Msamdars Week 9

Methods/Results

1. Why did you select this profile? In other words, why was it interesting to you?
   • I chose this profile because I saw the trend was very consistent. There was a clear trend of gene repression, followed by a period where gene expression was idled, followed by the last period of increased gene expression. I think that this is interesting because we can gain a clearer picture of what genes are activated initially, then repressed during cold shock.
2. How many genes belong to this profile?
   • 78 genes belong to this profile.
3. How many genes were expected to belong to this profile?
   • 47.1 genes were expected to belong to this profile.
4. What is the p value for the enrichment of genes in this profile?
   1. How many GO terms are associated with this profile at p < 0.05?
      • There are 8 terms
   2. How many GO terms are associated with this profile with a corrected p value < 0.05?
      • There are no terms.
   • The p-value is 0.000016 (1.6 x 10^-5).
5. 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)?
   1. GO:0003700
   2. GO:0045944
   3. GO:0055114
   4. GO:0016491
   5. GO:0005783
   6. GO:0046872

Acknowledgments

This week my team members included Emma Young, Ivy-Quynh Macaraeg, & DeLisa Madere. We worked in class together.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Other Links

Links
Mihir Samdarshi User Page
Assignment Pages	Personal Journal Entries	Shared Journal Entries
Week 1	Journal Week 1	Class Journal Week 1
Week 2	Journal Week 2	Class Journal Week 2
Week 3	FAS2/YPL231W Week 3	Class Journal Week 3
Week 4	Journal Week 4	Class Journal Week 4
Week 5	Database - AmtDB	Class Journal Week 5
Week 6	Journal Week 6	Class Journal Week 6
Week 7	Journal Week 7	Class Journal Week 7
Week 8	Journal Week 8	Class Journal Week 8
Week 9	Journal Week 9	Class Journal Week 9
Assignment Pages	Personal Journal Entries
Week 10	Journal Week 10
Week 11	Journal Week 11
Week 12/13	Journal Week 12/13
Team Project Links
Skinny Genes Team Page

References

1. LMU BioDB 2019. (2019). Week 9. Retrieved October 29, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9
2. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., ... & Harris, M. A. (2000). Gene ontology: tool for the unification of biology. Nature genetics, 25(1), 25.
3. Gene Ontology Consortium. (2018). The gene ontology resource: 20 years and still GOing strong. Nucleic acids research, 47(D1), D330-D338.
4. MediaWiki (2019). Category: Help. Retrieved October 29, 2019, from https://www.mediawiki.org/wiki/Category:Help