James C. Clements: Week 11

Responses to questions Given

These are responses to the questions from the protocol found on BIOL398-01/S11:Week 11

• Number of replicates for each timepoint:
  • t0: 3 replicates
  • t10: 7 replicates
  • t30: 6 replicates
  • t120: 4 replicates
  • t720: 4 replicates
  • t3600: 6 replicates
  • The number of replicates found in the excel file were more than the number of biologically independent replicates reported in the Schade paper. This could mean that some dependent replicates exist in the excel sheet.
• Find amounts of genes for different timepoints for given P values (Solutions are listed in order from t0, t10, t30, t120, t720, t3600)
  • How many genes have p value < 0.05?
    • 156 612 574 991 1507 930
  • What about p < 0.01?
    • 26 260 214 435 852 469
  • What about p < 0.001?
    • 2 69 52 110 268 154
  • What about p < 0.0001?
    • 0 14 6 15 46 29

• Perform this correction and determine whether and how many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction. (Solutions are listed in order from t0, t10, t30, t120, t720, t3600)
  • P =.05
    • 0 3 0 1 3 8
  • P = .01
    • 0 0 0 1 0 1
  • P = .001
    • 0 0 0 0 0 0
  • P = .0001
    • 0 0 0 0 0 0

• For timepoint with most genes significantly changed for P <.05, (720 minute timepoint in my analysis), find P <0.05 (assumed P value using Bonferroni correction since it was not specified) for different average log fold changes.
  • A>0
    • 0 genes
  • A>.25
    • 0 genes
  • A<0
    • 8 genes
  • A<-.25
    • 8 genes
• What criteria did Schade use? How does it compare?
  • Schade’s data is somewhat vague for how this part of the analysis was done. The genespring software was used perform the statistical analysis. It was not mentioned as to what type of statistical analysis was done, however. Some searching was done to determine Genespring’s method of determining a gene to have significant change, but it was not easily accessible.
• NSR1 Average fold change and P values. Is it significant?
  • AFC:
    • 0.6841 -0.7194 -3.1920 -3.6023 -1.7610 -0.4052
  • P:
    • 0.7557 0.0005864 0.001090 0.0004374 0.0001921 0.1391
  • No Significant change using Bonferroni correction for P = 5%, but without Bonferroni correction there is significant change at 10 minutes, 30 minutes, 120 minutes, 720 minutes, and 3600 minutes.

• Gene with lowest P value.
  • Index number 3328 was found for my data to have the smallest P value. This is systematic name YNL316C, standard name PHA2 used in the synthesis of Phenylalanine, an essential amino acid it only shows significant change at the 2 hour mark. The ALFC for this gene was -1.5751, so it was downregulated. It may be difficult for the cell to make proteins or amino acids at the 2 hour time point and thus the cell would downregulate the gene.