Anthony J. Wavrin Week 12

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  1. Why did you select this profile? In other words, why was it interesting to you?
    • I selected profile 48 because it had a very consistent trend that was up regulated from t0 to t60 but was down regulated at t120. This trend may hint that the significance is due to the cold shock instead of random chance.
  2. How many genes belong to this profile?
    • 42 genes (41.5 reported)
  3. How many genes were expected to belong to this profile?
    • 16.3 genes were expected to belong to this profile
  4. What is the p value for the enrichment of genes in this profile?
    • P value = 0.000000053
  5. How many GO terms are associated with this profile at p < 0.05?
    • 26 of 124
  6. How many GO terms are associated with this profile with a corrected p value < 0.05?
    • 0 of 124
  7. Select 10 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05). Look up the definitions for each of the terms at Gene Ontology. 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?
      1. GO:0034622 - The aggregation, arrangement and bonding together of a set of macromolecules to form a complex, carried out at the cellular level.
      2. GO:0003723 - Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
      3. GO:0022618 - The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.
      4. GO:0071826 - Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.
      5. GO:0000785 - The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
      6. GO:0022613 - A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.
      7. GO:0042254 - A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
      8. GO:0034470 - Any process that results in the conversion of one or more primary non-coding RNA (ncRNA) transcripts into one or more mature ncRNA molecules.
      9. GO:0032268 - Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
      10. GO:0016568 - The alteration of DNA, protein, or sometimes RNA, in chromatin, which may result in changing the chromatin structure.
    • There is one large problem with looking at statistical significance of changes of expression of go terms, it does not tell you if it is down regulated or up regulated during cold shock. In my case, I picked a profile that was up regulated during cold shock, so it is relatively safe to assume that these GO terms are up regulated. The main theme is that present in all of these go terms is the up regulation of ribosome biogenesis, ribosome assembly, and regulation of protein metabolic processes. This makes sense because, the cell is most likely changing expression in proteins to try and cope with this added stress. In order to do this, it must make more ribosomes so that it can translate these proteins. Additionally, it may need to break down other proteins to get raw materials to make the proteins mentioned earlier. Thus, it would make sense that ribosome biogenesis would be up regulated when there are going to be other proteins make.


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.

Transcription Factor  % of Genes Regulated
Ste12 23.8%
Rap1 21.4%
Ino4 19.0%
Rfx1 16.7%
Yap6 14.3%
Cin5 11.9%
Abf1 9.5%
Mcm1 9.5%
Tec1 9.5%
Cbf1 9.5%

2. Are Cin5, Gln3, Hmo1, and Zap1 on the list? What percentage of the genes in the cluster does they each regulate? How many genes do they each regulate?

Transcription Factor  % of Genes Regulated # of Genes Regulated
Cin5 11.9% 590 (5 in cluster)
Gln3 2.4% 668 (1 in cluster)
Hmo1 0% 1 (0 in cluster)
Zap1 4.8% 185 (2 in cluster)

3. Which transcription factors do you want to add to the model and why?

  • Ste12, Rap1, and Ino4 because they had the highest percentage of genes that they effected in cluster 48. They also had overlap among some of the genes they affected (PUF6 SSF2).

Powerpoint with YEASTRACT image

Regulation Matrix

Original Assignment