Info

[Nathan Salomonis]

Greetings Alessio,

Although the GenMAPP program is currently not supplied with a Dicty database
we have written a set of tutorials describing how users can create such
database and pathway maps to analyze their gene expression data within the
context of biological pathways and the entire Gene Ontology hierarchy. To
use these tools you must first install the program GenMAPP 2.0
(http://www.genmapp.org), download necessary gene and GO content files and
proceed through the below linked instructions.  We also provide user support
through our support email at: genmapp at gladstone.ucsf.edu.
 
Tutorials for Creating a New Species Specific GenMAPP Database:
http://www.genmapp.org/tutorials/Implementing-GenMAPP-2-for-non-supported-sp
ecies.pdf

Tutorial for Converting MAPPs between Species:
http://www.genmapp.org/tutorials/Converting-MAPPs-between-species.pdf

Alternatively, see:
http://www.genmapp.org/contribute.asp
http://www.genmapp.org/tutorials.html

Please note: GenMAPP 2.0 is a Windows compatible stand-alone program

Best Regards,
Nathan Salomonis
GenMAPP Development Group
http://www.genmapp.org


-----Original Message-----
From: owner-gofriends at genome.stanford.edu
[mailto:owner-gofriends at genome.stanford.edu] On Behalf Of Alessio Sillo
Sent: Friday, July 08, 2005 5:51 AM
To: gofriends at genome.stanford.edu
Subject: Info


Dear Go friends,

I write You because I have performed a microarray experiment using
Dictyostelium discoideum as experimental model.
After having calculated the statistics to select only significant
differentially expressed genes I would like to use GO annotations to
arrange my list of genes into groups.
I would like to do with Dicty genes what EASE
(www.geneontology.org/GO.tools.microarray.shtml#ease) does with human
genes, that is summarizing the predominant biological "theme" of a given
gene list. Given a list of genes resulting from a microarray or other
genome-scale experiment, EASE can rapidly calculate over-representation
statistics for every possible Gene Ontology term with respect to all genes
represented in the data set.

However, I have appreciated that the AmiGO gene ontology classifies Dicty
genes as well by biological process, molecular function and cellular
component.
How can I make a query in AmiGO with my list of differentially expressed
genes? Is there a query webpage where I can put my list of genes and I can
get them arranged in functional groups?

I look forward to hearing from You.

I will accept any suggestion with pleasure and gratitude.

Thanks a lot,


Alessio Sillo
Cell Biology Laboratory
Dept. Clinical and Biological Sciences
University of Torino
Italy

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--
This message is from the GOFriends moderated mailing list.  A list of public
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