CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction.

ABSTRACT:

Motivation

Identifying target promoters of active enhancers is a crucial step for realizing gene regulation and deciphering phenotypes and diseases. Up to now, several computational methods were developed to predict enhancer gene interactions, but they require either many epigenomic and transcriptomic experimental assays to generate cell-type (CT)-specific predictions or a single experiment applied to a large cohort of CTs to extract correlations between activities of regulatory elements. Thus, inferring CT-specific enhancer gene interactions in unstudied or poorly annotated CTs becomes a laborious and costly task.

Results

Here, we aim to infer CT-specific enhancer target interactions, using minimal experimental input. We introduce Cell-specific ENhancer Target pREdiction (C

SUBMITTER: Rapakoulia T 

PROVIDER: S-EPMC10666202 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature