# BIOL398-04/S15:Week 15

BIOL398-04: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

• This journal entry is due on Thursday, May 7 at midnight PDT (Wednesday night/Thursday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.
• The final oral presentation will be given on Thursday, May 7 at 8:00AM - 10:00AM.
• The final research report is due on Friday, May 8, 5:00PM, in hard copy to either Dr. Dahlquist (Seaver 218) or Dr. Fitzpatrick (UNH 2726)

## Individual Journal Assignment

• Store this journal entry as "username Week 15" (i.e., this is the text to place between the square brackets when you link to this page).
• Create the following set of links. (HINT: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.)
• Don't forget to add the "BIOL398-04/S15" category to the end of your wiki page.

For your assignment this week, you will keep an electronic laboratory notebook on your individual wiki page that records all the manipulations you perform on the data in preparation for your final presentation and paper.

• Your electronic lab notebook (individual journal entry) and shared journal entry are worth a total of 10 points for this week (like every week). You will be graded individually on this part of the assignment.
• Your final research presentation is worth a total of 60 points. You and your partner will receive the same grade on this part of the assignment.
• Your final written report is worth a total of 100 points. You will will write your paper individually and be graded individually for this part of the assignment.

REMINDER: you should "turn on" the file extensions using the instructions found on the Help page before beginning today's work.

### Final Research Report

• Your final paper for this course is an individual assignment.
• Prepare your final paper according to the guidelines below. To do this, you will be compiling and interpreting the results from the Week 11-14 journal assignments.

### Style Sheet

Use the following guidelines when formatting your paper.

• 1" margins
• double-spaced
• Times New Roman, 12 point font
• Number the pages
• Title page should include a descriptive title for your project, your name, the course number and name, and the date of submission
• There is no set length for this paper; it must be long enough to contain the content described below.

### Title

The function of the title is to identify the main result or message of the paper. It should be as specific as possible and name the organism(s) and strain(s) that you investigated. It can be a phrase or a sentence. What is the main result of your paper that you want to convey with the title?

### Introduction

The introduction gives the background information necessary to understand your paper. The introduction should be in the form of a logical argument that "funnels" from broad to narrow (you will need about 2-3 pages in length to adequately cover all of these points):

• States importance of the problem
• Why are we studying gene regulation and cold shock?
• States what is known about the problem
• Introduce the DNA microarray experiment that was performed.
• States what is unknown about the problem
• Little is known about which transcription factors regulate the early response to cold shock
• States clues that suggest how to approach the unknown
• Introduce the workflow of performing statistical analysis of the microarray data, clustering and GO term analysis, and finding candidate transcription factors with YEASTRACT
• States the question the paper is trying to address
• Using the model to estimate the relative contribution of each transcription factor to the regulation of gene expression
• Be sure to cite your sources according to the Guidelines for Literature Citations in a Scientific Paper instructions on the course home page. Each paragraph should have at a minimum, two in text citations.

### Methods

• This section will summarize the entire workflow for the project. This needs to be a narrative description of what you actually did, but it is not a protocol or recipe. You do not need to provide the actual protocol for what you did, but you do need to describe each step so that someone else with your level of expertise could follow what you did. For each of the items below, describe in words what you did and why.
1. A description of the experimental design for your assigned microarray datasets (for both you and your partner since you analyzed the wild type and one other strain) from the Week 11 Assignment
2. The statistical analysis steps you performed in Excel from the Week 11 Assignment
3. Using STEM for clustering from the Week 11 Assignment
4. Using YEASTRACT for identifying candidate transcription factors and for defining your network from the Week 12 Assignment
5. Creating your input sheet for the model from the Week 13 Assignment
6. Running the model from the Week 14 Assignment

### Results & Discussion

You will write a combined Results & Discussion section. This means that you will not have a separate Results section and a separate Discussion section, but that you will describe and interpret the results in the same section of the paper. The text of this section should be a narrative that describes and interprets each of the results from your gene regulation modeling project. In particular, include the items listed below. You need to describe each of the figures/tables in words in your text, it is not enough to just have the figures and tables alone.

