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

NK

Ontology Term

natural killer cellCL:0000623

Synonyms

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

NK cell

Category

Class of which the cell type is a subclass.

lymphocyteCL:0000542

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.

NKG7, KLRD1, KLRB1, GZMA, GZMB, GNLY, CCL4

Canonical Marker Genes

NKG2D (KLRK1), KLRB1, KLRG1, KLRC1, KLRC2, KLRC3, KLRF1, KLRD1

Rationale

There's no differential CD3 or TRAC expression here but plenty of cytotoxic markers, including KLR enzymes, which points to NK rather than T.

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/