DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks.

ABSTRACT: Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can capture genome-wide chromatin interactions mediated by a specific DNA-associated protein. The ChIA-PET experiments have been applied to explore the key roles of different protein factors in chromatin folding and transcription regulation. However, compared with widely available Hi-C and ChIP-seq data, there are not many ChIA-PET datasets available in the literature. A computational method for accurately predicting ChIA-PET interactions from Hi-C and ChIP-seq data is needed that can save the efforts of performing wet-lab experiments. Here we present DeepChIA-PET, a supervised deep learning approach that can accurately predict ChIA-PET interactions by learning the latent relationships between ChIA-PET and two widely us

SUBMITTER: Liu T 

PROVIDER: S-EPMC10368233 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature