Question: KEGG pathway per genes relation
0
gravatar for bharata1803
3.7 years ago by
bharata1803430
Japan
bharata1803430 wrote:

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.

kegg • 1.2k views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 3.7 years ago by bharata1803430

Can you show some example input and desired output?

ADD REPLYlink written 3.7 years ago by Endre Bakken Stovner880
1

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.

ADD REPLYlink written 3.7 years ago by bharata1803430
0
gravatar for EagleEye
3.7 years ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

Gene Set Clustering based on Functional annotation (GeneSCF)

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

Orelse 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/

 

ADD COMMENTlink modified 3.3 years ago • written 3.7 years ago by EagleEye6.4k
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