Question: KEGG cancer pathways
0
gravatar for Am.A
5.6 years ago by
Am.A20
SA
Am.A20 wrote:

How to retrieve genes in cancer pathways from KEGG databases?

is there any tutorial helps me for understanding pathways? 

gene • 2.4k views
ADD COMMENTlink modified 5.6 years ago by sedaghat.nafiseh20 • written 5.6 years ago by Am.A20

Do you know the cancer pathway ids?

ADD REPLYlink written 5.6 years ago by Haluk170

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

ADD REPLYlink written 5.6 years ago by Prakki Rama2.4k

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

ADD REPLYlink written 4.3 years ago by hlin1170

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.

ADD REPLYlink written 5.6 years ago by Siva1.7k

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?

 

ADD REPLYlink written 5.6 years ago by Am.A20

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.

ADD REPLYlink written 5.6 years ago by Siva1.7k
0
gravatar for sedaghat.nafiseh
5.6 years ago by
United States
sedaghat.nafiseh20 wrote:

Hello Amy,

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

Nafiseh

ADD COMMENTlink written 5.6 years ago by sedaghat.nafiseh20
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