Directly selecting cell-type marker genes for single-cell clustering analyses.
Cell Rep Methods
; 4(7): 100810, 2024 Jul 15.
Article
em En
| MEDLINE
| ID: mdl-38981475
ABSTRACT
In single-cell RNA sequencing (scRNA-seq) studies, cell types and their marker genes are often identified by clustering and differentially expressed gene (DEG) analysis. A common practice is to select genes using surrogate criteria such as variance and deviance, then cluster them using selected genes and detect markers by DEG analysis assuming known cell types. The surrogate criteria can miss important genes or select unimportant genes, while DEG analysis has the selection-bias problem. We present Festem, a statistical method for the direct selection of cell-type markers for downstream clustering. Festem distinguishes marker genes with heterogeneous distribution across cells that are cluster informative. Simulation and scRNA-seq applications demonstrate that Festem can sensitively select markers with high precision and enables the identification of cell types often missed by other methods. In a large intrahepatic cholangiocarcinoma dataset, we identify diverse CD8+ T cell types and potential prognostic marker genes.
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Base de dados:
MEDLINE
Assunto principal:
Análise de Célula Única
Idioma:
En
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
China