Anthony J. Wavrin Week 9

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11. Which gene has the smallest p value in your dataset (at any timepoint)? 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!) Look up the function of this gene at the Saccharomyces Genome Database and record it in your notebook. Why do you think the cell is changing this gene's expression upon cold shock?
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*The gene YIP1 has the ID YGR172C and has the smallest p value (p=1.24867 x 10^-5).  YIP1 is an "integral membrane protein required for the biogenesis of ER-derived COPII transport vesicles".  YIP1 is down regulated during cold shock, which makes sense because yeast is trying to survive, so trying to conserve energy by not transporting proteins from the ER via vesicles would make sense.
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[[BIOL398-03/S13:Week_9| Original Assignment]]
[[BIOL398-03/S13:Week_9| Original Assignment]]
{{template:Anthony J. Wavrin}}
{{template:Anthony J. Wavrin}}

Revision as of 02:17, 3 April 2013

Assignment 9

File of the spreadsheet with the statistics for dHMO1 is uploaded on Lionshare.

1. How many genes have p value < 0.05?

Time # of genes
15 385
30 544
60 434
90 204
120 190

2. What about p < 0.01?

Time # of genes
15 81
30 108
60 87
90 28
120 34

3. What about p < 0.001?

Time # of genes
15 8
30 10
60 6
90 5
120 4

4. What about p < 0.0001?

Time # of genes
15 0
30 1
60 1
90 1
120 0

5. Perform this correction and determine whether and how many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction.

  • There were no genes at any time point that has a p value < 0.05 after the Bonferroni correction.

6. 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?

  • 332

7. 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?

  • 212

8. Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05?

  • 306

9. How many have an average log fold change of < -0.25 and p < 0.05? (These are more realistic values for the fold change cut-offs because it represents about a 20% fold change which is about the level of detection of this technology.)

  • 198

10.Find NSR1 in your dataset. Is it's expression significantly changed at any timepoint? Record the average fold change and p value for NSR1 for each timepoint in your dataset.

  • There were no time points that had "significiantly" changed but, some time points were close to a p value of 0.05.
Time Avg Fold Change P Value
15 0.91 0.0385
30 1.19 0.0722
60 1.26 0.1618
90 -0.24 0.5704
120 -0.25 0.5507

11. Which gene has the smallest p value in your dataset (at any timepoint)? 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!) Look up the function of this gene at the Saccharomyces Genome Database and record it in your notebook. Why do you think the cell is changing this gene's expression upon cold shock?

  • The gene YIP1 has the ID YGR172C and has the smallest p value (p=1.24867 x 10^-5). YIP1 is an "integral membrane protein required for the biogenesis of ER-derived COPII transport vesicles". YIP1 is down regulated during cold shock, which makes sense because yeast is trying to survive, so trying to conserve energy by not transporting proteins from the ER via vesicles would make sense.



Original Assignment

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