GitHub - XinmengLiao/Open_MoA: Open MoA is a potent tool for identifying the underlying drug mechanism of actions (MoAs), core biological pathways, and key targets.

bioinformaticsdrug-discoverynetwork-analysistranscriptomicsr-package

Abstraction: R tool predicting drug mechanism of action via network topology

Key points:

Inputs transcriptomic data plus start/end points of a biological reaction; outputs context-specific weighted subnetworks with confidence scores and the shortest-path core pathway
Integrates three interaction databases: DrugBank v5.1.9 (drug-targets), STRING v11.5 (protein-protein interactions with combined scores), and RegNetwork (regulatory interactions)
Penalty scores on edges are derived from FDR values of perturbed genes; shortest path computed via igraph in R
HepG2 cell-line-specific subnetwork provided as a worked example using Human Protein Atlas and CCLE gene expression data
Published in Bioinformatics (2023): Liao et al., doi:10.1093/bioinformatics/btad666, PMID 37930015
Downstream analyses use DAVID (KEGG enrichment), Enrichr (OMIM), rWikipathways, and Cytoscape for visualization

Connections: Github · Drugbank · Drug Discovery · Network Analysis · Bioinformatics · Transcriptomics