# Difference between revisions of "Elizabeth Polidan Week9"

Elizabeth Polidan

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.

t15 t30 t60 t90 t120
4 4 4 5 5

Data errors replaced by single space: 108 occurences

Sanity Check

• Check the number of genes significantly changed. How many genes have p value < 0.05? p < 0.01? p < 0.001? p < 0.0001?
p t15 t30 t60 t90 t120
<.05 802 1213 1046 672 288
<.01 202 415 276 162 36
<.001 24 69 33 14 5
<.0001 2 8 4 0 2

Bonferroni correction

• Perform this correction and determine whether and how many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction.
p t15 t30 t60 t90 t120
<.05 0 1 0 0 0

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?
p t15 t30 t60 t90 t120
<.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.
Check for gene with smallest p-value. You can find this by sorting your data based on p value (but be careful that you don't cause a mismatch in the rows of your data!)
• 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.
Values for NSR1
t15 t30 t60 t90 t120
p value .0042 .0019 .0462 .1821 .5056
Avg LFC 1.57 2.06 1.66 -0.66 -0.14