Fibro

Ontology Term

fibroblastCL:0000057

Synonyms

Terms that have the same, or nearly the same, meaning as the selected cell type.

mesenchymal cells, stromal cells

Category

Class of which the cell type is a subclass.

stromal cellCL:0000499

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.

PDGFRA, PDGFRB, VIM, ADAMDEC1, LUM

Canonical Marker Genes

VIM, FN1, COL1A1, P4HA1, FAP

Rationale

VIM - mesenchymal origin ADAMDEC1 - often seen in gut fibroblasts PDGFRA/B - fibroblast migration markers

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/