• Number each of the figures sequentially and number each of the tables sequentially as they appear in your narrative. You can either embed your figures and tables in the appropriate place in the text or put them all at the end. Do not mix both styles, however.
• Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.
• Statistical analysis of the microarray data
• Create a table that reports the results of the statistical analysis of the DNA microarray data
• How many genes (and what percentage out of 6180) had an expression profile that was significantly different than zero at any timepoint (ANOVA) at the different p value cut offs (see your Week 11 Assignment)? Include the data for each of the strains that you and your partner analyzed (wt S. cerevisiae and the other strain).
• How do you interpret the p values?
• From the STEM analyis, include as figures the overall results (the screenshot showing all of the clusters) and then focus on the one you interpreted for your Week 11 Assignment.
• Include a table showing the GO results for that cluster (just the narrowed down list of terms that you have interpreted).
• Discuss what the p values for the cluster and for the GO term list mean.
• Discuss the biological interpretation of your GO terms.
• Note that in your presentation, you will not have enough time to discuss all of the GO terms. Focus on 3-4 terms to highlight in the presentation. In your paper, you can talk about all 10.
• Note also that in your paper you can focus in on the strain that you yourself analyzed, but that in your presentation you will need to discuss the results from both partners. You can choose to talk about terms that are similar between the two strains or terms that are different or some of each.
• Include a table that lists the transcription factors that you are working with and their enrichment p value from YEASTRACT (from the Week 12 Assignment). Include just the transcription factors that made it into your final network.
• Describe how and why you and your partner chose these transcription factors for your network.
• Include a figure of the unweighted network visualized with GRNsight.
• Modeling results (from the Week 14 Assignment)
• Include the following data tables that you created in Week 14 in your paper (Note that in your presentation you don't want to show the tables, but instead the bar charts and GRNsight visualizations because that lends itself to a visual presentation better.)
• Optimized weight parameters (w) when b was fixed and when b was optimized.
• Optimized production rates (P) when b was fixed and when b was optimized
• b parameters when b was optimized.
• Include the bar charts for the "fixed b" and "estimated b" weights.
• Show the individual plots for each transcription factor for each run. You will want to organize these so that they can be compared easily. For example, you might want to put the graphs for the same gene where b was fixed and estimated next to each other.
• Note that in your paper you should show all the plots, but that in your presentation, you will need to focus on just a few genes that have interesting properties that you want to show and discuss.
• Show the GRNsight visualization of the weighted network from the two runs, making sure that the genes are placed in the same relative location as each other an as the unweighted network figure.
• Interpret the results of the model simulation.
• Examine the graphs that were output by each of the runs. Which genes in the model have the closest fit between the model data and actual data? Which genes have the worst fit between the model and actual data? Why do you think that is? (Hint: how many inputs do these genes have?) How does this help you to interpret the microarray data?
• Which genes showed the largest dynamics over the timecourse? In other words, which genes had a log fold change that is different than zero at one or more timepoints. The p values from the Week 11 ANOVA analysis are informative here. Does this seem to have an effect on the goodness of fit (see question above)?
• Which genes showed differences in dynamics between the wild type and the other strain your group is using? Does the model adequately capture these differences? Given the connections in your network (see the visualization in GRNsight), does this make sense? Why or why not?
• Examine the bar charts comparing the weights and production rates between the two runs. Were there any major differences between the two runs? Why do you think that was? Given the connections in your network (see the visualization in GRNsight), does this make sense? Why or why not?
• Finally, based on the results of your entire project, which transcription factors are most likely to regulate the cold shock response and why?
• Relate the results of your project to the paper you presented for journal club in Week 10
• What future directions would you take if you were to continue this project?

### Acknowledgments

Acknowledge anyone that helped with your work (i.e., your classmates, instructors, and anyone else you had discussions with).

### Final Research Presentation

• You and your partner together will prepare a 15-20 minute PowerPoint presentation that will present the results of your final project. Please follow these guidelines when creating your presentation. You will need approximately 15-20 slides (1 slide per minute) for your presentation. You will be graded according to this rubric.
• Your presentation will include the same content as your final written report listed above, but formatted for a presentation.
• Title slide that gives the main take-home message as the title of your presentation, the authors, date, and venue (course number and title).
• Outline slide that is a summary of take-home messages of your talk (should mirror your conclusion slide)
• 1-2 introductory slides that give the background for your project
• You do not need to include any method slides; talk about your methods during your results slides, as appropriate.
• Figures from the Results & Discussion section of your paper described above (Note that your paper will have more figures than you have time for in the presentation. See the instructions above for how to select figures for your presentation.)
• Conclusion slide that mirrors your outline
• Future directions
• Acknowledgments
• References

## Shared Journal Assignment

• Store your shared journal entry in the shared Class Journal Week 15 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).