NicheNet: modeling intercellular communication by linking ligands to target genes
NicheNet: modeling intercellular communication by linking ligands to target genes
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DOI：
10.1038/s41592-019-0667-5
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发表时间：
2020-02-01
期刊：
影响因子：
48
通讯作者：
Saeys, Yvan
中科院分区：
文献类型：
--
作者：
Browaeys, Robin;Saelens, Wouter;Saeys, Yvan
缺乏模拟细胞间相互作用如何影响细胞基因表达的计算方法。我们提出了NICHENET(https://github.com/saeyslab/nichenetr)，)，这是一种通过将细胞的表达数据与信号和基因调控网络的先验知识相结合来预测相互作用的细胞之间的配体-靶连接的方法。我们将NicheNet应用于肿瘤和免疫细胞微环境数据，并证明了NicheNet可以推断活性配体及其对相互作用细胞的基因调控作用。NicheNet使用表达数据，结合先前建立在已知信号和基因调控网络上的模型，预测细胞间通信中的配体-目标连接。
Computational methods that model how gene expression of a cell is influenced by interacting cells are lacking. We present NicheNet (https://github.com/saeyslab/nichenetr), a method that predicts ligand-target links between interacting cells by combining their expression data with prior knowledge on signaling and gene regulatory networks. We applied NicheNet to tumor and immune cell microenvironment data and demonstrate that NicheNet can infer active ligands and their gene regulatory effects on interacting cells. NicheNet uses expression data, in combination with a previous model built on known signaling and gene regulatory networks, to predict ligand-target links in cell-to-cell communications.