Use Affymetrix Gene Expression Data in Cytoscape

Question

[daniel.rapoport]

Hi,

I have a number of gene expression data from mice, which were measured using Affymetrix Mouse Gene 1.1 chips. I would like to visualize the changes in expression as changes within the gene network with Cytoscape.

As far as I understand, the genes in Cytoscape are tagged/named according to the entrez-gene numbers/IDs, while the Affymetrix Expression Data are tagged/named according to their probe IDs. What would be the fastest way to map the Affymtrix-Data to the network (Entrez)-IDs?

I would be very grateful if someone could help me with this issue! Thank you very much,
Daniel

Answer 1

[pixie@bioinfo]

If you want to name your nodes in the network with gene IDs, you can download the latest gene annotation files from the Affymetrix website under Support -> Technical Documentation -> Annotation files. Choose your platform and the latest annotation file. Then either you can use a software like dChip or write a small script to just map the probe IDs to any of the annotations (gene ids, entrez ids, gene symbol) given in the file. The other option is to use any online tool like David, BioMart to do this.

[daniel.rapoport]

Thank you very much; that was helpful. I managed to assemble a lookup-table using David. I.e. a table with two columns:

Affy-ID (from)  Entrez-ID (to)
10165372       57282
....

Now, what would be the fastest way to proceed? You mentioned a "small script"; which scripting language / environment would you consider appropriate. I was thinking of merging all data into Igor Pro and rearrange the data using Igors Scripting language. Seems a bit awkward, though. Do you know of a smoother way to achieve the import into cytoscape?