Hivanson Week 9

Begin by recording in your wiki, the strain that you will analyze, the filename, the number of replicates for each strain and each time point in your data.

Strain name: ∆CIN5 strain

Filename: HI_BIOL367_S24_microarray-data_dCIN5.xcls

Number of replicates per strain: 4

Timepoints: 15 minutes, 30 minutes, 60 minutes, 90 minutes, 120 minutes

How many genes have p < 0.05? and what is the percentage (out of 6189)?

2290 genes; 37.0%

How many genes have p < 0.01? and what is the percentage (out of 6189)?

1380 genes; 22.3%

How many genes have p < 0.001? and what is the percentage (out of 6189)?

691 genes; 11.2%

How many genes have p < 0.0001? and what is the percentage (out of 6189)?

358 genes; 5.8%

How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?

151 genes; 2.4%

How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?

1453 genes; 23.5%

Find NSR1 in your dataset. What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values? What is its average Log fold change at each of the timepoints in the experiment?

Unadjusted p value: 6.37625E-08

Bonferroni-corrected p value: 0.000394626

B-H-corrected p value: 2.19237E-05

average Log fold change @ 15 minutes: 4.070025

average Log fold change @ 30 minutes: 3.611475

average Log fold change @ 60 minutes: 4.2985

average Log fold change @ 90 minutes: -2.900925

average Log fold change @ 120 minutes: -0.9315

NSR1 shows increased expression from time 15 minutes through 60 minutes. At 90 minutes, NSR1 expression decreases, and at 120 minutes, the expression of NSR1 remains decreased.

Excel microarray data

p value table slide for ∆CIN5

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