GenMAPP (Gene Map Annotator and Pathway Profiler) is a computer program designed for viewing and analyzing genome-scale data on MAPPs representing biological pathways and any other grouping of genes.
GenMAPP facilitates the analysis, organization and sharing of data produced in genomic-scale experiments, such as DNA microarray experiments. Instead of overwhelming researchers with long lists of un-annotated data, GenMAPP allows one to visualize gene expression data in a biological context with the graphical and more intuitive format of MAPPs.
A MAPP is a GenMAPP-produced file that graphically shows the biological relationship between genes or gene products. MAPPs can be used to group genes and view data by any organizing principle. Examples of the types of MAPPs that can be represented in GenMAPP are metabolic pathways, signal transduction cascades, sub cellular locations, gene families, or lists of genes associated with Gene Ontology categories. Each MAPP contains gene objects, which represent biological genes or gene products. The MAPP also contains symbols that depict other objects, such as receptors, membranes and ribosomes, and the relationships among the objects. Each gene object on a MAPP is identified by a gene identifier from one of the GenMAPP accepted gene ID systems. That gene identifier is used by the GenMAPP program to link information from a GenMAPP Gene Database to the gene object for annotation shown on a Backpage. The gene identifier is also used to link that gene object to data in an Expression Dataset for coloring the gene object.
Coloring of gene objects is done dynamically, based on criteria for the data determined by the user. For example, the user can tell GenMAPP to color all genes up-regulated in an experiment red and down-regulated blue. Since genes are colored and viewed dynamically, the user can easily switch criteria. For example, the user may wish to see which genes change with different fold cut-offs. Criteria can also be set to view the changes in gene expression on a MAPP at different disease stages or time points during an experiment.
Your raw data file of gene expression data must contain the gene identifiers for each row of data in the first column. The Expression Dataset Manager converts your raw data file, row by row, into the GenMAPP Expression Dataset format. As it converts, it searches the Gene Database for a match to the gene identifier. Once an Expression Dataset has been imported and customized with Color Sets, it can be applied to gene objects on MAPPs, coloring gene rectangles and displaying Gene Values according to the criteria met in the Color Set.
MAPPs for a standard set of biological pathways, as well as lists of functionally related genes from public sources such as the Gene Ontology Project, may be downloaded from the growing collection of MAPPs available through the Downloader. In addition, custom MAPPs for hypothesis testing may be drawn with the graphics tools provided by the GenMAPP program. These custom MAPPs may be shared with colleagues or posted for download through the Downloader for public distribution. Since no one can be an expert on every gene or biological pathway represented in a microarray experiment, contact information for the author of each MAPP is provided right on the graphic. Thus, GenMAPP can promote the efficient exchange of data and ideas between researchers.
The GenMAPP Program provides basic information about each gene on a MAPP. By clicking on a gene, a researcher can access information about that gene culled from the public databases. Moreover, hyperlinks to the database entries for that gene are provided so the researcher can rapidly access the latest information. Gene databases for a number of organisms are currently available through the Downloader. Updates to these databases and additional new databases for other model organisms are posted on a regular basis.
Although GenMAPP was designed specifically to visualize microarray data, GenMAPP can be used to view data from any large gene or protein dataset such as those generated from protein chips or other large-scale assays for protein function or interactions. In terms of gene expression data, GenMAPP accepts from both custom arrays and commercial microarrays such as Affymetrix GeneChips.
To provide these functions, the GenMAPP Program consists of a number of elements:
Although this help file contains detailed information, you may wish to view the Interactive Tutorial first. GenMAPP utilizes some features unique to the Windows operating system to navigate various functions of the program. Users unfamiliar with Windows should view the tips shown here.
Additional support for the GenMAPP program can be found by following this link to www.GenMAPP.org or by sending e-mail to genmapp@gladstone.ucsf.edu. If you use GenMAPP to analyze data for a publication, please cite this reference: Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR (2002) GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nature Genetics 31:19–20.
GenMAPP 2 has many new features and improvements. They are:
1. You can now use any number of species-specific Gene Databases, making the program much more flexible. This has allowed the use of additional gene ID systems and species with GenMAPP. Furthermore, users can customize and create new Gene Databases. Click here for details.
2. The accessory programs MAPPFinder and MAPPBuilder have been more fully integrated with the GenMAPP program. MAPPFinder 2 also has new features. Click here for details.
3. Entire sets of MAPPs can be exported at once to HTML for data exchange and display on web sites. See the section on MAPP Sets for details.
4. A Converter tool has been incorporated, to enable the automatic conversion of MAPPs and Expression Datasets between versions of GenMAPP. The Converter also makes it possible to switch gene IDs on MAPPs between gene ID systems.
5. The Drafting Board Menus have been reorganized to be more user-friendly. The Drafting Tools have been moved from a separate window to a Toolbar. The Change Color Sets function can now be accessed from the Toolbar.
6. A zoom feature has been implemented and can be accessed from the View menu or Toolbar.
7. Right-clicking on a Line Tool opens a window in which you can add a note that annotates the meaning of the line, arrow, ligand, receptor, or inhibition symbol.
8. A new Options menu allows you to control what is displayed in the Legend and at what size. It also allows you to control whether the MAPP Information Area displays on the MAPP and gives you options for how the MAPP is colored and if a MAPP opens already colored by an Expression Dataset.
9. The Backpage has been redesigned to show how the gene colors for each Color Set in the data table. The user also has the option of adding hyperlinks to a Remarks field in the Gene Finder, Expression Dataset, or Gene Database that will display on a gene’s Backpage.
10. GenMAPP now supports Expression Datasets with an unlimited number of columns.
11. When there are duplicate rows of data in an Expression Dataset that refer to the same gene, GenMAPP now colors the center of the gene object based on the mode, the most frequent criterion met, and colors the rim with the second-most frequent. Click here for details.
12. GenMAPPs Updater feature searches for any updates to the GenMAPP program online. If a newer version is found, the Updater will install it.
1. GenMAPP now allows for simultaneous display of data from multiple Color Sets on MAPPs. Gene boxes are partitioned into colored stripes that each represent a Color Set selected. This feature was designed to allow for efficient display of time-course data, but can be applied to many other situations.
2. MAPP Sets export of multiple Color Sets now include a summary view of all selected Color Sets. Similarly to viewing multiple Color Sets on a MAPP, gene boxes are partitioned into colored stripes that each represent a Color Set selected. Click here for details.
3. GenMAPP now allows a value from any Color Set to be displayed on the MAPP. The gene value displayed do not have to agree with the Color Set displayed. It is also possible to have no gene value displayed. Click here for details.
4. A set of polygon objects are now available in the Object Toolbox.
5. The order of Gene ID systems displayed in the Gene Finder and on the Backpage has been changed.