Question: Querying CTD database to find diseases associated with the given pathways.
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gravatar for omarrafiqued
8 weeks ago by
omarrafiqued50
omarrafiqued50 wrote:

I need all the diseases associated with the given pathways. The CTD database is to be queried to check if the over-represented pathways are known to be associated to the disease. The association between a disease and a pathway is inferred by the number of genes that the pathway shares with those associated to the disease.

I have two things:

  1. A downloaded association between pathway and disease from the CTD dataset at the following link:

    https://ctdbase.org/downloads/;jsessionid=428E5A2D36F9A54D509B536309FD0362#diseasepathways

  2. A list of over represented pathways. e.g Lysosome, Endocytosis and Phagosome with IDs hsa04142, hsa04144 and hsa04145 respectively.

Could someone tell me how to do it, in R or any other way.

ADD COMMENTlink written 8 weeks ago by omarrafiqued50

What have you tried so far, and where did it become difficult for you?

ADD REPLYlink written 6 weeks ago by Kevin Blighe340
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