1. MAPPFinder and You: An Introductory Presentation
Evan Montz & Zeb Russo
Loyola Marymount University Department of Biology
Biol 367
Oct. 26th, 2010

2. Outline MAPPFinder and the Gene Ontology Project How MAPPFinder works
MAPPFinder presents data in a variety of ways
Search and navigation in MAPPFinder

3. 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

4. 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

5. 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?

6. Outline MAPPFinder and the Gene Ontology Project How MAPPFinder works
MAPPFinder presents data in a variety of ways
Search and navigation in MAPPFinder

7. How MAPPFinder Works
Fig 1

8. 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

9. Outline MAPPFinder and the Gene Ontology Project How MAPPFinder works
MAPPFinder presents data in a variety of ways
Search and navigation in MAPPFinder

10. 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

11. Text representation of showing MAPPFinder results
Table 2

12. Graphical Representation of MAPPFinder Data (MAPPFinder Browser)
Fig 2

13. Graphical Representation cont.
Fig 3a

14. Graphical Representation cont.
Fig 3b+c

15. 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

16. Outline MAPPFinder and the Gene Ontology Project How MAPPFinder works
MAPPFinder presents data in a variety of ways
Search and navigation in MAPPFinder

17. 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

18. 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

19. 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

20. Acknowledgements
Margie and Andrew
Dr. Dionisio and Dr. Dahlquist