How many markers are needed to robustly determine a cell's type?

Fischer, Stephan, Gillis, Jesse (November 2021) How many markers are needed to robustly determine a cell's type? iScience, 24 (11). p. 103292. ISSN 2589-0042

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Abstract

Our understanding of cell types has advanced considerably with the publication of single-cell atlases. Marker genes play an essential role for experimental validation and computational analyses such as physiological characterization, annotation, and deconvolution. However, a framework for quantifying marker replicability and selecting replicable markers is currently lacking. Here, using high-quality data from the Brain Initiative Cell Census Network (BICCN), we systematically investigate marker replicability for 85 neuronal cell types. We show that, due to dataset-specific noise, we need to combine 5 datasets to obtain robust differentially expressed (DE) genes, particularly for rare populations and lowly expressed genes. We estimate that 10 to 200 meta-analytic markers provide optimal downstream performance and make available replicable marker lists for the 85 BICCN cell types. Replicable marker lists condense interpretable and generalizable information about cell types, opening avenues for downstream applications, including cell type annotation, selection of gene panels, and bulk data deconvolution.

Item Type:	Paper
Subjects:	Investigative techniques and equipment Investigative techniques and equipment > brain atlas organs, tissues, organelles, cell types and functions > cell types and functions > cell types organs, tissues, organelles, cell types and functions > cell types and functions > cell types organs, tissues, organelles, cell types and functions > cell types and functions > cell types organs, tissues, organelles, cell types and functions > cell types and functions organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons organs, tissues, organelles, cell types and functions Investigative techniques and equipment > assays > Single cell sequencing
CSHL Authors:	Fischer, Stephan Gillis, Jesse
Communities:	CSHL labs > Gillis Lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	19 November 2021
Date Deposited:	17 Nov 2021 15:53
Last Modified:	23 Jan 2024 21:04
PMCID:	PMC8571500
URI:	https://repository.cshl.edu/id/eprint/40421

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