CRUP: a comprehensive framework to predict condition-specific regulatory units.

ABSTRACT: We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell types and species, solely based on histone modification ChIP-seq data. Enhancers are subsequently assigned to different conditions and correlated with gene expression to derive regulatory units. We thoroughly test and then apply CRUP to a rheumatoid arthritis model, identifying enhancer-gene pairs comprising known disease genes as well as new candidate genes.

SUBMITTER: Ramisch A 

PROVIDER: S-EPMC6839171 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature