AhmadWeek12

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#Which transcription factors do you want to add to the model and why?
#Which transcription factors do you want to add to the model and why?
#*Just Ste12 and Rap1 because they are at such high percentages, well above the others.
#*Just Ste12 and Rap1 because they are at such high percentages, well above the others.
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#Regulation Matrix
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#*[[Image:Profile23GenesYeastract.jpg]]
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#*[[Image:RegulationMatrix_Documented_Ahmad.ppt]]
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*[[Image:Stem1.ppt]]
{{Salman Ahmad}}
{{Salman Ahmad}}

Current revision

Contents

Week 12 Journal Assignment

  1. Why did you select this profile? In other words, why was it interesting to you?
    • This profile was interesting to me because it has a pattern of staying at constant expression, followed by a slight repression, and ending with a higher expression than it started with.
  2. How many genes belong to this profile?
    • 256 genes belong to this profile
  3. How many genes were expected to belong to this profile?
    • 35.8 genes were expected to belong to this profile.
  4. What is the p value for the enrichment of genes in this profile?
    • The p-value is 2.1E-131 (very significant)
  5. How many GO terms are associated with this profile at a p-value of p < 0.05?
    • 533 have p-values below 0.05
  6. How many GO terms are associated with this profile at a corrected p-value of p < 0.05?
    • 116 have corrected p-values below 0.05
  7. 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?
    • General Metabolic Processes - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism. In cold, metabolic processes must have to change to maintain the integrity of the cell structure.
    • Cytoplasm- All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. The cytoplasm is important in cold shock because it needs to stay fluid and not become solid and sharp.
    • Small Molecule Metabolic Process- The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule. Small molecules here include monosaccharaides, but not disaccharides or polysaccharides.
    • 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.
    • Glycolysis- The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) into pyruvate, with the concomitant production of a small amount of ATP. Glycolysis begins with phosphorylation of a monosaccharide (generally glucose) on the sixth carbon by a hexokinase, and ends with the production of pyruvate. Pyruvate may be converted to ethanol, lactate, or other small molecules, or fed into the TCA cycle.
    • Monosaccharide Catabolic Process- The chemical reactions and pathways resulting in the breakdown of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. Breakdown of monosaccharides may cause warmth or keeping them intact could lower the freezing point of a solution.
    • Hexose Catabolic Process- The chemical reactions and pathways resulting in the breakdown of hexose, any monosaccharide with a chain of six carbon atoms in the molecule. This goes along with the last process, the monosaccharide catabolic process.
    • Intracellular Part- Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. It is important that the intracellular parts of the cell, mostly the organelles, are able to keep functioning even if the temperature is dropping.
    • Energy Derivation by Oxidation of Organic Compounds- The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released. The expression of this would likely change as the cell will have different energy needs at different temperatures.
    • Pyridine Nucleotide Metabolism- The chemical reactions and pathways involving a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base. Pyridine is important because it is a main component of DNA.
    • In this profile, the genes were first repressed and then expressed at a higher level later. I think that these genes were repressed because the cell thought the temperature would keep dropping until it got below freezing at which point it would be dangerous to continue doing these processes at the same rate. Once the cell realized that the temperature was actually a constant, it increased the expression of these genes, actually passing the starting point because it had to make up for the time it spent with these genes repressed.

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.
    • Ste12 34.4 %
    • Rap1 33.2 %
    • Fhl1 19.5 %
    • Sok2 16.0 %
    • Sko1 15.6 %
    • Yap6 14.1 %
    • Skn7 13.7 %
    • Msn2 12.9 %
    • Cin5 12.9 %
    • Yap5 11.7 %
  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 does they each regulate?
    • Cin5 is at 12.9%
    • Gln3 is at 1.6%
    • None of the other two
  3. Which transcription factors do you want to add to the model and why?
    • Just Ste12 and Rap1 because they are at such high percentages, well above the others.
  4. Regulation Matrix

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