FunGals

Effects of the Pesticide Thiuram:  Genome-wide Screening of Indicator Genes by Yeast DNA Microarray

Team Information
Project Manager: Michael Armas
Quality Assurance:  Iliana Crespin
Data Analysis: Emma Young, Kaitlyn Nguyen
Coder: Michael Armas

Methods and Results

Week 11

Setting up the Project

• Selected Michael Armas as team's Project Manager.
• Added the name of of selected project manager to the Project Manager guild page and Overview pages.
• Named the team FunGals and created FunGals home page on the wiki.
• The name of the team home page was the selected team name.
• Created a link to team's page on the course Main page.
• Created a template for FunGal with useful information and links that you will invoke on all pages that you will create for the project.
• Created a category using team name and included it the FunGal template so that it is used on all pages created for the project. Also included the category "Group Projects" in the template.
• Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
• Each team member should reflect on the team's progress (Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks):
  • What worked? What didn't work? What will I do next to fix what didn't work?
    • Michael Armas: Working with this team is a great pleasure! Everyone on the team is pulling their weight and providing information that contributes to the group work. Next time, as the project manager, I want to be more organized and come up with interim deadlines to make sure we are not cramming right before the actual deadline. In fact, I would have something small due every day than procrastinate until the end. However, with this team, we are making it work and doing exceptional work!
    • Kaitlyn Nguyen: What worked this week is starting the presentation formatting early, thus allocating the rest of the time to "filling in the missing parts" of the powerpoint. What also worked this week was team communication via group-chats. What didn't work this week was starting the individual assignment later, leaving less time to practicing and fully understanding the material from the journal article for the presentation in class. To fix what didn't work, I will start my individual assignment much earlier, to leave the rest of the time to focus on collaborative teamwork and group assignments. Knguye66 (talk) 23:37, 13 November 2019 (PST)
    • Emma Young: The team seems to work really well together. I think in upcoming weeks we will really thrive in working together. A foundation for communication has already been established and we have already started reviewing each others work and providing constructive criticism and help where it is needed. The main issue this week was a matter of timing. With the amount of work we had to do in the time frame given we were not able to meet up due to busy and conflicting prior engagements. This meant that we did not reach our full potential of working together effectively as a group this week. Next week, we hopefully will be able to set better deadlines and be able to have the ability to plan out time to work on this in a less rushed manner.
    • Iliana Crespin: Overall, this group has been great. Everyone has worked together and understands what must be done. In addition, each member is understanding of the special circumstances before the deadline of this assignment. The only thing that didn't work out was how scattered each of us were because of all the assignments that had to be completed from other classes. In addition, mandated plans (school- or work-related) popped up which made it difficult to contribute equally. For the future, I will make sure to manage my time better, because I have work and school. Therefore, by doing a fair share of certain things before classes/work, I will be able to contribute more.Icrespin (talk) 23:46, 13 November 2019 (PST)

Annotated Bibliography

1. Braconi, D., Bernardini, G., & Santucci, A. (2016). Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. Journal of Proteomics, 137, 19-34. DOI: 10.1016/j.jprot.2015.09.001
2. Hinkle, K. L., & Olsen, D. (2018). Exposure to the lampricide TFM elicits an environmental stress response in yeast. FEMS yeast research, 19(1), foy121. doi: 10.1093/femsyr/foy121
3. Iwahashi, Y., Hosoda, H., Park, J. H., Lee, J. H., Suzuki, Y., Kitagawa, E., ... & Iwahashi, H. (2006). Mechanisms of patulin toxicity under conditions that inhibit yeast growth. Journal of agricultural and food chemistry, 54(5), 1936-1942. doi: 10.1021/jf052264g.
4. Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
5. Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
6. Kitagawa, E., Momose, Y., & Iwahashi, H. (2003). Correlation of the Structures of Agricultural Fungicides to Gene Expression in Saccharomyces cerevisiaeupon Exposure to Toxic Doses. Environmental Science & Technology, 37(12), 2788–2793. doi: 10.1021/es026156b
7. Lu Yu, Na Guo, Rizeng Meng, Bin Liu, Xudong Tang, Jing Jin, Yumei Cui, Xuming Deng. Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 2010, 88 (1) , 219-229. DOI: 10.1007/s00253-010-2709-x.
8. Pierron, A., Mimoun, S., Murate, L. S., Loiseau, N., Lippi, Y., Bracarense, A. P. F., ... & Oswald, I. P. (2016). Intestinal toxicity of the masked mycotoxin deoxynivalenol-3-β-D-glucoside. Archives of toxicology, 90(8), 2037-2046. doi: 10.1007/s00204-015-1592-8

