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Bioinformatics 1 - Assignment 2

Background

Submit: Either using the submit function on DICE or by dropping a paper copy off at the ITO, level 4 Appleton Tower before the deadline. Any problems, please contact us well before the deadline.

This assignment is worth 25 marks. It is due 4pm on November 25th. Please remember that late assignments will not be marked. Plagiarism will be checked automatically, please read the guidelines and adhere to them completely. Make sure you show how you arrived at your solution. Please contact us to clarify anything you are unsure of.

The aim of this assignment is to explore some core molecular proteomics concepts. This assignment follows on directy from the work you did in assignment 1, you should use the same gene you have used there. However you may, if you wish, change your gene. If so, explain what the change was and why.

Q1

What is known about the function of the orthologues of your gene in mouse, fly or yeast? Select the one orthologue from any of the three species that is most informative. What has the study of this gene in a model species told us about how the disease might work. (10 marks)

Q2

Look at the protein encoded by your selected gene. Search for the known protein-protein interactions. How many proteins are in this list? Of this list of interactions, how many are also associated with the same disease? List those that are also implicated in the disease and explain how you investigated this. (10 marks)

Q3a.

Take all the proteins from Q2 and build a network of their interactions. Show a picture of this network highlighting your main protein. What is the position of your protein in this network, does it function as a hub? (5 marks).

OR
Q3b.

Take all the genes associated with the same disease that you can find (by any means). Build a protein-protein interaction network. Show a picture of this. What is the largest connected component? (5 marks)

If your protein/gene has no known interactions or less than 3 or 4, you may need to select another gene or seek advice.