James P. McDonald Week 12

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STEM

  1. Why did you select this profile? In other words, why was it interesting to you?
    • I chose profile 48. I did this because all the genes are consistently upregulated for the first 3 time points (t15, t30, t60) and then drop down around zero by t120. The genes appear to be responding similarly to the cold shock, suggesting consistent responses.
  2. How many genes belong to this profile?
    • 48 genes belong to this profile
  3. How many genes were expected to belong to this profile?
    • 28.4 genes were expected to belong to this profile
  4. What is the p value for the enrichment of genes in this profile?
    • p-value = 4.2E-4 (significant)
  5. How many GO terms are associated with this profile at p < 0.05?
    • 11 of 112
  6. How many GO terms are associated with this profile with a corrected p value < 0.05?
    • 0 of 112
  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 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?
      1. GO:0030684: Any complex of pre-rRNAs, ribosomal proteins, and associated proteins formed during ribosome biogenesis.
      2. GO:0006396: Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
      3. 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.
      4. 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.
      5. GO:0070647: A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to or removed from a target protein.
      6. GO:0034660: The chemical reactions and pathways involving non-coding RNA transcripts (ncRNAs).
      7. GO:0016070: The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
      8. 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.
      9. GO:0005730: A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
      10. GO:0006364: Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    • Explanation: I chose a profile where the genes were upregulated during cold shock. Looking at my GO terms they are involved in ribosome biosynthesis, assembly of ribosomes, RNA molecule synthesis, and transcription processes. This makes sense to me because when the cell is faced with cold shock it is trying to alter its protein expression through transcription processes. If the cell is make new proteins to cope with the cold shock it makes sense that the GO terms are all involved in the areas I previously mentioned

YEASTRACT

  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: 34.0 %
    • Rap1p: 19.1 %
    • Rfx1p: 14.9 %
    • Ino4p: 14.9 %
    • Sok2p: 12.8 %
    • Xbp1p: 10.6 %
    • Rpn4p: 10.6 %
    • Cin5p: 10.6 %
    • Mcm1p: 10.6 %
    • Yap6p: 8.5 %
  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?
    • Cin5: 10.6 %, 5 genes
    • Gln3: N/A
    • Hmo1: N/A
    • Zap1: 2.1 %, 1 gene
  3. Which transcription factors do you want to add to the model and why?
    • Ste12, Rap1, Rfx1, Ino4, Sok2. I would want to add these to the model because they had the highest percentages of genes they regulate in profile 48.

Powerpoint w/ YEASTRACT image

Excel of Regulation Matrix

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