CRM-TI: an enhanced pipeline for computationally assigning the target genes of cis-regulatory modules by considering comprehensive long-range regulation mechanisms.

Abstract

Metazoan transcriptional regulation is mediated by modular DNA segments termed To address these gaps, we developed CRM-Target Identifier (CRM-TI), a deep learning pipeline that integrates mechanisms of chromatin interactions and CRM ncRNA-transcription-related gene regulation. Using a chromosome-wise partitioning scheme, CRM-TI achieved an unbiased test auROC of 90.0%, outperforming existing methods by at least 10%. Additionally, considering both CRM-gene interactions and ncRNA-transcription-re