Question: How to map a drug target to corresponding KEGG pathway?
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gravatar for ayanava18
2.9 years ago by
ayanava1820
ayanava1820 wrote:

Can anybody please let me know the step by step procedure of how to map a drug target to corresponding KEGG pathway?

I wish to do something similar as mentioned in these papers :

'Information on the protein targets, transporters, and enzymes of a given drug was directly obtained from DrugBank. Each drug target was then mapped to the corresponding KEGG pathway through its protein-coding gene symbol [J Am Med Inform Assoc 2012;19:e28ee35]

The current study utilized 730 small-molecule clinically-approved drugs and 830 target proteins with solved structures .The protein targets were associated with 176 human related pathways extracted from the KEGG database [PLoS ONE 5(8): e12063]

target kegg drug pathway • 1.8k views
ADD COMMENTlink modified 2.9 years ago by Jean-Karim Heriche18k • written 2.9 years ago by ayanava1820

If you have the HGNC symbol or protein ID you can find the KEGG mappings to your targets via UniProtKB or Reactome

ADD REPLYlink written 2.9 years ago by Denise - Open Targets4.9k
1
gravatar for Jean-Karim Heriche
2.9 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

It's as it says in your first quote: Find the gene symbol of your drug target then check which KEGG pathway has it. KEGG uses Entrez gene IDs so you may as well find the Entrez gene ID of your drug target then look up which KEGG pathway contains it. This is simply done by entering the gene symbol or gene ID in the KEGG pathway search box.

ADD COMMENTlink written 2.9 years ago by Jean-Karim Heriche18k
0
gravatar for Antonio R. Franco
2.9 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

It depends upon what you call "drug" If it is a particular chemical compound not present regularly in a living cell, it will be out of the KEGG database

If present, you can find the corresponding KEGG code by using any of these services

  1. KEGG Compound. You give the name of the compound, and then it looks for the KEGG Code (manually)
  2. KAAS. KEGG Automatic nnotation Server.

There are some more servers available

To map to KEGG pathways you have several alternatives, like using the facilities present in the KEGG servers, or using programs such as MapMan, VANTED

There are more

ADD COMMENTlink written 2.9 years ago by Antonio R. Franco4.0k

You will see that by searching KEGG, you can find both, the code for compounds, and also for enzymes involved in pathways. This is important since the using of the right KEGG code avoid problems with spelling

ADD REPLYlink written 2.9 years ago by Antonio R. Franco4.0k
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