If you are using a version of GenMAPP 1.0 Beta that was released prior to September 13, 2001, you must follow these instructions to avoid losing gene identifications you have added to the Other category of your GenMAPP Database. (You can find the release number by clicking on the Help menu and choosing About GenMAPP. The release number is shown in the lower left-hand corner of the window. If it says 20010913, you do not need to worry about losing gene identifications. If it says 20010328, you must follow these instructions.) Before uninstalling your previous version of GenMAPP, go to C:\Program Files\GenMAPP and make a copy of the GenMAPP.gdb file (your GenMAPP Database), and store it somewhere else on your hard drive. Then uninstall your previous version of GenMAPP. After uninstalling, place the GenMAPP.gdb file back in the C:\Program Files\GenMAPP folder. Now install the updated version of GenMAPP following the directions below.

• Download the compressed GenMAPPSetup.exe installer from www.GenMAPP.org.
• Double-left-click on the icon to extract the files and install GenMAPP.
• If instructed, restart your computer.

To perform certain functions, such as updating, GenMAPP needs to know where you are planning to store your MAPPs and Expression Datasets. The first time you launch GenMAPP, an additional GenMAPP Data Paths window will ask you to choose a root folder where you want to store your MAPP files and Expression Datasets. GenMAPP will place the sample MAPP files and Expression Dataset packaged with the program in subfolders of that folder. For more MAPPs, download the complete MAPP Archive from www.GenMAPP.org. The new version of GenMAPP is packaged with an updated GenMAPP_New Database containing new and updated gene identifications from SwissProt and GenBank. When GenMAPP detects the new database, it will prompt you to update your database, MAPP files, and Expression Datasets with the new gene identifications. GenMAPP will only update MAPP files and Expression Datasets that are stored in the root folder you chose in the GenMAPP Data Paths window or subfolders of that. If you want to update your files please move them into these folders before proceeding.

Some European users have experienced difficulties using MAPPFinder due to their use of a comma "," as the decimal separator. 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.

Although MAPPFinder version 1.0 does not currently use the rat GeneOntology databases for analysis, a user can implement a MAPPFinder analysis on an existing rat GenMAPP gene expression dataset using the downloadable GeneOntology archive files (see MAPPArchive Download Area). After downloading the rat GeneOntology MAPPs along with the contributed MAPPArchives, install both of these sets of file folders into the MAPP directory in the GenMAPP folder of your hard drive (C:/GenMAPP/MAPPs is the default location). When the GeneOntology and Contributed MAPP archives are in the same folder (only rat MAPPs), begin using MAPPFinder, choose "Load Local MAPPs" and select the rat MAPP file directory you created, selecting mouse as the species (species is irrelevant for this excercise). Once completed, choose "Calculate New Results", select your rat dataset and choosen criterion criterion, and select only local MAPPs for your analysis. Upon running MAPPFinder, you will acheive similiar results to that of other MAPPFinder compatible species with your local archives. See MAPPFinder Help for more information on how to use MAPPFinder.

GenMAPP is a vector-based graphics program and thus has the intrinsic capacity to export MAPP images in a vector format. Although there currently, there is no supported vector export function within GenMAPP, users with an installed, 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 GenMAPP Database is currently built primarily using the SwissPROT database and GenBank accession numbers related within SwissPROT. As a result the GenBank accession numbers in the GenMAPP database tend to be full length cDNAs. Many current chip types link clone IDs and probes to Expressed Sequence Tags (ESTs), or cluster ID numbers (i.e. Unigene IDs) which have not been linked to SwissPROT and are therefore not in our database.

We are designing a new version of the GenMAPP database that uses Unigene to incorporate hundreds of thousands of ESTs. In the future nearly all EST identifiers will be in the GenMAPP database. This database and some improvements to GenMAPP will be released as GenMAPP 2.0 sometime in late 2002 to early 2003. In the mean time, there are a couple of temporary solutions for relating ESTs into GenMAPP. First, you can import them as "other" genes and then you will be able to use these gene IDs when constructing new MAPP files. However, none of your "other" genes will color genes on pre-existing MAPPs from GenMAPP. The second solution is to map your ESTs to full length cDNAs in the GenMAPP database. This can be most easily done using the Unigene database which can be downloaded from the NCBI. To obtain a full list of the GenBanks IDs in the GenMAPP database, you can open the database (GenMAPP.gdb) in Microsoft Access. The GenBank table contains all of the GenBanks that are accepted by GenMAPP. For additional help with mapping ESTs to full length sequences in GenMAPP please contact genmapp@gladstone.ucsf.edu.