Week 12/13

Milestone 3: Getting the data ready for analysis

1. Downloaded and examined the microarray dataset, compared it to the samples and experiment described in the journal club article.
   • Kitagawa et al. (2002)
   • downloaded and unzipped
   • file was downloaded but was PLC format
   • Mike figured out how to drag and drop it one to excel to open the file
2. Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, replicate number, and other information pertaining to each sample.
   • This "Metadata" sheet was created in Excel.
   • In collaboration with other groups, the Metadata sheet will be filled out so that nomenclature is consistent.
3. Come up with consistent column headers that summarize this information
   • As decided by all groups, the format for column headers is yeastStrain_treatmentOrMutation_concentrationAndUnits_dataType_timeAndUnits-replicateNumber.
     • For example, the Dahlquist Lab microarray data used strain_LogFC_timepoint-replicate number, as in wt_LogFC_t15-1.
4. Organize the data in a worksheet in an Excel workbook so that:
   • MasterIndex is in the first column, ID is in the second column
   • Data columns are to the right, in increasing chronological order, using the column header pattern you created
   • Replicates are grouped together
5. Data analysts (DA) set-up the ANOVA worksheet via referencing Week 8
   • Followed the steps for the ANOVA: Part I, Benjamini, Bonferroni, and p-value correction, as well as, perform a quick sanity check
6. DAs begin setting up for STEM analysis to complete the first stage of milestones and deliverables

• Each team member should reflect on the team's progress (Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks):
  • What worked? What didn't work? What will I do next to fix what didn't work?
    • Michael Armas: What worked this week was the communication between my guild and me, and my group and me. Everyone was able to help each other out and make sure the project is coming along smoothly. What didn't work this week for me was understanding exactly what I had to do to set up spreadsheets for data analysis. However, thanks to Mihir, I was able to understand how to create a metadata sheet and reach the milestone for this week. Before I leave class from now on, I will reassure myself that I understand the information by asking Dr. Dahlquist the best way to reach the week's milestone.
    • Kaitlyn Nguyen: This week, the pattern and organization to which each group member worked flowed smoothly as every member of the group knew exactly what each person was accomplishing. Having extra time in class and staying after class helped us jump-start on our tasks together and find out what assignments work best for each team member. What didn't work this week was that each milestone and part of this project works chronologically, whereby other members have to wait for the first person to finish his/her task before beginning theirs. As the days and weeks move on, it will be good to continue this method, but switch off on who starts the tasks first for the assignment. Knguye66 (talk) 18:44, 20 November 2019 (PST)
    • Emma Young: For this week I worked closely withKaitlyn to start the data analysis for the rest of the project. We worked with the whole team to analyze the data from the journal article and format for the rest of the data analysis. Mike worked with the other programers to formulate the metadata sheet and the format for the ANOVA sheet. More details on this can be found in his personal electronic notebook Marmas Week 12/13 Then Kaitlyn worked on the ANOVA analysis of the data. Iliana double checked the the results of the analysis the details can be found in Icrespin Journal Week 12/13. After the checks were completed and any errors were found, I ran a sanity check on the ANOVA data and then formatted the STEM worksheet for future analysis. The details about what [[User:Knguye66|Kaitlyn] and I did can be found in our shared journal Knguye66 Eyoung20 Week 12/13. As can be seen in this summary this week your group was really good at communicating and working together to work on this project. We worked really well together this week.
    • Iliana Crespin: For this week, it was a better organization on completing the assignment. There is more of a pattern of what should be done throughout each day to prepare for the deadline. What didn't work out for me is still trying to see how a QA can incorporate any work, since my teammates are great. For the next few weeks, I will try to continue double checking the work and contribute more. This contribution can include working with the data analysts and seeing how I can help out a bit more. In addition, texting teammates a bit more to remind any little things that must be due before the deadline. Icrespin (talk) 14:48, 21 November 2019 (PST)

