Matthew E. Jurek Week 12

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Matthew E. Jurek BIOL398-03/S13

Contents

Assignment Page

User Page

Analyzing and Interpreting STEM Results

  1. Why did you select this profile? In other words, why was it interesting to you?
    • I chose Profile 9 because it is down-regulated. My partner, Anthony, is focusing on a profile that is up-regulated. We thought it'd be interesting if we each explored a profile that behaved differently.
  2. How many genes belong to this profile?
    • There are 95 genes belonging to this profile.
  3. How many genes were expected to belong to this profile?
    • 23.9 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 for this profile is 3.3X10-29.
  5. How many GO terms are associated with this profile at p < 0.05?
    • 14 GO terms are associated with this p-value.
  6. How many GO terms are associated with this profile with a corrected p value < 0.05?
    • 1 GO term is associated with this corrected p-value.
  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?
    • Protein folding-The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    • Unfolded protein binding-Interacting selectively and non-covalently with an unfolded protein.
    • Cytoplasm-All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    • Cytosol-The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    • Response on stress-Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    • Regulation of phosphate metabolic process-Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
    • Protein Binding-Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    • Regulation of biological quality-Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
    • Carboxylic acid catabolic process-The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups.
    • Small molecule metabolic catabolic process-The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule.
    • I have chosen a profile that is down-regulated. I am not surprised that the GO terms related to protein folding, cytoplasmic behavior, and catabolism and metabolism. One GO term even dealt with stress response itself. As the yeast experiences cold shock, there are numerous implications on proteins. The cold temperatures degrade the proteins and that's why several of the GO terms relate to protein folding and binding. The cytosol and cytomplasm would also have to respond to the cold as they house everything wihtin the cell. Any changes within the cytoplasm could have major implications on all processes that happen in a cell. Metabolic and catabolic processes would also be impacted as the yeast strives to overcome cold temperatures.

Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes

  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 39.4%
    • Rap1p 30.9%
    • Sok2p 22.3%
    • Fhl1p 22.3%
    • Skn7p 22.3%
    • Swi4p 16.0%
    • Mbp1p 16.0%
    • Msn2p 16.0%
    • Yap6p 16.0%
    • Hsf1p 14.9%
  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- Regulates 13 genes for a total of 13%
    • Gln3- Regulates 5 genes for a total of 5.3%
    • Hmo1- Not on the list
    • Zap1- Regulates 2 genes for a total of 2.1%
  3. Which transcription factors do you want to add to the model and why?
    • I would add Ste12, Rap1 and Sok2. Looking at my cluster, these 3 transcription factors play a significant role in regulating the cluster.
  4. Regulation Matrix
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