Elizabeth Polidan Week12

Elizabeth Polidan

BIOL 398.03 / MATH 388

• Loyola Marymount University

• Los Angeles, CA, USA

• Email me through OpenWetWare

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Week 12 Assignment

1. STEM
   1. STEM Profiles
      • Media:All_Significant_Profiles.pdf
      • Selected profile #27
   2. Why did you select this profile? In other words, why was it interesting to you?
      • I liked the way many of the genes were upregulated and then went down, overshooting into the negative.
   3. How many genes belong to this profile? 81
   4. How many genes were expected to belong to this profile? 29.4
   5. What is the p value for the enrichment of genes in this profile? Bear in mind that in the week 2.00E-15
   6. How many GO terms are associated with this profile at p < 0.05? 19
   7. How many GO terms are associated with this profile with a corrected p value< 0.05? None
   8. Look up the definitions for each of the terms at http://geneontology.org. Write a paragraph that describes 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?
      • The 10 genes are involved in transcription and translation, assembling the ribosomal complex, maturation of rRNA, breakdown of mRNA. These activities are all in keeping with the description of yeast response to cold shock (Al-Fageeh, M.B. and Smales, C.M. 2006. Control and regulation of the cellular responses to cold shock: the responses in yeast and mammalian systems, Biochem. J., 397(Pt. 2) p. 247-259).
2. Yeastract.com
   1. What are the top 10 transcription factors in your results? List them on your wiki page with the percent of the genes in your cluster that they each regulate.
      • Ste12p - 33.3%
      • Rap1p - 17.3%
      • Tec1p - 14.8%
      • Phd1p - 11.1%
      • Ino4p - 11.1%
      • Sko1p - 9.9%
      • Yap6p - 9.9%
      • Fhl1p - 9.9%
      • Reb1p - 8.6%
      • Hcm1p - 8.6%
   2. Are Cin5, Gln3, Hmol, and Zapl on the list? What percentage of the genes in the cluster do they each regulate? How many genes do they each regulate?
      • Cin5p - 4.9% - 4 genes (BSC1, YGR250C, CIN5, SET6)
      • Gln3 - Not present
      • Hmo1 - Not present
      • Zap1p - 2.5% - 2 genes (ICL1, ZRT3)
   3. Which transcription factors do you want to add to the model and why?
      • Ste12p
      • Rap1p
      • Tec1p
      • Because they regulate the highest percentage of genes (see answer above for percentage values).
3. Regulation Network