Robert W Arnold Week 14

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Electronic Lab Notebook 14

Robert W Arnold

Week 14 Assignment

  • Opened up excel powerpoint.
  • Opened our data and multiplied all 2nd sets of data by -1 to normalize it.
  • Then averaged the 1st set of data with the new normalized data.
  • Then averaged A B C averages across the board. The spreadsheet can be seen down below under the Spreadsheet Updated title.
  • 680 or 2741 genes were found below .05 for P value.
  • 132 errors in 2741 genes were found by geneMAPP.
  • I began to look at increased factors, Alex looked at decreased.

Spreadsheet Updated

  • Here is updated spreadsheet. Included 2 more columns for each set of replicates, 3rd column in each in 2nd column multiplied by -1, 4th column is average of columns 1 and new column 3.
  • Here is the original excel file save as a .txt file for geneMAPP.
  • 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.
  • Here is the text file given back from geneMAPP with all of the information. Here is the file in excel form which will be used to filter results. Uploaded later will be this information after it is filtered for increasing and decreasing genes.
  • We looked at the top 10 genes with the lowest Pvalues and we obtained and the excel file for that can be found here.
  • Top ten decreasing GO terms looked at will be:
    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.

Data

  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

Media:Finalpresrwa.pptx

Links

Biol 368 Homepage

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