KEGNI:基因调控网络推理的知识图谱增强框架

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Pengxiao Li, Lin Li, Jingminjie Nan, Jiahuan Chen, Jielin Sun, Yanan Cao
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引用次数: 0

摘要

细胞类型特异性基因调控网络(GRNs)的推断是研究复杂调控机制的基本步骤。在这里,我们提出了KEGNI (Knowledge graph- enhanced Gene regulatory Network Inference,知识图增强基因调控网络推断),这是一个知识引导框架,它使用图自编码器来捕获基因调控关系,并结合知识图来推断基于scRNA-seq数据的grn。与使用scRNA-seq数据或配对scRNA-seq和scATAC-seq数据的多种方法相比,KEGNI显示出优越的性能。KEGNI可以识别驱动基因并阐明不同细胞背景下的调控机制。KEGNI的模块化设计支持为特定于上下文的任务集成各种知识图。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
KEGNI: knowledge graph enhanced framework for gene regulatory network inference
Inference of cell type-specific gene regulatory networks (GRNs) is a fundamental step in investigating complex regulatory mechanisms. Here, we present KEGNI (Knowledge graph-Enhanced Gene regulatory Network Inference), a knowledge-guided framework that employs a graph autoencoder to capture gene regulatory relationships and incorporates a knowledge graph to infer GRNs based on scRNA-seq data. KEGNI shows superior performance compared to multiple methods using scRNA-seq data or paired scRNA-seq and scATAC-seq data. KEGNI can identify driver genes and elucidate the regulatory mechanisms underlying distinct cellular contexts. The modular design of KEGNI supports the integration of various knowledge graphs for context-specific tasks.
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来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
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