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bioRxiv · 10.1101/566182

Uncovering hypergraphs of cell-cell interaction from single cell RNA-sequencing data

Tsuyuzaki, K.·Ishii, M.·Nikaido, I.
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Abstract

Complex biological systems can be described as a multitude of cell-cell interactions (CCIs). Recent single-cell RNA-sequencing technologies have enabled the detection of CCIs and related ligand-receptor (L-R) gene expression simultaneously. However, previous data analysis methods have focused on only one-to-one CCIs between two cell types. To also detect many-to-many CCIs, we propose scTensor, a novel method for extracting representative triadic relationships (hypergraphs), which include (i) ligand-expression, (ii) receptor-expression, and (iii) L-R pairs. When applied to simulated and empirical datasets, scTensor was able to detect some hypergraphs including paracrine/autocrine CCI patterns, which cannot be detected by previous methods.

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Tsuyuzaki, K., Ishii, M., Nikaido, I.. 2019-03-04. Uncovering hypergraphs of cell-cell interaction from single cell RNA-sequencing data. https://doi.org/10.1101/566182

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