Knguye66 Eyoung20 Week 15

Combined Individual Journals for Kaitlyn Nguyen and Emma Young (Data Analysts).

Purpose

The purpose of this assignment is to record our progress towards the FunGals group deliverables as the Data Analysts for this week and the future weeks to come. The purpose of week 12 specifically was to download and adapt the data to the formatting we need for analysis. Then to begin the analysis with ANOVA and preparations for STEM.

Methods and Results: Progress

Progress 11/26/19

Running Stem Methods

- Analyzing and Interpreting STEM Results -

1. Why did you select this profile? In other words, why was it interesting to you?
   • We collectively combined the 4 red profiles together because they had similar trends and to increase the number of genes for analysis (called "Red".) Similarly this was done to the 3 green profiles as well (upward trends), with the addition of the blue profile #29 added. We will call this group "Green".
2. How many genes belong to this profile?
   • Red (composed of Profile #9,26,34,11): 289
   • Green (Profile #40,42,18,29): 214
3. How many genes were expected to belong to this profile?
   • Red (composed of Profile #9,26,34,11): 51.5
   • Green (Profile #40,42,18,29): 48.5
4. What is the p value for the enrichment of genes in this profile?
   • Due to combining the profiles, we do not have p-values for the enrichment of genes in the 2 different groups.

Conclusion

The first stage of our group's project was completed via referencing Week 8 and using Microsoft Excel to complete the tasks. The excel file will be located in the FunGals page for viewing and download. We were able to successfully complete the ANOVA analysis and correct found mistakes. We were able to complete a sanity check with results showing. For the sanity check the unadjusted p- values showed 37.2% of the genes had a p<0.05, 18.16% had a p<0.01, 5.04% have p<0.001, and 0.87% have p<0.0001. The sanity check for the Bonferroni-corrected p-value 0.11% of the genes have p<0.05. For the sanity check on the Benjamini and Hochberg-corrected p-value 16.36% go the genes had a p <0.05. Finally we were able to prepare the Data to run STEM in the next step of working on this project.

Data and files

excel workbook

Acknowledgements

This section is in acknowledgement to partner Kaitlyn Nguyen (User:knguye66), Michael Armas (User:Marmas), as well as, Iliana Crespin (User:Icrespin), and Emma Young (User:eyoung20). We would also like to acknowledge Dr. Dahlquist (User:KDahlquist) for introducing and teaching the topic and direction of this assignment. Also to acknowledge that this is a shared electronic notebook between Kaitlyn Nguyen and Emma Young.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source." Knguye66 (talk) 18:49, 20 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) 16:40, 25 November 2019 (PST)

References

• 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

User Page

User:knguye66

Template Page

Template:knguye66

Table of all assignments and journal entries for BIO-367-01

Week	Individual Journal Entry	Shared Journal
Week 1	-	Class Journal Week 1
Week 2	knguye66 Week 2	Class Journal Week 2
Week 3	ILT1/YDR090C Week 3	Class Journal Week 3
Week 4	knguye66 Week 4	Class Journal Week 4
Week 5	DrugCentral Week 5	Class Journal Week 5
Week 6	knguye66 Week 6	Class Journal Week 6
Week 7	knguye66 Week 7	Class Journal Week 7
Week 8	knguye66 Week 8	Class Journal Week 8
Week 9	knguye66 Week 9	Class Journal Week 9
Week 10	knguye66 Week 10	Class Journal Week 10
Week 11	knguye66 Week 11	FunGals
Week 12/13	knguye66 Eyoung20 Week 12/13	FunGals
Week 15	knguye66 Eyoung20 Week 15	Class Journal Week 15

Eyoung20 user page

Assignment pages	Individual Journal	Class Journal
week 1	Eyoung20 journal week 1	Class Journal Week 1
week 2	Eyoung20 journal week 2	Class Journal Week 2
week 3	ASP1/YDR321W Week 3	Class Journal Week 3
week 4	Eyoung20 journal week 4	Class Journal Week 4
week 5	Ancient mtDNA Week 5	Class Journal Week 5
week 6	Eyoung20 journal week 6	Class Journal Week 6
week 7	Eyoung20 journal week 7	Class Journal Week 7
week 8	Eyoung20 journal week 8	Class Journal Week 8
week 9	Eyoung20 journal week 9	Class Journal Week 9
week 10	Eyoung20 journal week 10	Class Journal Week 10
week 11	Eyoung20 journal week 11	FunGals
week 12/13	Knguye66 Eyoung20 Week 12/13	FunGals
week 15	Knguye66 Eyoung20 Week 15	FunGals