A generalizable framework to comprehensively predict epigenome, chromatin organization, and transcriptome.

ABSTRACT: Many deep learning approaches have been proposed to predict epigenetic profiles, chromatin organization, and transcription activity. While these approaches achieve satisfactory performance in predicting one modality from another, the learned representations are not generalizable across predictive tasks or across cell types. In this paper, we propose a deep learning approach named EPCOT which employs a pre-training and fine-tuning framework, and is able to accurately and comprehensively predict multiple modalities including epigenome, chromatin organization, transcriptome, and enhancer activity for new cell types, by only requiring cell-type specific chromatin accessibility profiles. Many of these predicted modalities, such as Micro-C and ChIA-PET, are quite expensive to get in practice, an

SUBMITTER: Zhang Z 

PROVIDER: S-EPMC10325920 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature