Knguye66 Week 9

Microrray Data Analysis (wild type data)

Purpose

This week's assignment is to continue the Microarray Data Anaylsis for wild type data. Step 4 and 5 from Week 9 are featured: Viewing and Saving STEM results, and Analyzing and Interpreting STEM results. For reference and files, go to: knguye66 Week 8.

Methods/Results

After finishing the steps on Week 9 for Viewing and Saving STEM results on stem.jar, screenshots of each profile were placed on a powerpoint (see Data and Files below), and the Profile Gene Table and Profile GO Table list for each table were compressed and zipped into files. Following this step, Profile #45 was chosen to analyze and interpret.

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Analyzing and Interpreting STEM Results:

- Profile #45 -

• Why did you select this profile? In other words, why was it interesting to you?
• How many genes belong to this profile?
• How many genes were expected to belong to this profile?
• What is the p value for the enrichment of genes in this profile?
• How many GO terms are associated with this profile at p < 0.05?
• How many GO terms are associated with this profile with a corrected p value < 0.05?
• Look up the definitions for each of the terms at http://geneontology.org. In your research presentation, you will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor being deleted (for the groups working with deletion strain data)?

Data and Files

• Profile Genelist (zip file)
• Profile GOlist (zip file)
• "Interface options" & Significant Profiles (.pptx)

Acknowledgements

This section is in acknowledgement to partner Christina Dominguez (User:Cdomin12), as well as, Marcus Avila (User:Mavila9) and Jonar Cowan (User:Jcowan4). I would also like to acknowledge Dr. Dahlquist (User:KDahlquist) 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."

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

References

• GEO Accession viewer. (n.d.). Retrieved from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83656.
• Dahlquist, K. (2019, October 24). Week 8. In Wikipedia, Biological Databases. Retrieved 08:02, October 28, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9
• Gene Ontology. (n.d.). Retrieved from https://lmu.app.box.com/s/t8i5s1z1munrcfxzzs7nv7q2edsktxgl
• Gene Association. (n.d.) Retrieved from https://lmu.app.box.com/s/zlr1s8fjogfssa1wl59d5shyybtm1d49
• The Short Time-series Expression Miner (STEM) version 1.3.12. (n.d.). Retrieved from http://www.cs.cmu.edu/~jernst/stem/