Nick Rohacz: Week 11

Questions

1. t15 and t60 has 4 replicates, t30, t90, and t120 have 5 replicates.
2. We subtract the average and divide by the standard deviation to normalize the data. The dollar signs are just to keep the correct average and standard deviations cells used in each formula.
3. t15
   1. Pval < 0.05 = 817
   2. Pval < 0.01 = 208
   3. Pval < 0.001 = 25
   4. Pval < 0.0001 = 2
4. t30
   1. Pval < 0.05 = 1231
   2. Pval < 0.01 = 425
   3. Pval < 0.001 = 71
   4. Pval < 0.0001 = 8
5. t60
   1. Pval < 0.05 = 1071
   2. Pval< 0.01 = 292
   3. Pval < 0.001 = 41
   4. Pval < 0.0001 = 8
6. t90
   1. Pval < 0.05 = 684
   2. Pval < 0.01 = 164
   3. Pval < 0.001 = 14
   4. Pval < 0.0001 = 0
7. t120
   1. Pval < 0.05 = 295
   2. Pval < 0.01 = 37
   3. Pval < 0.001 = 5
   4. Pval < 0.0001 = 2
8. Pval < .05 after Bonferroni corrections
   1. t15: 0
   2. t30: 1
   3. t60: 3
   4. t90: 0
   5. t120: 0
9. t60 had the greatest number of genes that significantly changed at p < 0.05:
   1. AvgFC > zero: 2
   2. AvgFC < zero: 1
   3. AvgFC > 0.25 and p < 0.05: 2
   4. AvgFC > -0.25 and p < 0.05: 1
10. For Schade, genes were required to be at a 50% fold change, instead 20%, and the p-value for their analysis had to be less than .03, not .05. They used a different method, however, and used software for the calculations (GenePix) and we did ours in Excel. To get our p values, we used four or more trials, scaled and centered the data, averaged the trials, and then performed t-tests. Only after all this could we get p-values and filter the p-values to find significant data points. Schade only used two trials/datapoints, not 4 or 5. He also used different time intervals.
11. The expression of NSR1 greatly varied at t30.
    1. t15: AvgFC = 1.57; p = 0.0042
    2. t30: AvgFC = 2.06; p = 0.0019
    3. t60: AvgFC = 1.66; p = 0.0462
    4. t90: AvgFC = -.66; p = 0.1821
    5. t120: AvgFC = -.14; p = 0.5056
12. The gene with the smallest p value is YOL144W, otherwise known as NOP8. The p-value is 6.95892105234133E-09 at t60.
    1. The Saccharomyces Genome Database describes this gene as a "nucleolar protein required for 60S ribosomal subunit biogenesis."
    2. Two mutant phenotypes of this gene showed increased heat sensitivity at 37°C.
    3. The 60S ribosomal subunit the large ribosomal subunit of eukaryotes. At the time in which there was the smallest p-value (t60), the average log folding change was positive .91. Given that this gene is involved the translation process, I believe that the expression of YOL144W is increased because there is a greater need for translation of specific mRNA when it is cold. While other genes may be repressed because the protein that they code for is not needed, ribosomes involved in synthesizing necessary proteins would aid survival and prove beneficial in cold shock.

Nicholas A. Rohacz 02:44, 5 April 2011 (EDT)