Wednesday, January 05, 2005

GenMAPP 2.0 released

Got a mail in my inbox today informing me that GenMAPP, the popular pathway-mapping for microarray analysis, got released. I didn't try it yet and I hope that version 2.0 fix most shortcomings of the first version, which was an interface / file format nightmare. Here's the email :

"We are writing to inform you that GenMAPP 2.0 is now available to the public. GenMAPP (Gene Map Annotator and Pathway Profiler) is a computer program designed for viewing and analyzing gene expression data on maps representing biological pathways and other groupings of genes. GenMAPP 2.0 incorporates much of the feedback we received from hundreds of GenMAPP 1.0 users."

Read the full post for a list changes / features added.

Download GenMAPP 2.0 here:

New features in GenMAPP 2.0 include:

· GenMAPP 2.0 incorporates a flexible format to accept many different Gene ID systems in any number of Gene Databases for any number of species.

· We make available species-specific Gene Databases for Human, Drosophila, Mouse, Rat, Zebrafish, C. elegans and S. cerevisiae with relationships between the various Gene ID systems in the database. Genes on your MAPP may have MGI IDs, for example, but your Expression Datasets may be annotated with Unigene, and GenMAPP will make the connection.

· GenMAPP assists you in creating your own Gene Databases for any species, as well as customizing existing Gene Databases.

· GenMAPP 2.0 is fully integrated with the accessory programs MAPPFinder and MAPPBuilder.

· Entire sets of MAPPs, with information from your Expression Dataset, can be exported as interactive HTMLs, to enable convenient, interactive display of data on web sites (e.g.

· A user-friendly toolbar replaces the Drafting Board Menus in GenMAPP 2.0.

· With GenMAPP 2.0, you can zoom in and out on your MAPPs for optimum visualization.

· You can add notes to a Line Tool, to describe the meaning of the line, arrow, ligand, receptor, or inhibition symbol.

· The Backpage now has added information on how the gene colors for each Color Set in the data table. You also have the ability to add hyperlinks to a Remarks field in the Gene Finder, Expression Dataset, or Gene Database that will display on a gene’s Backpage.

· GenMAPP 2.0 accepts Expression Datasets with an unlimited number of columns.

New features in MAPPFinder 2.0 include:

· MAPPFinder 2.0 allows you to calculate results for multiple Criteria for a given Color Set simultaneously.

· You can export all highlighted MAPPs/GO terms in MAPP format concurrently.

· MAPPFinder 2.0 gives you the option of calculating the adjusted p-value for changes.

· Improved MAPPFinder output format that allows for easy identification of all genes associated with a GO term or MAPP.

Comment from an early beta tester of GenMAPP 2.0:

"GenMAPP is an incredibly useful program to put gene array findings into a biological context … the new version is hyperlinked to a variety of other databases… the new version of GenMAPP makes the use of the MAPPFinder program much easier, since it is incorporated directly into the menu."

Dr. Christine Konradi, Associate Professor of Psychiatry, Harvard University

Thank you,

GenMAPP Development Team
Gladstone Institute of Cardiovascular Disease/UCSF

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