Skinny Genes

Skinny Genes Links
BIOL Databases Main Page	Skinny Genes Project	Skinny Genes Template Page	Skinny Genes Deliverables	Members	Project Manager & Data Analysis: Yeabsira Mesfin	Quality Assurance: Jonar Cowan & Christina Dominguez	Data Analysis: David Ramirez	Coder: Mihir Samdarshi
				Assignment Pages	Week 11	Week 12/13	Week 15

Positions

Project Manager: Aby

Quality Assurance: Jonar & Christina

Data Analysis: Aby & David

Coder: Mihir

Files

Sample to Data Relationship Table

Journal Club Presentation

ANOVA Data (MOST UPDATED)

Network Data

Stem and GRNsight Network

Profile 39 Gene Table

Profile 39 GO list

Profile 39 Gene Table & Lists (.zip)

Rank by TF list

Zip file containing the Skinny Genes group database

GRNmap Output

GRNmap Input

fresh GRNmap output from @kdahlquist

• I redid the input file by copying and Paste special > Paste values into a new .xlsx file
• I then re-ran GRNmap
• Both the input and output files are visualized correctly in GRNsight. I think some formatting of the original input file that got carried through was messing up GRNsight, either that or the "threshold_b" sheet was out of order.

Annotated Bibliography

1. Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351. DOI: 10.1371/journal.pbio.0040351
2. Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. FEMS yeast research, 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
3. Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
4. Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. FEMS yeast research, 12(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
5. Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in Saccharomyces cerevisiae. Molecular microbiology, 95(3), 555-572. DOI: 10.1111/mmi.12886
6. Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., … Kschischo, M. (2012). Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling. PLoS Computational Biology, 8(6). doi: 10.1371/journal.pcbi.1002548
7. David: Gladfelter, A.S., Kozubowski, L., Zyla, T.R., and Lew, D.J. (2005) Interplay between septin organization, cell cycle and cell shape in yeast. J Cell Sci 118: 1617–1628. DOI: 10.1242/jcs.02286
8. David: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI: 10.1534/genetics.111.128314
9. Jonar: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351.
10. Jonar: Udensi, U. K., & Tchounwou, P. B. (2017). Potassium Homeostasis, Oxidative Stress, and Human Disease. International journal of clinical and experimental physiology, 4(3), 111–122. doi:10.4103/ijcep.ijcep_43_17

Schedule

Tasks	Date
Assigment for the Week: Project Manager: Create Sample/Data Relationship Table Data Analysists: download raw data, run ANOVA QAs and Coder: standardize the ID and Standard Names of the genes	11/19/19
Assignment for the Week: Data Analysists: Run STEM and prepare GRNsight network QAs: Discuss standard column headers for database with other groups Coder: Design and Create Database	11/24/19
Assignment for the Week: Data Analysists: Create GRNmap Input Worksheet and run GRNmap QAs and Coder: Finalize the Database	12/03/19
Assignment for the Week: Data Analysists, QAs, Coder: Begin working on Research Paper and Presentation	12/05/19
Final Presentation	12/10/19
Report submitted	12/13/19

Executive Summaries

Week 11

Aby's Reflection

• Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
  1. What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
  2. What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
  3. What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.

Jonar's Reflection

• Progress:
  1. What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
  2. What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
  3. What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

Jcowan4 (talk) 23:59, 13 November 2019 (PST)

Christina's Reflection

• Progress:
  1. What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
  2. What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
  3. What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

Cdomin12 (talk) 00:51, 26 November 2019 (PST)

Mihir's Reflection

• Progress:
  1. What worked?
     • We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
  2. What didn't work?
     • Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
  3. What will I do next to fix what didn't work?
     • Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.

Msamdars (talk) 20:16, 13 November 2019 (PST)

David's Reflection

• Progress:
  1. What worked? We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
  2. What didn't work? Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
  3. What will I do next to fix what didn't work? I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.

Dramir36 (talk) 00:01, 26 November 2019 (PST)

Week 12/13

Aby's Reflection

• Progress: This week David and I statistically analyzed the data using an ANOVA.
  1. What worked? The ANOVA was relatively easy to code using Excel.
  2. What didn't work? We were hoping to run STEM this week as well but had difficulty creating the ID's and Standard Names for the data.
  3. What will I do next to fix what didn't work? We reached out to Dr. Dahlquist in regards to changing the ID's and Standard Names and thus, we should be able to run STEM after a few more edits.

Ymesfin (talk) 11:10, 25 November 2019 (PST)

Jonar's Reflection

• Progress:
  1. What worked? What worked was how we divided what needed to be done and how we were in constant communication with each other.
  2. What didn't work? Early on we had problems with the standard name and gene ID, which caused us to get a little anxious about what were supposed to do. In essence, we needed to ask for help. (Which was done later on but not early enough)
  3. What will I do next to fix what didn't work? Overall, I think we are handling the project well but if we had to work on something it would probably better timing for project management.

Jcowan4 (talk) 19:25, 25 November 2019 (PST)

Christina's Reflection

• Progress:
  1. What worked? We were able to communicate in class to effectively figure out what we needs to be done on a timeline.
  2. What didn't work? It took a long to get past the step of finalizing the data into columns that had both the IDs and standard names. However, this was due to the fact that the data sheet had many repeated genes and a variety of different names for genes.
  3. What will I do next to fix what didn't work? Communicate better on how we can solve this problem as a group.

Mihir's Reflection

• Progress:
  • This week I worked on creating the format for encoding the entries into the database.

1. What worked?
   • This weekend we split up into our different guilds. I think that we worked well in those guilds, and it seemed like the pairs of Jonar and Christina and David and Aby worked well.
2. What didn't work?
   • I think that this week, we were a little too fractured because of how immediately we were required to split up following the official beginning of the project. There was a lack of communication when we were discussing how to fix the gene names of the spreadsheet. Even though our communication was good last week, because of a variety of reasons I think that we were not able to effectively relate information regarding our data and formatting to one another.
3. What will I do next to fix what didn't work?
   • I think this next week, we should take the time talk to each other regarding what he had accomplished between work sessions and what we planned on working on during the upcoming work session.

David's Reflection

• Progress:
  1. What worked? We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
  2. What didn't work? Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
  3. What will I do next to fix what didn't work? I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.

Dramir36 (talk) 00:02, 26 November 2019 (PST)