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Updated: Aug 3, 2025

Transcriptome Analysis of Single Cells

Transcriptome Analysis of Single Cells

Published on: April 25, 2011

exFINDER: identify external communication signals using single-cell transcriptomics data.

Changhan He¹, Peijie Zhou¹, Qing Nie^1,2

¹Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA.

Nucleic Acids Research

|April 7, 2023

Summary

This summary is machine-generated.

This study introduces exFINDER, a novel computational method to identify external signals received by cells. exFINDER enhances single-cell transcriptomics analysis by revealing crucial external signaling networks.

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A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

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Area of Science:

Cellular biology
Computational biology
Systems biology

Background:

Cells communicate and sense their environment to make decisions.
Single-cell transcriptomics and computational tools infer cell-cell communication via ligands and receptors.
Existing methods lack inference of external signals received by cells.

Purpose of the Study:

To present exFINDER, a method identifying external signals received by cells in single-cell transcriptomics data.
To uncover external signals activating target genes and infer external signal-target signaling networks (exSigNet).
To enable quantitative analysis of exSigNets and reveal external signal-associated cellular activities.

Main Methods:

Utilized prior knowledge of signaling pathways to identify external signals.
Developed exFINDER for inferring external signal-target signaling networks (exSigNet).
Applied exFINDER to single-cell RNA sequencing (scRNA-seq) datasets from various species.

Main Results:

Demonstrated accuracy and robustness of exFINDER in identifying external signals.
Revealed critical transition-related signaling activities and inferred key external signals and targets.
Successfully clustered signal-target paths and evaluated relevant biological events.

Conclusions:

exFINDER accurately identifies external signals received by cells using scRNA-seq data.
The method reveals external signal-associated activities and potential novel signaling cells.
exFINDER provides a robust framework for analyzing external signaling in cellular systems.