scSAGRN: Inferring gene regulatory networks from single-cell multi-omics using spatial association

IF 1.9 4区 生物学 Q2 BIOLOGY
Qing Ren, Mengdi Nan, Yuhan Fu, Xiang Chen, Yibing Ma, Yongle Shi, Jie Gao
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引用次数: 0

Abstract

Identifying the regulatory relationships between transcription factors and target genes is fundamental to understanding molecular regulatory mechanisms in biological processes including development and disease occurrence. Therefore, resolving the relationships between cis-regulatory elements and genes using single-cell multi-omics data is important for understanding transcriptional regulation. Here, scSAGRN is proposed as a framework for inferring gene regulatory networks from single-cell multi-omics. scSAGRN incorporates spatial association to compute correlations between gene expression and chromatin openness data, connects distal cis-regulatory elements to genes, infers gene regulatory networks and identifies key transcription factors. The approach is benchmarked using real single-cell datasets, and scSAGRN shows superior performance in TF recovery, peak-gene linkage prediction, and TF-gene linkage prediction compared to existing methods. Meanwhile, in human peripheral blood mononuclear cells dataset, mouse cerebral cortex dataset and mouse embryonic brain cells dataset, scSAGRN demonstrates its capability to infer gene regulatory networks and identify transcription factors. Overall, scSAGRN provides a reference for predicting transcriptional regulatory patterns from single-cell multi-omics data.
scSAGRN:利用空间关联推断单细胞多组学的基因调控网络
确定转录因子和靶基因之间的调控关系是理解包括发育和疾病发生在内的生物过程中的分子调控机制的基础。因此,利用单细胞多组学数据解决顺式调控元件与基因之间的关系对于理解转录调控具有重要意义。在这里,scSAGRN被提出作为从单细胞多组学推断基因调控网络的框架。scSAGRN采用空间关联来计算基因表达与染色质开放度数据之间的相关性,将远端顺式调控元件与基因连接起来,推断基因调控网络并识别关键转录因子。该方法使用真实的单细胞数据集进行了基准测试,与现有方法相比,scSAGRN在TF恢复、峰基因连锁预测和TF基因连锁预测方面表现出优越的性能。同时,在人外周血单个核细胞数据集、小鼠大脑皮层数据集和小鼠胚胎脑细胞数据集中,scSAGRN显示了其推断基因调控网络和鉴定转录因子的能力。总之,scSAGRN为单细胞多组学数据预测转录调控模式提供了参考。
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来源期刊
Biosystems
Biosystems 生物-生物学
CiteScore
3.70
自引率
18.80%
发文量
129
审稿时长
34 days
期刊介绍: BioSystems encourages experimental, computational, and theoretical articles that link biology, evolutionary thinking, and the information processing sciences. The link areas form a circle that encompasses the fundamental nature of biological information processing, computational modeling of complex biological systems, evolutionary models of computation, the application of biological principles to the design of novel computing systems, and the use of biomolecular materials to synthesize artificial systems that capture essential principles of natural biological information processing.
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