BIOL398-01/S11:Class Journal Week 12

Instructions

Formatting

• Link to your journal entry from your user page.
• Link back from the journal entry to your user page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "BIOL398-01/S11" category to the end of the wiki page (if someone has not already done so).

Class Responses

James C. Clements' Journal Entry

1. The part of the assignment that came most easily to me was figuring out what to do. The directions clearly stated exactly what to do for each step of the process. As nice as this was for me (being a student who is pressed for time because of his thesis and looming graduation), I'm not quite sure if this "cookbook recipe" format for assignments is the best way to go for upper-division coursework.
2. I have had difficulties with YEAST tract generating the list of genes grouped by transcription factor. The site persistently has given me an error message stating that it could not open a file.
3. I still don't understand what we're going to model.
4. Each p value gives us an idea of how significant the set of genes (or particular genes are). If we expect 5% of genes to perform in a certain way and we obtain data that states that 5% of our genes do just that, we've found nothing. If, on the other hand, our statistics determine that something should only happen 5% of the time and our experiments are able to induce it nearly 100% of the time, then it will be proven that that specific gene/cluster/profile has a significant role in the process.

James C. Clements 01:17, 12 April 2011 (EDT)

Alondra Vega's Journal Entry

1. The most easy thing about the assignment was working with STEM.
2. The most challenging was choosing the transcription factor and figuring out why it is important to cold shock. Also, I was never able to get the matrix to work.
3. I feel that I do not understand the p values and why we need all the different ones. Also, I am having trouble seeing the "big picture" for the project.
4. I will give this a try. The individual p values show how significant the expression of the gene was at a certain time point. The p-value per profile shows how significant the the expression of the cluster. Since the cluster are categorized by pathway or regulation of transcription factor, then it might show how significant the transcription factors are. the p value for the Go terms show the significance of the expression of the genes that are associated in that particular category.

Alondra Vega 23:28, 11 April 2011 (EDT)