Latent Variables Capture Pathway-Level Points of Departure in High-Throughput Toxicogenomic Data.

ABSTRACT: Estimation of points of departure (PoDs) from high-throughput transcriptomic data (HTTr) represents a key step in the development of next-generation risk assessment (NGRA). Current approaches mainly rely on single key gene targets, which are constrained by the information currently available in the knowledge base and make interpretation challenging as scientists need to interpret PoDs for thousands of genes or hundreds of pathways. In this work, we aimed to address these issues by developing a computational workflow to investigate the pathway concentration-response relationships in a way that is not fully constrained by known biology and also facilitates interpretation. We employed the Pathway-Level Information ExtractoR (PLIER) to identify latent variables (LVs) describing biological acti

SUBMITTER: Basili D 

PROVIDER: S-EPMC9019810 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature