One of the great current challenges in biology is to interpret large genomic datasets in the context of known biological pathways. The GenMAPP (Gene MicroArray Pathway Profiler) computer program provides a freely available tool for organizing, storing, analyzing, and sharing pathway information with gene expression data. The prototype program, called GenMAPP 1.0, can be used to analyze gene expression data on MAPPs representing biological pathways or any other functional grouping of genes. MAPPs are database files produced with the graphics tools in GenMAPP that depict the biological relationship between genes or gene products. GenMAPP also allows for automated analysis of gene expression data in the context of hundreds of known gene groupings using an auxiliary program, MAPPFinder, and the Gene Ontology database. Although GenMAPP 1.0 is a powerful analysis tool with hundreds of users, it has limitations that warrant major revisions to the software.
Our specific aims are: ? ? (1) To develop and maintain GenMAPP 3.0 as a robust, free, open-source application that adds drawing and editing enhancements and integrates MAPPFinder functions. Documentation and online tutorials will focus on the four major user groups: DNA-microarray users, journal readers, pathway experts, and biology students. ? ? (2) To redesign the underlying gene database to integrate data from the major genomic databases, including SWlSS-PROT, GenBank, RefSeq, LocusLink, Unigene, Gene Ontology, model organism databases, and custom user-specific databases. The MasterUpdate and MasterExtract open source programs will be developed to automatically build and update the gene database on a regular basis. The modular design of the new gene database will allow rapid updates and integration of species-specific databases at www.GenMAPP.org. Users can easily add custom databases for any other organism through a graphical user interface within the GenMAPP program itself. ? ? (3) To expand the import/export capabilities of GenMAPP with XML data exchange modules and improved HTML features that will allow cross-platform viewing of MAPPs. By capturing pathway information in a digital format, GenMAPP will act as a catalyst for sharing pathway information and building public pathway databases. With the completion these aims, GenMAPP 3.0 will provide a program that is robust, simple to use, and available without charge to the entire biological community. ? ?
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