Regarding Pathway gene association file for input gene list

[francina]

Hello,

I have used GenMAPP and MAPFinder for over-representation analysis using Gene ontology database.

I have to provide a supplementary table listing differentially expressed genes and the pathways, MAPP or GO term they are associated with.
Using GenMAPP or MApfinder is there a way to get a pathway gene association file or Gene ontology gene association file for the input genes in one file along with other information such as Entrez id, Zscore and P-values?

I have used :

GenMAPP version 2.0 and MAPFinder version 2.0

Denominator file : Mouse Genome 430 2.0

Input file contains affymetrix Mouse 430 array probe ids.

Gene database used: Mm-Std_20070817

Thank you for your help.

Best Regards,

Maggi

[Kristina Hanspers]

Hi Maggi,

We are no longer actively developing GenMAPP 2.1. Instead, we are now developing and supporting several other tools (listed below) that replace GenMAPP. I would highly recommend that you switch to one or more of these other tools. For your particular analysis, you can use GO-Elite, which will produce gene association files.

Let us know if you have additional questions.

GenMAPP-CS (http://www.genmapp.org/beta/genmappcs/)
This is the next generation of GenMAPP that we are developing. It is currently available as a beta version. GenMAPP-CS is developed as a set of specialized features in the Cytoscape environment, so it has the advantage of access to powerful network analysis features of Cytoscape and Cytoscape plugins. We will have the next version of GenMAPP-CS out in the next couple of months.

PathVisio (www.pathvisio.org)
PathVisio is very similar in use and features to GenMAPP, in fact it was modeled after GenMAPP originally. The difference is that PathVisio is actively developed and also provides a plug-in structure for advanced features.

GO-Elite (http://www.genmapp.org/go_elite/)
For over-representation analysis, I would recommend this over MAPPFinder. It was developed by a member of our group and it is also the over-representation analysis that is available in GenMAPP-CS.

Regards,

Kristina