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.

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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

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/