Elizabeth Polidan Week9: Difference between revisions
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{{Elizabeth Polidan}} | {{Elizabeth Polidan}} | ||
[[BIOL398-03/S13:Week_9|Week 9 Assignment]] | |||
'''Begin by recording in your wiki the number of replicates for each time point in your data.''' | '''Begin by recording in your wiki the number of replicates for each time point in your data.''' | ||
{| class="wikitable" style="text-align: right; color: green; border-collapse: collapse; border: 1px solid #000" | {| class="wikitable" style="text-align: right; color: green; border-collapse: collapse; border: 1px solid #000" border="1" cellpadding="2" | ||
! t15 | |+Number of replicates for each time step | ||
! Time | |||
! t15 | |||
! t30 | ! t30 | ||
! t60 | ! t60 | ||
Line 10: | Line 13: | ||
! t120 | ! t120 | ||
|- | |- | ||
| 4 | !Replicates | ||
| 4 | |||
| 4 | | 4 | ||
| 4 | | 4 | ||
Line 21: | Line 25: | ||
'''Sanity Check''' | '''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? | *Check the number of genes significantly changed. How many genes have p value < 0.05? p < 0.01? p < 0.001? p < 0.0001? | ||
{| class="wikitable" style="text-align: right; color: green; border-collapse: collapse; border: 1px solid #000" | {| class="wikitable" style="text-align: right; color: green; border-collapse: collapse; border: 1px solid #000" border="1" cellpadding="2" | ||
! | |+Number of genes changed with specified p-value | ||
! Time | |||
! t15 | ! t15 | ||
! t30 | ! t30 | ||
Line 61: | Line 66: | ||
'''Bonferroni correction''' | '''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. | *Perform this correction and determine whether and how many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction. | ||
{| class="wikitable" style="text-align: right; color: green; border-collapse: collapse; border: 1px solid #000" | {| class="wikitable" style="text-align: right; color: green; border-collapse: collapse; border: 1px solid #000" border="1" cellpadding="2" | ||
! | |+p-values after Bonferroni correction | ||
! Time | |||
! t15 | ! t15 | ||
! t30 | ! t30 | ||
Line 81: | Line 87: | ||
'''Magnitude and direction of gene expression''' | '''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? | *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? | ||
*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? | {| class="wikitable" style="text-align: right; color: green; border-collapse: collapse; border: 1px solid #000" border="1" cellpadding="2" | ||
*Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05? | |+Magnitude and direction of gene expression | ||
*How many have an average log fold change of < -0.25 and p < 0.05? | ! 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.''' | '''Check expression of NSR1. Find NSR1 in your dataset.''' | ||
*Is its expression significantly changed at any timepoint? | *Is its expression significantly changed at any timepoint? | ||
{| class="wikitable" style="text-align: right; color: green; border-collapse: collapse; border: 1px solid #000" border="1" cellpadding="2" | |||
|+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. | *Record the average fold change and p value for NSR1 for each timepoint in your dataset. | ||
Check for gene with smallest p-value. | **See the table above. | ||
'''Check for gene with smallest p-value. ''' | |||
*Which gene has the smallest p value in your dataset (at any timepoint)? | *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. | *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? | *Why do you think the cell is changing this gene's expression upon cold shock? | ||
**I don't know how to answer this. |
Latest revision as of 22:04, 25 April 2013
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.