BIOL368/F11:Week 14
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This journal entry is due on Wednesday, December 7 at midnight PST (Tuesday night/Wednesday morning). NOTE that the server is on Eastern Standard time (EST), therefore, midnight will register as 03:00.
Individual Journal Assignment
- Store this journal entry as "username Week 14" (i.e., this is the text to place between the square brackets when you link to this page).
- Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.
- Link to your journal entry from your user page.
- Link back from your journal entry to your user page.
- Link to this assignment from your journal entry.
- Don't forget to add the "BIOL368/F11" category to the end of your wiki page.
DNA Microarray Analysis
- Project work session to complete statistical analysis of your microarray data and MAPPFinder analysis.
- You will use Excel to calculate the average log fold changes and perform a modified t test for your experimental groups.
- We will be following the protocol on this page (with modifications): Sample Microarray Analysis for Vibrio cholerae.
- You will then use GenMAPP and MAPPFinder to find out which Gene Ontology terms are over-represented in the data.
- GenMAPP and MAPPFinder Protocols
- You will use Excel to calculate the average log fold changes and perform a modified t test for your experimental groups.
- Your presentation for Week 14 will be formatted similarly to your previous research presentations.
- Your presentation will be 15 minutes long (approximately 15 slides, one per minute). Include:
- Title slide
- Outline slide
- Background about your microarray dataset (from your journal club)
- The experimental design of the microarray experiment
- A table that lists the number of genes with significant changes in expression at the p value cut-offs of < 0.05, < 0.01, < 0.001, and Bonferroni-corrected p < 0.05.
- A list of the top 10 "most significant" genes and their functions.
- Tables that list the MAPPFinder results for increased and decreased gene expression.
- Discussion and interpretation of your results, in comparison to the original journal club paper.
- Upload your slides to the OpenWetware wiki by the Week 13 journal assignment deadline. You may make changes to your slides in advance of your presentation, but you will be graded on what you upload by the journal deadline.
- Use these Presentation Guidelines when preparing your PowerPoint slides.
- Your presentation will also be graded on the following Guide to critiquing talks.
- Your presentation will be 15 minutes long (approximately 15 slides, one per minute). Include:
- Store your journal entry in the shared BIOL368/F11:Class Journal Week 14 page. If this page does not exist yet, go ahead and create it.
- Link to the shared journal entry from your user page; this should be part of your template.
- Link the shared journal page to this assignment page.
- Sign your portion of the journal with the standard wiki signature shortcut (
~~~~). - Add the "BIOL368/F11" category to the end of the wiki page (if someone has not already done so).
Reflection
For your last reflection you will reflect on this entire semester:
- What are some of the things that you learned this semester in this class? Your answer could include biological/bioinformatics principles, personal or teamwork qualities, and/or technical skills.
- What will you take away from this class that you will still use a year from now?
