Paul Magnano: Week 12 Individual Journal

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Paul Magnano BIOL398-03/S13 User: Paul Magnano

Class Journals

Assignments/Individul Journals

Analyzing and Interpreting STEM Results

  • Profile #9 selected
  • Why did you select this profile? In other words, why was it interesting to you?
    • I selected this profile because it seemed interesting that the genes were immediately down-regulated at the early time points but later up-regulated as time increased. This seemed indicative of some necessary change being made and then corrected as the intended action resulted.
  • How many genes belong to this profile?
    • 170
  • How many genes were expected to belong to this profile?
    • 44
  • What is the p value for the enrichment of genes in this profile?
    • 2.0 E-49
  • How many GO terms are associated with this profile at p value <0.05?
    • 91
  • How many GO terms are associated with this profile with a corrected p value <0.05?
    • 8
  • Powerpoint of Screenshots

10 Gene Ontology Terms

  • protein folding: The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
  • cytosol: The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • chaperone binding: Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
  • unfolded protein binding: Interacting selectively and non-covalently with an unfolded protein.
  • ribosomal subunit: Either of the two subunits of a ribosome: the ribosomal large subunit or the ribosomal small subunit.
  • oxidoreductase activity: Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • NAD binding: Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
  • hexose metabolic process: The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule.
  • carbohydrate biosynthetic process: The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • monosaccharide metabolic process: The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
  • The cell changes expression of these genes during cold shock, so it can function better in the environment that cold shock would produce. For example in cold it is likely that most proteins will be folded, and not denatured as is common with excessive heat, therefore it is sensible that the cell might downregulate genes that assist in unfolded protein binding, as fewer unfolded proteins would be within the cell. Another example is with carbohydrate biosynthesis, in cold shock carbohydrates might not be formed for storage due to their quick usage. So in cold shock it would make sense to downregulate genes that control carbohydrate formation, as in the case of cold shock carbohydrate formation would not be the cells priority. The regulation of genes in response to cold shock is based on how to better suit the cells needs now that it must survive in a suddenly colder environment.


  • 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
    • Rap1p
    • Fhl1p
    • Sok2p
    • Skn7p
    • Yap5p
    • Cin5p
    • Yap1p
    • Yap6p
    • Phd1p
  • Are Cin5, Gln3, Hmo1, and Zap1 on the list? What percentage of the genes in the cluster does they each regulate? How many genes does they each regulate?
    • Yes Cin5 is on the list and it regulates 14.2% of the genes in the cluster. It regulates 24 genes.
  • Which transcription factors do you want to add to the model and why?
    • Ste12p
    • Rap1p
    • Fhl1p
  • Regulation matrix excel file
  • Matrix