Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome

Single-cell RNA-sequencing data has revolutionized our ability to understand of the patterns of cell–cell and ligand–receptor connectivity that influence the function of tissues and organs. However, the quantification and visualization of these patterns in a way that informs tissue biology are major...

Full description

Saved in:
Bibliographic Details
Published inScientific reports Vol. 12; no. 1; pp. 4187 - 12
Main Authors Raredon, Micha Sam Brickman, Yang, Junchen, Garritano, James, Wang, Meng, Kushnir, Dan, Schupp, Jonas Christian, Adams, Taylor S., Greaney, Allison M., Leiby, Katherine L., Kaminski, Naftali, Kluger, Yuval, Levchenko, Andre, Niklason, Laura E.
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 09.03.2022
Nature Publishing Group
Nature Portfolio
Subjects
631/114
631/114/1314
631/114/2114
631/114/2164
631/114/2408
631/114/2415
631/114/794
631/532
631/553
631/553/1833
Cell signaling
Computer applications
Humanities and Social Sciences
Ligands
multidisciplinary
Network topologies
Receptor mechanisms
Science
Science (multidisciplinary)
Online AccessGet full text

Cover

More Information
Summary:Single-cell RNA-sequencing data has revolutionized our ability to understand of the patterns of cell–cell and ligand–receptor connectivity that influence the function of tissues and organs. However, the quantification and visualization of these patterns in a way that informs tissue biology are major computational and epistemological challenges. Here, we present Connectome , a software package for R which facilitates rapid calculation and interactive exploration of cell–cell signaling network topologies contained in single-cell RNA-sequencing data. Connectome can be used with any reference set of known ligand–receptor mechanisms. It has built-in functionality to facilitate differential and comparative connectomics, in which signaling networks are compared between tissue systems. Connectome focuses on computational and graphical tools designed to analyze and explore cell–cell connectivity patterns across disparate single-cell datasets and reveal biologic insight. We present approaches to quantify focused network topologies and discuss some of the biologic theory leading to their design.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-022-07959-x