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

doi:10.1038/s41540-024-00388-8

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	Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles
	Wang, Yongcui; Wang, Yong
	2024
发表期刊	NPJ SYSTEMS BIOLOGY AND APPLICATIONS
卷号	10 期号:1 页码:62
摘要	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 significantly altered chromatin accessibility. Furthermore, the drug responsive enhancers were related to the pharmacogenomics genome-wide association studies (PGx GWAS). Stepping on the traditional drug-associated gene signatures, PERD holds the promise to enhance the causality of drug perturbation by providing candidate regulatory element of those drug associated genes.
DOI	10.1038/s41540-024-00388-8
WOS记录号	WOS:001235618600001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75997
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Wang, Yongcui,Wang, Yong. Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles[J]. NPJ SYSTEMS BIOLOGY AND APPLICATIONS,2024,10(1):62.
APA	Wang, Yongcui,&Wang, Yong.(2024).Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles.NPJ SYSTEMS BIOLOGY AND APPLICATIONS,10(1),62.
MLA	Wang, Yongcui,et al."Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles".NPJ SYSTEMS BIOLOGY AND APPLICATIONS 10.1(2024):62.

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