Re: Affy Data mapping in GM-CS

[Alex Pico]

Hi Jamie,

It sounds like you are doing everything correctly. The mapping from Affy IDs to WikiPathways should not be a problem. I can see that the pathway is using Ensembl IDs for the most part:

http://www.wikipathways.org/index.php/Pathway:WP2074

And this should be a fairly straightforward mapping for GenMAPP-CS.  My only concern here is with the database version you are using. That's a pre-release version that is awaiting a software update. It looks like these leaked through to the main release sometime today. Our mistake!  Please download the latest supported version:

http://bridgedb.org/data/gene_database/Mm_Derby_20110603.zip

Unzip it to your ~/GenMAPP-CS-Data/databases/ folder, then delete the 20120602 version. Then when you launch GenMAPP-CS it should find this one. It might show a red arrow indicating a newer version online, but do not update.

With this new version of the database, you will have to try remapping the dataset to the pathway. Might be easier to reimport the pathway and dataset?  If you still have trouble, send us the Affy file for further testing. Thanks!

 - Alex

On Wednesday, September 26, 2012 2:01:13 PM UTC-7, Jamie wrote:

Hi, I’m a new user of Genmapp-CS. I’m trying to map Affy expression data (mouse 430 2) for a particular wikipathway (Neural Crest Differentiation) and am following the online directions. The pathway loads ok and my expression data appears to load ok. But my data maps poorly onto the pathway: only 2 genes/nodes are mapped, but I know that my data has many more genes that should be mapped, based on reviewing gene symbols and probe set IDs listed at the wikipathway website. Maybe important to say that I'm judging the number mapped by creating criteria sets that should reveal all the mapped genes (upregulated = red; downregulated = green). I've tried swapping my expression data identifiers from Affy IDs to Entrez IDs, Ensembl IDs, or gene symbols, but I only ever get the 2 genes mapped. So I assume that the database (locally loaded Mm_Derby_20120602.bridge) does not have the same identifiers shown at the wikipathway website. But this is a guess. Or does this sound like another problem? Grateful for any helpful suggestions.

[Jamie]

Hi Alex, I attempted to send a thank you a couple days ago but seems that maybe it didn't post. But your suggestions fixed me up and the mapping was working fine. Any thoughts on how you could check in the future to make sure that you're using the most current version of the database? Thanks again.

Jamie

[Alexander Pico]

Glad to hear it! The color of the update/download arrow next to the species database selector in the GenMAPP-CS panel serves as an indicator of your database status. When it is green and active, it means there is a more up-to-date version available. Click it and the update is taken care of. 

However, this next series of databases planned for release will also require an updated version of GenMAPP-CS, so I'd just stick with the working version for now. 

 - Alex

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