ID conversion

[IngeH]

Dear sir/madam,

I am trying to import gene expression dataset in genmapp. However,
strangely when I am using the Illumina Gene IDs, it sais:
Gene not found in Illumina or any related system, in every line of 946
genes, that I try to import.
If I use the NM Refseq codes, it is not able to map it either and sais
again: Gene not found in RefSeq or any related system.

To give an overview of the first 10 genes:

NM_018866.1
NM_172537.2
NM_011498.4
NM_009465.3
NM_008605.3
NM_030690.2
NM_207105.1
NM_175498.3
NM_009977.2
XM_001480292.1
NM_010382.2

OR:
ILMN_2760019
ILMN_1258953
ILMN_1249378
ILMN_2651715
ILMN_1250421
ILMN_2682928
ILMN_2913716
ILMN_2622190
ILMN_1244891
ILMN_1239843
ILMN_1239102

I cannot imagine that there is something wrong with the probe
information I give, and I have no idea, what I am doing wrong! Can you
please help me?

Many thanks!

Kind regards,
Inge

[Kristina Hanspers]

Hi Inge,

We are no longer developing the “classic” GenMAPP program, and the
databases that are available are out of date. It is quite possible
that the problems you are seeing are due to outdated databases. I
would recommend switching to one of our other tools instead.

We are currently developing GenMAPP-CS (http://www.genmapp.org/beta/
genmappcs/) which is still in beta, but is available for use. This
program will eventually replace the classic GenMAPP.

If you prefer to work with non-beta software, I would highly recommend
PathVisio (www.pathvisio.org), which performs the same functions as
the classic GenMAPP (and more). If you are already familiar with
GenMAPP, this program will be easy to use since it was modeled after
GenMAPP. The databases available for PathVisio are up-to-date and more
extensive.

While PathVisio can perform over-representation analysis on pathways,
I would also recommend using GO-Elite (http://www.genmapp.org/
go_elite/) for over-representation on pathways and GO terms. This
program was developed in our lab, and is also incorporated into
GenMAPP-CS. You can use either a standalone application or run it
through a web interface.

Hope this helps.

Regards,

Kristina

Kristina Hanspers, ME
GenMAPP-CS Development Team
Bioinformatics Research Associate/Conklin Lab
Gladstone Institute of Cardiovascular Disease/UCSF
http://www.genmapp.org/beta/genmappcs/