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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
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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
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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
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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
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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