Inferring gene regulatory networks from single-cell transcriptomics based on graph embedding.

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Abstract

Gene regulatory networks (GRNs) encode gene regulation in living organisms, and have become a critical tool to understand complex biological processes. However, due to the dynamic and complex nature of gene regulation, inferring GRNs from scRNA-seq data is still a challenging task. Existing computational methods usually focus on the close connections between genes, and ignore the global structure and distal regulatory relationships.In this study, we develop a supervised deep learning framework, IGEGRNS, to infer gene regulatory networks from scRNA-seq data based on graph embedding. In the framework, contextual information of genes is captured by GraphSAGE, which aggregates gene features and neighborhood structures to generate low-dimensional embedding for genes. Then, the k most influential nodes in the whole graph are filtered through Top-k pooling. Finally, potential regulatory relationships between genes are predicted by stacking CNNs. Compared with nine competing supervised and unsupervised methods, our method achieves better performance on six time-series scRNA-seq datasets.Our method IGEGRNS is implemented in Python using the Pytorch machine learning library, and it is freely available at https://github.com/DHUDBlab/IGEGRNS.Supplementary data are available at Bioinformatics online.© The Author(s) 2024. Published by Oxford University Press.