Mstcl

Ontology Term

mast cellCL:0000097

Synonyms

Terms that have the same, or nearly the same, meaning as the selected cell type.

tissue basophil, histaminocyte, mastocyte, labrocyte

Category

Class of which the cell type is a subclass.

granulocyteCL:0000094

Ontology Assessment

Disagreements with any aspect of the Cell Ontology.

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Marker Gene Evidence

Gene markers used by researcher to assign this cell annotation.

TPSAB1, TPSB2, ANXA1, CD63, HDC, KIT

Canonical Marker Genes

KIT, FCER1A, CMA1, TPSAB1, TPSD2, HDC

Rationale

Mast cells are typically easy to identify in gut scRNAseq data as they cluster seperately and have high expression of tryptase (TPSA), chymase (CMA1), IgE receptors, and Histamine (HDC)

Inherited from celltype

Set of Labels Description

In this paper we used an automated iterative subclustering algorithm to find hundreds of cell state clusters, after which we merged unsupported clusters and annotated each resulting cluster with a better-known cell subtype. The high-res cell state clusters are annotated as subtype.gene1.gene2, so in some cases we didn't directly name some commonly named subtypes, such as pericytes. When we run DE on the resulting subtypes, we find many canonical and scRNA-suggested marker genes.

Annotation Method

both

Algorithm Name

ARBOL

Algorithm Version

v1.0

Algorithm URL

https://github.com/jo-m-lab/ARBOL/