GenMAPP Google Group

Re: Upcoming GenMAPP server maintenance

genm...@gladstone.ucsf.edu (GenMAPP Support) — Fri, 20 Nov 2009 22:05:55 UT

The server maintenance is taking longer than expected, and I don't
have an estimate on when service will be restored.

If you are looking for GenMAPP files (databases, pathways etc), please
let me know which files you need and I can send them to you.

Kristina

Re: Upcoming GenMAPP server maintenance

genm...@gladstone.ucsf.edu (GenMAPP Support) — Fri, 20 Nov 2009 22:55:11 UT

The server maintenance is taking longer than expected. I have no
estimate right now for when service will be restored.

If you need GenMAPP files (databases, pathways etc) from the
Downloader, please let me know which files you are interested in and I
can send them to you.

Kristina

Re: Upcoming GenMAPP server maintenance

tom.b...@gmail.com (tbair@eng.uiowa.edu) — Fri, 20 Nov 2009 20:17:38 UT

Any word on when the server will be back up?

On Nov 16, 3:43 pm, GenMAPP Support <genm...@gladstone.ucsf.edu>
wrote:

Re: data set

genm...@gladstone.ucsf.edu (GenMAPP Support) — Thu, 19 Nov 2009 21:50:01 UT

Hello Sridhar,

There are several public repositories of array data. A quick search
for "breast cancer" at two of these sites reveals many datasets that
may be relevant to you.

[link]

The format of the data on these sites varies between experiments, some

data set

raghunathan.srid...@gmail.com (sridhar) — Thu, 19 Nov 2009 21:08:06 UT

hi could suggest me some website for microarray data for breast cancer
data that is compatible for GenMAPP , i tried standford but as for the
GenMAPP requirements i not able to get the data

Upcoming GenMAPP server maintenance

genm...@gladstone.ucsf.edu (GenMAPP Support) — Mon, 16 Nov 2009 21:43:41 UT

The GenMAPP servers will be temporarily off-line due to scheduled
maintenance, starting on Wednesday November 18th. The server downtime
is estimated to be about 24 hours.

GenMAPP Development Team

Re: using own dataset

genm...@gladstone.ucsf.edu (GenMAPP Support) — Wed, 11 Nov 2009 20:09:07 UT

Hello Sridhar,

GenMAPP lets you import your own data to visualize it on GenMAPP
pathways and perform over-representation analysis to find significant
pathways. You an also draw your own pathways in GenMAPP, or edit
existing pathways.

Let me know if you have additional questions.

Regards,

using own dataset

raghunathan.srid...@gmail.com (sridhar) — Wed, 11 Nov 2009 19:25:28 UT

is it possible to use my own dataset of breast cancer data to build
pathways using genmapp and mappfinder.

Re: Affymetrix Human Gene 1.0 ST

genm...@gladstone.ucsf.edu (Kristina Hanspers) — Tue, 13 Oct 2009 18:04:51 UT

Hello Barbro,

The correct database to use for this array is the Hs-Std_20070818
database.

Regards,

Kristina

Affymetrix Human Gene 1.0 ST

bar...@wiki-eye-pedia.com (Barbro) — Tue, 13 Oct 2009 08:50:34 UT

Hi,
I'm trying to use GenMAPP to analyze data from the Human Gene 1.0 St
array from Affymtrix. I can find the Right Gene Database to use for
it. Can you please help me?

New pathway archive Arabidopsis thaliana

genm...@gladstone.ucsf.edu (GenMAPP Support) — Thu, 03 Sep 2009 17:19:47 UT

Dear GenMAPP users,

A new Contributed pathway archive for Arabidopsis is available for
download through the Downloader feature in GenMAPP
(At_MAPP_Archive_Contributed_2 0090902). The pathways included in this
archive were collected from WikiPathways ([link]).

Kristina Hanspers

New GDBs for Arabidopsis, Plasmodium, Vibrio, update to E. coli K12

kdahlqu...@lmu.edu (Kam Dahlquist) — Thu, 03 Sep 2009 15:52:44 UT

Dear GenMAPP Users,
We are pleased to announce the release of three new GenMAPP Gene
Databases for Arabidopsis thaliana, Plasmodium falciparum, Vibrio cholerae,
and an update to the Escherichia coli K12 Gene Database.
These databases were created automatically by the Bioinformatics Group at
Loyola Marymount University using a suite of programs called XMLPipeDB,

Re: Problems with MappFinder

genm...@gladstone.ucsf.edu (Kristina Hanspers) — Mon, 24 Aug 2009 20:53:57 UT

Hello Jai,

The IDs that are not importing are most likely new and since the
database is from 2007 they are not included.

However, the local MAPPs mode in MAPPFinder should still work. Can you
please send send the data (.gex) to genm...@gladstone.ucsf.edu so I
can test it?

Regards,

Kristina

Problems with MappFinder

meht...@mail.dcu.ie (jai) — Mon, 24 Aug 2009 10:18:12 UT

Hi,

Right now I am working on Bovine mRNA-seq data. So Basically I have
Ensembl Id as identifier.

In Genmapp there are two Bovine Gene Databse. Bt-Std_20060526.gdb and
Bt-Std_20070517.gdb.

When I use the 526.gdb, roughly 7181 of the identifiers out of 24,000
are not recognized. However when I use 517.gdb, around 3000 Ensembl

Re: [GenMAPP] Re: Problem importing data into MAPPBuilder

genm...@gladstone.ucsf.edu (GenMAPP) — Mon, 17 Aug 2009 03:51:31 UT

Hi Michal,

I just ran the test file you sent. The file ran fine, but
didn't return a results file since the Other ID is not
informative. It did generate a proper exception file that
indicated no ID was found, as it should. As Kristina
mentioned, to properly use MAPPBuilder (as a precursor for