KEGG cancer pathways

Question

[Am.A]

How to retrieve genes in cancer pathways from KEGG databases?

Is there any tutorial helps me for understanding pathways?

[Haluk]

Do you know the cancer pathway ids?

[Prakki Rama]

http://rest.kegg.jp/link/genes/H00031 ??

[hlin117]

Unfortunately, this link doesn't seem to work anymore.

[Siva]

You can get the KEGG disease database entries ("H" followed by 5 digit number) for several types of human cancers here.

You then can use the KEGG web service link Prakki Rama provided (for entry H00031) to get all the genes associated with your KEGG disease entries of interest.

[Am.A]

H00031 is a cancer? And the results are

ds:H00031   hsa:1048
ds:H00031   hsa:2064
ds:H00031   hsa:3856

Could you help me in understand the output?

[Siva]

Yes, H00031 is a disease entry ID for Breast cancer. You can find the description of the entry ID and other columns related to KEGG disease database here.

Regarding your second question, the first column is the disease entry ID and the second column is the list of genes related to the disease and diagnostic markers for the disease.

Answer 1

[sedaghat.nafiseh]

Hello Amy,

I think the easiest way is using R-packages. You can retrieve the name of genes in pathways through 'graphite' package.

Nafiseh