Reverse Engineering of Genetic Networks (Review meeting)基因网络的逆向工程（会议）.pptVIP

Reverse Engineering of Genetic Networks (Final presentation) Ji Won Yoon (s0344084) supervised by Dr. Dirk Husmeier. MSc in Informatics at Edinburgh University, J.Yoon@sms.ed.ac.uk Reverse Engineering What is reverse engineering of gene network? Past works Comparison of existing approaches to the reverse engineering of genetic networks, Mutual information relevance networks My own method Bayesian networks using Markov Chain Monte Carlo method Applying all methods to synthetic data generated from a gene network simulator. Applying to Biological data Diffuse large B cell Lymphoma gene expression data Arabidopsis gene expression data Relevance Network (Butte, 2000) Using mutual information MI(A, B) = H(A) – H(A|B) = H(B) – H(B|A) = MI(B, A) - Symmetric MI(A, B) = H(A) + H(B) – H(A, B) Mutual information is zero if two genes are independent. Pair wise relation Relevance Network (cont.) Relevance Network (Butte, 2000) Useful only to local relation due to pair wise relation. Important to select proper threshold to get good relations. Bootstrapping (Comparison of results in real data and in randomly permuted data) Difficulty to identify the relation with two parents due to the locality. MI(A, [B, C, D]) MI(A, B) MI(A, C) MI(A, D) Cannot detect XOR operation MI(A, C) = MI(B, C) = 0 No direction of edges due to symmetric property Fast and light computation. Useful for a number of genes My method (using mutual information) Based on Scale free network Crucial genes will have more connections than other genes. My method (Insertion step) Finding better parents and merging Clusters My method (Deletion step) Assumption The network generated from insertion step of my method is in stationary state in marginal log likelihood except one edge, which is investigated to check the connection Three case in an edge e X-Y, X-Y, and X Y My method (Deletion step) My method Mainly two steps Insertion and deletion steps My method Advantage