Monte Carlo Homework

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Use the genome.dat.csv file and the high-dnds.csv file for this question. You scan a genome looking for protein coding genes that show a sign of selection. You have save the names of the 100 genes with the highest Dn/Ds ratio in the high-dnds.csv file. You are interested if many of the genes that show a sign of selection might all be involved in the same cellular processes. You decide to find out if certain GO terms are associated with your list of 100 genes more often than you would expect by chance.

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You find that the most common GO term associated with your genes is GO term 58. Using a Monte Carlo determine if this GO term is present more often than you would expect? Assume an alpha level of 0.05

10 points

Yes GO term 58 is over represented in my genes experiencing strong selection

No GO term 58 is not over represented in my genes experiencing strong selection

Clear selection

In the last question you used an alpha level of 0.05. Use the Bonferroni approach to choose an appropriate p-value and answer the same question again.

10 points

Yes GO term 58 is over represented in my genes experiencing strong selection

No GO term 58 is not over represented in my genes experiencing strong selection

Clear selection

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