Elizabeth Polidan Week9
BIOL 398.03 / MATH 388
- Loyola Marymount University
- Los Angeles, CA, USA
Begin by recording in your wiki the number of replicates for each time point in your data.
Data errors replaced by single space: 108 occurences
- Check the number of genes significantly changed. How many genes have p value < 0.05? p < 0.01? p < 0.001? p < 0.0001?
- Perform this correction and determine whether and how many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction.
Only one gene was still significantly changed under this stringent correction.
Magnitude and direction of gene expression
- Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change greater than zero. How many meet these two criteria?
|<.05 & ALFC > 0||449||681||621||418||221|
|<.05 & ALFC > 0.25||439||668||609||398||191|
|<.05 & ALFC < -0.25||331||517||413||249||59|
- Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change less than zero. How many meet these two criteria? See table above, row 1.
- Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05? See table above, row 2.
- How many have an average log fold change of < -0.25 and p < 0.05? See table above, row 3.
Check expression of NSR1. Find NSR1 in your dataset.
- Is its expression significantly changed at any timepoint?
There was significant change at t=15, 30, and 60
- Record the average fold change and p value for NSR1 for each timepoint in your dataset.
- See the table above.
Check for gene with smallest p-value.
- Which gene has the smallest p value in your dataset (at any timepoint)?
- YOL159C has the smallest p-value of .0000024114 at t=30.
- Look up the function of this gene at the Saccharomyces Genome Database and record it in your notebook.
- YOL159C is listed in the Yeast Genome Database, but its function is listed as unknown.
- Why do you think the cell is changing this gene's expression upon cold shock?
- I don't know how to answer this.