Bobak Seddighzadeh Week 13

DNA Microarray Project

 * After struggling for several minutes with GenMAPP and our data, we finally got our data uploaded to GenMAPP
 * There were 70 errors while uploading
 * Here is our data saved from GenMAPP: [[Media:Leng Tai Yeast dataset.gex]]
 * After uploading, we specified the Inreased and Decreased values for both Carbon and Nitrogen limiting cultures
 * Orange correlated to increase; Blue correlated to decreased
 * From here, we used MAPPfinder to analyze our data
 * The results of our data are found in the following .txt files:
 * Carbon-Limited Increased Expression- [[Media:Increasedcarbonlimited.txt]]
 * Carbon-Limited Decreased Expression- [[Media:Decreasedcarbonlimited.txt]]
 * Nitrogen-Limited Increased Expression- [[Media:Increasednitrogenlimited.txt]]
 * Nitrogen-Limited Decreased Expression- [[Media:Decreasednitrogenlimited.txt]]
 * Here are the top 10 Gene Ontology terms for
 * Carbon-limited Decreased:
 * 1) Mitochondrial electron transport chain
 * 2) Energy Derivation by oxidation of organic compounds
 * 3) DNA Transposition
 * 4) Cellular Respiration
 * 5) Aerobic Respiration
 * 6) Amino acid permease activity
 * 7) Carbohydrate metabolism
 * 8) Cellular Carbohydrate metabolism
 * 9) ATP synthesis coupled electron transport
 * 10) Main Pathway of Carbohydrate Metabolism
 * Carbon-limited Increased:
 * 1) Nucleolus
 * 2) Cytoplasm organization and biogenesis
 * 3) Ribosome biogenesis and assembly
 * 4) Ribosome biogenesis
 * 5) rRNA processing
 * 6) rRNA Metabolism
 * 7) Nuclear lumen
 * 8) Membrane enclosed lumen
 * 9) Organelle lumen
 * 10) RNA Binding
 * Nitrogen-limited Decreased:
 * 1) Disaccharide metabolism
 * 2) Regulation of transcription from RNA polymerase to promoter
 * 3) Phosphotransferase activity/ Alcohol group as acceptor
 * 4) Trehalose metabolism
 * 5) Kinase Activity
 * 6) Transcription from RNA Polymerase to Promoter
 * 7) Carbohydrate metabolism
 * 8) Protein amino acid phosphorylation
 * 9) Protein Kinase activity
 * 10) Hydrolase activity/Hydrolyzing O-glycosyl compunds
 * Nitrogen-limited Increased:
 * 1) Cytosolic Ribosome
 * 2) Ribosome
 * 3) Structural Constituent of Ribosome
 * 4) Cytoplasm Organization and Biogenesis
 * 5) Ribosome Biogenesis and assembly
 * 6) Cytosolic Large Ribosomal Subunit
 * 7) Ribonucleoprotein complex
 * 8) Nucleolus
 * 9) Ribosme Biogenesis
 * 10) Large ribosomal subunit


 * We searched for the gene "HXT2" and clicked on the "Cell Surface Receptor Linked Signal Transduction" to get the following map:


 * We then clicked on the YCR072C gene to find its function which is a protein required for cell viability

Finding our data to work with

 * We opened our data with excel in order to filter our results to find significant changes and GO terms
 * The following is the criteria we used to cut the number of terms to about 20:
 * Permute p-value <0.05
 * Z score > 2
 * Number changed >3 and < 100
 * Percent Changed
 * Carbon-limited Increased: > 40%
 * Carbon-limited Decreased: > 60%
 * Nitrogen-Limited Increased: > 50%
 * Nitrogen-Limited Decreased: > 63%

Here are our 4 lists of about 20 GO terms each saved in Excel: [[Media:20 GO Terms for each culture.xls]]

Potential Explanations for Results:
In time of cold shock sugars metabolism was shown to be downregulated. This may seem counter intuitive at first because trehalose and glycogen are up-regulated in cold shock to counter the effects of freezing on the membrane. However, a good explanation for this has to with the fact the prolongued exposure resulted in acclimation making the up-regulation of those genes not necessary. Aminophopholipid transporters are going to be down regulated probably due to the fact that the cell has less aminophosopholipids available because they are in nitrogen limited conditions.
 * Nitrogen Limited Decreased Expression:

GMP expression is necessary for energy to carry about biological processes. Therefore, the upregulation of GMP makes sense. Ribsomes are going to need to be upregulated to make up for the slower enzyme kinetics. The increase in RNA methylation, RNA methyltransferase activity, tRNA methylation and tRNA methyltransferase activity, all indicate that new mRNA and tRNA molecules are being synthesized. Furthermore, biotin metabolism and biosynthesis is also upregulated. This makes sense because biotin is necessary for the production of fatty acids and fat and amino acid metabolism. This makes sense because lipids are often a long term energy source and since they are in nitrogen limited cultures they need another source of amino acids.
 * Nitrogen Limited Increased Expression:

The is an up regulation of the 20S subunit, ribosomal large subunit assembly and maintenance, and DNA directed RNA polymerase I complex. This indicates that the production of ribosomes are being up regulated which makes sense because enzyme kinetics have slowed and the cells compensates by making more ribosomes to possibly translate at a faster rate. snRNA binding, chaperon proteins, and transport vessicles have also been up regulated to allow proper processing and packaging of these proteins being made and expressed.
 * Carbon Limited Increased Expression:

For carbon limited cultures, there is a decrease in maltose metabolism, respiratory chain complex IV, cytochrome -c oxidase activity, as well as a couple other reductases. This indicates that glycolysis and cellular respiration is slowing because there is no glucose present to enter this pathway, so the cell compensates by down regulating many of the enzymes involved in the pathway.
 * Carbon Limited Decreased Expression: