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

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Cell Metadata

Endth/Ven

Ontology Term: vein endothelial cellCL:0002543
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: venous endothelial cell, endothelial cell of vein
CategoryClass of which the cell type is a subclass.: endothelial cellCL:0000115
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: PECAM1, PLVAP, CLDN5, VWF, MADCAM1, ACKR1, CPE
Canonical Marker Genes: CLDN5, PECAM1, VWF, MADCAM1
Rationale: PECAM1/PLVAP expressing endothelial cells. Compared to other endothelial cells, these display a high level of ACKR1, CPE, and MADCAM1 - attached DOIs suggesting these are venous endothelial cells.
Rationale DOI: 10.1369/0022155417753363 0.1038/s41467-022-33052-y

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: vein endothelial cellCL:0002543
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: venous endothelial cell, endothelial cell of vein
CategoryClass of which the cell type is a subclass.: endothelial cellCL:0000115
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: PECAM1, PLVAP, CLDN5, VWF, MADCAM1, ACKR1, CPE
Canonical Marker Genes: CLDN5, PECAM1, VWF, MADCAM1
Rationale: PECAM1/PLVAP expressing endothelial cells. Compared to other endothelial cells, these display a high level of ACKR1, CPE, and MADCAM1 - attached DOIs suggesting these are venous endothelial cells.
Rationale DOI: 10.1369/0022155417753363 0.1038/s41467-022-33052-y

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/