GenMAPP and MAPPFinder 2.0: Tools for Viewing and Analyzing Genomic and Proteomic Data Using Gene Ontology and Biological Pathways

Kam D. Dahlquist1, Scott W. Doniger2, Nathan Salomonis, Karen Vranizan, Steven C. Lawlor, and Bruce R. Conklin
1kadahlquist@vassar.edu, Department of Biology, Vassar College; 2sdoniger@gladstone.ucsf.edu, Gladstone Institute of Cardiovascular Disease

GenMAPP (Gene MicroArray Pathway Profiler) is a free, stand-alone program designed for viewing and analyzing gene expression and proteomic data on MAPPs representing biological pathways or any other functional grouping of genes. A MAPP is produced with the graphics tools in GenMAPP and depicts the biological relationship between genes or gene products. MAPP files are small database files that store identifiers for genes and vector coordinates for all objects on the MAPP. GenMAPP automatically color-codes the genes on the MAPP according to data and criteria supplied by the user. By integrating the Gene Ontology (GO) hierarchy and annotations into GenMAPP, we have developed a tool called MAPPFinder that creates a global gene expression profile across all areas of biology. MAPPFinder relates the gene expression dataset and the userís criterion for a meaningful gene expression change to the GO hierarchy and calculates a Z score and p value for each GO biological process, cellular component, and molecular function term. The p value indicates whether there is a significant over- or under-representation of genes meeting the userís criterion for that term. Results are displayed in a GO browser. Selecting a GO term in the browser opens the corresponding GenMAPP MAPP file containing a list, color coded by the expression data, of all of the genes associated with that term. These MAPPs are a starting point for curators to organize the genes into pathways and feed the information back into a public pathway database. GenMAPP and MAPPFinder 2.0 have new features that improve the functionality of both programs. The underlying gene database now includes gene identifiers from thirteen public gene and protein databases and contains data for nine species. Users can easily add gene tables for systems and species not currently supported. Also, entire sets of MAPPs can be exported to HTML for display on web sites. GenMAPP and MAPPFinder are available at www.GenMAPP.org.