Alex J. George 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:

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%