Elizabeth Polidan Week9
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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.
| 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?
| 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.
| 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?
| 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?
| 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.
