Preview Some illustrations of graphs in Integrative Gen.pptVIP

* * * * * * Preview: Some illustrations of graphs in Integrative Genomics Genomics ? Transcriptomics: Alternative Splicing Genomics ? Phenotype: Genetic Mapping Comparative Biology: Evolution of Networks Biological Graphs and their models/combinatorics Networks in Cellular Biology A. Metabolic Pathways Boehringer-Mannheim Enzyme catalyzed set of reactions controlling concentrations of metabolites B. Regulatory Networks Network of {Genes?RNA?Proteins}, that regulates each other transcription. C. Signaling Pathways Sreenath et al.(2008) Cascade of Protein reactions that sends signal from receptor on cell surface to regulation of genes. Dynamics - Inference - Evolution D. Protein Interaction Networks Some proteins stick together and appear together in complexes E. Alternative Splicing Graph (ASG) Determines which transcripts will be generated from a genes A repertoire of Dynamic Network Models To get to networks: No space heterogeneity ? molecules are represented by numbers/concentrations Definition of Biochemical Network: 1 2 3 k A set of k nodes (chemical species) labelled by kind and possibly concentrations, Xk. A set of reactions/conservation laws (edges/hyperedges) is a set of nodes. Nodes can be labelled by numbers in reactions. If directed reactions, then an inset and an outset. 1 2 7 Description of dynamics for each rule. ODEs – ordinary differential equations Mass Action Time Delay Stochastic Discrete: the reaction fires after exponential with some intensity I(X1,X2) updating the number of molecules Continuous: the concentrations fluctuate according to a diffusion process. Discrete Deterministic – the reactions are applied. Boolean – only 0/1 values. Number of Networks Interesting Problems to consider: The size of neighborhood of a graph? Given a set of subgraphs, who many graphs have them as subgraphs? Directed Acyclic Graphs - DAGs Connected undirected graphs undirec