Abstract
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.
Keywords
Computational biologyGeneGene expressionBiologyIntracellularRegulation of gene expressionCell biologyCellGene regulatory networkImmune systemGenetics
MeSH Terms
AnimalsCell CommunicationGene Regulatory NetworksHumansLigandsMiceModelsTheoreticalReceptorsCell SurfaceSequence AnalysisRNASignal TransductionSingle-Cell AnalysisTranscriptomeTumor Microenvironment
Affiliated Institutions
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Publication Info
- Year
- 2019
- Type
- article
- Volume
- 17
- Issue
- 2
- Pages
- 159-162
- Citations
- 1888
- Access
- Closed
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Cite This
Robin Browaeys,
Wouter Saelens,
Yvan Saeys
(2019).
NicheNet: modeling intercellular communication by linking ligands to target genes.
Nature Methods
, 17
(2)
, 159-162.
https://doi.org/10.1038/s41592-019-0667-5
Identifiers
- DOI
- 10.1038/s41592-019-0667-5
- PMID
- 31819264