Integrative prediction of gene expression with chromatin accessibility and conformation data.

ABSTRACT:

Background

Enhancers play a fundamental role in orchestrating cell state and development. Although several methods have been developed to identify enhancers, linking them to their target genes is still an open problem. Several theories have been proposed on the functional mechanisms of enhancers, which triggered the development of various methods to infer promoter-enhancer interactions (PEIs). The advancement of high-throughput techniques describing the three-dimensional organization of the chromatin, paved the way to pinpoint long-range PEIs. Here we investigated whether including PEIs in computational models for the prediction of gene expression improves performance and interpretability.

Results

We have extended our [Formula: see text] framework to include DNA contacts ded

SUBMITTER: Schmidt F 

PROVIDER: S-EPMC7003490 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature