Alex A. Cardenas Week 14

Electronic Notebook

• Computed the averages for A,B, and C along with multiplying all the c3/c5 by negative 1.
• Worked through the protocall and computed the Tstat values and the Pvalues along with changing some of the columns and rows.
• Filtered out the Pvalue column to find how many genes Pvalues were less than 0.05, 0.01, and 0.001.
  • Pvalue < 0.05 - 680 genes.
  • Pvalue < 0.01 - 228 genes.
  • Pvalue < 0.001 - 26 genes.
• The new spreadsheet can be found here.
• More modified spreadsheet can be found here.
• When making the geneMAPP, there were 132 errors found but this is insignificant because this is out of 2740 genes.
• geneMAPP excel file can be found here. The text file for geneMAPP can be found here.
• We looked at the top 10 genes with the lowest Pvalues, and the excel file can be found here.
• We also looked at the top 10 Gene Ontology terms and those can be found below.
  1. Pathogenesis
  2. Multi-organism process
  3. External encapsulating structure
  4. High-affinity iron ion transport
  5. Extracellular region
  6. Membrane Part
  7. Protein complex binding
  8. Immunoglobin binding
  9. Respiratory chain
  10. Periplasmic space

• Top ten increasing GO terms looked at will be:
  1. amine biosynthetic process
  2. cellular amino acid biosynthetic process
  3. cellular nitrogen compound biosynthetic process
  4. antiport activity
  5. branched chain family amino acid metabolic process
  6. aspartate family amino acid metabolic process
  7. threonine metabolic process
  8. oxidation reduction
  9. vitamin binding
  10. oxidoreductace activity

• Most Significant Genes
  1. SAR0633 - Q6GJ44 UniProt - Putative antiporter subunit mnhD2
  2. SAR1409 - Q6GH11 UniProt - Catalyzes the transfer of an acetyl group from acetyl-CoA to tetrahydrodipicolinate. INCREASED
  3. SAR2697 - Q6GDI4 UniProt - No other info INCREASED
  4. SAR2146 - Q6GF14 UniProt - Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate INCREASED
  5. SAR0689 - pseudogene
  6. SAR2771 - hypothetical protein
  7. SAR0278 - hypothetical protein
  8. SAR1563 - pseudogene
  9. SAR0820 - Q6GIM6 UniProt - Displays ATPase and GTPase activities. INCREASED
  10. SAR0353 - Q6GJW2 UniProt - Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation. INSCREASED

• This is a file that zeb put together. It deals with all the decreasing and increasing GO terms along with their screenshots. gene MRSA screenshots etc.

• Working on the powerpoint and so far it can be found here.
• The final powerpoint presentation can be found here.

Links

• Alex A. Cardenas
• Week 14 Assignment
• Alex A. Cardenas Week 2
• Alex A. Cardenas Week 3
• Alex A. Cardenas Week 4
• Alex A. Cardenas Week 5
• Alex A. Cardenas Week 6
• Alex A. Cardenas Week 7
• Alex A. Cardenas Week 8
• Alex A. Cardenas Week 9
• Alex A. Cardenas Week 10
• Alex A. Cardenas Week 11
• Alex A. Cardenas Week 12
• Alex A. Cardenas Week 14
• Class Journal Week 1
• Class Journal Week 2
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• Class Journal Week 5
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• Class Journal Week 14