THANK YOU FOR HELPING ME
There are 23221 human proteins with some Gene Ontology (GObiological process annotation. You conduct a gene expressionmicroarray experiment and identify 443 genes that are up-regulated;you can assume that the remaining 22778 (23221 â 443) genes are notup-regulated. Using GO, you note that 52 of the up-regulated genesare annotated as participating in the âNotch signaling pathwayâ.There are a total of 120 proteins in GO annotated with the termâNotch signaling pathwayâ.
1. Without using a calculator or computer, do you think you havean enrichment of Notch signaling pathway members in your list ofup-regulated genes? Describe your intuition for why there is orisnât enrichment of the GO term in your list. Hint: think in termsof percentages.
2. Fill out a contingency table that describes the overlapbetween up-regulated genes and âNotch signaling pathwayâ annotatedgenes. What distribution can be used to calculate the probabilityof observing this contingency table? Set up the formula and enterthe correct numbers for calculating the probability, but DO NOTcompute the probability.
3. How many contingency tables would be required to calculate ap-value for assessing significant enrichment of the Notch signalingpathway in your list of up-regulated genes? Note that the maximumnumber of genes that can be both up-regulated and belong to theNotch signaling pathway is 120.
4. Go to http://www.langsrud.com/fisher.htm and calculate thep-value (use right sided). Is finding 52 Notch signaling pathwayproteins in a list of 443 upregulated genes significant? Explainand cite the appropriate numbers.
THANK YOU FOR HELPING ME
There are 23221 human proteins with some Gene Ontology (GObiological process annotation. You conduct a gene expressionmicroarray experiment and identify 443 genes that are up-regulated;you can assume that the remaining 22778 (23221 â 443) genes are notup-regulated. Using GO, you note that 52 of the up-regulated genesare annotated as participating in the âNotch signaling pathwayâ.There are a total of 120 proteins in GO annotated with the termâNotch signaling pathwayâ.
1. Without using a calculator or computer, do you think you havean enrichment of Notch signaling pathway members in your list ofup-regulated genes? Describe your intuition for why there is orisnât enrichment of the GO term in your list. Hint: think in termsof percentages.
2. Fill out a contingency table that describes the overlapbetween up-regulated genes and âNotch signaling pathwayâ annotatedgenes. What distribution can be used to calculate the probabilityof observing this contingency table? Set up the formula and enterthe correct numbers for calculating the probability, but DO NOTcompute the probability.
3. How many contingency tables would be required to calculate ap-value for assessing significant enrichment of the Notch signalingpathway in your list of up-regulated genes? Note that the maximumnumber of genes that can be both up-regulated and belong to theNotch signaling pathway is 120.
4. Go to http://www.langsrud.com/fisher.htm and calculate thep-value (use right sided). Is finding 52 Notch signaling pathwayproteins in a list of 443 upregulated genes significant? Explainand cite the appropriate numbers.
