SC-MO-GRN-DB: A comprehensive repository for single-cell multiomic gene regulatory networks

Gene regulatory networks (GRNs) are essential models for understanding gene expression, cell differentiation, and cellular function. Existing GRN resources primarily focus on transcriptomic data and often overlook the epigenetic mechanisms of gene regulation, limiting evaluation and improvement of GRN inference methods. To address this challenge, we developed SC-MO-GRN-DB, a publicly accessible database of experimentally validated GRNs alongside tissue-matched single-cell multiomic datasets across human and mouse tissues. This repository includes ground-truth GRNs comprising over 22 million regulatory edges, curated from high-confidence experimental datasets. In addition, it hosts multiomic single-cell datasets totaling more than two million cells across six molecular modalities: single-cell RNA sequencing (scRNA-seq), chromatin accessibility (scATAC-seq), chromatin immunoprecipitation (scChIP-seq), DNA methylation (scDNA-Met), chromatin conformation (scHi-C), and gene perturbation screens (scCRISPR-seq). By offering standardized input datasets paired with experimentally supported ground-truth networks, SC-MO-GRN-DB provides a platform for the development, benchmarking, and validation of GRNs with single-cell multiomic data.