GRLGRN: graph representation-based learning to infer gene regulatory networks from single-cell RNA-seq data

• Published in: BMC bioinformatics Vol. 26; no. 1; pp. 108 - 19
• Main Authors: Wang, Kai, Li, Yulong, Liu, Fei, Luan, Xiaoli, Wang, Xinglong, Zhou, Jingwen
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 18.04.2025; BioMed Central; BMC
• Subjects: Ablation; Algorithms; Anopheles; Computational Biology - methods; Data mining; Datasets; Deep Learning; Drug development; Gene expression; Gene expression data; Gene regulatory network; Gene Regulatory Networks; Gene sequencing; Genes; Genetic regulation; Genetic research; Graph representation learning; Graph representations; Graphical representations; Heterogeneity; Humans; Implicit links; Links; Machine Learning; Methods; Neural networks; Noise measurement; Performance evaluation; Predictions; Ribonucleic acid; RNA; RNA sequencing; RNA-Seq - methods; Sequence Analysis, RNA - methods; Single-Cell Analysis - methods; Single-Cell Gene Expression Analysis; Stem cells; Transcription factors; China; Graph representation learning; Implicit links; Gene regulatory network; Gene expression data
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-025-06116-1

A gene regulatory network (GRN) is a graph-level representation that describes the regulatory relationships between transcription factors and target genes in cells. The reconstruction of GRNs can help investigate cellular dynamics, drug design, and metabolic systems, and the rapid development of single-cell RNA sequencing (scRNA-seq) technology provides important opportunities while posing significant challenges for reconstructing GRNs. A number of methods for inferring GRNs have been proposed in recent years based on traditional machine learning and deep learning algorithms. However, inferring the GRN from scRNA-seq data remains challenging owing to cellular heterogeneity, measurement noise, and data dropout. In this study, we propose a deep learning model called graph representational learning GRN (GRLGRN) to infer the latent regulatory dependencies between genes based on a prior GRN and data on the profiles of single-cell gene expressions. GRLGRN uses a graph transformer network to extract implicit links from the prior GRN, and encodes the features of genes by using both an adjacency matrix of implicit links and a matrix of the profile of gene expression. Moreover, it uses attention mechanisms to improve feature extraction, and feeds the refined gene embeddings into an output module to infer gene regulatory relationships. To evaluate the performance of GRLGRN, we compared it with prevalent models and performed ablation experiments on seven cell-line datasets with three ground-truth networks. The results showed that GRLGRN achieved the best predictions in AUROC and AUPRC on 78.6% and 80.9% of the datasets, and achieved an average improvement of 7.3% in AUROC and 30.7% in AUPRC. The interpretation discussion and the network visualization were conducted. The experimental results and case studies illustrate the considerable performance of GRLGRN in predicting gene interactions and provide interpretability for the prediction tasks, such as identifying hub genes in the network and uncovering implicit links.