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Unformatted text preview: ecture 15 : hylogenetics ECS 124 Theory and Practice of Bioinformatics Lecture 15 : Phylogenetics Instructor: Ilias Tagkopoulos [email protected] Office: Kemper 3063 and GBSF 5313 5/20/2010 1 UC Davis LAST TIME: Subgraphs and motifs c How to get information out of networks c Subgraph identification c Community structure c A network may consist of smaller subnetworks r sub raphs 5/20/2010 UC Davis 2 or subgraphs c Some of these subgraphs may be over represented in the network, i.e. have a higher frequency from what we would expect from random chance LAST TIME: Motif over representation 5/20/2010 UC Davis 3 Concentration FFL is the number of appearances of the motif divided by the number of appearances of all connected threenode subgraphs Milo et al., Science, 2002 LAST TIME: Issues with Motif Finding Issues with motif finding: c How many knode subgraphs should we be looking ? c Assume a network of 10,000 nodes. If we are to look for all 3node subgraphs, how many combinations 5/20/2010 UC Davis 4 do we have? What about for all 5node subgraphs? c 1.6e+11 and 8.3e+17 c How do we find isomorphic subgraphs c How do we calculate statistical significance ? How can we create random networks? c Pvalue Known motiffinding programs: mfinder (Uri Alon), NeMoFINDER (SeeKiong Ng) LAST TIME: Community structure c Some nodes of the network may be more closely connected than other nodes c A set of nodes whose members are strongly connected with each other, but loosely connected the rest of the network is called a mmunity 5/20/2010 UC Davis 5 to the rest of the network is called a community or a module PART IV: Phylogenetics c The study of evolutionary relatedness among various groups of organisms through genetic features and traits ....
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This note was uploaded on 05/30/2010 for the course ECS ECS 124 taught by Professor Tagkopoulos during the Spring '10 term at UC Davis.
 Spring '10
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