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