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Modeling Functional Genomics Datasets CVM8890-101 Lessons 4&5 10 July 2007 Bindu Nanduri Lesson 4: Introduction to pathways analysis. Theory and strategies for pathway analysis modeling in different species. Lesson 5: Tools for pathway analysis. Ingenuity, Pathway Studio, etc. Networks and pathways A network is a collection of interactions Pathways are a subset of networks All pathways are networks of interactions not all networks are pathways Young et. al: Transcriptional Regulatory Networks in Saccharomyces cerevisiae; Science 2002 A network is a collection of interactions Pathways are a subset of networks All pathways are networks of interactions, however not all networks are pathways! Pathway is a biological network that corresponds to a specific physiological process or phenotype Biological pathways Biological components interacting with each other over time to bring about a single biological effect Pathways can be broken down sub-pathways Some common pathways: signal transduction metabolic pathways, gene regulatory pathways Entities in one pathway can be found in others 3 types of interactions that can be mapped into pathways protein (enzyme) – metabolite (ligand) metabolic pathways protein – protein cell signaling pathways, protein complexes protein – gene genetic networks Available resources KEGG http://www.genome.jp/kegg/ BioCyc http://www.biocyc.org/ Reactome http://www.reactome.org/ GenMAPP http://www.genmapp.org/ BioCarta http://www.biocarta.com/ TransPATH http://www.biobaseinternational.com/pages/index.php?id=transpathda tabases Pathguide – the pathway resource list http://www.pathguide.org/ Network Topology (PPI) Network analysis and visualization tools Databases for analysis Text mining algorithms (e.g., natural language processing (NLP)) technologies Expert human curation Ingenuity Pathway Analysis http://www.ingenuity.com/products/pathways_analysis.html PathwayStudio http://www.ariadnegenomics.com/products/pathway-studio/ PathwayArchitect http://www.selectscience.net Cytoscape http://www.cytoscape.org/ Biological Networks http://biologicalnetworks.net/ GeneGO http://www.genego.com/ Nanduri etal (unpublished) GO term enrichment Nanduri etal (unpublished) Nanduri etal (unpublished) Nanduri etal (unpublished) Nanduri etal (unpublished)
