Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles.

ABSTRACT: Individual may response to drug treatment differently due to their genetic variants located in enhancers. These variants can alter transcription factor's (TF) binding strength, affect enhancer's chromatin activity or interaction, and eventually change expression level of downstream gene. Here, we propose a computational framework, PERD, to Predict the Enhancers Responsive to Drug. A machine learning model was trained to predict the genome-wide chromatin accessibility from transcriptome data using the paired expression and chromatin accessibility data collected from ENCODE and ROADMAP. Then the model was applied to the perturbed gene expression data from Connectivity Map (CMAP) and Cancer Drug-induced gene expression Signature DataBase (CDS-DB) and identify drug responsive enhancers with si

SUBMITTER: Wang Y 

PROVIDER: S-EPMC11139989 | biostudies-literature | 2024 May

REPOSITORIES: biostudies-literature