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KEGG cancer pathways

How to retrieve genes in cancer pathways from KEGG databases?

Is there any tutorial helps me for understanding pathways?

gene
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updated by Ram Ram • written by Am.A • Am.A

Do you know the cancer pathway ids?

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written by Haluk Haluk

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

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written by hlin117 • hlin117

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.

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written by Siva Siva

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?

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updated by Ram Ram • written by Am.A • Am.A

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.

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written by Siva Siva

1 answer

Hello Amy,

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

Nafiseh

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written by sedaghat.nafiseh • sedaghat.nafiseh

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