Given a set genes, I'd like to map the known regulatory relationships between them. My current way of doing this (when I had a small set of genes) was just to scour the literature and manually creating a Cytoscape network, but this becomes difficult as the list gets longer.
Intuitively, this information exists (or at least some of it) in KEGG pathways. It's just a matter of pulling all these interactions into a singular, custom network.
I've been looking into KEGGREST for this purpose and found this post that seems related: How To Get Kegg Pathway Interaction Network In A Tabular Format Easy To Manipulate? but at the time it was posted (over 6 years ago) there didn't seem to be a way to get the information I need. Someone involved with development said "there is heirarchical information hidden in the KO:pathway mapping that is usually discounted, and there isn't an existing resource to robustly process" and that KEGG Orthology was still in the process of being reintegrated in a way that satisfied liscensing issues. It's been a number of years now since this post and I'm not sure what the status of this is now.
There might be a way to do this without KEGG though. I just want something easier than manually looking back and forth between literature.
