray image.
   • Typically performed by the scanner software, although third party software packages do exist.
   • The image of the microarray slide and this quantitation are considered the "raw-est" form of the data.
   • Ideally, this type of raw data would be made publicly available upon publication.
   • In practice, the image data is usually not made available because the raw image file of one slide could be up to 100 MB in size.
   • Also, some journals do not require data deposition as a requirement for publication, so often published data are not actually available anywhere for download.
   • Microarray data is not centrally located in a single database. Some major sources are:
     • NCBI GEO
     • EBI ArrayExpress
     • Stanford Microarray Database
     • PUMAdb (Princeton Microarray Database)
     • In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
2. Calculate the ratio of red/green fluorescence
3. Log₂ transform the ratios
4. Normalize the log ratios on each microarray slide
5. Normalize the log ratios for a set of slides in an experiment
6. Perform statistical analysis on the log ratios
7. Compare individual genes with known data
8. Look for patterns (expression profiles) in the data (many programs are available to do this; we won't be doing this in class)
9. Perform Gene Ontology term enrichment analysis (we will use MAPPFinder for this)
10. Map onto biological pathways (we will use GenMAPP for this)

Preparation for Next Week's Journal Club

In preparation for the Journal Club, each individual will do the following assignment on their individual "username Week 7" pages.

1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries. Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources.
2. Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper. Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
   • What is the main result presented in this paper? (Hint: look at the last sentence of the introduction and restate it in plain English.)
   • What is the importance or significance of this work?
   • What were the limitations in previous studies that led them to perform this work?
   • What were the methods used in the study?
   • Briefly state the result shown in each of the figures and tables.
   • How do the results of this study compare to the results of previous studies (See Discussion).
3. Upload your completed PowerPoint slides to your journal page by the Week 7 journal deadline (you may make changes before your presentation Tuesday afternoon, but we will be evaluating the presentation you upload.)
   • For your PowerPoint presentation, you need to show each of the figures and tables in your article as part of your presentation. Do not have a separate section of your presentation for Methods. Instead, show each of the results (figures/tables) and just explain the methods used to obtain those results on that slide.
   • The length of your presentation should be about 15 minutes.

Journal Club Articles

<biblio>

1. Paper1 pmid=17588266

//Salomonis et al. (2007) link to full text

1. Paper2 pmid=12540299

//Doniger et al. (2003) link to full text

1. Paper3 pmid=10952301

//Heidelberg et al. (2000) link to full text

1. Paper4 pmid=12050664

//Merrell et al. (2002) link to full text, dataset (on this wiki) </biblio>

Groups

• To be determined

Shared Journal Assignment

• Store your journal entry in the shared Class Journal Week 7 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
• Link to your journal entry from your user page.
• Link back from the journal entry to your user page.
  • NOTE: you can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).

Reflection

• How do you think biotechnology like whole genome sequencing and microarrays will affect your future?
  • How will it affect your career?
  • How will it affect your personal life?
  • What pitfalls can you forsee and how would you suggest avoiding them?
• Please feel free to respond or comment on your classmates' reflections.