Paul Magnano: Week 12 Individual Journal

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

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.

YEASTRACT

• 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.