Hi,

I have a large data set from transcriptome analysis that I'm trying to use Mapman to show the differences in metabolic activity. I have gene expression data specified on a per-gene basis (i.e., Glyma01g00300). The glycine data set uses only the affy numbers, and there's not a good way to convert between them that I know about. Is there a way to use this mapping database with the glycine gene names rather than affy numbers?

Hi Alec,

Unfortunately, the only mapping we provide for soy bean to-date is affy-probe set identifier-based.
Using the procedure outlined by TAIR, probe sets can be mapped to the target gene(s) they will
match in an RNA sample (ftp://anonymous@ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/README).
Due to a lack of requests, we have not yet provided a mapping based on the gene identifiers. If you provide a
link/file containing the gene IDs and the respective sequences we can do the affy ID to gene ID mapping and
provide a gene ID based mapping for soy bean.

cheers,
marc

Marc,

Ah, I see. Unfortunately, we're doing a whole-genome comparison, so I think I'll do the mapping myself.

However, I need the list of the affy tags involved in MapMan's soybean database to do the mapping cleanly. Is there any way that I can get this? I don't need the whole set of pathway information in a flat format; just the affy tags involved.

-Alec

Hi Alec,

you can obtain the text or excel table containing the soybean mapping
from the mapman store (http://mapman.gabipd.org/web/guest/mapmanstore).
The first column of this file contains all the affy IDs. Since this list is not unique
(meaning affy ID may appear several times) i extracted the unique list and
attached it to the post.

best greetings,
Marc