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

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Cell Metadata

Endth/Lymph

Ontology Term: endothelial cell of lymphatic vesselCL:0002138
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: LEC, lymphatic endothelial cell
Category Class of which the cell type is a subclass.: endothelial cellCL:0000115
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CLDN5, LYVE1
Canonical Marker Genes: unknown
Rationale: This cluster does not differentially express PECAM1, PLVAP, or VWF, but does have some claudin CLDN5 expression. It also expresses VIM, which points to fibroblasts, but one of the highest DE genes is LYVE1 - a gene recently suggested as a lymphatic vessel endothelial cell marker (see doi)
Rationale DOI: 10.1073/pnas.242401399

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/

Ontology Term: endothelial cell of lymphatic vesselCL:0002138
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: LEC, lymphatic endothelial cell
Category Class of which the cell type is a subclass.: endothelial cellCL:0000115
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CLDN5, LYVE1
Canonical Marker Genes: unknown
Rationale: This cluster does not differentially express PECAM1, PLVAP, or VWF, but does have some claudin CLDN5 expression. It also expresses VIM, which points to fibroblasts, but one of the highest DE genes is LYVE1 - a gene recently suggested as a lymphatic vessel endothelial cell marker (see doi)
Rationale DOI: 10.1073/pnas.242401399

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/