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MAPPFinder and You: An Introductory Presentation Evan Montz & Zeb Russo Loyola Marymount University Department of Biology Biol 367 Oct. 26th, 2010 Outline • • • • MAPPFinder and the Gene Ontology Project How MAPPFinder works MAPPFinder presents data in a variety of ways Search and navigation in MAPPFinder MAPPFinder is a tool that organizes genes according to their GO ID • MAPPFinder integrates the Gene Ontology (GO) Project with GenMAPP • Compares an experimental to a control group • Generates a graphical representation of thousands of genes in their representative pathways as well as how they are regulated No tool previously linked gene expression data to the GO hierarchy • MAPPFinder used in conjunction with GenMAPP, a gene pathway profiler • Pathway profiling should be automated so as to explore all possible pathways • GenMAPP currently has 50 MAPPs (MicroArray Pathway Profiles), which is insufficient to cover all species • MAPPFinder created to connect GenMAPP to GO Project GO Consortium created a list of formal definitions • Describes biological processes, cellular components, and molecular functions • MAPPFinder calculates percentage of genes measured that meet user-created criterion • Using this plus a z score, can rank GO terms by relative amounts of change in gene expression based on the control Outline • • • • MAPPFinder and the Gene Ontology Project How MAPPFinder works MAPPFinder presents data in a variety of ways Search and navigation in MAPPFinder How MAPPFinder Works Fig Utilization of MAPPFinder as an Example • Analyzed publicly available mouse microarray data on cardiac development in 12.5 day old mouse embryo versus adult heart cells as the control • Locates genes in microarray and then finds associated GO terms Outline • • • • MAPPFinder and the Gene Ontology Project How MAPPFinder works MAPPFinder presents data in a variety of ways Search and navigation in MAPPFinder Genes Found by MAPPFinder Table 1 Text representation of showing MAPPFinder results Table 2 Graphical Representation of MAPPFinder Data (MAPPFinder Browser) Fig 2 Graphical Representation cont. Fig 3a Graphical Representation cont. Fig 3b+c MAPPFinder results confirm expectations • Highest upregulation was found in cell division and growth pathways • Highest downregulation was found in energy metabolism • Global view of gene expression changes allow to be put in context of other regulatory and developmental processes Outline • • • • MAPPFinder and the Gene Ontology Project How MAPPFinder works MAPPFinder presents data in a variety of ways Search and navigation in MAPPFinder MAPPFinder has many search and navigation functions • Can search by keyword or exact GO term • Can search by gene identifier to find associated GO terms • User can search GO tree to automatically to show all nodes with minimum # of genes, minimum % of genes meeting criterion, or minimum z-score Outline • • • • • MAPPFinder and the Gene Ontology Project How MAPPFinder works MAPPFinder presents data in a variety of ways Search and navigation in MAPPFinder MAPPFinder is a great addition to GenMAPP MAPPFinder is a great addition to GenMAPP • MAPPFinder works seamlessly with GenMAPP • Is free and is regularly updated • Expands with every new species and pathway mapped by researchers around the world Conclusions • MAPPFinder is an extremely effective tool that is capable of rapidly comparing microarray data to create a global gene expression profile. • MAPPFinder is capable of yielding important statistical data such as up regulation, down regulation, and z-scores Acknowledgements • Margie and Andrew • Dr. Dionisio and Dr. Dahlquist