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3 Apr 2018

Wnt signaling is required to promote division of intestinal cells; however, Notch is required for differentiation. Does Notch signaling promote differntiation of absorptive or secretory cells?

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Related questions

Most cell signaling pathways eventually regulate gene expression by regulating transcription factors in the nucleus. In class, we have discussed several pathways (e.g. Wnt, SMAD, NFkB, cAMP-dependent signaling, MAPK pathway, and Notch signaling) that result in transcriptional regulation by sending a protein into the nucleus. Choose 3 of these pathways and discuss: what the protein is that enters the nucleus, how it is activated by its signaling pathway, and whether the activated protein that enters the nucleus is directly responsible for binding to DNA or whether it exerts its effects by regulating transcription factors. Be specific and explain your answer.

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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 – 443) genes are notup-regulated. Using GO, you note that 52 of the up-regulated genesare annotated as participating in the “Notch signaling pathway”.There are a total of 120 proteins in GO annotated with the term“Notch signaling pathway”.

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 orisn’t 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 “Notch signaling pathway” 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.

For C. Elegans (anchor cell) is required induction of vulval development. Which cell express EGF receptor, EGF, Delta, Notch protein to figure out induction and the consequences of those proteins in the cells.

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