Whats the easiest way to make and quantify gene-drug-pathway interaction network?

Question

[dlmatera]

Nodes would be significantly altered genes and pathways, and the drugs of interest.

Im trying to narrow down a large list of drugs by quantifying how many differentially expressed pathways and genes they modulate. Im also curious what the best statistical test is to see if drugs "significantly" modulate signaling in a gene network?

This paper: https://www.medrxiv.org/content/10.1101/2020.05.06.20076687v1 does what I am trying to do (but for a different disease), but I'm having trouble figuring out how to quantify these interactions, beyond simply counting interactions and ranking drugs with more interactions as more favorable candidates

Any help is appreciated!