Paul Magnano: Week 12 Individual Journal: Difference between revisions
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*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? | *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. | **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 | |||
*[[Image:Image 1453115333.jpg|Matrix]] |
Revision as of 20:28, 11 April 2013
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.
- Which transcription factors do you want to add to the model and why?
- Ste12p
- Rap1p
- Fhl1p