Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade

TA

Ontology Term

transit amplifying cellCL:0009010

Synonyms

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

TACs, transit amplifying progenitor cell, transit-amplifying cell, transient amplifying cell, TAC, TA

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.

KRT8, KRT18, OLFM4, EPCAM, MKI67

Canonical Marker Genes

PCNA, KRT5, KRT8, CCND1

Rationale

These are clear epithelial cells based on OLFM4, KRT, EPCAM expression, but they also express some proliferative markers like MKI67 compared to other epithelial cells, so we called them transit amplifying

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/