The current GenMAPP has been written in Visual Basic and is therefore limited to computers running the Windows operating system. For other operating systems, we recommend the PathVisio program, which has the same functionality as GenMAPP in terms of pathway viewing and editing, data representation and analysis. For pathway and GO over-representation analysis, we also recommend the GO-Elite program.
The next version of GenMAPP will have a platform-independent implementation. For information on current open-source development of GenMAPP and how to participate, click here.

If you are upgrading from a previous version of GenMAPP (version 1.0 or 1.0 beta), you are not required to uninstall your previous version of GenMAPP, however, GenMAPP file associations (MAPP files and GEX files) will be associated with the latest installed version. Any custom MAPPs can be converted to GenMAPP 2 format using the Converter tool. Expression Datasets (Gex files) can also be converted, but we highly recommend that data be re-imported from scratch instead. Please see GenMAPP Help for more information.

GenMAPP distributed MAPP files are governed by the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported license. For details on this license, visit Creative Commons.

On August 12, 2004, we revised the GenMAPP acronym from "Gene MicroArray Pathway Profiler" to "Gene Map Annotator and Pathway Profiler". This change has been made in light of the fact that GenMAPP is now used for a wide variety of data types in addition to microarray data (e.g. gene trapping, SNPs, functional genomic experiments). The new GenMAPP definition reflects the use of GenMAPP to annotate pathways for use with any type of genomic data. If preparing a manuscript referencing the definition of GenMAPP, please use the new definition and additionally reference http://www.genmapp.org.

The next version of the GenMAPP software, GenMAPP-CS, is currently being developed and a beta version is expected in 2011. GenMAPP-CS is being developed as an open-source, Java-based program integrated into Cytoscape, and will include greatly expanded visualization and analysis options. Detailed development plans are available on our wiki. We are also developing WikiPathways, a community wiki for pathway curation and editing.
While GenMAPP 2.0 is no longer actively developed in its current form, it is still fully supported.

Data for use in GenMAPP must have a primary ID supported by GenMAPP. For a list of supported ID systems, see GenMAPP Help. If your data is not annotated with any of the supported ID systems, you have a variety of options. As a preferred method, please convert your primary GenBank accession numbers, clonal IDs, or microarray specific IDs to an ID supported by the Gene Database of interest. Several conversion tools are publicly available, see a list of common ones here.
In addition, the GenMAPP 2 Gene Databases allow for addition of any user-defined ID system. For details on how to customize a database or create a database for a non-supported species, see our Custom Database Manual or GenMAPP Help.
If none of these options apply, please contact us at: genmapp@gladstone.ucsf.edu

Some European users have experienced difficulties using MAPPFinder due to the use of a comma "," as the decimal separator on European-configured operating systems. MAPPFinder relies on SQL statements which use commas to separate variables in the query statement, so the comma decimal separator creates problems. To fix this problem, in Windows go to Start->Settings->Control Panel->Regional Options. In regional options, there is a tab menu called "Numbers." In this menu you'll see a text box titled "Decimal Symbol. Make sure that your decimal symbol is a period "." not a comma or any other character.

GenMAPP is a vector-based graphics program and thus has the intrinsic capacity to export MAPP images in a vector format. Although there currently isn't a supported vector export function within GenMAPP, users with an full version of Adobe Acrobat 4.0 or higher, have the ability to print as a PDF file from any vector based program. For more information on this product, go to: http://www.adobe.com/products/acrobat/main.html. The resulting exported PDF file can now be modified in a variety of vector based drawing programs (i.e. importing as PDF in Adobe Illustrator or changing the file extension to .eps for import into other drawing programs).

The pathways in the "KEGG_Converted" archive were converted using the KGML supplied by KEGG (V2). Sometimes the KGML does not exactly match the graphical representation given by KEGG and this is reflected in the GenMAPP MAPPs.

The EC numbers provided by KEGG are enzyme IDs, and have different genes associated with them for each respective species. On the KEGG website you can see these genes when you click on a colored EC box. In GenMAPP, we chose to display the gene names instead of the EC numbers, when available. In the case where an EC number has many genes associated with it, we attempt to show all associated genes.

These MAPPs are provided as a starting point for further curation. In some cases, you will be able to use a KEGG converted MAPP with some editing, instead of starting from scratch.

Currently, GenMAPP doesn't allow you to choose the number of significant digits to be displayed on the MAPPs. It will simply display the numbers as they appear in your raw input file. To change the way numbers are displayed on the MAPPs, change the data before import to GenMAPP. If you are working in Excel, you can do this by selecting the field of data you want to alter, and then choosing Format – Cells. Under the Number tab, you can set the number of decimal points to your liking.

Not at this time. Please carefully review each map.