Elizabeth Polidan Week9

Elizabeth Polidan

BIOL 398.03 / MATH 388

• Loyola Marymount University

• Los Angeles, CA, USA

• Email me through OpenWetWare

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Week 9 Assignment

Begin by recording in your wiki the number of replicates for each time point in your data.

Number of replicates for each time step

Time	t15	t30	t60	t90	t120
Replicates	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?

Number of genes changed with specified p-value

Time	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-values after Bonferroni correction

Time	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?

Magnitude and direction of gene expression

Time	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?

Values for NSR1

Time	t15	t30	t60	t90	t120
p value	.0042	.0019	.0462	.1821	.5056
Avg LFC	1.57	2.06	1.66	-0.66	-0.14

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.