# BIOL398-01/S11:Class Journal Week 12

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#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. | #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. | ||

#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. | #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. | ||

- | #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. | + | #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. We have the flexibility to say how large or small we want the p value to be, so it could be significant. |

[[User:Alondra Vega|Alondra Vega]] 23:28, 11 April 2011 (EDT) | [[User:Alondra Vega|Alondra Vega]] 23:28, 11 April 2011 (EDT) | ||

[[Category:BIOL398-01/S11]] | [[Category:BIOL398-01/S11]] | ||

[[Category: Biomathematical Modeling]] | [[Category: Biomathematical Modeling]] |

## Revision as of 02:05, 12 April 2011

## Contents |

## Instructions

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### Reflection

## Class Responses

### Sarah Carratt's Journal Entry

### Carmen E. Castaneda's Journal Entry

### James C. Clements' Journal Entry

- 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.
- 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.
- I still don't understand what we're going to model.
- 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)

### Nicholas A. Rohacz's Journal Entry

- The part of this assignment that came most easily to me was going through all the GO processes and making the graphs, not only because it was easy but because I enjoyed seeing how the genes were exactly regulated throughout the time points.
- The final step was most challenging because I could not get it to generate a jpeg even though the instructions matched exactly what was stated. I will check in class what was wrong.
- I still do not understand exactly what we are going to do with all of this data. I have a general idea but I would like to figure out the whole process, doing steps just breaks up the process for me and makes it harder to understand.
- The p values let us determine exaclty what was significant in each process. This lets us compare what was found to be significant to what we were predicting to be significant. If we find that every gene we thought was significant is significant in each p-value, then we can start to understand the process. However if we find a large number of genes that are significant that were not predicted to be significant, then we know we are either missing something or part of the experiment went wrong somewhere, hence the sanity test.

Nicholas A. Rohacz 01:30, 12 April 2011 (EDT)

### Alondra Vega's Journal Entry

- The most easy thing about the assignment was working with STEM.
- 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.
- 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.
- 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. We have the flexibility to say how large or small we want the p value to be, so it could be significant.

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