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

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Cell Metadata

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Ontology Term: endothelial cell of arteryCL:1000413
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: arterial endothelial cell
CategoryClass of which the cell type is a subclass.: endothelial cellCL:0000115
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: PLVAP, VWF, CLDN5, CAV1, GJA4
Canonical Marker Genes: unknown
Rationale: endothelial based on VWF, PLVAP, claudin 5 CLDN5. When compared to other endothelial clusters, these highly express CALD1 and some GJA4 expression (DOI) - suggesting artery endothelial cells
Rationale DOI: 10.1002/path.5751

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 arteryCL:1000413
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: arterial endothelial cell
CategoryClass of which the cell type is a subclass.: endothelial cellCL:0000115
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: PLVAP, VWF, CLDN5, CAV1, GJA4
Canonical Marker Genes: unknown
Rationale: endothelial based on VWF, PLVAP, claudin 5 CLDN5. When compared to other endothelial clusters, these highly express CALD1 and some GJA4 expression (DOI) - suggesting artery endothelial cells
Rationale DOI: 10.1002/path.5751

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/