Data and Files

Week 11

• Presentation file: Group Presentation

Week 12/13

excel workbook

1. Prepare your microarray data file for loading into STEM.
   • Insert a new worksheet into your Excel workbook, and name it "Thiuram_stem".
   • Select all of the data from your "Thiuram_ANOVA" worksheet and Paste special > paste values into your "Thiuram_stem" worksheet.
     • Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name".
     • Filter the data on the B-H corrected p value to be > 0.05 (that's greater than in this case).
       • Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu. Undo the filter. This ensures that we will cluster only the genes with a "significant" change in expression and not the noise.
     • Delete all of the data columns EXCEPT for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
     • Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
     • Save your work. Then use Save As to save this spreadsheet as Text (Tab-delimited) (*.txt). Click OK to the warnings and close your file.
       • Note that you should turn on the file extensions if you have not already done so.
2. Now download and extract the STEM software. Click here to go to the STEM web site.

Milestones

Tasks to be completed	Due Date
Write down Methods and Results for Week 12/13 Coder/designer: find out the column names and edit them, sample to data relationship table Data Analysis: ANOVA analysis and set-up, STEM set-up (will run STEM on Thursday) QA: make sure all data in original file actually made it into the database, let coder and analysts know if there are issues	Thursday, 12:00am, 11/19/19
Team Journal Assignment, continue writing down Methods and Results for Week 12/13 Data Analysis: finish editing missing information for ANOVA and (STRAIN) worksheet, run STEM Coder and QA: add standard names to genes, make sure all data in original file actually made it into the database, let coder and analysts know if there are issues	Tuesday, 12:00am, 11/26/19
	Thursday, 12:00am, 11/28/19
	Tuesday, 12:00am, 12/03/19
	Thursday, 12:00am, 12/05/19
Final Presentation	Tuesday, 12:00am, 12/10/19
Report submitted	Friday, 4:00 pm, 12/13/19

Acknowledgements

This section is in acknowledgement to partner Michael Armas, Iliana Crespin, Emma Young, and Kaitlyn Nguyen. I would also like to acknowledge Dr. Dahlquist for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
Marmas (talk) 23:40, 13 November 2019 (PST) Icrespin (talk) 23:46, 13 November 2019 (PST)

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source." Eyoung20 (talk) 23:57, 13 November 2019 (PST) Knguye66 (talk) 18:45, 20 November 2019 (PST)

Information and Links

FunGals Links
BIOL Databases Main Page	FunGals: Project Overview Page	Final Project Deliverables Requirements	FunGals: Final Project Deliverables
				Assignment Pages	Week 11	Week 12/13	Week 15

• Thiuram Article

User Pages

Knguye66 
Marmas
Icrespin
Eyoung20

Template Page

Template:FunGals

References

-Week 11-

• Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
• Dahlquist, K. (2019, November 7). Week 11. In Wikipedia, Biological Databases. https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11

-Week 12/13-

• Dahlquist, K. (2019, November 19). Data Analysis. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Data_Analysis
• Dahlquist, K. (2019, November 20). Final Project Deliverables. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables
• Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
• Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8