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 Discuss Z score (rating of how confident you are that the change isn’t by chance), was it upregulated a lot, downregulated a lot, or didn’t change that much at all?

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 1

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 Still don’t understand where the percentages are coming from, also the numbers for the gene change isn’t correct. Talk about methods and materials 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

Acknowledgements Margie and Andrew Dr. Dionisio and Dr. Dahlquist