Identifying compound-protein interactions with knowledge graph embedding of perturbation transcriptomics.

ABSTRACT: The emergence of perturbation transcriptomics provides a new perspective for drug discovery, but existing analysis methods suffer from inadequate performance and limited applicability. In this work, we present PertKGE, a method designed to deconvolute compound-protein interactions from perturbation transcriptomics with knowledge graph embedding. By considering multi-level regulatory events within biological systems that share the same semantic context, PertKGE significantly improves deconvoluting accuracy in two critical "cold-start" settings: inferring targets for new compounds and conducting virtual screening for new targets. We further demonstrate the pivotal role of incorporating multi-level regulatory events in alleviating representational biases. Notably, it enables the identificatio

SUBMITTER: Ni S 

PROVIDER: S-EPMC11602590 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature