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MAPPFinder, a new tool for microarray data analysis using GO

Scott Doniger sdoniger at
Mon Aug 26 09:36:46 PDT 2002

Dear GO friends,

I would like to announce the release of MAPPFinder, a new application for 
microarray data analysis using the annotations of the GO. MAPPFinder 
carries out an automated analysis of the entire GO, identifying those GO 
terms that are showing correlated gene expression changes in a microarray 
experiment. Using a user-defined criterion for a "significant" gene 
expression change, the percentage of genes meeting this criterion and a 
statistical score are calculated for each GO term. MAPPFinder uses the DAG 
structure to count the nested number of genes in a term and any child terms 
below it in the hierarchy. Using the nested numbers, rather than the number 
of genes associated with the individual nodes of the GO provides a more 
accurate measurement of the number of genes involved in a particular 
process, component, or function. The resulting gene expression profile is 
displayed as both a ranked list of GO terms and a GO browser painted with 
the MAPPFinder results, allowing the user to quickly identify those GO 
terms whose genes are showing interesting changes in their dataset. Once 
the interesting GO terms have been identified, selecting a GO term in the 
MAPPFinder browser builds the corresponding GenMAPP MAPP file. This MAPP 
file contains all of the genes associated with the selected term and all of 
its children. The MAPP is color-coded with the same criterion used in 
MAPPFinder, allowing the user to move from a global gene expression profile 
across the entire GO to the specific genes involved.

MAPPFinder and GenMAPP are available for download free of charge to the 
entire scientific community from The program release is a 
beta version, but is has been extensively tested. An comprehensive help 
file can be found at A 
manuscript describing this work in more detail is in preparation.

Please direct any questions/comments to GenMAPP at

Thank you,
Scott Doniger

Scott Doniger
GenMAPP Development Team
Bruce Conklin Lab
Gladstone Institute of Cardiovascular Disease/UCSF
Tel: (415) 695-3736
Fax: (415) 285-5632
Email: sdoniger at

Mailing Address
Gladstone Institutes
P.O. Box 419100
San Francisco, CA 94141-9100

Shipping Address
Gladstone Institutes
365 Vermont Street
San Francisco, CA 94103
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