Genome Evolution Course 2009-2010

www.yanaiweb.com/genome

Itai Yanai, Technion – Israel Institute of Technology

Tutorial Presentation as PDF or PP.

Problem Set #11 assigned January 4th, 2010

To be submitted as hard-copy in English or Hebrew on January 10^th, 2010 (at the beginning of class, 9:30am).

Problem 1: Irreducible Complexity. What problem does gene duplication pose for the argument from “irreducible complexity”?

Problem 2: Randomizing the network. Imagine that you are given a network with a certain number of nodes and edges connecting them, and are asked to randomize it such that afterwards it has the same number of nodes, edges, and degree distribution, but not necessarily the same topology. Describe an algorithm for generating such a randomized network beginning with the given network.

Problem 3. The age of a node. What does the Barabasi-Albert (scale-free) model predict regarding the age of the popular nodes of a network? In other words, would they tend to be more recent or ancient?

Problem 4. Network Evolution 1. Compare the genes involved in a network between two organisms. For this question use the KEGG database. Pick a network (pathway): http://www.genome.jp/kegg/pathway.html . You will see the ‘reference’ network summarizing everything known about the network in general. Select a genome and click ‘Go’. The green boxes indicate the presence of the gene(s) in the network, while the white indicate the absences of the genes in this organism when compared to the reference. Now, select another organism (why not go crazy and pick a very distant species?) and compare the presences of genes in the same network.

Problem 5. Network Evolution 2. By “rolling over” with the mouse on individual nodes in the network you will find information regarding genes. If multiple genes are described these correspond to gene duplication. In your network describe a few gene duplicates if present in this network. Are there different numbers of duplications in another organism?