KEGG pathway per genes relation

Question

[bharata1803]

Hello all,

After I search and study about KEGG pathway, I realized the node in KEGG pathway is group of genes. My question is, is there any tools that can decompose it per gene? Currently I'm in the middle of writing script to decompose it into per gene relationship. I just wondering if there is already tools to do that and I don't need to write by myself. Thank you.

[Endre Bakken Stovner]

Can you show some example input and desired output?

[bharata1803]

My output is basically just expanding each node in kegg pathway, which is usually in form of hsa:xxxxx gene code, to their own gene symbol. From the kegg genes database, each hsa:xxxxxx gene code consist of several genes. I just want to know per gene symbol for each node. I've finished writing the script so I think there is no problem anymore.

Answer 1

[EagleEye]

Gene Set Clustering based on Functional annotation (GeneSCF)

If you are looking for human genes. This could be the solution.

Or else if it is different organism, GeneSCF is in publication process which includes all organisms from KEGG. And also there are many features included.

Update GeneSCF v1.1: Support for more organisms and for information please follow http://genescf.kandurilab.org/