Secretory

Ontology Term

secretory cellCL:0000151

Synonyms

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

unknown

Category

Class of which the cell type is a subclass.

epithelial cellCL:0000066

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.

REG1A, REG1B, LCN2, SPINK1, REG3G, KRT18

Canonical Marker Genes

ALPI, MUC2, TFF3, CHGA, SYP, LYZ, DEFA5

Rationale

These are epithelial cells based. onKRT18 expression and they are not clearly fitting into goblet, EEC, paneth, or other specific secretory cell subsets, but they are high in SPINK1, REG1A/B, and LCN2. LCN2 and SPINK1 are secreted enzymes

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/