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

Mono

Ontology Term

monocyteCL:0000576

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.

myeloid cellCL:0000763

Ontology Assessment

Disagreements with any aspect of the Cell Ontology.

—

Marker Gene Evidence

Gene markers used by researcher to assign this cell annotation.

FTL, LYZ, CD14, FCN1, S100A8, S100A9

Canonical Marker Genes

CD14, CD16 (FCGR3A/B), CD64 (FCGR1A), CCR2, CSF1R, S100A8, S100A9

Rationale

This one has high AIF1, CD14, LYZ, FTL, all of which can be in macrophages. or monocytes. It is often difficult to discern macrophage from monocyte in gut data, but this one has higher CD14 as well as FCN1 and S100A8/9, so we went with monocyte

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/